identifier
stringlengths 11
32
| pdf_url
stringlengths 17
4.62k
⌀ | lang
stringclasses 120
values | error
stringclasses 1
value | title
stringlengths 2
500
⌀ | source_name
stringlengths 1
435
⌀ | publication_year
float64 1.9k
2.02k
| license
stringclasses 3
values | word_count
int64 0
1.64M
| text
stringlengths 1
9.75M
|
|---|---|---|---|---|---|---|---|---|---|
https://openalex.org/W2112223494
|
https://europepmc.org/articles/pmc4318176?pdf=render
|
English
| null |
Clinical and cost effectiveness of computer treatment for aphasia post stroke (Big CACTUS): study protocol for a randomised controlled trial
|
Trials
| 2,015
|
cc-by
| 9,871
|
* Correspondence: r.l.palmer@sheffield.ac.uk
1School of Health and Related Research, University of Sheffield, 107 Innovation
Centre, 217 Portobello, Sheffield S1 4DP, England
Full list of author information is available at the end of the article Clinical and cost effectiveness of computer
treatment for aphasia post stroke (Big CACTUS):
study protocol for a randomised controlled trial Clinical and cost effectiveness of computer
treatment for aphasia post stroke (Big CACTUS):
study protocol for a randomised controlled trial Rebecca Palmer1*, Cindy Cooper1, Pam Enderby1, Marian Brady2, Steven Julious3, Audrey Bowen4
and Nicholas Latimer5 Open Access Open Access Open Access © 2015 Palmer 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. TRIALS TRIALS Palmer et al. Trials (2015) 16:18
DOI 10.1186/s13063-014-0527-7 * Correspondence: r.l.palmer@sheffield.ac.uk
1School of Health and Related Research, University of Sheffield, 107 Innovation
Centre, 217 Portobello, Sheffield S1 4DP, England
Full list of author information is available at the end of the article
© 2015 Palmer 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. Background delivered with similar intensity [11]. Raymer et al. found
personal relevance or ‘salience’ of the language material be-
ing practiced to be important when targeting therapy [6]. While the optimum intensity remains unclear, it is gener-
ally acknowledged that for stroke rehabilitation regular, re-
petitive therapy practice is a factor in treatment success. g
Stroke is the largest cause of disability in the United
Kingdom with communication impairment affecting one
third of survivors [1]. Aphasia is the most common
communication impairment acquired post stroke. It is a
disorder of language which may affect understanding,
expression, reading and writing. Speech and language
therapy (SLT) is often received regularly initially but rarely
continues after the first few months. Medical instability,
fatigue and confusion may reduce full engagement with
language therapy in the early weeks post stroke, reducing
the opportunity for people to participate in treatment. There is evidence that people can continue to improve
their language skills for several years [2]. As the conse-
quences of aphasia remain a problem long term, investiga-
tion of interventions to reduce this health burden in the
chronic stages post stroke is crucial. The National Stroke
Strategy [1] recommends people receive rehabilitation for
as long as they benefit from it. Treatment of aphasia
that persists beyond the first few months post stroke is
often not available through NHS services in the United
Kingdom as ongoing therapy is costly through face-to-face
SLT and places greater demands on limited resources. The resources required to achieve intensive therapy in
the long term is prohibitive in the current financial cli-
mate and lower cost options for the support of repetitive
intensive practice are needed. Non-speech and language
therapy professionals have been employed successfully
to support therapy activity [4,12,13]. Computer therapy, developed for the treatment of apha-
sia, has been reported to be useful in the provision of tar-
geted language practice and provides opportunities for
independent home practice as part of a self-management
approach to maximise practice intensity, improving
outcomes for reading, spelling and expressive lan-
guage [13-17]. The Department of Health report, ‘Our
Health, Our Care, Our Say’ [18], recommends self-
management for long term conditions supported through
technological innovation [18]. However, to date, studies of
self-managed computer therapy for aphasia have been
limited to descriptive case series with only three reported
RCTs; two for treatment of reading disorders and one for
treatment of word finding [13,14,19]. Background Although these
studies were not fully powered, they indicate potential
effectiveness of computer therapy. Such computer-based
services for long term management of aphasia therapy
could provide a low cost therapy option which is accept-
able to patients and families. However, the actual cost ef-
fectiveness has not been definitively tested. p
g
Meta-analysis in a Cochrane review [2] of SLT for
aphasia following stroke suggests some effectiveness of
aphasia therapy [2]. Adequately powered randomized
controlled trials (RCTs) in this field are rare except for
recent studies of SLT intervention in the first few weeks
post stroke. Laska et al. [3] randomised 123 patients with
aphasia to receive 45 minutes of SLT a day for 21 days,
starting within two days of stroke onset, or no SLT
intervention. Severity of the aphasia was not reduced. A recently completed study, ACT NoW [4], randomised
170 people in hospital post stroke to SLT intervention or
attention control (informal conversation with paid visi-
tors) for up to four months. No significant differences be-
tween groups were shown and the authors suggested that
the intervention may have been provided too early in the
stroke pathway. As aphasia persists for many stroke survi-
vors, therapy in the longer term also warrants investiga-
tion using adequately powered RCTs. Although rapid
spontaneous recovery may occur in the first few months,
there is preliminary evidence to suggest targeted and in-
tensive SLT treatments can promote further improvement
in the latter months [5-7]. The StepbyStep© computerised approach to long term
aphasia therapy combines current evidence underpin-
ning language therapy with practical considerations of
treatment delivery. Skills of a qualified speech and lan-
guage therapist are used to select individually targeted
therapy exercises, computer software is provided for regu-
lar self-managed practice of therapy exercises and volun-
teers or assistant SLTs support language practice and
computer use [20]. A pilot study evaluating this approach
was carried out with 34 people with persistent aphasia. They were randomly assigned to using computer software
designed for treating aphasia, or usual long term care
(most frequently this was social support). On average
people with aphasia practiced their speech exercises on
the computer independently for 25 hours over five
months. The therapy showed statistically significant
improvement in the ability to use spoken words when
compared to usual care (P = 0.014). Abstract Background: Aphasia affects the ability to speak, comprehend spoken language, read and write. One third of
stroke survivors experience aphasia. Evidence suggests that aphasia can continue to improve after the first few
months with intensive speech and language therapy, which is frequently beyond what resources allow. The
development of computer software for language practice provides an opportunity for self-managed therapy. This
pragmatic randomised controlled trial will investigate the clinical and cost effectiveness of a computerised approach
to long-term aphasia therapy post stroke. Methods/Design: A total of 285 adults with aphasia at least four months post stroke will be randomly allocated to
either usual care, computerised intervention in addition to usual care or attention and activity control in addition to
usual care. Those in the intervention group will receive six months of self-managed word finding practice on their
home computer with monthly face-to-face support from a volunteer/assistant. Those in the attention control group
will receive puzzle activities, supplemented by monthly telephone calls. y
y
Study delivery will be coordinated by 20 speech and language therapy departments across the United Kingdom. Outcome measures will be made at baseline, six, nine and 12 months after randomisation by blinded speech and
language therapist assessors. Primary outcomes are the change in number of words (of personal relevance) named
correctly at six months and improvement in functional conversation. Primary outcomes will be analysed using a
Hochberg testing procedure. Significance will be declared if differences in both word retrieval and functional
conversation at six months are significant at the 5% level, or if either comparison is significant at 2.5%. A cost utility
analysis will be undertaken from the NHS and personal social service perspective. Differences between costs and
quality-adjusted life years in the three groups will be described and the incremental cost effectiveness ratio will be
calculated. Treatment fidelity will be monitored. Discussion: This is the first fully powered trial of the clinical and cost effectiveness of computerised aphasia
therapy. Specific challenges in designing the protocol are considered. Trial registration: Registered with Current Controlled Trials ISRCTN68798818 on 18 February 2014. Keywords: Speech and language therapy, Aphasia, Computerised intervention, Self-management, Long term
rehabilitation, RCT design, Stroke Palmer et al. Trials (2015) 16:18 Page 2 of 12 Background The results indi-
cated that self-managed computer therapy supported
by volunteers (a total of four hours on average) could help
people with aphasia to continue to practise, improving
their vocabulary and confidence talking [13]. Patients and Targeted therapies with good preliminary evidence to
date include constraint induced aphasia therapy (CIAT);
use of language in games to make, reject or clarify re-
quests for targeted items for 30 hours over 2 weeks
[5,8,9]. A systematic review of 10 studies conducted over
the decade concluded that evidence for this technique is
favourable [10]. Model oriented aphasia therapy (MOAT),
which tailors treatment according to a patient’s individual
symptoms, was found to be comparable to CIAT when Page 3 of 12 Palmer et al. Trials (2015) 16:18 carers found it an acceptable alternative to face-to-face
therapy [21]. Self-managed computer therapy could there-
fore improve the quality of life of people with persistent
aphasia at relatively low cost, and exploratory economic
analysis has suggested considerable potential for the inter-
vention to prove cost effective [13,22]. months or more post stroke, with persistent aphasia who
are randomly allocated to either: usual care, self-managed
computerised speech and language therapy in addition to
usual care or attention control in addition to usual care. Each participant will be in the trial for 12 months. Partic-
ipants will be identified and recruited over an 18-month
period in total, and 15 months at each site. Each partici-
pant will receive their intervention for six months, with
follow-up at six, nine and 12 months. The study has an in-
ternal pilot phase with criteria for progression to comple-
tion of the full RCT. There are no formal statistical criteria
for stopping the trial early. Decisions to stop the trial early
on grounds of safety or futility will be made by inde-
pendent data management and ethics committee mem-
bers. The protocol conforms to the Consolidated Standards
of Reporting Trials (CONSORT) guidelines for non-
pharmacological studies (Figure 1) [23]. The aim of this study is to provide definitive evidence of
the clinical and cost effectiveness of targeted, intensive
speech and language impairment-based therapy interven-
tion for word finding delivered through self-managed
computer exercise for persisting post-stroke aphasia. This
builds on the pilot RCT which explored possible effects,
and informed measures, feasibility, recruitment rates, ad-
herence, cost effectiveness analysis and a power calcula-
tion. The primary objectives of the study are: The study protocol was approved by Leeds West research
ethics committee (reference number: 13/YH/0377). Add-
itional approval was granted for Scotland by the Scotland
A research ethics committee (reference number: 14/SS/
0023). The University of Sheffield is the sponsor. The trial
is registered with the International Standard Randomised
Controlled Trials database ISRCTN (reference number:
68798818) and is commissioned by the National Institute
for Health Research. 1. To establish whether self-managed computerised
speech and language therapy for aphasia related
word finding problems after stroke increases the
ability to use vocabulary of personal importance
(impairment). 2. To establish whether self-managed computerised speech
and language therapy for word finding problems after
stroke improves functional communication ability in
conversation (activity). Background The current study was commissioned by the United
Kingdom National Institute for Health Research, having
considered the limitations in the current evidence base. Methods/Design 5. Ability to retrieve 10 to 90% of words on the
Comprehensive Aphasia Test Naming Objects
subtest (score of 5 to 43 out of 48); Inclusion criteria Inclusion criteria
Participants will be included if they meet the following
criteria: Inclusion criteria
Participants will be included if they meet the following
criteria: Secondary objectives include investigating the generalisa-
tion of treatment to retrieval of untreated words (impair-
ment); the use of treated words in conversation; the carer
perception of communication effectiveness (participation)
and identification of any possible adverse events. Carers’
own quality of life will be measured. Fidelity to treatment
will also be monitored. 1. Aged 18 or over; 2. Diagnosis of stroke(s); 3. Onset of stroke at least four months prior to
randomisation; 4. Diagnosis of aphasia, subsequent to stroke, as
confirmed by a trained speech and language therapist; Ethics approval
Th
t d
t The primary objectives of the study are: Participants 3. To investigate whether patients receiving self-managed
computerised speech and language therapy perceive
greater changes in social participation and quality of
life (participation). A total of 285 participants who have a diagnosis of apha-
sia as a consequence of a stroke will be recruited from
approximately 20 speech and language therapy depart-
ments across the United Kingdom. The study will also
be advertised at voluntary groups and using posters in
libraries and GP surgeries in each locality so that potential
participants can self-present to the local research team. 4. To establish whether self-managed computerised
speech and language therapy is cost effective for
persistent aphasia post stroke. 5. To identify whether any effects of the intervention
are evident 12 months after therapy has begun. Screening for eligibility
l
b l
ll b
bl Eligibility will be established on the first visit. The speech
and language therapist will request verbal consent to carry
out the Naming Objects subtest of the Comprehensive
Aphasia Test [24]. This test is used in routine practice and
will establish the severity of the word finding deficit. If the
word finding score is less than 10%, or greater than 90%,
an explanation will be given that this type of computer
therapy is not suitable for them. If the potential partici-
pant has eligible word finding scores, the research speech
and language therapist will ask them to try a simple repe-
tition task to confirm their repetition ability, followed by a
matching task on the computer to confirm ability to see
the screen and perform simple computer related actions. Exclusion criteria Participants will be excluded from the study if they meet
any of the following criteria: 1. They have another pre-morbid speech and
language disorder caused by a neurological deficit
other than stroke (a formal diagnosis can be
reported by the participant or relatives and
confirmed by the recruiting speech and language
therapist). 2. They require treatment for a language other than
English (as the software is in English). 3. They are currently using the StepbyStep© computer
programme or other computer speech therapy
aimed at word retrieval and/or naming. Outcome measures
Primary 1. Change in the number of words (personally relevant
to the participant) named correctly at 6 months
from baseline will be measured by a naming task of
100 pictures presented on the computer. Methods/Design
Design The study will use a pragmatic, parallel group randomised
controlled adjunct trial design. The intervention under test
or attention control will be delivered in addition to usual
care. Outcomes will be compared for people who are four 6. Ability to perform a simple matching task in
StepByStep with at least 50% accuracy (to confirm
sufficient vision and cognitive ability) and Palmer et al. Trials (2015) 16:18 Page 4 of 12 Figure 1 Progression of participants through the trial (CONSORT diagram). SLT = speech and language therapist; ITT = intention to treat. Palmer et al. Trials (2015) 16:18 Page 5 of 12 7. Ability to repeat at least 50% of words in a simple
word repetition task in the StepByStep© program. 7. Ability to repeat at least 50% of words in a simple
word repetition task in the StepByStep© program. therapist at each site will request verbal consent from
the potential participant to carry out part A of the CST. The result will indicate the style of information they are
most likely to understand in part B. Participants will be
given sufficient time to consider their participation be-
fore informed consent is taken by a research speech and
language therapist. Participants providing their own in-
formed consent will be provided with an aphasia-friendly
consent form. If potential participants with severe aphasia
indicate an interest, a relative (in Scotland this will be the
person’s legal representative or nearest relative) will be
asked to read an information sheet detailing their respon-
sibility, and will be asked to sign a carer declaration on be-
half of their relative with aphasia (in Scotland they will be
asked to sign a consent form). For those participants with
a carer, the carer will be asked if they are willing to
complete some outcome measures related to their own
quality of life and perception of their relative’s commu-
nication ability. They will be provided with the carer
information sheet detailing their potential involvement and
will be asked to sign a separate consent form. Informed
consent will be obtained from each participant where they
are able to give it, or consent or carer declaration will be
obtained by the carer or legal representative where the par-
ticipant is interested in participating, but is unable to pro-
vide their own fully informed consent. Baseline assessment
I iti l
t Initial assessment will be performed by the local re-
search speech and language therapist once informed
consent has been given. This will include collection of
the following demographic data: aphasia type, age, gen-
der, time post-onset of stroke and type and location of
stroke (if known). Baseline information will also include
results of the standardised naming test - Naming Objects
subtest of the Comprehensive Aphasia Test (performed as
part of eligibility testing during screening) and the Com-
prehension of Spoken Sentences subtest of the CAT to
provide information on the comprehension ability of the
participants [24]. Baseline measures relating to the study
outcomes are summarised in Table 1. Procedures
Identification Potential participants will be contacted by the research
speech and language therapist in each project centre and
provided with information on the project. They will be
contacted within a fortnight to establish whether they
are interested in knowing more about the study. If they
are interested, the research speech and language therap-
ist will make an appointment to visit them at home. The
number of those contacted but who cannot be followed
up on or who are not interested in learning more and
the reason for this will be recorded. Recruitment The level of support required to enable a person with
aphasia to provide informed consent is dependent upon
the severity and profile of the aphasia. In order to pro-
vide information in a format consistent with each indi-
vidual's language ability, a consent support tool (CST)
will be used [25]. The research speech and language 2. Change in functional communication will be measured
by blinded ratings of video-recorded conversations
between unfamiliar speech and language therapists
blinded to treatment allocation and participants at
six months. Conversations will be structured around Page 6 of 12 Palmer et al. Trials (2015) 16:18 Table 1 Summary of measures
Outcome
Measure
Method of collection
Change in word finding ability
Naming of 100 personally relevant words
Taken at baseline by blinded SLT recruiting
participant 6, 9 and 12 months by separate
blinded SLT. Change in functional communication
10-minute videoed conversations structured
around topics of personal interest. Activity
scale of TOMS used to measure conversational
ability
Conversations at baseline by blinded SLT. Separate blinded SLT follows same topic
guide at 6, 9 and 12 months. Videos
randomised and rated centrally by blinded
assessors. Change in patient perception of
communication and quality of life
COAST self-reported questionnaire. Administered by blinded SLT at baseline. Separate blinded SLT at 6, 9, and 12 months. Generalisation to untreated words
Naming Objects subtest from Comprehensive
Aphasia Test
As above
QALYs for cost effectiveness
EQ-5D for patient and carer (accessible and by proxy)
As above
Carer quality of life
Carer COAST and CarerQol
Self-administered
Cost of intervention
Diaries of time spent on intervention
Self-administered by SLTs, SLTAs and volunteers
Cost of usual care
Diaries of time spent on usual care
SLT collects data from usual treating therapists and
participants at baseline, 3, 6, 9 and 12 months
Carer perception of change in
communication
Carer COAST
Collected by blinded SLT at baseline. Separate
blinded SLT at 6, 9, and 12 months. Negative effects of treatment
Patient diary to record any difficulties and/or negative
impacts of intervention
Patients and carers - central team to send monthly
letter reminding to send back in prepaid envelope. Intervention adherence
Software tailoring checklists. Volunteer and/or
assistant feedback forms. Software key files. Puzzle
book and telephone support feedback. Completed by SLT, monitored by central study team. Self-managed practice monitored by central study
team. Puzzle book completion and telephone support
recorded by member of central study team. Key secondary
I
t Improvement in patient perception of communication
will be measured using the Communication Outcomes
After Stroke (COAST) questionnaire at six months - a
patient-centred, patient-reported measure of commu-
nication related activity, participation and quality of
life [27]. Randomisation, blinding and allocation concealment
Following baseline assessment, the participant will be
randomised to one of the three trial intervention arms. Randomisation will be performed by an online random-
isation system developed and maintained through the
Sheffield Clinical Trials Research Unit (CTRU). The ran-
domisation sequence will be generated in advance by the
trial statistician. Randomisation will be stratified by
centre (as heterogeneity between centres is expected),
and according to severity of word retrieval at baseline,
based on percentage scores on the Naming Objects sub-
test of the Comprehensive Aphasia Test (severe = 10 to
34%, moderate = 35 to 64%, and mild = 65 to 90%). The Recruitment SLT = speech and language therapist; TOMS = Therapy Outcome Measures; COAST = Communication Outcomes After Stroke questionnaire; SLTA speech and
language therapy assistant. Method of collection Change in functional communication 10-minute videoed conversations structured
around topics of personal interest. Activity
scale of TOMS used to measure conversational
ability Collected by blinded SLT at baseline. Separate
blinded SLT at 6, 9, and 12 months. Patients and carers - central team to send monthly
letter reminding to send back in prepaid envelope. Completed by SLT, monitored by central study team. Self-managed practice monitored by central study
team. Puzzle book completion and telephone support
recorded by member of central study team. topics of personal relevance to the participants by the
speech and language therapist performing an
assessment to ensure the sensitivity of the measure. The same topic guide will be followed by blinded
speech and language therapists performing outcome
measures. Independent speech and language therapists
blinded to treatment allocation and measurement time
point will rate the videoed conversations at the project
coordinating centre using the activity scale of the
Therapy Outcome Measures (TOMS) [26]. Generalisation of treatment to retrieval of untreated
words will be measured using the Naming Objects subtest
from the Comprehensive Aphasia Test. Carer perception
of communication effectiveness will be measured using
the Carer COAST questionnaire [28]. Carer quality of life
will be measured using the last five items of the Carer
COAST questionnaire [28] and the CarerQol question-
naire [29]. Negative effects of treatment will be reported
through diaries. Table 1 summarises the main measures
and methods of data collection. Follow-up assessments
will be conducted within one month of the target time
point. Blinding This is a single blind study. The patient participants are
not blind to their treatment allocation. The speech and
language therapists performing baseline assessments will
do this prior to randomisation. A second speech and
language therapist at each site, blinded to group alloca-
tion, will perform follow-up assessments. The speech
and language therapist setting up the treatment will ask
participants not to discuss treatment with the person
coming to carry out the follow-up measures. It is pos-
sible that unblinding will happen during conversation
and the speech and language therapists will be asked to
record instances of this. A primary outcome is func-
tional communication in conversation. Video recordings
of conversations will be presented in random order to
speech and language therapists in the project coordinat-
ing centre to rate, blind to treatment allocation and
follow-up time. The chief investigator, study manager,
statisticians and health economist will all be blind to
group allocation. Regular self-managed practice
The participant will then be asked to work through the
exercises on the computer and be encouraged to
practise each day for 20 to 30 minutes. Participants will
be given a six-month period to work though the therapy
material on the computer and practise using the new
vocabulary in their daily lives. As this is a pragmatic
trial, those participants who have the software installed
on their own computers will not be prevented from
continuing to practise if they wish, following the six-month
supported intervention time. Any continued use of
software beyond the six months will be recorded. Other secondary Evidence of treatment effect will be measured by repeat-
ing all outcome measures at nine and 12 months from
baseline, in addition to the primary end point of 6 months. The nine-month time point is included as an interim
measure as drop out from the study was found to increase
over time in the pilot study [13]. Page 7 of 12 Palmer et al. Trials (2015) 16:18 Qualified speech and language therapist assessment,
tailoring of exercises and monitoring
The speech and language therapist at each site will
tailor computer exercises to the individual using 100
words of personal relevance chosen by the participant. Photographs imaging the 100 words will be selected
from those existing in the software, or can be added
from a digital camera or from image stores on a
computer. The computer software (StepbyStep© by
Steps Consulting Ltd, Gloucester, UK) [30] enables the
speech and language therapist to select exercises using
these words that follow steps in the therapy process
that the therapist would take if delivering it face to
face. The speech and language therapist bases the
selection of exercises on language skills demonstrated
in the initial language assessments. The speech and
language therapist will provide initial demonstration of
the software exercises, check that the individual is able
to use the software and monitor the appropriateness of
the tailored exercises. This is expected to take only
three to four hours, based on the pilot study [13], as
the computer intervention is predominantly self-managed
by the patient. research speech and language therapist will then inform
the participant which group they have been allocated to
and draw their attention to the description of this group
in the information sheet. Treatment fidelity The speech and language therapists delivering this inter-
vention will receive training on how to set up appropriate
exercise steps. To enable monitoring of the treatment fi-
delity, they will be asked to complete a checklist which
guides their selection of exercises based on the participant
language profile identified during assessment. These will
be reviewed centrally by the study quality monitor. Encrypted and anonymised key files from the partici-
pants’ software will be returned to the study team to
enable comparison of a random selection of exercises
provided with the corresponding checklist completed. As this is a self-managed intervention, adherence of
the participants in using the intervention as intended
will be monitored. This will be achieved through volun-
teer or assistant visits with reminders to practise daily
and assistance with using the full range of exercises set. The speech and language therapist will also monitor
practice through feedback forms provided by the volun-
teer or assistant. In addition, the software key files
returned to the study coordinating team centrally will be
reviewed for total practice time and patterns of practice
over the six-month treatment period. Practice with the
computer for a minimum of 20 minutes three times a
week at home on average will be considered per protocol
to account for periods of illness and holiday. Volunteer
and assistant adherence will be monitored through their
feedback forms to the speech and language therapists
who will record amounts of support provided. A mini-
mum of four hours in total per patient will be consid-
ered per protocol. Adherence to the attention control
group will be monitored by recording information re-
garding the number of puzzles completed and the fre-
quency and duration of telephone support calls received. Usual care will be recorded across the study period for
all groups. Attention and activity control arm The third group in
this study intends to control for the potential impact of ele-
ments of the intervention which of themselves do not pro-
vide or require specific speech and language intervention. Participants randomised to this arm will be provided
with generalised activities to carry out and general atten-
tion in addition to usual care. On allocation to this
group, the speech and language therapists conducting
baseline assessments will provide books of standard puz-
zles that can be purchased from most supermarkets or
high street shops. Interventions
l language therapist; encourage the use of new words
in everyday situations, conversation and discussions
with family about how to encourage use and encourage
re-use of completed exercises over time. The participants will be able to contact the volunteer
or SLTA by telephone for technical advice on computer
use between planned visits if necessary. Volunteers and
SLTAs will be asked to complete a feedback form on
each face-to-face session with a participant and send it
to the therapist to enable them to provide tailored
advice and support. They therapists are also encouraged
to meet with all the volunteers/SLTAs together every two
months for support and discussion of issues arising. The majority of the practice time involved in the
intervention is self-managed by the participant through
regular use of the aphasia computer software. The
therapists, SLTAs and volunteers will be asked to
keep diaries of resource use showing direct and indir-
ect (telephone and computer set up) time spent and
therapist grade (see Table 1). Interventions
l Usual care control arm Usual care for this pragmatic
study may consist of participation in a range of activities
to a greater or lesser extent. Usual care varies across the
country in terms of type, frequency and length of provision,
and is dependent upon available resources in each locality. Findings from the pilot study confirmed that usual care for
four months or more following a stroke may include: face-
to-face speech and language therapy targeting language im-
pairment (reading, writing, speaking or understanding);
therapy focussing on compensatory communication strat-
egies, provision of communication aids or psychological
support; attendance at voluntary support groups or infor-
mal communication support from family and friends. Usual
care will be recorded retrospectively for three months prior
to the study and throughout the study on the case report
forms for all groups. Those who are randomised to the usual
care group will not receive any project specific intervention. Volunteer support to assist with treatment adherence
and carry over into daily activity Volunteer support to assist with treatment adherence
and carry over into daily activity
To enhance treatment adherence, the speech and
language therapist will provide training to local
volunteers who already have a working relationship
with the SLT department or SLT assistants based in the
department. They will use the three-hour training
programme and instruction book (University of
Sheffield, Sheffield, UK) developed and evaluated
during the pilot study. The volunteer will be asked
to visit the participant once a month for an hour, or
every two weeks for half an hour (to suit the patient),
carrying out the following tasks: provide technical
assistance; observe and encourage use of computer
exercises; check results and discuss difficulties; assist
the participant to move on to harder tasks in the
therapy process pre-programmed by the speech and Self-managed computerised therapy intervention A
structured intervention is proposed in addition to usual
care as tested in the pilot study. The intervention targets
word retrieval as it is one of the challenges most fre-
quently experienced by people with aphasia, restricting
their communication. The three components of the inter-
vention are as follows: Page 8 of 12 Palmer et al. Trials (2015) 16:18 Palmer et al. Trials (2015) 16:18 if necessary, again, mimicking the access to the volun-
teers and SLTAs and type of attention available in the
intervention arm. Treatment fidelity Each book will contain enough activ-
ities for one to be carried out each day for at least a
month. Examples of puzzles include getting through a
maze, spotting the difference between pictures, matching
objects that are the same, word searches, Sudoku and so
forth. The SLT will provide age appropriate puzzle books
that match the participant’s linguistic ability as indicated
by the baseline assessments. Puzzle books will be colour
coded into levels of easy, medium and hard by the clini-
cians on the research team centrally and a leaflet will be
provided to give speech and language therapists guid-
ance on skills required for each level. Data and statistical analysis
Sample size The study aims to recruit 285 participants
across 20 speech and language therapy departments
(study sites and centres). The sample size of 285 patients
in total (95 per arm) is the maximum sample size esti-
mate across the two primary endpoints (word finding
ability and functional conversation ability) and key sec-
ondary endpoint (patient perception of communication
ability) for 90% power and a two-sided significance level
of 5%. A member of the research team will contact the par-
ticipants or their carer by telephone or email (whichever
is preferred by the participant) once a month to provide
the attention similar to that given by volunteers in the
intervention arm. They will ask if they are enjoying the
activities, how many they have managed to do, whether
they would like a new puzzle book sent to them for the
coming month and whether they would like the same
level of difficulty or an easier or harder one. The partici-
pants will also have access to these contact details to en-
able them to ask for easier or harder books at any time Assumptions for the sample size calculation For im-
provement in word retrieval the estimated effect size is Palmer et al. Trials (2015) 16:18 Page 9 of 12 checking will be conducted throughout the study and
prior to any analysis of the data. 10%, with a standard deviation (SD) of 17.38%, from an
analysis of covariance (based on results of the pilot study
[13]). For assessment of conversation the estimated ef-
fect size is 0.45 of a SD (with a correlation between
baseline and outcome of 0.5 previously observed in the
ACT NoW study). Treatment fidelity For patient-rated improvement using
the COAST questionnaire the estimated effect size is
7.2, with a standard deviation (SD) of 13.5 (with an as-
sumed correlation between baseline and outcome of 0.5). The observed dropout rate was 5 out of 33 (15%; 95% CI: 5
to 32%) in the pilot study, which translated to a completion
rate of 28/33 (85%; 95% CI: 68 to 95%) [31]. Primary and key secondary endpoints for the compari-
sons of control to intervention and active control to
intervention will be analysed using a Hochberg testing
procedure, which allows for an investigation of all three
endpoints whilst maintaining the overall type I error at
5% [32]. This approach has the advantage of not inflat-
ing the sample size while maintaining the type I error
rate at 5%. Significance will be declared for the comparison of
usual care to intervention if and only if both primary
outcomes, word retrieval and conversation, are signifi-
cant at the 5% level, or if either comparison is significant
at 2.5%. If and only if significance is declared for both
primary outcomes, a similar comparison of attention
control to intervention will be made. Significance will be
declared for the comparison of attention control to inter-
vention if and only if both word retrieval and conversation
are significant at the 5% level, or if either comparison is
significant at 2.5%. Internal pilot The initial phase of the study will be conducted as an in-
ternal pilot trial and will include clear criteria to inform de-
cisions about progression. Data from the internal pilot will
be included in the final analysis. The internal pilot trial will
be limited to six sites (over 25% of the total), representative
of the sites which will be in the substantive study. However,
during this phase we will recruit and commence set-up
processes for all the intended sites. The progression criteria
will be reviewed eight months from site set-up of the sixth
site in the internal pilot trial. We are estimating that this
will be approximately halfway through the recruitment
phase, at 22 months from contract start. If and only if significance is declared for the comparison
of attention control to intervention for both comparisons
will the key secondary outcome measure (patient percep-
tion of communication and related quality of life, mea-
sured using the COAST rating scale) be used in a further
comparison of usual care to intervention. If and only if
this comparison is significant at the 5% level will the inter-
vention be compared to attention control based on the
COAST questionnaire (see Figure 2). The progression will be based on achieving the follow-
ing criteria: recruitment of no fewer than 30 participants
(10% of the target for the full trial), a minimum partici-
pant retention rate of 65%, 80% of participants having
been offered a volunteer and 70% of participants con-
tinuing to be supported by the same volunteer for their
six-month treatment period. Primary analysis will take an intention-to-treat approach
(ITT) for all key measures, and further exploratory ana-
lysis of participants who complied with the intervention
will be undertaken using the same statistical tests, accord-
ing to the per protocol principle (PP). Only patients with
post-randomisation observations will be included in the
primary analysis at six months. A sensitivity analysis re-
sponses will be imputed as appropriate with details pro-
vided in the statistical analysis plan. Quality monitoring
Th
h
d l The speech and language therapists carrying out out-
come measures will receive training on how to deliver
the assessments reliably, including scoring criteria and
benchmarking of scoring video-recorded assessments
with other assessors. Site monitoring visits will also be
carried out within the first six months of recruitment
(and more frequently if required) to check accurate
completion of case report forms, adherence to the
protocol for taking consent and discussion of any is-
sues arising. Health economic analysis A cost utility analysis will be undertaken from the NHS
and personal social service (PSS) perspective. Due to the
use of volunteers to help participants with their use of
the computer program we will undertake a supplemen-
tary analysis taking a societal perspective. Costs will be
estimated for individual patients, including intervention
costs and SLT support and coordination time (collected
through diaries as shown in Table 1), combined with
standard costing sources [33]. In the pilot study we col-
lected other resource use data (on, for example, GP and
hospital visits and prescribed medications) via patient
and carer diaries, but these did not show important dif-
ferences between treatment groups and we will not col-
lect such data in the full trial. The EQ-5D questionnaire
will be administered at every data collection time point
(see Table 1) and will be combined with standard valu-
ation sources to measure the QALYs gained in each
treatment arm [34]. An accessible version of the EQ-5D
designed for people with aphasia was trialled in the pilot
study. This has not been validated but represents a way
in which EQ-5D scores can be elicited directly from pa-
tients. We will administer this version of the EQ-5D
alongside the standard version which will be completed
by carers (where the participant has a carer) by proxy. EQ-5D and CarerQoL scores will also be elicited from
carers (Table 1). Statistical analysis Patients with at least one post-randomisation observa-
tion will be included in the analysis. Missing data will be
described using summary statistics. Data will be checked
and cleaned blind to the actual treatment allocation. Data Figure 2 Statistical testing procedure. COAST = Communication Outcomes After Stroke questionnaire. Palmer et al. Trials (2015) 16:18 Palmer et al. Trials (2015) 16:18 Page 10 of 12 Page 10 of 12 The mean difference in percentage improvement of
words named correctly between the treatment and con-
trol groups, adjusted for baseline naming ability, will be
analysed using an analysis of covariance (ANCOVA). Terms for treatment and baseline will be fitted into the
model. Assumptions underlying the analyses will be
assessed by inspection of residual plots. Homogeneity of
variance will be assessed by plotting the studentised re-
siduals against the predicted values from the model,
whilst Normality will be assessed by use of Normal
probability plots. If the assumptions for the analysis of
variance are violated then appropriate transformations
may be applied or alternative analyses may be performed. Similar analyses will be undertaken for the endpoints of
functional conversation ability (measured by the activity
scale of the Therapy Outcome Measures and patient-
reported communication outcomes (the COAST ques-
tionnaire). The endpoints at nine and 12 months will be
similarly analysed for exploratory purposes. Likewise an
investigation of trends over time will be made. QALY gained, however results were uncertain and the
value of obtaining further (perfect) information was very
high (expected value of perfect information (EVPI) was
approximately £37 million). This model will be updated
with data from the full trial. The third attention control
group will be added to the model. Differences between
costs and QALYs in the three groups will be described
and an incremental analysis will be performed with
ICERs calculated. Probabilistic sensitivity analysis will
be undertaken to allow the production of cost effect-
iveness acceptability curves [33] and value of informa-
tion analyses [35]. Discussion Chronic aphasia has a considerable impact on a person’s
ability to participate in many personal, social and work
activities. Despite evidence of the potential for continued
language improvement over time with intensive practice
of targeted, salient language therapy exercises, opportun-
ities to participate in such ongoing therapy are limited
due to resource pressures. There is preliminary evidence
of the potential for computer software developed for
aphasia therapy to provide new opportunities for on-
going aphasia therapy for patients to participate in for as
long as they wish and/or benefit. Indeed, there is an in-
crease in the software options being developed for inde-
pendent language practice. In order for health services
or private practitioners and the public to invest in this
option it is crucial to know whether such interventions
are clinically and cost effective. This protocol describes
the first fully powered RCT of long term aphasia therapy
delivered through self-managed computerised language
exercises, with the support of volunteers or assistants. The protocol also describes the process for the first full
economic analysis of a computerised aphasia intervention. The therapy under investigation is a complex interven-
tion of word finding therapy for aphasia. Previous stud-
ies, including the pilot study informing this protocol,
have shown that people with aphasia learn the words
that are meaningful to them more successfully than
those they have little functional need for. As in many re-
habilitation interventions, this therapy is driven by the We developed a Markov model to estimate the cost ef-
fectiveness of the computer intervention alongside our
previous pilot study. Model parameters were informed
by clinical data from the trial. We estimated that the
intervention was likely to be cost effective, with an in-
cremental cost effectiveness ratio (ICER) of £3,058 per Palmer et al. Trials (2015) 16:18 Page 11 of 12 Page 11 of 12 patient’s own goals. Communication needs to achieve
different goals are discussed with the therapist and a
range of words key to achieving those goals are identi-
fied. The personalisation of the therapy goals requires
some personalisation in the measurement of whether
they have been achieved. The design of outcome mea-
sures which can be used to make group comparisons
whilst maintaining accurate measurement of individual
goals was a challenge. Discussions resulted in two pri-
mary outcome measures. Discussion The first measures word find-
ing ability whereby all participants have comparable
word finding scores from naming 100 pictures. Measure-
ment of word finding of personally meaningful and use-
ful words is achieved by allowing the 100 words to be
different for each individual according to their goals. Similarly, the second measures ability to communicate
in conversation. All conversations are rated using the ac-
tivity scale of the TOMS so group comparisons can be
made. Measurement of individual goals is maintained by
structuring the conversations around the communication
areas identified as personally relevant by each individual. sufficiently to provide informed consent and therefore
need the involvement of a carer, relative or legal represen-
tative. In addition, the reading deficits make completion of
standard questionnaire tools such as the EQ-5D difficult
and unreliable. We therefore developed and tested an ac-
cessible EQ-5D which uses illustrations and visually repre-
sented extent of difficulty. There are three groups in the study. Introducing a
three-way comparison increases the required sample size
and therefore poses a potential threat to the power of
the study if recruitment is insufficient. However, a three-
way comparison is not required here as the first question
to answer is whether the computerised intervention is
more effective than usual care alone. Only if the answer
to the first question is positive is there a need to ask
whether it is the speech and language therapy compo-
nents that cause the effectiveness shown. In this case a
second comparison of computer intervention to activity
and/or attention control needs to be carried out. The
Hochberg analysis was chosen to allow for these con-
secutive comparisons, thus also maintaining a more
achievable sample size. Other key issues in designing the protocol arose from
the pragmatic nature of the study. First of all, in order to
recruit sufficient numbers of participants, at least 20
speech and language departments are required across
the United Kingdom. This will allow generalisation of
the results to the population of the United Kingdom. However, we expect considerable variation in the usual
care provided to people with aphasia in the long term
post stroke, with some sites providing impairment based
interventions face to face for several months, and others
limiting their service provision to hospital care or for a
few weeks post-hospital discharge only. The intervention
being tested could be implemented in addition to any
existing services in practice. Authors’ contributions RP is the chief investigator of the study and led the protocol design and the
writing of this manuscript. CC, PE, MB and AB contributed to the design of
the protocol and helped to draft the manuscript. SJ carried out the power
calculation and designed the analysis plan. NL designed and wrote the
health economic sections of the protocol. All co-authors read and approved
the manuscript. Abbreviations ANCOVA: Analysis of covariance; CAT: CIAT, Constraint induced aphasia
therapy; COAST: Communication Outcomes After Stroke; CST: Consent
support tool; CTRU: Clinical Trials Research Unit; EVPI: Estimated value of
perfect information; ICER: Incremental cost effectiveness ratio;
ISRCTN: International standard randomised controlled trial number;
MOAT: Model oriented aphasia therapy; NHS: National Health Service;
NIHR: National Institute of Health Research; PSS: Personal social service;
QALYs: Quality-adjusted life years; RCT: Randomised control trial; SLT: speech
and language therapy; SLTA: Speech and language therapy assistant;
TOM: Therapy Outcome Measures. Discussion The study therefore uses
an adjunct design whereby patients continue to receive
any ongoing care. This may have the added benefit of
recruiting those patients who would not wish to be
randomised away from usual care. To account for the
heterogeneity expected, the randomisation is to be
stratified by site, ensuring representation of different
models of usual care in each study group. Finally, the set-up of 20 individual speech and lan-
guage therapy departments to participate in the study is
a considerable challenge, in which service support and
excess treatment costs must be negotiated at each site
independently, with a large range of local policies and fi-
nancial restrictions across the United Kingdom. Competing interests There are challenges in involving people with aphasia
in research, as they often have difficulty reading or un-
derstanding spoken language. The protocol for obtaining
informed consent therefore needed careful consideration. In order to adhere to the Mental Capacity Act (2005) in
England and the Adults with Incapacity Act (2000) in
Scotland, a consent support tool has been included to
identify reading and spoken comprehension ability of indi-
viduals and recommend the style of information that is
likely to best inform each individual. The tool also identi-
fies those participants whose aphasia severity is such that
they
are
unlikely
to
understand
the
information g
The authors declare they have no competing interests. The authors declare they have no competing interests. Trial status The study has received ethical approval and fifteen partici-
pants have been recruited from the first five sites set up. References Submit your next manuscript to BioMed Central
and take full advantage of:
• Convenient online submission
• Thorough peer review
• No space constraints or color figure charges
• Immediate publication on acceptance
• Inclusion in PubMed, CAS, Scopus and Google Scholar
• Research which is freely available for redistribution
Submit your manuscript at
www.biomedcentral.com/submit Submit your next manuscript to BioMed Central
and take full advantage of:
• Convenient online submission
• Thorough peer review
• No space constraints or color figure charges
• Immediate publication on acceptance
• Inclusion in PubMed, CAS, Scopus and Google Scholar
• Research which is freely available for redistribution
Submit your manuscript at
www.biomedcentral.com/submit Received: 22 August 2014 Accepted: 19 December 2014 24. Swinburn K, Porter G, Howard D. Comprehensive Aphasia Test. London:
Psychology Press; 2004. 25. Jayes M, Palmer R. Initial evaluation of the consent support tool: a
structured procedure to facilitate the inclusion and engagement of people
with aphasia in the informed consent process. Int J Speech Lang Pathol. 2013;16:159–68. Acknowledgements This report is independent research funded by the National Institute for
Health Research (Health Technology Assessment number: 12/21/01AB;
Clinical and cost effectiveness of aphasia computer therapy compared with
usual stimulation or attention control long term post stroke (CACTUS)). RP is Page 12 of 12 Page 12 of 12 Palmer et al. Trials (2015) 16:18 Palmer et al. Trials (2015) 16:18 partially funded by an NIHR/HEFCE (Higher Education Council for England)
senior academic clinical lectureship. AB is partially funded by the National
Institute for Health Research Collaboration for Leadership in Applied Health
Research and Care (NIHR CLAHRC), Greater Manchester. MB is partially
funded by the Chief Scientist Office (CSO), Scottish Government Health and
Social Care Directorates. The views expressed in this article are those of the
authors and not necessarily those of the NHS, CSO, NIHR or the Department
of Health. partially funded by an NIHR/HEFCE (Higher Education Council for England)
senior academic clinical lectureship. AB is partially funded by the National
Institute for Health Research Collaboration for Leadership in Applied Health
Research and Care (NIHR CLAHRC), Greater Manchester. MB is partially
funded by the Chief Scientist Office (CSO), Scottish Government Health and
Social Care Directorates. The views expressed in this article are those of the
authors and not necessarily those of the NHS, CSO, NIHR or the Department
of Health. 15. van de Sandt-Koenderman M. Aphasia rehabilitation and the role of computer
technology: can we keep up with modern times? Int J Speech Lang Pathol. 2011;13:21–7. 16. Fink R, Breecher A, Schwarz M, Robey R. A computer-implemented protocol
for treatment of naming disorders: evaluation of clinician-guided and partially
self-guided instruction. Aphasiology. 2002;16:1061–86. 17. Mortley J, Wade J, Enderby P. Superhighway to promoting a client-therapist
partnership: using the internet to deliver word-retrieval computer therapy
monitored remotely with minimal speech and language therapy input. Aphasiology. 2004;18:193–211. On behalf of the Big CACTUS project we would like to thank Liz Cross, Madeleine
Harrison, Helen Hughes, Tim Chater, Ellen Bradley and Annabelle Allison. gy
18. Department of Health. Our Health, Our Care, Our Say: a New Direction for
Community Services. London: Her Majesty’s Government; 2006. References 1. Department of Health. National Stroke Strategy. London: Department of
Health; 2007. 1. Department of Health. National Stroke Strategy. London: Department of
Health; 2007. 26. Enderby PM, John A, Petheram B. Therapy Outcome Measures for
Rehabilitation Professionals. Chichester: John Wiley& Sons Ltd; 2006. 2. Brady MC, Kelly H, Godwin J, Enderby P. Speech and language therapy for
aphasia following stroke. Cochrane Database Syst Rev. 2012;5:CD000425. 2. Brady MC, Kelly H, Godwin J, Enderby P. Speech and language therapy for
aphasia following stroke. Cochrane Database Syst Rev. 2012;5:CD000425. 27. Long A, Hesketh A, Paszek G, Booth M, Bowen A. Development of a reliable
self-report outcome measure for pragmatic trials of communication therapy
following stroke: the Communication Outcome after Stroke (COAST) scale. Clin Rehabil. 2008;22:1083–94. 3. Laska A, Kahan T, Helblom A, Murray V, Von Arbin MA. Randomized
controlled trial on very early speech and language therapy in acute stroke
patients with aphasia. Cerebrovasc Dis Extra. 2011;1:66–74. 3. Laska A, Kahan T, Helblom A, Murray V, Von Arbin MA. Randomized
controlled trial on very early speech and language therapy in acute stroke
patients with aphasia. Cerebrovasc Dis Extra. 2011;1:66–74. 28. Long AF, Hesketh A, Bowen A, on behalf of the ACT NoW Study. Communication outcome after stroke: a new measure of the carer's
perspective. Clin Rehabil. 2009;23:846–56. 4. Bowen A, Hesketh A, Patchick E, Young A, Davies L, Vail A, et al. Clinical
effectiveness, cost effectiveness and service users’ perceptions of early,
well-resourced communication therapy following a stroke, a randomised
controlled trial (The ACT NoW Study). Health Technol Assess. 2012;16:26. 29. Brouwer W, van Exel N, van Gorp B, Redekop W. The CarerQol instrument: a
new instrument to measure care-related quality of life of informal caregivers
for use in economic evaluations. Qual Life Res. 2006;15:1005–2. 5. Meinzer M, Djundja D, Barthel G, Elbert T, Rockstroh B. Long term stability of
improved language functions in chronic aphasia after constraint-induced
aphasia therapy. Stroke. 2005;36:1462–6. 5. Meinzer M, Djundja D, Barthel G, Elbert T, Rockstroh B. Long term stability of
improved language functions in chronic aphasia after constraint-induced
aphasia therapy. Stroke. 2005;36:1462–6. 30. Steps Consultancy Ltd: StepbyStep© software. [http://www.aphasia-software.com] 31. Julious SA. Sample Sizes for Clinical Trials. London: Chapman and Hall; 20 6. Raymer A, Beeson P, Holland A, Kendall D, Maher L, Martin N, et al. Translational research in aphasia: from neuroscience to neurorehabilitation. J Speech Lang Hear Res. 2008;51:259–75. 6. Author details
1 19. Katz R, Wertz R. The efficacy of computer-provided reading treatment for
chronic aphasic adults. J Speech Lang Hear Res. 1997;40:493–507. 1School of Health and Related Research, University of Sheffield, 107 Innovation
Centre, 217 Portobello, Sheffield S1 4DP, England. 2Nursing, Midwifery and
Allied Health Professions Research Unit, Glasgow Caledonian University,
Cowcaddens Road, Glasgow G40BA, England. 3Medical Statistics Group, School
of Health and Related Research, University of Sheffield, Regent Court, Regent
Street, Sheffield S1 4DA, England. 4Reader, School of Psychological Sciences,
University of Manchester (MAHSC), Joint theme lead - Patient-Centred Care,
NIHR CLAHRC Greater Manchester, Centre for Stroke and Vascular Research,
CSB, Salford Royal NHS Foundation Trust, Stott Lane, Salford M6 8HD, England. 5Senior Research Fellow in Health Economics, Health Economics and Decision
Science, ScHARR, University of Sheffield, Regent Court, 30 Regent Street,
Sheffield S1 4DA, England. 20. Palmer R, Mortley J. How I offer impairment therapy (2): from idealism
to realism, step by step. Speech & Language Therapy in Practice. 2011; Winter:29–32. 21. Palmer R, Enderby P, Paterson G. Using computers to enable self-management
of aphasia therapy exercises for word finding: the patient and carer perspective. Int J of Language and Communication Dis. 2013;48:508–21. 22. Latimer NR, Dixon S, Palmer R. Cost-utility of self-managed computer therapy
for people with aphasia. Int J Technol Assess Health Care. 2013;29:402–9. 23. Boutron I, Moher D, Altman D, Schulz K, Ravaud P, for the Consort group. Extending the CONSORT statement to randomized trials of nonpharmacologic
treatment: explanation and elaboration. Ann Intern Med. 2008;148:295–309. Received: 22 August 2014 Accepted: 19 December 2014 Received: 22 August 2014 Accepted: 19 December 2014 References Raymer A, Beeson P, Holland A, Kendall D, Maher L, Martin N, et al. Translational research in aphasia: from neuroscience to neurorehabilitation. J Speech Lang Hear Res. 2008;51:259–75. 32. Hochberg Y, Tamhane AC. Multiple Comparison Procedures. New York:
Wiley; 1987. 33. Curtis L. Unit Costs of Health and Social Care. University of Kent at
Canterbury: Personal and Social Services Research Unit; 2011. 33. Curtis L. Unit Costs of Health and Social Care. University of Kent at
Canterbury: Personal and Social Services Research Unit; 2011. 7. Kurland J, Baldwin K, Tauer C. Treatment-induced neuroplasticity following
intensive naming therapy in a case of chronic Wernicke’s aphasia. Aphasiology. 2010;24:737–51. 7. Kurland J, Baldwin K, Tauer C. Treatment-induced neuroplasticity following
intensive naming therapy in a case of chronic Wernicke’s aphasia. Aphasiology. 2010;24:737–51. 34. Dolan P. Modeling valuations for EuroQol health states. Med Care. 1997;35:1095–108. 8. Pulvermuller F, Berthier M. Aphasia therapy on a neuroscience basis. Aphasiology. 2008;22:563–99. 35. Griffin S, Welton NJ, Claxton K. Exploring the research decision space: the
expected value of information for sequential research designs. Med Decis
Making. 2010;30:155–62. 35. Griffin S, Welton NJ, Claxton K. Exploring the research decision space: the
expected value of information for sequential research designs. Med Decis
Making. 2010;30:155–62. 9. Pulvermuller F, Neininger B, Elbert T, Mohr B, Rockstroh B, Koebbel P, et al. Constraint induced therapy of chronic aphasia after stroke. Stroke. 2001;32:1621. 9. Pulvermuller F, Neininger B, Elbert T, Mohr B, Rockstroh B, Koebbel P, et al. Constraint induced therapy of chronic aphasia after stroke. Stroke. 2001;32:1621. 9. Pulvermuller F, Neininger B, Elbert T, Mohr B, Rockstroh B, Koebbel P, et al. Constraint induced therapy of chronic aphasia after stroke. Stroke. 10. Cherney L, Patterson J, Raymer A, Frymark T. Evidence-based systematic review:
effects of intensity of treatment and constraint-induced language therapy for
individuals with stroke-induced aphasia. J Speech Lang Hear Res. 2008;51:1282–99. Submit your next manuscript to BioMed Central
and take full advantage of: and take full advantage of:
• Convenient online submission
• Thorough peer review
• No space constraints or color figure charges
• Immediate publication on acceptance
• Inclusion in PubMed, CAS, Scopus and Google Scholar
• Research which is freely available for redistribution
Submit your manuscript at
www.biomedcentral.com/submit 11. Barthel G, Meinzer M, Djundja D, Rockstroh B. Intensive language therapy in
chronic aphasia: which aspects contribute most? Aphasiology. 2008;22:408–21. • Convenient online submission 12. David R, Enderby P, Bainton D. Treatment of acquired aphasia: speech
therapists and volunteers compared. J Neurol Neurosurg Psychiatr. 1982;45:957–61. • Thorough peer review 13. Palmer R, Enderby P, Cooper C, Latimer N, Julious S, Paterson G, et al. Computer therapy compared with usual care for people with long standing
aphasia post stroke: a pilot randomized controlled trial. Stroke. 2012;43:1904–11. 14. Cherney LR. Oral Reading for Language in Aphasia (ORLA): evaluating the
efficacy of computer-delivered therapy in chronic nonfluent aphasia. Top
Stroke Rehabil. 2010;17:423–31. 14. Cherney LR. Oral Reading for Language in Aphasia (ORLA): evaluating the
efficacy of computer-delivered therapy in chronic nonfluent aphasia. Top
Stroke Rehabil. 2010;17:423–31. Submit your manuscript at
www.biomedcentral.com/submit
|
https://openalex.org/W2802258562
|
https://europepmc.org/articles/pmc5949354?pdf=render
|
English
| null |
Understanding Activation Patterns in Shared Circuits: Toward a Value Driven Model
|
Frontiers in human neuroscience
| 2,018
|
cc-by
| 11,585
|
Understanding Activation Patterns
in Shared Circuits: Toward a Value
Driven Model
Lisa Aziz-Zadeh 1,2* Emily Kilroy 1,2 and Giorgio Corcelli 3 Lisa Aziz-Zadeh 1,2*, Emily Kilroy 1,2 and Giorgio Corcelli 3 1Brain and Creativity Institute, University of Southern California, Los Angeles, CA, United States, 2Division of Occupational
Science and Occupational Therapy, University of Southern California, Los Angeles, CA, United States, 3Department of
Economics, University of Southern California, Los Angeles, CA, United States Over the past decade many studies indicate that we utilize our own motor system to
understand the actions of other people. This mirror neuron system (MNS) has been
proposed to be involved in social cognition and motor learning. However, conflicting
findings regarding the underlying mechanisms that drive these shared circuits make
it difficult to decipher a common model of their function. Here we propose adapting
a “value-driven” model to explain discrepancies in the human mirror system literature
and to incorporate this model with existing models. We will use this model to explain
discrepant activation patterns in multiple shared circuits in the human data, such that
a unified model may explain reported activation patterns from previous studies as a
function of value. Keywords: mirror neuron system, motor learning, social cognition, shared neural networks, value-based decision
making REVIEW REVIEW
published: 07 May 2018
doi: 10.3389/fnhum.2018.00180 Reviewed by: Lei Xu,
University of Electronic Science and
Technology of China, China
Tetsuo Yamamori,
RIKEN Brain Science Institute (BSI),
Japan University of Electronic Science and
Technology of China, China
Tetsuo Yamamori,
RIKEN Brain Science Institute (BSI),
Japan *Correspondence:
Lisa Aziz-Zadeh
lazizzad@usc.edu The MNS (inferior frontal gyrus [IFG], ventral premotor cortex [vPMC] and posterior parietal
cortex [PPC]) responds both when one executes an action and when one observes someone else
make the same action (e.g., opening a bottle of champagne and watching someone else perform
the action; Rizzolatti and Craighero, 2004). Data also indicate that some mirror neurons may also
respond to the sounds of actions (Kohler, 2002). Because observing others activates one’s own
motor systems, it is thought that the MNS is important for action and social understanding. That
is, part of how we may understand other people’s actions and intentions is by simulating their
actions onto our own motor representations (Keysers et al., 2004). Received: 13 December 2017
Accepted: 17 April 2018
Published: 07 May 2018 INTRODUCTION Edited by:
Lucina Q. Uddin,
University of Miami, United States
Reviewed by:
Lei Xu,
University of Electronic Science and
Technology of China, China
Tetsuo Yamamori,
RIKEN Brain Science Institute (BSI),
Japan Edited by: Edited by:
Lucina Q. Uddin,
University of Miami, United States Understanding other people’s actions and feelings is an essential component of successful social
interactions. Recent neuroscience data indicate that the neural mechanisms involved in processing
one’s own actions, sensations and emotions are also involved in perceiving and understanding
the actions, sensations and emotions of others (Gallese and Goldman, 1998; Keysers et al., 2004,
2010; Keysers and Gazzola, 2009). These ‘‘shared circuits’’ are thought to constitute pre-reflective
processes in social cognition, involving automatic and intuitive levels of representation (Coricelli,
2005). Such shared circuits include the mirror neuron system (MNS), the pain matrix and the
somatosensory cortices. Citation: Aziz-Zadeh L, Kilroy E and Corcelli G
(2018) Understanding Activation
Patterns in Shared Circuits: Toward a
Value Driven Model. Front. Hum. Neurosci. 12:180. doi: 10.3389/fnhum.2018.00180 Since the discovery of the MNS, it has been suggested that other brain regions might also be
active both for processing one’s own experiences as well for processing the experiences of other
people. For example, there is evidence for a shared neural system for processing disgust, where
human subjects use the same neural regions in the anterior insula for the physical experience May 2018 | Volume 12 | Article 180 Frontiers in Human Neuroscience | www.frontiersin.org 1 Shared Circuits and Value Aziz-Zadeh et al. of disgust as well as for perceiving another person experience
disgust (facial expressions), has also been shown (Wicker et al.,
2003). A similar social mirroring mechanism is thought to exist
for emotion and pain processing as well as somatosensation. Previous research indicates that we process other people’s pain
by activating the neural systems that processes pain in our own
bodies. This ‘‘pain matrix’’ includes the insula, anterior and
middle cingulate gyrus and somatosensory cortices (Singer et al.,
2004; Avenanti et al., 2005; Jackson et al., 2006; Bufalari et al.,
2007; Di Cesare et al., 2015), though it has been suggested that
this network responds to a variety of salient stimuli (Lannetti
and Mouraux, 2010). In addition, watching another person being
touched (e.g., watching a snake slither up another person’s
leg or being brushed up against by a cat) activates our own
secondary somatosensory cortices (Keysers et al., 2004; Meyer,
2011). Keysers et al. (2004) reported that observing another
person’s leg being stroked activated the secondary somatosensory
cortex (SII) bilaterally, the same as when the person was touched
themselves. Such ‘‘shared neural circuits’’ involved in processing
one’s own experiences as well as the experiences of other people,
might be an important neural basis of social cognition. (Gallese and Goldman, 1998), the context (Liepelt et al., 2009), or
their physical body (Buccino et al., 2004). Following an empirical
Bayes inference, the model states that our prior expectations of an
action have an associated standard deviation. A predication error
is generated by the comparison between the predicted action and
the actual observed action. Thus, they theorize that predictive
coding may provide a computational framework for inferring the
causes of sensory information. Citation: In the case of action observation,
causes may include goals, intentions and motor commands and
sensory inputs may include observed kinematics. Thus, when we
observe someone swing a tennis racket and hit a ball, we may
use the same models that we use to perform the action ourselves
to infer motor commands and kinematics from the observed
actions of other people. A discrepancy in prediction error would
result in greater MNS activation, which may reflect increased
demands to learn, predict, or assimilate to novel actions (Cross
et al., 2007). Cross and her colleagues utilized this predictive model for
the MNS to build a model that used predictability as a metric
to explain fMRI results (Cross et al., 2012; Diersch et al.,
2013). In their U-shaped model, observed actions that are
extremely high or extremely low in predictability activated the
MNS most strongly, while observed actions that are moderately
predictable activated the MNS the least (Figure 1). However,
when considering the neural efficiency theory, one would expect
that increased familiarity with an action would result in a
more efficient use of neural resources while perceiving that
action. Cross and colleagues (Gardner et al., 2017) recently
tested this theory and proposed adjusting the quadratic U-shaped
predicative model to a cubic model to account for changes
in neural efficiency upon increased familiarity with an action Discrepancy in Research Findings
Regarding Activation of Shared Neural
Circuits The idea that we utilize our own sensorimotor representations
to process and understand other people has been the focus of
much recent research. However, there has been a great deal
of discrepant findings in what drives activity in these shared
neural circuits (e.g., MNS, somatosensory cortices, pain matrix,
emotion-related brain regions). Some research groups have
shown increased activity in shared circuits for observing liked
individuals (Singer et al., 2006) or individuals more similar to the
self (Xu et al., 2009) while other studies show the opposite (Fox
et al., 2013; Losin et al., 2014). Some groups find more activity
for observing actions for which one has expertise (Raichle et al.,
2001; Cross et al., 2006, 2009; Beudel et al., 2011; Liew et al.,
2011; Gardner et al., 2015), while other groups find that novelty
drives activation patterns (Cross et al., 2012; Aziz-Zadeh, 2013;
Grossmann et al., 2013; Liew et al., 2013; Tipper et al., 2015). These discrepant findings (discussed further in ‘‘Relation of the
Value Model to Human Data’’ section) not only raise important
questions about what drives activity in shared neural circuits, but
also their function. FIGURE 1 | Familiarity Model: a representation of the predictability model
proposed by Cross et al. (2012). The horizontal axis represents predictability of
an action and the vertical axis represents activity in mirror neuron regions. In
2017, Cross and her colleagues updated this to a cubic model (Gardner et al.,
2017). PREVIOUS MODELS One model that has previously been put forward to better
understand the function of the MNS and its activation patterns
utilizes the notion of predictive modeling. In this model,
Kilner et al. (2007) utilize largely established forward or
generative models that are critical to motor control (Miall and
Wolpert, 1996; Wolpert et al., 2003; Kilner et al., 2007; Neal
and Kilner, 2012). They extend the same model for action
observation. The predictive coding account posits that the MNS
is involved in creating predications of other people’s actions Frontiers in Human Neuroscience | www.frontiersin.org TOWARD AN EXPLANATORY MODEL Recent neurophysiological findings may shed light on an
underlying mechanism that modulates the MNS. Single cell
recordings in monkeys indicate that subjective value drives
activity in mirror neurons in F5 (Caggiano et al., 2012). That
is, mirror neurons respond to the observation of actions that
are valuable to the monkey, such as picking up a banana as
compared to picking up a pretzel or another food item they are
not fond of (see Figure 2). Even observation of actions that from
the offset are arbitrary to a monkey, once paired with reward,
elicit a stronger response in mirror neurons than actions that are
not paired with reward (Caggiano et al., 2012). The researchers
posit that through connections with reward circuits in the basal
ganglia, mirror neurons are especially attuned to observation of
actions that are subjectively valuable to the observer (Caggiano
et al., 2012). These findings are reminiscent of findings from
a previous study by Platt and Glimcher (1999) showing that
activity in the lateral intraparietal area (LIP), a brain region
involved in transferring visual information to motor actions in
the monkey as well as a region later shown to have mirror
neurons (Shepherd et al., 2009), is correlated with expected value. Here, we define value as the subjective importance, worth or
usefulness of something. Subjective value can be modulated by
reward, learning, valence, motivation and social context. While OMPFC neurons encode value, they are not modulated
by the location in space a reward is given or the motor
response associated with a reward. This is in contrast to
other value processing brain regions, in which value modulates
activity related to sensory or motor processes (Conen and
Padoa-Schioppa, 2016). Thus indirect reward processing could
modulate sensorimotor regions. For example, the anterior
cingulate cortex (ACC) represents quantitative reward prediction
errors (Amiez et al., 2006; Matsumoto and Hikosaka, 2007; Seo
and Lee, 2007) especially of actions (Matsumoto and Hikosaka,
2007). Thus, its activity is closely tied to action selection and it
may therefore be an important component for action observation
as well. The anticipation of a large reward also triggers strong
neuronal activation patterns in motor networks (Roesch and
Olson, 2003, 2004, 2007; Wallis and Kennerley, 2010). The
frontal eye fields, and the premotor cortex modulate attentional
resources using the reward signal (Wallis and Kennerley, 2010)
as do parietal regions (Platt and Glimcher, 1999). FIGURE 1 | Familiarity Model: a representation of the predictability model
proposed by Cross et al. (2012). The horizontal axis represents predictability of
an action and the vertical axis represents activity in mirror neuron regions. In
2017, Cross and her colleagues updated this to a cubic model (Gardner et al.,
2017). FIGURE 1 | Familiarity Model: a representation of the predictability model
proposed by Cross et al. (2012). The horizontal axis represents predictability of
an action and the vertical axis represents activity in mirror neuron regions. In
2017, Cross and her colleagues updated this to a cubic model (Gardner et al.,
2017). Frontiers in Human Neuroscience | www.frontiersin.org May 2018 | Volume 12 | Article 180 2 Shared Circuits and Value Aziz-Zadeh et al. (Gardner et al., 2017). However, as we will delineate in ‘‘Relation
of the Value Model to Human Data’’ section, the U-shaped model
cannot explain why individuals with stroke show more activity
for observation of actions made with the paretic rather than the
non-paretic hand (the non-paretic hand is highly predictable
while the paretic hand is moderately predictable, Garrison et al.,
2013). Nor can it explain why observation of an action made by
an amputee’s residual limb (highly unpredictable) and a typical
hand action (highly predictable) should differ in their activation
levels (Liew et al., 2013). While the cubic model has more
potential to explain these results, the shape of the model remains
largely unknown, and thus it is difficult to determine where many
moderately familiar stimuli (e.g., paretic hand) would fit in the
cubic model. For a stroke patient, a paretic hand is somewhere in
the middle for familiarity, and in the cubic model, since the shape
of it is vague, somewhere in the middle can either be high MNS
activity or low MNS activity. Furthermore, while it is likely that
familiarity and expertise modulate shared circuits, it seems that
other factors, such as value, valance, etc., are needed to further
explain these results. Indeed, there is a need to understand
shared circuits as broader networks that are tied with emotion
processing, reward systems and other circuits along with the
sensorimotor networks within which they are commonly seen. FIGURE 2 | Mirror neuron activity is modulated by subjective value. As
presented by Caggiano et al. (2012), the figure illustrates neural activity from
single cell recordings of an exemplary mirror neuron in F5 of a monkey while it
was presented with three different rewards: the most rewarding treat
symbolized by a banana (blue coloring), a less relished reward indicated by the
pretzel (green coloring) and an non-preferred food item represented by an “X”
(red coloring). Taken from: Caggiano et al. (2012). FIGURE 2 | Mirror neuron activity is modulated by subjective value. As
presented by Caggiano et al. (2012), the figure illustrates neural activity from
single cell recordings of an exemplary mirror neuron in F5 of a monkey while it
was presented with three different rewards: the most rewarding treat
symbolized by a banana (blue coloring), a less relished reward indicated by the
pretzel (green coloring) and an non-preferred food item represented by an “X”
(red coloring). Taken from: Caggiano et al. (2012). FIGURE 2 | Mirror neuron activity is modulated by subjective value. As
presented by Caggiano et al. (2012), the figure illustrates neural activity from
single cell recordings of an exemplary mirror neuron in F5 of a monkey while it
was presented with three different rewards: the most rewarding treat
symbolized by a banana (blue coloring), a less relished reward indicated by the
pretzel (green coloring) and an non-preferred food item represented by an “X”
(red coloring). Taken from: Caggiano et al. (2012). dopamine, produced in the VTA, which is known to be
involved with processing both natural and conditioned rewards. Interestingly, ventromedial regions of the VTA and substantia
nigra compacta (SNc) may be involved in coding value, while
dorsolateral regions of the SNc may be involved in coding
motivational salience (Matsumoto and Hikosaka, 2009). From
the VTA, dopamine signals are most strongly projected to the
ventral striatum/nucleus accumbens (NAc). The NAc in turn is
thought to encode reward signals from the VTA. While striatal
neurons are thought to be involved in reward learning, they
do not seem to encode the specific reward. By contrast, orbital
and medial prefrontal (OMPFC) neurons seem to process the
specific nature of the reward (Schultz, 2000; Schultz et al., 2000). In the vmPFC, they may also be involved in the assessment
and assignment of the personal value of the stimulus (Kim and
Johnson, 2013). Frontiers in Human Neuroscience | www.frontiersin.org TOWARD AN EXPLANATORY MODEL The parietal MNS is thought to include the posterior parietal cortex (PPC) while the frontal MNS is
thought to include the ventral premotor cortex (vPMC) and the inferior frontal gyrus (IFG). STS = superior temporal sulcus. For brevity, we don’t include every region
of salient, emotion and reward systems, only primary nodes most likely to be directly related to the MNS. We also note that components of the reward system also
process saliency, as discussed in “Toward an Explanatory Model” section. to the premotor cortex, the study by Caggiano et al. (2012)
on mirror neurons indicate this is true regardless of whether
the reward is for the self or for another person. Again though,
the direct pathways between mirror neuron regions and reward
processing regions remains to be further explored, with current
data showing indirect pathways to motor areas (Haber et al.,
2000). As we delineate in Figure 3, such indirect pathways
could allow not only reward signals to modulate the MNS,
but also other factors such as salience, emotion and other
cognitive processes. With regard to salience, while parts of the
striatum code for this factor (Matsumoto and Hikosaka, 2009)
and saliency is an important factor for processing one stimulus
over another, it should be distinguished by motivational value,
which is a separate factor. That is to say, all valuable stimuli may
be salient (and thus chosen for further processing), but not all
salient stimuli are valuable. future actions from more ambiguous prior observed actions,
and the authors argued that ambiguous actions which need to
be learned may be tied with more reward processing (Diersch
et al., 2013). Pairing a value model with the prediction models
may outcome as a tetrahedron model that combines the cubic
model of Gardner et al. (2017) and adds to the dimension of
value-driven modulation, though such a model is probably still
underestimating the complexity added by other dimensions, such
as valence and saliency. The need for Bayesian theories of brain
processing to incorporate value, emotion and valence processing
has previously been expressed by other researchers (Joffily and
Coricelli, 2013). TOWARD AN EXPLANATORY MODEL With regards While the latter studies indicate that reward affects activity
in the MNS, the direct neural pathways between monkey area
F5 and prefrontal reward regions remain unknown. Previous
studies indicate reward modulates neuronal activity during
goal-directed actions in many parts of the brain, including
mid-brain (ventral tegmental area [VTA], substantia nigra [SN]),
basal ganglia and prefrontal cortex (Schultz, 2000; Schultz et al.,
2000). This modulation is facilitated by the neurotransmitter May 2018 | Volume 12 | Article 180 3 Shared Circuits and Value Aziz-Zadeh et al. FIGURE 3 | Integrating the proposed value-driven model with the Bayesian model of mirror neuron system (MNS) processing. Following processing in visual brain
regions, information flows along established MNS pathways (Iacoboni, 2005) as well as along emotion processing/salience regions (anterior insula, anterior cingulate
cortex [ACC], amygdala) and reward processing regions (substantia nigra reticulate [SNr], substantia nigra compacta [SNc], ventral tegmental area [VTA], ventral
striatum/nucleus accumbens [NAc]). Here we integrate Bayesian models, which include prediction error signals (green arrows), and generative model processing
(blue arrows, Kilner et al., 2007), with emotion and salience processing (pink arrows) and reward processing (red arrows). Indirect reward processing is depicted with
dashed red lines. All of these processes modulate the MNS. The parietal MNS is thought to include the posterior parietal cortex (PPC) while the frontal MNS is
thought to include the ventral premotor cortex (vPMC) and the inferior frontal gyrus (IFG). STS = superior temporal sulcus. For brevity, we don’t include every region
of salient, emotion and reward systems, only primary nodes most likely to be directly related to the MNS. We also note that components of the reward system also
process saliency, as discussed in “Toward an Explanatory Model” section. FIGURE 3 | Integrating the proposed value-driven model with the Bayesian model of mirror neuron system (MNS) processing. Following processing in visual brain
regions, information flows along established MNS pathways (Iacoboni, 2005) as well as along emotion processing/salience regions (anterior insula, anterior cingulate
cortex [ACC], amygdala) and reward processing regions (substantia nigra reticulate [SNr], substantia nigra compacta [SNc], ventral tegmental area [VTA], ventral
striatum/nucleus accumbens [NAc]). Here we integrate Bayesian models, which include prediction error signals (green arrows), and generative model processing
(blue arrows, Kilner et al., 2007), with emotion and salience processing (pink arrows) and reward processing (red arrows). Indirect reward processing is depicted with
dashed red lines. All of these processes modulate the MNS. Frontiers in Human Neuroscience | www.frontiersin.org Observation of Significant or Insignificant
Others Discrepant findings and tasks make the synthesis of the results
difficult to interpret. In some instances, it appears that the IFG
is sensitive not only to self-recognition (Kaplan et al., 2008) but
also to the perceived closeness or value, such as observing a
partner or an important political or social figure (Shah et al.,
2001; Ishai et al., 2002; Taylor et al., 2009). However, these
studies are not sufficient to detangle the ‘‘like me’’ from a
‘‘value’’ model since information about value was not collected
from participants. Furthermore, ‘‘like me’’ characteristics can be
correlated with value in some situations making these variables
difficult to detangle. That is, similarity may be confounded by
value (the more similar, the more value; (Mitchell et al., 2011;
Tamir and Mitchell, 2013). Perhaps a way to disentangle the value
model from the ‘‘like me’’ model is to consider a study where you
compare situations in which you judge characteristics of similar
vs. dissimilar others as well as features you value. For example,
you may be similar with another person in that you are both
smokers, but you consider smoking to be a negative value. By
contrast, you may be similar with another person in that you both
have athletic physiques, and you value this physique very much. Future studies such as this need to be explored. Depending on the situation, observing either a loved one (Cheng
et al., 2010) or an enemy (Fox et al., 2013) in pain can be
equally meaningful and valuable for the observer and elicit
more activity in the underlying shared circuits (Cheng et al.,
2010; Fox et al., 2013). For example, if you are being pursued
by an enemy, seeing them trip over and crouch with pain is
highly relevant information to process, perhaps more so than
observing a neutral or liked individual in pain (e.g., your child). In other circumstances, observing your child slam their finger
in a door is the most relevant information to process. Thus,
the significance or valence of a relationship cannot be the
key-determining factor, but rather the meaning and value of the
observed experience. Similarly, watching someone of the same
race or a different race can be equally valuable information
to an observer depending on the background, situation and
circumstance of the people involved. Observation of Significant or Insignificant
Others Therefore, while some have
previously argued that shared circuits are more active for those
‘‘like me’’ (Molnar-Szakacs and Uddin, 2013) we argue instead
that activation patterns may be better explained by the value
of the observed action and actor to the self, which depends on
goals, relationships, personal history, context, environment and
motivational state. Such a model may be able to explain the
data better than the ‘‘like me’’ model which is built purely on
motoric or physical similarity and familiarity. This could explain
why in some cases individuals very different from the self can
activate the MNS (Aziz-Zadeh et al., 2012; Fox et al., 2013), while
in other cases more similar others activate the system (Calvo-
Merino et al., 2005, 2006; Bangert et al., 2006). Furthermore, we
note that the ‘‘like me’’ model has an implicit value consideration. Thus, the ‘‘like me’’ model may be simplified by thinking instead
in terms of value. p
Nevertheless, dissimilar to the ‘‘like me’’ model, the value
driven model could explain reported findings of increased
activity in MNS regions for both familiar (Hadjikhani et al.,
2007; Avenanti et al., 2010; Liew et al., 2011) and unfamiliar
individuals (Qin and Northoff, 2011; Aziz-Zadeh et al., 2012). Furthermore it could explain discrepant findings such as why
some reports indicate increased activity in MNS regions for
human agents than robotic or non-human agents (Tai et al.,
2004; Costantini et al., 2005; Engel et al., 2008; Chaminade
et al., 2010; Miura et al., 2010; Shimada, 2010) while others find
more activity for robotic as compared to human agents (Cross
et al., 2012, etc.). With regard to familiar individuals, in a study
by Losin et al. (2012), individuals observed and imitated an
unfamiliar hand action performed by actors of different races. The researchers found that neural activity during imitation was
modulated by race of the actor that participants were imitating. Specifically, more activity was elicited in Caucasian and Asian
participants when observing African American actors than any
other race, including their own. The authors suggested that
perceived social status (i.e., African Americans having the lowest
perceived social status; Fiske et al., 1999) might be reflected
in neural activity during imitation. In other words, activity
was modulated by the perceived value of the actor and not
by similarity to the participant (‘‘like me’’ model). RELATION OF THE VALUE MODEL TO
HUMAN DATA We extend this value-driven model from the monkey data to
better explain discrepant activation patterns in multiple shared
circuits in the human data, such that a unified model may
explain reported activation patterns from previous studies as a
function of value. Below we discuss findings from shared circuit
research and explain their results from a value driven perspective. We focus here particularly on the MNS and pain matrix, as
there is more data on these shared circuits than the others. Here we organize shared circuit studies along three categories:
(1) observation of significant others; (2) observation of action
familiarity; and (3) observations of actions to be learned. We extend this value-driven model from the monkey data to
better explain discrepant activation patterns in multiple shared
circuits in the human data, such that a unified model may
explain reported activation patterns from previous studies as a
function of value. Below we discuss findings from shared circuit
research and explain their results from a value driven perspective. In our view, while the Kilner and Friston’s prediction
model (also utilized by Cross et al., 2012) is an elegant one,
and provides an excellent framework to understand the MNS,
there is a need to understand the MNS circuit with broader
networks that are tied with emotion processing, reward systems,
saliency and other networks within which they are commonly
seen (Caggiano et al., 2012). Here, we specifically propose a
modification to the model such that preferred predictive models
are those that are meaningful and valued. Indeed one study
found increased activity in the caudate, as well as typical MNS
regions, when participants had to predict another person’s May 2018 | Volume 12 | Article 180 4 Aziz-Zadeh et al. Shared Circuits and Value Frontiers in Human Neuroscience | www.frontiersin.org Observation of Actions That Need to Be
Learned or Relearned We extend ‘‘value’’ to also incorporate the need for motor
or social learning. Clearly, if there is a need to learn an
observed action, then there is more value in observing that action
and we would expect increased activity in the mirror system. Thus, as mentioned earlier, individuals who have different
bodies than ourselves (e.g., an individual with an amputated
limb) are people whose bodies we need to learn more about. Hence, some results show that there is more MNS activity
in typically developing individuals when observing individuals
performing actions with amputated limbs (Liew et al., 2013). Furthermore, some studies have shown that observing actions
with novel kinematics also yields increased activity in the
MNS as compared to more familiar actions (Cross et al.,
2012). Observed actions that are unfamiliar to individuals
compared to familiar actions can preferentially engage the MNS
when performed by nonconspecifics. These findings can be
understood in terms of the value model. In some situations,
understanding the actions and intentions of action regardless
of who is performing it is more valuable when the goal of the
action is important, such as when an action is being learned. Indeed, goal-directed actions recruit shared circuit networks
more than ambiguous or non-goal directed actions (Iacoboni
et al., 2005). Similarly, a stroke patient finds more value in
observing an actor’s counterpart to the paretic hand rather than
the non-paretic hand perform actions (Garrison et al., 2013). Again, it may be more valuable to understand the actions of a However, familiarity with the action does not always
correspond to more MNS activity. Some studies indicate no
significant differences in key MNS regions when participants
viewed human vs. robotic hand actions (Gazzola et al.,
2007), or hands vs. geometric objects making goal directed
actions (Ramsey and Hamilton, 2010). In fact some studies
find increased MNS activation when observing non-human
(e.g., robots) compared to human actions (Cross et al., 2012;
Saygin and Stadler, 2012). Furthermore, it has been found that
observing actions made by a limb that you do not have (e.g., a
residual limb in an amputee) activates the MNS more than a limb
that you do have (e.g., a hand; Liew et al., 2011). Thus, action
familiarity cannot explain these discrepant results. However, in
a value model, this discrepancy could be explained by looking
at the value to the viewer behind the observed actions. Observation of Significant or Insignificant
Others A follow
up study by the same group tested this theory by recruiting
African American subjects to participate in the same experiment. Indeed, African American and European Americans activated
MNS regions more when observing African American actors
than when observing European Americans ones (Losin et al.,
2014; see also Avenanti et al., 2010). The authors posit that social
status, rather than racial similarity, is responsible for this racial
modulation during observation. This theory of perceived social
status supports a ‘‘value’’ driven model of the MNS such that
perceived value of an individual is driving activity in this system. Finally, such a model would predict that socially relevant stimuli,
like individuals facing toward the observer rather than away from In human studies, the value assigned to others is often
determined quantitatively by comparing the activity elicited by
viewing close family members in contrast to strangers. However,
the complexity of human relationships makes interpreting
quantitative data in regard to the value of a given individual
difficult. In studies comparing self vs. non-self faces, researchers
typically find differences in the bilateral and right IFG (Uddin
et al., 2005; Heckendorf et al., 2016). However, when comparing
personally familiar vs. unfamiliar faces (i.e., personally familiar
faces vs. famous faces or one’s own child vs. a familiar but
unrelated child), findings often indicate activity in the anterior
paracingulate cortex, posterior superior temporal sulcus and
precuneous suggesting personal knowledge retrieval (Gobbini
and Haxby, 2007). The majority of studies do not report MNS
brain region activation when comparing familiar and unfamiliar
faces (Ida Gobbini et al., 2004; Leibenluft et al., 2004; for review,
with a few exceptions, see Natu and O’Toole, 2011). This may
be because they focus on face perception rather than action
observation. However other studies do find IFG activation; Ishai
et al. (2002) reported IFG activation during familiar (famous)
vs. unfamiliar face processing and Taylor et al. (2009) reported
similar results when individuals viewed their partner’s faces
compared to a stranger’s. May 2018 | Volume 12 | Article 180 Frontiers in Human Neuroscience | www.frontiersin.org 5 Shared Circuits and Value Aziz-Zadeh et al. Observation of Action Familiarity Calvo-Merino et al. (2005) reported that ballet dancers show
increased activation in the MNS when watching ballet as
compared to martial arts than those with no ballet expertise. Indeed, a number of studies indicate increased MNS activity for
observed actions that are more familiar to the viewer or that
the viewer has expertise in performing (Buccino et al., 2004;
Järveläinen et al., 2004; Calvo-Merino et al., 2005, 2006; Cross
et al., 2006; Wright et al., 2010). For example, when participants
think they are observing the actions of another human being as
opposed to a robot or inanimate agent, there have been reports
of increased MNS activity (Wheatley et al., 2007) and motor
priming. As we previously mentioned, this has led some people
to propose that action familiarity drives activation in the MNS
(see Figure 1). Indeed, familiarity may have at least two effects: reduction
of uncertainty (e.g., in action execution), and facilitation of
automatic responses (e.g., motor repertoire for ballet dancers). Reduction of uncertainty interacts with value in that individuals
prefer familiar contexts to unfamiliar ones (ambiguity aversion,
discounting unfamiliar contexts due to entropy, Calvo-Merino
et al., 2006; Gazzola et al., 2007). Thus, in some cases, higher
activation in the MNS for familiar observed actions can be
explained because it is more valued and because it activates
automatically. We explore how novel actions may show increased
MNS activity in the ‘‘Observation of Actions That Need to be
Learned or Relearned’’ section. Increased shared circuit activation for familiar actions
is also observed in other sensory domains such as the
auditory domain (Ricciardi et al., 2009). In a study by
Ricciardi et al. (2009), congenitally blind individuals activated
a premotor–temporoparietal cortical network in response to the
sounds of actions (e.g., hammering). These regions overlapped
both with MNS areas found in sighted participants in response to
seeing or hearing an action, and with the brain response elicited
by motor pantomime of the same actions. Furthermore, the MNS
showed significantly greater activity to motor familiarity (actions
previously performed by an individual) than to unfamiliar action
sounds in both sighted and blind individuals. Observation of Significant or Insignificant
Others Activity in MNS and mentalizing regions (i.e., temporal-parietal
junction [TPJ]) has been observed to increases when European
American and Chinese participants view similar race actors
performing actions compared to non-similar actors as well as
when viewing unfamiliar hand actions compared to familiar
actions in the same individuals (Van Overwalle and Baetens,
2009; Liew et al., 2011). Depending on the complexity of the
situation and level of individual engagement, it is thought that
multiple networks contribute differently to the understanding
of actions (Liew et al., 2011). A ‘‘like me’’, ‘‘familiarity’’, or
even a saliency model cannot explain the dynamic activation
patterns seen in these studies, where a value driven model may
be better able. The MNS activates with increased familiarity and
unfamiliarity depending on the task and individual engagement. The value of the observed action does not necessitate that the
individual be familiar with the actor or action. the observer, should show modulation in the MNS (Kilner et al.,
2007). We note that in these examples, it is possible that value
can interact with saliency and both factors are important for
increased processing in the MNS (see Figure 3). Frontiers in Human Neuroscience | www.frontiersin.org RELEVANCE TO CLINICAL POPULATIONS To conclude the review, we speculate that in some instances,
clinical cases may arise from abnormal function between value
processing and sensorimotor processing. Here we will specifically
consider data on individuals with autism spectrum disorder
(ASD; Dapretto et al., 2006; Williams, 2008; Kana et al.,
2011). Research suggests that the MNS may be important for
understanding ASD for several reasons. First, extensive research
has identified impairments in imitation and motor ability in
individuals with ASD (Rogers et al., 2003; Mostofsky et al.,
2006; Williams et al., 2006; Williams, 2008; Vanvuchelen et al.,
2011). A recent meta-analysis and a systematic review concluded
that motor coordination deficits, including but not limited
to imitation, are present in individuals with ASD (even in
studies that controlled for age and IQ), and that this should
be considered a cardinal feature of ASD (Williams et al., 2004;
Fournier et al., 2010). Based on evidence that the MNS is strongly
involved in imitation (Koski et al., 2002; Heiser et al., 2003;
Iacoboni, 2005), it has been proposed that individuals with
ASD who have imitation deficits (Williams et al., 2004) may
also have a deficit in the MNS (Dapretto et al., 2006; Williams
et al., 2006; Oberman and Ramachandran, 2007), potentially
along with deficits in other networks. Several studies support this
hypothesis, showing differential MNS functioning in individuals
with ASD as compared to typically developing individuals
(Dapretto et al., 2006; Williams, 2008; Kana et al., 2011). However, a few behavioral studies have indicated no imitation
deficits, or ‘‘hyper imitation’’ deficits, in high functioning
individuals with ASD, and no differential MNS functioning
in individuals with ASD (Hamilton et al., 2007; Press et al.,
2010; Spengler et al., 2010). These discrepant findings can arise
from a number of factors. Some of the latter studies used adult
populations (Press et al., 2010; Spengler et al., 2010), which is
problematic because the one study that examined the effects of
age on the AON found increased activity in this system as a
function of age in individuals with ASD (Bastiaansen et al., 2011). Other studies that failed to find between-group differences had
small sample sizes (Avikainen et al., 1999) or used many ASD
subjects with autism impairment scores in the normal range
(Raymaekers et al., 2009). Heterogeneity of symptomology in
ASD may also be an important factor to consider. In general, more research on MNS development is needed. RELEVANCE TO CLINICAL POPULATIONS While some researchers suggest that the MNS is present
at birth (Lepage and Théoret, 2007), there is only indirect
evidence of this. In adults, several studies posit that during
action observation and execution, MNS activity may be detected
by desynchronization of the electroencephalogram (EEG) mu
rhythm recorded over motor regions (Muthukumaraswamy
et al., 2004; Ferrari et al., 2012). Similar EEG results have been
found with human infants (Southgate et al., 2010; Marshall
and Meltzoff, 2011; Nyström et al., 2011) and monkey infants
(Ferrari et al., 2012) during action observation and execution. Furthermore, data indicate that mu desynchronization during
action observation is predicted by the infant’s own motor abilities
(van Elk et al., 2008). Thus MNS activity is modulated by
development (Woodward and Gerson, 2014). A previous study
indicated that the mu rhythm in infants is sensitive to action
goals (Southgate et al., 2010) and the researchers argue that this
allows infants to predict the outcomes of other people’s actions
(Southgate et al., 2009, 2010). However, the degree to which
this activation pattern is related to social cognitive and reward
functioning remains unknown. Future longitudinal studies may
focus on integrating social behavioral data with neural data
on the MNS during development. Indeed abnormalities in the
development of social abilities has been correlated with less
activity in the MNS (Dapretto et al., 2006), and a longitudinal
study may better decipher if there is a directionality to the data. This would then have implications for clinical cases as well. However, if a MNS deficit in ASD is true for at least a
subgroup of individuals with ASD, it may be that impairments
arise not just from abnormalities in the MNS regions, but also
between interactions between the MNS circuit and the reward
circuits. Indeed, a few studies have shown that individuals
with ASD have an impairment in processing social rewards
as compared to monetary rewards (Lin et al., 2012), and
social as compared to monetary reward learning is associated
with decreased frontostriatal activations in ASD (Scott-Van
Zeeland et al., 2010). Furthermore, mutations in genes within
the mesolimbic dopamine pathway have been linked to ASD
(Hettinger et al., 2008; Staal, 2015), as have mutations in the Finally, more work on structural cortical changes to MNS
regions through development are needed. Specifically, the
prefrontal cortical thickness progresses in an inverted U-shaped
pattern from infancy to one’s mid-20s (Sowell et al., 2002). Observation of Actions That Need to Be
Learned or Relearned In the first
study discussed here by Calvo-Merino et al. (2005), it is likely that
a ballet dancer would likely find observing ballet more ‘‘valuable’’
or meaningful than observing martial arts. Furthermore, learning
the kinematics of a novel effector (e.g., a residual limb), or a novel
agent (a robot) performing a dance, may be more meaningful. Furthermore, deciphering the underlying mechanisms of action
understanding becomes more difficult when familiarly with
actions and actors interact. The interplay between familiar and
unfamiliar actions performed by similar or non-similar raced
actors can elicit multiple neural systems as complexity increases. May 2018 | Volume 12 | Article 180 6 Shared Circuits and Value Aziz-Zadeh et al. dopamine transporter (DAT; Bowton et al., 2014). Indeed, the
social motivation theory of ASD (Dawson et al., 2005) suggests
that children with ASD do not find social stimuli rewarding. In other words, children with ASD do not value or find the
same social information rewarding to the same extent as typically
developing children. Therefore, if individuals with ASD do not
value the same stimuli, then according to our proposed model,
they would elicit less activity in MNS regions. In fact, the value
driven model fits with results suggesting that in children with
ASD, MNS activity and sociality traits (as measured by subsets
of established social assessments, e.g., Social Responsiveness
Scale; Constantino et al., 2003) are positively related (Dapretto
et al., 2006). Children who have higher scores in sociality find
social reward stimuli more valuable, and therefore would have
higher levels of MNS activation. Indeed, a recent study in a
non-clinical group of participants indicated that individuals with
more autistic traits assigned less value to viewing human bodies
in natural motion compared to human bodies in robot-like
motion or non-human control motion (Williams and Cross,
2018). Future studies comparing the subjective value of social and
nonsocial stimuli would be useful to determine the relationship
between ASD, the MNS, and value. paretic hand over the non-paretic depending on the environment
and situation. paretic hand over the non-paretic depending on the environment
and situation. Frontiers in Human Neuroscience | www.frontiersin.org May 2018 | Volume 12 | Article 180 REFERENCES Bowton, E., Saunders, C., Reddy, I. A., Campbell, N. G., Hamilton, P. J.,
Henry, L. K., et al. (2014). SLC6A3 coding variant Ala559Val found in two
autism probands alters dopamine transporter function and trafficking. Transl. Psychiatry 4:e464. doi: 10.1038/tp.2014.90 Amiez, C., Joseph, J. P., and Procyk, E. (2006). Reward encoding in
the monkey anterior cingulate cortex. Cereb. Cortex 16, 1040–1055. doi: 10.1093/cercor/bhj046 Buccino, G., Lui, F., Canessa, N., Patteri, I., Lagravinese, G., Benuzzi, F.,
et al. (2004). Neural circuits involved in the recognition of actions
performed by nonconspecifics: an fMRI study. J. Cogn. Neurosci. 16, 114–126. doi: 10.1162/089892904322755601 Avenanti, A., Bueti, D., Galati, G., and Aglioti, S. M. (2005). Transcranial
magnetic stimulation highlights the sensorimotor side of empathy for pain. Nat. Neurosci. 8, 955–960. doi: 10.1038/nn1481 Avenanti, A., Sirigu, A., and Aglioti, S. M. (2010). Report racial bias reduces
empathic sensorimotor resonance with other-race pain. Curr. Biol. 20,
1018–1022. doi: 10.1016/j.cub.2010.03.071 Bufalari, I., Aprile, T., Avenanti, A., Di Russo, F., Aglioti, S. M., Psicologia, D.,
et al. (2007). Empathy for pain and touch in the human somatosensory cortex. Cereb. Cortex 17, 2553–2561. doi: 10.1093/cercor/bhl161 Avikainen, S., Kulomäki, T., and Hari, R. (1999). Normal movement reading
in Asperger subjects. Neuroreport 10, 3467–3470. doi: 10.1097/00001756-
199911260-00001 Caggiano, V., Fogassi, L., Rizzolatti, G., Casile, A., Giese, M. A., and Thier, P. (2012). Mirror neurons encode the subjective value of an observed action. Proc. Natl. Acad. Sci. U S A 109, 11848–11853. doi: 10.1073/pnas.1205553109 Calvo-Merino, B., Glaser, D. E., Grèzes, J., Passingham, R. E., and Haggard, P. (2005). Action observation and acquired motor skills: an fMRI study with
expert dancers. Cereb. Cortex 15, 1243–1249. doi: 10.1093/cercor/bhi007 Aziz-Zadeh, L. (2013). ‘‘Embodied semantics for language related to actions: a
review of fMRI and neuropsychological research,’’ in Language and Action in
Cognitive Neuroscience, eds Y. Coello and A. Bartolo (East Sussex: Psychology
Press), 273–283. Calvo-Merino, B., Grèzes, J., Glaser, D. E., Passingham, R. E., Haggard, P.,
Grezes, J., et al. (2006). Seeing or doing? Influence of visual and motor
familiarity in action observation. Curr. Biol. 16, 1905–1910. doi: 10.1016/j.cub. 2006.07.065 Aziz-Zadeh, L., Sheng, T., Liew, S. L., and Damasio, H. (2012). Understanding
otherness: the neural bases of action comprehension and pain empathy
in a congenital amputee. Cereb. Cortex 22, 811–819. doi: 10.1093/cercor/
bhr139 Chaminade, T., Zecca, M., Blakemore, S. J., Takanishi, A., Frith, C. D.,
Micera, S., et al. (2010). RELEVANCE TO CLINICAL POPULATIONS It is likely that these structural changes in the IFG reflect
differing activation patterns in the MNS and can be linked
with behavioral development. In addition, neural connectivity
to other brain systems, such as the reward network, salience May 2018 | Volume 12 | Article 180 Frontiers in Human Neuroscience | www.frontiersin.org 7 Shared Circuits and Value Aziz-Zadeh et al. system and emotion processing systems are likely to change
throughout development. This may be reflected in differences
found between mu desynchronization in infants compared to
adults (Marshall and Meltzoff, 2011). Linking the structural
brain, EEG and behavioral data together will be important
for better understanding the MNS and its connections with
other neural systems (e.g., reward systems, saliency network,
etc.) through development and potentially allow for a better
understanding of clinical disorders. studies ‘‘valued’’ things differently. With a value driven model,
one would predict that this type of comparison would result in a
positive correlation between activity in the MNS, reward system
and the value an individual contributed to a given condition
or stimuli. Future studies are needed to further explore this
hypothesis. ACKNOWLEDGMENTS We would like to thank Kathleen Garrison, Sook-Lei Liew,
Sharon Cermak, and S. Butterfill for thoughtful comments and
discussion during the development of this manuscript. CONCLUSION In sum, previous theories have yet to satisfy current literature
findings. Here we propose adapting the ‘‘value-driven’’ model
of the MNS proposed for monkeys to humans. Specifically, the
role of the dopamine reward circuit and emotion processing
in modulating MNS activity needs to be an important part of
any future model of the MNS, or other shared circuits. After
reviewing previous findings through the lens of this new model’s
framework, we find to better explain discrepant activation
patterns in multiple shared circuits in the human data. FUNDING Research reported in this publication was supported by the
Eunice Kennedy Shriver National Institute of Child Health
and Human Development of the National Institutes of Health
under Award Number R01HD079432. The content is solely the
responsibility of the authors and does not necessarily represent
the official views of the National Institutes of Health. Further research should be conducted to test if indeed this
model can explain reported activation patterns from previous
studies as a function of value. In order to test this model, one
would need to be able to determine ‘‘value’’ of a stimulus to an
individual. So logically then, to account for previous discrepant
results, one would need to show that the cohorts in the different AUTHOR CONTRIBUTIONS LA-Z conceived the review article and wrote the first draft of the
manuscript with EK. GC edited and contributed to sections of the
manuscript. REFERENCES doi: 10.1016/j.neuroimage.2006.01.033 Haber, S. N., Fudge, J. L., and McFarland, N. R. (2000). Striatonigrostriatal
pathways in primates form an ascending spiral from the shell to the dorsolateral
striatum. J. Neurosci. 20, 2369–2382. doi: 10.1523/JNEUROSCI.20-06-02369. 2000 Cross, E. S., Hamilton, A. F. D. C., Kraemer, D. J. M., Kelley, W. M., and
Grafton, S. T. (2009). Dissociable substrates for body motion and physical
experience in the human action observation network. Eur. J. Neurosci. 30,
1383–1392. doi: 10.1111/j.1460-9568.2009.06941.x Hadjikhani, N., Joseph, R. H., Snyder, J., and Tager-Flusberg, H. (2007). Abnormal
activation of the social brain during face perception in autism. Hum. Brain
Mapp. 28, 441–449. doi: 10.1002/hbm.20283 Cross, E. S., Liepelt, R., Hamilton, H. F., Parkinson, J., Ramsey, R., Stadler, W.,
et al. (2012). Robotic movement preferentially engages the action observation
network. Hum. Brain Mapp. 33, 2238–2254. doi: 10.1002/hbm.21361 Hamilton, A. F. D. C., Brindley, R. M., and Frith, U. (2007). Imitation and
action understanding in autistic spectrum disorders: how valid is the hypothesis
of a deficit in the mirror neuron system? Neuropsychologia 45, 1859–1868. doi: 10.1016/j.neuropsychologia.2006.11.022 Cross, E. S., Schmitt, P. J., and Grafton, S. T. (2007). Neural substrates of contextual
interference during motor learning support a model of active preparation. J. Cogn. Neurosci. 19, 1854–1871. doi: 10.1162/jocn.2007.19.11.1854 Heckendorf, E., Huffmeijer, R., Bakermans-Kranenburg, M. J., and van
IJzendoorn, M. H. (2016). Neural processing of familiar and unfamiliar
children’s faces: effects of experienced love withdrawal, but no effects of neutral
and threatening priming. Front. Hum. Neurosci. 10:231. doi: 10.3389/fnhum. 2016.00231 Dapretto, M., Davies, M. S., Pfeifer, J. H., Scott, A. A., Sigman, M.,
Bookheimer, S. Y., et al. (2006). Understanding emotions in others: mirror
neuron dysfunction in children with autism spectrum disorders. Nat. Neurosci. 9, 28–30. doi: 10.1038/nn1611 Heiser, M., Iacoboni, M., Maeda, F., Marcus, J., and Mazziotta, J. C. (2003). The
essential role of Broca’s area in imitation. Eur. J. Neurosci. 17, 1123–1128. doi: 10.1046/j.1460-9568.2003.02530.x Dawson, G., Webb, S. J., and McPartland, J. (2005). Understanding the nature
of face processing impairment in autism: insights from behavioral and
electrophysiological studies. Dev. Neuropsychol. 27, 403–424. doi: 10.1207/
s15326942dn2703_6 Hettinger, J. A., Liu, X., Schwartz, C. E., Michaelis, R. C., and Holden, J. J. A. (2008). A DRD1 haplotype is associated with risk for autism spectrum disorders
in male-only affected sib-pair families. Am. J. Med. Genet. B Neuropsychiatr. Genet. 147, 628–636. doi: 10.1002/ajmg.b.30655 Di Cesare, G., Di Dio, C., Marchi, M., and Rizzolatti, G. REFERENCES Brain response to a humanoid robot in areas
implicated in the perception of human emotional gestures. PLoS One 5:e11577. doi: 10.1371/journal.pone.0011577 Bangert, M., Peschel, T., Schlaug, G., Rotte, M., Drescher, D., Hinrichs, H.,
et al. (2006). Shared networks for auditory and motor processing in
professional pianists: evidence from fMRI conjunction. Neuroimage 30,
917–926. doi: 10.1016/j.neuroimage.2005.10.044 Cheng, Y., Chen, C., Lin, C.-P., Chou, K.-H., and Decety, J. (2010). Love hurts: an
fMRI study. Neuroimage 51, 923–929. doi: 10.1016/j.neuroimage.2010.02.047 Bastiaansen, J. A., Thioux, M., Nanetti, L., van der Gaag, C., Ketelaars, C.,
Minderaa, R., et al. (2011). Age-related increase in inferior frontal gyrus
activity and social functioning in autism spectrum disorder. Biol. Psychiatry
69, 832–838. doi: 10.1016/j.biopsych.2010.11.007 Conen, K. E., and Padoa-Schioppa, C. (2016). The dynamic nature of value-based
decisions. Nat. Neurosci. 19, 866–867. doi: 10.1038/nn.4329 Constantino, J. N., Davis, S. A., Todd, R. D., Schindler, M. K., Gross, M. M.,
Brophy, S. L., et al. (2003). Validation of a brief quantitative measure
of autistic traits: comparison of the social responsiveness scale with the
Autism Diagnostic Interview-Revised. J. Autism Dev. Disord. 33, 427–433. doi: 10.1023/A:1025014929212 Beudel, M., Zijlstra, S., Mulder, T., Zijdewind, I., and de Jong, B. M. (2011). Secondary sensory area SII is crucially involved in the preparation of familiar
movements compared to movements never made before. Hum. Brain Mapp. 32, 564–579. doi: 10.1002/hbm.21044 May 2018 | Volume 12 | Article 180 Frontiers in Human Neuroscience | www.frontiersin.org Frontiers in Human Neuroscience | www.frontiersin.org 8 Aziz-Zadeh et al. Shared Circuits and Value Coricelli, G. (2005). Two-levels of mental states attribution: from automaticity to
voluntariness. Neuropsychologia 43, 294–300. doi: 10.1016/j.neuropsychologia. 2004.11.015 Gobbini, M. I., and Haxby, J. V. (2007). Neural systems for recognition of
familiar faces. Neuropsychologia 45, 32–41. doi: 10.1016/j.neuropsychologia. 2006.04.015 Costantini, M., Galati, G., Ferretti, A., Caulo, M., Tartaro, A., Romani, G. L.,
et al. (2005). Neural systems underlying observation of humanly impossible
movements: an fMRI study. Cereb. Cortex 15, 1761–1767. doi: 10.1093/cercor/
bhi053 Grossmann, T., Cross, E. S., Ticini, L. F., Daum, M. M., and Luca, F. (2013). Action observation in the infant brain: the role of body form and motion Action
observation in the infant brain: the role of body form and motion. Soc. Neurosci. 8, 22–30. doi: 10.1080/17470919.2012.696077 Cross, E. S., Hamilton, A. F. D. C., and Grafton, S. T. (2006). Building a
motor simulation de novo: observation of dance by dancers. Neuroimage 31,
1257–1267. REFERENCES (2015). Expressing our
internal states and understanding those of others. Proc. Natl. Acad. Sci. U S A
112, 10331–10335. doi: 10.1073/pnas.1512133112 Iacoboni, M. (2005). Neural mechanisms of imitation. Curr. Opin. Neurobiol. 15,
632–637. doi: 10.1016/j.conb.2005.10.010 Diersch, N., Mueller, K., Cross, E. S., Stadler, W., Rieger, M., and Schütz-
Bosbach, S. (2013). Action prediction in younger versus older adults: neural
correlates of motor Familiarity. PLoS One 8:e64195. doi: 10.1371/journal.pone. 0064195 Iacoboni, M., Molnar-Szakacs, I., Gallese, V., Buccino, G., Mazziotta, J. C., and
Rizzolatti, G. (2005). Grasping the intentions of others with one’s own mirror
neuron system. PLoS Biol. 3:e79. doi: 10.1371/journal.pbio.0030079 Engel, A., Burke, M., Fiehler, K., Bien, S., and Rosler, F. (2008). How moving
objects become animated: the human mirror neuron system assimilates
non-biological movement patterns. Soc. Neurosci. 3, 368–387. doi: 10.1080/
17470910701612793 Ida Gobbini, M., Leibenluft, E., Santiago, N., and Haxby, J. V. (2004). Social and
emotional attachment in the neural representation of faces. Neuroimage 22,
1628–1635. doi: 10.1016/j.neuroimage.2004.03.049 1628–1635. doi: 10.1016/j.neuroimage.2004.03.049 Ishai, A., Haxby, J. V., and Ungerleider, L. G. (2002). Visual imagery of famous
faces: effects of memory and attention revealed by fMRI. Neuroimage 17,
1729–1741. doi: 10.1006/nimg.2002.1330 Ferrari, P. F., Vanderwert, R. E., Paukner, A., Bower, S., Suomi, S. J., and Fox, N. A. (2012). Distinct EEG amplitude suppression to facial gestures as evidence for
a mirror mechanism in newborn monkeys. J. Cogn. Neurosci. 24, 1165–1172. doi: 10.1162/jocn_a_00198 Jackson, P. L., Rainville, P., and Decety, J. (2006). To what extent do we share the
pain of others? Insight from the neural bases of pain empathy. Pain 125, 5–9. doi: 10.1016/j.pain.2006.09.013 Fiske, S. T., Xu, J., Cuddy, A. C., and Glick, P. (1999). (Dis)respecting versus
(Dis)liking: status and interdependence predict ambivalent stereotypes of
competence and warmth. J. Soc. Issues 55, 473–489. doi: 10.1111/0022-4537. 00128 Järveläinen, J., Schürmann, M., and Hari, R. (2004). Activation of the human
primary motor cortex during observation of tool use. Neuroimage 23, 187–192. doi: 10.1016/j.neuroimage.2004.06.010 Fournier, K. A., Hass, C. J., Naik, S. K., Lodha, N., and Cauraugh, J. H. (2010). Motor coordination in autism spectrum disorders: a synthesis and meta-
analysis. J. Autism Dev. Disord. 40, 1227–1240. doi: 10.1007/s10803-010-0981-3 Joffily, M., and Coricelli, G. (2013). Emotional valence and the free-energy
principle. PLoS
Comput. Biol. 9:e1003094. doi:
10.1371/journal.pcbi. 1003094 Fox, G. R., Sobhani, M., and Aziz-Zadeh, L. (2013). REFERENCES D. C. (2010). Triangles have goals too:
understanding action representation in left aIPS. Neuropsychologia 48,
2773–2776. doi: 10.1016/j.neuropsychologia.2010.04.028 Liew, S. L., Sheng, T., and Aziz-Zadeh, L. (2013). Experience with an amputee
modulates one’s own sensorimotor response during action observation. Neuroimage 69, 138–145. doi: 10.1016/j.neuroimage.2012.12.028 Lin, A., Rangel, A., and Adolphs, R. (2012). Impaired learning of social compared
to monetary rewards in autism. Front. Neurosci. 6:143. doi: 10.3389/fnins.2012. 00143 Raymaekers, R., Wiersema, J. R., and Roeyers, H. (2009). EEG study of the mirror
neuron system in children with high functioning autism. Brain Res. 1304,
113–121. doi: 10.1016/j.brainres.2009.09.068 Losin, E. A. R., Cross, K. A., Iacoboni, M., and Dapretto, M. (2014). Neural
processing of race during imitation: self-similarity versus social status. Hum. Brain Mapp. 35, 1723–1739. doi: 10.1002/hbm.22287 Ricciardi, E., Bonino, D., Sani, L., Vecchi, T., Guazzelli, M., Haxby, J. V.,
et al. (2009). Do we really need vision? How blind people ‘‘See’’ the actions
of others. J. Neurosci. 29, 9719–9724. doi: 10.1523/JNEUROSCI.0274-09. 2009 Losin, E. A. R., Iacoboni, M., Martin, A., Cross, K. A., and Dapretto, M. (2012). Race modulates neural activity during imitation. Neuroimage 59, 3594–3603. doi: 10.1016/j.neuroimage.2011.10.074 Rizzolatti, G., and Craighero, L. (2004). The mirror-neuron system. Annu. Rev. Neurosci. 27,
169–192. doi:
10.1146/annurev.neuro.27.070203. 144230 Marshall, P. J., and Meltzoff, A. N. (2011). Neural mirroring systems: exploring
the EEG µ rhythm in human infancy. Dev. Cogn. Neurosci. 1, 110–123. doi: 10.1016/j.dcn.2010.09.001 Roesch, M. R., and Olson, C. R. (2003). Impact of expected reward on
neuronal activity in prefrontal cortex, frontal and supplementary eye fields
and premotor cortex. J. Neurophysiol. 90, 1766–1789. doi: 10.1152/jn.00019. 2003 Matsumoto, M., and Hikosaka, O. (2007). Lateral habenula as a source of negative
reward signals in dopamine neurons. Nature 447, 1111–1115. doi: 10.1038/
nature05860 Roesch, M. R., and Olson, C. R. (2004). Neuronal activity related to reward value
and motivation in primate frontal cortex. Science 304, 307–310. doi: 10.1126/
science.1093223 Matsumoto, M., and Hikosaka, O. (2009). Two types of dopamine neuron
distinctly convey positive and negative motivational signals. Nature 459,
837–841. doi: 10.1038/nature08028 Roesch, M. R., and Olson, C. R. (2007). Neuronal activity related to anticipated
reward in frontal cortex: does it represent value or reflect motivation? Ann. N
Y Acad. Sci. 1121, 431–446. doi: 10.1196/annals.1401.004 Meyer, K. (2011). Primary sensory cortices, top-down projections and conscious
experience. Prog. Neurobiol. 94, 408–417. doi: 10.1016/j.pneurobio.2011. 05.010 Rogers, S. J., Hepburn, S. L., Stackhouse, T., and Wehner, E. (2003). REFERENCES doi: 10.1111/j.2044-8295.2011.02053.x Neal, A., and Kilner, J. M. (2012). Europe PMC funders group what is simulated in
the action observation network when we observe actions? Eur. J. Neurosci. 32,
1765–1770. doi: 10.1111/j.1460-9568.2010.07435.x Kohler, E. (2002). Hearing sounds, understanding actions: action representation
in mirror neurons. Science 297, 846–848. doi: 10.1126/science.1070311 Nyström, P., Ljunghammar, T., Rosander, K., and von Hofsten, C. (2011). Using
mu rhythm desynchronization to measure mirror neuron activity in infants. Dev. Sci. 14, 327–335. doi: 10.1111/j.1467-7687.2010.00979.x Koski, L., Wohlschläger, A., Bekkering, H., Woods, R. P., Dubeau, M. C.,
Mazziotta, J. C., et al. (2002). Modulation of motor and premotor activity
during imitation of target-directed actions. Cereb. Cortex 12, 847–855. doi: 10.1093/cercor/12.8.847 Oberman, L. M., and Ramachandran, V. S. (2007). The simulating social mind:
the role of the mirror neuron system and simulation in the social and
communicative deficits of autism spectrum disorders. Psychol. Bull. 133,
310–327. doi: 10.1037/0033-2909.133.2.310 Lannetti, G. D., and Mouraux, A. (2010). From the neuromatrix to the pain matrix
(and back). Exp. Brain Res. 205, 1–12. doi: 10.1007/s00221-010-2340-1 Leibenluft, E., Gobbini, M. I., Harrison, T., and Haxby, J. V. (2004). Mothers’
neural activation in response to pictures of their children and other children. Biol. Psychiatry 56, 225–232. doi: 10.1016/j.biopsych.2004.05.017 Platt, M. L., and Glimcher, P. W. (1999). Neural correlates of decision
variables
in
parietal
cortex. Nature
400,
233–238. doi:
10.1038/
22268 Lepage, J. F., and Théoret, H. (2007). The mirror neuron system: grasping
others’ actions from birth? Dev. Sci. 10, 513–523. doi: 10.1111/j.1467-7687. 2007.00631.x Press, C., Richardson, D., and Bird, G. (2010). Intact imitation of emotional
facial actions in autism spectrum conditions. Neuropsychologia 48, 3291–3297. doi: 10.1016/j.neuropsychologia.2010.07.012 Liepelt, R., Ullsperger, M., Obst, K., Spengler, S., von Cramon, D. Y., and
Brass, M. (2009). Contextual movement constraints of others modulate motor
preparation in the observer. Neuropsychologia 47, 268–275. doi: 10.1016/j. neuropsychologia.2008.07.008 j
y
g
Qin, P., and Northoff, G. (2011). How is our self related to midline regions and the
default-mode network? Neuroimage 57, 1221–1233. doi: 10.1016/j.neuroimage. 2011.05.028 Raichle, M. E., MacLeod, A. M., Snyder, A. Z., Powers, W. J., Gusnard, D. A., and
Shulman, G. L. (2001). A default mode of brain function. Proc. Natl. Acad. Sci. U S A 98, 676–682. doi: 10.1073/pnas.98.2.676 Liew, S. L., Han, S., and Aziz-Zadeh, L. (2011). Familiarity modulates mirror
neuron and mentalizing regions during intention understanding. Hum. Brain
Mapp. 32, 1986–1997. doi: 10.1002/hbm.21164 Ramsey, R., and Hamilton, A. F. REFERENCES Witnessing hateful people
in pain modulates brain activity in regions associated with physical pain and
reward. Front. Psychol. 4:772. doi: 10.3389/fpsyg.2013.00772 Kana, R. K., Wadsworth, H. M., and Travers, B. G. (2011). A systems level analysis
of the mirror neuron hypothesis and imitation impairments in autism spectrum
disorders. Neurosci. Biobehav. Rev. 35, 894–902. doi: 10.1016/j.neubiorev.2010. 10.007 Gallese, V., and Goldman, A. (1998). Mirror neurons and the mind-reading. Trends Cogn. Sci. 2, 493–501. doi: 10.1016/S1364-6613(98)01262-5 Kaplan, J. T., Aziz-Zadeh, L., Uddin, L. Q., and Iacoboni, M. (2008). The self across
the senses: an fMRI study of self-face and self-voice recognition. Soc. Cogn. Affect. Neurosci. 3, 218–223. doi: 10.1093/scan/nsn014 Gardner, T., Aglinskas, A., and Cross, E. S. (2017). Using guitar learning to
probe the Action Observation Network’s response to visuomotor familiarity. Neuroimage 156, 174–189. doi: 10.1016/j.neuroimage.2017.04.060 Keysers, C., and Gazzola, V. (2009). Expanding the mirror: vicarious activity
for actions, emotions, and sensations. Curr. Opin. Neurobiol. 19, 666–671. doi: 10.1016/j.conb.2009.10.006 Gardner, T., Goulden, N., and Cross, E. S. (2015). Dynamic modulation of
the action observation network by movement familiarity. J. Neurosci. 35,
1561–1572. doi: 10.1523/JNEUROSCI.2942-14.2015 Keysers, C., Kaas, J. H., and Gazzola, V. (2010). Somatosensation in social
perception. Nat. Rev. Neurosci. 11, 417–428. doi: 10.1038/nrn2833 Garrison, K. A., Aziz-Zadeh, L., Wong, S. W., Liew, S. L., and Winstein, C. J. (2013). Modulating the motor system by action observation after stroke. Stroke
44, 2247–2253. doi: 10.1161/STROKEAHA.113.001105 Keysers, C., Wicker, B., Gazzola, V., Anton, J.-L., Fogassi, L., and Gallese, V. (2004). A touching sight: SII/PV activation during the observation and
experience of touch. Neuron 42, 335–346. doi: 10.1016/S0896-6273(04)00156-4 Gazzola,
V.,
Rizzolatti,
G.,
Wicker,
B.,
and
Keysers,
C. (2007). The
anthropomorphic brain: the mirror neuron system responds to human
and robotic actions. Neuroimage 35, 1674–1684. doi: 10.1016/j.neuroimage. 2007.02.003 Kilner, J. M., Friston, K. J., and Frith, C. D. (2007). Predictive coding: an account
of the mirror neuron system. Cogn. Process. 8, 159–166. doi: 10.1007/s10339-
007-0170-2 May 2018 | Volume 12 | Article 180 Frontiers in Human Neuroscience | www.frontiersin.org 9 Aziz-Zadeh et al. Shared Circuits and Value Kim, K., and Johnson, M. K. (2013). Activity in ventromedial prefrontal
cortex during self-related processing: positive subjective value or personal
significance? Soc. Cogn. Affect. Neurosci. 10, 494–500. doi: 10.1093/scan/
nsu078 Natu, V., and O’Toole, A. J. (2011). The neural processing of familiar and
unfamiliar faces: a review and synopsis. Br. J. Psychol. 102, 726–747. REFERENCES Child Neurol. 44, 4–16. doi: 10.1111/j.1469-
8749.2002.tb00253.x Williams, J. H., Waiter, G. D., Gilchrist, A., Perrett, D. I., Murray, A. D., and
Whiten, A. (2006). Neural mechanisms of imitation and ‘‘mirror neuron’’
functioning in autistic spectrum disorder. Neuropsychologia 44, 610–621. doi: 10.1016/j.neunet.2006.02.001 Spengler, S., Bird, G., and Brass, M. (2010). Hyperimitation of actions is
related to reduced understanding of others’ minds in autism spectrum
conditions. Biol. Psychiatry 68, 1148–1155. doi: 10.1016/j.biopsych.2010. 09.017 Williams, J. H. G., Whiten, A., and Singh, T. (2004). A systematic review of action
imitation in autistic spectrum disorder. J. Autism Dev. Disord. 34, 285–299. doi: 10.1023/b:jadd.0000029551.56735.3a Staal, W. G. (2015). Autism, DRD3 and repetitive and stereotyped behavior,
an overview of the current knowledge. Eur. Neuropsychopharmacol. 25,
1421–1426. doi: 10.1016/j.euroneuro.2014.08.011 Wolpert, D. M., Doya, K., and Kawato, M. (2003). A unifying computational
framework for motor control and social interaction. Philos. Trans. R. Soc. B
Biol. Sci. 358, 593–602. doi: 10.1098/rstb.2002.1238 Woodward, A. L., and Gerson, S. A. (2014). Mirroring and the development of
action understanding. Philos. Trans. R. Soc. Lond. B Biol. Sci. 369:20130181. doi: 10.1098/rstb.2013.0181 Tai, Y. F., Scherfler, C., Brooks, D. J., Sawamoto, N., and Castiello, U. (2004). The
human premotor cortex is ‘‘mirror’’ only for biological actions. Curr. Biol. 14,
117–120. doi: 10.1016/s0960-9822(04)00006-5 Tamir, D. I., and Mitchell, J. P. (2013). Anchoring and adjustment during
social
inferences. J. Exp. Psychol. Gen. 142,
151–162. doi:
10.1037/
a0028232 Wright, M. J., Bishop, D. T., Jackson, R. C., and Abernethy, B. (2010). Functional
MRI reveals expert-novice differences during sport-related anticipation. Neuroreport 21, 94–98. doi: 10.1097/WNR.0b013e328333dff2 Taylor, M. J. M., Arsalidou, M., Bayless, S. S. J., Morris, D., Evans, J. W., and
Barbeau, E. J. (2009). Neural correlates of personally familiar faces: parents,
partner and own faces. Hum. Brain Mapp. 30, 2008–2020. doi: 10.1002/hbm. 20646 Xu, X., Zuo, X., Wang, X., and Han, S. (2009). Do you feel my pain? Racial group
membership modulates empathic neural responses. J. Neurosci. 29, 8525–8529. doi: 10.1523/JNEUROSCI.2418-09.2009 Tipper, C. M., Signorini, G., and Grafton, S. T. (2015). Body language in the brain:
constructing meaning from expressive movement. Front. Hum. Neurosci. 9:450. doi: 10.3389/fnhum.2015.00450 Conflict of Interest Statement: 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. Uddin, L. Q., Kaplan, J. T., Molnar-Szakacs, I., Zaidel, E., and Iacoboni, M. (2005). REFERENCES Understanding others’ actions and goals
by mirror and mentalizing systems: a meta-analysis. Neuroimage 548, 564–584. doi: 10.1016/j.neuroimage.2009.06.009 Shepherd, S. V., Klein, J. T., Deaner, R. O., and Platt, M. L. (2009). Mirroring of
attention by neurons in macaque parietal cortex. Proc. Natl. Acad. Sci. U S A
106, 9489–9494. doi: 10.1073/pnas.0900419106 Vanvuchelen, M., Roeyers, H., and De Weerdt, W. (2011). Imitation assessment
and its utility to the diagnosis of autism: evidence from consecutive clinical
preschool referrals for suspected autism. J. Autism Dev. Disord. 41, 484–496. doi: 10.1007/s10803-010-1074-z Shimada, S. (2010). Deactivation in the sensorimotor area during observation
of a human agent performing robotic actions. Brain Cogn. 72, 394–399. doi: 10.1016/j.bandc.2009.11.005 Wallis, J. D., and Kennerley, S. W. (2010). Heterogeneous reward signals in
prefrontal cortex. Curr. Opin. Neurobiol. 20, 191–198. doi: 10.1016/j.conb.2010. 02.009 Singer, T., Seymour, B., O’Doherty, J., Kaube, H., Dolan, R. J., and Frith, C. D. (2004). Empathy for pain involves the affective but not sensory components of
pain. Science 303, 1157–1162. doi: 10.1126/science.1093535 Wheatley, T., Milleville, S. C., and Martin, A. (2007). Distinct roles for the social
network and mirror system. Psychol. Sci. 18, 469–474. doi: 10.1111/j.1467-9280. 2007.01923.x Singer, T., Seymour, B., O’Doherty, J. P., Stephan, K. E., Dolan, R. J., and
Frith, C. D. (2006). Europe PMC Funders Group Empathic neural responses
are modulated by the perceived fairness of others. Nature 439, 466–469. doi: 10.1038/nature04271 Wicker, B., Keysers, C., Plailly, J., Royet, J. P., Gallese, V., and Rizzolatti, G. (2003). Both of us disgusted in My insula: the common neural basis of seeing and
feeling disgust. Neuron 40, 655–664. doi: 10.1016/S0896-6273(03)00679-2 Southgate, V., Johnson, M. R., El Karoui, I., and Csibra, G. (2010). Motor system
activation reveals infants’ on-line prediction of others’ goals. Psychol. Sci. 21,
355–359. doi: 10.1177/0956797610362058 Williams, J. H. G. (2008). Self-other relations in social development and autism:
multiple roles for mirror neurons and other brain bases. Autism Res. 1, 73–90. doi: 10.1002/aur.15 Southgate, V., Johnson, M. H., Osborne, T., and Csibra, G. (2009). Predictive
motor activation during action observation in human infants. Biol. Lett. 5,
769–772. doi: 10.1098/rsbl.2009.0474 Williams, E. H., and Cross, E. S. (2018). Decreased reward value of
biological motion among individuals with autistic traits. Cognition 171, 1–9. doi: 10.1016/j.cognition.2017.10.017 Sowell, E. R., Trauner, D. A., Gamst, A., and Jernigan, T. L. (2002). Development
of cortical and subcortical brain structures in childhood and adolescence:
a structural MRI study. Dev. Med. REFERENCES Imitation
performance in toddlers with autism and those with other developmental
disorders. J. Child Psychol. Psychiatry 44, 763–781. doi: 10.1111/1469-7610. 00162 Miall, R. C., and Wolpert, D. M. (1996). Forward models for physiological motor
control. Neural Netw. 9, 1265–1279. doi: 10.1016/s0893-6080(96)00035-4 Mitchell, J. P., Schirmer, J., Ames, D. L., and Gilbert, D. T. (2011). Medial
prefrontal cortex predicts intertemporal choice. J. Cogn. Neurosci. 23, 857–866. doi: 10.1162/jocn.2010.21479 Saygin, A. P., and Stadler, W. (2012). The role of appearance and motion
in action prediction. Psychol. Res. 76, 388–394. doi: 10.1007/s00426-012
-0426-z Miura, N., Sugiura, M., Takahashi, M., Sassa, Y., Miyamoto, A., Sato, S., et al. (2010). Effect of motion smoothness on brain activity while observing a dance:
an fMRI study using a humanoid robot. Soc. Neurosci. 5, 40–58. doi: 10.1080/
17470910903083256 Schultz, W. (2000). Multiple reward signals in the brain. Nat. Rev. Neurosci. 1,
199–207. doi: 10.1038/35044563 Schultz, W., Tremblay, L., and Hollerman, J. R. (2000). Reward processing in
primate orbitofrontal cortex and basal ganglia. Cereb. Cortex 10, 272–283. doi: 10.1093/cercor/10.3.272 Molnar-Szakacs, I., and Uddin, L. Q. (2013). Self-processing and the default mode
network: interactions with the mirror neuron system. Front. Hum. Neurosci. 7:571. doi: 10.3389/fnhum.2013.00571 Scott-Van Zeeland, A. A., Dapretto, M., Ghahremani, D. G., Poldrack, R. A., and
Bookheimer, S. Y. (2010). Reward processing in autism. Autism Res. 3, 53–67. doi: 10.1002/aur.122 Mostofsky, S. H., Dubey, P., Jerath, V. K., Jansiewicz, E. M., Goldberg, M. C., and
Denckla, M. B. (2006). Developmental dyspraxia is not limited to imitation in
children with autism spectrum disorders. J. Int. Neuropsychol. Soc. 12, 314–326. doi: 10.1017/s1355617706060437 Seo, H., and Lee, D. (2007). Temporal filtering of reward signals in the dorsal
anterior cingulate cortex during a mixed-strategy game. J. Neurosci. 27,
8366–8377. doi: 10.1523/JNEUROSCI.2369-07.2007 Muthukumaraswamy, S. D., Johnson, B. W., and McNair, N. A. (2004). Mu rhythm
modulation during observation of an object-directed grasp. Cogn. Brain Res. 19,
195–201. doi: 10.1016/j.cogbrainres.2003.12.001 Shah, N. J., Marshall, J. C., Zafiris, O., Schwab, A., Zilles, K., Markowitsch, H. J.,
et al. (2001). The neural correlates of person familiarity: a functional magnetic May 2018 | Volume 12 | Article 180 Frontiers in Human Neuroscience | www.frontiersin.org 10 Aziz-Zadeh et al. Shared Circuits and Value resonance imaging study with clinical implications. Brain 124, 804–815. doi: 10.1093/brain/124.4.804 resonance imaging study with clinical implications. Brain 124, 804–815. doi: 10.1093/brain/124.4.804 Van Overwalle, F., and Baetens, K. (2009). Frontiers in Human Neuroscience | www.frontiersin.org REFERENCES Self-face recognition activates a frontoparietal ‘‘mirror’’ network in
the right hemisphere: an event-related fMRI study. Neuroimage 25, 926–935. doi: 10.1016/j.neuroimage.2004.12.018 Copyright © 2018 Aziz-Zadeh, Kilroy and Corcelli. 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 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. Copyright © 2018 Aziz-Zadeh, Kilroy and Corcelli. 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 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. van Elk, M., van Schie, H. T., Hunnius, S., Vesper, C., and Bekkering, H. (2008). You’ll never crawl alone: neurophysiological evidence for experience-
dependent
motor
resonance
in
infancy. Neuroimage
43,
808–814. doi: 10.1016/j.neuroimage.2008.07.057 May 2018 | Volume 12 | Article 180 Frontiers in Human Neuroscience | www.frontiersin.org 11
|
https://openalex.org/W2917647459
|
https://bmcendocrdisord.biomedcentral.com/track/pdf/10.1186/s12902-019-0339-6
|
English
| null |
Performance of HbA1c versus oral glucose tolerance test (OGTT) as a screening tool to diagnose dysglycemic status in high-risk Thai patients
|
BMC endocrine disorders
| 2,019
|
cc-by
| 5,890
|
(2019) 19:23 (2019) 19:23 Thewjitcharoen et al. BMC Endocrine Disorders (2019) 19:23
https://doi.org/10.1186/s12902-019-0339-6 Thewjitcharoen et al. BMC Endocrine Disorders
https://doi.org/10.1186/s12902-019-0339-6 Open Access Performance of HbA1c versus oral glucose
tolerance test (OGTT) as a screening tool to
diagnose dysglycemic status in high-risk
Thai patients Yotsapon Thewjitcharoen*
, Amia Jones Elizabeth, Siriwan Butadej, Soontaree Nakasatien, Phawinpon Chotwanvirat,
Ekgaluck Wanothayaroj, Sirinate Krittiyawong, Tinapa Himathongkam and Thep Himathongkam © The Author(s). 2019 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: Dysglycemic status defined by prediabetes and diabetes is known to be related with future risk of
diabetic complications and cardiovascular diseases. Herein, we aimed to determine the diagnostic accuracy of
glycated hemoglobin (HbA1c) when compared with oral glucose tolerance test (OGTT) as a reference test in
identifying dysglycemic status among high-risk Thai patients receiving care in an out-patient setting. Methods: An 11-year retrospective cross-sectional study of high-risk Thai patients who underwent OGTT during
2007–2017 was analysed. The OGTT was used as a reference test to identify subjects of dysglycemic status. The
diagnostic accuracy of HbA1c and the agreement between HbA1c and OGTT were examined. Validated Thai
diabetes risk score, Thai cardiovascular risk score (Thai CV risk score), and visceral fat area (VFA) were also compared
in each glycemic status from OGTT as surrogate markers for future diabetes and cardiovascular diseases. Results: A total of 512 subjects (females 60.5%, mean age of 50.3 ± 12.7 years, BMI of 26.5 ± 4.6 kg/m2) were
reviewed. Normal glucose tolerance (NGT) was found in 220 patients (43.0%), impaired glucose tolerance (IGT) in
191 patients (37.3%), and diabetes in 101 patients (19.7%). The prevalence of diabetes using OGTT was
approximately two times higher than those defined by HbA1c (19.7% versus 11.1%). There were poor agreements
between the classifications of prediabetes and diabetes defined by OGTT and HbA1c (Cohen’s Kappa 0.154 and 0. 306, respectively). Using a cut-off value for HbA1c ≥6.5% as a threshold for HbA1c-defined criteria of diabetes,
sensitivity was 32% (95% CI 23–41%) and specificity was 94% (95% CI 92–96%). The optimal cut-off HbA1c value
for detecting diabetes by Youden’s index was at HbA1c 6.2%. Thai CV risk score was much higher among the
OGTT-defined diabetes group when compared with the NGT group (median score 10 vs. 3, p-value < 0.001). Conclusions: Despite the practicality and validity of HbA1c as a diagnostic test, our study suggested that HbA1c as
a screening tool for diabetes in high-risk Thai patients is much inferior to OGTT. With limitations of HbA1c,
physicians should continue to advocate OGTT as a screening tool for the identification of dysglycemic status in
high-risk Thai patients. Keywords: HbA1c, OGTT, Dysglycemia, Performance, Diagnostic accuracy * Correspondence: kamijoa@hotmail.com
Diabetes and Thyroid Center, Theptarin Ho * Correspondence: kamijoa@hotmail.com
Diabetes and Thyroid Center, Theptarin Hospital, Bangkok, Thailand * Correspondence: kamijoa@hotmail.com
Diabetes and Thyroid Center, Theptarin Hospital, Bangkok, Thailand Methods We reviewed a sample of high-risk adult Thai patients,
aged 15 and older, who underwent 75-g OGTT and had
an HbA1c value within 3 months of OGTT procedure
during the study period of 2007–2017 at Theptarin
Hospital, Bangkok, Thailand. Most subjects underwent
OGTT due to high risk for diabetes such as having a
body mass index (BMI) ≥25 kg/m2 or having abdominal
obesity, Thai diabetes risk score ≥6, have a history of
IFG, or a family history of diabetes. Thai diabetes risk
score is a validated risk score calculated using factors
including age, sex, BMI, waist circumference (WC),
hypertension, and family history of diabetes for predict-
ing diabetes over 12 years in Thai people [15]. Subjects
were excluded from this study if they had a history of
diagnosed diabetes, had hematologic or endocrinologic
disorders or on medications that would interfere with
glucose metabolism. Subjects that are pregnant during
the OGTT and subjects with other nationalities were
also excluded. Only the results of the first OGTT in the
study period were used for the analysis. Data were collected on baseline characteristics such
as, age, sex, blood pressure, BMI, WC, history of dia-
betes in first-degree relatives, previously documented
cardiovascular diseases, history of smoking, hyperten-
sion, plasma lipid profiles, and statin usage. Visceral fat
area (VFA) calculated using body composition analysis
within 1 year of OGTT was retrieved. A Thai cardiovas-
cular risk score (Thai CV risk score) developed from
Electricity Generating Authority of Thailand (EGAT)
study [16] was also calculated to evaluate the risk in in-
dividual for future cardiovascular diseases. Thai CV risk
score aimed to quantify the estimated 10-year absolute
cardiovascular risk for each individual. Variables used
for calculating include age, sex, smoking status, diabetes
status, WC, height, systolic blood pressure, and/or total
cholesterol, HDL, LDL [17]. Standards for Reporting of
Diagnostic Accuracy Studies (STARD) 2015 checklist
was followed with HbA1c as the index test and OGTT
as a reference standard to ensure the proper methods
for studying diagnostic accuracy test [18]. This study
was reviewed and approved by the Theptarin Hospital
ethics committee (EC No.07/2017). Currently, there are three glucose-based diagnostic
methods with specific cut-off points for diagnosing
dysglycemic status [3, 8]. HbA1c is the latest method
and the most convenient screening tool for dysglycemia,
but it is also known to be less sensitive than the oral
glucose tolerance test (OGTT). Background g
Approximately 451 million (8.8%) adults worldwide are
expected to have diabetes, and the number is estimated
to reach 693 million (9.9%) by the year 2045 [1]. In the
Western Pacific Region, including Thailand, the preva-
lence of diabetes is estimated to increase up to 15% in
2045 [2]. Dysglycemia, both diabetes and prediabetes,
has been defined using diabetic retinopathy as a specific
complication of diabetes and these hyperglycemic states
are associated with cardiovascular diseases and meta-
bolic syndromes [3]. Prediabetes includes individuals
with impaired fasting glucose (IFG) or impaired glucose
tolerance
(IGT)
or
elevated
glycated
hemoglobin
(HbA1c) [4]. According to previous studies [5, 6], up to
70% of people with prediabetes will eventually develop
overt diabetes during their lifetime. The annual inci-
dence of progression from prediabetes to diabetes is
around 5–10% depending on the population characteris-
tics and the definition of prediabetes (6–9% in subjects
with isolated IFG, 4–6% in those with isolated IGT, up
to 15–19% among those with both IFG and IGT, and
subjects with HbA1c levels from 5.7–6.4% have a
7.5-year predicted risk of 43.1% for incident of diabetes). Moreover, individuals with prediabetes are at an in-
creased risk of cardiovascular diseases (CVD) and pre-
mature mortality when compared with subjects with
normoglycemia [7]. Thewjitcharoen et al. BMC Endocrine Disorders (2019) 19:23 Thewjitcharoen et al. BMC Endocrine Disorders (2019) 19:23 Page 2 of 8 Page 2 of 8 and OGTT in diagnosing dysglycemic status among
high-risk Thai patients. Methods It is still debatable
whether HbA1c or OGTT should be the preferred test
for diagnosing diabetes [9, 10]. The results from the
Detection Strategies for Type 2 Diabetes and Impaired
Glucose Tolerance (DETECT-2) study [11] which in-
cluded more than 40,000 participants with gradable ret-
inal photographs from five countries did not support the
superiority of OGTT over HbA1c or fasting plasma
glucose (FPG). Also, the effect of race/ethnicity on
HbA1c level were apparent [12, 13]. A previous study
from a community-based diabetes prevention program
in high-risk Thai participants [14] revealed that 51% of
total participants were positive for dysglycemia (defined
by either FPG or OGTT) and the prevalence of diabetes
classified by OGTT was two times higher than those
defined by FPG (11.0% versus 5.4%). Unfortunately, no
study was done to evaluate the clinical utility of HbA1c
compared with OGTT to diagnose dysglycemia in Thai
participants. The objectives of this study were to exam-
ine the diagnostic accuracy of HbA1c using OGTT as a
reference standard to identify subjects of dysglycemic
status and also evaluate the agreement between HbA1c Demographic and clinical characteristics g
p
Of the 618 subjects without prior history of diabetes
who underwent OGTT from 2007 to 2017, 512 subjects
met the inclusion criteria for analysis as shown in Fig. 1. Of these subjects, 74.8% had Thai diabetes risk score ≥6
out of the total score of 17, 62.9% had a history of IFG
prior to the study, 59.4% had a BMI ≥23 kg/m2. Accord-
ing to the results of OGTT, dysglycemia was found in al-
most 60% of the subjects (37.3% found IGT and 19.7%
was diagnosed with diabetes). Table 1 shows the clinical
characteristics and laboratory data of the 512 partici-
pants that are categorized into 3 groups including NGT,
IGT, and DM. The mean age of all subjects was 50.3 ±
12.7 years and the mean BMI was 26.5 ± 4.6 kg/m2. Compared to the NGT group, the IGT and DM groups
were significantly older (p = 0.001) and tended to have
higher BMI but did not reach statistical significance (p =
0.189). As shown in Table 1, there were significant
differences in HbA1c in each glycemic spectrum (HbA1c
5.6 ± 0.4% in NGT, 5.8 ± 0.5% in IGT, 6.1 ± 0.5% in DM,
p-value < 0.001). Moreover, Thai CV risk score was
much higher in DM group when compared with NGT Laboratory investigation y
g
After fasting for at least 8–12 h, OGTT was performed
2 h after the ingestion of a standard 75-g glucose load. Plasma glucose was measured by enzymatic hexokinase
method (Roche Diagnostics Cobas analyzer). Measure-
ment of HbA1c was done by electrochemiluminescence
immunoassay using Abbott Diagnostics core laboratory
(from 2007 to 2008) and Roche Diagnostics Cobas
Analyzer (from 2009 to 2017). The HbA1c test was
DCCT-aligned assay and was accredited by the National
Glycohemoglobin Standardization Program (NGSP). Definition of prediabetes and diabetes Definition of prediabetes and diabetes
In this study, the definition is based on 2018 American
Diabetes Association (ADA) criteria [3]. Diabetes was
defined as subjects with 2-h plasma glucose from OGTT
≥200 mg/dL and/or HbA1c ≥6.5% and/or FPG of ≥126
mg/dL. The term “prediabetes” refers to IFG (FPG 100–
125 mg/dL), IGT (2-h plasma glucose from OGTT at Page 3 of 8 Thewjitcharoen et al. BMC Endocrine Disorders (2019) 19:23 Page 3 of 8 Page 3 of 8 Thewjitcharoen et al. BMC Endocrine Disorders 140–199 mg/dL) or an HbA1c level of 5.7–6.4%. Normal
glucose tolerance (NGT) was defined as subjects who
had 2-h plasma glucose less than 140 mg/dL. and OGTT was analyzed using Cohen’s kappa coeffi-
cients (K). The receiver operating characteristic (ROC)
curves, plotted by using sensitivity and 1-specificity,
were used to calculate the performance of the HbA1c as
area under curves (AUC) in diagnosing prediabetes and
diabetes using the OGTT as the reference. All statistical
analyses were conducted using the Statistical Package for
the Social Sciences (version 22.0; SPSS, Chicago, IL, USA). Statistical analysis Continuous variables were presented as mean (±stand-
ard deviation, SD) or median (interquartile range), and
categorical variables were presented as proportions. Subjects were divided into 3 groups NGT, IGT, and DM
according to OGTT criteria. Clinical characteristics were
compared using one-way ANOVA and post hoc analysis. P-value ≤0.05 was considered statistically significant. The diagnostic accuracy of HbA1c to diagnose diabetes
when OGTT was used as the reference standard was
expressed in four dimensions (sensitivity, specificity,
positive likelihood ratio and negative likelihood ratio). The Youden’s index which combines sensitivity and spe-
cificity into a single measure (sensitivity + specificity - 1)
was calculated at selected HbA1c thresholds to define
diabetes from OGTT. The agreement between HbA1c Fig. 1 Flow diagram of the study according to Standards for Reporting of Diagnostic Accuracy Studies (STARD) Fig. 1 Flow diagram of the study according to Standards for Reporting of Diagnostic Accuracy Studies (STARD) Thewjitcharoen et al. Statistical analysis BMC Endocrine Disorders (2019) 19:23 Page 4 of 8 Table 1 Clinical characteristics and laboratory data of analyzed subjects classified by OGTT (N = 512)
Overall (n = 512)
NGT (n = 220, 42.9%)
IGT (n = 191, 37.3%)
DM (n = 101, 19.7%)
p-value
Female (%)
60.5%
58.6%
58.6%
68.3%
0.205
Age (years)
50.3 ± 12.7
48.4 ± 12.8
50.3 ± 11.4
54.3 ± 14
0.001
BMI (kg/m2)
26.5 ± 4.6
26.1 ± 4.7
26.7 ± 4.5
27.0 ± 4.6
0.189
Systolic BP (mmHg)
126 ± 16
124 ± 16
126 ± 15
131 ± 15
< 0.001
Diastolic BP(mmHg)
74 ± 11
74 ± 11
75 ± 11
74 ± 11
0.578
Fasting plasma glucose
103 ± 12
98 ± 9
103 ± 11
112 ± 15
< 0.001
2-h plasma glucose
155 ± 51
111 ± 19
163 ± 17
236 ± 29
< 0.001
Hypertension
31.8%
27.7%
32.5%
39.6%
0.103
History of smoking
10.4%
11.0%
11.1%
7.9%
0.422
Statin usage
37%
34%
40%
40%
0.370
History of CVD
2.3%
1.8%
2.1%
4.0%
0.339
Family History of DM
60.2%
57.7%
59.7%
66.3%
0.339
HbA1c (%NGSP)
5.8 ± 0.5
5.6 ± 0.4
5.8 ± 0.5
6.1 ± 0.5
< 0.001
Total Cholesterol (mg/dL)
199 ± 39
199 ± 39
198 ± 40
200 ± 36
0.949
Fasting Triglyceride (mg/dL)
138 ± 83
128 ± 75
149 ± 102
138 ± 48
0.081
HDL (mg/dL)
53 ± 15
55 ± 16
51 ± 15
52 ± 12
0.048
LDL (mg/dL)
125 ± 37
125 ± 38
126 ± 39
124 ± 30
0.883
VFAa (cm2)
130 ± 39
129 ± 41
131 ± 39
129 ± 34
0.963
WC (cm)
94.5 ± 13
94.1 ± 13
94.9 ± 13
94.7 ± 12
0.909
Thai DM risk score (points)
9 ± 4
8 ± 4
9 ± 3
10 ± 3
0.003
Thai CV risk scoreb (points)
4 (1–10)
3 (1–7)
4 (1–9)
10 (2–19)
< 0.001
a Available in 268/512 overall subjects (107/220 in NGT, 112/191 in IGT, 49/101 in DM)
b Displayed as median (IQR) Diagnostic accuracy of HbA1c Diagnostic accuracy of HbA1c group (median score 3 vs. 10, p-value < 0.001). Based on
Thai diabetes risk score, the distribution of OGTT-based
DM prevalence varied from 11% in low-risk category
(score ≤2) to 25% in very high-risk category (score ≥11)
as shown in Fig. 2. Figure 3 shows diabetes prevalence was twice as high
when defined by OGTT as when defined by HbA1c
(19.7% versus 11.1%, p-value < 0.001). However in diag-
nosing prediabetes, HbA1c as diagnostic criteria for Fig. 2 The distribution of OGTT-based prevalence of DM based on Thai diabetes risk score Fig. 2 The distribution of OGTT-based prevalence of DM based on Thai diabetes risk score Fig. 2 The distribution of OGTT-based prevalence of DM based on Thai diabetes risk score Thewjitcharoen et al. BMC Endocrine Disorders (2019) 19:23 Page 5 of 8 Fig. 3 Diagram showing discordants in diagnosis of a) Prediabetes defined by 2-h OGTT and HbA1c of ≥6.5%. b Diabetes defined by IGT and
HbA1c of 5.7–6.4% prediabetes (HbA1c 5.7–6.4%) can detect up to 235
(45.9%) subjects while only 191 (37.3%) subjects were
classified as IGT from OGTT. Sensitivity, specificity,
positive predictive value, and negative predictive value
for detecting selected type 2 diabetes mellitus at differ-
ent HbA1c thresholds are displayed in Table 2. The sen-
sitivity of recommended cut-off HbA1c (HbA1c ≥6.5%)
is only 32% (95% CI 23–41%) but with high specificity of
94% (95% CI 92–96%) by using OGTT as the reference
diagnosis. The best optimal cut-off HbA1c threshold to
diagnose diabetes per OGTT criteria was found at 6.2%
(Youden’s index 0.391). was considered a fair agreement between the two tests. However in diagnosing prediabetes, AUC from the ROC
curve is 0.54. Thus, HbA1c could not be used to dis-
criminate subjects with IGT. The Kappa value of 0.154
(95% CI 0.067–0.241), indicated that there was no agree-
ment between the two tests in diagnosing prediabetes. Discussions In this study we found dysglycemia in almost 60% of
high-risk adult Thai patients based on the results of
OGTT in a hospital setting. Compared to OGTT,
HbA1c has lower sensitivity but higher specificity in
diagnosing diabetes. The optimal cut-off HbA1c point to
diagnose diabetes was found at 6.2% per OGTT criteria
which is lower than the current HbA1c-based criteria of
diabetes. Such findings suggest that physicians should
advocate OGTT as a screening tool for the identification
of dysglycemic status in high-risk Thai patients. Alterna-
tively, a lower cut-off point for HbA1c might be suitable
for high-risk Thai patients. The agreement between HbA1c and OGTT In vivo studies in humans indi-
cated that there is a 70% decrease in beta-cell glucose re-
sponsiveness by the time that individual has developed
IGT [19]. Primary prevention by lifestyle modifications
and pharmacological therapy had been shown to be ef-
fective, especially in IGT patients [20–22]. Early detec-
tion for primary prevention is therefore critical to
prevent future diabetes and cardiovascular diseases. The
low reproducibility, intense sweetness problem and in-
convenience in terms of costs and time consumption
often hampered physicians’ decision to routinely use
OGTT. However, previous studies from our group and
others confirmed the possibility and practicality to use
this test as an essential diagnostic procedure for both
diagnosis and screening of diabetes [14, 23–25]. Cur-
rently, IGT does not receive much attention from
healthcare providers [26]. Perceived barriers for both
patients and clinicians should be corrected and the indi-
viduals with IGT should be identified to receive inter-
ventions on modifiable risk factors for T2DM and
cardiovascular disease. g
Our results in terms of discordance between HbA1c
and OGTT were consistent with other studies in Asian
population. A study in Japan showed concordance of
HbA1c to diagnose prediabetes with Kappa value of 0.10
and AUC of 0.65 [32]. In Singapore, a study showed that
HbA1c is more consistent in prediabetes but also had
lower sensitivity [33]. Those findings indicated that a
substantial number of diabetes cases would be missed
by using the HbA1c test alone compared with OGTT
[34, 35]. It should be noted that the agreement in diag-
nosing prediabetes and diabetes do not reflect how one
test would be better than the other. A previous study in
Chinese population suggested the use of both HbA1c and
plasma glucose [36]. Some studies recommended raising
HbA1c cut-off points for prediabetes and diabetes in
obese subjects [37, 38]. We recommend using both
HbA1c and OGTT to capture the full spectrum of dysgly-
cemic status in high-risk patients. A recent population-
based study in Vietnam [39] showed the prevalence of
diabetes to be at 12.3% and prediabetes at 40.1% based on
HbA1c criteria which are similar to our study. Therefore,
prediabetes detected by the HbA1c should be further
explored in the Asia Pacific region in order to maximize
the role of HbA1c in early detection of dysglycemic
status. The agreement between HbA1c and OGTT g
We evaluated the agreement represented by the ROC
curves between the classification of prediabetes and
diabetes defined by OGTT and HbA1c in Fig. 4. The
diagnostic ability of HbA1c for prediabetes and diabetes
are represented by the ROC curves. In diabetes group,
the AUC was 0.74 indicating that HbA1c was an accept-
able test to diagnose diabetes. The agreement, repre-
sented by kappa value of 0.306 (95% CI 0.180–0.433), The natural history of T2DM is characterized by a
progressive decline in beta-cell function, a process that Table 2 Sensitivity, specificity, positive likelihood ratio, and negative likelihood ratio for detecting selected type 2 diabetes mellitus
at different HbA1c thresholds
HbA1c (%NGSP))
Sensitivity
Specificity
Positive Likelihood Ratio
Negative Likelihood Ratio
Youden’s Index
5.7
78% (70–86%)
48% (43–53%)
1.51 (1.31–1.73)
0.45 (0.31–0.66)
0.264
5.8
74% (66–83%)
58% (53–62%)
1.75 (1.49–2.06)
0.45 (0.32–0.63)
0.319
5.9
69% (60–78%)
65% (60–69%)
1.96 (1.63–2.36)
0.47 (0.35–0.64)
0.340
6.0
63% (54–73%)
72% (67–76%)
2.25 (1.81–2.78)
0.51 (0.39–0.66)
0.351
6.1
57% (48–67%)
79% (75–83%)
2.68 (2.09–3.44)
0.54 (0.43–0.68)
0.360
6.2
54% (45–64%)
85% (81–88%)
3.55 (2.66–4.74)
0.54 (0.43–0.67)
0.391
6.3
46% (36–55%)
89% (86–92%)
4.07 (2.80–5.75)
0.61 (0.51–0.74)
0.344
6.4
38% (28–47%)
91% (89–94%)
4.42 (2.95–6.62)
0.68 (0.58–0.80)
0.291
6.5
32% (23–41%)
94% (92–96%)
5.21 (3.24–8.38)
0.73 (0.64–0.83)
0.256 y, positive likelihood ratio, and negative likelihood ratio for detecting selected type 2 diabetes mellitus Thewjitcharoen et al. BMC Endocrine Disorders (2019) 19:23 Page 6 of 8 Fig. 4 Area under the receiver operating characteristic curve (AUC) for a) concordance between OGTT and HbA1c in diagnosis of prediabetes
(AUC = 0.54) b) concordance between OGTT and HbA1c in diagnosis of diabetes (AUC = 0.74) Fig. 4 Area under the receiver operating characteristic curve (AUC) for a) concordance between OGTT and HbA1c in diagnosis of prediabetes
(AUC = 0.54) b) concordance between OGTT and HbA1c in diagnosis of diabetes (AUC = 0.74) individuals from Southeast Asia is known to interfere with
some HbA1c assay [30]. But the prevalence of major thal-
assemia (beta-thalassemia and beta-thalassemia associated
with other Hb anomalies) varies among different regions
in each country [31]. Therefore, HbA1c is still a valuable
tool for early diagnosis of dysglycemia in the Southeast
Asia region if we understand the limitations of its use. is accelerated by obesity. Funding No source of funding was applied in this retrospective study. The agreement between HbA1c and OGTT With respect to HbA1c criteria for diabetes,
our study suggests additional research on the optimal
HbA1c cut-off points to identify diabetes in high-risk
Southeast Asia patients. Glycated hemoglobin was endorsed as one of the cri-
teria for diagnosis of prediabetes and diabetes by ADA
in 2010 [27] and by the World Health Organization
(WHO) in 2011 [8] based on its equal sensitivity and
specificity to other methods as a predictor of prevalent
retinopathy. However, it needed to emphasize that the
quality assurance tests are in place and assays are stan-
dardized to criteria aligned to the international reference
values [28]. Also, it should be ensured that there are no
conditions present which preclude accuracy of HbA1c
measurement [29]. The use of HbA1c can avoid the
requirements for individual to fast or to have adequate
carbohydrate intakes before OGTT testing. Hemoglobin-
opathies especially thalassemia which affects 5–10% of Page 7 of 8 Page 7 of 8 Page 7 of 8 Thewjitcharoen et al. BMC Endocrine Disorders (2019) 19:23 Thewjitcharoen et al. BMC Endocrine Disorders (2019) 19:23 Various DM risk scores based on clinical characteris-
tics have been developed to identify individuals at high
risk of having undiagnosed T2DM. However, risk scores
developed in Caucasian populations might not apply to
populations of other ethnic groups. A validated DM risk
score in Thai population [15] was developed from a co-
hort study of employees of a state enterprise, the EGAT
in which male made up more than 75% of total partici-
pants [16]. The included variables were age, sex, BMI,
waist circumference, history of hypertension, and his-
tory of diabetes in parents or siblings. Our findings in
this study confirmed the clinical utility of this simple
risk score for different populations which were at
higher risk of developing T2DM and with the major-
ity being female. Around one fourths of subjects with
very-high Thai diabetes risk score of ≥11 were found
to have diabetes from OGTT. Therefore, screening
patients using the simple score can be effective in
identifying subjects at risk. However, our data also
suggested that at-risk individuals identified in hospital
settings should receive OGTT screening even those
with low to moderate risk classifications (scores less
than 6 out of 17). Publisher’s Note Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. Received: 9 September 2018 Accepted: 9 January 2019 Received: 9 September 2018 Accepted: 9 January 2019 Abbreviations ADA: American Diabetes Association; AUC: Area under curves; BMI: Body
mass index; CVD: Cardiovascular disease; DETECT-2 study: Detection
strategies for type 2 diabetes and impaired glucose tolerance study;
EGAT: Electricity Generating Authority of Thailand; FPG: Fasting plasma
glucose; HbA1c: Glycated hemoglobin; IFG: Impaired fasting glucose;
IGT: Impaired glucose tolerance; NGSP: National glycohemoglobin
standardization program; NGT: Normal glucose tolerance; OGTT: Oral glucose
tolerance test; ROC curve: Receiver operating characteristic curve;
T2DM: Type 2 diabetes; VFA: Visceral fat area; WC: Waist circumference;
WHO: World Health Organization Availability of data and materials The datasets analyzed during the current study are available from the
corresponding author on reasonable request. Conclusions Our study found that diabetes prevalence is almost 2
times higher when diagnosed using OGTT than when
using HbA1c which implies the limitations of HbA1c as
a screening tool for diabetes in high-risk Thai patients. This is the first study to explore the role of HbA1c in
diagnosing dysglycemic status in high-risk Thai patients. OGTT should continue to advocate as a screening tool
for identification of dysglycemic status in particular
population. Acknowledgements The authors wish to thank Professor Dr. Rajata Rajatanavin, Faculty of
Medicine, Mahidol University for his thoughtful comments and generous
advice and the staffs of Theptarin Hospital for all their help and support. Part
of this manuscript was previously presented as a poster at the annual
Endocrine meeting 2018, Chicago, USA. The authors acknowledge some limitations in the
present study. Firstly, the inherit weakness of poor re-
peatability from OGTT itself and single testing episode
only might impact the misclassification of glycemic sta-
tus. However, our results reflect real-life practice which
limited the chance to repeat OGTT in daily service. Sec-
ondly, our study assumed that a single OGTT represents
the gold standard for the presence of the disease is de-
batable. The decision of which test to use for diagnosis
of prediabetes and diabetes is left to clinical judgement
of physicians because each diagnostic test has advan-
tages and disadvantages. Thirdly, this study is based on
high-risks individuals in outpatients setting only. Thus,
the prevalence in this study would differ from that of the
general healthy population. Fourthly, there is also
emerging
evidence
that
mid-OGTT
glucose
time
points may be equally or even more predictive of fu-
ture risk of diabetes or retinopathy than the 2-h glu-
cose level [40, 41]. Our present study evaluated data
from the traditional post-load 2-h plasma glucose
level. The role and cut-off for mid-OGTT glucose
level need to be further studied in other populations. Finally, the data are retrospective cross-sectional in
nature and we cannot conclude the overall progres-
sion of future diabetes, cardiovascular diseases, or
other future co-morbidities for each individual. Fur-
ther prospective follow up study should be conducted
to evaluate our approach in using both OGTT and
HbA1c to capture dysglycemia in high-risk patients
and evaluate risks for long-term diabetic and cardio-
vascular complications. Authors’ contributions TY, AEJ, and CP performed the statistical analyses, interpreted the data and
drafted the manuscript. BS, NS, CP, WE, KS, HT, and HT contributed to the
statistical analyses, interpretation of the data and revised the manuscript
critically before submission. WE, KS, and HT made substantial contributions
to the discussion of results. They revised the manuscript critically before
submission. All authors read and approved the final manuscript. Ethics approval and consent to participate This retrospective study is approved by the Ethics board committee of
Theptarin Hospital (No.07/2017). No inform consent to participant was
required as a retrospective study. Consent for publication
Not applicable. Competing interests
h
h
d
l
h Competing interests
The authors declare that they have no competing interests. References Optimal Hemoglobin A1c
Levels for Screening of Diabetes and Prediabetes in the Japanese
Population. J Diabetes Res. 2015;2015:932057. 6. Buysschaert M, Medina JL, Bergman M, Shah A, Lonier J. Prediabetes and
associated disorders. Endocrine. 2015;48:371–93. 7. Ford ES, Zhao G, Li C. Pre-diabetes and the risk for cardiovascular disease: a
systematic review of the evidence. J Am Coll Cardiol. 2010;55:1310–7. 33. Chai JH, Ma S, Heng D, Yoong J, Lim WY, Toh SA, et al. Impact of analytical
and biological variations on classification of diabetes using fasting plasma
glucose, oral glucose tolerance test and HbA1c. Sci Rep. 2017;7:13721. 8. World Health Organization. Use of glycated Haemoglobin (HbA1c) in the
diagnosis of diabetes mellitus: abbreviated report of a WHO consultation. Geneva: WHO Press; 2011. 34. Cohen RM, Haggerty S, Herman WH. HbA1c for the diagnosis of diabetes
and prediabetes: is it time for a mid-course correction? J Clin Endocrinol
Metab. 2010;95:5203–6. 9. Sacks DB. A1C versus glucose testing: a comparison. Diabetes Care. 2011;34:
518–23. 35. Meijnikman AS, De Block CEM, Dirinck E, Verrijken A, Mertens I, Corthouts B,
et al. Not performing an OGTT results in significant underdiagnosis of
(pre)diabetes in a high risk adult Caucasian population. Int J Obes. 2017;41:
1615–20. 10. Malkani S, DeSilva T. Controversies on how diabetes is diagnosed. Curr Opin
Endocrinol Diabetes Obes. 2012;19:97–103. 11. Colagiuri S, Lee CM, Wong TY, Balkau B, Shaw JE, Borch-Johnsen K. DETECT-
2 collaboration writing group: glycemic thresholds for diabetes-specific
retinopathy: implications for diagnostic criteria for diabetes. Diabetes Care. 2011;34:145–50. 36. Zhang YH, Ma WJ, Thomas GN, Xu YJ, Lao XQ, Xu XJ, et al. Diabetes and pre-
diabetes as determined by glycated haemoglobin A1c and glucose levels in a
developing southern Chinese population. PLoS One. 2012;7:e37260. 12. Gallagher EJ, Le Roith D, Bloomgarden Z. Review of hemoglobin A(1c) in
the management of diabetes. J Diabetes. 2009;1:9–17. 37. Li J, Ma H, Na L, Jiang S, Lv L, Li G, et al. Increased hemoglobin A1c
threshold for prediabetes remarkably improving the agreement between
A1c and oral glucose tolerance test criteria in obese population. J Clin
Endocrinol Metab. 2015;100:1997–2005. 13. Davidson MB, Schriger DL. Effect of age and race/ethnicity on HbA1c levels
in people without known diabetes mellitus: implications for the diagnosis
of diabetes. Diabetes Res Clin Pract. 2010;87:415–21. 38. Camacho JE, Shah VO, Schrader R, Wong CS, Burge MR. References 1. Cho NH, Shaw JE, Karuranga S, Huang Y, da Rocha Fernandes JD, Ohlrogge
AW, et al. IDF diabetes atlas: global estimates of diabetes prevalence for
2017 and projections for 2045. Diabetes Res Clin Pract. 2018;138:271–81. Page 8 of 8 Page 8 of 8 Page 8 of 8 Page 8 of 8 Thewjitcharoen et al. BMC Endocrine Disorders (2019) 19:23 2. International Diabetes Federation. IDF Diabetes Atlas, 8th edn. Brussels,
Belgium: International Diabetes Federation; 2017. http://www.diabetesatlas.org 2. International Diabetes Federation. IDF Diabetes Atlas, 8th edn. Brussels, International Diabetes Federation. IDF Diabetes Atlas, 8th edn. Brusse 27. American Diabetes Association. Diagnosis and classification of diabetes
mellitus. Diabetes Care. 2010;33(Suppl1):S62–9. 3. American Diabetes Association (ADA). 2. Classification and Diagnosis of 3. American Diabetes Association (ADA). 2. Classification and Diagnosis of
Diabetes: Standards of medical Care in Diabetes-2018. Diabetes Care. 2018;
41(Suppl 1):S13–27. 28. International Expert Committee Report on the Role of the A1C assay in the
diagnosis of diabetes. Diabetes Care 2009;32:1327–1334. diagnosis of diabetes. Diabetes Care 2009;32:1327–1334. Diabetes: Standards of medical Care in Diabetes-2018. Diabetes Care. 2018;
41(Suppl 1):S13–27. 29. Rohlfing C, Wiedmeyer HM, Little R, Grotz VL, Tennill A, England J, et al. Biological variation of glycohemoglobin. Clin Chem. 2002;48:1116–8. Biological variation of glycohemoglobin. Clin Chem. 2002;48:1116 4. Mirasol R, Thai AC, Salahuddin AA, Tan K, Deerochanawong C, Mohamed M,
et al. A consensus of key opinion leaders on the Management of pre-
diabetes in the Asia-Pacific Region. J ASEAN Fed Endocr Soc. 2017;32:6–13. 4. Mirasol R, Thai AC, Salahuddin AA, Tan K, Deerochanawong C, Mohamed M,
et al. A consensus of key opinion leaders on the Management of pre- 30. Nasir NM, Thevarajah M, Yean CY. Hemoglobin variants detected by
hemoglobin A1c (HbA1c) analysis and the effects on HbA1c measurements. Int J Diabetes Dev Ctries. 2010;30:86–90. . Edelstein SL, Knowler WC, Bain RP, Andres R, Barrett-Connor EL, Dowse GK, 5. Edelstein SL, Knowler WC, Bain RP, Andres R, Barrett-Connor EL, Dowse GK,
et al. Predictors of progression from impaired glucose tolerance to NIDDM:
an analysis of six prospective studies. Diabetes. 1997;46:701–10. 31. Fucharoen S, Weatherall DJ. Progress Toward the Control and Management
of the Thalassemias. Hematol Oncol Clin North Am. 2016;30:359–71. of the Thalassemias. Hematol Oncol Clin North Am. 2016;30:359– an analysis of six prospective studies. Diabetes. 1997;46:701–10. 32. Shimodaira M, Okaniwa S, Hanyu N, Nakayama T. References Performance of A1C
versus OGTT for the diagnosis of prediabetes in a community-based
screening. Endocr Pract. 2016;22:1288–95. 14. Aekplakorn W, Tantayotai V, Numsangkul S, Sripho W, Tatsato N,
Burapasiriwat T, et al. Detecting prediabetes and diabetes: agreement
between fasting plasma glucose and Oral glucose tolerance test in Thai
adults. J Diabetes Res. 2015;2015:396505. 39. Ho-Pham LT, Do TT, Campbell LV, Nguyen TV. HbA1c-Based Classification
Reveals Epidemic of Diabetes and Prediabetes in Vietnam. Diabetes Care. 2016;39:e93–4. 15. Aekplakorn W, Bunnag P, Woodward M, Sritara P, Cheepudomwit S,
Yamwong S, et al. A risk score for predicting incident diabetes in the Thai
population. Diabetes Care. 2006;29:1872–7. 40. Jagannathan R, Sevick MA, Fink D, Dankner R, Chetrit A, Roth J, et al. The 1-
hour post-load glucose level is more effective than HbA1c for screening
dysglycemia. Acta Diabetol. 2016;53:543–50. 16. Vathesatogkit P, Woodward M, Tanomsup S, Ratanachaiwong W, Vanavanan
S, Yamwong S, et al. Cohort profile: the electricity generating authority of
Thailand study. Int J Epidemiol. 2012;41:359–65. 41. Paddock E, Looker HC, Piaggi P, Knowler WC, Krakoff J, Chang DC. One-hour
plasma glucose compared with two-hour plasma glucose in relation to
diabetic retinopathy in American Indians. Diabetes Care. 2018;41:1212–7. 17. Thai CV risk score. https://med.mahidol.ac.th/cardio_vascular_risk/thai_cv_
risk_score/tcvrs_en.html (Accessed 8 Dec 2017). 18. Cohen JF, Korevaar DA, Altman DG, Bruns DE, Gatsonis CA, Hooft L, et al. STARD 2015 guidelines for reporting diagnostic accuracy studies:
explanation and elaboration. BMJ Open. 2016;6:e012799. 19. Ferrannini E, Gastaldelli A, Miyazaki Y, Matsuda M, Mari A, DeFronzo RA. Beta-cell function in subjects spanning the range from normal glucose
tolerance to overt diabetes: a new analysis. J Clin Endocrinol Metab. 2005;90:493–500. 19. Ferrannini E, Gastaldelli A, Miyazaki Y, Matsuda M, Mari A, DeFronzo RA. Beta-cell function in subjects spanning the range from normal glucose
tolerance to overt diabetes: a new analysis. J Clin Endocrinol Metab. 2005;90:493–500. 20. Tuomilehto J, Lindstrom J, Eriksson JG, Valle TT, Hamalainen H, Ilanne-
Parikka P, et al. Finnish diabetes prevention study group: prevention of type
2 diabetes mellitus by changes in lifestyle among subjects with impaired
glucose tolerance. N Engl J Med. 2001;344:1343–50. 21. Knowler WC, Barrett-Connor E, Fowler SE, Hamman RF, Lachin JM, Walker
EA, et al. Diabetes prevention program research group: reduction in the
incidence of type 2 diabetes with lifestyle intervention or metformin. N Engl
J Med. 2002;346:393–403. 22. Thewjitcharoen et al. BMC Endocrine Disorders (2019) 19:23 26.
Karuranga S, Wiebke Ohlrogge A. The time bomb of IGT. Diabetes Res Clin
Pract. 2018;138:288–90. 24.
Tabák AG, Herder C, Rathmann W, Brunner EJ, Kivimäki M. Prediabetes: a
high-risk state for diabetes development. Lancet. 2012;379:2279–90. References Pan XR, Li GW, Hu YH, Wang JX, Yang WY, An ZX, et al. Effects of diet and
exercise in preventing NIDDM in people with impaired glucose tolerance. The Da Qing IGT and diabetes study. Diabetes Care. 1997;20:537–44. 23. Chotwanvirat P, Thewjitcharoen Y, Parksook W, Krittiyawong S, Hutaphat K,
Nakasatien S, et al. Development of New Lemon-Lime Flavored Beverage for
OGTT: Acceptability and Reproducibility. J Med Assoc Thail. 2016;99:497–504. 24. Tabák AG, Herder C, Rathmann W, Brunner EJ, Kivimäki M. Prediabetes: a
high-risk state for diabetes development. Lancet. 2012;379:2279–90. 25. Abdul-Ghani MA, Williams K, DeFronzo RA, Stern M. What is the best
predictor of future type 2 diabetes? Diabetes Care. 2007;30:1544–8. 26. Karuranga S, Wiebke Ohlrogge A. The time bomb of IGT. Diabetes Res Clin
Pract. 2018;138:288–90.
|
https://openalex.org/W3046224654
|
https://zenodo.org/records/3969272/files/RaTG13%20anomalies.pdf
|
English
| null |
Anomalies in BatCoV/RaTG13 sequencing and provenance
|
Zenodo (CERN European Organization for Nuclear Research)
| 2,020
|
cc-by
| 4,150
|
ABSTRACT To this date, the most critical piece of evidence on the purposed “natural origin” theory of
SARS-CoV-2, was the sequence known as RaTG13, allegedly collected from a single fecal sample
from Rhinolophus Affinis. Understanding the provenance of RaTG13 is critical on the ongoing
debate of the Origins of SARS-CoV-2. However, this sample is allegedly “used up” and therefore
can no longer be accessed nor sequenced independently [1], and the only available data was the
3 related Genbank accessions: MN996532.1, SRX7724752 and SRX8357956. We report these datasets possessed multiple significant anomalies, and the provenence of the
promised claims of RaTG13 or it’s role in proving a “probable bat origin”[2] of SARS-CoV-2 can
not be satisfied nor possibly be confirmed. Daoyu Zhang Daoyu Zhang d Telomere-like repeat sequences within the first 20 reads of
of traces of Telomere-like repeats in total RNA of most cells,
raction of the total cellular RNA within real biological samples,
the first 100 reads. RaTG13 contained an anomalous amount
3% of the dataset and exist in nearly any set of 10 reads within
xt highest content of such repeats within any other sample of
merely 4% of these repeats, which does not show up in the
ere-like repeats are not detected in the first 100 reads of any
24693 lacked such reads within the first 100 reads of the
724693 did not show any Telomere-like repeats. 6% all-N sequences that were exactly 35nt long, which is not
atasets that had the same design section. n SRX7724752. Figure 1: The reads that contained Telomere-like repeat sequences within the first 20 reads of
SRX7724752. Despite the theoretical presence of traces of Telomere-like repeats in total RNA of most cells,
such repeats comprise only a tiny fraction of the total cellular RNA within real biological samples,
and normally does not show up in the first 100 reads. RaTG13 contained an anomalous amount
of such repeats, which comprises 63% of the dataset and exist in nearly any set of 10 reads within
this dataset. In comparison, the next highest content of such repeats within any other sample of
similar context on NCBI, contained merely 4% of these repeats, which does not show up in the
first 20 reads of the dataset. Telomere-like repeats are not detected in the first 100 reads of any
other datasets examined. In comparison, the related SRX7724693 lacked such reads within the first 100 reads of the
dataset. Figure 2: the first 100 reads in SRX7724693 did not show any Telomere-like repeats. In addition, SRX7724752 contained 6% all-N sequences that were exactly 35nt long, which is not
found at levels any close in other datasets that had the same design section. Figure 3: an example of All-N read in SRX7724752. Figure 1: The reads that contained Telomere-like repeat sequences within the first 20 reads of
SRX7724752. Fi
1 Th
d th t
t i
d T l
lik
t
ithi
th
fi t 20
d
f Figure 1: The reads that contained Telomere-like repeat sequences within the first 20 reads of
SRX7724752. Despite the theoretical presence of traces of Telomere-like repeats in total RNA of most cells,
such repeats comprise only a tiny fraction of the total cellular RNA within real biological samples,
and normally does not show up in the first 100 reads. RaTG13 contained an anomalous amount
of such repeats, which comprises 63% of the dataset and exist in nearly any set of 10 reads within
this dataset. In comparison, the next highest content of such repeats within any other sample of
similar context on NCBI, contained merely 4% of these repeats, which does not show up in the
first 20 reads of the dataset. Telomere-like repeats are not detected in the first 100 reads of any
other datasets examined. In comparison, the related SRX7724693 lacked such reads within the first 100 reads of the
dataset. dataset.
Figure 2: the first 100 reads in SRX7724693 did not show any Telomere-like repeats.
In addition, SRX7724752 contained 6% all-N sequences that were exactly 35nt long, which is not
found at levels any close in other datasets that had the same design section.
Figure 3: an example of All-N read in SRX7724752. Anomalous enrichment of non-attributable and low-match
data within SRX7724752 Anomalous enrichment of non-attributable and low-match
data within SRX7724752 Anomalous enrichment of non-attributable and low-match
data within SRX7724752 data within SRX7724752 Figure 4: BLAST result of 100 random reads obtained from RaTG13 using BLASTn. In addition to the anomalous enrichment of repeats, The vast majority of the non-repeat
sequences in SRX7724752 does not show any clear matches when examined using BLASTn. With
matching results ranging from nearly all domains of life—all of which were partial and low-quality
matches, including that of bats. Only 2 out of 7 Non-repeat and non-PolyN sequences from the first 20 reads from SRX7724752
had any matches, and the match was only partial matches to certain hypothetical proteins Only 2 out of 7 Non-repeat and non-PolyN sequences from the first 20 reads from SRX7724752
had any matches, and the match was only partial matches to certain hypothetical proteins Figure 5: the BLASTn result of the 2 non-repeat and non-PolyN sequences in the first 20 reads of
SRX7724752. The rest can not be matched to any known organisms. Figure 5: the BLASTn result of the 2 non-repeat and non-PolyN sequences in the first 20 reads of
SRX7724752. The rest can not be matched to any known organisms. metadata. Fecal matter [3], is primarily bacteria by composition. All other fecal swabs prepared using the
methods indicated by the metadata correctly showed the presence of bacteria as the majority of
the reads. In contrast, SRX7724272 contained only 0.65% bacteria-like reads, all of which were
16S rRNA. Figure 6: Phylogenetic analysis of SRX7724272. Figure 6: Phylogenetic analysis of SRX7724272. Figure 7: A set of 9 Swabs. The only ones that matches RaTG13 by metadata on Genbank. None of
them had more Eukarya-like reads than Bacteria-like reads. In addition to the anomalous depletion of bacterial-like reads, SRX7724272 also lacked Figure 7: A set of 9 Swabs. The only ones that matches RaTG13 by metadata on Genbank. None of
them had more Eukarya-like reads than Bacteria-like reads. In addition to the anomalous depletion of bacterial-like reads, SRX7724272 also lacked discernible reads from bacterial mRNA. discernible reads from bacterial mRNA. Figure 8: BLAST hits of bacterial non-ribosomal RNA genome on SRX7724272 and another swab
from Rhinolophus Affinis under the same library preparation section. Figure 8: BLAST hits of bacterial non-ribosomal RNA genome on SRX7724272 and another swab
from Rhinolophus Affinis under the same library preparation section. Observation of anomalous and unexpected data within
SRX7724752 Figure 9: Phyllostomus Discolor, or Pale spear-nosed bat, a species of bat native to the Americas,
is found in high abundance within SRX7724752. Figure 10: A sequence which was matched to a bat mRNA clone in the first 96 nucleotides, but
then matching nothing on the later nucleotides. This match end with a T. Figure 9: Phyllostomus Discolor, or Pale spear-nosed bat, a species of bat native to the Americas,
is found in high abundance within SRX7724752. igure 9: Phyllostomus Discolor, or Pale spear-nosed bat, a species of bat native to the Americas,
s found in high abundance within SRX7724752. Figure 10: A sequence which was matched to a bat mRNA clone in the first 96 nucleotides, but
then matching nothing on the later nucleotides. This match end with a T. Figure 10: A sequence which was matched to a bat mRNA clone in the first 96 nucleotides, but
then matching nothing on the later nucleotides. This match end with a T. Figure 10: A sequence which was matched to a bat mRNA clone in the first 96 nucleotides, but
then matching nothing on the later nucleotides. This match end with a T. Figure 10: A sequence which was matched to a bat mRNA clone in the first 96 nucleotides, bu
then matching nothing on the later nucleotides. This match end with a T. igure 10: A sequence which was matched to a bat mRNA clone in the first 96 nucleotides, but
hen matching nothing on the later nucleotides. This match end with a T. Figure 11: a viral sequence fused to a mRNA-like sequence Again overlapping on an A Figure 11: a viral sequence fused to a mRNA-like sequence. Again overlapping on an A. Of the only 3 sequences within the viral reads within SRX7724752 that displays fusion of different
sequences, only one sequence matches that of a canonical coronavirus subgenomic mRNA leader,
another one was the read illustrated in Figure.11, while the third one was a non-canonical fusion
of two non-TRS regions in the RaTG13 genome. Figure 12: an anomalous fusion of two non-canonical regions of the RaTG13 genome. The fusion
again happens on a T. Figure 12: an anomalous fusion of two non-canonical regions of the RaTG13 genome. The fusion
again happens on a T. Figure 12: an anomalous fusion of two non-canonical regions of the RaTG13 genome. The fusion
again happens on a T. Figure 13: the only canonical sgRNA-like read* in SRX7724752. Furthermore, SRX7724752 contained significant amount of reads that had higher query coverage
on the DNA sequence than on the corresponding mRNA. This most likely indicate a clonal, rather
than cDNA, library, was responsible for most of the bat-like reads observed in SRX7724752. re 13: the only canonical sgRNA-like read* in SRX7724752. Figure 13: the only canonical sgRNA-like read* in SRX7724752. Figure 13: the only canonical sgRNA-like read* in SRX7724752. Furthermore, SRX7724752 contained significant amount of reads that had higher query coverage
on the DNA sequence than on the corresponding mRNA. This most likely indicate a clonal, rather
than cDNA, library, was responsible for most of the bat-like reads observed in SRX7724752. Furthermore, SRX7724752 contained significant amount of reads that had higher query coverage
on the DNA sequence than on the corresponding mRNA. This most likely indicate a clonal, rather
than cDNA, library, was responsible for most of the bat-like reads observed in SRX7724752. Figure 14: a read from SRX7724752 which have higher coverage on the clone than on the
corresponding mRNA. E.g. the read contained nucleotide sequences that were not supposed to
be transcribed in actual cells/bats. Figure 14: a read from SRX7724752 which have higher coverage on the clone than on the
corresponding mRNA. E.g. the read contained nucleotide sequences that were not supposed to
be transcribed in actual cells/bats. Inability of SRX8357956 to prove the promises claimed in [5] Figure 15: A complete analysis [4] of all Amplicon sequences in SRX8357956. Including the
location of these amplicons and the similarity of such amplicon to the RaTG13 and SARS-CoV-2
genome. Figure 15: A complete analysis [4] of all Amplicon sequences in SRX8357956. Including the
location of these amplicons and the similarity of such amplicon to the RaTG13 and SARS-CoV-2
genome. Chuan Xiao et.al claimed that RaTG13 contained all the 3 S1 variable loops that were previously
considered unique in SARS-CoV-2. [5] However, such claims can not be verified using the
amplicons listed in SRX8357956. Chuan Xiao et.al claimed that RaTG13 contained all the 3 S1 variable loops that were previously
considered unique in SARS-CoV-2. [5] However, such claims can not be verified using the
amplicons listed in SRX8357956. Figure 16: a thorough analysis of the amplicons located on the S locus of RaTG13 in SRX8357956. Notice that the last 4 amplicons sequenced in 14/10/2018 was of very low quality matches, and
matched other organisms—including Mouse(mus musculus). Figure 16: BLAST result of the non-RaTG13 matched parts of Amplicons 25, 24 and 23 in
SRX8357956 Figure 16: a thorough analysis of the amplicons located on the S locus of RaTG13 in SRX8357956. Notice that the last 4 amplicons sequenced in 14/10/2018 was of very low quality matches, and
matched other organisms—including Mouse(mus musculus). Figure 16: a thorough analysis of the amplicons located on the S locus of RaTG13 in SRX8357956. Notice that the last 4 amplicons sequenced in 14/10/2018 was of very low quality matches, and
matched other organisms—including Mouse(mus musculus). Figure 16: BLAST result of the non-RaTG13 matched parts of Amplicons 25, 24 and 23 in
SRX8357956
Using the remaining amplicons, the 3 variable loops, GTNGIKR, HKSNK and VIFSQ was obtained. Figure 16: a thorough analysis of the amplicons located on the S locus of RaTG13 in SRX8357956. Notice that the last 4 amplicons sequenced in 14/10/2018 was of very low quality matches, and
matched other organisms—including Mouse(mus musculus). Figure 16: BLAST result of the non-RaTG13 matched parts of Amplicons 25, 24 and 23 in
SRX8357956
Using the remaining amplicons, the 3 variable loops, GTNGIKR, HKSNK and VIFSQ was obtained. Figure 16: a thorough analysis of the amplicons located on the S locus of RaTG13 in SRX8357956. Notice that the last 4 amplicons sequenced in 14/10/2018 was of very low quality matches, and
matched other organisms—including Mouse(mus musculus). Inability of SRX8357956 to prove the promises claimed in [5] Figure 16: a thorough analysis of the amplicons located on the S locus of RaTG13 in SRX8357956. Notice that the last 4 amplicons sequenced in 14/10/2018 was of very low quality matches, and
matched other organisms—including Mouse(mus musculus). her organisms—including Mouse(mus musculus). Figure 16: BLAST result of the non-RaTG13 matched parts of Amplicons 25, 24 and 23 in
SRX8357956
Using the remaining amplicons, the 3 variable loops, GTNGIKR, HKSNK and VIFSQ was obtained. Figure 16: BLAST result of the non-RaTG13 matched parts of Amplicons 25, 24 and 23 in Figure 16: BLAST result of the non-RaTG13 matched parts of Amplicons 25, 24 and 23 in
SRX8357956 Figure 16: BLAST result of the non-RaTG13 matched parts of Amplicons 25, 24 and 23 in
SRX8357956 Using the remaining amplicons, the 3 variable loops, GTNGIKR, HKSNK and VIFSQ was obtained Using the remaining amplicons, the 3 variable loops, GTNGIKR, HKSNK and VIFSQ was obtained. This is vastly different from the variable loops possessed by SARS-CoV-2, which were GTNGTKR,
HKNNK and GDSSSG. Therefore, the promise of Chuan Xiao et. Al does not hold upon raw data
analysis. Probable discontinuities in RaTG13 sequencing in SRX8357956 Probable discontinuities in RaTG13 sequencing in SRX8357956 Figure 17: Detailed analysis of the early amplicons located in the nsp12 RdRp region of RaTG13 in
SRX8357956. Within the amplicons labeled “7896”, there were 2 sites of overlap—the first overlap, a region
158bp in length, contained only 2nt difference—all C-T transitions—to SARS-CoV-2. Such
transitions easily arise in passage, and are probable sequencing errors from a degraded/passaged
sample of DNA. Figure 17: Detailed analysis of the early amplicons located in the nsp12 RdRp region of RaTG13 in
SRX8357956. Figure 17: Detailed analysis of the early amplicons located in the nsp12 RdRp region of RaTG13 in
SRX8357956. Within the amplicons labeled “7896”, there were 2 sites of overlap—the first overlap, a region
158bp in length, contained only 2nt difference—all C-T transitions—to SARS-CoV-2. Such Within the amplicons labeled “7896”, there were 2 sites of overlap—the first overlap, a region
158bp in length, contained only 2nt difference—all C-T transitions—to SARS-CoV-2. Such
transitions easily arise in passage, and are probable sequencing errors from a degraded/passaged
sample of DNA. The second overlap, one with BtCoV/4991, contained only 1 C-T transition, which have a probable
origin in the primers used to generate the amplicons in the first place. DISCUSSIONS
Origins of the anomalies in SRX7724752
Figure 18A: Origin of repeating sequences in SRX7724752. The only satiable explanation for the anomalous enrichment of the Telomere-like repeats in
SRX7724752, involves the self-amplification of such sequences in a PCR reaction with little to no
template. Origins of the anomalies in SRX7724752 Origins of the anomalies in SRX7724752 Figure 18A: Origin of repeating sequences in SRX7724752. Figure 18A: Origin of repeating sequences in SRX7724752. he only satiable explanation for the anomalous enrichment of the Telomere-like repeats in
RX7724752, involves the self-amplification of such sequences in a PCR reaction with little to no
emplate. Normally, with significant amount of template, the random primers normally used in RT-PCR
amplifies most sequences evenly and outcompetes the repeat sequences in the reaction, and the
result was an accurate reflection of such repeats within cellular samples—extremely poor. However, in samples that have little to no template, such that the random primers/random
hexamers used in the reaction were not able to prime the amplification of most sequences—e.g. the amount of normal templates within the reaction falls below the timescale needed for the
amplification of the repeating sequences, Repeating sequences, of which telomere-like repeats
forms the vast majority of it in the environment and in most samples, can self-amplify in a
primer-independent fashion, eventually reaching very high dominance, through repeated
denaturing, sliding, reannealing and extension. As this is a linear process, the self-amplification process is very slow, and is normally
outcompeted by the normal amplicons as long as any usable amount of templates were present. Therefore, the presence of anomalously enriched telomere-like repeats within SRX7724752
indicate that the original sample couldn’t have contained enough templates for the generation of
the complete genome, through any means possible. Figure 18B: Origin of the random matched sequences and partial sequences in SRX7724752
The majority of the sequences that were not repeats, when BLASTed, does not match any known
organisms. There were also many sequences that matches—only partially, to many diverse
organisms. What was striking, is, however, is that these matches often ends with an “A” or a “T”. The most possible explanation of this anomaly is that the Library preparation process of
ILLUMINA RNA-seq, which include strand synthesis and A-T ligation to adaptors, were fed dsDNA
rather than ssRNA, as input. Such dsDNA input may be PCR products, or it may be a pre-made
ILLUMINA sequencing library—Certain mRNA-like reads were inadvertently inverted, indicating
double-stranded cDNA was likely used instead of single stranded mRNA. Origins of the anomalies in SRX7724752 Figure 18B: Origin of the random matched sequences and partial sequences in SRX7724752 Figure 18B: Origin of the random matched sequences and partial sequences in SRX7724752 The majority of the sequences that were not repeats, when BLASTed, does not match any known
organisms. There were also many sequences that matches—only partially, to many diverse
organisms. What was striking, is, however, is that these matches often ends with an “A” or a “T”. The most possible explanation of this anomaly is that the Library preparation process of
ILLUMINA RNA-seq, which include strand synthesis and A-T ligation to adaptors, were fed dsDNA
rather than ssRNA, as input. Such dsDNA input may be PCR products, or it may be a pre-made
ILLUMINA sequencing library—Certain mRNA-like reads were inadvertently inverted, indicating
double-stranded cDNA was likely used instead of single stranded mRNA. The majority of the sequences that were not repeats, when BLASTed, does not match any known
organisms. There were also many sequences that matches—only partially, to many diverse
organisms. What was striking, is, however, is that these matches often ends with an “A” or a “T”. The most possible explanation of this anomaly is that the Library preparation process of
ILLUMINA RNA-seq, which include strand synthesis and A-T ligation to adaptors, were fed dsDNA
rather than ssRNA, as input. Such dsDNA input may be PCR products, or it may be a pre-made
ILLUMINA sequencing library—Certain mRNA-like reads were inadvertently inverted, indicating
double-stranded cDNA was likely used instead of single stranded mRNA. Figure 20a: the match analysis between different genomic fragments of RaTG13, of the sole
sgRNS-like read* in SRX7724752. *:Figure 13 Despite being sgRNA-like in the first glance, analysis of the exact overlapping region of thi
particular read reveal that this region is identical to BtCoV/ZC45 and BtCoV/ZXC21—indicating it’
identity as likely being a consensus primer. Despite being sgRNA-like in the first glance, analysis of the exact overlapping region of this
particular read reveal that this region is identical to BtCoV/ZC45 and BtCoV/ZXC21—indicating it’s
identity as likely being a consensus primer. Figure 20b: BLAST result of CTCTCGATCTCTTGTAGATCTGTTCTCTAAACGAAC. This particular sequence have extended overlap to the beginning of the N gene, which was
coincidentally at the end of the last 2017/06/17 amplicon. This indicate it was most likely the
product of mispriming, rather than a true sgRNA-like read. Figure 20b: BLAST result of CTCTCGATCTCTTGTAGATCTGTTCTCTAAACGAAC. Origins of the anomalies in SRX7724752 This particular sequence have extended overlap to the beginning of the N gene, which was
coincidentally at the end of the last 2017/06/17 amplicon. This indicate it was most likely the
product of mispriming, rather than a true sgRNA-like read. cDNA This dataset is likely subjected to probe-capture sequencing similar to these other datasets—the
use of a positive-sense CoV probe resulted in the selective presentation of the negative ssDNA
strand of the ligation products to show up. This is supported by the observation that while most
of the virus-like reads were on the negative strand, the Repeats does not show a bias in strand
polarity, and the mRNA-like reads have a much higher chance of being on the wrong polarity for
RNA-seq. This is likely due to the ligation process being used. cDNA Phyllostomus Discolor, a species of bat native to Mexico and southern United states, leaves
numerous Full-length 100% matched reads that don’t match anything else. Coincidentally,
Mexico is one of the major supplier of bat guano used for fertilizer and other commercial
purposes[6]. The confirmed presence of this particular bat species, suggest the use of a
commercial dried bat guano matrix as the bulk of the sample being sequenced. As in
PRJNA494391[7] which synthetic metagenome samples were constructed using cDNA amplicons
and a specific material matrix to simulate realistic metagenomic reads of a desired virus in a
sample. Traces of the original template used in the megaprimer PCR process can be seen as traces of
low-matched virus-like reads within this dataset, which are found across the entire RaTG13
genome. g
Figure 21: Read coverage of SRX7724752 on the RaTG13 genome. The red pixels represent
significant mismatches on the reads in the dataset. The Bacterial-like reads in SRX7724752 is also likely a synthetic 16S library—as the only other
dataset with Telomere-like repeats(4%), still contained significant amount of bacterial mRNA. Figure 21: Read coverage of SRX7724752 on the RaTG13 genome. The red pixels represent
significant mismatches on the reads in the dataset. The Bacterial-like reads in SRX7724752 is also likely a synthetic 16S library—as the only other
ataset with Telomere-like repeats(4%), still contained significant amount of bacterial mRNA. Figure 22a: a bacterial mRNA read in SRX7724696, the only other dataset on NCBI that contained
Telomere-like repeats in the first 100 reads of the dataset. Total amt. of repeats=4% Figure 22a: a bacterial mRNA read in SRX7724696, the only other dataset on NCBI that contained
Telomere-like repeats in the first 100 reads of the dataset. Total amt. of repeats=4% Figure 22a: a bacterial mRNA read in SRX7724696, the only other dataset on NCBI that contained
Telomere-like repeats in the first 100 reads of the dataset. Total amt. of repeats=4% Figure 22a: a bacterial mRNA read in SRX7724696, the only other dataset on NCBI that contained
Telomere-like repeats in the first 100 reads of the dataset. Total amt. of repeats=4% Figure 22b: the same species of bacteria in SRX7724752. No significant matches were found. Figure 22b: the same species of bacteria in SRX7724752. No significant matches were found. CONCLUSION The raw data of BtCoV/RaTG13 Contained multiple anomalies that signifies that the original
sample could not have contained enough RNA template for the extraction of a complete viral
genome as in MN996532.1 Furthermore, many of these anomalies points toward the fraudulent use of a mixed DNA library,
rather than genuine mRNA, for the sequencing of SRX7724752, evident by the presence of
widespread A-T ligation of unrelated dsDNA fragments that can only happen if the same library
preparation process have been ran on dsDNA instead of ssRNA. which would constitute Academic
fraud. Therefore, the sequencing of BtCoV/RaTG13 can not be considered to be valid or honest as is,
and any publications, including [2], and other publications that cites or use RaTG13 as critical
pieces of evidence or proof, must be immediately invalidated and retracted. REFERENCES
[1] https://www.thetimes.co.uk/article/seven-year-covid-trail-revealed-l5vxt7jqp
[2] Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of
probable bat origin. Nature. 2020;579(7798):270-273. doi:10.1038/s41586-020-2012-7 REFERENCES [3] Rose C, Parker A, Jefferson B, Cartmell E. The Characterization of Feces and Urine: A Review of
the Literature to Inform Advanced Treatment Technology. Crit Rev Environ Sci Technol. 2015;45(17):1827-1879. doi:10.1080/10643389.2014.1000761
[4] https://telegra.ph/RaTG13-07-06
[5] Xiao C, Li X, Liu S, Sang Y, Gao SJ, Gao F. HIV-1 did not contribute to the 2019-nCoV genome. Emerg
Microbes
Infect. 2020;9(1):378-381. Published
2020
Feb
14. doi:10.1080/22221751.2020.1727299
[6] https://www.planetnatural.com/product/mexican-bat-guano/
[7] Paskey, A.C., Frey, K.G., Schroth, G. et al. Enrichment post-library preparation enhances the
sensitivity of high-throughput sequencing-based detection and characterization of viruses from
complex samples. BMC Genomics 20, 155 (2019). https://doi.org/10.1186/s12864-019-5543-2 [7] Paskey, A.C., Frey, K.G., Schroth, G. et al. Enrichment post-library preparation enhances the
sensitivity of high-throughput sequencing-based detection and characterization of viruses from
complex samples. BMC Genomics 20, 155 (2019). https://doi.org/10.1186/s12864-019-5543-2
|
https://openalex.org/W3172642863
|
https://fbj.springeropen.com/track/pdf/10.1186/s43093-021-00067-8
|
English
| null |
The impacts of interaction of audit litigation and ownership structure on audit quality
|
Future business journal
| 2,021
|
cc-by
| 12,713
|
1 GCC stands for Gulf Cooperation Council. This Council consists of six
countries: Saudi Arabia, Kuwait, Qatar, United Arab Emirates, Bahrain and
Oman. Abstract This study examines the impact of the interactions of audit litigation and ownership structure on audit quality by Big
4 and non-Big 4 audit firms in Oman. This study uses modified audit opinion as proxies for audit quality, binary varia-
ble for audit litigation and percentage of shares owned by large shareholders and minority shareholders (consisting of
Arab [non-GCC] shareholders) for ownership structure. The study uses size, risk, types of activity and ages of the firms
as control variables. For the analysis and explanation of results descriptive statistics, correlation, regression techniques
and T-test are used. Based on a sample of 107 listed companies on Muscat Securities Market (MSM) for 2013–2017, we
find that audit litigation has a significant impact on audit quality for Big 4 audit firms, but not for non-Big 4 audit firms. Also, the results indicate that there is no difference between Big 4 and non-Big 4 audit firms as far as litigation risk is
concerned. Keywords: Audit litigation, Audit quality, Ownership structure, Emerging economy, Oman
JEL Classification: M40, M42, G32 JEL Classification: M40, M42, G32 Ownership structure is defined in terms of size of
shareholders as well as the identity or nationality. Muscat
Securities Market (MSM) is totally regulated by CMA. There are two groups of shareholders in terms of size:
large shareholders which include three types of inves-
tor’s nationalities; Omani, Arab-GCC (Gulf Coopera-
tion Council) and foreign and the minority shareholders
group which includes only one type of investor that is
Arab non-GCC. Large shareholders are those who hold a
sizable fraction of all voting shares in the firms, whereas
the minority shareholders are those who hold a less siz-
able fraction of these shares. © The Author(s) 2021. 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/. *Correspondence: mawih@du.edu.om
2 Accounting Department, Dhofar University, Dhofar, Oman
Full list of author information is available at the end of the article Riyadh Jassim AL Abdullah1 and Mawih Kareem AL Ani2* Riyadh Jassim AL Abdullah1 and Mawih Kareem AL Ani2* Future Business Journal Future Business Journal AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19
https://doi.org/10.1186/s43093-021-00067-8 Open Access © The Author(s) 2021. 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/. Introduction Since 2005, the Capital Market Authority (CMA) which
is responsible for the control of the audit firms in Oman
issued warning letters to some audit firms, suspended
one audit firm from conducting audits for firms regu-
lated by CMA for one year and suspended eight audit
firms for three months due to their violations of articles
of the Omani Commercial Companies. Thus, the cred-
ibility of audited financial statements issued by audit
firms remains questionable. Since 2000, the number of
litigations related to audit issues has increased to 32,000
[4]. Out of these, 2250 cases were against the Big 4 firms. Prior researches [2, 22, 25, 29, 54] assess the impact of
audit litigation and ownership structure separately on
audit quality, rather than exploring the combined impact
of both the audit litigation and ownership structure on
audit quality. This study fills the gap in the literature
by evaluating audit litigations and auditees’ ownership
structures on audit quality.1 Omani data were used for the evaluation due to acces-
sibility of data and for filling the gap in literature on the
impact of audit litigations and auditees’ ownership struc-
ture on audit quality of Big 4 or non-Big 4. Data related
to ownership structure and audit quality were collected
from MSM reports, while the data of audit litigation were
retrieved from CMA reports. All these data were offi-
cially from CMA. Audit litigation: with focus on Oman In general, there are two types of litigations against audit
firms; the first is carried out by government authority or
any authorized audit associations and the second is car-
ried out by audit clients. This study is within the domain
of the first type. i
Litigation against an audit firm can arise from carrying
out audit services in companies having publicly or pri-
vately traded securities. Furthermore, litigation against
an audit firm covers audit services (e.g., audit of financial
statements) as well as non-audit services (e.g., prepara-
tion of tax report, assurance services, consultancy ser-
vices, etc.). Audit litigation may also arise from violations
of laws such as company law, securities acts, contract law
or/and any other regulations [6]. In the relevant literature, the term “audit litigation
risk” is used to refer to the possibility that legal action is
executed due to dissatisfaction with an auditor’s or audit
firm’s actions, inaction, products, services and/or other
activity [19]. According to Kim and Skinner [31], the liti-
gation risk is the risk of securities class action lawsuits,
as opposed to the risk of legal action brought by govern-
ment agencies/departments. This study embraces this
distinction and, accordingly, defines the audit litigation
risk as the class action lawsuit, as opposed to the risk of
legal action brought about by government agencies in the
context of Oman, particularly, i.e., the legal action carried
out by the Ministry of Commerce and Industry and CMA
in Oman. There are many possible direct and indirect impacts
of the litigations cases in Oman on the auditor, auditor’s
behavior, audit firm, audit profession, auditees and finan-
cial community in general. Damaged reputation of audi-
tor and audit firms, significant monetary costs associated
with litigation and declarations of bankruptcy of audit
firms are examples of direct impacts of litigation related
to audit activities [6, 44]. Changes in ownership struc-
ture, indirect monetary costs associated with auditor
litigation such as investments to enhance quality control,
significant negative market reaction to companies that
were audited by litigation audit firm and effects related
to new client acceptance where the litigation audit firms
are less likely to receive new engagements are examples
of indirect effects of auditor litigation [28]. The paper’s structure is given as follows. In “Audit
litigation: with focus on Oman” section elaborates
audit litigations in general and in Oman in particu-
lar. AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Page 2 of 14 The findings of this study contribute to the literature
on audit litigation and audit quality in several ways. First, to the best of our knowledge, this is the first
study that examines interactions between audit litiga-
tion and ownership structure on audit quality in the
Omani environment and elsewhere. Prior studies [2,
22, 25, 29, 54] tend to assess the association between
audit litigation and audit quality separately from the
associations between auditees’ ownership structure
and audit quality. These studies use two variables:
ownership structure as an independent variable and
audit quality as a dependent variable, and they report
positive or negative results for the two variables. Another group of prior studies that discuss the asso-
ciation between ownership structure and audit quality
is moderated by only one factor such as earnings man-
agement [32], audit fees [27] or risk [52]. On the other
hand, one of the most important issues regarding audit
litigation is the relationship between audit litigation
and audit quality. Most of scientific works here con-
cluded that there is a significant relationship between
audit litigation and audit quality [12, 20, 26, 35, 49,
51]. Second, with the imposition of the requirement
by CMA that Omani firms must comply with Inter-
national Financial Reporting Standards (IFRS) and
International Auditing Standards (IAS) and increasing
global trades and business transactions, both auditors
and auditees face a constant challenge of meeting the
reporting and auditing expectations. Accordingly, an
increasing number of audit litigations have been moti-
vating local audit firms to ensure quality in compliance
with the international rules and regulations. We use
this opportunity to investigate the extent of the impact
of both audit litigation and auditees’ ownership struc-
ture on meeting the increasing challenge on disclosure
and compliance. Third, our findings contribute to the
literature on Big 4 audit firms. Although there is wide
evidence in the literature that Big 4 audit firms provide
a high level of audit quality, this paper extends this line
of research by examining the effect of audit litigation
on audit quality. Literature review and hypotheses development
Audit quality and audit litigation In Oman as in elsewhere, auditing plays a crucial role
in adding credibility to financial statements. However,
the accountancy and audit affairs are not under the con-
trol of well-established profession. Government agencies
have the full responsibility in this regard. There are two
governmental agencies that govern this profession: CMA
and the Ministry of Commerce and Industry. However,
there is no independent agency regulating and control-
ling the external auditors. In 2016, the Association of
Chartered Accountants of Oman was established but
only allowed offering consultancy role and providing
support to the audit profession. The regulatory frame-
work consists of three sources of regulations to organize
the profession. These are the Commercial Company Law
No. 4 issued in 1974 and its amendments, Accounting
and Auditing law through Royal Decree No 77 was issued
in 1986 followed by a number of amendments and CMA
Code of Corporate Governance Regulation was issued in
2002 followed by a number of amendments. These laws
and regulations include many general rules of auditing
such as independence, registration, auditor rights and
obligations, formulation of audit committees, penalties,
auditor’s qualifications and the relationships between
external auditing and internal auditing. y
g
Most of the researches in the area of audit quality used
DeAngelo’s [13] definition of audit quality. According to
DeAngelo (12: 186), “the audit quality is defined as the
probability that a misstatement in the accounts of the
audited entity is discovered and reported by the auditor
as assessed by the market.” Practically, prior studies used
different proxies to measure the audit quality. The com-
mon proxies are Big and non-big auditor (audit firm size),
discretionary accruals, audit fees, accrual quality, going-
concern or modified opinions, meet or beat the quarterly
earnings target and audit fees [43]. El Deeb and Ramadan
[16] provide a comprehensive discussion with respect to
audit quality proxies that are used in the literature. Like
Chen et al. [10] and Wong et al. [51] and due to avail-
ability of information, we will measure the audit quality
by the issuance of modified audit opinions. On average,
within the period of this study in Oman, the Big 4 audit
firms issued around 58 (54%) modified audit reports for
107 listed companies, while around (21) 20% modified
audit reports were issued by non-Big 4 audit firms, which
means that the total modified report is 79. Audit litigation: with focus on Oman In “Literature review and hypotheses develop-
ment” section is about the relevant literature and
development of hypotheses. Section four is about the
methodology. In “Empirical analysis” and “Results
and discussion” sections, respectively, present the
empirical analysis and discuss the results. Conclu-
sion, limitations of the current paper and suggestions
for further research are included in “Conclusion”
section. f
Unfortunately, there is no formal statistics about the
litigation cases against the auditors in the Arab countries
or GCC countries including Oman. Oman CMA through Inspection and Examination
Department is an authorized agency that is responsi-
ble for controlling the audit firms working in Oman. CMA states that “CMA emphasizes that all audit firms
must comply with the applicable laws and regulations
to enhance professionalism, confidence and credibility.” AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Page 3 of 14 auditor. Audit committee of the clients is given a vital
role in recruiting the auditor. Second, in the Omani
audit market, there are 19 audit firms and offices recog-
nized by CMA and registered in the Ministry of Com-
merce and Industry and grouped into three types of
audit firms: Big 4 audit firms, non-Big 4 audit firms and
local audit offices. By the end of 2017, 73% of listed com-
panies were audited by Big 4 audit firms and 27% were
audited by non-Big 4 audit firms. Third, the auditors of
listed companies should be appointed by the board of
directors and shareholders on a yearly basis, and rotated
each four-year period. Fourth, the financial statements
of listed companies are prepared according to IFRS and
audited according to IASs. Fifth, it is allowed to the audit
firm to provide only three types of non-audit services,
namely audit-related services, taxation advisory services
and investigation of matters arriving from auditor’s find-
ings or observations to by their clients, and it should be
reviewed and approved by the audit committee. Finally,
the audit market in Oman is very small and the competi-
tion between auditor firms is very high [5]. The CMA issued around six warning letters and suspen-
sion decisions related to accounting and auditing issues
against some audit firms in Oman: both Big 4 and non-
Big 4 since 2005. These warning letters and suspension
decisions became audit litigations due to violating the
IFRS and IASs. It must be emphasized that CMA has the
required judicial power. Audit litigation: with focus on Oman A significant limitation is related to data on litigious
cases in Oman. Court lawsuits and settlements between
auditors and clients are generally unavailable because
cases are often resolved privately without public disclo-
sure of the agreed settlements. Information on lawsuits is
available for only 6 of the unknown total lawsuits. Up to date, in Oman, there are many lawsuit cases but
only six cases were carried out against some audit firms. The cases covered Big 4 audit firms and non-Big 4 audit
firms and are related to accounting and auditing issues. The total clients (i.e., auditees) of these two types of audit
firms are 32 listed companies out of 107 on MSM. Fifteen
out of 32 auditees are clients of the non-Big 4 audit firms
and 17 are clients of Big 4 audit firms. The remaining
numbers, i.e., 75 companies, were audited by non-Big 4
and Big 4 audit firms that were not subjected to litigation
cases. Literature review and hypotheses development
Audit quality and audit litigation Also,
Nelson and Mohamed-Rusdi [39] find significant positive
relationship between audit fees and firms with larger for-
eign ownership and government ownership but find no
relationship between audit fees and managerial owner-
ship. The appropriate interpretation for this positive rela-
tionship is that in some business environment the audit
quality is more important for foreign investors who are
ready to pay more fees for audit quality. Also, Eshghali-
zadeh [17] and Ali and Lesage [3] find mixed results. For
example, Ali and Lesage [3] find three types of results: a
negative relationship between audit fees and government
shareholdings; a positive relationship between audit
fees and institutional shareholdings; and no relationship
between audit fees and family shareholdings. The dif-
ferent results can be justified because each group in the
ownership structure has different objectives and power. Family shareholders focus on achieving short-term
profits rather than on long term objectives [9]. There-
fore, family ownership causes companies to pay lower
fees for the audit process. In contrast, higher audit fees
are acceptable by institutional and foreign shareholders
because they believe that this sends positive signal to the
market about the quality of their performance in order to
attract more investments [3]. El Deeb and Abdel Megeid
[15] find that audit firm size in terms of Big 4 audit firm
and non-Big 4 audit firm reflecting an audit quality plays
a vital role in enhancing capital structure decisions. In
particular, they find that auditor type as one of proxies
of corporate governance has positive association with Because audit quality is an important theme in audit-
ing; many researchers discuss it in their studies. Empiri-
cally, more attention is given to the association between
audit quality and audit fees [1], audit committee [36],
ownership structure [29], audit firm size and earnings
management [16, 32], firm performance [45], non-audit
fees [50] and corporate governance [22]. Recently, the discussion of the association between
audit quality and audit litigation is increased. Lennox and
Li [35] conclude that the audit quality will improve fol-
lowing litigation against the auditor. Catanach et al. [8]
find that Big 4 auditors are less likely to accept new audit
engagements relative to small auditors related to clients
with high-risk litigation. Badertscher et al. [6] find that
higher litigation risk is arising from public equity owner-
ship (governmental ownership). Baldauf et al. Literature review and hypotheses development
Audit quality and audit litigation Within the first
group, 9 modified audit reports were issued by litigated
Big 4 and 10 by litigated non-Big 4 audit firms, while 49
and 11 reports issued by non-litigated non-Big 4. There are some important facts related to the audit-
ing in Oman. First, according to Article 111 of Omani
Company Law no. 4 issued in 1974, all joint-stock and
limited liability companies must be subjected to external
auditing by one local or foreign qualified and recognized The issue of audit quality is one of the most attrac-
tive and controversial in both emerging and developed
markets. There are many empirical evidences that the
low level of audit quality is one of the main reasons for AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Page 4 of 14 addressed by even single paper whether covering the
Omani or GCC countries. financial, corporate and auditing scandals [48], Say-
yar et al. [45]. On the other hand, high level of audit
quality can improve some firm characteristics such as
performance and financial reporting as well as audit
characteristics such as independence of the auditor and
the level of audit fees [45]. Because most of the prior studies use different meas-
ures of ownership structure (such as large sharehold-
ers, managerial ownership and family ownership), some
results illustrate either single or mixed relationship
between ownership and audit characteristics. It is very
rare that prior studies are congruent in their results. There are always mixed results. For example, Lennox
[34] examines the relationship between audit firm size
and management ownership structure and finds negative
relationship, which means that the probability of recruit-
ing a large audit firm is lower as management owner-
ship increases. Kasai [27] finds a negative relationship
between audit fees and institutional ownership struc-
ture. Basically, the reason for this negative relationship
is that the audit client prefers to save audit fees rather
than increase the audit quality. On the other hand, in the
multi-different results studies, the mixed results are com-
mon. For example, Zureigat [54] finds positive relation-
ship between audit firm size as a proxy for audit quality
and foreign and institutional ownership structures. On
the other hand, the relationship between audit quality
and ownership structure is found to be negative. Literature review and hypotheses development
Audit quality and audit litigation [7] find a
positive association between risk aversion of auditor and
audit quality, which means that recruiting a risk-averse
auditor will improve the audit quality. Franz et al. [20]
suggested that audit litigation is a measure of audit qual-
ity and therefore the market interprets audit litigation as
an indicator of a low level of audit quality. Czerney et al. [12] found that higher level of litigation will improve
the quality of financial reports because the auditor will
increase the audit efforts to improve the audit quality.h f
These results are consistent with the argument that
potential clients perceive litigation against audit firms as
an indicator of lower audit quality. This has many adverse
effects such as decrease in the audit fees, decrease in the
new engagements of new clients, decrease in the bar-
gaining power of the auditor and decrease in the finan-
cial reporting quality of the client’s financial statement. Therefore, the first hypothesis is: H#1 There is a statistically negative relationship
between audit litigation and audit quality. H#3 There is no statistical relationship between minor-
ity ownership and audit quality. Audit litigation is likely to damage both audit charac-
teristics such as auditor’s reputation and audit quality
and client characteristics such as firm value, performance
and ownership structure. The ownership structure as
defined in this study consists of two groups of sharehold-
ers; large shareholders and minority shareholders. Large
shareholders are an important mechanism for corporate
governance which may affect the audit litigation. There
are two perspectives for the relationship between audit
litigations and large shareholders. The positive perspec-
tive refers to the case that the large shareholders increase
their percentage of shares that they own to get more
control and power to prevent the audit litigations in the
future. For example, Fan et al. [19: 15] indicate that the
“litigation auditors have competing incentives regard-
ing new client acceptance decisions following a lawsuit.”
Also, large shareholders are providers of capital and they
possess the ability to reduce cost of capital, increase share
price and influence strategic decisions. Therefore, they
might increase their ownership to protect their capi-
tal and to exercise more control and power [41]. On the
other hand, large shareholders can take some actions
against litigation auditor to avoid possible losses in the
future. For example, Skinner and Srinivasan [47] discuss
some negative consequences for audit litigations. First,
around one quarter of the clients left the auditor after
the audit litigation was announced. Second, future cli-
ents may believe that the litigation auditors provide lower
audit quality and, accordingly, they become less willing to
engage with those auditors compared with non-litigation
auditors. This perspective is justified by small sharehold-
ers who are ready to shift to those companies audited
by non-litigation auditors if they expect that the perfor-
mance of the company will decrease because of the audit
litigations. In the area of audit quality, prior studies examine the
relationship between ownership structure as an inde-
pendent variable and audit quality as a dependent vari-
able. These studies find positive and/or negative effects
of ownership structure on some variables such as audit
quality, audit fees and audit firm size. On the other hand,
audit litigation or lawsuit is only discussed in relation to
many audit characteristics such as audit fees and audit
firm size. i
In this study, the Omani shareholders, shareholders
from GCC countries and foreign shareholders are con-
sidered as the large shareholders. Ownership structure, audit quality and audit litigation Ownership structure, audit quality and audit litigation
One of the most important topics in accounting, audit-
ing and finance is ownership structure and how it
changes or behaves based on certain circumstances. In the area of auditing, there are many papers that dis-
cuss the relationship between ownership structure and
audit characteristics such as audit firm size, audit fees
and independence of auditor. However, this area is not AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Page 5 of 14 capital structure decisions (e.g., reduction in financial
leverage). capital structure decisions (e.g., reduction in financial
leverage). According to [41], the minority shareholders are
not interested in controlling the company and making
managerial strategic decisions. Nurdin et al. [40] con-
cluded that minority shareholders have negative effect
on the optimal level of leverage because they slow the
adjustment process toward the optimal level of leverage. Accordingly, the third hypothesis is: g
It seems that the prior literature examines many types
of ownership structure individually and collectively. Ownership structures such as large shareholder, foreign
ownership, institutional ownership, family ownership,
block ownership, managerial ownership, employee’s
ownership, government ownership, retail ownership and
domestic ownership are exhaustively examined. Owner-
ship structure in Omani firms is characterized by “stable
shareholders.” The largest institutional and single share-
holders do typically exceed a 5% of shares, but only some
individual shareholders and institutional shareholders
own around 30% or more of shares. According to the clas-
sification by MSM, the structure of ownership of listed
companies in MSM is different. This structure is defined
based on one general criterion that is the ownership
identity/nationality of investor, Omani or non-Omani. Omani investor is all Omani individuals or institutions
who can buy or sell shares in MSM. Non-Omani investor
has three clusters: the investor from GCC countries that
have the same characteristics of Omani investors, the
Arab investor from outside GCC countries and the last
one being the foreign investor. Foreign investor is defined
as percentage share held by companies which are incor-
porated inside Omani or those foreign investors inside
Oman. GCC investors are those investors or institutions
in the other GCC countries outside Oman, and Arab
non-GCC investors are those investors or institutions
from all other Arab countries. Methods
Sample and datah and to avoid the conflict of interest with the manag-
ers because of such conflict increase in case of owner-
ship concentration [37]. Thus, large shareholders will
be attracted by the companies which present financial
statements audited by non-litigation auditors because
this type of auditors reflects high level of audit quality
[33]. On the other hand, large shareholders are hold-
ing high percentage of shares in their companies, which
means that they can control the managers by using other
control mechanisms (such as board of director, board
committees and ownership structure) rather than resort-
ing to external auditing [46]. Accordingly, the fourth
hypothesis is: This study attempts to investigate the effect of interaction
of audit litigation and ownership structure on audit qual-
ity for listed companies on the MSM. The total number of
companies listed on the MSM at the end of the 2017 was
107 distributed among three sectors: banking and finance
companies (31), industrial companies (41) and service
companies (35). Since 2005, six audit litigation cases were
diagnosed by CMA related to accounting and auditing
issues. The study sample consists of all 107 companies
which equal 535 observations. Data about ownership
structure and audit firms were collected from the annual
reports for the listed companies and report of the MSM. In this report, 73% of listed companies are audited by
Big 4 audit firms and 27% are audited by non-Big 4 audit
firms by the end of 2017. H#4 There is no statistical effect of the interaction
between large shareholder ownership and audit litigation
on audit quality. i
For each audit litigation case, we have four groups;
clients of litigation Big 4 audit firms and clients of non-
litigation Big 4 audit firms, clients of litigation non-Big 4
audit firms and clients of non-litigation non-Big 4 audit
firms. Tables 1 and 2 show the statistics for each group. Mustafa et al. [38] discuss the relationship between
minority shareholders and audit quality and they con-
clude that the minority shareholders have motivation
to increase audit quality. According to agency theory,
minority shareholders have a feeling of high level of
risk due to many reasons. They might feel that they
do not access reliable accounting information; their
investments are not protected because managers
might not use the company’s fund properly and there
is the possibility of conflict of interest between them
and both managers and large shareholders. H#3 There is no statistical relationship between minor-
ity ownership and audit quality. This is because these
three types of shareholders have the majority percentage
of shares in all listed companies on MSM since they own
around 96% of the shares. In addition, the GCC coun-
tries shareholders have the same rights as Omani share-
holders. The Arab non-GCC countries shareholders are
considered as minority shareholders because they own
around 4% by the end of 2017. Based on the above dis-
cussion, the second hypothesis is: There is not a known prior study on the extent of inter-
actions between audit litigation and ownership on audit
quality. According to Hay et al. [24] as cited by Kouaib
and Jarboui [32], the existing and potential large share-
holders are requesting auditors who offer better audit
and non-audit services to increase the quality of finan-
cial reporting of the companies to protect their benefits H#2 There is a statistically positive relationship
between large shareholder ownership and audit quality. AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Page 6 of 14 Table 1 Number of clients of audit litigation and non-litigations audit firms
Sector
Big 4 audit firms
Non-Big 4 audit firms
Total
Clients of
litigation
Clients of non-
litigation
Total
Clients of
litigation
Clients of non-
litigation
Total
Finance and banking
8
19
27
1
3
4
31
Industrial
6
17
23
13
5
18
41
Services
3
25
28
1
6
7
35
Total
17
61
78
15
14
29
107 Table 1 Number of clients of audit litigation and non-litigations audit firms Definition of the variablesh more easily. The control variables help to define the rela-
tionship between the independent and dependent vari-
able in the model [21]. Our choice of control variables
follows prior research. In this study, we use four control
variables; age, size, risk and activity of the client because
most of the studies have employed these variables in their
models. The study uses a regression approach to control for the
effect of the ownership structure on audit quality under
the audit litigations. In this study, we model owner-
ship structure rates as a function of audit quality under
the audit litigation. There are four groups of variables:
dependent variable, independent variables, moderating
variable and control variables. According to Collier et al. [11], age and size of the firm
are determinants of risk. They conclude that the younger
firms and smaller firms face many threats which create
many types of risk. In the area of auditing, we expect that
companies are more (less) likely to be litigious if they are
younger (older). Also, we expect that companies are more
(less) likely to be litigious if they are smaller (larger) in
size. In this study, age of the company is measured by the
number of years since date of establishment (algorithm),
while size of the company is measured by algorithm of
total assets. The moderating variable is the ownership structure
which is measured by four concentrations as per the clas-
sification of MSM: Large
shareholders
(LS1) = Omani
ownership
(OMO). Large shareholders (LS2) = GCC countries owner-
ship (GCCO). Large shareholders (LS3) = Foreign ownership (FO). Minority shareholders (MS) = Arab (non-GCC)
ownership (AO). Large
shareholders
(LS1) = Omani
ownership
(OMO). Large shareholders (LS2) = GCC countries owner-
ship (GCCO). Large shareholders (LS3) = Foreign ownership (FO). Minority shareholders (MS) = Arab (non-GCC)
ownership (AO). Leverage is the third control variable which refers to
the financial strength of the client firms [6]. Risk of the
company is measured by debt-to-equity ratio. We control
for risk or leverage because the audit litigation is borne
by the auditor of the client. The independent variable is Audit Litigations (ALs)
against the audit firms which is measured by binary vari-
able, 1 if audit litigation and otherwise 0.h Finally, we control for activity of the clients because the
audit litigations are different between the clients across
the sectors in the MSM. Methods
Sample and datah This indi-
cates that the minority shareholders need to mitigate
and reduce all of the above-mentioned risks through
using non-litigation auditors. Accordingly, the fifth
hypothesis is i
Based on Table 1, there are 17 (17/78 = 22%) audit
clients audited by litigation Big 4 audit firms and 15
(15/29 = 52%) audit clients audited by litigation non-Big
4 audit firms. For better clarity and differentiation, this
study will make four types of analysis: • The effect of audit litigation on audit quality moder-
ated by ownership structure of the clients of litigation
Big 4 audit firms. gi
• The effect of audit litigation on audit quality moder-
ated by ownership structure of the clients of litigation
non-Big 4 audit firms. H#5 There is no statistical effect of interaction of
minority shareholder ownership and audit litigation on
audit quality. i
• Establishing the differences between the clients of
litigation and clients of non-litigation of Big 4 audit
firms. i
• Establishing the differences between the clients of
litigation and clients of non-litigation of non-Big 4
audit firms. AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Page 7 of 14 Table 2 Variables and definitions
Variable
Code
Definition
Moderating variables
Large shareholder
LS1
The percentage of shares (%) owned by Omani investors
Large shareholder
LS2
The percentage of shares (%) owned by GCC countries investors
Large shareholder
LS3
The percentage of shares (%) owned by Foreign investors
Minority shareholders
MS
The percentage of shares (%) owned by Arab non-GCC invertors
Independent variable
Audit litigations
ALs
Binary variable, 1 if audit litigation and otherwise 0
Dependent variable
Audit quality
AQ
Binary variable, 1 if modified audit report and otherwise 0
Control variables
Size of the company
S
Algorithm of total assets
Age of the company
AG
Algorithm of years
Leverage
R
Debt-to-equity ratio
Activity of the clients
AC
Type of sector that the company belongs to it, dummy vari-
ables: Banking and finance (1), industrial (2) and services (3) Table 2 Variables and definitions Model#1: The effect of interaction of audit litigation
and ownership structure on audit quality for the cli-
ents of Big 4 audit firms. Definition of the variablesh The activity of the clients is
measured by dummy variable: banking and finance (1),
industrial (2) and service (3). The dependent variable is the audit quality which is
measured by the modified audit report issued by audit
firm as a binary variable, 1 if modified audit report and
otherwise 0. The third group of variables is control variables. These
variables are added in the regression model that are not
of interest in themselves but are included to reduce the
aggregate bias for every additional relevant variable that
we include in the models. These variables are kept con-
stant so the changes in other variables can be observed According to the types of analysis and variables, the
models are as follows: Model#1: The effect of interaction of audit litigation
and ownership structure on audit quality for the cli-
ents of Big 4 audit firms. AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Page 8 of 14 Page 8 of 14 Table 3 Descriptive statistics
Variables N
Minimum Maximum Mean
Std. deviation
Statistics Statistics
Statistics
Statistics Statistics
LS1
107
0.01
1.00
0.7782
0.24751
LS2
107
0.00
0.99
0.1421
0.21830
LS3
107
0.00
0.65
0.0750
0.14573
MS
107
0.00
0.17
0.0040
0.01927
R
107
0.00
1.70
0.3095
0.29872
AG
107
4.00
45.00
25.3832
9.99589
S
107
2.24
7.00
4.6509
0.81814
AC
107
1.00
3.00
2.0374
0.78818
ALs
107
0.00
1.00
0.3084
0.46401
AQ
107
0.00
1.00
0.7383
0.44162 Table 3 Descriptive statistics the rate of audit litigations is around 22% during the
period of the study. Table 3 also reports descriptive sta-
tistics for the control variables: age, risk, activity and
size of the firm. For example, the mean value of age
of these companies is 24 years, which means that they
have good experiences in the business. The mean value
of risk indicates that these companies are funded by
debts with 31% and owner equity provides 69%. the rate of audit litigations is around 22% during the
period of the study. Table 3 also reports descriptive sta-
tistics for the control variables: age, risk, activity and
size of the firm. For example, the mean value of age
of these companies is 24 years, which means that they
have good experiences in the business. The mean value
of risk indicates that these companies are funded by
debts with 31% and owner equity provides 69%. Definition of the variablesh Table 3 allows us to observe, in a descending order,
that the mean value of Omani large shareholders (LS1)
is around 78%, GCC countries large shareholders
(LS2) is around 14%, then foreign shareholders (LS3) is
around 7.5% and finally Arab shareholders (MS) is 0.4%. This means that in all listed companies, Omani, GCC
courtiers and foreign investors (large shareholders)
own a very high percentage of shares against minority
shareholders (Arab non-GCC) which give these three
groups more capital concentration, control and power. The mean of risk is positive, 30.95%, which means that
the owner equity is the main source for the listed com- In this model, we have two types of clients. The first is
clients of litigation of Big 4 audit firms, and the second is
the clients of non-litigation of Big 4 audit firms. There-
fore, the model is: AQbig4 =αit + βit + β1LS1it + β2LS2it + β3LS3it +β 4MSit
+ β5ALsit + β6LS1it ∗ALsit + β7LS2it ∗ALsit + β8LS3it ∗ALsit
+ β9MSit ∗ALsit + β10AGit + β11Sit + β12Rit + β13ACit+ ∈it. Model#2: The effect of interaction of audit litigation
and ownership structure on audit quality for the cli-
ents of non-Big 4 audit firms. Model#2: The effect of interaction of audit litigation
and ownership structure on audit quality for the cli-
ents of non-Big 4 audit firms. panies, and there are a limited number of Omani com-
panies which are highly in debt. The mean of activity,
2.0374, indicates that the high number of listed com-
panies is in the industrial sector which is equal to 68%
of total listed companies. The result shows that the
majority of the listed companies (73.83%) have modi-
fied audit reports, which means that the audit quality is In this model, we also have two types of clients. The
first is clients of litigation of non-Big 4 audit firms, and
the second is the clients of non-litigation of non-Big 4
audit firms. Therefore, the model is: AQnonbig4 =αit + βit + β1LS1it + β2LS2it + β3LS3it +β 4MSit
+ β5ALsit + β6LS1it ∗ALsit + β7LS2it ∗ALsit + β8LS3it ∗ALsit
+ β9MSit ∗ALsit + β10AGit + β11Sit + β12Rit + β13ACit+ ∈it. it + βit + β1LS1it + β2LS2it + β3LS3it +β 4MSit
+ β5ALsit + β6LS1it ∗ALsit + β7LS2it ∗ALsit + β8LS3it ∗ALsit
+ β9MSit ∗ALsit + β10AGit + β11Sit + β12Rit + β13ACit+ ∈it. Definition of the variablesh AQnonbig4 =αit + βit + β1LS1it + β2LS2it + β3LS3it +β 4MSit
+ β5ALsit + β6LS1it ∗ALsit + β7LS2it ∗ALsit + β8LS3it ∗ALsit
+ β9MSit ∗ALsit + β10AGit + β11Sit + β12Rit + β13ACit+ ∈it. In both models, we add the following variables: high. There are around 31% of audit clients audited by
litigation audit firms during the period of the study. The
means of both the size and age show that all listed com-
panies have quite enough experience to deal with risk. αit = constant. β = beta. εit = error term. ith = firm. tth = period.tth = period. In both models, we add the following variables:
αit = constant. β = beta. εit = error term. ith = firm.
tth = period.tth = period. Descriptive statistics Al
T bl
5
ll
t
l d
th t
t
l
i
Table 4 Multicollinearity test and correlation matrix (N = 107)
*Correlation is significant at the 0.05 level (2-tailed)
LS1
LS2
LS3
MS
R
AG
S
AC
ALs
AQ
LS1
1
LS2
0.021
1
LS3
− 0.156
− 0.108
1
MS
0.037
− 0.074
− 0.090
1
R
− 0.049
0.080
− 0.038
0.028
1
AG
0.161
− 0.188
0.015
− 0.002
− 0.126
1
S
− 0.128
0.065
0.145
− 0.194*
− 0.075
− 0.141
1
AC
0.174
− 0.086
− 0.179
0.089
− 0.166
0.048
− 0.096
1
ALs
0.021
− 0.059
0.064
− 0.108
− 0.158
− 0.062
0.198*
− 0.161
1
AQ
0.093
− 0.126
0.064
− 0.241*
0.126
− 0.176
− 0.011
0.001
− 0.201*
1
Table 5 Regression results between ALs and AQ
R-square = 13.7%, F-value = 4.477, P-value = 0.038
Dependent variable = AQ
Model
B
T-Value
Sig
1
(Constant)
0.777
2.925
0.004
R
0.002
0.700
0.486
AG
− 0.161
− 1.828
0.070
S
0.053
0.083
0.934
AC
− 0.010
− 0.107
0.915
ALs
− 0.204
− 2.102
0.038
Table 6 Regression results between ownership and AQ
R2 = 16.8%, F-value = 7.557, P-value = 0.001
Dependent variable = AQ
Model
B
T-value
Sig
2
(Constant)
2.631
15.004
0.000
LS1
0.032
0.980
0.330
LS2
− 0.497
− 3.032
0.003
LS3
0.157
0.980
0.330
MS
− 0.288
− 2.312
0.023
R
0.097
1.522
0.133
AG
− 0.232
− 2.515
0.014
S
− 0.053
− 0.549
0.585
AC
0.047
0.815
0.418 Table 4 Multicollinearity test and correlation matrix (N = 107)
*Correlation is significant at the 0.05 level (2-tailed)
LS1
LS2
LS3
MS
R
AG
S
AC
ALs
AQ
LS1
1
LS2
0.021
1
LS3
− 0.156
− 0.108
1
MS
0.037
− 0.074
− 0.090
1
R
− 0.049
0.080
− 0.038
0.028
1
AG
0.161
− 0.188
0.015
− 0.002
− 0.126
1
S
− 0.128
0.065
0.145
− 0.194*
− 0.075
− 0.141
1
AC
0.174
− 0.086
− 0.179
0.089
− 0.166
0.048
− 0.096
1
ALs
0.021
− 0.059
0.064
− 0.108
− 0.158
− 0.062
0.198*
− 0.161
1
AQ
0.093
− 0.126
0.064
− 0.241*
0.126
− 0.176
− 0.011
0.001
− 0.201*
1 Table 4 Multicollinearity test and correlation matrix (N = 107) AQ *Correlation is significant at the 0.05 level (2-tailed) Table 5 Regression results between ALs and AQ
R-square = 13.7%, F-value = 4.477, P-value = 0.038
Dependent variable = AQ
Model
B
T-Value
Sig
1
(Constant)
0.777
2.925
0.004
R
0.002
0.700
0.486
AG
− 0.161
− 1.828
0.070
S
0.053
0.083
0.934
AC
− 0.010
− 0.107
0.915
ALs
− 0.204
− 2.102
0.038
Table 6 Regression results between ownership and AQ
Model
B
T-value
Sig
2
(Constant)
2.631
15.004
0.000
LS1
0.032
0.980
0.330
LS2
− 0.497
− 3.032
0.003
LS3
0.157
0.980
0.330
MS
− 0.288
− 2.312
0.023
R
0.097
1.522
0.133
AG
− 0.232
− 2.515
0.014
S
− 0.053
− 0.549
0.585
AC
0.047
0.815
0.418 Table 5 Regression results between ALs and AQ On the other hand, there are negative significant cor-
relations between audit quality (AQ) and both minor-
ity shareholders (MS) and audit litigation (ALs) at 0.05. Descriptive statistics These results indicated that if the percentage of MS
increases, the AQ decreases and vice versa and if the
percentage of ALs increases, the AQ decreases and vice
versa. Therefore, a negative and significant impact of audit liti-
gations on audit quality is clearly discerned. R2 is 13.7%,
which means that the model explains 13.7% of variation
in AQ. This result agrees with that of Lennox and Li [34]. This is consistent with the first hypothesis that the audit
litigation of Big 4 audit firms has negative consequences
on the audit quality. According to Hair et al. [23], the presence of high cor-
relations (generally 0.80 and above) is the first indicator
of substantial multicollinearity. As shown in Table 4, the
correlations between the independent variables including
control variable are low and below 0.80. This result indi-
cates that no multicollinearity problem occurs for all the
study variables. Also, Table 5 allows us to conclude that control vari-
ables do not have an effect on the audit quality, which
means that the association between audit litigations
and audit quality does not change because of size, risk,
age and sector and the audit litigations have this effect
on audit quality regardless of the control variables. For
example, the audit quality decreases if there is any audit
litigation against the auditor for large size client as well
for low size client. Results and discussioni Model 1: Big 4 audit firms’ litigation and non‑litigation
Audit litigation and audit quality (Testing Hypothesis#1)hi The first hypothesis is regarding the relationship between
audit litigation and audit quality. Table 5 indicates that
this relationship is significant at 0.05 and the audit litiga-
tion has negative impact on audit quality (F-value = 4.477,
P-value = 0.038 < 0.05, t-statistic = − 2.102).fi Descriptive statistics Table 3 provides descriptive statistics for the sample
used to estimate the models. The mean value of depend-
ent variable (LS1) indicates that Omani ownership rate
is 78% of total of shares in the companies audited by Big
4 audit firms, while the other three ownership struc-
tures represent around 22%. The mean value of audit
litigation by Big 4 audit firms is 21.79%, which means The multicollinearity is a computational difficulty that
appears when two or more independent variables are
highly correlated. From Table 4, the autocorrelation
refers only to positive correlation between audit liti-
gation and size of companies and negative correlation
between size and minority shareholders but it only is
weakly correlated with each other. AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Page 9 of 14 On the other hand, there are negative significant cor-
relations between audit quality (AQ) and both minor-
ity shareholders (MS) and audit litigation (ALs) at 0.05. These results indicated that if the percentage of MS
increases, the AQ decreases and vice versa and if the
percentage of ALs increases, the AQ decreases and vice
versa. According to Hair et al. [23], the presence of high cor-
relations (generally 0.80 and above) is the first indicator
of substantial multicollinearity. As shown in Table 4, the
correlations between the independent variables including
Therefore, a negative and significant impact of audit liti-
gations on audit quality is clearly discerned. R2 is 13.7%,
which means that the model explains 13.7% of variation
in AQ. This result agrees with that of Lennox and Li [34]. This is consistent with the first hypothesis that the audit
litigation of Big 4 audit firms has negative consequences
on the audit quality. Discussion of results of Model 1 According to the results of model 1, the audit litigation
has inverse impact on audit quality in the Big 4 audit
firms’ sample. This means the audit quality is a sensitive
issue for the Big 4 audit firms and their clients where
the audit quality decreases if the size of audit litigation
against Big 4 audit firms increases. The Big 4 audit firms
are more risk averse to the damage of their reputation
from financial and economic scandals and audit fail-
ures. This result is consistent with the findings of Esh-
leman and Guo [18] who find that Big 4 audit firms do
perform higher audit quality, which means they are more
likely to issue going-concern reports. Big 4 audit firms
have many advantages such as high audit fees, large share
market and more new engagements every year, high level
of bargaining power with clients and authorized audit-
ing associations and high level of audit quality and finan-
cial reporting quality of the client’s financial statements. These results suggest that Big 4 audit firms are likely to
lose most of these advantages in case of audit litigation,
especially in the highly competitive audit market like
that of Oman. For example, Fan et al. [19] conclude that
litigation audit firms have fewer new engagements fol-
lowing the litigation. Another example is introduced by
Hay et al. [24] about audit fees who find that audit fees
for litigated auditor are significantly lower than those of
non-litigated auditor. Therefore, the audit quality and
audit litigations have a priority for 4 big audit firms in
that they tend to keep their reputation and audit qual-
ity at a high level. There are many evidences that these i
Model 1: Big 4 audit firms’ litigation and non-litiga-
tion: interaction of ownership structure and audit liti-
gation on audit quality (Testing Hypotheses #4 and 5) In this subsection, the effect of interaction of ownership
structure and audit litigation on audit quality is tested. Table 7 indicates that GCC ownership (LS2) and minor-
ity ownership (MS) structures have inverse significant
relationship with audit quality at 0.05 as the coefficients
of LS2 and MS are (− 0.904) and (− 0.287), respectively. The other two interactions between ownership structures
(Omani and Foreign) and audit litigation do not have any
effect on audit quality. R2 is 13.2%, which means that the
model of interaction explains 13.2% of variation in AQ. Model 1: Further analysisif According to the results of Table 6, LS2 and MS have
significant negative effect on audit quality at 0.05 as the
coefficients of LS2 and MS are (− 0.497) and (− 0.288),
respectively. R2 is 16.8%, which means that the model
explains 16.8% of variation in AQ which is more than the
previous R2 between ALs and AQ. These results indicate
that any increase in GCC countries shareholders own-
ership as large shareholders and minority sharehold-
ers inversely effect on audit quality. We think that if the
GCC countries shareholders ownership and minority
shareholders are increased, the audit quality decreases
because these two categorizes have very less control on
the managers and auditors. Therefore, they might use liti-
gated auditor to audit their financial statements. Also, for
control variables group, there is only one variable with
impact on the audit quality, that is, age of the firm. As the
age of a company increases, the audit quality decreases. This result is consistent with the reality in Oman where
companies that have more age tend to use service of liti-
gation audit firms. In order to find any differences between litigated Big 4
and non-litigated Big 4 regarding audit quality, we use
t-test for two samples. Table 8 shows that there are no
differences between litigation Big 4 and non-litigation Big
4 regarding audit quality because the value in the “Sig. (2-tailed)” (0.104) is more than 0.05. This means there is
no difference in the audit quality for the litigation Big 4
and non-litigation Big 4 audit firms. Both types of firm
consider audit quality as an important criterion for their
audit work and reputation. and 3) Table 6 shows the results of hypotheses 2 and 3 for Big 4
audit firms: As for the coefficient of the audit litigations (ALs), it
is negative (− 0.204) and significant (P-value = 0.038). AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Page 10 of 14 Table 7 Interaction between LS, MS and ALs on AQ
R2 = 13.2%, F-value = 2.763, P-value = 0.034
Dependent variable = AQ
Model
B
T-value
Sig
1
(Constant)
0.800
14.730
0.000
LS1ALs
0.015
0.085
0.932
LS2ALs
− 0.904
− 1.691
0.035
LS3ALs
− 0.483
− 0.836
0.406
MSALs
− 0.287
− 2.375
0.020
Table 8 T-test results
* Correlation is significant at the 0.05 level (2-tailed)
Levene’s
test for
equality of
variances
t-test for equality of
means
F
Sig
T
df
Sig. (2-tailed)
AQ equal variances assumed
Equal variances not assumed
9.057
0.104
2.116
1.862
76
24
0.038
0.075 Discussion of results of Model 1 Of these findings, it is noted that in the Omani con-
text, the type of an auditor (i.e., Big 4 audit litigation or
non-litigation) from the perspective of Omani and GCC
investors does not have impact on audit quality. On the
other hand, from the perspective of Arab non-GCC and
foreign investors it appears that they do have significant
impact on audit quality. AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Page 11 of 14 Table 9 Chi-square tests and symmetric measures (ALs and AQ)
*Correlation is significant at the 0.05 level (2-tailed)
Value
Df
Asymp. Sig
Approx. Sig
Pearson Chi-square
0.514
28
0.474
Nominal by nominal Phi
− 0.133
0.474
Cramer’s V
0.133
0.474
No. of valid cases
29 Table 10 Chi-square tests and symmetric measures (Ownership
structure and audit quality)
Pearson Chi-square
LS1
LS2
LS3
MS
Value
15.651
6.319
10.228
3.770
Df
15
11
9
3
Asymp. Sig. (2-sided)
0.406
0.851
0.322
0.287
Phi
0.735
0.467
0.594
0.361
Cramer’s V
0.735
0.467
0.594
0.361
No. of valid cases
29
29
29
29 Table 10 Chi-square tests and symmetric measures (Ownership
structure and audit quality) *Correlation is significant at the 0.05 level (2-tailed) issues are important for Big 4 audit firms. For example,
Ernst & Young has created the position of vice chairman
of quality and risk management. PricewaterhouseCoop-
ers (PwC) has established a grading system similar to the
one used by credit-rating agencies such as Moody’s and
Standard and Poor’s [53]. Also, clients under the auditing
of an auditor who engages in audit litigation there would
be at a higher risk of losing some of their advantages such
as a decrease in the market fair value of shares. issues are important for Big 4 audit firms. For example,
Ernst & Young has created the position of vice chairman
of quality and risk management. PricewaterhouseCoop-
ers (PwC) has established a grading system similar to the
one used by credit-rating agencies such as Moody’s and
Standard and Poor’s [53]. Also, clients under the auditing
of an auditor who engages in audit litigation there would
be at a higher risk of losing some of their advantages such
as a decrease in the market fair value of shares. Table 11 Chi-square tests and symmetric measures Table 11 Chi-square tests and symmetric measures
Pearson Chi-square
LS1
LS2
LS3
MS
Value
12.313
9.870
8.175
2.328
Df
15
11
9
3
Asymp. Sig. Ownership structure and audit quality Based on Table 10, it seems that Sig. of Chi-square of all
ownership structures is greater than 0.05, which means
that there is no statistically significant relationship
between ownership structures and audit quality. In this
case, both ownership structures and audit quality are
independent and audit quality is not affected by owner-
ship structures. Furthermore, to test the strength of this
relationship, we use Phi and Cramer’s V. The result of the
test indicates there is a very weak relationship. Model 2: Non‑Big 4 audit firms’ litigation and non‑litigation
Since the sample of non-Big 4 audit firms is small
(N = 29), it is probable that data do not follow the normal
distribution. For this reason, we will use the nonparamet-
ric tests to examine the hypotheses of this model. Audit litigation and audit quality Table 9 shows that the value of Chi-square is 0.514 and
P-value is 0.474. This result tells us that there is no sta-
tistically significant relationship between audit litigation
and audit quality, which means both audit litigation and
audit quality are independent and audit quality is not
affected by audit litigation. Furthermore, in order to test
the strength of the relationship, we use Phi and Cramer’s
V and it seems that the strength of relationship between
the variables is very weak. Interaction between ownership structure and audit litigation
on audit quality Based on Table 11, it seems that Sig. of Chi-square of all
interactions is greater than 0.05, which means that there
is no statistically significant relationship between inter-
actions and audit quality. In this case, both interactions
and audit quality are independent and audit quality is not
affected by interaction between ownership structure and
audit litigation. Again, in order to test the strength of this
relationship, we use Phi and Cramer’s V. There is still a
very weak relationship. Discussion of results of Model 1 (2-sided)
0.655
0542
0.517
0.507
Phi
0.652
0.583
0.531
0.283
Cramer’s V
0.652
0.583
0.531
0.283
No. of valid cases
29
29
29
29 Empirical evidence shows that there is statistically
negative significant effect of large shareholders No. 2
(GCC countries shareholders) and minority shareholders
(Arab non-GCC) on audit quality of firms audited by Big
4. Also, there is statistically no significant effect of large
shareholders No. 1 and 3 (GCC countries shareholders)
and minority shareholders (Arab non-GCC) on audit
quality. These results do not provide incentives to audi-
tors to deliver high-quality audit and, accordingly, con-
strain their behavior to avoid any audit litigation. It seems
that Big 4 audit firms are unable to deliver audit quality
in the presence of Omani and foreign shareholders own-
ership. We believe that this situation is justified because
the audit market in Oman is small, number of competi-
tive audit firms is less few, and the auditing is governed
by public agencies which will reduce the effect of owner-
ship structure on audit quality. Conclusionh Table 13 T-test for comparison between litigation Big 4 versus
litigation non-Big 4 audit firms This study examines how the audit litigation affects the
audit quality moderated by the ownership structure. In
this study, two models were tested: the audit litigation
and audit quality moderated by ownership structure of
clients audited by Big 4 audit firm and non-Big 4 audit
firm. Regarding the first model, our results show that the
audit quality is a sensitive issue for the Big 4 audit firms
and their clients where the audit quality will decrease
if the size of audit litigation against Big 4 audit firms is
increased. The result based on hypothesis testing pro-
vides insignificant effect of audit litigation on the own-
ership structure of Omani companies listed on MSM for
both clients. While most of prior studies conclude that
there is a significant relationship between ownership
structure and audit quality, audit fees and other audit
characteristics, the result of this study is different. In
the first model, the effect of audit litigation on the own-
ership structure of clients audited by Big 4 audit firms
was tested. The result of the test indicates that there is
no significant effect of audit litigation on the ownership
structure. This means that ownership structure of listed
Omani companies does not change because of the audit
litigations against the Big 4 audit firm. Specifically, the
ownership structure of clients has weaker sensitivity
toward the audit litigations of both Big 4 and non-Big 4
audit firms. Thus, the evidence of this study suggests that
audit litigations are significantly less likely to cause any
change in the ownership structure. Table 13 T-test for comparison between litigation Big 4 versus
litigation non-Big 4 audit firms
Bignon
N
Mean
SD
SE mean
AQ
1.00
17
0.5556
0.51131
0.12052
0.00
15
0.6667
0.48795
0.12599
Levene’s test
for equality of
variances
F = 1.455, Sig = 0.237, t-statistics = − 0.635, − 0.637,
Sig. (2-tailed) = 0.530,0.529 quality, we use Mann–Whitney test. Results of Table 12
indicate that there are no statistically significant differ-
ences between litigated non-Big 4 and non-litigated non-
Big 4 audit firms (U = 92.5, P = 0.592). Further analysisi In order to find any differences between litigation non-
Big 4 and non-litigation non-Big 4 regarding audit Page 12 of 14 AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Table 12 Test statistics
Grouping variable: ALs
a Not corrected for ties
AQ
Mann–Whitney U
92.500
Wilcoxon W
212.500
Z
− 0.704
Asymp. Sig. (2-tailed)
0.481
Exact Sig. [2*(1-tailed Sig.)]
0.591a not subject them to greater litigation risk [14, 18, 42]. The size of the damage award in judgments against Big
4 audit firms can also be larger for the same reason [30]. As a result, investors are more likely to sue Big 4 audit
firms, along with the involved company and manage-
ment for the recovery of some of their losses. A different
but related argument is that large auditors have stronger
incentives to provide high quality audits because they
have more invaluable reputations. Table 12 Test statistics CMA: Capital Market Authority; GCC: Gulf Cooperation Council; MSM: Muscat
Securities Market; IFRS: International Financial Reporting Standards; IAS: Inter-
national Auditing Standards; OMO: Omani ownership; LS2: large shareholders;
GCCO: GCC countries ownership; LS3: large shareholders; FO: foreign owner-
ship; MS: minority shareholders; AO: Arab (non-GCC) ownership; ALs: audit
litigations; AQ: audit quality; S: size of the company; AG0: age of the company;
R: leverage; AC: activity of the clients. Acknowledgements
Not applicable. 16. El Deeb MS, Ramadan M (2020) The impact of financial distress, firm size,
and audit quality on earnings’ management evidence from companies
listed in the Egyptian stock exchange. Alexandria J Account Res 4(3):1–48 References 1. Abdul-Rahman OA, Benjamin AO, Olayinka OH (2017) Effect of audit fees
on audit quality: evidence from cement manufacturing companies in
Nigeria. Eur J Account Audit Finance Res 5(1):6–17 1. Abdul-Rahman OA, Benjamin AO, Olayinka OH (2017) Effect of audit fees
on audit quality: evidence from cement manufacturing companies in
Nigeria. Eur J Account Audit Finance Res 5(1):6–17 g
2. Al Qadasi A, Abidin S (2018) The effectiveness of internal corporate
governance and audit quality: the role of ownership concentration-
Malaysian evidence. Corp Gov 18(2):233–253. https://doi.org/10.1108/
CG-02-2017-0043 3. Ali CB, Lesage C (2013) Audit pricing and nature of controlling sharehold-
ers: evidence from France. China J Account Res 6(1):21–34. https://doi.
org/10.1016/j.cjar.2012.08.002 g
j j
4. Audit Analytics (2019) https://www.auditanalytics.com/contact?subject=
Risk 5. Baatwah SR (2016) Audit tenure and financial reporting in Oman: does
rotation affect the quality? Risk Gov Control Financial Mark Inst 6(3):16–27 5. Baatwah SR (2016) Audit tenure and financial reporting in Oman: does
rotation affect the quality? Risk Gov Control Financial Mark Inst 6(3):16–27
6. Badertscher B, Jorgensen B, Katz S, Kinney W Jr (2014) Public equity and
audit pricing in the United States. J Account Res 52(2):303–339 6. Badertscher B, Jorgensen B, Katz S, Kinney W Jr (2014) Public equity and
audit pricing in the United States. J Account Res 52(2):303–339 7. Baldauf J, Pummerer E, Steller M (2012) Audit quality, litigation and risk
aversion—An analytical analysis of the influence of risk aversion on audit
quality. All Innsbruck University, Austria 8. Catanach A, Irving J, Williams S, Walker P (2011) An ex post examination
of auditor resignations. Account Horiz 25(2):267–283 9. Charbel S, Elie B, Georges S (2013) Impact of family involvement in
ownership management and direction on financial performance of the
Lebanese firms. Int Strateg Manag Rev 1(1–2):30–41 10. Chen CJP, Chen S, Su X (2001) Profitability regulation, earnings manage-
ment, and modified audit opinions: evidence from China. Audit J Pract
20(2):9–30. https://doi.org/10.2308/aud.2001.20.2.9 10. Chen CJP, Chen S, Su X (2001) Profitability regulation, earnings manage-
ment, and modified audit opinions: evidence from China. Audit J Pract
20(2):9–30. https://doi.org/10.2308/aud.2001.20.2.9 11. Collier BL, Haughwout AF, Kunreuther HC, Michel-Kerjan EO, Stewart MA
(2017) Firms’ management of infrequent shocks. NBER Working Paper No. 22612. NBER Program(s): Public Economics 11. Collier BL, Haughwout AF, Kunreuther HC, Michel-Kerjan EO, Stewart MA
(2017) Firms’ management of infrequent shocks. NBER Working Paper No. 22612. NBER Program(s): Public Economics 12. Received: 9 December 2020 Accepted: 13 April 2021
Published: 9 June 2021 Received: 9 December 2020 Accepted: 13 April 2021
Published: 9 June 2021 g
p
Those limits constitute a motivation for further
research. We suggest extending the study period to
include more audit litigation cases. This will allow get-
ting more robust results. Also, we suggest that other
audit quality proxies can be used such as audit fees and
discretionary accruals in addition to modified audit
report to get more comprehensive results. Since 2016,
the Association of Chartered Accountants of Oman
was created as a potential player in the audit market. Here, we expect that this relationship will take some
roles and responsibilities from the government to
organize the audit market. In this regard, we predict
that the number of audit litigations will increase which
allows us to conduct more studies in Oman. Also, in the
future studies, all GCC countries shall be included in
such studies because these countries have almost the
same audit market characteristics and ownership struc-
tures. We suggest that future researches should study
the effect of audit litigation on audit quality moderated
by other types of ownership structures such as fam-
ily ownership, institutional ownership and managerial
ownership to see how the different structure can effect
on the audit quality. Availability of data and materials is only 5 years (2013–2017) which is a short period. Second, due to non-availability of all necessary annual
reports and other related data, we use only one proxy
to measure the audit quality, that is, the modified audit
report. There are other proxies such as audit fees, audit
risk and discretionary accruals which are not used in
this study. Third, Oman as an emerging economy has
very few number of audit litigations because the audit
market is very small and it is governed by the govern-
mental agencies. Fourth, we use the taxonomy of own-
ership structure as declared by MSM. However, other
structures (family ownership, institutional ownership
and managerial ownership) are not used. The datasets generated and/or analyzed during the current study are available
in the Muscat Securities Market Web site repository, www.msm.gov.com References Czerney K, Lisic L, Wu B, Zhang J (2019) Big 4 auditors, litigation risk, and
disclosure tone. Working paper, University of Nebraska, Virginia Tech, and
University of Minnesota. https://papers.ssrn.com/sol3/papers.cfm?abstr
act_id=3351230 Competing interests The authors declare that they have no competing interests. Author details
1 1 Accounting Department, Bayan University, Baghdad, Iraq. 2 Accounting
Department, Dhofar University, Dhofar, Oman. Authors’ contributions MA reviewed the literature and analyzed, interpreted and discussed the
results. He is the only contributor in writing the manuscript. RJAA read, revised
and approved the final manuscript. 17. Eshghalizadeh A (2014) Study the relationship between audit fees by
ownership structure of accepted companies in Tehran Stock Exchange. Appl Math Eng Manag Technol 2(4):521–527 17. Eshghalizadeh A (2014) Study the relationship between audit fees by
ownership structure of accepted companies in Tehran Stock Exchange. Appl Math Eng Manag Technol 2(4):521–527 18. Eshleman JD, Guo P (2014) Do Big 4 auditors provide higher audit quality
after controlling for the endogenous choice of auditor? Audit J Pract
Theory 33(4):197–219 18. Eshleman JD, Guo P (2014) Do Big 4 auditors provide higher audit quality
after controlling for the endogenous choice of auditor? Audit J Pract
Theory 33(4):197–219 Funding
There is no source of funding. Further Analysis: litigation Big 4 vs. litigation non‑Big 4
audit firmsf We further examine whether there are any differences
between litigation Big 4 and litigation non-Big 4 audit
firms regarding the audit quality. Table 13 presents the
results of this comparison. The sample is restricted to liti-
gation Big 4 and non-Big 4 audit firms. The results indi-
cate that there are no statistically significant differences
(Levene’s test for equality of variances: F-value = 1.455,
P-value = 0.237) between the two samples regarding
audit quality, which means that the audit quality is an
important issue for both Big 4 and non-Big 4 audit firms. i
According to Czerney et al. [12], many studies indi-
cate that Big 4 audit firms provide relatively higher audit
quality than the other audit firms such as non-Big 4
audit firms. For example, compared to non-Big 4 audit
firms, Big 4 audit firms are associated with less litigation
because of the Big 4 audit firms are more conservative
and sensitive regarding their reputation. In the second model, the results show that there is no
statistically significant relationship between audit litiga-
tion and audit quality. Also, the results tell us that there
is no statistically significant relationship between owner-
ship structures and audit quality. The effect of the inter-
action between ownership structure and audit litigation
on audit quality is very weak. One of the most important issues in the dichotomy of
Big 4 and non-Big 4 audit firms is the differences in com-
pany characteristics between Big 4 and non-Big 4 clients. In this study, we address one difference between them,
that is, audit litigations. Finally, the results indicate that there is no statistically
difference between the two samples (Big 4 and non-Big
4) regarding audit quality, which means that the audit
quality is an important issue for both Big 4 and non-Big
4 audit firms.h An important motivation for Big 4 firms when pro-
viding high-quality audit is that their “deep pockets” do i
There are certain limitations in the data gathering
and analysis processes. First, the time series examined AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Page 13 of 14 Availability of data and materials 14. Dye R (1993) Auditing standards, legal liability, and auditor wealth. J Polit
Econ 101(5):887–914 Abbreviations CMA: Capital Market Authority; GCC: Gulf Cooperation Council; MSM: Muscat
Securities Market; IFRS: International Financial Reporting Standards; IAS: Inter-
national Auditing Standards; OMO: Omani ownership; LS2: large shareholders;
GCCO: GCC countries ownership; LS3: large shareholders; FO: foreign owner-
ship; MS: minority shareholders; AO: Arab (non-GCC) ownership; ALs: audit
litigations; AQ: audit quality; S: size of the company; AG0: age of the company;
R: leverage; AC: activity of the clients. 13. DeAngelo LE (1981) Auditor size and auditor quality. J Account Econ
3(3):183–199 13. DeAngelo LE (1981) Auditor size and auditor quality. J Account Econ
3(3):183–199 14. Dye R (1993) Auditing standards, legal liability, and auditor wealth. J Polit
Econ 101(5):887–914 14. Dye R (1993) Auditing standards, legal liability, and auditor wealth. J Polit
Econ 101(5):887–914 15. El Deeb MS, Sobhy NA (2017) An exploration of corporate social respon-
sibility disclosure determinants, corporate governance and capital struc-
ture in the Egyptian stock exchange market. Egyp Account Rev 6:1–44 15. El Deeb MS, Sobhy NA (2017) An exploration of corporate social respon-
sibility disclosure determinants, corporate governance and capital struc-
ture in the Egyptian stock exchange market. Egyp Account Rev 6:1–44 Funding
h Funding
There is no source of funding. There is no source of funding. Page 14 of 14 AL Abdullah and AL Ani Futur Bus J 2021, 7(1):19 Page 14 of 14 19. Fan Y, Li, C, Nagarajan N (2015) Auditor litigation, audit office pricing and
client acceptance. Paper presented in 2015 Auditing Section Midyear
Conference and Doctoral Consortium. January, 15–17, 2015: Miami,
Florida, USA 38. Mustafa AS, Barwari AS, Mohammed NH (2018) Minority Sharehold-
ers’ rights and audit quality: empirical evidence from Turkey. J Account
Finance Audit Stud 4(4):27–44. https://doi.org/10.32602/jafas.2018.003 39. Nelson SP, Mohamed-Rusdi NF (2015) Ownership structures influence on
audit fee. J Account Emerg Econ 5(4):457–478. https://doi.org/10.1108/
JAEE-05-2013-0027 20. Franz D, Crawford D, Johnson EN (1998) The impact of litigation against
an audit firm on the market value of non litigating clients. J Account
Audit Financ 13(2):117–134 40. Nurdin N, Kartini D, Fani M, Kaltum U (2016) Small Shareholders’ interven-
tion in the determination of Firm’s Leverage. Int J Econ Commerce Manag
IV 4:26–40 21. Frölich M (2006) Non-parametric regression for binary dependent vari-
ables. Economet J 9(3):511–540 22. Gajevszky A (2014) Audit quality and corporate governance: evidence
from the Bucharest Stock Exchange. J Econ Soc Dev 1(2):1–11 41. Oktorina M, Wedari LK (2015) An empirical investigation on owner-
ship characteristics activities of the audit committee, and audit fees in
companies listed on Indonesia stock exchange. Appl Finance Account
1(1):20–29 23. Hair JF, Black WC, Babin BJ, Anderson RE, Tatham RL (2006) Multivariate
data analysis, 6th edn. Prentice Hall, New Jersey data analysis, 6th edn. Prentice Hall, New Jersey 42. Palmrose ZV (1988) An analysis of auditor litigation and audit service
quality. Account Rev 63(1):55–73 24. Hay DC, Knechel WR, Wong N (2006) Audit fees: a meta-analysis of
the effect of supply and demand attributes. Contemp Account Res
23(1):141–191 43. Rajgopal S, Suraj S, Zheng X (2020) Measuring audit quality, Working
paper. https://ssrn.com/abstract=3504037 or https://doi.org/10.2139/
ssrn.3504037 25. Imanzadeh P, Lalepour M (2013) The effect of corporate governance
mechanisms on auditing quality of firms accepted in Tehran Stock
Exchange. Appl Math Eng Manag Technol 1(3):58–63 44. Rothenberg NR (2020) Auditor reputation concerns, legal liability, and
standards. Account Rev 95(3):371–391 26. Kang M, Lee H-Y, Mande V, Woo Y-S (2019) Audit firm attributes and audi-
tor litigation risk. J Account Finance Business Stud 55(4):639–675 45. Funding
h https://doi.org/10.1016/j.
jacceco.2013.10.002 35. Lennox C, Li B (2014) Accounting misstatements following lawsuits
against auditors. J Account Econ 57(1):58–75. https://doi.org/10.1016/j.
jacceco.2013.10.002 53. YU DM (2007) The Effect of Big four Size on Audit quality, Unpub-
lished Ph.D. Dissertation. Faculty of the Graduate School. University of
Missouri–Columbia. 53. YU DM (2007) The Effect of Big four Size on Audit quality, Unpub-
lished Ph.D. Dissertation. Faculty of the Graduate School. University of
Missouri–Columbia. 36. Miko NU, Kamardin H (2015) Impact of audit committee and audit quality
on preventing earnings management in the pre- and post-Nigerian
Corporate Governance Code 2011. Procedia Soc Behav Sci 172:651–657. https://doi.org/10.1016/j.sbspro.2015.01.415 54. Zureigat QM (2011) The effect of ownership structure on audit quality:
evidence from Jordan. Int J Bus Soc Sci 2(10):38–46 54. Zureigat QM (2011) The effect of ownership structure on audit quality:
evidence from Jordan. Int J Bus Soc Sci 2(10):38–46 p
g
j
p
37. Mitra S, Hossain M, Deis DR (2007) The empirical relationship between
ownership characteristics and audit fees. Rev Quant Finance Account
28(3):257–285. https://doi.org/10.1007/s11156-006-0014-7 37. Mitra S, Hossain M, Deis DR (2007) The empirical relationship between
ownership characteristics and audit fees. Rev Quant Finance Account
28(3):257–285. https://doi.org/10.1007/s11156-006-0014-7 Funding
h Sayyar HR, Basiruddin S, Abdul Rasid Z, Elhabib MA (2015) The impact of
audit quality on firm performance: evidence from Malaysia. J Adv Rev Sci
Res 10(1):1–19 g
27. Kasai N (2014) Ownership structure, audit fees, and audit quality in Japan,
Publisher: Shiga University, Faculty of Economics, Japan Publisher: Shiga University, Faculty of Economics, Japan 46. Sharma N (2017) Corporate governance mechanisms in India. Int J Adv
Res Dev 2(5):132–137 28. Khalil S, Mazboudi M (2016) Client acceptance and engagement pricing
following auditor resignations in family Firms. Audit A J Pract Theory
35(4):137–158. https://doi.org/10.2308/ajpt-51489 47. Skinner DJ, Srinivasan S (2012) Audit quality and auditor reputation:
evidence from Japan. Account Rev 87(5):1737–1765. https://doi.org/10.
2308/accr-50198 p
g
jp
29. Khasharmeh H, Joseph N (2017) Does ownership structure affects
audit quality: evidence from Bahrain? Global J Account Econ Finance
4(3):92–100 48. Soltani B (2014) The anatomy of corporate Fraud: a comparative analysis
of high profile American and European corporate scandals. J Bus Ethics
120(2):251–274 30. Khurana IK, Raman KK (2004) Litigation risk and the financial reporting
credibility of Big4 versus non-Big 4 audits: evidence from Anglo-Ameri-
can countries. Account Rev 79(2):473–498 49. Sun J, Guoping L (2011) Client-specific litigation risk and audit quality
differentiation. Manag Audit J 26(4):300–316 31. Kim ID, Skinner J (2012) Measuring securities litigation risk. J Account
Econ 53(1–2):290–310. https://doi.org/10.1016/j.jacceco.2011.09.005 50. Svanström T (2013) Non-audit services and audit quality: evidence from
private firms. Eur Account Rev 22(2):337–366. https://doi.org/10.1080/
09638180.2012.706398 32. Kouaib A, Jarboui A (2014) External audit quality and ownership structure
interaction and impact on earnings management of industrial and com-
mercial Tunisian sectors. J Econ Finance Adm Sci 19(37):78–89 51. Wong RMK, Firth MA, Lo AWY (2018) The impact of litigation risk on the
association between audit quality and auditor size: evidence from China. J Int Financ Manag Acc 29(3):280–311 33. Labelle R, Piot C (2003) Governance, audit et manipulations comptables. Revue du Financier 139:84–90 33. Labelle R, Piot C (2003) Governance, audit et manipulations comptables. Revue du Financier 139:84–90 52. Yeung WH, Lento C (2018) Ownership structure, audit quality, board
structure, and stock price crash risk: evidence from China. Global Finance
Journal 37(2):1–24 34. Lennox C (2005) Management ownership and audit firm size. Contemp
Account Res 22(1):205–227 34. Lennox C (2005) Management ownership and audit firm size. Contemp
Account Res 22(1):205–227 35. Lennox C, Li B (2014) Accounting misstatements following lawsuits
against auditors. J Account Econ 57(1):58–75. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations.
|
https://openalex.org/W3042027277
|
https://www.nature.com/articles/s42005-020-0394-3.pdf
|
English
| null |
Interferometric and fluorescence analysis of shock wave effects on cell membrane
|
Communications physics
| 2,020
|
cc-by
| 7,097
|
1 Department of Mechanical Engineering, The University of Tokyo, Tokyo 113-8656, Japan. 2 Department of Chemistry, Massachusetts Institute of
Technology, Cambridge, MA 02139, USA. 3 Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
4 Department of Bioengineering, The University of Tokyo, Tokyo 113-8656, Japan. 5 Department of Precision Engineering, The University of Tokyo, Tokyo 113-
8656, Japan. ✉email: kei@bmpe.t.u-tokyo.ac.jp; kanelson@mit.edu COMMUNICATIONS PHYSICS | (2020) 3:124 | https://doi.org/10.1038/s42005-020-0394-3 | www.nature.com/commsphys Interferometric and fluorescence analysis of shock
wave effects on cell membrane Yusuke Ito
1, David Veysset
2,3, Steven E. Kooi3, Dmitro Martynowych2,3, Keiichi Nakagawa
4,5✉&
Keith A. Nelson2,3✉ Yusuke Ito
1, David Veysset
2,3, Steven E. Kooi3, Dmitro Martynowych2,3, Keiichi Nakagawa
4,5✉&
Keith A. Nelson2,3✉ Yusuke Ito
1, David Veysset
2,3, Steven E. Kooi3, Dmitro Martynowych2,3, Keiichi Nakagawa
4,5✉&
Keith A. Nelson2,3✉ Shock waves generated by laser pulses have been gaining attention for biological and medical
applications in which shock-induced cell membrane deformation influences cell permeation. However, the mechanisms through which the deformation of cell membranes affects per-
meability remain mostly unknown because of the difficulty of observing in real time the
transient and dynamic behaviors of the shock waves and the cells. Here we present an all-
optical measurement method that can quantitatively capture the pressure distribution of the
propagating shock wave and simultaneously monitor the dynamic behavior of cell mem-
branes. Using this method, we find that the profile of the shock wave dictates the cell
membrane permeation. The results suggest a possible mechanism of membrane permeation
where sharp pressure gradients create pores on the membrane. Our measurement will foster
further understanding of the interaction of shock waves with cells, while the proposed
mechanism advances biological and medical applications of shock waves. 1 ARTICLE COMMUNICATIONS PHYSICS | https://doi.org/10.1038/s42005-020-0394-3 B B
iological and medical applications of shock waves have been
attracting interest in both clinical and scientific studies1–3. The applications involve a broad range of techniques, such
as damage induction on cancer cells4,5, delivery of DNA vaccines
or anticancer chemotherapeutics into diseased cells6,7, treatment
of tissues3,8, and transformation of filamentous fungi9–11 and
bacteria12–15. The cell membrane, which works as a barrier and
also as a gate between the interior of a cell and outside envir-
onment, plays an important role in mediating such physiological
effects. Membranes are sensitive to mechanical force and expected
to deform under the mechanical constraints resulting from the
interaction with a shock16,17. However, because the direct
observation of the interaction in real time has not been achieved,
the determinative mechanisms causing the membrane permea-
tion remain largely unclear. duration, 800-nm wavelength) was focused into a thin phosphate-
buffered saline (PBS) liquid layer that included carbon nano-
particles, fluorescent dyes, and HeLa cells. Using a cylindrical lens
with a 200-mm focal length and an achromatic doublet with a
30-mm focal length, as shown in Fig. Interferometric and fluorescence analysis of shock
wave effects on cell membrane 1b, the focused laser line
had a length of 750 µm and a width of 6 µm. The liquid was
confined between 100-µm-thick and 200-µm-thick glass windows
separated by a 10-µm polymer spacer, yielding a 10–20-µm thick
liquid layer. Upon laser absorption by the carbon nanoparticles,
two counter-propagating planar shock waves were generated in the
liquid layer and remained mostly confined in the plane due to the
impedance mismatch between the liquid and the glass substrates21. p
q
g
To perform quantitative measurement of the shock pressure
distribution with both high spatial and temporal resolution,
interferometric images were acquired with a Mach-Zehnder
interferometer and a variably-delayed probe laser pulse. The
probe pulse, generated by another amplified Ti:sapphire system
(150-fs pulse duration, 400-nm wavelength), was synchronized
with the pump pulse and delivered to the liquid layer colinearly
with the pump pulse, as shown in Fig. 1b. The time delay between
the pump and the probe pulses was adjusted using a delay
generator controlling the timing of the two laser systems. Because
the jitter of the synchronization was 20 ns, the time difference
between the pump and probe pulses was measured by photo-
detectors in every experiment. By comparing the interferograms
obtained before and after the generation of shock waves, the
change in refractive index induced by the density change in the
liquid following the shock front was directly extracted. Note that
a short probe pulse duration was necessary to avoid blurring of
the shock image, but precise timing between the pump and probe
pulses was not needed. Better understanding has been impeded by the incompatibility
of conventional medical shock wave devices based on piezo-
electric, electrohydraulic, or electromagnetic methods8 or of
hydrophone measurement of underwater shock profiles18 with
direct real-time observation of individual cells as they interact
with and respond to shock. Additionally, in biological studies,
shock waves are commonly generated in petri dishes or vials
containing a number of cells in a culture solution, and the effects
of shock waves are investigated after removing the culture solu-
tion19, preventing monitoring of the dynamic behavior of indi-
vidual cells. In contrast, shock waves generated by focused
ultrashort laser pulses can be microscopically targeted4,6,19,20 and
synchronized with real-time optical probes. Results Experimental method. Figure 1 shows the experimental setup. We generated planar shock waves by cylindrically focusing the
pump laser beam into a line, as illustrated in Fig. 1a. A picose-
cond laser pump pulse (amplified Ti:sapphire system, 300-ps a
b
Cylindrically focused
pump pulse
Glass
substrates
10–20 μm
Liquid layer
Cells
Laser-focused
line
Propagating
shock waves
Probe pulse
λ = 400 nm, τ = 150 fs
Pump pulse
λ = 800 nm, τ = 300 ps
Argon-ion laser
λ = 488 nm, CW
Fluorescence
λ = 518 nm
BS
BS
DM
DM
DM
Liquid
layer
Sample
f300
f30
f30
f30
f30
f300
f500
f1000
CCD
CCD
Cylindrical
f200
Fig. 1 Optical apparatus for analyzing cell membrane interactions with and responses to shock. a Sample assembly. Cells are placed in a thin liquid layer
that contains fluorescent dyes. A cylindrically focused pump pulse (red beam) irradiates a line in the plane of the liquid layer. Two counter-propagating
shock waves are launched and remain confined in the plane. b Optical setup. A cylindrical-lens configuration shapes the pump pulse into a line focus. Interferometric imaging is performed using a Mach-Zehnder configuration and a variably-delayed probe pulse (blue beams). The probe beam is split into
two arms and recombined using two beam splitters (BS). The sample plane is imaged onto a charge-coupled device (CCD) using a two-lens telescope. A
continuous-wave (CW) argon-ion-laser beam (azure) is delivered to the sample plane through a dichroic mirror (DM) to induce dye fluorescence (green)
which is imaged onto another CCD. For each laser and fluorescence, λ is the wavelength. τ is the pulse duration of each laser. The focal length of lens is
indicated such as f300 where 300 is measured in millimeters. a
Cylindrically focused
pump pulse
Glass
substrates
10–20 μm
Liquid layer
Cells
Laser-focused
line
Propagating
shock waves b a b
Probe pulse
λ = 400 nm, τ = 150 fs
Pump pulse
λ = 800 nm, τ = 300 ps
Argon-ion laser
λ = 488 nm, CW
Fluorescence
λ = 518 nm
BS
BS
DM
DM
DM
Liquid
layer
Sample
f300
f30
f30
f30
f30
f300
f500
f1000
CCD
CCD
Cylindrical
f200 Cylindrically focused
pump pulse Probe pulse
λ = 400 nm, τ = 150 fs Argon-ion laser
λ = 488 nm, CW Argon-ion laser
λ = 488 nm, CW Liquid
layer Glass
substrates Laser-focused
line Propagating
shock waves line Fig. Interferometric and fluorescence analysis of shock
wave effects on cell membrane Here we present an optically-based system that can produce
controlled shock waves on a microscopic scale, acquire the shock
pressure distribution quantitatively, and monitor the dynamic
behavior of cell membranes in response to shock. Our measure-
ments allow changes of cell membranes to be associated with
quantitative characteristics of shock waves. To visualize the dynamic behavior of the cell membrane, we
distributed outside the cells fluorescent dyes having no cell
membrane permeability under normal conditions. The mem-
brane was observed as the interface between fluorescent and dark
regions. Transport of dye molecules from outside to inside the
cells resulting from shock-induced membrane permeability was
observed as the appearance and increase of fluorescence inside
the cell. In this study, fluorescein isothiocyanate (FITC) dextran
of average molecular weight 3000–5000 Da was used; the
molecules can permeate into cells when the size of the pores on Results The peak pressures at 25, 47, and 80 ns were
52.8 ± 8.2,
46.3 ± 4.8, and
47.7 ± 3.5 MPa,
corresponding
to
density changes of 23.3 ± 3.3 mg cm−3, 20.6 ± 2.0 mg cm−3, and
21.1 ± 1.5 mg cm−3, respectively. The full widths at half max-
imum (FWHM) of the shock waveforms were 13.2 ± 0.2 µm,
16.2 ± 0.8 µm, and 21.3 ± 1.2 µm, respectively. The shock wave
propagated with a speed of 1458 ± 15 m s−1, which corresponded
to the acoustic speed in water (≈1450 m s−1) (see Supplementary
Fig. 3a and Supplementary Note 3 for details). Interferometric analysis. Interferograms of shock waves propa-
gating in the liquid (in the absence of cells) were recorded to
characterize the shock waves generated in our setup. Figure 2a–c
shows images recorded with increasing probe pulse delays at a
pump pulse energy of 200 ± 50 µJ. The shock fronts are obser-
vable as distortions in the interferogram fringes. To quantitatively
analyze the pressure profile of the shock, the interferometric
images were converted to 2D phase images through a 2D Fourier
transform method with a Hann function for spectrum apodiza-
tion22. After phase unwrapping, 2D phase images were obtained
before and after laser excitation and subtracted to obtain the
optical phase change profile (see Supplementary Fig. 1 and Sup-
plementary Note 1). The extracted phase change Δφ was con-
verted to the change in refractive index Δn based on the relation The FWHM of each shock waveform at different propagation
distance is plotted in Fig. 2h. It expanded as the shock wave
propagated. According to the linear fitting shown as the red line,
the initial FWHM at the laser-focused line was estimated to be
9.1 µm, and it expanded with the slope of 0.16. The peak
pressures of shock waves at different propagation distances had
large variations (see Supplementary Fig. 3b and Supplementary
Note 3 for details) because of the fluctuations of the thickness of
the liquid layer and the pump pulse energy. Despite the large
variations in the peak pressures, the FWHM consistently
indicated the clear (and well-known25) lengthening of the tail
of the shock wave with propagation. Δn ¼ Δφ
2π
λ
l ;
ð1Þ ð1Þ where λ is the wavelength of the probe pulse and l is the thickness
of the liquid layer. Results g a
t = 25 ns
Focused line
d c
t = 80 ns b
t = 47 ns g b
t = 4 t = 47 ns f h h f d 0
-50
50 (MPa)
f 50 (MPa)
0
-50
50 (MPa)
0
-50
50 (MPa)
e
f e 0
-50
50 (MPa)
e 0
-50
50 (MPa)
d Fig. 2 Interferograms and analyzed shock waveforms. a–c Interferometric images show Fig. 2 Interferograms and analyzed shock waveforms. a–c Interferometric images showing shock wave propagation at three different time delays t. Arrows indicate the propagation direction of the shock fronts. Bubbles are formed at the laser focused area and appear as a black line on the images. Each
image was recorded from a different sample region. Scale bars, 50 µm. d–f Spatial distributions of pressure extracted from a–c, respectively. g Comparison
of shock waveforms at different time delays as a function of the distance from the laser-focused line. h Full width at half maximum (FWHM) of each shock
waveform as a function of the position of shock front with respect to the laser-focused line. The error bars indicate the standard deviation. cells becomes larger than that of FITC dextran. The fluorescent
molecules were excited by a continuous-wave argon-ion-laser
beam with a wavelength of 488 nm. Light was emitted with a
wavelength of 518 nm and separated from the excitation light
using a dichroic mirror. This in situ monitoring was conducted in
real time with a high-sensitivity charge-coupled device (CCD)
camera. shock conditions for densities ranging from 1.00 to 1.21 g cm−3. Shock pressures associated with the measured density changes
were calculated using the Tait equation of state of water24. The
uncertainty of the pressures is related to the uncertainty of the
density changes, which mainly originated from the uncertainty of
the liquid thickness l. The calculated pressure distributions with various time delays
corresponding to the three images in Fig. 2a–c are shown
respectively in Fig. 2d–f. x = 0 µm corresponds to the position at
the laser-focused line. The pressure drop near x = 0 µm was
caused by temperature increase (see Supplementary Fig. 2 and
Supplementary Note 2 for details). The shock waveforms along
the horizontal line defined by the multiple arrows in Fig. 2a–c are
plotted in Fig. 2g. Results 1 Optical apparatus for analyzing cell membrane interactions with and responses to shock. a Sample assembly. Cells are placed in a thin liquid layer
that contains fluorescent dyes. A cylindrically focused pump pulse (red beam) irradiates a line in the plane of the liquid layer. Two counter-propagating
shock waves are launched and remain confined in the plane. b Optical setup. A cylindrical-lens configuration shapes the pump pulse into a line focus. Interferometric imaging is performed using a Mach-Zehnder configuration and a variably-delayed probe pulse (blue beams). The probe beam is split into
two arms and recombined using two beam splitters (BS). The sample plane is imaged onto a charge-coupled device (CCD) using a two-lens telescope. A
continuous-wave (CW) argon-ion-laser beam (azure) is delivered to the sample plane through a dichroic mirror (DM) to induce dye fluorescence (green)
which is imaged onto another CCD. For each laser and fluorescence, λ is the wavelength. τ is the pulse duration of each laser. The focal length of lens is
indicated such as f300 where 300 is measured in millimeters. COMMUNICATIONS PHYSICS | (2020) 3:124 | https://doi.org/10.1038/s42005-020-0394-3 | www.nature.com/commsphys 2 ARTICLE COMMUNICATIONS PHYSICS | https://doi.org/10.1038/s42005-020-0394-3 0
-50
50 (MPa)
0
-50
50 (MPa)
0
-50
50 (MPa)
a
b
c
t = 25 ns
t = 47 ns
t = 80 ns
Focused line
d
e
f
g
h
Fig. 2 Interferograms and analyzed shock waveforms. a–c Interferometric images showing shock wave propagation at three different time delays t. Arrows indicate the propagation direction of the shock fronts. Bubbles are formed at the laser focused area and appear as a black line on the images. Each
image was recorded from a different sample region. Scale bars, 50 µm. d–f Spatial distributions of pressure extracted from a–c, respectively. g Comparison
of shock waveforms at different time delays as a function of the distance from the laser-focused line. h Full width at half maximum (FWHM) of each shock
waveform as a function of the position of shock front with respect to the laser-focused line. The error bars indicate the standard deviation. COMMUNICATIONS PHYSICS | (2020) 3:124 | https://doi.org/10.1038/s42005-020-0394-3 | www.nature.com/commsphys Results The thickness of the liquid layer ranged from
10 to 20 µm. Although the polymer spacer between the glass
substrates was 10-µm thick, distortion of the substrates caused the
variation of the liquid layer thickness. Therefore, the thickness
within the imaging field of view was measured before each
experiment with an uncertainty of 1.4 µm. The change in the
refractive index Δn was then translated into density change Δρ: Δρ ¼ Δn
0:322 ½g cm3
ð2Þ ð2Þ Fluorescence analysis. To monitor the dynamic behavior of cell
membrane simultaneously with interferometric imaging of the using an empirically determined formula for water23, valid under using an empirically determined formula for water23, valid under COMMUNICATIONS PHYSICS | (2020) 3:124 | https://doi.org/10.1038/s42005-020-0394-3 | www.nature.com/commsphys 3 ARTICLE COMMUNICATIONS PHYSICS | https://doi.org/10.1038/s42005-020-0394-3 -80
0
80 (MPa)
Pressure (MPa)
x (µm)
y (µm)
a
t = 84 ns
Cell #1
Cell #2
Cell #3
Focused line
c
t = 10 s
Cell #1
Cell #2
Cell #3
d
t = 150 s
Cell #1
Cell #2
Cell #3
e
t = 300 s
Cell #1
Cell #2
Cell #3
b
f
Cell #1
Cell #2
Cell #3
Bubbles
Fig. 3 Interferometric and fluorescence analysis. a Interferometric
image showing a propagating shock wave and three cells with a time
delay of 84 ns. An arrow indicates the propagation direction of the
shock front. Scale bar, 50 µm. b Extracted spatial distribution of pressure
c–e Fluorescence images showing the permeation behavior of the
fluorescent molecules into the cells. Images were recorded c 10 s, d 150 s
and e 300 s after the pump pulse was delivered (time indicated by t). Scal
bars, 50 µm. f Normalized brightness inside the cells with increasing time
after delivering the pump pulse obtained by fluorescence imaging. -80
0
80 (MPa)
Pressure (MPa)
x (µm)
y (µm)
d
t = 150 s
Cell #1
Cell #2
Cell #3
b
Cell #1
Cell #2
Cell #3 a
t = 84 ns
Cell #1
Cell #2
Cell #3
Focused line -80
0
80 (MPa)
Pressure (MPa)
x (µm)
y (µm)
b
Cell #1
Cell #2
Cell #3 capillary forces prevented them from collapsing on a much
shorter time scale. As time increased, the brightness inside cells
#1 and #2, labeled in Fig. 3, increased. Discussion
h f e
t = 300 s
Cell #1
Cell #2
Cell #3 f Despite the slight difference between the locations of cells #1 and
#2, the time-dependences of their brightness changes differed
substantially. The difference may stem from either variability
between the cells or in the shock properties. To identify the
origin, we measured the brightness changes of 53 cells located at
different distances away from laser-focused lines in order to
investigate the time dependence of permeation behavior at dif-
ferent distances from the shock excitation region. The results shown in Fig. 4a clearly indicate that the closer the
cells were located to the laser-focused line, the faster the bright-
ness of the cells increased. Because Fig. 2h showed that FWHM of
the shock waveform increased with the propagation of the shock
wave, the FWHM may affect the brightness change. To verify this
hypothesis, the cells were divided into two groups; one with
permeation of the fluorescent molecules at 300 s after the shock
delivery and the other without permeation. As shown in Fig. 4b,
the two groups were compared after calculating the FWHM at
the position of each cell (see Supplementary Fig. 5 and Fig. 3 Interferometric and fluorescence analysis. a Interferometric Fig. 3 Interferometric and fluorescence analysis. a Interferometric
image showing a propagating shock wave and three cells with a time
delay of 84 ns. An arrow indicates the propagation direction of the
shock front. Scale bar, 50 µm. b Extracted spatial distribution of pressure. c–e Fluorescence images showing the permeation behavior of the
fluorescent molecules into the cells. Images were recorded c 10 s, d 150 s,
and e 300 s after the pump pulse was delivered (time indicated by t). Scale
bars, 50 µm. f Normalized brightness inside the cells with increasing time
after delivering the pump pulse obtained by fluorescence imaging. g
y
image showing a propagating shock wave and three cells with a time
delay of 84 ns. An arrow indicates the propagation direction of the
shock front. Scale bar, 50 µm. b Extracted spatial distribution of pressure. c–e Fluorescence images showing the permeation behavior of the
fluorescent molecules into the cells. Images were recorded c 10 s, d 150 s,
and e 300 s after the pump pulse was delivered (time indicated by t). Scale
bars, 50 µm. Discussion
h f Normalized brightness inside the cells with increasing time
after delivering the pump pulse obtained by fluorescence imaging. b
a
Fig. 4 Effect of a shock wave on cell permeation. a Normalized brightness
inside each cell located at different distance away from the laser-focused
line and at increasing time after the pump pulse was delivered. b Comparison of full width at half maximum (FWHM) of shock waveform
at the position of each cell belonging to one of two groups: with permeation
(n = 19 cells, red circles) and without permeation (n = 16 cells, blue
diamonds) of fluorescent molecules at 300 s after the pump pulse was
delivered. The box plot shows the middle value of the data set (central line),
the 25th percentile (bottom of the box), and the 75th percentile (top of the
box) with a set of whiskers determined by the 1.5 interquartile ranges. Data
were compared by conducting a two-tailed t-test using all data points and
by calculating the probability value (p value). .org/10.1038/s42005-020-0394-3 | www.nature.com/commsphys b
a b a a shock, fluorescence imaging was used. Images were recorded for
300 s or longer with a frame rate of 0.5 Hz in a single experiment. An interferogram recorded 84 ns after the pump pulse irradiated
the liquid layer, where cells are present, is shown in Fig. 3a. The
pressure distribution extracted from the interferogram is shown
in Fig. 3b. The pressure distribution indicates that the shock wave
propagated with no visible disturbance after encountering the cell;
the impedance mismatch between the water and the cell being
small, the shock was not reflected or attenuated significantly by
the cell26. The difference between the pressure distributions (peak
pressure and pressure at the tail) shown in Figs. 2d–f and 3b
arises from the fluctuations of the thickness of the liquid layer and
the pump pulse energy independent from the presence of the
cells. As shown in Fig. 3c–e, we captured the permeation behavior
of the fluorescent molecules into the cells after cell-shock inter-
action, from which membrane disruption can be inferred argu-
ably at scales below the optical resolution. The laser-focused line
observed in Fig. 3a evolved after 10 s into large bubbles (Fig. 3c
and Supplementary Fig. 4) that collapsed prior to 150 s (Fig. 3d). Results The increase in the
brightness indicates that pores were generated in the cell mem-
branes, and that fluorescent molecules permeated the cell mem-
branes when the pore size increased sufficiently. Pores can be
generated due to a non-uniform pressure distribution on the
membrane28. Blebs, the cellular protrusions, were observed
around all three cells after the shock wave passed as shown in
Fig. 3d,
e. Blebbing
occurs
due
to
local
rupture
of
membrane–cytoskeleton attachments in regions of high pressure
in cells29. Therefore, the results may indicate that the pressure is
unequally distributed and locally increased on the membrane
during the passage of the shock wave. The brightness changes
inside the cells were plotted in Fig. 3f by averaging the brightness
inside each cell and normalizing it by comparing the brightness
inside and outside the cell. In cells #1 and #2, the brightness
started to increase 94 s and 158 s after the shock, respectively, and
saturated at ~300 s. Permeation was not observed in cell #3
throughout the observation. b t = 84 ns c
t = 10 s
Cell #1
Cell #2
Cell #3
Bubbles Discussion
h Bubbles normally collapse much faster in conventional experi-
ments when they are not constrained27; however, because the
bubbles were sandwiched between glass walls in our setup, the shock, fluorescence imaging was used. Images were recorded for
300 s or longer with a frame rate of 0.5 Hz in a single experiment. An interferogram recorded 84 ns after the pump pulse irradiated
the liquid layer, where cells are present, is shown in Fig. 3a. The
pressure distribution extracted from the interferogram is shown
in Fig. 3b. The pressure distribution indicates that the shock wave
propagated with no visible disturbance after encountering the cell;
the impedance mismatch between the water and the cell being
small, the shock was not reflected or attenuated significantly by
the cell26. The difference between the pressure distributions (peak
pressure and pressure at the tail) shown in Figs. 2d–f and 3b
arises from the fluctuations of the thickness of the liquid layer and
the pump pulse energy independent from the presence of the
cells. As shown in Fig. 3c–e, we captured the permeation behavior
of the fluorescent molecules into the cells after cell-shock inter-
action, from which membrane disruption can be inferred argu-
ably at scales below the optical resolution. The laser-focused line
observed in Fig. 3a evolved after 10 s into large bubbles (Fig. 3c
and Supplementary Fig. 4) that collapsed prior to 150 s (Fig. 3d). Bubbles normally collapse much faster in conventional experi-
ments when they are not constrained27; however, because the
bubbles were sandwiched between glass walls in our setup, the Sample characterization. The thickness of the liquid layer was calculated
according to the Beer-Lambert law. The thickness l can be expressed as Sample characterization. The thickness of the liquid layer was calculated
according to the Beer-Lambert law. The thickness l can be expressed as l ¼ 1
α1
log10
I IB
I0 IB
;
ð3Þ ð3Þ where α1 is the absorption coefficient of the liquid, I and I0 are the brightness
detected by a CCD after the probe pulses transmitted through the liquid sample
and a pure water in the glass substrates, respectively, and IB is the brightness of the
background without the probe pulses. α1 = 93 cm−1 was measured for the wave-
length of 400 nm using a UV-VIS spectrometer. The effect of the reflection by the
glass surfaces on the accuracy of the thickness measurement was canceled by using
the same glass substrates for the brightness measurements of the liquid sample and
the pure water. For canceling the variation of the probe pulse energies and the
noise from the CCD, the exposure time of the CCD was set to 20 ms, so that the
variation and the noise were averaged by the 20 probe pulses with a repetition rate
of 1 kHz. The thickness was calculated by the brightness of each pixel on the CCD
and averaged. A standard deviation of the thickness was measured to be 1.4 µm. It
was calculated by comparing the 20 different images taken by moving the sample a
few micrometers in a plane before the experiments. Because most conventional methods could not analyze the
influence of shock pressure distribution on individual cells, the
key parameter causing membrane permeation has not been
clarified. Although previous studies32–34 suggested the contribu-
tion of peak pressure, rise time or impulse, direct evaluation
through quantitative analysis of the shock profile has not been
achieved. Conversely, our method allows such analyses which
demonstrate the crucial effect of FWHM. We anticipate that
future studies considering different shock parameters, as well as
cell conditions, will advance the understanding of the mechan-
isms leading to membrane permeation. Regarding shock para-
meters, modulating the spatial and temporal profiles of the laser
pulse will permit control of not only the FWHM but also the peak
pressure, rise time, fall time, impulse and number of shocks. Because our system allows the generation of shock waves and
quantitative analyses of shock parameters and cell permeability at
the same time, the shock parameters can be further optimized
through direct observations. COMMUNICATIONS PHYSICS | https://doi.org/10.1038/s42005-020-0394-3 COMMUNICATIONS PHYSICS | https://doi.org/10.1038/s42005-020-0394-3 Supplementary Note 4 for details). The results of a t-test
demonstrated that there was a significant difference between the
two groups regarding the FWHM. When the propagation dis-
tance is under 70 µm, the FWHM is typically smaller than the
diameter of the cells (~20 µm). Therefore, this suggests that at
short distance the shock wave is narrow enough to create both
low- and high-pressure regions within a cell during the passage of
the wave. This non-uniform pressure distribution creates pores
on the membrane, resulting in fluorescent molecule penetration
into the cell through the pores. On the other hand, when the
propagation distance of the shock wave becomes larger, the
FWHM typically exceeds the diameter of the cells. In this situa-
tion, the cell cytoplasm is more homogeneously compressed and
released rather than being affected by the gradient of the pressure
field in the cell during the passage of the shock wave, therefore
limiting pore formation in the cell membrane and preserving the
membrane impermeability to the fluorescent molecules. This
explains why permeation was not observed in cell #3 in Fig. 3f. Although microjets and secondary shock waves can be generated
when the bubbles collapse30,31, the cells were located away from
the laser-focused line, and therefore, the bubble collapse is
expected to little effect on the cells. In addition, we anticipate
capillary effects to slow down bubble collapse (or prevent it
entirely), consequently reducing the emission of secondary shock
wave. diameter, glass substrates (Schott D263®). A photoresist (SU-8 2015, MicroChem®)
was coated and developed on the 200-µm-thick substrate to form a ring-patterned
spacer. The spacer had an outer diameter of 22 mm, an inner diameter of 19 mm,
and a thickness of 10 µm to ensure separation between the substrates. Cell preparation. HeLa cells were maintained in DMEM supplemented with 10%
(v/v) fetal bovine serum and 1% (v/v) Pen Strep at 37 °C and 5% CO2 in a T-75
flask. When the cells reached ~80% confluence, the growth media was aspirated. Trypsin-EDTA 0.25% (2 mL) was added to the cells and incubated for 15 min at
37 °C and 5% CO2. To quench the trypsin, DMEM supplemented with 10% (v/v)
fetal bovine serum and 1% (v/v) Pen Strep (8 mL) was added to the flask. Data availability The data that support the findings of this work are available from the corresponding
author upon reasonable request. The data that support the findings of this work are available from the corresponding
author upon reasonable request. Sample characterization. The thickness of the liquid layer was calculated
according to the Beer-Lambert law. The thickness l can be expressed as The optimization will contribute to
the more effective use of shock waves in the biotechnological and
clinical applications. Normalization of brightness. For the normalization, the average of the brightness
of 100 pixels inside each cell was divided by a reference brightness, which was
the average of the brightness of 100 pixels outside the cell. The reference area was
10 µm away from each cell. The brightness inside the cells was above zero before
the generation of the shock, because the fluorescence from the fluorescent mole-
cules existing between the cells and the glass substrate was detected. Reporting summary. Further information on research design is available in
the Nature Research Reporting Summary linked to this article. Code availability y
The codes used for the data collection and analysis are available from the corresponding
author upon reasonable request. The codes used for the data collection and analysis are available from the corresponding
author upon reasonable request. In summary, we have presented an all-optical measurement
system that can produce a planer shock wave whose spatial
profile, propagation through cells, and effects on cell membrane
behavior can be monitored. Our results demonstrate the influence
of the profile of the shock wave on membrane permeation, where
shocks that are shorter temporally and spatially are more likely to
make cells permeable to fluorescent dye. The results suggest a
possible mechanism of membrane permeation due to sharp
pressure gradients, i.e. non-uniform pressure distribution in the
cell that deforms cell membranes and causes pore formation. Our
all-optical measurement will foster further understanding of the
interaction of shock waves with cells, while the proposed
mechanism may guide the formulation of optimal conditions for
biological and medical applications of shock waves. Received: 10 March 2020; Accepted: 17 June 2020; Received: 10 March 2020; Accepted: 17 June 2020; References 1. Seah, B. C.-Q. & Teo, B. M. Recent advances in ultrasound-based transdermal
drug delivery. Int. J. Nanomed. 13, 7749–7763 (2018). 2. Battula, N., Menezes, V. & Hosseini, H. A miniature shock wave driven micro-
jet injector for needle-free vaccine/drug delivery. Biotechnol. Bioeng. 113,
2507–2512 (2016). 3. Mani-Babu, S., Morrissey, D., Waugh, C., Screen, H. & Barton, C. The
effectiveness of extracorporeal shock wave therapy in lower limb
tendinopathy. Am. J. Sports Med. 43, 752–761 (2015). 4. Steinhauser, M. O. & Schmidt, M. Destruction of cancer cells by laser-induced
shock waves: recent developments in experimental treatments and multiscale
computer simulations. Soft Matter 10, 4778–4788 (2014). ARTICLE ARTICLE COMMUNICATIONS PHYSICS | https://doi.org/10.1038/s42005-020-0394-3 In all,
7.5 mL of the dissociated cells in media were transferred to a 15 mL falcon tube and
spun at 500 rcf for 3 min. The supernatant was removed and the pellet was
resuspended in 250 µL of PBS. COMMUNICATIONS PHYSICS | (2020) 3:124 | https://doi.org/10.1038/s42005-020-0394-3 | www.nature.com/commsphys Sample preparation. The liquid sample was made by mixing a 0.4 wt% carbon
nanoparticles, a 2 wt% of FITC dextran of average molecular weight 3000–5000 Da
(FD4, Sigma-Aldrich®), and cells in PBS (Sigma-Aldrich®). The carbon con-
centration was yielded by diluting black ink (Winsor & Newton Ink®) 50x in PBS.
The liquid was enclosed between a 100 µm-thick and a 200 µm-thick, 1 inch- Fig. 4 Effect of a shock wave on cell permeation. a Normalized brightness Fig. 4 Effect of a shock wave on cell permeation. a Normalized brightness Fig. 4 Effect of a shock wave on cell permeation. a Normalized brightness
inside each cell located at different distance away from the laser-focused
line and at increasing time after the pump pulse was delivered. inside each cell located at different distance away from the laser-focused
line and at increasing time after the pump pulse was delivered b Comparison of full width at half maximum (FWHM) of shock waveform
at the position of each cell belonging to one of two groups: with permeation
(n = 19 cells, red circles) and without permeation (n = 16 cells, blue
diamonds) of fluorescent molecules at 300 s after the pump pulse was
delivered. The box plot shows the middle value of the data set (central line),
the 25th percentile (bottom of the box), and the 75th percentile (top of the
box) with a set of whiskers determined by the 1.5 interquartile ranges. Data
were compared by conducting a two-tailed t-test using all data points and
by calculating the probability value (p value). COMMUNICATIONS PHYSICS | (2020) 3:124 | https://doi.org/10.1038/s42005-020-0394-3 | www.nature.com/commsphys 4 COMMUNICATIONS PHYSICS | https://doi.org/10.1038/s42005-020-0394-3 COMMUNICATIONS PHYSICS | https://doi.org/10.1038/s42005-020-0394-3 7. Azagury, A., Khoury, L., Enden, G. & Kost, J. Ultrasound mediated
transdermal drug delivery. Adv. Drug Deliv. Rev. 72, 127–143 (2014). 30. Lauterborn, W. & Vogel, A. Shock wave emission by laser generated bubbles. in Bubble Dynamics and Shock Waves, 67–103 (Springer, Berlin, 2013). https://doi.org/10.1007/978-3-642-34297-4_3 8. Zelle, B. A., Gollwitzer, H., Zlowodzki, M. & Bühren, V. Extracorporeal shock
wave therapy: current evidence. J. Orthop. Trauma 24, S66–S70 (2010). p
g
31. Li, Z. G., Liu, A. Q., Klaseboer, E., Zhang, J. B. & Ohl, C. D. Single cell
membrane poration by bubble-induced microjets in a microfluidic chip. Lab
Chip 13, 1144–1150 (2013). 9. Magaña-Ortíz, D. et al. A novel and highly efficient method for genetic
transformation of fungi employing shock waves. Fungal Genet. Biol. 56, 9–16
(2013). 9. Magaña-Ortíz, D. et al. A novel and highly efficient method for genetic p
32. Doukas, A. G. & Flotte, T. J. Physical characteristics and biological effects of
laser-induced stress waves. Ultrasound Med. Biol. 22, 151–164 (1996). 10. Gómez-Lim, M. A., Ortíz, D. M., Fernández, F. & Loske, A. M. Transformation of Fungi Using Shock Waves, 209–219 (Springer, Cham, 2015). https://doi.org/10.1007/978-3-319-10142-2_21 33. Mulholland, S. E., Lee, S., McAuliffe, D. J. & Doukas, A. G. Cell loading with
laser-generated stress waves: the role of the stress gradient. Pharm. Res. 16,
514–518 (1999). p
g
11. Loske, A. M. Medical and Biomedical Applications of Shock Waves. (Springer,
Cham, 2017). https://doi.org/10.1007/978-3-319-47570-7 34. Kodama, T., Hamblin, M. R. & Doukas, A. G. Cytoplasmic molecular
delivery with shock waves: importance of impulse. Biophys. J. 79, 1821–1832
(2000). p
g
12. Jagadeesh, G., Nataraja, K. & Udayakumar, M. Shock waves can enhance
bacterial transformation with plasmid DNA. Curr. Sci. 87, 734–735 (2004). 13. Divya Prakash, G., Anish, R. V., Jagadeesh, G. & Chakravortty, D. Bacterial
transformation using micro-shock waves. Anal. Biochem. 419, 292–301
(2011). Acknowledgements We thank A. A. Maznev (MIT, USA) for discussion on the project, and C. Fadzen and B. Pentelute (MIT, USA) for sample preparation. This material is based upon work sup-
ported in part by the U. S. Army Research Office through the Institute for Soldier We thank A. A. Maznev (MIT, USA) for discussion on the project, and C. Fadzen and B. Pentelute (MIT, USA) for sample preparation. This material is based upon work sup-
ported in part by the U. S. Army Research Office through the Institute for Soldier
Nanotechnologies under Cooperative Agreement Number W911NF-18-2-0048 14. Loske, A. M., Campos-Guillen, J., Fernández, F. & Castaño-Tostado, E. Enhanced shock wave-assisted transformation of Escherichia coli. Ultrasound
Med. Biol. 37, 502–510 (2011). Nanotechnologies, under Cooperative Agreement Number W911NF-18-2-0048. Nanotechnologies, under Cooperative Agreement Number W911NF-18-2-0048. 15. Campos-Guillén, J., Fernández, F., Pastrana, X. & Loske, A. M. Relationship
between plasmid size and shock wave-mediated bacterial transformation. Ultrasound Med. Biol. 38, 1078–1084 (2012). Author contributions 16. Steinbach, P., Hofstädter, F., Nicolai, H., Rössler, W. & Wieland, W. In vitro
investigations on cellular damage induced by high energy shock waves. Ultrasound Med. Biol. 18, 691–699 (1992). D.V., K.N., and K.A.N. designed the experiments. Y.I., D.V., S.E.K., and K.N. constructed
the experimental setup. Y.I. and K.N. conducted the experiments. D.V. developed the
code to extract the pressure distribution from the interferogram. Y.I. analyzed the data. D.M. aided in performing experiments and interpreting the results. D.V., K.N., and
K.A.N. supervised the work. Y.I. wrote the paper and all authors contributed to
improvement of the paper. D.V., K.N., and K.A.N. designed the experiments. Y.I., D.V., S.E.K., and K.N. constructed
the experimental setup. Y.I. and K.N. conducted the experiments. D.V. developed the
code to extract the pressure distribution from the interferogram. Y.I. analyzed the data. D.M. aided in performing experiments and interpreting the results. D.V., K.N., and
K.A.N. supervised the work. Y.I. wrote the paper and all authors contributed to
improvement of the paper. 17. Ohl, C.-D. & Wolfrum, B. Detachment and sonoporation of adherent HeLa-
cells by shock wave-induced cavitation. Biochim. Biophys. Acta Gen. Subj. 1624, 131–138 (2003). 18. Schoeffmann, H., Schmidt-Kloiber, H. & Reichel, E. Time-resolved
investigations of laser-induced shock waves in water by use of
polyvinylidenefluoride hydrophones. J. Appl. Phys. 63, 46–51 (1988). The authors declare no competing interests. The authors declare no competing interests. Correspondence and requests for materials should be addressed to K.N. or K.A.N. Reprints and permission information is available at http://www.nature.com/reprints Reprints and permission information is available at http://www.nature.com/reprints Methods 5. Moosavi-Nejad, S. F., Hosseini, S. H. R., Satoh, M. & Takayama, K. Shock
wave induced cytoskeletal and morphological deformations in a human renal
carcinoma cell line. Cancer Sci. 97, 296–304 (2006). Sample preparation. The liquid sample was made by mixing a 0.4 wt% carbon
nanoparticles, a 2 wt% of FITC dextran of average molecular weight 3000–5000 Da
(FD4, Sigma-Aldrich®), and cells in PBS (Sigma-Aldrich®). The carbon con-
centration was yielded by diluting black ink (Winsor & Newton Ink®) 50x in PBS. The liquid was enclosed between a 100 µm-thick and a 200 µm-thick, 1 inch- 6. Tirlapur, U. K. & König, K. Cell biology: targeted transfection by femtosecond
laser. Nature 418, 290–291 (2002). 6. Tirlapur, U. K. & König, K. Cell biology: targeted transfection by femtosecond
laser. Nature 418, 290–291 (2002). 5 /doi.org/10.1038/s42005-020-0394-3 | www.nature.com/commsphy Additional information 20. Antkowiak, M., Torres-Mapa, M. L., Stevenson, D. J., Dholakia, K. & Gunn-
Moore, F. J. Femtosecond optical transfection of individual mammalian cells. Nat. Protoc. 8, 1216–1233 (2013). Supplementary information is available for this paper at https://doi.org/10.1038/s42005-
020-0394-3. Supplementary information is available for this paper at https://doi.org/10.1038/s42005-
020-0394-3. 21. Veysset, D., Мaznev, A. A., Pezeril, T., Kooi, S. & Nelson, K. A. Interferometric analysis of laser-driven cylindrically focusing shock waves in a
thin liquid layer. Sci. Rep. 6, 24 (2016). Correspondence and requests for materials should be addressed to K.N. or K.A.N. Correspondence and requests for materials should be addressed to K.N. or K.A.N. Competing interests y
y
y
pp
y
19. Chakravarty, P., Qian, W., El-Sayed, M. A. & Prausnitz, M. R. Delivery of
molecules into cells using carbon nanoparticles activated by femtosecond laser
pulses. Nat. Nanotechnol. 5, 607–611 (2010). The authors declare no competing interests. Reprints and permission information is available at http://www.nature.com/reprints y
p
22. Takeda, M. & Mutoh, K. Fourier transform profilometry for the automatic
measurement of 3-D object shapes. Appl. Opt. 22, 3977 (1983). Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. 23. Yadav, H. S. et al. Measurement of refractive index of water under high
dynamic pressures. J. Appl. Phys. 44, 2197–2200 (1973). 24. Gojani, A. B., Ohtani, K., Takayama, K. & Hosseini, S. H. R. Shock Hugoniot
and equations of states of water, castor oil, and aqueous solutions of sodium
chloride, sucrose and gelatin. Shock Waves 26, 63–68 (2016). 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 license, and indicate if changes were made. The images or other third party
material in this article are included in the article’s Creative Commons license, unless
indicated otherwise in a credit line to the material. If material is not included in the
article’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. To view a copy of this license, visit http://creativecommons.org/
licenses/by/4.0/. g
25. Pezeril, T. et al. Direct visualization of laser-driven focusing shock waves. Phys. Rev. Lett. 106, 214503 (2011). 26. Kobayashi, K., Yoshida, S., Saijo, Y. & Hozumi, N. Acoustic impedance
microscopy for biological tissue characterization. Ultrasonics 54, 1922–1928
(2014). 27. Akhatov, I. et al. Collapse and rebound of a laser-induced cavitation bubble. Phys. Fluids 13, 2805–2819 (2001). 28. Adhikari, U., Goliaei, A. & Berkowitz, M. L. Mechanism of membrane
poration by shock wave induced nanobubble collapse: a molecular dynamics
study. J. Phys. Chem. B 119, 6225–6234 (2015). 29. Charras, G. T., Yarrow, J. C., Horton, M. A., Mahadevan, L. & Mitchison, T. J. Non-equilibration of hydrostatic pressure in blebbing cells. Nature 435,
365–369 (2005). © The Author(s) 2020 COMMUNICATIONS PHYSICS | (2020) 3:124 | https://doi.org/10.1038/s42005-020-0394-3 | www.nature.com/commsphys 6
|
https://openalex.org/W4393234792
|
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0297596&type=printable
|
English
| null |
Cause and preventability of in-hospital mortality after PCI: A statewide root-cause analysis of 1,163 deaths
|
PloS one
| 2,024
|
cc-by
| 6,334
|
PLOS ONE RESEARCH ARTICLE Editor: Shukri AlSaif, Saud Al-Babtain Cardiac
Centre, SAUDI ARABIA Editor: Shukri AlSaif, Saud Al-Babtain Cardiac
Centre, SAUDI ARABIA Editor: Shukri AlSaif, Saud Al-Babtain Cardiac
Centre, SAUDI ARABIA
Received: October 11, 2023
Accepted: January 9, 2024
Published: March 27, 2024
Copyright: © 2024 Moroni 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. Objectives To systematically analyze the cause and circumstances of in-hospital mortality in a large,
multi-center, statewide cohort. Copyright: © 2024 Moroni 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. Methods In-hospital deaths after PCI occurring at 39 hospitals included in the Blue Cross Blue Shield
of Michigan Cardiovascular Consortium (BMC2) between 2012 and 2014 were retrospec-
tively reviewed using validated methods. A priori PCI-related mortality risk was estimated
using the validated BMC2 model. Data Availability Statement: Regarding data
availability, all relevant data necessary to replicate
the study findings are within the paper. The authors
are unable to share the raw data, due to contractual
agreements between participating institutions and
the BMC2 registry that prohibit data sharing with
external agencies. However, the analysis code and
metadata to support the study figures is available
on request from Annemarie Forrest, Program
Manager BMC2 (avassalo@med.umich.edu). OPEN ACCESS Citation: Moroni F, Seth M, Changezi HU, Karve M,
Arora DS, Sharma M, et al. (2024) Cause and
preventability of in-hospital mortality after PCI: A
statewide root-cause analysis of 1,163 deaths. PLoS ONE 19(3): e0297596. https://doi.org/
10 1371/journal pone 0297596 Cause and preventability of in-hospital
mortality after PCI: A statewide root-cause
analysis of 1,163 deaths Francesco Moroni1,2, Milan Seth3, Hameem U. ChangeziID4, Milind Karve5, Dilip S. Arora6,
Manoj Sharma7, Elizabeth Pielsticker8, Aaron D. Berman9, Daniel Lee10, M. Imran Qureshi11, Lorenzo Azzalini12, Devraj Sukul3, Hitinder S. GurmID3* 1 Division of Cardiology, Berne Cardiovascular Research Center and Heart and Vascular Center, School of
Medicine, University of Virginia, Charlottesville, Virginia, United States of America, 2 Deparment of Medicine,
Università Milano-Bicocca, Milan, Italy, 3 Department of Internal Medicine, Division of Cardiovascular
Medicine, University of Michigan, Ann Arbor, Michigan, United States of America, 4 McLaren Flint Cardiology,
Flint, Michigan, United States of America, 5 Division of Cardiology, Sparrow Health, Lansing, Michigan,
United States of America, 6 Corewell Health South Lakeland, St Joseph, Michigan, United States of America,
7 Division of Cardiology, Covenant HealthCare, Saginaw, Michigan, United States of America, 8 Heart and
Vascular Service Line, Henry Ford-Jackson, Jackson, Michigan, United States of America, 9 Division of
Cardiology, Corewell Health William Beaumont University Hospital, Royal Oak, Michigan, United States of
America, 10 McLaren Bay Heart and Vascular, Bay City, Michigan, United States of America, 11 Division of
Cardiology, DMC Sinai Grace Hospital, Detroit, Michigan, United States of America, 12 Department of
Medicine, Division of Cardiology, University of Washington, Seattle, Washington, United States of America a1111111111
a1111111111
a1111111111
a1111111111
a1111111111 * hgurm@med.umich.edu Background Mortality is the most devastating complication of percutaneous coronary interventions
(PCI). Identifying the most common causes and mechanisms of death after PCI in contem-
porary practice is an important step in further reducing periprocedural mortality. PLOS ONE PLOS ONE Conclusions In-hospital mortality after PCI is rare, and primarily related to pre-existing critical acute car-
diovascular condition. However, approximately 10% of deaths were preventable. Further
research is needed to characterize preventable deaths, in order to develop strategies to
improve procedural safety. Results A total of 1,163 deaths after PCI were included in the study. Mean age was 71±13 years,
and 507 (44%) were women. Left ventricular failure was the most common cause of death
(52% of cases). The circumstance of death was most commonly related to prior acute 1 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 PLOS ONE Statewide analysis of 1,163 deaths following PCI cardiovascular condition (61% of cases). Procedural complications were considered contrib-
uting to mortality in 235 (20%) cases. Death was rated as not preventable or slightly prevent-
able in 1,045 (89.9%) cases. The majority of the deaths occurred in intermediate or high-risk
patients, but 328 (28.2%) deaths occurred in low-risk patients (<5% predicted risk of mortal-
ity). PCI was considered rarely appropriate in 30% of preventable deaths. Funding: The author(s) received no specific
funding for this work. Funding: The author(s) received no specific
funding for this work. Competing interests: I have read the journal’s
policy and the authors of this manuscript have the
following competing interests: Dr. Azzalini received
consulting fees from Teleflex, Abiomed, GE
Healthcare, Asahi Intecc, Philips, Abbott Vascular,
Reflow Medical, and Cardiovascular Systems, Inc.;
is on the advisory board of GE Healthcare; and
owns equity in Reflow Medical. Devraj Sukul
reports no relevant financial disclosures. Hitinder
Gurm receives research support from Blue Cross
and Blue Shield of Michigan. He is the co-founder
of, owns equity in, and is a consultant to Amplitude
Vascular Systems. He also owns equity in Jiaxing
Bossh Medical Technology Partnership and is a
consultant for Osprey Medical. He is the chair of
the Clinical Events Committee for the
PERFORMANCE trial sponsored by Contego
Medical. All other authors have nothing to disclose. This does not alter our adherence to PLOS ONE
policies on sharing data and materials. Introduction Percutaneous Coronary Intervention (PCI) is one of the most common procedures performed
in the United States and worldwide [1]. Although uncommon, periprocedural mortality is the
most serious complication of the procedure. Early experience with PCI in the 1990s suggested
that most patients who died after the intervention had experienced a procedural complication
[2]. This observation supported the use of periprocedural mortality as a surrogate marker for
procedural quality in PCI. Several states have thus implemented public reporting of clinical
outcomes after PCI. While advocates suggest that public reporting increases transparency and
may improve outcomes in cardiovascular care, others suggest that it may foster unwanted con-
sequences such as the adoption of risk-averse practices which may ultimately prevent patients
from receiving procedures that are indicated and potentially lifesaving [3,4]. Abbreviations: PCI, percutaneous coronary
intervention; BMC2, Blue Cross, Blue Shield of
Michigan Cardiovascular Consortium; HIPAA,
Health Insurance Portability and Accountability Act
of 1996; IRB, institutional review board; ASD,
Absolute Standardized Difference. To add to the controversy, more recent data using standardized, validated approaches to
root-cause analysis in the setting of contemporary practice, have shown that periprocedural
mortality after PCI is rarely the direct result of a procedural complication, whereas, in most
instances, it is due to the increased acuity and comorbid conditions of patients treated in the
catheterization laboratory [5,6]. However, a small number of deaths were deemed preventable. The aim of the present work was to systematically review the causes, circumstances and pre-
ventability of death after PCI in a large, state-wide cohort using a validated approach to (1)
assess the risks associated with the procedure itself and (2) identify the most common causes
of death, with the overarching goal of promoting further research aimed at improving the
overall safety of PCI. Data abstraction, cause, circumstance and preventability of death
adjudication Each mortality event was independently reviewed locally by either committee of interventional
cardiologists or an operator other than the one who performed the original procedure using stan-
dardized forms provided by the BMC2 coordinating site. Anonymized case review data were sub-
sequently forwarded to a central database for subsequent analysis purpose. Each review
encompassed 4 major evaluations for each case: appropriateness of the indication to perform PCI,
cause of death, circumstance of death, and preventability of death. The appropriateness of PCI
indication was evaluated according to intersocietal Appropriate Use Criteria for Coronary Revas-
cularization that were available at that time, as well as consideration of additional clinical data that
may be relevant in categorizing appropriateness [9]. Briefly, the indication to PCI was categorized
as “appropriate”, “may be appropriate” or “rarely appropriate” according to guideline indication. Cause of death was determined to be ventricular failure, arrhythmic, neurological, respira-
tory, infectious, hemorrhagic/vascular, or “other” for each patient, in accordance to previously
validated methods [5]. The cause of death was defined as the precipitating factor for the
patient’s demise, independent of the presenting problem on admission. In case the reviewing
committee felt unable to attribute death to a single cause, more than one cause could be listed. Death was ascribed to one or more of the following circumstances [5]: 1. Procedural complication: new disease state or acute worsening of a pre-existing disease
state directly attributable to the procedure (e.g., coronary perforation). 2. Pre-existing acute cardiovascular cause: new cardiovascular diagnosis within the 14 days
before PCI which was not worsened by the procedure (e.g., acute myocardial infarction). 3. Pre-existing chronic cardiovascular cause: pre-existing cardiovascular condition diagnosed
>14 days before PCI which was not acutely worsened by the procedure (e.g., chronic heart
failure). 4. Pre-existing, non-cardiovascular cause: pre-existing non-cardiovascular condition, either
acute or chronic (e.g., cancer). 5. Post-procedural complication: event occurring during the hospital stay, after the procedure
and not related to it (e.g., ventilator-associated pneumonia). Table 1 summarizes causes and circumstances of death. The preventability of death was
determined by each reviewer based on a thorough review of each patient’s medical record. Pre-
ventability was graded using a previously validated 6-point Likert scale [5]: 0 was defined as an
unpreventable death; 1, slightly preventable; 2, moderately preventable; 3, mostly preventable; 4,
strongly preventable; and 5, entirely or certainly preventable. Study population The original study population included all patients undergoing PCI, between January 2012
and December 2014, at 39 hospitals participating in the Blue Cross, Blue Shield of Michigan
Cardiovascular Consortium (BMC2) Registry who participated in the mortality review pro-
cess. Cases with periprocedural mortality (i.e., mortality during/after PCI during the index
admission) were the focus of the present analysis. The details of BMC2 database were previ-
ously reported [7]. Briefly, the BMC2 is a HIPAA-compliant multi-center, statewide database
collecting anonymized data regarding PCI procedural details and outcomes at all non-federal
hospitals in the state of Michigan. Data is collected by on-site registered nurse coordinators, PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 2 / 12 PLOS ONE Statewide analysis of 1,163 deaths following PCI and includes demographic and clinical characteristics, procedural details, and in-hospital out-
comes of patients undergoing PCI procedures. Data quality and the inclusion of consecutive
procedures is ensured by ad hoc queries, random chart reviews, detailed site audits by an expe-
rienced nurse auditor, and a series of diagnostic routines included in the database. The Univer-
sity of Michigan IRB has waived the need for prior IRB approval for studies performed using
BMC2 data since no patient identifiers are collected [8]. PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 Data abstraction, cause, circumstance and preventability of death
adjudication We defined the concept of pre-
ventability as follows: “including or subsequent to the initial decision to perform cardiac cathe-
terization, the managing physician could have pursued a different treatment plan, thereby
impacting mortality.” This was included in the instructions to reviewers with the data collection
form and provided examples as previously described by Valle and colleagues [5]. An example of 3 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 PLOS ONE Statewide analysis of 1,163 deaths following PCI Table 1. Causes and circumstances of death, as adjudicated by reviewers. Causes of death
Ventricular failure
• Left
• Right
Arrhythmia
Neurological cause
Respiratory failure
Infection
Hemorrhagic/Vascular
Other
Circumstance of death
Procedural complication
New disease state or acute worsening of a pre-existing disease state directly
attributable to the procedure (e.g., coronary perforation). Pre-existing acute
cardiovascular
New cardiovascular diagnosis within the 14 days before PCI which was not
worsened by the procedure (e.g., acute myocardial infarction). Pre-existing, chronic
cardiovascular
Pre-existing cardiovascular condition diagnosed >14 days before PCI which was
not acutely worsened by the procedure (e.g., chronic heart failure). Pre-existing,
noncardiovascular
Pre-existing non-cardiovascular condition, either acute or chronic (e.g., cancer). Post-procedural complication
Event occurring during the hospital stay, after the procedure and not related to it
(e.g., ventilator-associated pneumonia). https://doi.org/10.1371/journal.pone.0297596.t001 https://doi.org/10.1371/journal.pone.0297596.t001 entirely preventable deaths might be air embolization triggering hemodynamic collapse and
death while an unpreventable death might include a patient presenting with out of hospital car-
diac arrest, undergoing successful PCI and subsequently dying from anoxic brain injury. In addition to the aforementioned evaluation, each patient’s “a priori” risk of PCI-associ-
ated mortality was estimated based on pre-procedural clinical characteristics using the vali-
dated BMC2 mortality prediction model [10]. A procedure was considered to be low risk if the
predicted risk of death was <5%. Statistical analysis Continuous variables are reported as mean ± standard deviation, and categorical variables as
number and percentage. The independent-samples Student’s t-test was used to compare con-
tinuous variables with normal distribution, and the Wilcoxon signed rank test was used to
compare continuous variables with a non-normal distribution. Chi-square test was used to
compare differences between categorical variables. To assess differences in baseline covariate
distributions, the Absolute Standardized Difference (ASD) statistic was reported in addition to
the p-value for a statistical comparison [11]. The ASD provides a measure univariate imbal-
ance that is robust to the impact of large sample size seen in statistical testing, where very small
and likely insignificant differences can reach statistical significance (ie p< 0.05) in large sam-
ples. An ASD of 10% was used to identify variables with substantial imbalance between
groups. A 2-tailed p-value <0.05 was considered statistically significant. All analyses were per-
formed with R version 4.1.0 (R Core Team, Vienna, Austria). PLOS ONE Statewide analysis of 1,163 deaths following PCI Table 2. Baseline clinical characteristics. Discharged alive
Deceased (with death review)
P-value
ASD (%)
N
89,922
1,163
Females
29841 (33.2)
507 (43.6)
<0.001
21.50%
Age—mean (SD)
65.11 (11.96)
71.13 (12.85)
<0.001
48.50%
Race/ethnicity:
White (%)
76979 (85.6)
990 (85.1)
0.672
1.40%
Black (%)
10257 (11.4)
147 (12.6)
0.205
3.80%
Asian (%)
932 (1.0)
13 (1.1)
0.899
0.80%
Hispanic origin (%)
1173 (1.3)
23 (2.0)
0.064
5.20%
BMI—mean (SD)
30.61 (7.30)
29.34 (10.38)
<0.001
14.10%
Current smoker (%)
26220 (29.2)
301 (25.9)
0.016
7.30%
Diabetes (%)
34891 (38.8)
524 (45.1)
<0.001
12.70%
Dyslipidemia (%)
73889 (82.2)
785 (67.6)
<0.001
34.30%
Chronic Lung Disease (%)
17369 (19.3)
267 (23.0)
0.002
8.90%
eGFR—mean (SD)
69.80 (24.93)
52.65 (26.50)
<0.001
66.60%
Currently on dialysis (%)
2180 (2.4)
66 (5.7)
<0.001
16.60%
Prior CHF (%)
14936 (16.6)
312 (26.8)
<0.001
25.00%
Prior MI (%)
31807 (35.4)
397 (34.2)
0.408
2.50%
Prior PAD (%)
14559 (16.2)
260 (22.4)
<0.001
15.70%
Prior PCI (%)
41519 (46.2)
370 (31.8)
<0.001
29.80%
Prior CABG (%)
16827 (18.7)
163 (14.0)
<0.001
12.70%
LVEF—mean (SD)
52.01 (12.79)
37.20 (16.94)
<0.001
98.70%
BMI, body mass index; CABG, coronary artery bypass graft; CHF, congestive heart failure; eGFR, estimated glomerular filtration rate; LVEF, left ventricular ejection
fraction; MI, myocardial infarction; PAD, peripheral artery disease; PCI, percutaneous coronary intervention; SD, standard deviation. htt
//d i
/10 1371/j
l
0297596 t002 Table 2. Baseline clinical characteristics. BMI, body mass index; CABG, coronary artery bypass graft; CHF, congestive heart failure; eGFR, estimated glomerular filtration rate; LVEF, left ventricular ejection
fraction; MI, myocardial infarction; PAD, peripheral artery disease; PCI, percutaneous coronary intervention; SD, standard deviation. BMI, body mass index; CABG, coronary artery bypass graft; CHF, congestive heart failure; eGFR, estimated glomerular filtr
fraction; MI, myocardial infarction; PAD, peripheral artery disease; PCI, percutaneous coronary intervention; SD, standard https://doi.org/10.1371/journal.pone.0297596.t002 procedure was 2 days. Average age was 71±13 years, 507 (44%) were women and 85% self-
identified as white. Compared with patients discharged alive, patient who died in the hospital
were significantly older (71±13 vs 65±12 years of age, p<0.001) and were more likely to have
diabetes (45% vs 39%, p<0.001), chronic lung disease (23% vs 19%, p = 0.002), chronic kidney
disease (mean estimated glomerular filtration rate [eGFR] 52 vs 70 ml/min, p<0.001) and had
a history of congestive heart failure (27% vs 17%, p<0.001) or peripheral artery disease (22%
vs 16%, p<0.001). PLOS ONE Notably, patient who died tended to have more impaired left ventricular
function (left ventricular ejection fraction 37±17% vs 52±13%, p<0.001). All baseline clinical
characteristics of the patient population are summarized in Table 2. Patient who died in hospital were more likely to present with acute coronary syndrome:
28% presented with non-ST-elevation myocardial infarction, while 58% presented with ST-ele-
vation myocardial infarction. As expected, the proportion of patients presenting with myocar-
dial infarction was higher among patients who died compared with patients who were
discharged alive (86% vs 37%, p<0.001). The a priori predicted risk of mortality was signifi-
cantly higher among patients who died compared with those who did not (22.9±21.0% vs 1.2
±4.8%, p<0.001). PCI indication and a priori risk are summarized in Table 3. Results Among 91,308 unique PCIs performed during the study period at the 39 centers contributing
to the present analysis, 1,386 deaths occurred, resulting in an overall in-hospital mortality after
PCI of 1.5%. Of these deaths, 1,163 (83.9%) were independently reviewed. Death occurred
within 19 days from the procedure in 95% of cases, and median length of stay after the 4 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 PLOS ONE Table 3. Clinical presentation and procedural characteristics. Discharged alive
Deceased (with death review)
P-value
ASD (%)
N
89,922
1,163
Predicted risk of death (percent)—mean (SD)
1.18 (4.32)
22.99 (21.04)
<0.001
143.60%
CAD Presentation (%)
<0.001
128.60%
No symptom, no angina
3719 (4.1)
29 (2.5)
Symptom unlikely to be ischemic
1986 (2.2)
13 (1.1)
Stable angina
9141 (10.2)
16 (1.4)
Unstable angina
41569 (46.2)
109 (9.4)
NSTEMI
20431 (22.7)
320 (27.5)
STEMI or equivalent
13061 (14.5)
676 (58.1)
Cardiogenic shock on presentation
1559 (1.7)
556 (47.8)
<0.001
1.262
Radial access
22407 (24.9)
96 (8.3)
<0.001
0.46
Left Main PCI (%)
2419 (2.7)
126 (10.8)
<0.001
32.90%
Multivessel PCI (%)
10240 (11.4)
224 (19.3)
<0.001
22.00%
Atherectomy device used (%)
991 (1.1)
22 (1.9)
0.016
6.50%
MCS (%)
<0.001
51.10%
MCS in place at start of procedure
79 (0.1)
24 (2.1)
MCS inserted after PCI has begun
76 (0.1)
59 (5.1)
MCS inserted during procedure and prior to PCI
521 (0.6)
73 (6.3)
No MCS
89246 (99.2)
1007 (86.6)
Aspirin
86793 (96.5)
1042 (89.6)
<0.001
0.275
P2Y12 inhibitor
Clopidogrel
58915 (65.5)
609 (52.4)
<0.001
0.27
Prasugrel
16548 (18.4)
62 (5.3)
<0.001
0.413
Ticagrelor
11209 (12.5)
119 (10.2)
0.025
0.07
GP IIb/IIIa inhibitor
21534 (23.9)
496 (42.6)
<0.001
0.405
Periprocedural anticoagulation
Low molecular weight heparin
2974 (3.3)
36 (3.1)
0.75
0.012
Unfractionated Heparin
68435 (76.1)
992 (85.3)
<0.001
0.235
Bivalirudin
40098 (44.6)
346 (29.8)
<0.001
0.311
Direct thrombin inhibitor (other)
228 (0.3)
5 (0.4)
0.373
0.03
ASD = absolute standardized difference; CAD = coronary artery disease; MCS = mechanical circulatory support; NSTEMI = non-ST elevation myocardial infarction; Table 3. Clinical presentation and procedural characteristics. ASD = absolute standardized difference; CAD = coronary artery disease; MCS = mechanical circulatory support; NSTEMI = non-ST elevation myocardial infarction;
PCI = percutaneous coronary intervention; SD = standard deviation; STEMI = ST elevation myocardial infarction. https://doi.org/10.1371/journal.pone.0297596.t003 (33.5%) cases. The most commonly observed cause of death was left ventricular failure, occur-
ring in 603 (51.8%) of cases. Other common causes of death were fatal arrhythmias in 281
(24.2%) patients, neurologic complications in 207 (17.8%) and respiratory failure, which
occurred in 194 (16.7%) patients (Fig 1). Circumstances of death were considered multifactorial in 345 (29.6%) subjects. h
f d
h
d
d Circumstances of death were considered multifactorial in 345 (29.6%) subjects. Appropriateness of PCI indication, causes, circumstances and
preventability of death PCI indication was considered appropriate, i.e. class I or II according to the appropriate use
criteria, in 1,071 (92.1%) of cases. Cause of death was considered multi-factorial in 390 5 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 Statewide analysis of 1,163 deaths following PCI https://doi.org/10.1371/journal.pone.0297596.t003 PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 PLOS ONE The most common circumstance of death was a pre-existing acute cardiac condition, Circumstances of death were considered multifactorial in 345 (29.6%) subjects. The most common circumstance of death was a pre-existing acute cardiac condition,
which was present in 714 (61.4%) cases. Other common circumstances of death were prior
chronic cardiac condition (in 254 [21.8%] subjects) and prior acute or chronic non-cardiac
conditions (in 262 [22.5%] individuals). Procedural complications were considered to con-
tribute to the circumstance of death in 235 (20.2%) cases. Fig 2 shows circumstances of
death. Death was rated as unpreventable or only slightly preventable in 1,045 (89.9%) of
cases. 6 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 PLOS ONE Statewide analysis of 1,163 deaths following PCI Fig 1. Causes of death in the study population. Each bar represents the percentage of each adjudicated cause of death for the overall population (green) and
stratified per a priori risk of death (blue, low risk i.e. <5% of a priori estimated risk of death and red, non-low risk procedures). LV = left ventricular. https://doi.org/10.1371/journal.pone.0297596.g001 Fig 1. Causes of death in the study population. Each bar represents the percentage of each adjudicated cause of death for the overall population (green) and
stratified per a priori risk of death (blue, low risk i.e. <5% of a priori estimated risk of death and red, non-low risk procedures). LV = left ventricular. https://doi.org/10.1371/journal.pone.0297596.g001 A priori PCI risk and appropriateness, causes, circumstances and
preventability of death According to the validated BMC2 mortality prediction model, 328 (28.2%) deaths occurred
after low-risk procedures. Notably, low-risk PCI were more likely to be rated as rarely appro-
priate (11.0% vs 6.1%, p<0.001). Cause of death in low-risk PCI was less likely to be left ven-
tricular failure compared to non-low risk procedures (41.8% vs 55.8%, p<0.0001). On the
other hand, bleeding and vascular complications were more commonly observed (13.1% vs Fig 2. Circumstances of death in the study population. Each bar represents the percentage of each adjudicated circumstance of death for the overall
population (green bar) and stratified per a priori risk of death (blue, low risk i.e. <5% of a priori estimated risk of death and red, non-low risk procedures). https://doi.org/10.1371/journal.pone.0297596.g002 Fig 2. Circumstances of death in the study population. Each bar represents the percentage of each adjudicated circumstance of death for the overall
population (green bar) and stratified per a priori risk of death (blue, low risk i.e. <5% of a priori estimated risk of death and red, non-low risk procedures). https://doi.org/10.1371/journal.pone.0297596.g002 PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 7 / 12 PLOS ONE Statewide analysis of 1,163 deaths following PCI 5.9%, p = 0.0001). Similarly, circumstances of death were more commonly multifactorial
(39.9% vs 25.6%, p<0.0001), and encompassed prior acute cardiovascular conditions less fre-
quently than non-low risk procedures (45.1% vs 67.8%, p<0.0001). Procedural complications
and post-procedural complications were more common in patients dying after low-risk PCI
(39.0% vs 12.8%, p<0.0001 and 21.9% vs 8.5%, p<0.0001, respectively). In terms of procedural complications, catheter-induced coronary dissection was reported
in 5 (0.4%) cases, while coronary perforation in 3 (0.3%) patients. Bleeding events were
reported in 58 (4.9%) subjects, and only 1 periprocedural stroke was reported. Death was rated as largely preventable more frequently in low-risk interventions compared
to non-low risk procedures (15.8% vs 5.3%, p<0.0001). Preventable deaths after PCI Of the 96 deaths after PCI that were considered largely preventable, 62 (64%) were considered
moderately preventable, 33 (34%) mostly preventable and only 1 death strongly preventable
and attributed to vascular complications related to the intervention. Cause of death was multi-
factorial in 32 (33%) of cases. LV failure remained the most common cause of death, occurring
in approximately 36 (37%) of cases, followed by arrhythmia in 25 (26%) of cases and bleeding
and vascular complications in 22 (23%) of cases. Circumstance of death was most commonly
procedural complications (70% of deaths). Notably, coronary perforation was indicated as the
primary cause of death in 3 patients, while coronary dissection in 4 patients. Post-procedural
complications accounted for 28% of preventable deaths, while non-cardiac causes accounted
for 9%. PCI was considered rarely appropriate in 30% of preventable deaths. Fig 3 shows the
relationship between preventability, appropriateness and a priori estimated risk, while S1 Fig
displays the same relationship in the elective subgroup and S2 Fig displays the relationship in
the emergent subgroup. PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 Discussion The main results of the present work are: 1) in-hospital death after elective PCI is uncommon,
2) death most commonly occurs in patients who present acutely with myocardial infarction,
especially if complicated by shock, and is most commonly secondary to a pre-existing acute
cardiovascular condition, 3) in the vast majority of cases, death was considered unpreventable,
and 4) deaths in low-risk patients undergoing PCI for rarely appropriate indications were
most likely to be preventable. Our findings thus corroborate and extend prior work in two
important ways. Firstly, our findings from a statewide analysis of mortality following PCI confirm work
from other contemporary reports. Our findings are in stark juxtaposition to the early PCI
experience published in the 1990s, when the majority of deaths were ultimately traceable to
procedural complications [2,12]. Indeed, similar to contemporary reports of PCI practice, the
majority of deaths were attributed to pre-existing acute conditions [5,6,13]. In the work by
Valle et al., approximately 92% of the 85 deaths analyzed were not attributable to any proce-
dural factor but either imputable to a pre-existing acute cardiac condition (most commonly, in
approximately 63% of cases) or a post-procedural, noncardiac complication (approximately
16% of cases) [5]. Notably, death was rated as unpreventable or only slightly preventable in
69% of cases [5]. Moroni et al. recently reported similar findings in a cohort of 166 subjects
[13]. Notably, in the latter study 93% of subjects had presented with acute myocardial infarc-
tion, and 45% were in overt shock at the time of the procedure [13]. Indeed, the majority of
deaths were unpreventable or slightly preventable, and secondary to pre-existing acute cardio-
vascular conditions. [13] Finally, Bricker et al. reported on 1,674 deaths in the 30-day period PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 8 / 12 PLOS ONE Statewide analysis of 1,163 deaths following PCI Fig 3. Relation between preventability, appropriateness and a priori estimate of the risk of death. Each dot represent a single case. Adjudicated
preventability of death is plotted on the x-axis as an ordinal variable (from unpreventable to mostly preventable). A priori the risk of death using the BMC2
model is plotted on the y-axis. Inappropriate PCI indications are indicated by a red dot, while non-inappropriate cases are in light blue. The underlying
box plot shows median (thick line), interquartile range (box) and range (whiskers) of the distribution of estimated risk of mortality. PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 Discussion Median and interquartile
range are reported as explicit numbers at the bottom of the plot. BMC2, Blue Cross Blue Shield of Michigan; IQR, interquartile range. Fig 3. Relation between preventability, appropriateness and a priori estimate of the risk of death. Each dot represent a single case. Adjudicated
preventability of death is plotted on the x-axis as an ordinal variable (from unpreventable to mostly preventable). A priori the risk of death using the BMC2
model is plotted on the y-axis. Inappropriate PCI indications are indicated by a red dot, while non-inappropriate cases are in light blue. The underlying
box plot shows median (thick line), interquartile range (box) and range (whiskers) of the distribution of estimated risk of mortality. Median and interquartile
range are reported as explicit numbers at the bottom of the plot. BMC2, Blue Cross Blue Shield of Michigan; IQR, interquartile range. https://doi.org/10.1371/journal.pone.0297596.g003 https://doi.org/10.1371/journal.pone.0297596.g003 https://doi.org/10.1371/journal.pone.0297596.g003 following PCI [6]. In an experience from the Veteran Affairs Healthcare System, up to 74% of
deaths were considered unpreventable, and only one-third were attributable to cardiac causes. Only 8% were traceable to a procedural complication [6]. Our results confirm and expand
findings from previous literature. First, our study population was very large, comparable to
that of Bricker et al., but encompassed a higher proportion of female subject, and encompassed
institutions varying from tertiary referral centers, academic centers and community hospitals
contributing to the generalizability of our results. Second, while uncommon, preventable deaths do occur and a significant proportion
(approximately 30%) of preventable deaths occurred in procedures that were deemed to be of
low value and could potentially be avoided. In proportion, preventable deaths were more likely 9 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 PLOS ONE Statewide analysis of 1,163 deaths following PCI to occur in the setting of procedural complications. Notably, however, coronary perforation,
which is among the most dreaded PCI complication, was exceedingly rare, as previously
reported [14]. These data suggest that systems focusing on optimizing appropriateness of PCI
might be an effective strategy to reduce preventable deaths from PCI. Discussion In addition, deaths in
patients deemed to be of low predicted risk of mortality were more likely to have a higher like-
lihood of being preventable and a targeted assessment of such procedures might be more effec-
tive at optimizing procedural safety than a broader approach of reviewing all deaths at
mortality and morbidity conferences that is commonly followed in many hospitals. Along
those same lines, risk guided approaches might be also impactful for guiding regional and
national focused quality efforts and research studies. Finally, given the infrequent occurrence
of preventable death, our data support a more nuanced approach to using mortality for public
reporting and ranking institutions on quality [15]. Limitations The present work does have some limitations that need to be acknowledged. First, approxi-
mately 16% of death cases within the study period were not included in the analysis, due to
inability of some centers to develop the appropriate process for case review. Second, case
review and preventability of death adjudication were performed locally, which may have intro-
duced some heterogeneity in the classification of deaths. The use of centrally generated, stan-
dardized forms as well as centralized training on root-cause analysis and event adjudication
may have mitigated the latter. Our data originate from a State with a strong culture of quality
improvement and collaboration and may or may not be directly applicable to all types of clini-
cal practice patterns [16]. Finally, some of the data has been collected and generated close to a
decade ago, which may not fully reflect contemporary practice and indications for PCI. Conclusion In-hospital mortality after PCI is rare, and mainly secondary to pre-existing critical acute con-
dition, with procedural complications being a contributing factor in one-fifth of cases. How-
ever, 10% of deaths were considerate preventable, and was often observed in patients
undergoing low risk procedures deemed to be poorly rated on appropriateness. Our data sup-
port further research to characterize preventable deaths in order to develop strategies to fur-
ther enhance procedural safety. Supporting information S1 Fig. Estimated baseline mortality risk by preventability: Elective PCI. This plot shows
median (thick line), interquartile range (box) and range (whiskers) of the distribution of esti-
mated risk of mortality among the subset of patients undergoing elective percutaneous coro-
nary intervention (PCI). Each dot represents a single case. Adjudicated preventability of death
is plotted on the x-axis as an ordinal variable (from unpreventable to mostly preventable). A
priori the risk of death using the BMC2 model is plotted on the y-axis. Inappropriate PCI indi-
cations are indicated by a red dot, while non-inappropriate cases are in light blue. Median and
interquartile range for the a priori risk of death are reported as explicit numbers at the bottom
of the plot. BMC2, Blue Cross Blue Shield of Michigan; IQR, interquartile range. (DOCX) S2 Fig. Estimated baseline mortality risk by preventability rating: Acute coronary syn-
drome. This plot shows median (thick line), interquartile range (box) and range (whiskers) of
the distribution of estimated risk of mortality among the subset of patients undergoing 10 / 12 PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 PLOS ONE Statewide analysis of 1,163 deaths following PCI percutaneous coronary intervention (PCI) for an urgent or emergent indication, including
acute coronary syndromes, cardiogenic shock and cardiac arrest. Each dot represents a single
case. Adjudicated preventability of death is plotted on the x-axis as an ordinal variable (from
unpreventable to mostly preventable). A priori the risk of death using the BMC2 model is plot-
ted on the y-axis. Inappropriate PCI indications are indicated by a red dot, while non-inappro-
priate cases are in light blue. Median and interquartile range for the a priori risk of death are
reported as explicit numbers at the bottom of the plot. BMC2, Blue Cross Blue Shield of Michi-
gan; IQR, interquartile range. (DOCX) Writing – original draft: Francesco Moroni, Milan Seth. Writing – original draft: Francesco Moroni, Milan Seth. Writing – review & editing: Milan Seth, Hameem U. Changezi, Milind Karve, Dilip S. Arora,
Manoj Sharma, Elizabeth Pielsticker, Aaron D. Berman, Daniel Lee, M. Imran Qureshi, Writing – review & editing: Milan Seth, Hameem U. Changezi, Milind Karve, Dilip S. Arora,
Manoj Sharma, Elizabeth Pielsticker, Aaron D. Berman, Daniel Lee, M. Imran Qureshi, Lorenzo Azzalini, Devraj Sukul, Hitinder S. Gurm. Lorenzo Azzalini, Devraj Sukul, Hitinder S. Gurm. Lorenzo Azzalini, Devraj Sukul, Hitinder S. Gurm. Lorenzo Azzalini, Devraj Sukul, Hitinder S. Gurm. Conceptualization: Hameem U. Changezi. Conceptualization: Hameem U. Changezi. Formal analysis: Milan Seth. Methodology: Milan Seth. Methodology: Milan Seth. Visualization: Milan Seth. Visualization: Milan Seth. Visualization: Milan Seth. Writing – original draft: Francesco Moroni, Milan Seth. References ACCF/SCAI/STS/
AATS/AHA/ASNC/HFSA/SCCT 2012 appropriate use criteria for coronary revascularization focused
update: a report of the American College of Cardiology Foundation Appropriate Use Criteria Task PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 11 / 12 PLOS ONE Statewide analysis of 1,163 deaths following PCI Force, Society for Cardiovascular Angiography and Interventions, Society of Thoracic Surgeons, Ameri-
can Association for Thoracic Surgery, American Heart Association, American Society of Nuclear Cardi-
ology, and the Society of Cardiovascular Computed Tomography. J Thorac Cardiovasc Surg. 2012;
143(4):780–803. https://doi.org/10.1016/j.jtcvs.2012.01.061 PMID: 22424518. Force, Society for Cardiovascular Angiography and Interventions, Society of Thoracic Surgeons, Ameri-
can Association for Thoracic Surgery, American Heart Association, American Society of Nuclear Cardi-
ology, and the Society of Cardiovascular Computed Tomography. J Thorac Cardiovasc Surg. 2012;
143(4):780–803. https://doi.org/10.1016/j.jtcvs.2012.01.061 PMID: 22424518. Force, Society for Cardiovascular Angiography and Interventions, Society of Thoracic Surgeons, Ameri-
can Association for Thoracic Surgery, American Heart Association, American Society of Nuclear Cardi-
ology, and the Society of Cardiovascular Computed Tomography. J Thorac Cardiovasc Surg. 2012;
143(4):780–803. https://doi.org/10.1016/j.jtcvs.2012.01.061 PMID: 22424518. 10. 10. Gurm HS, Seth M, Kooiman J, Share D. A novel tool for reliable and accurate prediction of renal compli-
cations in patients undergoing percutaneous coronary intervention. J Am Coll Cardiol. 2013; 61
(22):2242–8. https://doi.org/10.1016/j.jacc.2013.03.026 PMID: 23721921. 11. Austin PC. Balance diagnostics for comparing the distribution of baseline covariates between treatment
groups in propensity-score matched samples. Stat Med. 2009; 28(25):3083–107. https://doi.org/10. 1002/sim.3697 PMID: 19757444; PubMed Central PMCID: PMC3472075. 12. Rathore S, Grayson AD, Sastry S, Gray TP, Beynon R, Jackson M, et al. Circumstances and mode of
in-hospital death following 9,914 consecutive patients undergoing percutaneous coronary interventions
in the northwest of England. J Invasive Cardiol. 2008; 20(8):386–90. Epub 2008/08/09. PMID:
18688060. 13. Moroni F, Gurm HS, Gertz Z, Abbate A, Azzalini L. In-Hospital Death Among Patients Undergoing Per-
cutaneous Coronary Intervention: A Root-Cause Analysis. Cardiovasc Revasc Med. 2022; 40s:8–13. Epub 20220226. https://doi.org/10.1016/j.carrev.2022.01.021 PMID: 35232664. 14. Rakowski T, Węgiel M, Siudak Z, Plens K, Dziewierz A, Birkemeyer R, et al. Prevalence and Predictors
of Coronary Artery Perforation During Percutaneous Coronary Interventions (from the ORPKI National
Registry in Poland). Am J Cardiol. 2019; 124(8):1186–9. Epub 20190725. https://doi.org/10.1016/j. amjcard.2019.07.021 PMID: 31439282. 15. Sukul D, Bhatt DL, Seth M, Zakroysky P, Wojdyla D, Rumsfeld JS, et al. Appropriateness and Out-
comes of Percutaneous Coronary Intervention at Top-Ranked and Nonranked Hospitals in the United
States. JACC Cardiovasc Interv. 2018; 11(4):342–50. Epub 20171112. https://doi.org/10.1016/j.jcin. PLOS ONE | https://doi.org/10.1371/journal.pone.0297596
March 27, 2024 References 1. Tsao CW, Aday AW, Almarzooq ZI, Alonso A, Beaton AZ, Bittencourt MS, et al. Heart Disease and
Stroke Statistics-2022 Update: A Report From the American Heart Association. Circulation. 2022; 145
(8):e153–e639. Epub 20220126. https://doi.org/10.1161/CIR.0000000000001052 PMID: 35078371. 2. Malenka DJ, O’Rourke D, Miller MA, Hearne MJ, Shubrooks S, Kellett MA, Jr., et al. Cause of in-hospital
death in 12,232 consecutive patients undergoing percutaneous transluminal coronary angioplasty. The
Northern New England Cardiovascular Disease Study Group. Am Heart J. 1999; 137(4 Pt 1):632–8. Epub 1999/05/01. https://doi.org/10.1016/s0002-8703(99)70215-2 PMID: 10223894. 3. Hannan EL, Kilburn H, Racz M Jr., Shields E, Chassin MR. Improving the outcomes of coronary artery
bypass surgery in New York State. Jama. 1994; 271(10):761–6. PMID: 8114213. 4. Narins CR, Dozier AM, Ling FS, Zareba W. The influence of public reporting of outcome data on medical
decision making by physicians. Arch Intern Med. 2005; 165(1):83–7. https://doi.org/10.1001/archinte. 165.1.83 PMID: 15642879. 5. Valle JA, Smith DE, Booher AM, Menees DS, Gurm HS. Cause and circumstance of in-hospital mortal-
ity among patients undergoing contemporary percutaneous coronary intervention: a root-cause analy-
sis. Circ Cardiovasc Qual Outcomes. 2012; 5(2):229–35. Epub 2012/03/01. https://doi.org/10.1161/
CIRCOUTCOMES.111.963546 PMID: 22373903. 6. Bricker RS, Valle JA, Plomondon ME, Armstrong EJ, Waldo SW. Causes of Mortality After Percutane-
ous Coronary Intervention. Circ Cardiovasc Qual Outcomes. 2019; 12(5):e005355. Epub 2019/05/21. https://doi.org/10.1161/CIRCOUTCOMES.118.005355 PMID: 31104472. 7. Kline-Rogers E, Share D, Bondie D, Rogers B, Karavite D, Kanten S, et al. Development of a multicen-
ter interventional cardiology database: the Blue Cross Blue Shield of Michigan Cardiovascular Consor-
tium (BMC2) experience. J Interv Cardiol. 2002; 15(5):387–92. https://doi.org/10.1111/j.1540-8183. 2002.tb01072.x PMID: 12440182. 8. Gurm HS, Seth M, Dixon S, Kraft P, Jensen A. Trends in Contrast Volume Use and Incidence of Acute
Kidney Injury in Patients Undergoing Percutaneous Coronary Intervention: Insights From Blue Cross
Blue Shield of Michigan Cardiovascular Collaborative (BMC2). JACC Cardiovasc Interv. 2018; 11
(5):509–11. https://doi.org/10.1016/j.jcin.2017.10.018 PMID: 29519389. 9. Patel MR, Dehmer GJ, Hirshfeld JW, Smith PK, Spertus JA, Masoudi FA, et al. References 2017.10.042 PMID: 29471947. 16. Share DA, Campbell DA, Birkmeyer N, Prager RL, Gurm HS, Moscucci M, et al. How a regional collabo-
rative of hospitals and physicians in Michigan cut costs and improved the quality of care. Health Aff (Mill-
wood). 2011; 30(4):636–45. https://doi.org/10.1377/hlthaff.2010.0526 PMID: 21471484. 12 / 12
|
https://openalex.org/W4293427773
|
https://www.researchsquare.com/article/rs-1298140/latest.pdf
|
English
| null |
Fine mapping of a recessive leaf rust resistance locus on chromosome 2BS in wheat accession CH1539
|
Molecular breeding
| 2,022
|
cc-by
| 7,972
|
Research Article Keywords: Wheat, Leaf rust, Seedling resistance, Fine-mapping
Posted Date: February 7th, 2022
DOI: https://doi.org/10.21203/rs.3.rs-1298140/v1
License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full
License Page 1/20 Page 1/20 Page 1/20 Page 1/20 Abstract Leaf rust, caused by Puccinia triticina (Pt), is one of the most important fungal diseases of wheat worldwide. The
wheat accession CH1539 showed a high level of resistance to leaf rust. A mapping population of 184 recombinant
inbred lines (RILs) was developed from a cross between the resistant accession CH1539 and the susceptible
cultivar SY95-71. The RILs showed segregating infection responses to Puccinia triticina Eriks. (Pt) race THK at the
seedling stage. Genetic analysis showed that leaf rust resistance was controlled by a monogenic gene, and the
potential locus was temporarily named LrCH1539. Bulked segregant analysis (BSA) using a 35K DArTseq array
located LrCH1539 on the short arm of chromosome 2B. Subsequently, a genetic linkage map of LrCH1539 was
constructed using the developed 2BS chromosome-specific markers, and its flanking markers were sxau-2BS136
and sxau-2BS81. An F2 subpopulation with 3619 lines was constructed by crossing the resistant and susceptible
lines selected from the RIL population. The inoculation identification results showed that LrCH1539 was
recessively inherited and was fine-mapped to a 779.4-kb region between markers sxau-2BS47 and sxau-2BS255 at
the end of 2BS. The linkage marker analysis showed that the positions of LrCH1539 and Lr16 were the same, but
the identification results of the resistance spectrum indicated that the causal genes of the two might be different. The resistant materials reported in this study and the cosegregation marker can be used for marker-assisted
selection breeding of leaf rust-resistant wheat cultivars. Introduction In this study, genetic analysis was performed on the resistance of the RIL Page 2/20 Page 2/20 constructed by CH1539 and a susceptible parent using the race THK. BSA combined with a wheat DArTseq array
was used to determine the gene locus of resistance to leaf rust; a subpopulation was constructed to fine map this
gene, and a cosegregation marker was developed to better use the germplasm. constructed by CH1539 and a susceptible parent using the race THK. BSA combined with a wheat DArTseq array
was used to determine the gene locus of resistance to leaf rust; a subpopulation was constructed to fine map this
gene, and a cosegregation marker was developed to better use the germplasm. Plant materials and Pt races An RIL mapping population containing 184 F2:10 lines was developed from the cross between the resistant
accession CH1539 and the susceptible cultivar SY95-71. The accession CH1539 developed by the College of
Agriculture, Shanxi Agricultural University (Shanxi Key Laboratory of Crop Genetics and Molecular Improvement)
has a high level of resistance to leaf rust, and the wheat cultivar SY95-71 developed in the 1990s by the Wheat
Research Institute of Sichuan Agricultural University is susceptible to prevalent Pt races in China. The susceptible
control is Mingxian 169. Additionally, a high-resolution mapping population comprising 3619 F2 plants was
constructed by crossing resistant line #36 and susceptible line #4 of the RIL population. The wheat cultivar Selkirk was donated by Wentao Zhang, Gansu Academy of Agricultural Sciences, and RL6005
was provided by Dr. Minjie Liu, College of Plant Protection, Shanxi Agricultural University, China. A set of core
germplasms containing 262 wheat varieties that are widely used in Chinese breeding programs (Chen et al. 2020)
was used to detect the frequency of the LrCH1539 allele. The pathotype of P. triticina was collected from the wheat-growing region in northern China through single spore
separation and pure culturing. The Pt race was designated according to the system of Long and Kolmer (1989)
and provided by Dr. Minjie Liu. A total of 31 races were used in the experiment (Table S1). The avir/vir formulas for
THK were as follows: Lr3ka, Lr9, Lr13, Lr14b, Lr18, Lr21, Lr24, Lr25, Lr28, Lr29, Lr38/Lr1, Lr2a, Lr2b, Lr2c, Lr3,
Lr3bg, Lr10, Lr11, Lr12, Lr14a, Lr15, Lr16, Lr17, Lr20, Lr22a, Lr22b, Lr23, Lr26, Lr30, Lr32, Lr33, Lr36 and Lr39. Introduction Leaf rust, caused by Puccinia triticina Eriks. (Pt), is a worldwide disease of wheat (Huerta-Espino et al. 2011;
Kolmer 2005). It occurs more frequently than other rusts and is more common worldwide (Ellis et al. 2014). In
recent years, leaf rust has become an increasingly significant disease in the major wheat production regions of
China (Li et al. 2014; Zhang et al. 2020), and more than 15 million hectares of wheat are affected by leaf rust
annually (Gao et al. 2019). The use of disease-resistant cultivars is the most efficient and environmentally friendly
way to prevent yield losses from this disease worldwide (Pink 2002). To date, 80 permanently named and numerous temporarily designated leaf rust resistance genes (Lr genes) and
quantitative trait loci (QTLs) have been reported in wheat (Kumar et al. 2021). Although the number of designated
Lr genes is increasing annually, new LR races with new virulence(s) that can overcome some of these Lr genes will
likely occur (Ren et al. 2015). Lr genes such as Lr1, Lr3, Lr3bg, Lr10, Lr11, Lr14a, Lr16, and Lr26, which are
common in Chinese wheat cultivars, have been nearly ineffective when applied alone (Gao et al. 2019; Li et al. 2010; Zhao et al. 2013). Therefore, to ensure the genetic resistance of wheat, it is essential to identify new or
effective resistance genes in different germplasms of wheat varieties or related species worldwide. Meanwhile, fully use the discovered resistance resources and improve the efficiency of breeding selection, it is
necessary to develop more effective selection markers for resistance genes, which will also lay the foundation for
cloning genes and studying their resistance mechanisms. Currently, only few race-specific seedling resistance
genes (including Lr1, Lr10, Lr14a, and Lr21) and few adult plant resistance genes (including Lr22a, Lr34, and Lr67)
have been cloned (Cloutier et al. 2007; Feuillet et al. 2003; Huang et al. 2003; Kolodziej et al. 2021; Krattinger et al. 2009; Moore et al. 2015; Thind et al. 2017). The remaining large number of leaf rust resistance genes/QTLs have
not been finely mapped and cannot be efficiently used in marker-assisted selection (MAS). The wheat accession CH1539 developed by our laboratory has shown a high level of resistance to leaf rust in the
field environment for many years. Testing for seedling reactions In the greenhouse, resistance identification of the tested material and the susceptible control Mingxian 169 was
carried out using Pt races at the seedling stage. Seeds were planted in a plastic growth chamber with five plants
for each line and repeated twice. When the first leaves were fully expanded, inoculations were performed by
dusting with urediniospores. Inoculated seedlings were subsequently incubated in the dark at 18°C and 100%
relative humidity (RH) for 24 h. The seedlings were then placed in a growth chamber at 16-21°C and 70% RH. The
infection types (ITs) were scored approximately 14 days later based on the 0-4 Stakman Scale modified by Roelfs
et al. (1992). ITs: 0 = no visible symptoms; necrotic or chlorotic flecks without any uredinia; 1 = small uredinia
surrounded by necrosis; 2 = small to medium uredinia surrounded by chlorotic or necrosis; 3 = medium-sized
uredinia without chlorosis or necrosis; 4 = large-sized uredinia without chlorosis or necrosis. “+” and “-” were used
when uredinia were somewhat larger or smaller than normal for the ITs. ITs of 0-2 and 3-4 were considered
resistant and susceptible, respectively (Kertho et al. 2015). A chi-square (χ2) test was used to determine whether the observed segregation ratio of the phenotypic data fits the
expected genetic ratios. The χ2 analysis was performed in Microsoft Excel (version 2010) using the ‘chitest’
function to calculate the χ2 and p-value. DNA extraction and bulk segregant analysis (BSA) DNA extraction and bulk segregant analysis (BSA) Page 3/20 Page 3/20 The genomic DNA of all tested wheat lines was extracted using a modified CTAB method (Hill-Ambroz et al. 2002)
and detected by 1% agarose electrophoresis. The concentration was measured, and the DNA samples were diluted
to a final concentration of 50 ng/µL and stored at -20°C for later use. BSA was performed to determine the chromosomal location of leaf rust resistance in CH1539. Equal amounts of
DNA from 21 homozygous resistant RILs (HR, ITs: 0-1) and 21 homozygous susceptible RILs (HS, ITs: 3-4) were
pooled to constitute the respective resistant and susceptible bulks. The two parents and bulks were genotyped with
the wheat 35K DArTseq array (Diversity Arrays Technology Pty Ltd). Polymorphic SNPs between parents were
considered to be associated with LrCH1539 when the score values of resistant bulk and CH1539, susceptible bulk
and SY95-71 were consistent. The sequences of DArTseq markers linked to resistance were blasted against the
genome assembly of T. aestivum cv. Chinese Spring (CS) [International Wheat Genome Sequencing Consortium
(IWGSC) RefSeq v1.0, https://urgi.versailles.inra.fr/download/iwgsc/IWGSC_RefSeq_Annotations/v1.0/] (IWGSC
2018) to obtain their physical positions. SSR marker assays and genotyping Based on the results of polymorphic SNPs in the array, the specific-chromosome SSR primers were developed and
named with the prefix “sxau” (Shanxi Agricultural University) followed by a consecutive number. A total of 157
designed markers and twelve markers linked with known Lr genes were used to screen the parents and bulks to
confirm their polymorphism before genotyping the entire RIL population, and the screened markers were then used
to construct a linkage map. Another 120 specific chromosome markers were also designed for fine mapping
LrCH1539. Information of the markers located on the linkage map in this paper is listed in Table S2. PCR amplification was performed on a C1000 Touch thermal cycler. The PCR amplification reaction mixture
volume was 10 µL: 5.0 µL of 2×Taq PCR Master Mix (Tiangen Biochemical Incorporation, Beijing), 2.0 µL of ddH2O,
1.0 µL (2 mmol/µL) of each primer, and 1.0 µL (50 ng/µL) of DNA template. PCR amplification program: pre-
denaturation at 94°C for 5 min; denaturation at 94°C for 30 s, renaturation at 55-68°C (determined by the annealing
temperature of each primer) for 30 s, extension at 72°C for 60 s, a total of 35 cycles; final extension at 72°C for 10
min and preservation at 12°C. The PCR amplification products were detected by electrophoresis through 8%
nondenaturing polyacrylamide gels (the mass ratio of Acr to Bis was 29:1) for 50-70 min. After silver nitrate
staining and formaldehyde solution dyeing, the results were photographically observed. Genetic linkage map and gene annotation The linkage map for the CH1539/SY95-71 RIL population was constructed using the JoinMap v4.0 software
(www.kyazma.nl), and the Kosambi map function was used to convert recombination rates to centimorgans
(Kosambi 1943). A logarithm of odds (LOD) of 3.0 was set to declare genetic linkages. MapDraw V2.1 was used to
draw the linkage map (Liu and Meng 2003). The flanking markers were subjected to BLAST against IWGSC RefSeq v1.0 to obtain the physical location of the
target gene. Then, gene annotation of the refined LrCH1539 interval was retrieved from the above mentioned
IWGSC RefSeq v1.0. Expression data for the genes in leaf tissues and under pathogen treatment were obtained
using the Wheat Expression Browser database (http://www.wheat-expression.com, Ramírez-González et al. 2018). The reaction of parents and RILs to Pt races The parents CH1539 and SY95-71 and the RIL population were evaluated for their reactions to the Pt race THK at
the seedling stage. CH1539 developed hypersensitive flecks with small- to medium-sized uredinia to the race THK,
indicating a highly resistant reaction (Fig. 1); however, SY95-71 developed large-sized uredinia without chlorosis to
THK, indicating a highly susceptible reaction (Fig. 1). The susceptible Mingxian 169 developed large-sized uredinia
without chlorosis (Fig. 1). Meanwhile, the RILs were segregated for their reaction to THK, and the reactions ranged from highly resistant
(IT=;1) to highly susceptible (IT=4). Of the 184 RILs evaluated, 86 (two missing data) and 91 lines were resistant,
and 96 and 93 lines were susceptible in the two duplications, respectively. The segregation of resistant and
susceptible RILs fit a single gene segregation ratio of 1:1 (Table 1). Through the phenotypic analysis of the three
groups of F2 subpopulations, the separation of resistant lines and susceptible lines conformed to a separation
ratio of 1:3 (Table 1), indicating that the resistance of CH1539 to Pt race THK is controlled by a single recessive
gene, tentatively named LrCH1539. Table 1
The number of plants in response to Pt race THK in RILs derived from the cross CH1539 × SY95-71 and three F2
groups (F2-1, F2-2, F2-3) derived from the cross lines #36 × #4. Group
Resistance reaction
Theoretical ratio (R:S)
χ2
P value
R
S
RILs-rep1
86
96
1:1
0.71
0.60
RILs-rep2
91
93
1:1
3.00
0.91
F2-1
38
128
1:3
0.88
0.65
F2-2
126
370
1:3
2.47
0.88
F2-3
64
199
1:3
2.17
0.86
The infection type (IT) was scored in a 0-4 scale (Roelfs et al. 1992). IT 0-2, resistant; IT 3-4, susceptible. χ2
(0.05, 1) = 3.841. Molec lar Mapping of LrCH1539 Table 1 The infection type (IT) was scored in a 0-4 scale (Roelfs et al. 1992). IT 0-2, resistant; IT 3-4, susceptible. χ2
(0.05, 1) = 3.841. A total of 106 SNPs showed polymorphisms between the DNA bulks after genotyping by the 35K DArTseq array. According to the physical location of the polymorphic SNPs, 60 (56.6%) of these SNPs were located on
chromosome 2B, and no more than 11 (10.4%) were located on other single chromosomes (Fig. 2A). These results
indicated that SNPs in 2B were extremely likely to be associated with the resistance locus. Result Page 4/20 Page 4/20 Fine mapping of LrCH1539 To narrow down the region containing LrCH1539, we generated 3619 F2 individuals to screen for new crossovers
between sxau-2BS81 and sxau-2BS136, and 33 crossovers were identified. Among the 33 crossovers, 12 showed
recombination between the marker sxau-2BS136 and LrCH1539, while 21 showed recombination between the
marker sxau-2BS81 and LrCH1539. Based on the 2.4 Mb interval of CS RefSeq v1.0, more primers were designed
and tested on the contrasting parents and bulks. Four markers (sxau-Q2BS3, sxau-Q2BS5, sxau-2BS210, and sxau-
2BS255) were polymorphic and used with sxau-2BS47 to examine 33 crossovers. The obtained results indicated
that the closest flanking markers of LrCH1539 were sxau-2BS47 (with one recombination event) and sxau-2BS255
(with six recombination events), and the marker cosegregating with LrCH1539 was sxau-2BS210 (Fig. 4). These
results suggest that the LrCH1539 locus is located in a 779.4 kb region between markers sxau-2BS47 and sxau-
2BS255 (6,226,584 bp–7,005,940 bp) in CS RefSeq v1.0. The reaction of parents and RILs to Pt races For the polymorphic SNPs distributed on chromosome 2B, the average number of polymorphic SNPs contained in
each 10 Mb was calculated using 10 Mb as a sliding window. The obtained results showed that the most
polymorphic SNPs in the physical range of 0-20 Mb accounted for more than 78.3% (47) of polymorphic SNPs on
2B. (Fig. 2B). Therefore, it is speculated that there is a leaf rust resistance site at the end of the short arm of
chromosome 2B. Page 5/20 Page 5/20 Page 5/20 Chromosome-specific SSR markers in the region were developed and then screened on the parents and bulks to
confirm polymorphisms before being genotyped on the entire population; 35 polymorphic markers were successful
in distinguishing the contrasting parents and bulks. Among the 12 markers linked to known Lr genes, one KASP
and two SSR markers linked to Lr16 were also polymorphic between parents and bulks. A genetic map was
constructed using one KASP and 16 SSR markers genotyped on the 184 F2:10 individuals, resulting in a linkage
group spanning 16.0 cM. LrCH1539 was preliminarily located between the SSR markers sxau-2BS81/Xwmc764
and sxau-2BS136 in an interval of 1.1 cM and coseparated with sxau-2BS47 and 2BS-5175914_kwm849 (Fig. 3). According to the physical position of the markers sxau-2BS81 and sxau-2BS136 in the CS1.0 reference genome,
LrCH1539 was located in the 2.4 Mb region between 5.7 and 8.1 Mb (Fig. 3). Comparison with reported Lr genes in chromosome 2B The linked markers of the Lr gene reported on chromosome 2BS were used to detect contrasting parents and bulks
(Table 2, Fig. S1). The obtained results showed that no polymorphisms of Xgwm630, Xbarc55, Xbarc7, sun471,
and Sr39F2/R3 were observed between CH1539 and SY95-71, and none of the characteristic bands of Sr39F2/R3
were amplified. Xwmc770, Xgwm374, and Xgwm429b were polymorphic between parents, but they were not
polymorphic between R-bulk and S-bulk. These results suggested that these markers were not linked to LrCH1539. Page 6/20 Page 6/20 Page 6/20 Table 2
The reported Lr genes on chromosome 2BS in wheat
Gene
Genetic
method
Type of
resistance
Source
Linkage marker
Reference
Name
Polymorphism
in parents
Linked to
phenotype
Lr13
recessive
partially
dominant
APR
common
wheat
Xbarc55
No
No
Zhang et
al. 2016
Xbarc7
No
No
Dyck et
al. 1966
Xgwm630
No
No
Seyfarth
et al. 2000
Lr16
N
ASR
common
wheat
Xwmc764
Yes
Yes
Kassa et
al. 2017
Xwmc661
Yes
Yes
Lr23
recessive
partially
dominant
ASR
durum
wheat
Xsun471
No
No
Chhetri et
al. 2017
McIntosh
and Dyck,
1975
Lr35
N
APR
T. speltoides
Sr39F2/R3
No
No
Gold et
al. 1999
Lr48
Recessive
APR
common
wheat
Xgwm429b
Yes
No
Saini et
al. 2002
Bansal et
al. 2008
LrA2K
N
ASR
common
wheat
Xwmc770
Yes
No
Sapkota
et al. 2019
LrZH22
dominant
ASR
common
wheat
Xgwm374
Yes
No
Wang et
al. 2016
LrCH1539
Recessive
ASR
common
wheat
N: No relevant descriptions were found in the literature. LrCH1539 has a genetic distance of 0.8 cM from Xwmc764, cosegregated with KASP marker 2BS-
5175914_kwm849 (Fig. 3), and has a linkage relationship with CAPS markers kwm847 and dCAPS markers
kwm747 transformed from KASP markers 2BS-5175914_kwm847 and 2BS-5194460_kwm747, respectively (Fig. S1). Resistance spectrum analysis of LrCH1539 and Lr16
The wheat accessions CH1539 and RL6005 showed different disease responses to 31 Chinese Pt races (Fig. 5,
Table S1). Twelve of 31 Pt races, including DHK, FHK, FKT, KHJ, PGL, PHS, PKJ, PKT, PRK, PTK, THK, and TKK, Discussion The wheat accession CH1539 is a valuable source of genetic variation for biotic resistance, such as powdery
mildew and stripe rust resistance (data not shown), and has a high level of resistance to leaf rust in the field. In
this study, the recessive seedling resistance gene LrCH1539 was characterized on the short arm of chromosome
2B in CH1539. Previous studies have identified several permanently and tentatively designated Lr genes on chromosome 2BS,
including Lr13, Lr16, Lr23, Lr35, Lr48, Lr73, LrZH22, and LrA2K. Based on the integrated genetic maps (Maccaferri
et al. 2015), the markers flanked or linked with the reported genes were far from Xwmc764 and Xwmc661, which
were flanked to LrCH1539 (Fig. 7A). Meanwhile, there was no linkage relationship between these markers and
LrCH1539 (Table 2, Fig. S1), which indicates that the genes Lr13, Lr23, Lr48, LrZH22, and LrA2K are distinct from
LrCH1539. Lr35 is an adult-plant resistance gene located on a translocation chromosome fragment extracted from
Aegilops speltoides (Gold et al. 1999). The selection marker Sr39F2/R3 of Lr35 could not be amplified in CH1539,
and there is no Triticum speltoides in the pedigree of CH1539. Therefore, LrCH1539 cannot be Lr35. The dominant gene Lr73 is located between XwPt-4453 and XwPt-8760 on 2BS (Park et al. 2014), and its genetic
position overlaps with LrCH1539 (Fig. 7A). The gene Lr73, sometimes referred to as the “fossil” gene, only exists in
Morocco and some other Australian wheat cultivars (Park et al. 2014); thus, it is considered not to exist in the
Chinese wheat background. Furthermore, unlike Lr73, LrCH1539 in this study is a recessive gene. The molecular markers coseparated with Lr16 are also linked or coseparated with LrCH1539. Meanwhile, on the
physical map, LrCH1539 is included in the region of Lr16 (Fig. 7B). CH1539, RL6005, and Selkirk were genotyped
and analyzed with markers sxau-2BS210, sxau-2BS255, sxau-2BS47, sxau-Q2BS3, sxau-Q2BS5, kwm847, and
kwm747 (Table S3). According to the genotyping results of three genotypes with seven markers, CH1539, RL6005,
and Selkirk had the same haplotype (combination of marker alleles). Therefore, LrCH1539 and Lr16 may be in the
same chromosome interval. However, the original sources of Lr16 are believed to be five wheat cultivars, Warden, Exchange, Selkirk, Etoile de
Choisy, and Columbus (Harrison et al. 2015), while the pedigree of CH1539 does not correlate with Lr16. CH1539
and RL6005 produced different LR resistance responses to 13 Pt races, including THK. Resistance spectrum analysis of LrCH1539 and Lr16 The wheat accessions CH1539 and RL6005 showed different disease responses to 31 Chinese Pt races (Fig. 5,
Table S1). Twelve of 31 Pt races, including DHK, FHK, FKT, KHJ, PGL, PHS, PKJ, PKT, PRK, PTK, THK, and TKK, Page 7/20 Page 7/20 were avirulent to LrCH1539 but virulent to Lr16 (Fig. 5). The race PBB was avirulent to Lr16 but virulent to
LrCH1539. Distribution of the LrCH1539 allele in wheat varieties The cosegregating marker sxau-2BS210 of LrCH1539 had genotyped 262 varieties which are widely used as core
germplasms in Chinese breeding programs. Only 12 (4.6%) of these varieties showed the presence of the resistant
CH1539 allele, and the rest showed the presence of the susceptible SY95-71 allele. These 12 wheat varieties
include two Italian varieties (Funo and St2422/464) and ten Chinese varieties (Laomai, Hongmangmai,
Yangmai158, Kelao 4, Ji’nan 17, Xiaoyan 6, Shaannong 7859, Fan 6, Zhengmai 9023, Yanzhan 1) (Fig. 6). Discussion It is assumed that the
differences in the response of CH1539 and RL6005 to leaf rust are not only due to differences in the genetic
background but may also result from differences in the candidate genes for LrCH1539 and Lr16. Page 8/20 The wheat core germplasms were genotyped using the cosegregating marker sxau-2BS210 of LrCH1539; the
CH1539 allele was detected in 12 cultivars, and the remaining 250 cultivars were the SY95-71 allele. Of the 12
cultivars, Funo and St2422/464 are Italian varieties introduced in China in the 1950s and 1970s, respectively, and
have been widely used as parents in breeding programs. Five of eight Chinese wheat varieties, Yangmai 158,
Xiaoyan 6, Fan 6, Zhengmai 9023, and Yanzhan 1, all have Funo and/or St2422/464 genetic backgrounds (Wu et
al. 1993; Xu et al. 2009; Yuan et al. 1981; Zou 1991). The remaining two varieties, Laomai and Hongmangmai, are
Chinese landraces. The former is distributed in Shaanxi Province, China, and the latter is distributed in Shandong,
Hebei, and Shanxi provinces. In summary, the CH1539 allele of LrCH1539 is distributed over a wide range but at a
very small frequency, representing only 4.6% of the tested germplasms. Among the 12 detected germplasms, three
(25%) had a “Funo” genetic background, and four (33.3%) had a “St2422/464” genetic background. Therefore, the
CH1539 allele of LrCH1539 has good application potential. LrCH1539 was mapped to 6,226,584-7,005,940 bp on chromosome arm 2BS (Chinese Spring RefSeq v.1.0). There
were 42 annotated genes in this region, including 14 low confidence genes and 28 high confidence genes (IWGSC
2018). To predict the LrCH1539 gene, we analyzed the expression profiles of genes in the candidate region after
being induced by pathogens using the wheat expVIP expression platform. Since symptoms of LR resistance begin
from the early seedling stage and are maintained to the adult stage, we hypothesized that the LrCH1539 allele
should be expressed in leaves throughout the entire growth period. Nine of 42 candidate genes were expressed
(above two transcripts per million) in at least ten RNA-seq samples (leaves and stress-disease, n=99) at different
developmental stages (Table S4). Eight of the nine expressed genes were high-confidence genes, which may be
related to plant disease resistance. Discussion Gene annotation of the corresponding region in Chinese Spring revealed that the gene TraesCS2B01G012400
encodes the Avr9/Cf-9 rapidly elicited protein, which is a protein produced after the plant resistance gene Cf-9
recognizes pathogens and plays a pivotal role during plant defense responses (Rowland et al. 2005; van den Burg
et al. 2008). The gene TraesCS2B01G012600 encodes the StAR-related lipid transfer protein (LTP), and LTP has
been classified as a member of the pathogenesis-related (PR) proteins belonging to the PR-14 group (Van Loon et
al. 1999). Overexpression of LTP genes enhances resistance to plant pathogens and plays an important role in
plant long-distance systemic signaling in tobacco (Sarowar et al. 2009). McLaughlin et al. (2015) found that LTP
can increase the glutathione content and enhance Arabidopsis resistance to a trichothecene mycotoxin;
Kirubakaran et al. (2008) identified a new antifungal lipid transfer protein from wheat. Li et al. (2006) used the
transient overexpression method to study the role of cloned LTP1 in wheat-powdery mildew interactions, and the
obtained results indicated obvious effectiveness of LTP1 in powdery mildew resistance. The gene
TraesCS2B01G012800 encodes a peptidyl-prolyl cis-trans isomerase. The activity domain of this enzyme is a
common feature of immunophilins that are ubiquitous in organisms (Fisher et al. 1989). Pogorelko et al. (2014)
characterized three Arabidopsis thaliana immunophilin genes involved in the plant defense response against
Pseudomonas syringae, and the research showed that Arabidopsis knock-out mutations in these immunophilins
result in an increased susceptibility to P. syringae, whereas overexpression of these genes alters the transcription
profile of pathogen-related defense genes and led to enhanced resistance. These genes are essential in the biotic
stress response of plant resistance to pathogens. However, based on the available data, we cannot determine the
LrCH1539 gene, which requires more experimental evidence. Conclusions Page 9/20 A recessive seedling stage LR resistance gene, LrCH1539, located within a 779.4 kb physical region (6,226,584 bp-
7,005,940 bp) on 2BS, was characterized in wheat accession CH1539, and the cosegregating marker sxau-2BS210
was developed. LrCH1539 and Lr16 are at the same position on the chromosome but differ in their resistance
spectra. Consent for publication Not applicable. Conflict of interest The authors declare no competing interests. Supplementary information The online version contains supplementary material available at XXXX. Declarations Author contribution DS performed the experiments; DS and LQ analyzed the data, carried out the bioinformatics
work and wrote the manuscript; XZ and ZC conceived and supervised the experiments; XZ and XL administrated
the project; LC, HG, SZ and FC investigated the phenotype; ZC revised the manuscript. All authors have read and
approved the final manuscript. Funding This work was supported by the Shanxi Province S & T Cooperation and Exchange Special Program; the
State Key Laboratory of Integrative Sustainable Dryland Agriculture (in preparation), Shanxi Agricultural University
(202002-3); the Key Science & Technology Project in Shanxi Province (201903D211003-2); and the Biological
Breeding Engineering (YZGC093). Ethics approval Not applicable. Consent to participate Not applicable. Consent to participate Not applicable. Consent for publication Not applicable. References 1. Bansal UK, Hayden MJ, Venkata BP, Khanna R, Saini RG, Bariana HS (2008) Genetic mapping of adult plant
leaf rust resistance genes Lr48 and Lr49 in common wheat. Theor Appl Genet 117:307–312. https://doi.org/10.1007/s00122-008-0775-6 1. Bansal UK, Hayden MJ, Venkata BP, Khanna R, Saini RG, Bariana HS (2008) Genetic mapping of adult plant
leaf rust resistance genes Lr48 and Lr49 in common wheat. Theor Appl Genet 117:307–312. https://doi.org/10.1007/s00122-008-0775-6 2. Chen F, Jia H, Zhang X, Qiao L, Li X, Zheng J, Guo H, Powers C, Yan L, Chang Z (2019) Positional cloning of
PmCH1357 reveals the origin and allelic variation of the Pm2 gene for powdery mildew resistance in wheat. Crop J 7(6):771–783. https://doi.org/10.1016/j.cj.2019.08.004 3. Chhetri M, Bariana H, Wong D, Sohail Y, Hayden M, Bansal U (2017) Development of robust molecular markers
for marker-assisted selection of leaf rust resistance gene Lr23 in common and durum wheat breeding
programs. Mol Breeding 37:21. https://doi.org/10.1007/s11032-017-0628-6 4. Cloutier S, McCallum BD, Loutre C, Banks TW, Wicker T, Feuillet C, Keller B, Jordan MC (2007) Leaf rust
resistance gene Lr1, isolated from bread wheat (Triticum aestivum L.) is a member of the large psr567 gene
family. Plant Mol Biol 65:93–106. https://doi.org/10.1007/s11103-007-9201-8 4. Cloutier S, McCallum BD, Loutre C, Banks TW, Wicker T, Feuillet C, Keller B, Jordan MC (2007) Leaf rust
resistance gene Lr1, isolated from bread wheat (Triticum aestivum L.) is a member of the large psr567 gene
family. Plant Mol Biol 65:93–106. https://doi.org/10.1007/s11103-007-9201-8 5. Dyck PL, Samborski DJ, Anderson RG (1966) Inheritance of adult-plant leaf rust resistance derived from the
common wheat varieties exchange and Frontana. Can J Genet Cytol 8(4):665–671. https://doi.org/10.1139/g66-082 5. Dyck PL, Samborski DJ, Anderson RG (1966) Inheritance of adult-plant leaf rust resistance derived from the
common wheat varieties exchange and Frontana. Can J Genet Cytol 8(4):665–671. https://doi.org/10.1139/g66-082 Page 10/20 6. Ellis JG, Lagudah ES, Spielmeyer W, Dodds PN (2014) The past, present and future of breeding rust resistant
wheat. Front Plant Sci 5:641. https://doi.org/10.3389/fpls.2014.00641 6. Ellis JG, Lagudah ES, Spielmeyer W, Dodds PN (2014) The past, present and future of breeding rust resistant
wheat. Front Plant Sci 5:641. https://doi.org/10.3389/fpls.2014.00641 7. Feuillet C, Travella S, Stein N, Albar L, Nublat A, Keller B (2003) Map-based isolation of the leaf rust disease
resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. Proc Natl Acad Sci USA
100(25):15253–15258. https://doi.org/10.1073/pnas.2435133100 8. References Fisher G, Wittmann-Liebold B, Lang K, Kiefhaber T, Schmid FX (1989) Cyclophilin and the peptidyl-prolyl cis-
trans isomerase are probably identical proteins. Nature 337:476–478. https://doi.org/10.1038/337476a0 9. Gao P, Zhou Y, Gebrewahid TW, Zhang P, Yan X, Li X, Yao Z, Li Z, Liu D (2019) Identification of known leaf rust
resistance genes in common wheat cultivars from Sichuan province in China. Crop Prot 115:122–129. https://doi.org/10.1016/j.cropro.2018.09.012 10. Gold J, Harder D, Townley-Smith F, Aung T, Procunier J (1999) Development of a molecular marker for rust
resistance genes Sr39 and Lr35 in wheat breeding lines. Electron J Biotechnol 2(1):35–40. doi: 10.2225/vol2-
issue1-fulltext-1 11. Harrison NR, Fritz AK, Glasscock JI, Ahmed S, Messina DN, Amand PS, Fellers JP (2015) Using RNA
sequencing and in silico subtraction to identify resistance gene analog markers for Lr16 in wheat. Plant
Genome 8(2). https://doi.org/10.3835/plantgenome2014.08.0040 12. Hill-Ambroz KL, Brown-Guedira GL, Fellers JP (2002) Modified rapid DNA extraction protocol for high
throughput microsatellite analysis in wheat. Crop Sci 42(6):2088–2091. doi:10.2135/cropsci2002.2088 13. Huang L, Brooks SA, Li W, Fellers JP, Trick HN, Gill BS (2003) Map-based cloning of leaf rust resistance gene
Lr21 from the large and polyploid genome of bread wheat. Genetics 164(2):655–664. doi:
10.1093/genetics/164.2.655 14. Huerta-Espino J, Singh RP, Germán S, McCallum BD, Park RF, Chen WQ, Bhardwaj SC, Goyeau H (2011) Global
status of wheat leaf rust caused by Puccinia triticina. Euphytica 179:143–160. https://doi.org/10.1007/s10681-011-0361-x 15. Kassa MT, You FM, Hiebert CW, Pozniak CJ, Fobert PR, Sharpe AG, Menzies JG, Humphreys DG, Harrison NR,
Fellers JP, McCallum BD, McCartney CA (2017) Highly predictive SNP markers for efficient selection of the
wheat leaf rust resistance gene Lr16. BMC Plant Biol 17:45. https://doi.org/10.1186/s12870-017-0993-7 16. Kertho A, Mamidi S, Bonman JM, McClean PE, Acevedo M (2015) Genome-wide association mapping for
resistance to leaf and stripe rust in winter-habit hexaploid wheat landraces. PLoS ONE 10(6):e0129580. https://doi.org/10.1371/journal.pone.0129580 17. Kirubakaran SI, Begum SM, Ulaganathan K, Sakthivel N (2008) Characterization of a new antifungal lipid
transfer protein from wheat. Plant Physiol Biochem 46(10):918–927. https://doi.org/10.1016/j.plaphy.2008.05.007 17. Kirubakaran SI, Begum SM, Ulaganathan K, Sakthivel N (2008) Characterization of a new antifungal lipid
transfer protein from wheat. Plant Physiol Biochem 46(10):918–927. https://doi.org/10.1016/j.plaphy.2008.05.007 18. Kolmer JA (2005) Tracking wheat rust on a continental scale. Curr Opin Plant Biol 8:441–449. https://doi.org/10.1016/j.pbi.2005.05.001 18. Kolmer JA (2005) Tracking wheat rust on a continental scale. Curr Opin Plant Biol 8:441–449. https://doi.org/10.1016/j.pbi.2005.05.001 19. References Li ZF, Xia XC, He ZH, Li X, Zhang LJ, Wang HY, Meng QF, Yang WX, Li GQ, Liu DQ (2010) Seedling and slow
rusting resistance to leaf rust in Chinese wheat cultivars. Plant Dis 94(1):45–53. https://doi.org/10.1094/PDIS-94-1-0045 25. Li ZF, Lan CX, He ZH, Singh RP, Rosewarne GM, Chen XM, Xia XC (2014) Overview and application of QTL for
adult plant resistance to leaf rust and powdery mildew in wheat. Crop Sci 54:1907–1925. https://doi.org/10.2135/cropsci2014.02.0162 25. Li ZF, Lan CX, He ZH, Singh RP, Rosewarne GM, Chen XM, Xia XC (2014) Overview and application of QTL for
adult plant resistance to leaf rust and powdery mildew in wheat. Crop Sci 54:1907–1925. https://doi.org/10.2135/cropsci2014.02.0162 26. Liu RH, Meng JL (2003) MapDraw: a Microsoft Excel macro for drawing genetic linkage maps based on given
genetic linkage data. Hereditas (Beijing) 25(3):317–321 (In Chinese) 26. Liu RH, Meng JL (2003) MapDraw: a Microsoft Excel macro for drawing genetic linkage maps based on given
genetic linkage data. Hereditas (Beijing) 25(3):317–321 (In Chinese) 27. Long DL, Kolmer JA (1989) A North American system of nomenclature for Puccinia recondita f. sp. tritici. Phytopathology 79:525–529. doi: 10.1094/Phyto-79-525 27. Long DL, Kolmer JA (1989) A North American system of nomenclature for Puccinia recondita f. sp. tritici. Phytopathology 79:525–529. doi: 10.1094/Phyto-79-525 28. Maccaferri M, Zhang J, Bulli P, Abate Z, Chao S, Cantu D, Bossolini E, Chen X, Pumphrey M, Dubcovsky J
(2015) A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a
worldwide collection of hexaploid spring wheat (Triticum aestivum L.). G3 5. 449–465. https://doi.org/10.1534/g3.114.014563. 3 28. Maccaferri M, Zhang J, Bulli P, Abate Z, Chao S, Cantu D, Bossolini E, Chen X, Pumphrey M, Dubcovsky J
(2015) A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a
worldwide collection of hexaploid spring wheat (Triticum aestivum L.). G3 5. 449–465. https://doi.org/10.1534/g3.114.014563. 3 29. McCartney CA, Somers DJ, McCallum BD, Thomas J, Humphreys DG, Menzies JG, Brown PD (2005)
Microsatellite tagging of the leaf rust resistance gene Lr16 on wheat chromosome 2BSc. Mol Breeding
15:329–337. https://doi.org/10.1007/s11032-004-5948-7 29. McCartney CA, Somers DJ, McCallum BD, Thomas J, Humphreys DG, Menzies JG, Brown PD (2005)
Microsatellite tagging of the leaf rust resistance gene Lr16 on wheat chromosome 2BSc. Mol Breeding
15:329–337. https://doi.org/10.1007/s11032-004-5948-7 30. McIntosh RA, Dyck PL (1975) Cytogenetical studies in wheat. VII. References Kolodziej MC, Singla J, Sánchez-Martín J, Zbinden H, Šimková H, Karafiátová M, Doležel J, Gronnier J, Poretti
M, Glauser G, Zhu W, Köster P, Zipfel C, Wicker T, Krattinger SG, Keller B (2021) A membrane-bound ankyrin
repeat protein confers race-specific leaf rust disease resistance in wheat. Nat Commun 12:956. https://doi.org/10.1038/s41467-020-20777-x 19. Kolodziej MC, Singla J, Sánchez-Martín J, Zbinden H, Šimková H, Karafiátová M, Doležel J, Gronnier J, Poretti
M, Glauser G, Zhu W, Köster P, Zipfel C, Wicker T, Krattinger SG, Keller B (2021) A membrane-bound ankyrin
repeat protein confers race-specific leaf rust disease resistance in wheat. Nat Commun 12:956. https://doi.org/10.1038/s41467-020-20777-x 20. Kosambi DD (1943) The estimation of map distances from recombination values. Ann Eugen 12:172–175 Page 11/20 Page 11/20 21. Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller
B (2009) A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323(5919):1360–1363. doi: 10.1126/science.1166453 22. Kumar S, Bhardwaj SC, Gangwar OP, Sharma A, Qureshi N, Kumaran VV, Khan H, Prasad P, Miah H, Singh GP,
Sharma K, Verma H, Forrest KL, Trethowan RM, Bariana HS, Bansal UK (2021) Lr80: A new and widely
effective source of leaf rust resistance of wheat for enhancing diversity of resistance among modern cultivars. Theor Appl Genet 134:849–858. https://doi.org/10.1007/s00122-020-03735-5 22. Kumar S, Bhardwaj SC, Gangwar OP, Sharma A, Qureshi N, Kumaran VV, Khan H, Prasad P, Miah H, Singh GP,
Sharma K, Verma H, Forrest KL, Trethowan RM, Bariana HS, Bansal UK (2021) Lr80: A new and widely
effective source of leaf rust resistance of wheat for enhancing diversity of resistance among modern cultivars. Theor Appl Genet 134:849–858. https://doi.org/10.1007/s00122-020-03735-5 23. Li A, Meng C, Zhou R, Ma Z, Jia J (2006) Assessment of lipid transfer protein (LTP1) gene in wheat powdery
mildew resistance. Agric Sci China 5(4):241–249. https://doi.org/10.1016/S1671-2927(06)60045-X 23. Li A, Meng C, Zhou R, Ma Z, Jia J (2006) Assessment of lipid transfer protein (LTP1) gene in wheat powdery
mildew resistance. Agric Sci China 5(4):241–249. https://doi.org/10.1016/S1671-2927(06)60045-X 24. Li ZF, Xia XC, He ZH, Li X, Zhang LJ, Wang HY, Meng QF, Yang WX, Li GQ, Liu DQ (2010) Seedling and slow
rusting resistance to leaf rust in Chinese wheat cultivars. Plant Dis 94(1):45–53. https://doi.org/10.1094/PDIS-94-1-0045 24. References gene Lr23 for reaction to Puccinia recondita
in Gabo and related cultivars. Aust J BioI Sci 28(2):201–211. doi:10.1071/bi9750201 30. McIntosh RA, Dyck PL (1975) Cytogenetical studies in wheat. VII. gene Lr23 for reaction to Puccinia recondita
in Gabo and related cultivars. Aust J BioI Sci 28(2):201–211. doi:10.1071/bi9750201 31. McLaughlin JE, Bin-Umer MA, Widiez T, Finn D, McCormick S, Tumer NE (2015) A lipid transfer protein
increases the glutathione content and enhances Arabidopsis resistance to a trichothecene mycotoxin. PLoS
ONE 10(6):e0130204. https://doi.org/10.1371/journal.pone.0130204 32. Moore JW, Herrera-Foessel S, Lan C, Schnippenkoetter W, Ayliffe M, Huerta-Espino J, Lillemo M, Viccars L,
Milne R, Periyannan S, Kong X, Spielmeyer W, Talbot M, Bariana H, Patrick JW, Dodds P, Singh R, Lagudah E
(2015) A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat. Nat
Genet 47:1494–1498. https://doi.org/10.1038/ng.3439 32. Moore JW, Herrera-Foessel S, Lan C, Schnippenkoetter W, Ayliffe M, Huerta-Espino J, Lillemo M, Viccars L,
Milne R, Periyannan S, Kong X, Spielmeyer W, Talbot M, Bariana H, Patrick JW, Dodds P, Singh R, Lagudah E
(2015) A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat. Nat
Genet 47:1494–1498. https://doi.org/10.1038/ng.3439 33. Park RF, Mohler V, Nazari K, Singh D (2014) Characterisation and mapping of gene Lr73 conferring seedling
resistance to Puccinia triticina in common wheat. Theor Appl Genet 127. https://doi.org/10.1007/s00122-014-
2359-y. :2041-2049 33. Park RF, Mohler V, Nazari K, Singh D (2014) Characterisation and mapping of gene Lr73 conferring seedling
resistance to Puccinia triticina in common wheat. Theor Appl Genet 127. https://doi.org/10.1007/s00122-0
2359-y. :2041-2049 34. Pink DA (2002) Strategies using genes for non-durable disease resistance. Euphytica 124:227–236. https://doi.org/10.1023/A:1015638718242 34. Pink DA (2002) Strategies using genes for non-durable disease resistance. Euphytica 124:227–236. https://doi.org/10.1023/A:1015638718242 Page 12/20 35. Pogorelko GV, Mokryakova M, Fursova OV, Abdeeva I, Piruzian ES, Bruskin SA (2014) Characterization of three
Arabidopsis thaliana immunophilin genes involved in the plant defense response against Pseudomonas
syringae. Gene 538(1):12–22. https://doi.org/10.1016/j.gene.2014.01.029 36. Ramírez-González RH, Borrill P, Lang D et al (2018) The transcriptional landscape of polyploid wheat. Science
361(6403):eaar6089. doi: 10.1126/science.aar6089 37. Ren XL, Liu TG, Liu B, Gao L, Chen WQ (2015) Postulation of seedling leaf rust resistance genes in 84 Chinese
winter wheat cultivars. J Integr Agric 14(10):1992–2001 38. Roelfs AP, Singh RP, Saari EE (1992) Rust diseases of wheat: Concepts and methods of disease management. CIMMYT, Mexico, D.F. 39. References Rowland O, Ludwig AA, Merrick CJ, Baillieul F, Tracy FE, Durrant WE, Fritz-Laylin L, Nekrasov V, Sjölander K,
Yoshioka H, Jones JD (2005) Functional analysis of Avr9/Cf-9 rapidly elicited genes identifies a protein
kinase, ACIK1, that is essential for full Cf-9-dependent disease resistance in tomato. Plant Cell 17(1):295-310. doi: 10.1105/tpc.104.026013 40. Saini RG, Kaur M, Singh B, Sharma S, Nanda GS, Nayar SK, Gupta AK, Nagarajan S (2002) Genes Lr48 and
Lr49 for hypersensitive adult plant leaf rust resistance in wheat (Triticum aestivum L.). Euphytica 124:365–
370. https://doi.org/10.1023/A:1015762812907 41. Sapkota S, Hao Y, Johnson J, Lopez B, Bland D, Chen Z, Sutton S, Buck J, Youmans J, Mergoum M (2019)
Genetic mapping of a major gene for leaf rust resistance in soft red winter wheat cultivar AGS 2000. Mol
Breeding 39:8. https://doi.org/10.1007/s11032-018-0909-8 42. Sarowar S, Kim YJ, Kim KD, Hwang BK, Ok SH, Shin JS (2009) Overexpression of lipid transfer protein (LTP)
genes enhances resistance to plant pathogens and LTP functions in long-distance systemic signaling in
tobacco. Plant Cell Rep 28:419–427. https://doi.org/10.1007/s00299-008-0653-3 43. Seyfarth R, Feuillet C, Schachermayr G, Messmer M, Winzeler M, Keller B (2000) Molecular mapping of the
adult-plant leaf rust resistance gene Lr13 in wheat (Triticum aestivum L.). Journal of Genetics and Breeding
54(3):193–198 44. Thind AK, Wicker T, Šimková H, Fossati D, Moullet O, Brabant C, Vrána J, Doležel J, Krattinger SG (2017) Rapid
cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nat Biotechnol
35:793–796. https://doi.org/10.1038/nbt.3877 45. van den Burg HA, Tsitsigiannis DI, Rowland O, Lo J, Rallapalli G, Maclean D, Takken FL, Jones JD (2008) The
F-box protein ACRE189/ACIF1 regulates cell death and defense responses activated during pathogen
recognition in tobacco and tomato. Plant Cell 20(3):697–719. https://doi.org/10.1105/tpc.107.056978 46. Van Loon LC, Van Strien EA (1999) The families of pathogenesis-related proteins, their activities and
comparative analysis of PR-1 type proteins. Physiol Mol Plant Pathol 55(2):85–97. https://doi.org/10.1006/pmpp.1999.0213 46. Van Loon LC, Van Strien EA (1999) The families of pathogenesis-related proteins, their activities and
comparative analysis of PR-1 type proteins. Physiol Mol Plant Pathol 55(2):85–97. https://doi.org/10.1006/pmpp.1999.0213 47. Wang C, Yin G, Xia X, He Z, Zhang P, Yao Z, Qin J, Li Z, Liu D (2016) Molecular mapping of a new temperature-
sensitive gene LrZH22 for leaf rust resistance in Chinese wheat cultivar Zhoumai 22. Mol Breeding 36:18. https://doi.org/10.1007/s11032-016-0437-3 47. References (In Chinese) References Wang C, Yin G, Xia X, He Z, Zhang P, Yao Z, Qin J, Li Z, Liu D (2016) Molecular mapping of a new temperature-
sensitive gene LrZH22 for leaf rust resistance in Chinese wheat cultivar Zhoumai 22. Mol Breeding 36:18. https://doi.org/10.1007/s11032-016-0437-3 48. Wu J, Gu SY, Xing YZ, Qian J (1993) The wheat cultivar Yangmai 158.Seed Science and Technology. (05):45. (In Chinese) 48. Wu J, Gu SY, Xing YZ, Qian J (1993) The wheat cultivar Yangmai 158.Seed Science and Technology. (05):45. (In Chinese) 49. Xu WG, Hu L, Wang GS, Zhang L, Dong HB, Li Y, Zhang JY, Zan XC, Qi XL, Li CX, Zhao MZ (2009) Breeding
strategies of high quality and wide regional adaptability wheat variety Zhengmai 9023 and relevant thoughts 49. Xu WG, Hu L, Wang GS, Zhang L, Dong HB, Li Y, Zhang JY, Zan XC, Qi XL, Li CX, Zhao MZ (2009) Breeding
strategies of high quality and wide regional adaptability wheat variety Zhengmai 9023 and relevant thoughts Page 13/20 Page 13/20 on wheat high yield breeding.Journal of Henan Agricultural Sciences(09):14–18. (In Chinese) on wheat high yield breeding.Journal of Henan Agricultural Sciences(09):14–18. (In Chinese) 50. Zhang P, Hiebert CW, McIntosh RA, McCallum BD, Thomas JB, Hoxha S, Singh D, Bansal U (2016) The
relationship of leaf rust resistance gene Lr13 and hybrid necrosis gene Ne2m on wheat chromosome 2BS. Theor Appl Genet 129:485-493. https://doi.org/10.1007/s00122-015-2642-6 51. Zhang L, Xiao Y, Gao Y, Zhao N, An Y, Yang W, Meng Q, Yan H, Liu D (2020) Race and virulence analysis of
Puccinia triticina in China during 2011 to 2013. Plant Dis 104:2095–2101. https://doi.org/10.1094/PDIS-01-
20-0047-RE 52. Zhao LN, Ren XD, Hu YY, Zhang N, Yang WX, Liu DQ (2013) Evaluation of wheat leaf rusts resistance of 23
Chinese wheat mini-core collections. Scientia Agricultura Sinica 46(3):441–450. doi: 10.3864/j.issn.0578-
1752.2013.03.001(In Chinese) 52. Zhao LN, Ren XD, Hu YY, Zhang N, Yang WX, Liu DQ (2013) Evaluation of wheat leaf rusts resistance of 23
Chinese wheat mini-core collections. Scientia Agricultura Sinica 46(3):441–450. doi: 10.3864/j.issn.0578-
1752.2013.03.001(In Chinese) 53. Zou YL (1991) Breeding of sister lines of high-yield and rust-resistant wheat variety ‘Fan 6’.Journal of Yibin
University(01):1–8, 34. (In Chinese) 53. Zou YL (1991) Breeding of sister lines of high-yield and rust-resistant wheat variety ‘Fan 6’.Journal of Yibin
University(01):1–8, 34. (In Chinese) 53. Zou YL (1991) Breeding of sister lines of high-yield and rust-resistant wheat variety ‘Fan 6’.Journal of Yibin
University(01):1–8, 34. Figures Figure 1
The phenotype of resistant parent CH1539, susceptible parent SY95-71, and susceptible control Mingxian 169
about 14 days after inoculation with Pt race THK. Figure 1 Figure 1 The phenotype of resistant parent CH1539, susceptible parent SY95-71, and susceptible control Mingxian 169
about 14 days after inoculation with Pt race THK. Page 14/20 Figure 2
Distributions of the polymorphic SNPs in each chromosome by 35K DArTseq array (A) and positions of SNPs in
chromosome 2B (B). Distributions of the polymorphic SNPs in each chromosome by 35K DArTseq array (A) and positions of SNPs in
chromosome 2B (B). Page 15/20 Page 15/20 Figure 3
Genetic map of wheat chromosome 2BS showing the location of leaf rust resistance gene LrCH1539. The 2BS
physical map was based on the IWGSC CS1.0 genomic sequence. Figure 3 Genetic map of wheat chromosome 2BS showing the location of leaf rust resistance gene LrCH1539. The 2BS
physical map was based on the IWGSC CS1.0 genomic sequence. Page 16/20 Page 16/20 Figure 4
Fine mapping of LrCH1539. Phenotypes and genotypes of seven F2 crossovers (including F2-416, F2-466, F2-1690,
F2-2375, F2-651, F2-1616, F2-1559) are showed. The name and phenotype of F2 individuals were labeled in the left
and right, respectively. Black, white, and gray blocks present genomic regions of CH1539, SY95-71 and
heterozygous, respectively. a: The phenotype of F2:3 lines was segregated. c: indicated the number of crossovers. Figure 4
Fine mapping of LrCH1539. Phenotypes and genotypes of seven F2 crossovers (including F2-416, F2-466, F2-1690,
F2-2375, F2-651, F2-1616, F2-1559) are showed. The name and phenotype of F2 individuals were labeled in the left
and right, respectively. Black, white, and gray blocks present genomic regions of CH1539, SY95-71 and
heterozygous, respectively. a: The phenotype of F2:3 lines was segregated. c: indicated the number of crossovers. Figure 5 Figure 4 Fine mapping of LrCH1539. Phenotypes and genotypes of seven F2 crossovers (including F2-416, F2-466, F2-1690,
F2-2375, F2-651, F2-1616, F2-1559) are showed. The name and phenotype of F2 individuals were labeled in the left
and right, respectively. Black, white, and gray blocks present genomic regions of CH1539, SY95-71 and
heterozygous, respectively. a: The phenotype of F2:3 lines was segregated. c: indicated the number of crossovers. Figure 5 Page 17/20 Page 17/20 Phenotype of susceptible parent SY95-71 (1), RL6005 carried with Lr16 (2), resistant parent CH1539 (3), and the
resistant line #72 (4) after inoculation with Pt race KHJ (A), PHS(B), PKJ(C), PKT(D) and PRK(E). Figure 6
PCR profiles of the marker sxau-2BS210 co-separated with LrCH1539 in several Chinese core germplasms in
breeding programs. The arrowhead indicated co-segregating PCR amplicons linked to LrCH1539. Numbers on th
left are the size in bp of the DNA ladder. Figure 6 Figure 7 (A) LrCH1539 identified in the present study and Pt genes previously mapped were positioned based on the
integrated genetic map (Maccaferri et al. 2015). RD: Relative distance. The centromere region is displayed in black. The confidence interval of the gene is indicated with black lines. (B) The physical position of LrCH1539 compared
with the previously reported Lr genes for seedling resistance to leaf rust on 2BS (10-Mb tick size map). The black
bar indicates an interval harboring an Lr gene flanked by two markers, and the dot indicates a single marker
representing an Lr gene. (A) LrCH1539 identified in the present study and Pt genes previously mapped were positioned based on the
integrated genetic map (Maccaferri et al. 2015). RD: Relative distance. The centromere region is displayed in black. The confidence interval of the gene is indicated with black lines. (B) The physical position of LrCH1539 compared
ith th
i
l
t d L
f
dli
i t
t l
f
t
2BS (10 Mb ti k i
) Th bl
k (A) LrCH1539 identified in the present study and Pt genes previously mapped were positioned based on the
integrated genetic map (Maccaferri et al. 2015). RD: Relative distance. The centromere region is displayed in black. The confidence interval of the gene is indicated with black lines. (B) The physical position of LrCH1539 compared
with the previously reported Lr genes for seedling resistance to leaf rust on 2BS (10-Mb tick size map). The black
bar indicates an interval harboring an Lr gene flanked by two markers, and the dot indicates a single marker
representing an Lr gene. Figure 6 PCR profiles of the marker sxau-2BS210 co-separated with LrCH1539 in several Chinese core germplasms in
breeding programs. The arrowhead indicated co-segregating PCR amplicons linked to LrCH1539. Numbers on the
left are the size in bp of the DNA ladder. Page 18/20 Figure 7
(A) LrCH1539 identified in the present study and Pt genes previously mapped were positioned based on the
integrated genetic map (Maccaferri et al. 2015). RD: Relative distance. The centromere region is displayed in b
The confidence interval of the gene is indicated with black lines. (B) The physical position of LrCH1539 compa
with the previously reported Lr genes for seedling resistance to leaf rust on 2BS (10-Mb tick size map) The bla Supplementary Files his is a list of supplementary files associated with this preprint. Click to download. SupplementryFigure1.png SupplementryFigure1.png Page 19/20 Page 19/20 20220126LrCH15392BSTableS14.xlsx 20220126LrCH15392BSTableS14.xlsx Page 20/20
|
https://openalex.org/W3165209919
|
https://medvis.vidar.ru/jour/article/download/1009/636
|
Russian
| null |
Metastasesin the pancreas: radiation methods assessment of cryodestruction
|
Medicinskaâ vizualizaciâ
| 2,021
|
cc-by
| 11,061
|
Авторы подтверждают отсутствие конфликтов интересов. Авторы подтверждают отсутствие конфликтов интересов. Авторы подтверждают отсутствие конфликтов интересов. р
р
у
ф
р
Для цитирования: Гальчина Ю.С., Карельская Н.А., Кармазановский Г.Г., Степанова Ю.А., Ионкин Д.А.,
Сташкив В.И., Чжао А.В. Метастазы в поджелудочной железе: лучевые методы оценки криодеструкции. Медицинская визуализация. 2021; 25 (1): 35–53. https://doi.org/10.24835/1607-0763-813 Поступила в редакцию: 02.10.2019. Принята к печати: 08.05.2020. Опубликована o оступила в редакцию: 02.10.2019. Принята к печати: 08.05.2020. Опубликована online: 22. в редакцию: 02.10.2019. Принята к печати: 08.05.2020. Опубликована online: 22.03.2021. Метастазы в поджелудочной железе:
лучевые методы оценки криодеструкции © Гальчина Ю.С.1*, Карельская Н.А.1, Кармазановский Г.Г.1, 2,
Степанова Ю.А.1, Ионкин Д.А.1, Сташкив В.И.1, Чжао А.В.1 ирургии имени А.В. Вишневского” Минздрава России; 117997 Москва, ул. Большая Серпуховская, д. 2
едерация ОУ ВО “РНИМУ имени Н.И. Пирогова” Минздрава России; 117997 Москва, ул. Островитянова, д. 1, Рос
ерация ИМУ имени Н.И. Пирогова” Минздрава России; 117997 Москва, ул. Островитянова, д. 1, Российская Метастазы в поджелудочной железе – достаточно редко встречающееся опухолевое поражение этого
органа. Согласно литературным данным, доля метастазов среди злокачественных опухолей поджелудоч-
ной железы варьирует от 1,8 до 4%. р
ру
,
В статье представлены три клинических наблюдения метастазов опухолей в поджелудочной железе –
метастазов меланомы, светлоклеточного рака почки, рака легкого. Все пациенты были оперированы с
использованием методов криохирургического воздействия с положительной динамикой в послеопераци-
онном периоде наблюдения. Также приведен краткий обзор литературы по проблеме метастатического поражения подже
железы и предложена тактика ведения таких пациентов. Ключевые слова: метастазы в поджелудочной железе, криодеструкция, КТ, МРТ Keywords: pancreatic metastases, cryodestruction, CT, MRI ISSN 1607-0763 (Print); ISSN 2408-9516 (Online)
https://doi.org/10.24835/1607-0763-813 ISSN 1607-0763 (Print); ISSN 2408-9516 (Online)
https://doi.org/10.24835/1607-0763-813 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT Metastasesin the pancreas: radiation
methods assessment of cryodestruction © Yulia S. Galchina1*, Natalya A. Karelskaja1, Grigory G. Kаrmаzаnovsky1, 2,
Yulia A. Stepanova1, Dmitry A. Ionkin1, Vladislava I. Stashkiv1, Aleksey V. Chzhao1 © Yulia S. Galchina1*, Natalya A. Karelskaja1, Grigory G. Kаrmаzаnovsky1, 2,
Yulia A. Stepanova1, Dmitry A. Ionkin1, Vladislava I. Stashkiv1, Aleksey V. Chzhao1 Введение ния. В качестве методов хирургического лечения
метастазов в поджелудочной железе описано
применение радиочастотной абляции и криодест-
рукции. В основе радиочастотной абляции лежит
термическое повреждение клеток при прохож де-
нии через них высокочастотного тока [8]. Приме-
нение этого метода при лечении метастатическо-
го рака поджелудочной железы описано в единич-
ных наблюдениях [9, 10]. Метод криодеструкции
основан на действии сверхнизких температур на
ткани, вследствие воздействия развивается не-
кроз [11]. Применение криодеструкции при мета-
статическом поражении поджелудочной железы
в литературе описано также в единичных клиниче-
ских наблюдениях [12, 13]. Метастазы в поджелудочной железе – доста-
точно редко встречающееся опухолевое пораже-
ние этого органа. По литературным данным, час-
тота метастатических новообразований в подже-
лудочной железе варьирует от 1,8 до 4% среди
всех ее новообразований [1, 2]. Наиболее часто в поджелудочной железе встре-
чаются метастазы светлоклеточного рака почки
и рака легкого. Гораздо реже в поджелудочную
железу метастазируют аденокарциномы желудоч-
но-кишечного тракта (толстой и тонкой кишки, пи-
щевода, желудка, желчного пузыря), рак щитовид-
ной и молочной железы, кожи, мочевого пузыря,
эндометрия и яичников [1–3]. В медицинской литературе также описано ме-
тастатическое поражение поджелудочной железы
при более редких первичных опухолях [4–7]. За период 2012–2019 гг. в ФГБУ “НМИЦ хирур-
гии имени А.В. Вишневского” Минздрава России
были обследованы и проходили лечение 14 паци-
ентов с метастатическим поражением поджелу-
дочной железы. В данной статье приведено 3 кли-
нических наблюдения, когда пациентам была
выпол нена криодеструкция метастатических оча-
гов в поджелудочной железе. M.A. Túlio и соавт. в 2018 г. представили редкое
клиническое наблюдение метастаза в поджелудоч-
ную железу нейроэндокринной карциномы шейки
матки в терминальной стадии [7]. В 2011 г. G.A. Falk описал единичный случай
метастаза аденоидной кистозной карциномы кор-
ня языка в поджелудочную железу. Ранее пациент
уже был оперирован в 1994 г. по поводу аденоид-
ной кистозной карциномы корня языка с после-
дую щей радиотерапией. Спустя 10 лет у пациента
выявлена опухоль головки поджелудочной железы. Была проведена пилоросохраняющая панкреато-
дуоденальная резекция. При морфологическом
исследовании в головке поджелудочной железы
верифицирован метастаз аденоидной кистозной
карциномы. Отмечается, что вторичное поражение
поджелудочной железы было выявлено спустя
189 мес после операции по поводу первичной опу-
холи [4]. © Yulia S. Galchina1*, Natalya A. Karelskaja1, Grigory G. Kаrmаzаnovsky1, 2,
Yulia A. Stepanova1, Dmitry A. Ionkin1, Vladislava I. Stashkiv1, Aleksey V. Chzhao1 sky National Medical Research Center of Surgery; 27, Bol'shaya Serpukhovskaia str., Moscow 117997, Russ .V. Vishnevsky National Medical Research Center of Surgery; 27, Bol'shaya Serpukhovskaia str., Moscow 117
Federation 1 A.V. Vishnevsky National Medical Research Center of Surgery; 27, Bol'shaya Serpukhovskaia str., Moscow
Federation 2 Pirogov Russian National Research Medical University of the Ministry of Health of Russia; house 1, Ostrivityanova str., Moscow
117997, Russian Federation Metastases in the pancreas are rather rare tumor lesion of this organ. According to different data, the incidence
of metastatic pancreatic lesions varies from 1.8 to 4% of all pancreatictumors. The article presents three clinical observations of metastases of melanoma, renal clearcell cancer, lung cancer
in the pancreas. All patients were treatedusing cryosurgical methods with positive dynamics in the postoperative
period. p
A brief review of the literature discussing metastatic lesions of the pancreas is also done, and the
treatment tactics of these patients is described. Keywords: pancreatic metastases, cryodestruction, CT, MRI MEDICAL VISUALIZATION
2021, V. 25 , N1 35 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT Conflict of interest. The authors declare no conflict of interest. The study had no sponsorship. For citation: Galchina Yu.S., Karelskaya N.A., Karmazanovsky G.G., Stepanova Yu.A., Ionkin D.A., Stashkiv V.I.,
Chzhao A.V. Metastasesin the pancreas: radiation methods assessment of cryodestruction. Medical Visualization. 2021; 25 (1): 35–53. https://doi.org/10.24835/1607-0763-813 Conflict of interest. The authors declare no conflict of interest. The study had no sponsorship. For citation: Galchina Yu.S., Karelskaya N.A., Karmazanovsky G.G., Stepanova Yu.A., Ionkin D.A., Stashkiv V.I.,
Chzhao A.V. Metastasesin the pancreas: radiation methods assessment of cryodestruction. Medical Visualization. 2021; 25 (1): 35–53. https://doi.org/10.24835/1607-0763-813 Published online: 22.03.2021. Accepted for publication: 08.05.2020. Клиническое наблюдение 1 Пациент 62 лет с диагнозом “метахронный светло-
клеточный рак почек, метастаз светлоклеточного рака
почки в головке поджелудочной железы”. Анамнез: в 2010 г. выявлена опухоль левой почки,
выполнена нефрэктомия слева, верифицирован свет-
локлеточный рак левой почки; в 2013 г. выявлена опу-
холь единственной правой почки, гиперваскулярный
метастаз в головке поджелудочной железы размером
15 мм, выполнена лапароскопическая резекция единст-
венной правой почки, верифицирован светлоклеточный
рак правой почки. В 2016 г. при контрольном УЗИ выявлено увеличение
размера метастаза в головке поджелудочной железы
до 15 мм, пациент направлен на КТ. По данным КТ 2016 г. в головке поджелудочной железы мягкотканное гипер-
васкулярное образование размером 18 мм (метастаз
светлоклеточного рака почки, рис. 1). Состояние после
нефрэктомии слева, резекции правой почки, данных
о рецидиве опухоли правой почки не получено. По дан-
ным МРТ 2016 г. в головке поджелудочной железы со-
лидной структуры образование, умеренно ограничиваю-
щее диффузию (значения на ADC в опухоли 0,9 мм2/с,
в неизмененной паренхиме 1,8 мм2/с) (рис. 2). Как правило, метастатическое поражение под-
желудочной железы клинически протекает бессимп-
томно и выявляется при исследованиях, которые
проводятся в рамках динамического наблюдения
пациентов по поводу основного заболевания [2]. Алгоритм лечения при метастатическом пора-
жении поджелудочной железы четко не опреде-
лен, в зависимости от объема поражения выпол-
няется резекция железы или проводится химиоте-
рапия. Методом паллиативного лечения является
локальная термодеструкция очагового образова- МЕДИЦИНСКАЯ ВИЗУАЛИЗАЦИЯ
2021, том 25, №1 36 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT Рис. 1. Компьютерные томограммы с внутривенным контрастным усилением, в головке поджелудочной железы
определяется гиперваскулярное мягкотканное образование (стрелка). а – артериальная фаза; б – венозная фаза. а
б а б а б Рис. 1. Компьютерные томограммы с внутривенным контрастным усилением, в головке поджелудочной железы
определяется гиперваскулярное мягкотканное образование (стрелка). а – артериальная фаза; б – венозная фаза. а Рис. 2. МР-томограммы, в головке поджелудочной железы определяется мягкотканное образование (стрелка). а – Т2ВИ; б – Т2 SPAIR; в – DWI, b = 600; г – ADC (по данным DWI, ADC умеренное ограничение диффузии). а
в
г
б б а б а г в г в Рис. 2. МР-томограммы, в головке поджелудочной железы определяется мягкотканное образование (стрелка). а – Т2ВИ; б – Т2 SPAIR; в – DWI, b = 600; г – ADC (по данным DWI, ADC умеренное ограничение диффузии). Пациенту с единственной почкой с учетом почечной
недостаточности по данным лабораторного исследова-
ния, локализации метастатического очага была выпол-
нена криодеструкция метастатического очага в головке
поджелудочной железы. Клиническое наблюдение 1 правой почке данных о рецидиве опухоли в ложе удален-
ной левой почки, метастазов в печени, а также увеличен-
ных лимфатических узлов не выявлено. В головке подже-
лудочной железы по ее передней поверх ности одиноч-
ный метастатический узел размерами 20 × 15 мм. правой почке данных о рецидиве опухоли в ложе удален-
ной левой почки, метастазов в печени, а также увеличен-
ных лимфатических узлов не выявлено. В головке подже-
лудочной железы по ее передней поверх ности одиноч-
ный метастатический узел размерами 20 × 15 мм. После мобилизации передней поверхности под-
желудочной железы при помощи аппарата “КРИО-МТ”
с аппликатором площадью рабочей части 2 см2 была
выполнена трехкратная криодеструкция с экспозицией
по 3 мин. Хирургическое вмешательство: криодеструкция ме-
тастаза рака почки в головке поджелудочной железы из
срединного лапаротомного доступа. По данным ревизии, интраоперационного УЗИ
(ИОУЗИ) патологических изменений в единственной MEDICAL VISUALIZATION
2021, V. 25 , N1 37 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT Рис. 3. Образование в головке поджелудочной железы
(стрелка), ПЭТ/КТ с ФДГ. а – КТ, артериальная фаза; б
КТ, венозная фаза; в – ПЭТ с РФП. Отмечается гетеро
генное по периферии накопление образованием кон
трастного вещества, накопления РФП не отмечено. а
б
в Рис. 4. Ультразвуковое изображение поджелудочной
железы (В-режим), в головке железы определяется
зона незначительно пониженной эхогенности. P
M а а б б Рис. 4. Ультразвуковое изображение поджелудочной
железы (В-режим), в головке железы определяется
зона незначительно пониженной эхогенности. Данные ПЭТ/КТ с ФДГ через 16 мес после операции:
выявлено гетерогенное, преимущественно по перифе-
рии, накопление контрастного вещества выявлявшимся
до выполнения криодеструкции метастазом в головке
поджелудочной железы, очаговой фиксации РФП в ме-
тастазе в головке поджелудочной железы не выявлено
(рис. 3). в в Данные УЗИ органов брюшной полости и забрюшин-
ного пространства через 18 мес после операции: в го-
ловке поджелудочной железы зона пониженной эхоген-
ности с нечеткими контурами размером 19 мм. При ду-
плексном сканировании кровоток в этой зоне не лоци-
ровался (рис. 4). Данные МРТ органов брюшной полости через 18 мес
после операции: в головке поджелудочной железы уча-
сток измененного сигнала размером 21 мм с четкими
контурами, прилежащий к неизмененному панкреати-
ческому протоку, умеренно ограничивающий диффу-
зию по данным DWI, ADC (значения на ADC 1–1,2
мм2/с, в неизмененной паренхиме 1,9 мм2/с). Других
изменений паренхиматозных органов метастатическо-
го характера, данных о рецидиве в ложе удаленной
левой почки, рецидиве опухоли правой почки не выяв-
лено (рис. 5). Рис. 3. Образование в головке поджелудочной железы
(стрелка), ПЭТ/КТ с ФДГ. Клиническое наблюдение 1 а – КТ, артериальная фаза; б –
КТ, венозная фаза; в – ПЭТ с РФП. Отмечается гетеро-
генное по периферии накопление образованием кон-
трастного вещества, накопления РФП не отмечено. Таким образом, через 4 мес после выполнения крио-
деструкции метастаза рака почки в головке поджелу-
дочной железы по данным ПЭТ/КТ не было выявлено
накопления контрастного вещества, РФП метастазом,
через 16 мес по данным ПЭТ/КТ выявлено гетероген-
ное, преимущественно по периферии, накопление кон-
трастного вещества метастазом. Через 18 мес после
криодеструкции увеличение значений измеряемого
коэф фициента диффузии (ИКД) в метастазе с 0,9 до
1,2 мм2/с. При УЗИ с дуплексным сканированием через
18 мес кровоток в метастазе не регистрировался. Увеличения размеров образования за весь период на-
блюдения не выявлено. Послеоперационный период протекал без осложне-
ний, признаков усиления существовавших до операции
проявлений хронической почечной недостаточности от-
мечено не было. Пациент был выписан в удовлетвори-
тельном состоянии на 9-е сутки после оперативного
вмешательства. Данные ПЭТ/КТ с ФДГ через 4 мес после операции:
данных о наличии очагов патологической фиксации
радио фармпрепарата (РФП) и очагов патологического
накопления контрастного вещества на уровне исследо-
вания, в том числе в головке поджелудочной железы,
не выявлено. МЕДИЦИНСКАЯ ВИЗУАЛИЗАЦИЯ
2021, том 25, №1 38 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT Рис. 5. МР-изображения. а – Т2 SPAIR; б – DWI, b = 600;
в – ADC. В головке поджелудочной железы участок
измененного сигнала с четкими контурами умеренно
ограничивает диффузию по данным DWI, ADC (стрелка). а
б
в а а иссле довании динамики не было выявлено. При бронхо-
скопии в 2016 г.: просвет левого верхнедолевого бронха
в проксимальном отделе был незначительно сужен,
в дистальном отделе обтурирован опухолевой тканью
белесоватого цвета. С учетом данных рентгенологи-
ческих и эндоскопических исследований в 2016 г. боль-
ному была выполнена расширенная верхняя лобэкто-
мия слева. При гистологическом исследовании был ве-
рифицирован метастаз меланомы. В 2017 г. при контрольном исследовании ПЭТ/КТ
были выявлены метастазы в надключичных лимфатиче-
ских узлах, была проведена полихимиотерапия. б б Спустя 10 мес с момента обнаружения метастаза
в веществе головного мозга при ПЭТ/КТ с ФДГ был также
выявлен гиперметаболический очаг в теле поджелудоч-
ной железы с блоком панкреатического протока (рис. 6). Спустя 10 мес с момента обнаружения метастаза
в веществе головного мозга при ПЭТ/КТ с ФДГ был также
выявлен гиперметаболический очаг в теле поджелудоч-
ной железы с блоком панкреатического протока (рис. 6). Клиническое наблюдение 1 У пациента с прогрессированием опухолевого про-
цесса (появление новых метастатических очагов на фо-
не химиотерапии) после проведения ряда хирургиче-
ских вмешательств без выявленного первичного очага
меланомы было принято решение отказаться от выпол-
нения обширной резекции поджелудочной железы. Была выполнена криодеструкция метастатического оча-
га в поджелудочной железе. в в Оперативное вмешательство: криодеструкция мета-
стаза меланомы в поджелудочной железе из верхнесре-
динного лапаротомного доступа. На операции: по передней поверхности начальных
отделов тела поджелудочной железы определялось
округлое, плотное образование до 2,5–3 см – метастаз
меланомы. При ИОУЗИ было подтверждено наличие метастаза в
поджелудочной железе. Иных очаговых образований
в поджелудочной железе по данным ИОУЗИ и пальпаторно
не было выявлено. Также не выявлены изменения желуд-
ка, стенок кишки, почек, органов малого таза, брюшины. Рис. 5. МР-изображения. а – Т2 SPAIR; б – DWI, b = 600;
в – ADC. В головке поджелудочной железы участок
измененного сигнала с четкими контурами умеренно
ограничивает диффузию по данным DWI, ADC (стрелка). С применением аппарата “КРИО-01” (Еламед) при
помощи аппликатора диаметром 3 см было произведе-
но 3 сеанса криодеструкции метастатического очага
в теле поджелудочной железы продолжительностью
по 3 мин. Клиническое наблюдение 2 В НМИЦ хирургии имени А.В. Вишневского обратил-
ся пациент 63 лет для дообследования и решения во-
проса о тактике лечения. При контрольной ПЭТ/КТ с ФДГ через 5 мес после
оперативного вмешательства: очагов патологической
фиксации РФП в поджелудочной железе не было выяв-
лено. Размеры образования в теле поджелудочной
желе зы уменьшились в 2 раза по сравнению с доопера-
ционными данными (рис. 7). Из анамнеза: пациент болен с июня 2015 г., когда
появились жалобы на общее недомогание, слабость,
головные боли. Была выполнена МРТ головного мозга,
выявлена опухоль левой лобной доли с выраженным
перифокальным отеком. В 2016 г. больному было вы-
полнено удаление опухоли левой лобной доли головно-
го мозга. Гистологический диагноз: метастаз мелано-
мы. Проведено 3 курса полихимиотерапии. В 2015 г. при
КТ было выявлено периферическое образование верх-
ней доли левого легкого. После проведения таргетной
терапии, полихимиотерапии при контрольном КТ- При МРТ органов брюшной полости через 9 мес:
в теле поджелудочной железы нечетко визуализировал-
ся участок измененного сигнала размером 19 мм, огра-
ничивающий диффузию по данным ДВИ, ИКД-карт
анало гично неизмененной паренхиме поджелудочной
железы (рис. 8). Таким образом, у пациента на протяжении всего пе-
риода наблюдения по результатам двух методов иссле- MEDICAL VISUALIZATION
2021, V. 25 , N1 39 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT Рис. 6. ПЭТ/КТ с ФДГ. а – КТ, венозная фаза; б – очаг патологической фиксации РФП (стрелка). а
б Рис. 6. ПЭТ/КТ с ФДГ. а – КТ, венозная фаза; б – очаг патологической фиксации РФП (стрелка). а
б б а а б Рис. 6. ПЭТ/КТ с ФДГ. а – КТ, венозная фаза; б – очаг патологической фиксации РФП (стрелка) б Рис. 7. ПЭТ/КТ с ФДГ. а – КТ, венозная фаза, уменьшение размеров образования поджелудочной железы; б – пато-
логической фиксации РФП образованием в теле поджелудочной железы не выявлено (стрелка). а
б а б а Рис. 7. ПЭТ/КТ с ФДГ. а – КТ, венозная фаза, уменьшение размеров образования поджелудочной железы; б – пато-
логической фиксации РФП образованием в теле поджелудочной железы не выявлено (стрелка). Рис. 8. МР-томограммы. а – Т1 FS; б – DWI, b = 600. В теле поджелудочной железы нечетко визуализируется участок
измененного сигнала, ограничивающий диффузию аналогично неизмененной паренхиме поджелудочной железы
(стрелка). а
б а б б а Рис. 8. МР-томограммы. а – Т1 FS; б – DWI, b = 600. В теле поджелудочной железы нечетко визуализируется участок
измененного сигнала, ограничивающий диффузию аналогично неизмененной паренхиме поджелудочной железы
(стрелка). Клиническое наблюдение 2 дования была отмечена динамика в виде уменьшения
размеров метастаза в теле поджелудочной железы
и снижения степени фиксации РФП метастазом. дования была отмечена динамика в виде уменьшения
размеров метастаза в теле поджелудочной железы
и снижения степени фиксации РФП метастазом. Пациент предъявлял жалобы на умеренные боли
в эпигастральной области. Из анамнеза: в 2015 г. был оперирован по поводу
опухоли левого легкого в объеме левосторонней пуль-
монэктомии. Клиническое наблюдение 3 Клиническое наблюдение 3 В НМИЦ хирургии имени А.В. Вишневского обратил-
ся пациент 60 лет для планового обследования. При КТ в НМИЦ хирургии имени А.В. Вишневского
от 2018 г.: в теле поджелудочной железы солидное гипо- МЕДИЦИНСКАЯ ВИЗУАЛИЗАЦИЯ
2021, том 25, №1 40 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT б а Рис. 9. Компьютерные томограммы с контрастным усиле нием, в теле поджелудочной железы определяется гипова-
скулярное новообразование (стрелка). а – артериальная фаза; б – венозная фаза. а
б б а Рис. 9. Компьютерные томограммы с контрастным усиле нием, в теле поджелудочной железы определяется гипова-
скулярное новообразование (стрелка). а – артериальная фаза; б – венозная фаза. а б Рис. 10. Компьютерные томограммы с контрастным усилением, размер, структура, характер контрастирования
образования в теле поджелудочной железы и степень локальной распространенности прежние (стрелка). а – арте-
риальная фаза; б – венозная фаза. а
б б а Рис. 10. Компьютерные томограммы с контрастным усилением, размер, структура, характер контрастирования
образования в теле поджелудочной железы и степень локальной распространенности прежние (стрелка). а – арте-
риальная фаза; б – венозная фаза. васкулярное образование размером 50 мм, с бугристыми
контурами, с распространением изменений на ретропан-
креатическую клетчатку. Селезеночная вена и артерия
проходили в структуре опухолевого инфильтрата (рис. 9). логическое исследование. Других изменений метаста-
тического характера при ревизии выявлено не было. С применением аппарата “КРИО-01” (Еламед) при
помощи аппликатора диаметром 3 см была произве-
дена криодеструкция опухоли тела поджелудочной
железы доступом через ее переднюю поверхность на-
конечниками диаметром 30 мм (центр) и 20 мм (на 14 и
19 часах) из 3 точек с экспозицией по 3 мин. С учетом локализации очага, местной распростра-
ненности процесса и соматического состояния пациен-
та было принято решение о проведении криодеструк-
ции метастаза в теле поджелудочной железы. Оперативное вмешательство: криодеструкция опу-
холи тела поджелудочной железы. При гистологическом исследовании биопсийного
материала: в операционном материале были выявлены
участки опухоли, имеющей строение, соответствующее
плоскоклеточному раку с очагами ороговения. В теле поджелудочной железы визуально и пальпа-
торно определялась плотная бугристая округлая не-
смещаемая опухоль размерами 60 мм. Из опухоли тела
железы взята биопсия, направлена на плановое гисто- Послеоперационный период протекал без ослож-
нений. Пациент был выписан в удовлетворительном MEDICAL VISUALIZATION
2021, V. 25 , N1 41 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT внекле точная среда потенцировала выход внутри-
клеточных кристаллов воды во внеклеточное про-
странство с разрушением мембран клеток и дена-
турацией белка, что неизбежно приводило к не-
крозу и апоптозу клеток. В последующем в зоне
криовоздействия автор наблюдал развитие фи-
броза [19]. Обсуждение Криохирургические технологии применяются
в абдоминальной хирургии с начала 60–70-х годов
прошлого столетия [14]. Развитие криохирургии
в СССР в 80-е годы прошлого столетия началось
с работ по изучению криовоздействия на печень
и поджелудочную железу в эксперименте, позже
результаты были внедрены в практику [15]. Воз-
можность мониторирования криовоздействия при
помощи ИОУЗИ в начале 80-х годов (Onik G.M.,
1982) стимулировала внедрение криодеструкции
в клиническую практику [16]. Новый этап развития
криохирургии начался в 1990-х годах за счет рас-
пространения современных методов лучевой ди-
агностики и появления новых моделей криогенной
аппаратуры [17]. Так, в 1991 г. российские иссле-
дователи доложили о возможности использования
криохирургии в комбинации с лучевой терапией
при местнораспространенном раке поджелудоч-
ной железы [11]. По данным литературы, криодеструкция при-
меняется при опухолях печени в рамках радикаль-
ных и паллиативных вмешательств, при местно-
рас пространенных первичных опухолях поджелу-
дочной железы [18, 21]. Метастатическое поражение поджелудочной
железы встречается гораздо реже, чем первичные
опухоли [1]. При метастазах в поджелудочной железе при-
менение криовоздействия описано в единичных
исследованиях. Так, L. Niu и соавт. в зависимости
от метода лечения разделили в своем исследова-
нии 106 пациентов на 4 группы: пациенты, кото-
рым выполнена криоиммунотерапия (31 человек),
пациенты, которым выполнена криотерапия
(36 человек), пациенты, которым выполнена крио-
терапия иммунотерапия (17 человек) и химио-
терапия (22 человека). Общая выживаемость по-
сле диагностики метастатического рака поджелу-
дочной железы была оценена после 4-летнего на-
блюдения. Медиана общей выживаемости была
выше в группах пациентов, которым выполнялась
криоиммунотерапия (13 мес) и криотерапия
(7 мес), чем в группе пациентов, которым выпол-
нялась химиотерапия (3,5 мес; p < 0,001). У паци-
ентов, которым выполнялась криоиммунотерапия
и криотерапия, медиана общей выживаемости
была выше после множественных криодеструк-
ций, чем после однократной криодеструкции
(p = 0,0048 и 0,041 соответственно). На основании
результатов проведенного исследования авторы
сделали вывод, что криоиммунотерапия значи-
тельно увеличила общую выживаемость при мета-
статическом раке поджелудочной железы. Мно-
жественные сеансы криодеструкции были связа-
ны с лучшим прогнозом выживаемости [12]. В 2002 г. S.J. Kovach и соавт. привели первую
фазу клинических испытаний применения криохи-
рургии при раке поджелудочной железы. В иссле-
дование было включено 9 пациентов с нерезекта-
бельными опухолями поджелудочной железы, ко-
торым выполнены сеансы криодеструкции под
ультразвуковым контролем. Все вмешательства
прошли без осложнений, с положительным клини-
ческим эффектом [18]. Механизмы криовоздействия и ультраструктур-
ные морфологические изменения в опухолевой тка-
ни после криовоздействия изучал N.N. Korpan [19]. Так, уже к 2007 г. в эксперименте N.N. Клиническое наблюдение 3 Стенки сосудов малого калибра также
подвергались некрозу. Сосуды крупного калибра
в эксперименте оказались более устойчивы к воз-
действию сверхнизких температур ввиду наличия
хорошо выраженной коллагеновой стромы сосу-
да, которая под воздействием сверхнизких темпе-
ратур не разрушается, и в дальнейшем стенка
реге нерирует, а также вследствие большего объе-
ма кровотока в просвете крупных сосудов и соот-
ветственно менее эффективного криовоздейст-
вия [20]. состо янии на 8-е сутки после оперативного вмешатель-
ства, болевой синдром был полностью купирован. При контрольной КТ через 3 мес в НМИЦ хирургии
имени А.В. Вишневского: образование в поджелудоч-
ной железе не увеличилось в размере по сравнению
с дооперационными данными, степень локальной рас-
пространенности прежняя (рис. 10). Таким образом, при динамическом наблюдении зо-
ны криодеструкции через 3 мес размеры образования
и степень местной распространенности были прежние. Обсуждение Korpan
описал структурные изменения после криодест-
рукции ткани поджелудочной железы у экспери-
ментальных животных (собак) и наблюдал зону
криовоздействия в динамике. Криодеструкция
проводилась при температурах −80 °С и −100 °С. Было доказано, что в первые часы после воздей-
ствия в зоне криодеструкции развивается отек,
хоро шо отграниченный морфологически от неиз-
мененной ткани. В тканях при криовоздействии
происходит кристаллизация внутриклеточной
и внеклеточной жидкости. Гиперосмолярная P. Jin и соавт. провели ретроспективный анализ
результатов лечения пациентов с первичным ра- P. Jin и соавт. провели ретроспективный анализ
результатов лечения пациентов с первичным ра- МЕДИЦИНСКАЯ ВИЗУАЛИЗАЦИЯ
2021, том 25, №1 42 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT ком поджелудочной железы и метастазами в под-
желудочной железе. В исследование было вклю-
чено 66 пациентов: с первичными опухолями под-
желудочной железы – 34 пациента, с метастатиче-
скими опухолями – 32. В 1-й группе у 12 пациентов
выполнена радикальная операция, у 3 – криодест-
рукция опухоли поджелудочной железы. Медиана
выживаемости у пациентов после радикальных
операций составила 23 мес (от 2 до 50 мес), у па-
циентов, которым выполнялась криодеструкция, –
12 мес (от 6 до 19 мес). Во второй группе 8 паци-
ентам выполнены радикальные операции, крио-
деструкция опухоли выполнена 3 пациентам. При
анализе медианы выживаемости пациентов вто-
рой группы значимых различий результатов в груп-
пах пациентов, которым была выполнена ради-
кальная операция, и пациентов, которым была
выполнена криодеструкция, не получено. Пока-
затели выживаемости 1 и 2 года для этих пациен-
тов составили 38,1 и 16,6% соответственно [13]. По мнению исследователей [12, 13], применение
криодеструкции при метастатическом поражении
поджелудочной железы оправдано. Более того,
результаты криодеструкции, дополненные соот-
ветствующей химиотерапией, могут быть сопоста-
вимы с результатами радикальных оперативных
вмешательств [12, 13, 21]. новом обследовании была выявлена опухоль в те-
ле поджелудочной железы. Дифференциальная
диагностика проводилась между первичной опу-
холью и вторичным поражением поджелудочной
железы. При биопсии был верифицирован мета-
стаз плоскоклеточного рака легкого. При динами-
ческом КТ-контроле после криодеструкции увели-
чения размеров образования, а также увеличения
степени локальной распространенности процесса
не было выявлено. Заключение Метастазы в поджелудочной железе встреча-
ются относительно редко. При выявлении очаго-
вых изменений в поджелудочной железе и форми-
ровании предварительного диагноза необходимо
учитывать анамнез, так как метастатическое пора-
жение поджелудочной железы может выявляться
в отдаленные сроки после выявления первичной
опухоли. Наиболее часто в поджелудочной железе
встречаются метастазы почечно-клеточного рака. Единственными радикальным методами лечения
при метастазах в поджелудочной железе являются
радикальные оперативные вмешательства. В си-
туациях, когда выполнение радикального опера-
тивного вмешательства невозможно либо риск
радикальной операции очень высок вследствие
распространенности процесса или тяжелого со-
стояния пациента, оправдано применение метода
криодеструкции опухоли. Результаты криодест-
рукции метастатических очагов в поджелудочной
железе, дополненной соответствующей химиоте-
рапией, могут быть сопоставимы с радикальными
оперативными вмешательствами. Для достиже-
ния наилучших результатов лечения данная группа
пациентов должна получать помощь в многопро-
фильных центрах с командой специалистов (хи-
рурги, лучевые диагносты, химиотерапевты). [
]
В нашем исследовании в двух представленных
клинических наблюдениях у пациентов, которым
была выполнена криодеструкция метастазов
в поджелудочной железе, было выявлено стойкое
уменьшение болевого синдрома. В первом на-
блюдении у пациента с метастазом почечно-кле-
точного рака до 6 мес при КТ и ПЭТ с ФДГ не было
выявлено патологического накопления контраст-
ного вещества и РФП в ранее выявленном очаге,
вероятно, за счет снижения васкуляризации опу-
холи. Через 2,5 года при контрольной КТ было от-
мечено периферическое контрастное усиление,
однако размеры метастаза не увеличились. При
магнитно-резонансной томографии было отмече-
но повышение значений ИКД в очаге за период
наблюдения, вероятно, за счет снижения клеточ-
ности в очаге. Во втором случае у пациента с мета-
стазом меланомы в поджелудочную железу за пе-
риод наблюдения было выявлено стойкое умень-
шение размеров метастаза более чем в 2 раза,
отсутствие накопления РФП в очаге при ПЭТ/КТ. При магнитно-резонансной томографии степень
ограничения диффузии в очаге аналогична огра-
ничению диффузии неизмененной паренхимой
поджелудочной железы. В третьем случае у паци-
ента через 3 года после пульмонэктомии при пла- Clinical observation 1. Most often, metastases of clear cell renal cell
carci noma and lung cancer form in the pancreas. Less often, adenocarcinomas of the gastrointestinal
tract (colon and small intestine, esophagus, stomach,
and gallbladder), thyroid and breast cancer, skin,
bladder, endometrium, and ovarian cancer metasta-
size to the pancreas [1-3]. A 60-year-old patient visited A.V. Vishnevsky NMRC of
Surgery for a routine examination of renal cell carcinoma. Medical history: In 2010, a left nephrectomy was per-
formed for cancer of the left kidney. In 2013, cancer of the
right kidney was detected, and laparoscopic resection of the
right kidney was performed. Histologically, in both cases,
clear cell renal cell carcinoma was verified. For the first time,
a vascularized soft tissue formation measuring 15 mm in the
head of the pancreas was detected by ultrasound in 2013. A control ultrasound revealed an increase in the size of the
formation in the head of the pancreas to 18 mm in 2016. In the medical literature, secondary lesions of the
pancreas and more rare primary tumors are also de-
scribed [4–7]. M.A. Túlio et al. presented a rare clinical case of
pancreatic metastasis in terminal stage of neuroendo-
crine cervical carcinoma in 2018 [7]. According to the computed tomography at A.V. Vish-
nevsky NMRC of Surgery dated 2016, a soft-tissue hyper-
vascular formation with clear, even contours was detected in
the head of the pancreas; it accumulated a contrast agent in
the arterial and venous phases of the study mainly, isodense
parenchyma of the pancreas in the native and delayed
phases of the study, measuring 18 mm. The left kidney was
removed. Nephrosclerosis of the right kidney were identi-
fied; there was no evidence of tumor recurrence. G.A. Falk described a single case of metastasis
of adenoid cystic carcinoma of the tongue root to the
pancreas in 2011. Previously, the patient had already
underwent a surgery for adenoid cystic carcinoma
of the tongue root in 1994, followed by radiotherapy. 10 years later, the patient developed pain-free jaun-
dice and generalized itching. Retrograde cholangio-
pancreatography revealed a narrowing of the termi-
nal part of the choledochus. Pylorus-preserving pan-
creatoduodenal resection was performed. Morpho-
logical examination revealed metastasis of adenoid
cystic carcinoma in the head of the pancreas. It is
noted that a secondary lesion of the pancreas was
detected 189 months after the surgery for the pri-
mary tumor [4]. Clinical observation 1. CT-examination: The status after left nephrectomy, re-
section of the right kidney. Small hypervascular formation of
the pancreas head. Considering the medical history, sec-
ondary origin are probable (Fig. 1) In August 2016, MRI was performed: an oval-shaped
formation with uneven clear contours,18 mm in size was
determined in the head of the pancreas along the anterior
surface; the formation moderately limited diffusion accord-
ing to DWI, ADC data (ADC values 0.9–1 mm2/s). The pan-
creatic duct was not dilated. The left kidney was removed. Nephrosclerosis of the right kidney were identified; there
was no evidence of tumor recurrence. As a rule, metastatic pancreatic lesion is clinically
asymptomatic and is detected during follow-up ex-
amination of patients for the underlying disease [2]. The treatment strategy for metastatic pancreatic
lesion is not clearly defined: depending on the volume
of the lesion, resection of the gland or chemotherapy
are performed. Palliative treatment methods include
local thermal destruction of the focal formation. RF ablation and cryodestruction are also described in
cases of pancreatic metastases. RF ablation is based
on thermal damage to cells, when a high-frequency
current passes through them [8]. The use of this
method in the treatment of metastatic pancreatic
cancer is described in single observations [9, 10]. The cryodestruction method is based on the effect of
ultra-low temperatures on the tissue, causing its ne-
crosis [11]. The use of cryodestruction in secondary
pancreatic lesions is also recorded in the literature
in rare single clinical observations [12, 13]. MR-examination: The status after left nephrectomy, re-
section of the right kidney. MR-image of neoplasm in the
pancreas head (metastasis) (Fig. 2). MR-examination: The status after left nephrectomy, re-
section of the right kidney. MR-image of neoplasm in the
pancreas head (metastasis) (Fig. 2). It was decided to carry out cryodestruction of metasta-
sis in the head of the pancreas in the patient with a single
kidney and renal failure, considering the solitary nature of
the lesion and its localization. Surgical intervention: Cryoablation of metastasis of re-
nal cancer in the head of the pancreas from the midline ap-
proach. When the abdominal cavity examination, there was no
ascite. The peritoneum was shiny and smooth. There were
no pathological changes in liver, stomach, loops of the small
and large intestine, and pelvic organs. The left kidney was
removed. The resected right kidney was enlarged. Abnormal
formation was not determined by palpation. Introduction in the A.V. Vishnevsky National Medical Research
Center of Surgery of the Ministry of Health of the
Russian Federation. The article presents 3 clinical
cases, in which cryodestruction was performed in the
setting of metastatic foci in the pancreas. Metastases to the pancreas are a rather rare onco-
logical lesion of this organ. According to the literature
data, frequency of metastatic neoplasms in the pan-
creas varies from 1.8% to 4% among all pancreatic
neoplasms [1, 2]. Участие авторов Гальчина Ю.С. – сбор и обработка материала, напи-
сание и редактирование текста. Карельская Н.А. – концепция и дизайн исследова-
ния, подготовка и редактирование текста, утверждение
окончательного варианта статьи. Кармазановский Г.Г. – концепция и дизайн исследо-
вания, подготовка и редактирование текста, утвержде-
ние окончательного варианта статьи. Степанова Ю.А. – подготовка и редактирование тек-
ста, утверждение окончательного варианта статьи. Степанова Ю.А. – подготовка и редактирование тек-
ста, утверждение окончательного варианта статьи. Ионкин Д.А. – подготовка и редактирование текста. Сташкив В.И. – перевод текста на английский язык. Чжао А.В. – подготовка и редактирование текста. MEDICAL VISUALIZATION
2021, V. 25 , N1 43 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT Clinical observation 1. From 2012 to 2019, 14 patients with a metastatic
lesion of the pancreas were examined and treated МЕДИЦИНСКАЯ ВИЗУАЛИЗАЦИЯ
2021, том 25, №1 44 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT Fig. 1. CT scans with contrast enhancement, hypervascular tumor (arrow) in the head of the pancreas. a – arterial phase;
b – venous phase. a
b a b a b contrast enhancement, hypervascular tumor (arrow) in the head of the pancreas. a – arterial phase; Fig. 1. CT scans with contrast enhancement, hypervascular tumor (arrow) in the head of the pancreas. a – arterial phase;
b – venous phase. b a Fig. 2. MRI tomograms, tumor (arrow) in the head of the pancreas. a – T2VI; b – T2 SPAIR; c – DWI, b = 600; d – ADC
(according to DWI, ADC moderate diffusion limitation). a
c
d
b a b a c d d c Fig. 2. MRI tomograms, tumor (arrow) in the head of the pancreas. a – T2VI; b – T2 SPAIR; c – DWI, b = 600; d – ADC
(according to DWI, ADC moderate diffusion limitation). According to the intra-operative US, there were no
pathological changes in the last kidney, formations in the
liver, as well as enlarged lymph nodes. In the area of the
head of the pancreas along the anterior surface, a single
metastatic node measuring 15 × 20 mm was determined. chronic renal failure. The patient was discharged in satisfac-
tory condition on the 9th day after surgery. After 4 months, PET-CT with FDG was performed: there
were no data for the presence of focal pathological fixation
of the radiopharmaceutical agent and foci of pathological
accumulation of the contrast agent at the study level, in-
cluding in the pancreatic parenchyma. The anterior surface of the soft pancreas was mobilized. In the area of the head, a single dense node with dimensions
of 15 × 20 mm was revealed on the front surface. Using the
CRYO-MT device with an applicator of 2 cm body in area,
three cryodestructions with a 3-minute exposure were per-
formed. PET-CT with FDG after 16 months revealed hetero-
geneous peripheral accumulation of contrast agent by for-
mation in the head of the pancreas was noted, but no ac-
cumulation of FDG was observed (Fig. 3). Clinical observation 1. The postoperative period was uneventful: there were no
signs of intensification of the existing manifestations of Ultrasound of the abdominal cavity and retroperitoneal
space after 18 months: in the head of the pancreas, an area MEDICAL VISUALIZATION
2021, V. 25 , N1 45 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT Fig. 3. The tumor in the head of the pancreas (arrow), PET
CT with FDG. a – CT arterial phase; b – CT venous phase
c– PET with FDG. A peripheral heterogeneous accumulatio
is noted by the formation of a contrast medium; accumulatio
of FDG not noted. a
b
c Fig. 4. Ultrasound image of the pancreas (B-mode), in the
head of the pancreas, a zone of slightly reduced echogenicity
is determined. P
M a a Fig. 4. Ultrasound image of the pancreas (B-mode), in the
head of the pancreas, a zone of slightly reduced echogenicity
is determined. Fig. 5. MR images. a – T2 SPAIR; b – DWI, b = 600; c –
ADC. In the pancreatic head is detected tumor with well-
definedcontours, according to DWI, ADC moderate diffusion
limitation (arrow). a
b
c b Fig. 4. Ultrasound image of the pancreas (B-mode), in the
head of the pancreas, a zone of slightly reduced echogenicity
is determined. b a a c c b b Fig. 3. The tumor in the head of the pancreas (arrow), PET/
CT with FDG. a – CT arterial phase; b – CT venous phase;
c– PET with FDG. A peripheral heterogeneous accumulation
is noted by the formation of a contrast medium; accumulation
of FDG not noted. c c of reduced echogenicity with indistinct contours measuring
18.8 mm was determined. During duplex scanning, the
blood flow in this area was not localized (Fig. 4). MRI of the abdominal organs after 18 months: in the
head of the pancreas, a zone of the altered signal 21 mm in
size, with clear contours, moderately limiting diffusion ac-
cording to DWI, ADC (ADC values 1–1.2 mm2/s), adjacent to
the pancreatic duct, was determined. No other areas of the
pathological signal in the parenchyma of the gland were
detected. The pancreatic duct was no more than 3 mm
along the entire length (Fig. 5). of reduced echogenicity with indistinct contours measuring
18.8 mm was determined. During duplex scanning, the
blood flow in this area was not localized (Fig. 4). Clinical observation 2. A 63-year-old patient visited A.V. Vishnevsky NMRC of
Surgery for further examination and treatment strategy de-
cision. During the revision, there was no exudate in the ab-
dominal cavity. The peritoneum was shiny and smooth. The
peripheral lymph nodes were not enlarged. The omental
bursa was opened. On the anterior surface of the initial
parts of the pancreas body, a rounded, dense formation up
to 2.5–3 cm in size – a melanoma metastasis – located in
the projection of the superior mesenteric vein, was identi-
fied. Medical history: the patient considered himself ill since
June 2015, when complaints of general ailment, weakness,
and headaches appeared. An MRI of the brain was per-
formed, and a tumor of the left frontal lobe with pronounced
perifocal edema was detected. On August 19, 2016, the
patient underwent removal of the tumor of the left frontal
lobe of the brain. Histological diagnosis: metastasis of mel-
anoma. 3 courses of polychemotherapy (monochemothera-
py with Temodal, target therapy with Zelboraf) were per-
formed. In 2015, computed tomography revealed a periph-
eral formation of the upper lobe of the left lung. After tar-
geted therapy and polychemotherapy, CT scans of the chest
organs showed no dynamics. Bronchoscopy dated August
26, 2016: lumen of the left upper lobe bronchus in the
proximal part was slightly narrowed, in the distal part it was
obstructed by a whitish tumor tissue. Taking into account
the X-ray and endoscopic data, the patient underwent an
extended upper lobectomy on the left lung. Histological ex-
amination revealed metastasis of melanoma. An intra-operative US confirmed the presence of metas-
tasis in the pancreas. No other focal formations were de-
tected according to the intra-operative US and palpatory
data. No pathological changes were noted in stomach, in-
testinal loops, kidneys, and pelvic organs. Using the “CRYO-01” device (Elamed, Russia) with an
applicator of 3 cm in diameter, three 3-minute sessions of
cryodestruction of a metastatic lesion in the body of the
pancreas were performed. During control PET-CT with FDG 5 months after surgery,
foci of pathological fixation of the radiopharmaceutical
agent in the pancreas were not detected. The size of the
formation in the pancreas body decreased by 2 times com-
pared to the preoperative data (Fig. 7). In the future, a follow-up PET-CT examination revealed
metastases in the supraclavicular lymph nodes, for which
polychemotherapy was performed. Clinical observation 1. MRI of the abdominal organs after 18 months: in the
head of the pancreas, a zone of the altered signal 21 mm in
size, with clear contours, moderately limiting diffusion ac-
cording to DWI, ADC (ADC values 1–1.2 mm2/s), adjacent to
the pancreatic duct, was determined. No other areas of the
pathological signal in the parenchyma of the gland were
detected. The pancreatic duct was no more than 3 mm
along the entire length (Fig. 5). Fig. 5. MR images. a – T2 SPAIR; b – DWI, b = 600; c –
ADC. In the pancreatic head is detected tumor with well-
definedcontours, according to DWI, ADC moderate diffusion
limitation (arrow). МЕДИЦИНСКАЯ ВИЗУАЛИЗАЦИЯ
2021, том 25, №1 46 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT Fig. 6. PET/CT with FDG. a – CT venous phase; b – is the focus of pathological fixation of the FDG (arrow). a
b a b T/CT with FDG. a – CT venous phase; b – is the focus of pathological fixation of the FDG (arrow). Thus, there was no accumulation of contrast agent in CT
and FDG in PET-CT in the formation of pancreatic head for
4–6 months; after 16–18 months, there was an accumulation
of contrast agent in contrast enhanced computed tomo-
graphy. During the observation period, magnetic resonance
imaging showed an increase in the measured diffusion coef-
ficient in the formation from 0.9 mm2/s to 1.2 mm2/s. During
ultrasound duplex scanning, the blood flow in the formation
was not recorded. No increase in the size of the formation
was detected during the entire observation period. metabolic focus in the body of the pancreas, blocking the
pancreatic duct (Fig. 6). The patient suffered from a persis-
tent pain in the epigastric region. It was decided to refuse to perform an extensive resec-
tion of the pancreas in the patient with the progression of
the oncological process (the appearance of new second-
ary formations in the setting of chemotherapy), after sev-
eral surgical interventions, without a primary focus of
melanoma. Cryoablation of the metastatic lesion was per-
formed. Surgical intervention: Cryodestruction of melanoma
metastasis in the pancreas from the upper-midline access. Clinical observation 2. According to the MRI of the abdomen after 9 months:
in the body of the pancreas, a section of the altered signal
with a size of 19 mm, limiting the diffusion similarly to the
unchanged pancreatic parenchyma, was indistinctly visua-
lized (Fig. 8). 10 months after the discovery of a secondary focus in
the brain substance, PET-CT with FDG revealed a hyper- MEDICAL VISUALIZATION
2021, V. 25 , N1 47 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT Fig. 7. PET/CT with FDG. a – CT venous phase, a decrease in the size of the tumor of the pancreas; b – pathological fixation
of the FDG in the tumor of the body of the pancreas was not detected (arrow). a
b b a a b Fig. 7. PET/CT with FDG. a – CT venous phase, a decrease in the size of the tumor of the pancreas; b – pathological fixation
of the FDG in the tumor of the body of the pancreas was not detected (arrow). Fig. 8. MR-tomograms. a – T1 FS; b – DWI, b = 600. In the body of the pancreas, a tumor that not clear visualized, with
moderate diffusion limitation similarly unchanged pancreatic parenchyma (arrow). a
b b a a b a Fig. 8. MR-tomograms. a – T1 FS; b – DWI, b = 600. In the body of the pancreas, a tumor that not clear visualized, with
moderate diffusion limitation similarly unchanged pancreatic parenchyma (arrow). Thus, according to the results of two research methods,
the patient showed dynamics such as a decrease in the size
of the metastasis in the pancreatic body and a decrease
in the fixation of the radiopharmaceutical agent by the me-
tastasis during the entire follow-up period. the focus, the local prevalence of the process, and the so-
matic state of the patient. Surgical intervention: Cryodestruction of the pancreatic
body tumor from the bi-ribbed transverse access. On surgery, there was no exudate in the abdominal cav-
ity. The peritoneum was smooth, clean, shiny, without visible
pathological changes. The liver was visually brilliant, of nor-
mal color and tight-elastic consistency, without focal lesions
visually and by palpation. Visible loops of the small and large
intestines, the stomach had no peculiarities. The gallblad-
der was not changed. Entrance to the omental bursa was
made. Clinical observation 2. In the body of the pancreas, a dense, bumpy, round-
ed, non-displaced tumor with dimensions of 6.0 × 5.0 cm
was detected visually and by palpation. A biopsy was taken
from the tumor of the gland body and sent for a planned
histological examination. Clinical observation 3. A 60-year-old patient visited A.V. Vishnevsky NMRC of
Surgery for a routine examination. The patient complained of moderate pain in the epigas-
tric region. Medical history: In 2015, he was operated on for a neo-
plasm in the root of the left lung in the volume of a left-sided
pulmonectomy. According to the computed tomography at A.V. Vish-
nevsky NMRC of Surgery dated 2018: a hypovascular for-
mation of 50 mm in size with bulging contours was deter-
mined in the body of the pancreas. The splenic vein and ar-
tery were located within the formation (Fig. 9). Using the “CRYO-01” device (Elamed, Russia), with an
applicator of 3 cm in diameter, cryodestruction of the tumor
of the pancreatic body was performed by access through its
anterior surface with tips of 30 mm (center) in diameter and
20 mm (at 14 o'clock and 19 o'clock) from 3 points with a
3-minute exposure. CT-examination: formation of the pancreatic body, a dif-
ferential diagnosis should be made between primary tumor
and metastasis. It was decided to perform cryodestruction
of the pancreatic formation, considering the localization of МЕДИЦИНСКАЯ ВИЗУАЛИЗАЦИЯ
2021, том 25, №1 48 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT a b Fig. 9. CT scans with contrast enhancement, in the body of the pancreas, a hypovascular neoplasm is determined (arrow). a – arterial phase; b – venous phase. a
b b a a b Fig. 9. CT scans with contrast enhancement, in the body of the pancreas, a hypovascular neoplasm is determined (arrow). a – arterial phase; b – venous phase Fig. 9. CT scans with contrast enhancement, in the body of the pancreas, a hypovascular neoplasm is determined (arrow). a – arterial phase; b – venous phase. Fig. 10. CT scans with contrast enhancement, size, structure, pattern of contrast enhancement tumor in the body of the
pancreas and degree of local prevalence former (orange arrow). a – arterial phase; b – venous phase. a
b b a Fig. 10. CT scans with contrast enhancement, size, structure, pattern of contrast enhancement tumor in the body of the
pancreas and degree of local prevalence former (orange arrow). a – arterial phase; b – venous phase. Discussion Histological examination of the biopsy material revealed
areas of the tumor with a structure corresponding to squa-
mous cell carcinoma with cornification foci. Cryosurgical technologies have been used in ab-
dominal surgery since the beginning of the 60–70s
of the last century [14]. Development of cryosurgery
in the USSR started in the 80s with the study of cryo-
exposure on liver and pancreas in an experiment, later
the results were implemented in the clinic [15]. In the
early 80's, possibility of monitoring cryopreservation
using intraoperative ultrasound (Onik G. M., 1982)
stimulated introduction of cryodestruction in clinical
practice (Korpan N. N. [16]). A new stage of cryosur-
gery development began in the 1990s due to spread of The postoperative period was uneventful. The patient
was discharged in a satisfactory condition on the 8th day
after surgery, the pain syndrome was completely managed. According to the control CT in 3 months at A.V. Vish nevsky
NMRS of Surgery: the formation in the pancreas did not in-
crease in size in comparison with the preoperative data, the
degree of local prevalence remained the same (Fig. 10). Thus, the size of the formation and the degree of local
prevalence remained the same, when the cryodestruction
zone was observed dynamically after 3 months. MEDICAL VISUALIZATION
2021, V. 25 , N1 49 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT modern methods of radiological diagnostics and emer-
gence of new models of cryogenic equipment [17]. Thus, in 1991, Russian researchers reported on the
possibility of using cryosurgery in combination with ra-
diotherapy for locally advanced pancreatic cancer [11]. modern methods of radiological diagnostics and emer-
gence of new models of cryogenic equipment [17]. Thus, in 1991, Russian researchers reported on the
possibility of using cryosurgery in combination with ra-
diotherapy for locally advanced pancreatic cancer [11]. dian OS was higher in the cryoimmunotherapy
(13 months) and cryotherapy (7 months) groups than
in the chemotherapy group (3.5 months; both
P < 0.001). It was also higher in the cryoimmunother-
apy group compared with the cryotherapy (P < 0.05)
and immunotherapy groups (5 months; P < 0.001). Both the cryoimmunotherapy group and the cryo-
therapy group were characterized by higher median
OS was after multiple cryoablations than after a single
cryoablation (P = 0.0048 and 0.041, respectively). Based on the study, the authors concluded that cryo-
immunotherapy significantly increased OS in meta-
static pancreatic cancer. Discussion Multiple cryoablation ses-
sions were associated with a better prognosis [12]. In 2002, S.J. Kovach et al. presented the first
phase of clinical trials of the use of cryosurgery in
pancreatic cancer. The study included 9 patients
with unresectable pancreatic tumors, who underwent
10 sessions of cryodestruction under ultrasound con-
trol. All interventions were performed without compli-
cations, with a positive clinical effect [18]. N.N. Korpan actively studied the principle of expo-
sure and ultrastructural morphological changes in tu-
mor tissue [19]. p
g
[
]
P. Jin et al. have conducted a retrospective analysis
of the results of treatment of patients with primary pan-
creatic cancer and metastases in the pancreas. The
study included 66 patients: 34 patients with primary
pancreatic tumors, and 32 patients with metastatic tu-
mors. In the first group, 32 patients had verified adeno-
carcinoma, one patient had serous cystadenocarci-
noma, and one patient had malignant insulinoma. In
the second group, metastases of lung cancer, clear
cell renal cell carcinoma, stomach cancer, melanoma,
colon cancer, endometrial cancer, uterine leiomyosar-
coma, cholangiocarcinoma, ovarian cancer, esopha-
geal cancer, and lymphoma were verified. In patients
of the first group, radical surgery was performed in
12 cases, and cryodestruction of the pancreatic tu-
mor was performed in 3 cases. The median survival
constituted 23 months (from 2 to 50 months) in pa-
tients after radical surgery; in patients who underwent
cryodestruction, it was 12 months (from 6 to 19
months). In the second group, 8 patients underwent
radical surgery, and 3 patients underwent cryode-
struction of the tumor. When analyzing the median
survival rate of patients in the second group, there
were no significant differences in the results of pa-
tients who underwent radical surgery and patients
who underwent cryodestruction. For these patients,
the survival rates of 1 and 2 years were 38.1% and
16.6%, respectively [13]. So, in 2007, N.N. Korpan described structural
changes after cryodestruction of pancreatic tissue in
experimental animals (dogs) and observed the cryo-
preservation zone in dynamics. Cryodestruction of
tissues occurred at temperatures of −80 °C and
−100 °C. It was proved that in the first hours after ex-
posure, edema develops in the cryodestruction zone,
which was well separated morphologically from the
unchanged tissue. In the tissues, the intracellular
and extracellular fluid crystallizes during cryopreser-
vation. Discussion Hyperosmolar extracellular medium potenti-
ates release of intracellular water crystals into the
extracellular space with the destruction of cell mem-
branes and protein denaturation, which inevitably
leads to cell necrosis and apoptosis. Subsequently,
fibrosis develops in the cryopreservation zone [19]. The walls of small-caliber blood vessels are also sub-
jected to necrosis. In the experiment, large-caliber
vessels were more resistant to the effects of ultra-low
temperatures due to the presence of a well-defined
collagen stroma of the vessel, which does not col-
lapse under the influence of ultra-low temperatures
and, subsequently, regenerates the wall; and due to
the greater volume of blood flow in the lumen of a
large vessel [20]. According to the literature, cryodestruction is used
in liver tumors as part of radical and palliative interven-
tions, and in locally advanced primary pancreatic tu-
mors [18, 21]. Thus, according to the researchers [12, 13], the
use of cryodestruction in metastatic lesions of the
pancreas is justified. Moreover, the results of cryode-
struction combined with an appropriate chemothera-
py may be compared with radical surgical intervention
ones [12, 13, 21]. Metastatic lesions of the pancreas are much less
common than primary tumors [1]. In case of metastases in the pancreas, the use of
cryotherapy is described in single studies. For in-
stance, L. Niu et al. divided 106 patients of their study
into four groups, depending on the treatment method:
cryoimmunotherapy (31 patients), cryotherapy
(36 patients), immunotherapy (17 patients) and
chemotherapy (22 patients). Overall survival (OS)
after metastatic pancreatic cancer being diagnosed
was evaluated after 4 years of observation. The me- In our study, patients who underwent cryodestruc-
tion of metastases in the pancreas showed a persis-
tent reduction in pain syndrome in two presented
clinical cases. In the first case, the patient with metas-
tasis of renal cell carcinoma had been showing no
pathological accumulation of contrast agent and radi-
opharmaceutical agent in the previously identified fo- МЕДИЦИНСКАЯ ВИЗУАЛИЗАЦИЯ
2021, том 25, №1 50 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT cus during CT and PET with fluoride deoxyglucose up
to 6 months. Probably, it relates to decrease in vascu-
larization and necrosis formation, later developing in
fibrosis in the central parts of the neoplasm. After
2.5 years, a control CT scan showed peripheral con-
trast enhancement, but the size of the metastasis re-
mained the same. Discussion MRI showed an increase in the val-
ues of the measured diffusion coefficient in the focus
during the observation period. In the second case, the
patient with melanoma metastasis in the pancreas
showed a persistent decrease in the size of the metas-
tasis by more than 2 times and no accumulation of
RPh in the focus at PET-CT during the follow-up peri-
od. Magnetic resonance imaging showed no restric-
tion of diffusion. In the third case, the patient was di-
agnosed with a tumor in the body of the pancreas
during a routine examination 3 years after pneumo-
nectomy. Differential diagnosis was made between
the primary tumor and the secondary lesion of the
pancreas. During the biopsy, metastasis of squamous
cell lung cancer was verified. Dynamic CT control after
cryodestruction showed no increase in size of the for-
mation and no increase in degree of vascular invasion. term after detection of the primary tumor. Most often,
metastases of renal cell carcinoma occur in the pan-
creas. The only radical method of treatment for me-
tastases in the pancreas include radical surgical inter-
vention. In cases when radical surgical intervention is
not possible, or the risk of radical surgery exceeds
reasonable limits due to prevalence of the process or
poor condition of the patient, it is justified to use the
method of cryodestruction of the tumor. The results of
cryodestruction of metastatic foci in the pancreas,
combined with an appropriate chemotherapy, may be
compared with the ones of radical surgical interven-
tions. To achieve the best treatment results, this group
of patients should receive care in centers equipped
with a team of specialists of different profiles, such as
surgeons, diagnosticians, chemotherapists. Conclusion Stepanova Y.A. – text preparation and editing, approval
of the final version of the article. Secondary lesion of pancreas is a rare malignant
neoplasm. When identifying focal changes in the pan-
creas and making a preliminary diagnosis, it is neces-
sary to take into account medical history, since meta-
static damage to the pancreas may occur in the long Ionkin D.A. – text preparation and editing. Stashkiv V.I. – translation of the text into English. Stashkiv V.I. – translation of the text into English. Chzhao A.V. – text preparation and editing. Authors’ participation Galchina Yu.S. – collection and processing of material,
writing and editing text. Karelskaja N.A. – concept and design of the study, text
preparation and editing, approval of the final version of the
article. Kаrmаzаnovsky G.G. – concept and design of the study,
text preparation and editing, approval of the final version of
the article. Список литературы Onkol. 1991; 37: 695–700. 6. Shi L., Guo Z., Wu X. Primary pulmonary primitive
neuroectodermal tumor metastasis to the pancreas: a rare
case with seven-year follow-up. Diagn. Pathol. 2013;
8 (1): 64–70. http://doi.org/10.1186/1746-1596-8-51 12. Niu L., Chen J., He T.L., Liao M., Yuan Y., Zeng J., Li J.,
Zuo J., Xu K. Combination treatment with comprehensive
cryoablation and immunotherapy in metastatic pancreatic
cancer. Pancreas. 2013; 42 (7): 1143–1149. http://doi.org/10.1097/MPA.0b013e3182965dde. 7. Kopke Túlio M.A.C.B., Horta M.S.F., Bispo M.C.S., Bana E. Costa T.S.N., Chagas C.M.D.B.R. Pancreatic Meta stases
as the Initial Manifestation of a Neuroendocrine Carcinoma
of the Uterine Cervix. Pancreas. 2018; 47 (2): e4–e5. http://doi.org/10.1097/MPA.0000000000000979 http://doi.org/10.1097/MPA.0b013e3182965dd 13. Jin P., Ji X., Ren H., Tang Y., Hao J. Resection or cryosurgery
relates with pancreatic tumor type: Primary pancreatic
cancer with previous non-pancreatic cancer or secondary
metastatic cancer within the pancreas. Pancreatology. 2014; 14 (1): 64–70. 8. Goldberg S.N. Radiofrequency tumor ablation: principles
and techniques. Eur. J. Ultrasound. 2001; 13: 129–147. 9. Carrafiello G., Laganà D., Recaldini C., Dionigi G., Boni L.,
Bacuzzi A., Fugazzola C. Radiofrequency ablation of
a pan creatic metastasis from renal cell carcinoma: case
report. Surg. Laparosc. Endosc. Percutan Tech. 2008;
18 (1): 64–66. http://doi.org/10.1097/SLE.0b013e3181592a13 14. Stucke K., Kachlert F. Morphological studies on cryogenic
surgery of the liver. Acta Hepatosplenol. 1970; 17 (6):
416–422. 15. Кубышкин В.А., Ионкин Д.А., Кунгурцев С.В., Чжао А.В. История криохирургии. Хирургия. Журнал им. Н.И. Пиро-
гова. 2015; 5: 62–74. 10. Crinò S.F., D'Onofrio M., Bernardoni L., Frulloni L.,
Iannelli M., Malleo G., Paiella S., Larghi A., Gabbrielli A. EUS-guided Radiofrequency Ablation (EUS-RFA) of Solid
Pancreatic Neoplasm Using an 18-gauge Needle
Electrode: Feasibility, Safety, and Technical Success. J. Gastrointest. Liver Dis. 2018; 27 (1): 67–72. http://doi.org/10.15403/jgld.2014.1121.271.eus. 16. Korpan N.N. Basics of cryosurgery. Wien; New York:
Shringer-Verlag, 2001. 325 p. 17. Ионкин Д.А., Степанова Ю.А., Шуракова А.Б., Чжао
А.В. Технические особенности и результаты примене-
ния криодеструкции при раке поджелудочной железы. Клиническая практика. 2016; 3: 22–33. 11. Patiutko Iu.I., Barkanov A.I., Kholikov T.K., Lagoshnyĭ A.T.,
Li L.I., Samoĭlenko V.M., Afrikian M.N., Savel'eva E.V. The
combined treatment of locally disseminated pancreatic
cancer using cryosurgery. Vopr. Onkol. 1991; 37: 695–
700. 18. Kovach S.J., Hendrickson R.J., Cappadona C.R.,
Schmidt C.M., Groen K., Koniaris L.G., Sitzmann J.V. Cryoablation of unresectable pancreatic cancer. Surgery. 2002; 131 (4): 463–464. 19. Korpan N.N. Cryosurgery: ultrastructural changes in
pancreas tissue after low temperature exposure. Technol. Cancer Res. Treat. 2007; 6: 59–67. 12. Список литературы Niu L., Chen J., He T.L., Liao M., Yuan Y., Zeng J., Li J.,
Zuo J., Xu K. Combination treatment with comprehensive
cryoablation and immunotherapy in metastatic pancreatic
cancer. Pancreas. 2013; 42 (7): 1143–1149. http://doi.org/10.1097/MPA.0b013e3182965dde. 20. Yu H.B., Ge C.L., Huang Z.H., Wang H., Liu Z.Y., Zhang J.R. Effect of targeted argon-helium cryoablation on the portal
region in canine livers. J. South. Med. University. 2009; 29
(3): 538–540. ( )
http://doi.org/10.1097/MPA.0b013e3182965dde 13. Jin P., Ji X., Ren H., Tang Y., Hao J. Resection or cryosurgery
relates with pancreatic tumor type: Primary pancreatic
cancer with previous non-pancreatic cancer or secondary
metastatic cancer within the pancreas. Pancreatology. 2014; 14 (1): 64–70. 21. McKinnon G., Temple W.J., Wiseman D.A., Saliken J.C. Cryosurgery for Malignant Tumours of the Liver. Canadian
J. Surg. 1996; 39: 401–406. ( )
14. Stucke K., Kachlert F. Morphological studies on cryogenic
surgery of the liver. Acta Hepatosplenol. 1970; 17 (6):
416–422. References 1. Adsay N.V., Andea A., Basturk O., Kilinc N., Nassar H.,
Cheng J.D. Secondary tumors of the pancreas: an analysis
of a surgical and autopsy database and review of the
literature. Virchows Arch. 2004; 444 (6): 527–535. http://doi.org/10.1007/s00428-004-0987-3 15. Kubyshkin V.A., Ionkin D.A., Kungurtsev S.V., Zhao A.V. History of cryosurgery. Pirogov Russian Journal of Surgery
= Khirurgiya. Zhurnal imeni N.I. Pirogova. 2015; 5: 62–74. (In Russian) (
)
16. Korpan N.N. Basics of cryosurgery. Wien; New York:
Shringer-Verlag, 2001. 325 p. 2. Yoon W.J., Ryu J.K., Kim Y.T., Yoon Y.B., Kim S.W., Kim
W.H. Clinical features of metastatic tumors of the pancreas
in Korea: a single-center study. Gut and Liver. 2011; 5 (1):
61. http://doi.org/10.5009/gnl.2011.5.1.61 17. Ionkin D.A., Stepanova Yu.A., Shurakova A.B., Zhao A.V. Technical features and results of the use of cryodestruction
in pancreatic cancer. Clinicheskaya praktika. 2016; 3:
22–33. (In Russian) 3. Faure J.P., Tuech J.J., Richer J.P., Pessaux P., Arnaud J.P.,
Carretier M. Pancreatic metastasis of renal cell carcinoma:
presentation, treatment and survival. J. Urol. 2001;
165 (1): 20–22. http://doi.org/10.1097/00005392-200101000-00005 Carretier M. Pancreatic metastasis of renal cell carcinoma:
presentation, treatment and survival. J. Urol. 2001;
165 (1): 20–22. http://doi.org/10.1097/00005392-200101000-00005 (
)
18. Kovach S.J., Hendrickson R.J., Cappadona C.R.,
Schmidt C.M., Groen K., Koniaris L.G., Sitzmann J.V. Cryoablation of unresectable pancreatic cancer. Surgery. 2002; 131 (4): 463–464. 165 (1): 20–22. http://doi.org/10.1097/00005392-200101000-00005 http://doi.org/10.1097/00005392-200101000-000 4. Falk G.A., El-Hayek K., Morris-Stiff G., Tuthill R.J.,
Winans C.G. Adenoid cystic carcinoma of the base of the
tongue: late metastasis to the pancreas. Int. J. Surg. Case
Rep. 2011; 2 (1): 1–3. 19. Korpan N.N. Cryosurgery: ultrastructural changes in
pancreas tissue after low temperature exposure. Technol. Cancer Res. Treat. 2007; 6: 59–67. Rep. 2011; 2 (1): 1–3. http://doi.org/10.1016/j.ijscr.2010.08.003
Á 20. Yu H.B., Ge C.L., Huang Z.H., Wang H., Liu Z.Y., Zhang J.R. Effect of targeted argon-helium cryoablation on the portal
region in canine livers. J. South. Med. University. 2009; 29
(3): 538–540. p
;
( )
http://doi.org/10.1016/j.ijscr.2010.08.003
Á p //
g/
/j j
5. Gómez J.A., Sánchez Á.A., Cecilia D.M., Nieto R.D., de la
Rúa, J.R., Martínez A.V., Febres E.L., Ruiz J.P., Peña S.R. Uterine leiomyosarcoma metastasis to the pancreas:
report of a case and review of the literature. J. Gastrointest. Cancer. 2012; 43 (2): 361–363. http://doi.org/10.1007/s12029-010-9172-x 21. McKinnon G., Temple W.J., Wiseman D.A., Saliken J.C. Cryosurgery for Malignant Tumours of the Liver. Canadian
J. Surg. 1996; 39: 401–406. Список литературы 6. Shi L., Guo Z., Wu X. Primary pulmonary primitive
neuroectodermal tumor metastasis to the pancreas: a rare
case with seven-year follow-up. Diagn. Pathol. 2013;
8 (1): 64–70. http://doi.org/10.1186/1746-1596-8-51 1. Adsay N.V., Andea A., Basturk O., Kilinc N., Nassar H.,
Cheng J.D. Secondary tumors of the pancreas: an analysis
of a surgical and autopsy database and review of the
literature. Virchows Arch. 2004; 444 (6): 527–535. http://doi.org/10.1007/s00428-004-0987-3 7. Kopke Túlio M.A.C.B., Horta M.S.F., Bispo M.C.S., Bana
E. Costa T.S.N., Chagas C.M.D.B.R. Pancreatic
Metastases as the Initial Manifestation of a Neuroendocrine
Carcinoma of the Uterine Cervix. Pancreas. 2018; 47 (2):
e4–e5. http://doi.org/10.1097/MPA.0000000000000979 2. Yoon W.J., Ryu J.K., Kim Y.T., Yoon Y.B., Kim S.W., Kim
W.H. Clinical features of metastatic tumors of the pancreas
in Korea: a single-center study. Gut and Liver. 2011; 5 (1):
61. http://doi.org/10.5009/gnl.2011.5.1.61 8. Goldberg S.N. Radiofrequency tumor ablation: principles
and techniques. Eur. J. Ultrasound. 2001; 13: 129–147. 3. Faure J.P., Tuech J.J., Richer J.P., Pessaux P., Arnaud J.P.,
Carretier M. Pancreatic metastasis of renal cell carcinoma:
presentation, treatment and survival. J. Urol. 2001;
165 (1): 20–22. http://doi.org/10.1097/00005392-200101000-00005 9. Carrafiello G., Laganà D., Recaldini C., Dionigi G., Boni L.,
Bacuzzi A., Fugazzola C. Radiofrequency ablation of
a pan creatic metastasis from renal cell carcinoma: case
report. Surg. Laparosc. Endosc. Percutan Tech. 2008;
18 (1): 64–66. http://doi.org/10.1097/SLE.0b013e3181592a13 4. Falk G.A., El-Hayek K., Morris-Stiff G., Tuthill R.J.,
Winans C.G. Adenoid cystic carcinoma of the base of the
tongue: late metastasis to the pancreas. Int. J. Surg. Case
Rep. 2011; 2 (1): 1–3. http://doi.org/10.1016/j.ijscr.2010.08.003
Á 10. Crinò S.F., D'Onofrio M., Bernardoni L., Frulloni L.,
Iannelli M., Malleo G., Paiella S., Larghi A., Gabbrielli A. EUS-guided Radiofrequency Ablation (EUS-RFA) of Solid
Pancreatic Neoplasm Using an 18-gauge Needle
Electrode: Feasibility, Safety, and Technical Success. J. Gastrointest. Liver Dis. 2018; 27 (1): 67–72. http://doi.org/10.15403/jgld.2014.1121.271.eus. 5. Gómez J.A., Sánchez Á.A., Cecilia D.M., Nieto R.D., de la
Rúa, J.R., Martínez A.V., Febres E.L., Ruiz J.P., Peña S.R. Uterine leiomyosarcoma metastasis to the pancreas:
report of a case and review of the literature. J. Gastrointest. Cancer. 2012; 43 (2): 361–363. http://doi.org/10.1007/s12029-010-9172-x http://doi.org/10.15403/jgld.2014.1121.271.eus 11. Patiutko Iu.I., Barkanov A.I., Kholikov T.K., Lagoshnyĭ A.T.,
Li L.I., Samoĭlenko V.M., Afrikian M.N., Savel'eva E.V. The MEDICAL VISUALIZATION
2021, V. 25 , N1 51 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT combined treatment of locally disseminated pancreatic
cancer using cryosurgery. Vopr. Onkol. 1991; 37: 695–700. combined treatment of locally disseminated pancreatic
cancer using cryosurgery. Vopr. References МЕДИЦИНСКАЯ ВИЗУАЛИЗАЦИЯ
2021, том 25, №1 52 КЛИНИЧЕСКОЕ НАБЛЮДЕНИЕ | CASE REPORT Для корреспонденции*: Гальчина Юлия Сергеевна – 117997 Москва, ул. Большая Серпуховская, д. 27. НМИЦ хирургии имени
А.В. Вишневского. Тел.: +7-926-903-23-57 (моб.). E-mail: jgalchina@gmail.com Гальчина Юлия Сергеевна – аспирант ФГБУ “НМИЦ хирургии имени А.В. Вишневского” Минздрава России, Москва. https://orcid. org/0000-0001-9063-4565 Карельская Наталья Александровна – канд. мед. наук, старший научный сотрудник отделения рентгенологических и магнитно-
резонансных методов исследования с кабинетом ультразвуковой диагностики ФГБУ “НМИЦ хирургии имени А.В. Вишневского” Минздрава
России, Москва. https://orcid.org/0000-0001-8723-8916 Кармазановский Григорий Григорьевич – член-корр. РАН, доктор мед. наук, профессор, заведующий отделением рентгенологии
и магнитно-резонансных исследований с кабинетом ультразвуковой диагностики ФГБУ “НМИЦ хирургии имени А.В. Вишневского”
Минздрава России; профессор кафедры лучевой диагностики и терапии медико-биологического факультета ФГБОУ ВО “РНИМУ имени
Н.И. Пирогова” Минздрава России, Москва. https://orcid.org/0000-0002-9357-0998 рогова” Минздрава России, Москва. https://orcid.org/000 Степанова Юлия Александровна – доктор мед. наук, Ученый секретарь ФГБУ “НМИЦ хирургии имени А.В. В
России, Москва. https://orcid.org/0000-0002-5793-5160 ександровна – доктор мед. наук, Ученый секретарь ФГБУ “НМИЦ хирургии имени А.В. Вишневского” Минздрав
://orcid.org/0000-0002-5793-5160 Ионкин Дмитрий Анатольевич – канд. мед. наук, старший научный сотрудник отделения хирургии печени и поджелудочной железы ФГБУ
“НМИЦ хирургии имени А.В. Вишневского” Минздрава России, Москва. https://orcid.org/0000-0002- 4903-5293 Сташкив Владислава Ивановна – ординатор ФГБУ “НМИЦ хирургии имени А.В. Вишневского” Минздрава России, Москва. https://orcid.org/0000-0002-7349-1192. Чжао Алексей Владимирович – доктор мед. наук, профессор, заместитель директора по связям с регионами ФГБУ “НМИЦ хирургии
имени А.В. Вишневского” Минздрава России, Москва. https://orcid.org/0000-0002-0204-8337 Contact*: Yulia S. Galchina – 27, Bolshaya Serpuhovskaya str., 117997, Moscow, Russia, A.V. Vishnevsky National Medical Research Center
of Surgery. Phone: +7-926-903-23-57. E-mail: jgalchina@gmail.com Yulia S. Galchina – graduate student of A.V. Vishnevsky National Medical Research Center of Surgery, Moscow. https://orcid.o duate student of A.V. Vishnevsky National Medical Research Center of Surgery, Moscow. https://orcid.org/0000-0001-9063-456 Natalya A. Karelskaja – Cand. of Sci. (Med.), the senior research of X-ray and magnetic resonance studies department with ultrasound
of A.V. Vishnevsky National Medical Research Center of Surgery, Moscow. https://orcid.org/0000-0001-8723-8916 Grigory G. Kаrmаzаnovsky – сorresponding member of the Russiаn Асаdemy of Sсienсes, Doct. of Sci. (Med.), Professor, Heаd of X-ray and mag-
netic resonance studies department with ultrasound of A.V. Vishnevsky National Medical Research Center of Surgery; Professor of radiology depart-
ment of Pirogov Russian national research medical university, Moscow. https://orcid.org/0000-0002-9357-0998 Yulia A. Stepanova – Doct. of Sci. (Med.), Scientific Secretary of A.V. Vishnevsky National Medical Research Center of Surgery, Moscow. https://orcid.org/0000-0002-5793-5160. Dmitry A. Ionkin – Cand. of Sci. References (Med.), Senior Researcher of the liver and pancreas surgery department of A.V. Vishnevsky National Medical Research
Center of Surgery, Moscow. https://orcid.org/0000-0002- 4903-5293 I. Stashkiv – Resident in the specialty “radiology” of A.V. Vishnevsky National Medical Research Center of Surgery, Moscow
d.org/0000-0002-7349-1192. p //
g/
Aleksey V. Chzhao – Doct. of Sci. (Med.), Professor, Deputy Director for Regional Relations of A.V. Vishnevsky National Medical Research Center
of Surgery, Moscow. https://orcid.org/0000-0002-0204-8337 MEDICAL VISUALIZATION
2021, V. 25 , N1 MEDICAL VISUALIZATION
2021, V. 25 , N1 53
|
https://openalex.org/W3179334637
|
https://www.mdpi.com/1660-4601/18/14/7457/pdf?version=1626165456
|
English
| null |
The Relation between Physical Education Teachers’ (De-)Motivating Style, Students’ Motivation, and Students’ Physical Activity: A Multilevel Approach
|
International journal of environmental research and public health/International journal of environmental research and public health
| 2,021
|
cc-by
| 13,034
|
Citation: Van Doren, N.; De Cocker,
K.; De Clerck, T.; Vangilbergen, A.;
Vanderlinde, R.; Haerens, L. The
Relation between Physical Education
Teachers’ (De-)Motivating Style,
Students’ Motivation, and Students’
Physical Activity: A Multilevel
Approach. Int. J. Environ. Res. Public
Health 2021, 18, 7457. https://
doi.org/10.3390/ijerph18147457 Keywords: Self-Determination Theory; physical education; physical activity; motivating style; con-
trolling style; motivation; gender; lesson topic The Relation between Physical Education Teachers’
(De-)Motivating Style, Students’ Motivation, and Students’
Physical Activity: A Multilevel Approach 1,*
, Katrien De Cocker 1
, Tom De Clerck 1, Arwen Vangilbergen 1, Ruben Vanderlinde 2
1 1
Department of Movement and Sports Sciences, Faculty of Medicine and Health Sciences, Ghent University,
9000 Ghent, Belgium; Katrien.DeCocker@Ugent.be (K.D.C.); Tom.DeClerck@Ugent.be (T.D.C.);
Arwen.Vangilbergen@Ugent.be (A.V.); Leen.Haerens@Ugent.be (L.H.)
2
Department of Educational Studies, Faculty of Psychology and Educational Sciences, Ghent University,
9000 Ghent, Belgium; Ruben.Vanderlinde@ugent.be
*
Correspondence: nele.vandoren@ugent.be 1
Department of Movement and Sports Sciences, Faculty of Medicine and Health Sciences, Ghent University,
9000 Ghent, Belgium; Katrien.DeCocker@Ugent.be (K.D.C.); Tom.DeClerck@Ugent.be (T.D.C.);
Arwen.Vangilbergen@Ugent.be (A.V.); Leen.Haerens@Ugent.be (L.H.) g
*
Correspondence: nele.vandoren@ugent.be Abstract: Research suggests that physical education (PE) teachers can play a crucial role in the
promotion of students’ physical activity. Grounded in Self-Determination Theory, this study investi-
gated how students’ perceptions of PE teachers (de-)motivating style relate to students’ device-based
physical activity levels during PE. Moreover, it was examined whether students’ motivation plays
an intervening role in this relation and whether students’ physical activity differs according to
their gender and lesson topic. A sample of 302 secondary school students aged between 11 and
16 years (M = 13.05, SD = 1.04) completed a questionnaire assessing their perceptions of teachers’
(de-)motivating style and their personal motivation toward PE. Students also wore ActiGraph GT3X
accelerometers during the PE lesson. Multilevel structural equation modeling revealed that the
teachers’ motivating style had a significant positive relation with students’ autonomous motivation,
both at the student level and the class level, and teachers’ controlling style had a significant positive
relation with students’ controlled motivation and amotivation at both levels. However, in terms of
students’ physical activity levels, students’ gender, the lesson topic, and teachers’ controlling style
seemed to be more decisive than students’ motivation and teachers’ motivating style.
Citation: Van Doren, N.; De Cocker,
K.; De Clerck, T.; Vangilbergen, A.;
Vanderlinde, R.; Haerens, L. The
Relation between Physical Education
Teachers’ (De-)Motivating Style,
Students’ Motivation, and Students’
Physical Activity: A Multilevel
Approach. Int. J. Environ. Res. Public
Health 2021, 18, 7457. https://
doi.org/10.3390/ijerph18147457
Academic Editors: Angel Abos,
Javier Sevil-Serrano,
Luis Garcia-Gonzalez and Paul
B. Tchounwou
Received: 31 May 2021
Accepted: 11 July 2021
Published: 13 July 2021
Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
published maps and institutional affil-
iations. Copyright: © 2021 by the authors. International Journal of
Environmental Research
and Public Health International Journal of
Environmental Research
and Public Health 1. Introduction The benefits of an active lifestyle during adolescence have been widely demon-
strated [1]. For instance, adolescents who are physically active not only perform better at
school [2,3], they also sleep better [4] and have less anxiety and depressive symptoms [5]. As active adolescents are more likely to remain physically active in adulthood [6–8], they
are also expected to gain physical and psychological health benefits in later life. These
benefits include reduced risks of cardiovascular diseases, metabolic syndrome, overweight
and obesity, cancer, osteoporosis, diabetes type 2, and depression [1,9]. As such, the
World Health Organization [10] recommends adolescents to participate in at least 60 min
of moderate- to vigorous-intensity physical activity (MVPA) every day. However, many
adolescents do not reach this global recommendation [7,11,12]. Moreover, adolescents’
physical activity levels decline rapidly through adolescence, whereby adolescents between
the age of 12 and 15 years display the highest decline [13,14]. Therefore, the promotion of
physical activity is necessary for this age group. Research suggests that physical education
(PE-) teachers can play a crucial role in this promotion [15,16]. One way is to increase
physical activity levels during PE. In this respect, the US Health People 2010 recommends Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
published maps and institutional affil-
iations. 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/). Int. J. Environ. Res. Public Health 2021, 18, 7457. https://doi.org/10.3390/ijerph18147457 https://www.mdpi.com/journal/ijerph Int. J. Environ. Res. Public Health 2021, 18, 7457 2 of 17 students to participate in MVPA for at least 50% of the PE lesson [17]. However, research
reveals that most students participate in MVPA for less than 50% of the lesson. For instance,
Fairclough and Stratton [18] found that students engage in MVPA between only 27% and
47% of the effective PE lesson time. Furthermore, it appears that students’ physical ac-
tivity levels during the PE lesson depend on a range of factors such as the goal of the
lesson [19], the lesson topic [20], and students’ gender [21]. Indeed, it has been shown that
students’ physical activity levels during the PE lesson largely vary according to the lesson
topic [20,22]. 1.1. Students’ Motivation for PE To examine students’ motivation and teachers’ (de-)motivating style, we rely on Self-
Determination Theory (SDT) [27], which is a broad and well-evidenced theory on human
behavior and motivation that distinguishes amotivation from controlled motivation and
autonomous motivation. Amotivation refers to a complete absence of motivation [27]. An
amotivated student feels incapable to engage in PE or claims to have no idea why he/she
should participate [20]. Introjected and external regulation are two controlled forms of motivation, as they
involve a feeling of pressure, coercion or obligation [20]. Externally regulated students will
engage in PE to avoid a punishment or criticism, obtain a reward or appreciation (e.g., gain
good grades), or meet external expectations [20,28]. Introjected regulation manifests when
students feel pressure that originates from themselves [27]. For example, a student engages
in PE to avoid a negative internal state (e.g., guilt, shame) or to gain a positive internal
state (e.g., increasing self-esteem, achieving social recognition) [29]. Identified regulation, integrated regulation, and intrinsic motivation constitute au-
tonomous types of motivation because they are volitional in nature [20]. Identified regula-
tion occurs when a student understands the personal relevance of the activity [20,28]. For
instance, a student puts effort into the warm-up of the PE lesson when he/she understands
that a good warm-up prevents injuries [20]. Integrated regulation is defined as engagement
in a behavior as a result of the harmonization of the behavior with the indivudal’s personal
values and ideals [20]. For instance, a student engages in PE because he/she values sports,
social interaction, and being in good shape [28]. Intrinsic motivation, the highest quality
form of motivation, is characterized by interest, enjoyment, satisfaction, and choice [29]. For example, a student engages in PE because he/she finds pleasure and accomplishment
in the activity and enjoys the experience of learning new things [30]. These qualitatively different forms of motivation relate differently to important out-
comes in PE. Autonomous motivation for PE is associated with higher concentration [31],
greater enjoyment [32,33], and more effort [31,32,34]. Controlled motivation and amotiva-
tion for PE have been positively related to boredom [32] and unhappiness [33]. 1. Introduction For example, students displayed lower MVPA levels during racket games
when compared to all other topics (i.e., ball games, artistic sports, and fitness training) [20];
lower vigorous physical activity in artistic sports when compared to fitness training [22];
and lower physical activity levels during individual activities when compared to team
activities [18,23]. Even though findings are inconsistent across studies, all these studies
consistently confirm the variability in percentage time spent in MVPA according to the les-
son topic. Furthermore, boys are generally more active than girls [21,24]. The present study
aims to build on this work by investigating how secondary school students’ objectively
measured physical activity levels differ according to the lesson topic and students’ gender,
while also examining relations with students’ motivation [20] and teachers’ (de-)motivating
style [25,26]. 1.2. Teachers’ (De-)Motivating Style According to SDT, a teacher can foster students’ autonomous motivation by adopting
a need-supportive motivating style, which is characterized by autonomy-supporting,
structuring and relatedness-supportive teaching behaviors [37,38]. When being autonomy-
supportive, teachers identify, nurture, and develop students’ interests, preferences, and
personal goals [37]. Autonomy-supportive strategies include offering choice [39,40], using
inviting language instead of controlling language [41], and accepting students’ input [42]. When providing structure, teachers give students clear information about what to do
and how to do it to achieve the desired outcomes [43]. Structuring strategies include
communicating transparent expectations [44,45], giving step-by-step guidelines [44,46],
and using positive and constructive feedback [47,48]. Finally, when being relatedness-
supportive, teachers show noticeable interest and (emotionally) support their students [49]. Relatedness-supportive strategies include being warm and caring, offering affection and
unconditional regard, and devoting extensive energy, time, and resources in students [25]. g
g
gy
In contrast, a teacher will elicit students’ controlled motivation and amotivation by
displaying a need-thwarting motivating style, which is characterized by controlling, chaotic,
and cold teaching behaviors [50]. When being controlling, teachers ignore the students’
perspective and instead pressure students to act, think, or feel in a specific way [37]. When
being chaotic, teachers state unclear goals, and teachers do no inform students how to
achieve these goals. Lastly, when being cold, teachers are unfriendly or even reject or
exclude students [51]. In general, SDT-based research suggests that teachers who adopt a motivating style
will stimulate their students toward higher engagement [52], health-related well-being [53],
and physical activity through the development of autonomous motivation for PE [54,55]. Specifically, an autonomy-supportive style has been related to students’ need satisfaction,
autonomous motivation, and positive course-related outcomes in PE, such as effort and ex-
ercise intention [56]. In addition, (a small number of) studies in the PE context have related
a structuring motivating style to autonomous motivation, enjoyment, perceived importance
of PE, and exercise intention [57]. Lastly, studies regarding a relatedness-supportive style
are generally scarce. One experimental study found that students’ perceptions of teachers’
relatedness-supportive style were positively related to confidence in their teachers’ ability
and enjoyment [58]. However, most studies focused solely on one aspect of a motivating
style [59,60], with an autonomy-supportive motivating style being the most commonly
investigated. Furthermore, most of these studies fully relied on self-reported measures to
assess students’ physical activity levels, risking the issue of shared method variance. 1.1. Students’ Motivation for PE In studies
using device-based measurements (i.e., heart-rate monitors, pedometers, accelerometers),
autonomous motivation for PE is positively related to higher levels of physical activity
levels during PE [20] and during leisure time [35], while controlled motivation and amoti-
vation were unrelated to physical activity levels during PE [20] and during leisure time [35]. In comparison to the number of studies investigating the relation between students’ motiva-
tion and their physical activity levels using self-reported measures, the number of studies Int. J. Environ. Res. Public Health 2021, 18, 7457 3 of 17 3 of 17 using device-based measurements such as pedometers and accelerometers is scarce [26,36]. Overall, the abovementioned studies stress the importance of enhancing students’ au-
tonomous motivation for PE to achieve higher physical activity levels during PE. 1.3. Premise of This Study The objective of this study is to investigate the relation between teachers’ motivating
style (that is an autonomy-supportive, structuring, and relatedness-supporting teaching
style), and demotivating style (i.e., controlling) and students’ physical activity levels during
PE, and determine if this relation can be indirectly explained by the quality of students’
motivation toward PE (i.e., autonomous, controlled, amotivation). In doing so, this study
builds on previous research by (1) focusing on all aspects of a teachers’ motivating style,
(2) including an aspect of teachers’ need-thwarting style, (3) assessing physical activity
levels during the PE lesson by means of devices (accelerometers), and (3) taking both the
lesson topic as well as students’ gender into account. Based on SDT [27] and previous research findings [20,46,53,63], multiple hypotheses
are put forward: we expect that when students perceive their teacher as more need-
supportive, their autonomous motivation for PE will be fostered, while their controlled
motivation and amotivation for PE will be lower (H1a). When a teacher is perceived to be
more controlling, we hypothesize that students’ controlled motivation and amotivation
will be fostered, while their autonomous motivation will be lower (H1b). In turn, we expect
students’ autonomous motivation will relate to higher physical activity levels during
the PE lesson (H2). Theoretically, we would expect that students’ controlled motivation
and amotivation will relate to lower physical activity levels during the PE lesson. Yet,
empirical evidence does not show such relations. Therefore, we examine relations between
controlled motivation and amotivation and physical activity in a more explorative manner. In line with previous research, we further expect boys to be more physically active than
girls (H3), and we will explore how students’ physical activity varies according to the
lesson topic. In addressing these hypotheses, we decomposed the variance at the student
level (i.e., individual) and the class level (i.e., contextual), because the extent to which
students experience the teacher as need-supportive is likely to depend on both individual
(e.g., their personality) and teacher level (e.g., how need-supportive the teacher actually
is) factors. Such decomposement allows examining at the student level how individual
students’ perceptions of the teacher style relate to their personal motivation for PE and in
turn their activity levels. 1.2. Teachers’ (De-)Motivating Style To our
knowledge, only two studies used accelerometers to determine students’ physical activity
levels during PE [25,26]. Both intervention studies, one in elementary school children
and the other in secondary school children, showed that positive changes in teachers’
motivating style can increase students’ MVPA during PE. In addition, studies on teachers’ need-thwarting style have mainly focused on a con-
trolling style, showing that teachers who adopt a controlling style will stimulate students’
controlled motivation and amotivation [52], and maladaptive outcomes, such as fear of
failure and less engagement [52,54,61]. Moreover, one study found that students’ percep-
tions of teachers’ controlling style were negatively related to students’ physical activity
levels during leisure time, as measured by accelerometers [62]. Yet, to the best of our
knowledge, relations with objectively measured physical activity levels during PE have
not been previously examined. Int. J. Environ. Res. Public Health 2021, 18, 7457 4 of 17 1.3. Premise of This Study At the same time, it allows to examine at the class level whether
classes are on average more active, more autonomously motivated, and less controlled
motivated and amotivated when teachers are generally perceived as more need-supportive
and less controlling. 2.2. Measures Students’ situational motivation for PE was assessed using the validated Behavioral
Regulations in Physical Education Questionnaire (BRPEQ) [20]. The BRPEQ is an adapted
Dutch version of the Behavioral Regulations in Exercise Questionnaire (BREQ-II) [64] and
consists of 20 items that were rated on a five-point Likert scale ranging from 1 (completely
disagree) to 5 (completely agree). Eight items were used to determine autonomous moti-
vation. For example: “I put effort in this PE lesson because I liked this PE lesson”. While
SDT proposes autonomous motivation consists of three different regulations (i.e., identified
regulation, integrated regulation, and intrinsic motivation), we did not collect data on
integrated regulation, as the BRPEQ only measures identified regulation and intrinsic
motivation. Another eight items measured controlled motivation, such as “I put effort in
this PE lesson because I would feel guilty if I didn’t put effort in the PE lesson”. Lastly,
four items referred to amotivation. For instance: “I don’t see why I would put effort in this
PE lesson”. The Cronbach’s alpha for autonomous motivation, controlled motivation, and
amotivation was respectively 0.85, 0.76, and 0.66. p
y
To determine students’ perceptions of teachers’ (de-)motivating style, students were
asked to fill out the Dutch version of Teacher as Social Context Questionnaire (TASCQ) [65,66]
and the Psychologically Controlling Teaching (PCT) [50], respectively. The translation
followed the guidelines of the International Test Commission [67] and has previously been
used and validated in other studies [54,61]. The TASCQ measures autonomy-support
(6 items), structure (5 items), and relatedness-support (6 items), while the PCT measures
control (9 items). All items had to be answered on a five-point Likert scale ranging from
1 (completely disagree) to 5 (completely agree). An example of an autonomy-support item
is “During this PE lesson, my teacher gave me lots of choices about how I can deal with the
exercises”. An example of a structure item is “During this PE lesson, my teacher clarified
what he/she expects of me”. An example of a relatedness-support item is “My teacher likes
me”. An example of a controlling item is “During the PE lesson, my teacher made me feel
guilty when I dissatisfied him/her”. The Cronbach’s alpha was 0.71 for autonomy-support,
0.69 for structure, 0.78 for relatedness-support, and 0.77 for control. pp
To determine students’ physical activity during PE, Actigraph GT3x (+) accelerometers
were used. 2.1. Participants and Data Collection For this cross-sectional study, 260 Flemish secondary schools were contacted by e-mail
or telephone. When the PE teachers were interested in participating in this study, the
teacher was provided with extra information by e-mail, telephone, or personal contact. If the teacher agreed to participate, one of their classes was chosen to participate in the
study. In total, 29 PE teachers from 22 different secondary schools participated in this
study (8.46% response rate), of which 18 teachers were men (62.07%) and 11 teachers
were female (37.93%). Teachers who provided their age and years of experience (N = 16)
were on average 39.5 (SD = 11.38) years old and had on average 17.66 (SD = 11.52) years
experience. For every PE teacher, one class from grades 8 to 10 was chosen, with students’
age ranging between 11 and 16 years. In total, 302 students participated in this study. Of
the 299 students who provided their sex (N = 299), 159 were boys (53.18%) and 140 were
girls (46.82%). Students providing their age (N = 228) were on average 13.05 years old
(SD = 1.04). The average number of students per class was 10.41 (SD = 3.86). The lesson
topics could be grouped in one of four categories [20]: ball games (e.g., volleyball, handball,
soccer; 7 classes, or 24.14%), artistic sports (e.g., gymnastics, dance, rope skipping; 6 classes,
or 20.69%), fitness training (e.g., running, fitness track; 11 classes, or 37.93%), and racket
games (badminton, table tennis; 5 classes, or 17.24%). All participating teachers and Int. J. Environ. Res. Public Health 2021, 18, 7457 5 of 17 students, as well as the parents of the students, signed an informed consent form. The
study was approved by the Ethical Committee of Ghent University (EC: 2017/0213). All participating PE teachers filled out a short questionnaire that provided information
regarding their sex, age, and years of experience. At the start of the PE lesson, the students
were mounted with an accelerometer. Since the number of available accelerometers was
limited (N = 15), accelerometers were randomly assigned to students who signed the
informed consent form and were present on the day of the study. Students wore the ac-
celerometer on their right hip using an elastic belt. 2.1. Participants and Data Collection At the end of the PE lesson, the students
who wore an accelerometer were asked to individually fill out a set of questionnaires
to determine their gender, age, motivation for PE, and their perceptions of the teachers’
(de-)motivating style. It took about 10 to 15 min for students to fill out the questionnaire. 2.3. Data Analyses To further check the validity of the measures (BRPEQ, TASCQ, and PCT), confir-
matory factor analysis (CFA) was used in Mplus [71]. Amotivation consisted of 4 items,
autonomous and controlled motivation each consisted of 8 items, teachers’ motivating
style consisted of 17 items, and teachers’ controlling style consisted of 9 items. Model
fit was determined by using normed chi-square (normed χ2), root mean square error of
approximation (RMSEA), comparative fit index (CFI), and standardized root-mean-square
residual (SRMR). For a good model fit, normed χ2 should be < 2; RMSEA < 0.05 (< 0.08 is
acceptable), CFI > 0.95 (> 0.90 is acceptable), and SRMR < 0.05 (< 0.08 is acceptable) [72]. CFA revealed an acceptable to good model fit for three out of four parameters (χ2 = 1717.83,
df = 979; CFI = 0.80; RMSEA = 0.05; SRMR = 0.07). Preliminary analyses were executed using SPSS 25.0 (descriptive statistics and bivari-
ate Pearson correlations); and similar to previous studies [54], structural equation modeling
(SEM) in Mplus [71] was used to investigate the research questions. Given the nested struc-
ture of the data, multilevel SEM analyses were conducted, with students at the first level
and classes (or teachers) at the second level. To determine the model fit of the SEM model,
the same fit indices as with the CFA were used [72]. First, a null model was estimated to
evaluate how much of the variation in percentage of lesson time spent in MVPA could
be attributed to both levels (student and teacher). Thereafter, student gender and lesson
topic were included separately into the null model to evaluate the relation between both
predictors and MVPA. To account for the lesson topic, three dummy variables were created
(i.e., artistic sports, fitness training, and racket games) and contrasted against the reference
group (ball games). To find out which lesson topics were significantly differed from one
other, all possible group comparisons were performed by changing the reference group. Second, a multilevel SEM model was tested. It was decided to use a two-level model,
since the school and class level were largely confounded (e.g., for 20 out of the 22 schools,
the number of teachers per school was N = 1). Furthermore, a three-level model did not
yield a better fit than a two-level model, and the variance at the school level was zero. 2.2. Measures Actigraph accelerometers are known to be valid and reliable measures to objec-
tively assess duration, frequency, and intensity of physical activity among youth [68,69]. Furthermore, Actigraph GT3x accelerometers are omnidirectional accelerometers that
are sensitive to movements in all three axes. The Actigraph GT3x accelerometer detects
movements over pre-specified time periods called epochs that were set on fifteen-second
intervals. Movements within each epoch are converted to ‘activity counts’ with the use of
the ‘Actilife’ programme. Then, these activity counts are interpreted to determine minutes
spent at different activity intensities (e.g., moderate and vigorous) by using cut-off points. The current study focused on MVPA because this type of physical activity is recommended
for public health [15,17]. Similar to previous research [21,62], the cut-off points for physical
activity of Evenson et al. [70] were used to determine MVPA (>2296). To determine MVPA
during the PE lesson, the raw scores were converted into percentage of time spent in Int. J. Environ. Res. Public Health 2021, 18, 7457 6 of 17 6 of 17 MVPA by dividing the raw scores by lesson time. In Belgium, PE is grouped in one or
two blocks of 50 min. For all participating classes, class schedules were consulted. Time
spent in MVPA was calculated as a percentage of the 50 or 100 min’ lesson hours, which
included the time spent to go to the gym and to get changed as well as the actual lesson
time. By using percentages, comparison between classes was made possible, since the
duration of the PE lessons was different from one lesson to another (either 50 min or 100
min, respectively 18 and 11 classes). 3.1. Preliminary Analysis Descriptive statistics (means, standard deviations) and bivariate Pearson correlations
are shown in Table 1. In Supplementary Tables S1–S6, correlation coefficients between the
study variables are presented separately for boys and girls, and per lesson topic. On aver-
age, the students engaged in MVPA during 19.03% (SD = 10.87%; 9.52 min per lesson) of
the lesson, with only 3.31% of the students achieving the recommended amounts of MVPA
during the PE lesson (2.65% of the boys and 0.66% of the girls). In addition, correlations
showed that autonomy-support, structure, and relatedness-support were significantly and
positively associated with autonomous motivation, while these were negatively correlated
with amotivation. Only autonomy-support was significantly and positively related to con-
trolled motivation, and structure showed a trend toward a significant positive correlation
with controlled motivation. Furthermore, a controlling style was negatively associated
with autonomous motivation, and it was positively correlated with controlled motivation
and amotivation. Moreover, small but significant positive relations were found between
students’ autonomous motivation and students’ MVPA during PE on the one hand and
between teachers’ autonomy-support and students’ MVPA during PE on the other hand. Lastly, a trend toward a significant relation was found between teachers’ relatedness-suport
and students’ MVPA during PE (see Table 1). Table 1. Descriptive statistics and bivariate Pearson correlations. Table 1. Descriptive statistics and bivariate Pearson correlations. Variable
N
Mean
(SD)
2
3
4
5
6
7
8
9
10
1. Percentage of
MVPA during PE
302
19.03
(10.87)
0.17 **
0.04
−0.09
0.17 **
−0.02
0.10 $
0.09
−0.08
−0.02
2. Autonomous
motivation
302
3.83
(0.73)
0.09
−0.41 **
0.39 **
0.32 **
0.46 **
0.45 **
−0.17 **
−0.23 **
3. Controlled
motivation
302
1.77
(0.61)
0.29 **
0.15 *
0.06
0.04
0.10 $
0.38 **
−0.08
4. Amotivation
302
1.53
(0.65)
−0.14 *
−0.16 **
−0.20 **
−0.19 **
0.30 **
0.08
5. Perceived
teachers’
autonomy-
support
301
3.30
(0.77)
0.55 **
0.63 **
0.85 **
−0.02
−0.04
6. Perceived
teachers’ structure
301
3.51
(0.80)
0.60 **
0.85 **
−0.01
−0.02
7. Perceived
teachers’
relatedness-
support
301
3.58
(0.70)
0.86 **
−0.15 *
−0.05
8. Perceived
teachers’
motivating style
301
3.47
(0.65)
−0.07
−0.04
9. Perceived
teachers’
controlling style
301
1.71
(0.60)
−0.04
10. 2.3. Data Analyses Therefore, using a three-level model did not seem justified, and the data were treated as a
two-level model. In this full model, the indirect effect of the teachers’ (de-)motivating style
onto the percentage of lesson time spent in MVPA via students’ autonomous motivation,
controlled motivation, and amotivation was tested. In this full model, both individual
students’ perceptions of the (de-)motivating teaching style and motivations, as well as
average class perceptions of the (de-)motivating teaching style and motivations were in-
cluded as respectively group-mean centered and grand-mean centered variables. This
allowed examining relations at the student level as well as at the class level. The full model
was controlled for students’ gender and for lesson topic. For all these analyses, a p-value
inferior to 0.05 was considered statistically significant, and a p-value inferior to 0.10 was
considered to reveal a trend toward significance. Due to missing data for age in 74 of 302 students, we did not include students’ age as
a covariate in the full model. In order to estimate the stability of the full model without
students’ age, we decided to conduct sensitivity analyses by comparing this full model
with a model controlled for students’ age, hereby relying on multiple imputations for
handling the missing data for age. Multiple imputations are considered one of the most
highly recommended methods for dealing with missing data [73]. In line with previous Int. J. Environ. Res. Public Health 2021, 18, 7457 7 of 17 research, five imputed datasets were created, stored, and analyzed [74]. Subsequently,
results are combined according to the rules suggested by Rubin [75]. research, five imputed datasets were created, stored, and analyzed [74]. Subsequently,
results are combined according to the rules suggested by Rubin [75]. 3.1. Preliminary Analysis Students’ age
228
13.05
(1.04)
** Correlation is significant at the 0.01 level; * Correlation is significant at the 0.05 level; $ correlation showed a trend towards significance at
the 0.10 level; MVPA moderate- to vigorous-intensity physical activity, PE physical education. ** Correlation is significant at the 0.01 level; * Correlation is significant at the 0.05 level; $ correlation showed a trend towards significance at
the 0.10 level; MVPA moderate- to vigorous-intensity physical activity, PE physical education. 3. Results 3.1. Preliminary Analysis 3.2. Main Analysis Next, direct relations between teachers’ (de-)motivating style and students’ physical
activity levels at both the student and class level were tested (hereby controlling for gender
and lesson topic). For this model, a good fit was obtained (χ2 = 0.00, df = 0; CFI = 1.00;
RMSEA < 0.001; SRMR within < 0.001; SRMR between < 0.001). The relations between
teachers’ motivating style and students’ physical activity levels was significant on neither
level (student level: β = −0.71; p = 0.18; class level: β = 0.83; p = 0.89). The relation between
teachers’ controlling style and students’ physical activity levels was not significant on the
student level (β = 0.62; p = 0.37). However, this relation was significant and negative on
the class level (β = −13.31; p = 0.02) (
p
)
Finally, students’ motivation (at both levels) was included in the multilevel model
(see Figure 1). Results indicated that teachers’ motivating style was significantly and
positively related to autonomous motivation at both the student (β = 0.47; p < 0.001)
and class level (β = 0.66; p = 0.02). Teachers’ motivating style was also significantly and
positively related to controlled motivation at the student level (β = 0.11; p = 0.03), but
not at the class level (β = 0.16; p = 0.51). Teachers’ motivating style was significantly and
negatively related to amotivation at the student level (β = −0.14; p = 0.05), and it displayed
a trend toward a significant negative relation with amotivation at the class level (β = −0.34;
p = 0.08). Furthermore, teachers’ controlling style was significantly and positively related to
controlled motivation and amotivation at both the student (controlled motivation: β = 0.37;
p < 0.001; amotivation: β = 0.29; p < 0.001) and class level (controlled motivation: β = 0.47;
p < 0.001; amotivation: β = 0.54; p = 0.001). Teachers’ controlling style displayed a trend
toward a significant negative relation with autonomous motivation at the student level
(β = −0.14; p = 0.06), yet it was not significantly related to autonomous motivation at the
class level (β = −0.38; p = 0.26). Autonomous motivation showed a trend toward a significant positive relation with
students’ percentage of the lesson time spent in MVPA on the student level (β = 1.27;
p = 0.10) but not at the class level (β = 1.05; p = 0.84). 3.2. Main Analysis A two-level null model for percentage of lesson time spent in MVPA was estimated
and revealed that 21.61% of the variability was accounted for by student differences and
78.39% was accounted for by class differences. Inclusion of gender revealed that boys
(22.63%, SE = 2.21) displayed a significantly higher percentage of time spent in MVPA than
girls (18.78%, SE = 1.21). Student gender explained 9% of the student differences. Second,
the relation between the lesson topics and students’ MVPA levels was investigated. The
lesson topic explained 17.32% of the class differences. Specifically, the mean percentage Int. J. Environ. Res. Public Health 2021, 18, 7457 8 of 17 8 of 17 of lesson time spent in MVPA in the multilevel model was 28.12% (SE = 5.12) during
ball games, 24.05% (SE = 3.61) during artistic sports, 24.60% (SE = 1.77) during fitness
training, and 25.48% (SE = 1.52) during racket games. Students were significantly less
active during fitness training when compared to ball games (p < 0.05; see Table 2), although
the differences between ball games and racket games displayed a trend toward significance,
with students being more active in ball games (p = 0.08). Table 2. Means and standard deviations in percentages of MVPA (percentage of class time) during
PE as a function of lesson topic. Lesson Topic
M (SE)
β
Ball games
28.12 (5.12) a
Artistic sports
24.05 (3.61) a,b
−4.07
Fitness training
24.60 (1.77) b
−3.51 *
Racket games
25.78 (1.51) a,b
−2.64
MVPA moderate- to vigorous-intensity physical activity, PE physical education. Note. Values in parentheses are
standard errors. * p < 0.05. Regression equations were repeated several times by changing the reference category
to obtain coefficients for all combinations of lesson topic. A mean is significantly different from another mean
(p < 0.05) if they have different superscripts. Table 2. Means and standard deviations in percentages of MVPA (percentage of class time) during
PE as a function of lesson topic. MVPA moderate- to vigorous-intensity physical activity, PE physical education. Note. Values in parentheses are
standard errors. * p < 0.05. Regression equations were repeated several times by changing the reference category
to obtain coefficients for all combinations of lesson topic. A mean is significantly different from another mean
(p < 0.05) if they have different superscripts. 3.2. Main Analysis However, none of the indirect
effects via autonomous motivation were significant. Moreover, controlled motivation and
amotivation were not associated with the percentage of lesson time spent in MVPA neither
at the student level nor at the class level. Thus, also the indirect effects via controlled
motivation and amotivation were not significant. Surprisingly, in the full model, teachers’
motivating style displayed a trend toward a significant negative relation with students’
percentage of the lesson time spent in MVPA on the student level (β = −1.27; p = 0.06). Only the direct relation between teachers’ controlling style and students’ percentage of
lesson time spent in MVPA remained significant on the class level (β = −13.78; p = 0.001). Int. J. Environ. Res. Public Health 2021, 18, 7457
style display
the le
o
ti 9 of 17 Yet, these results need to be interpreted with care, since no good model fit was obtained
(χ2 = 66.19, df = 6; CFI = 0.75; RMSEA = 0.18; SRMR within = 0.07; SRMR between = 0.06). n MVPA remained significant on the class level (β = −13.78; p = 0.001). Yet, these results
eed to be interpreted with care, since no good model fit was obtained (χ2 = 66.19, df = 6;
FI = 0.75; RMSEA = 0.18; SRMR within = 0.07; SRMR between = 0.06). Yet, these results need to be interpreted with care, since no good model fit was obtained
(χ2 = 66.19, df = 6; CFI = 0.75; RMSEA = 0.18; SRMR within = 0.07; SRMR between = 0.06). n MVPA remained significant on the class level (β = −13.78; p = 0.001). Yet, these results
eed to be interpreted with care, since no good model fit was obtained (χ2 = 66.19, df = 6;
FI = 0.75; RMSEA = 0.18; SRMR within = 0.07; SRMR between = 0.06). Yet, these results need to be interpreted with care, since no good model fit was obtaine
(χ2 = 66.19, df = 6; CFI = 0.75; RMSEA = 0.18; SRMR within = 0.07; SRMR between = 0.0
in MVPA remained significant on the class level (β = −13.78; p = 0.001). Yet, these results
need to be interpreted with care, since no good model fit was obtained (χ2 = 66.19, df = 6;
CFI = 0.75; RMSEA = 0.18; SRMR within = 0.07; SRMR between = 0.06). Figure 1. 3.2. Main Analysis Full model with teachers’ (de-)motivating style as a possible predictor for students’ MVPA during PE when
taking both students’ gender and lesson topic into account. βs are presented at both the student level (first number) and
the class level (β student level/β class level); $ p < 0.1; * p < 0.05; ** p < 0.01; *** p < 0.001; MVPA moderate- to vigorous-
intensity physical activity; PE physical education. Black lines indicate a significant relation on both the student and class
level, while gray full lines indicate only a significant or trend to significant relation on one of the two levels. Finally, gray
dashed lines indicate that no significant relations were found. Figure 1. Full model with teachers’ (de-)motivating style as a possible predictor for students’ MVPA during PE when taking
both students’ gender and lesson topic into account. βs are presented at both the student level (first number) and the class
level (β student level/β class level); $ p < 0.1; * p < 0.05; ** p < 0.01; *** p < 0.001; MVPA moderate- to vigorous-intensity
physical activity; PE physical education. Black lines indicate a significant relation on both the student and class level, while
gray full lines indicate only a significant or trend to significant relation on one of the two levels. Finally, gray dashed lines
indicate that no significant relations were found. Figure 1. Full model with teachers’ (de-)motivating style as a possible predictor for students’ MVPA during PE when
aking both students’ gender and lesson topic into account. βs are presented at both the student level (first number) and
he class level (β student level/β class level); $ p < 0.1; * p < 0.05; ** p < 0.01; *** p < 0.001; MVPA moderate- to vigorous-
ntensity physical activity; PE physical education. Black lines indicate a significant relation on both the student and class
evel, while gray full lines indicate only a significant or trend to significant relation on one of the two levels. Finally, gray
dashed lines indicate that no significant relations were found. Figure 1. Full model with teachers’ (de-)motivating style as a possible predictor for students’ MVPA during PE when taking
both students’ gender and lesson topic into account. . Sensitivity Analyses
3.3. Sensitivity Analyses A two-level model that controlled for students’ age was estimated and revealed sim-
r results when compared to the abovementioned results, confirming the stability of the
esented model. Only two small differences were found on the student level: teachers’
otivating style now displayed a significant negative relation with students’ physical ac-
ity levels during PE (β = −1.28; p = 0.05), and the p-value displaying the relation between
udents’ autonomous motivation and their physical activity levels during PE was now
9 instead of 0.10 (β = 1.26). In Supplementary Figure S1, the model controlled for stu-
nts’ age is shown. A two-level model that controlled for students’ age was estimated and revealed
similar results when compared to the abovementioned results, confirming the stability of
the presented model. Only two small differences were found on the student level: teachers’
motivating style now displayed a significant negative relation with students’ physical
activity levels during PE (β = −1.28; p = 0.05), and the p-value displaying the relation
between students’ autonomous motivation and their physical activity levels during PE was
now 0.09 instead of 0.10 (β = 1.26). In Supplementary Figure S1, the model controlled for
students’ age is shown. 3.2. Main Analysis βs are presented at both the student level (first number) and the class
level (β student level/β class level); $ p < 0.1; * p < 0.05; ** p < 0.01; *** p < 0.001; MVPA moderate- to vigorous-intensity
physical activity; PE physical education. Black lines indicate a significant relation on both the student and class level, while
gray full lines indicate only a significant or trend to significant relation on one of the two levels. Finally, gray dashed lines
indicate that no significant relations were found. 4.1. Physical Activity Levels during the PE Lesson Results revealed that students engaged in MVPA for only 19.03% of the PE lesson
on average, which is even lower than the percentages found in previous reviews (e.g.,
34.7%, [76]; 46.8%, [18]). Furthermore, only 3.31% of present students scored equal to or
above 50%, which is also lower in comparison to previous studies (e.g., 12.8%, [20]). These
results show that this study sample does not meet the recommended amount of MVPA
during PE (50% of the PE lesson, [17]). It is important to note that percentage time spent
in MVPA was calculated consulting the class schedule, hereby including time spent to
go to the gym and to get changed. Therefore, percentages found in this study are lower
compared to other studies [18,76]. In the study of Lonsdale et al. [26], percentage time spent
in MVPA was calculated by recording start and finish times of each lesson as indicated by
the school bell. This method is similar to the method used in this study, and similar results
were found. In addition, the estimated model including students’ physical activity levels and
the topic of the lesson revealed that there were significant differences between students’
physical activity levels during the lesson, implying that albeit being taught by the same
teacher, students’ physical activity levels differed from one another. Yet, our analyses
also showed that class differences (78.39%) outweighed student differences (21.61%). This
suggests that not only students’ personal characteristics have to be taken into account (e.g.,
students’ gender), but particularly class or teacher-related variables will explain differences
in activity levels (e.g., lesson topic). Aelterman et al. [20] also reported similar distributions
with 63% of the variability in MVPA being accounted for by the class level in their study. 4.2. Relations between Teachers’ Motivating Style, Students’ Motivation, and Students’ Physical
Activity Levels during PE 4.2. Relations between Teachers’ Motivating Style, Students’ Motivation, and Students’ Physical
Activity Levels during PE In the current study, we investigated the relation between teachers’ (de-)motivating
style and students’ motivation. In line with our hypothesis, teachers’ motivating style
was significantly and positively related to students’ autonomous motivation both at the
student and the class level. This is an important finding as SDT-related research in PE
highlights the importance of enhancing students’ autonomous motivation for PE to achieve
positive outcomes, such as higher concentration [31], greater enjoyment [32,33], and more
effort [31,32,34]. Discussion
4. Discussion Given the low physical activity levels in adolescence, the promotion of physical
activity is a big concern worldwide in this age group [10]. Research suggests that PE
teachers can play a crucial role in this promotion [15,16]. Grounded in SDT, this study
investigated how students’ perceptions of PE teachers (de-)motivating style relate to their
motivation for PE and in turn to their physical activity levels during the PE lesson as
measured by means of device-based measures. Moreover, it was also examined how
students’ gender and the lesson topic relate to students’ physical activity levels during PE. Overall, the results suggest that teachers’ motivating style is positively related to students’
autonomous motivation for PE both at student and class level. Teachers’ motivating
style is also negatively related to students’ amotivation for PE at the student level and
showed a trend toward a significant negative relation to students’ amotivation at the class Int. J. Environ. Res. Public Health 2021, 18, 7457 10 of 17 level. Furthermore, teachers’ controlling style is positively related to students’ controlled
motivation and amotivation for PE on both levels. These results are in line with the
theoretical tenets of SDT [27]. In terms of students’ physical activity levels, students’
gender, the lesson topic, and teachers’ controlling style seemed to be more decisive than
students’ motivation and teachers’ motivating style. 4.1. Physical Activity Levels during the PE Lesson Moreover, teachers’ motivating style displayed a significant negative
relation with students’ amotivation on the student level, and it showed a trend toward a
negative relation on the class level. In addition, teachers’ controlling style was significantly
and positively related to students’ controlled motivation and amotivation on both levels. This reveals that it is important to minimize teachers’ controlling style and optimize
teachers’ motivating style, since controlled motivation and amotivation for PE is related to
negative outcomes, such as boredom [32] and unhappiness [33]. Moreover, these results
stress the importance of examining both teachers’ motivating and demotivating styles. This
is shown in the relatively unique and differential pathways between teachers’ motivating
and controlling style and students’ motivation, with teachers’ motivating style fostering a
bright pathway and teachers’ controlling style supporting a dark pathway [54]. Furthermore, as relations were found both at the student and at the class level, we
can conclude that it is not only when students personally perceive their teachers as more
motivating or controlling that their personal motivation is affected. There also appear to be
class-level relations or contextual effect. When teachers are generally perceived as more
motivating, their classes display higher levels of autonomous motivation. When teachers
are generally perceived as more controlling, their classes display higher levels of controlled
motivation and amotivation for PE. These findings suggests that teachers’ (de-)motivating Int. J. Environ. Res. Public Health 2021, 18, 7457 11 of 17 11 of 17 style is not only important for students’ personal motivation but is equally important for
the classes’ motivation in general. style is not only important for students’ personal motivation but is equally important for
the classes’ motivation in general. g
In addition to these relations between teachers’ (de-)motivating style and students’
motivation, an important question was whether these variables were related to students’
physical activity levels during PE. In the presented model, only a trend toward a signif-
icant positive relation was found betweens students’ autonomous motivation and their
MVPA during PE on the student level. Although we hypothesized, based on previous
research [54,55], that teachers who adopt a motivating style will stimulate their students
toward being physically active through the development of autonomous motivation for
PE, this assumption was only partially confirmed by our model. 4.1. Physical Activity Levels during the PE Lesson Note that the correlation
table displayed a significant positive relation between students’ autonomous motivation,
teachers’ autonomy support, and students’ physical activity levels, and a trend toward a
significant relation between teachers’ relatedness support and students’ physical activity
levels. This suggests that students display higher levels of physical activity when they
are autonomously motivated and when they perceive their teachers as more autonomy
and relatedness supportive. Yet, these relations do not hold in the full model (when ac-
counting for students’ gender, lesson topic, and the hierarchical structure of the data);
therefore, no indirect relation was obtained. In the full model, the direct relation between
a need-supportive teaching style and MVPA during PE even became negative on the stu-
dent level. In line with the findings of the full model, a recently conducted intervention
study in elementary school children also showed that enhanced perceived support from
teachers did not affect students’ physical activity levels [77]. These findings contrast prior
research that found positive relations between teachers’ motivating style [25] or students’
autonomous motivation and physical activity levels during PE [20]. Moreover, relations
between students’ controlled motivation and amotivation and students’ physical activity
levels during PE were not significant. Although, we expected, based on theoretical insights
that amotivated students and controlled motivated students would be less active, this
assumption was not confirmed by our model. However, this finding is in line with prior
empirical research using device-based measures [20]. p
g
A significant direct relation was found between teachers’ controlling style and students’
physical activity levels during PE at the class level, with classes perceiving their teachers as
more controlling displaying lower percentages of lesson time spent in MVPA. One could
assume that students would have no choice but being active with a controlling teacher. Yet, this appeared not to be the case. Previous research on teachers’ controlling style
mainly focused on relations with physical activity during leisure time and not physical
activity during PE. In line with the findings of the current research, Koka et al. [62] found
a significant negative relation between teachers’ controlling style and students’ MVPA
levels during leisure time (as measured by means of accelerometers). On the other hand,
Rodrigues et al. [78] found no significant direct relation between teachers thwarting style
(i.e., controlling, chaotic, and cold) and students’ intention to continue exercising. 4.3. Students’ Physical Activity Levels According to Students’ Gender and Lesson Topic Results of the current study confirmed that students’ physical activity levels vary
according to students’ gender. In line with our expectations, we found that boys engaged
in more MVPA than girls. This finding is in line with many studies that also revealed
that girls were less active during the PE lessons [21,24]. Furthermore, students’ gender
explained 9% of the variability in students’ physical activity levels during PE, which is in
line with the study of Aelterman et al. (6%, [20]). Moreover, lesson topic accounted for 17.32% of the class differences, which is in
line with the findings of Aelterman et al. [20], who reported that lesson topic accounted
for 19% of the class differences. In addition, students in the present study accumulated
more MVPA during ball games. While only differences between ball games and fitness
training reached significance, an inspection of the averages suggests that ball games differed
from the three other lesson topics. The unequal distribution of the topics with an under- Int. J. Environ. Res. Public Health 2021, 18, 7457 12 of 17 12 of 17 representation of racket games and artistic sports may have influenced our results. Overall,
this finding favoring ball games in terms of students’ activity levels is in line with the study
by Erwin et al. [23]. This study found that students displayed higher physical activity
levels during team activities in comparison to individual activities, and Fairclough and
Stratton [18] showed that students’ physical activity levels were the highest during team
games in comparison to individual games, individual activities, and movement activities. However, in contrast to our findings, Aelterman et al. [20] found that students particularly
engaged in less MVPA during racket games when compared to all other topics (i.e., ball
games, artistic sports, and fitness training). Delextrat et al. [22] showed that students
engaged in more MVPA during fitness training compared to artistic sports, while no such
differences were found in the current study. Even though findings clearly differ across
studies, all these studies consistently confirm the variability in percentage time spent in
MVPA according to the lesson topic. It appeared in the current study that lesson topic is more decisive for students’ MVPA
levels during PE than teachers’ motivating style. In contrast to our expectations, we even
found a trend toward a significant negative relation between teachers’ motivating style
and students’ activity levels at the student level. 4.4. Practical Implications A major concern rising from the results of this study is that students spent very
low percentages of time in MVPA during the PE lesson. If increasing students’ MVPA
levels during the lesson is the sole goal, it might be worthwhile to consider ball games, as
students appear to accumulate more MVPA during these activities. Yet, it is important to
acknowledge that PE has many other goals that are equally important. For instance, a major
goal of PE is to enhance students’ personal and social skills [79], which may not necessarily
be achieved more easily during ball games when compared to other lesson topics. Teachers
are also recommended to adopt a motivating style to benefit both students’ and classes’
autonomous motivation for PE, while at the same time minimizing their controlling style
to minimize students’ and classes’ controlled motivation and amotivation. Thus, future
intervention studies should not only focus on developing teachers’ motivating style (an
autonomy-supportive, structuring, and relatedness-supportive style), but should also raise
awareness among teachers about the detrimental effects of a teachers’ controlling style and
discourage teachers from adopting such a style. 4.3. Students’ Physical Activity Levels According to Students’ Gender and Lesson Topic To our knowledge, only one other study
investigated teachers’ motivating style in relation to students’ physical activity levels
during PE while taking the lesson topic into account [23]. These authors showed that lesson
topic may interact with teachers’ style as students displayed the highest physical activity
levels in lessons with team activities without the provision of choice as well as in lessons
with individual activities with the provision of choice. The correlations of the current study
also revealed that particularly teachers’ autonomy-support is related to students’ physical
activity levels. Thus, it is possible that certain motivating strategies such as offering choice
are of larger influence for students’ physical activity levels than others. Secondly, it appears
that certain motivating strategies exert a different effect depending on lesson topic [23],
which is an issue that is worth further exploration. 4.5. Limitations and Future Directions First, the study used a cross-sectional study design. As such, the observed relations
between teachers’ (de-)motivating style and students’ motivation during PE might be
interpreted in both ways. For example, students who are more autonomously motivated
are more positive toward the teachers’ approach, while students with higher controlled
motivation and amotivation are more negative toward the teachers’ approach. Future
research could use a longitudinal study design to investigate the causal and long-term
effects of a teachers’ motivating style on student’s physical activity levels. Secondly, it is worth mentioning that selection bias might have occurred, since the
accelerometers were randomly given to students who were present in the class and had Int. J. Environ. Res. Public Health 2021, 18, 7457 13 of 17 13 of 17 their informed consent form with them. Therefore, students that were eager to participate
in this research may have been more likely to be selected in this research. By no means can
the sample of the current study be considered representative of the entire population. p
y
p
p p
Thirdly, only 228 out of 302 students provided information regarding their age. There-
fore, we were not able to include students’ age in the full model in our study. Sensitivity
analyses indicated that the full model was similar to a model in which the missing data
regarding students’ age were imputed, hereby relying on multiple imputations. While
this method is recommended in case of missing data, this method has a few pitfalls, with
multiple imputations assuming that missing data are missing at random being the main
pitfall [80]. Finally, in the multilevel SEM analyses, we focused on teachers’ motivating style as a
whole. Future research should opt to investigate the relation between specific motivating
styles and/or strategies and students’ physical activity levels during PE. Moreover, future
research could also add other teachers’ demotivating styles (e.g., chaos and coldness) to
the model. 5. Conclusions In conclusion, results suggest that teachers’ motivating style is positively related to
students’ autonomous motivation at both the student and the class level, and teachers’
controlling style is positively related to students’ controlled motivation and amotivation
on both levels. However, in terms of students’ physical activity levels during PE, students’
gender, the lesson topic, and teachers’ controlling style seemed to be more decisive than
students’ motivation and teachers’ motivating style. Supplementary Materials: The following are available online at https://www.mdpi.com/article/10
.3390/ijerph18147457/s1, Figure S1: Full model with teachers’ (de-)motivating style as a possible
predictor for students’ MVPA during PE, when taking students’ gender, students’ age and lesson topic
into account (using imutations), Table S1: Descriptive statistics and bivariate Pearson correlations for
boys; Table S2: Descriptive statistics and bivariate Pearson correlations for girls; Table S3: Descriptive
statistics and bivariate Pearson correlations for ball games; Table S4: Descriptive statistics and
bivariate Pearson correlations for artistic sports; Table S5: Descriptive statistics and bivariate Pearson
correlations for fitness training; Table S6: Descriptive statistics and bivariate Pearson correlations for
racket games. Author Contributions: Conceptualization, N.V.D., L.H. and K.D.C.; methodology, N.V.D.; L.H. and
A.V.; data collection, A.V.; formal analysis, N.V.D. and T.D.C.; investigation, N.V.D., T.D.C., L.H.,
K.D.C. and R.V.; resources, L.H.; data curation, N.V.D., L.H.; writing—original draft preparation,
N.V.D.; writing—review and editing, all co-authors.; visualization, N.V.D.; supervision, L.H., K.D.C. and R.V.; project administration, L.H.; All authors have read and agreed to the published version of
the manuscript. Funding: The research was funded by the following research grant of the Flemish Research
Foundation-Flanders (FWO): 1510317N. Institutional Review Board Statement: The study was conducted according to the guidelines of the
Declaration of Helsinki and according to the guidelines for good clinical practice (ICH/GCP). The
study was approved by the Committee for Medical Ethics affiliated with UZ Gent (UZG 2017/0213
approved on 17 March 2017). Informed Consent Statement: Informed consent was obtained from all subjects involved in the study. Data Availability Statement: Data gathered in this study are not available for public access, since
the informed consents did not ask for permission to share data publicly. Data remain confidential
according to the ethical approval process of the Committee for Medical Ethics and is held on secure
and password protected servers. Acknowledgments: The authors thank the students and PE teacher for their participation in data
collection, and Femke Van duyse for her help with the data collection. 5. Conclusions Conflicts of Interest: The authors declare no conflict of interest. Conflicts of Interest: The authors declare no conflict of interest. Int. J. Environ. Res. Public Health 2021, 18, 7457 14 of 17 References 12. Troiano, R.; Berrigan, D.; Dodd, K.; Mâsse, L.; Tilert, T.; McDowell, M. Physical activity in the united stated measured by
acceleromter. Med. Sci. Sports Exerc. 2008, 40, 181–188. [CrossRef] 13. Cooper, A.R.; Goodman, A.; Page, A.S.; Sherar, L.B.; Esliger, D.W.; van Sluijs, E.M.; Andersen, L.B.; Anderssen, S.; Cardon, G.;
Davey, R.; et al. Objectively measured physical activity and sedentary time in youth: The International children’s accelerometry
database (ICAD). Int. J. Behav. Nutr. Phys. Act. 2015, 12, 113. [CrossRef] y
14. Dumith, S.C.; Gigante, D.P.; Domingues, M.R.; Kohl, H.W., 3rd. Physical activity change during adolescence: A systematic review
and a pooled analysis. Int. J. Epidemiol. 2011, 40, 685–698. [CrossRef] [PubMed] 15. Pate, R.; Davis, M.; Robinson, T.; Stone, E.; McKenzie, T.; Young, J. Promoting physical activity in children and youth: A
leadership role for schools: A scientific statement from the American Heart Association Council on nutrition, physical activity,
and metabolism (Physical Activity Committee) in collaboration with the Councils on Cardiovascular Disease in the Young and
Cardiovascular Nursing. Circulation 2006, 114, 1214–1224. [PubMed] g
16. Centers for Disease Control and Prevention. Physical Education and Physical Activity. Available online: https://www.cdc.gov/
healthyschools/physicalactivity/index.htm (accessed on 28 May 2021). y
p y
y
y
17. Regulatory Issues—Department of Health and Human Services Recombinant DNA Advisory Committee National Institutes of
Health: Minutes of Meeting. June 14, 1999. Hum. Gene Ther. 2000, 11, 1369–1382. [CrossRef] [PubMed] 18. Fairclough, S.; Stratton, G. Physical Activity Levels in Middle and High School Physical Education: A Review. Pediatr. Exerc. Sci. 2005, 17, 217–236. [CrossRef] 19. Haerens, L.; Aelterman, N.; Meester, A.D.; Tallir, I. Educating teachers in health pedagogies. In Routledge Handbook of Physical
Education Pedagogies Publisher: Routledge International Handbooks; Routledge: Abingdon, UK, 2016. 20. Aelterman, N.; Vansteenkiste, M.; Keer, H.V.; Berghe, L.V.d.; Meyer, J.D.; Haerens, L. Students’ Objectively Measured Physical
Activity Levels and Engagement as a Function of Between-Class and BetweenStudent Differences in Motivation Toward Physical
Education. J. Sport Exerc. Psychol. 2012, 34, 457–480. [CrossRef] J
p
y
21. Gråstén, A.; Yli-Piipari, S.; Huhtiniemi, M.; Salin, K.; Seppälä, S.; Lahti, J.; Hakonen, H.; Jaakkola, T. Predicting accelerometer-
based physical activity in physical education and total physical activity: The Self-determination Theory approach. J. Hum. Sport
Exerc. 2019, 14. [CrossRef] 22. Delextrat, A.; Esser, P.; Beale, N.; Bozon, F.; Eldridge, E.; Izadi, H.; Johansen-Berg, H.; Wheatley, C.; Dawes, H. References 1. Janssen, I.; LeBlanc, A.G. Systematic review of the health benefits of physical activity and fitness in school-aged children and
youth. Int. J. Behav. Nutr. Phys. Act. 2010, 7, 40. [CrossRef] y
y
2. Biddle, S.J.H.; Ciaccioni, S.; Thomas, G.; Vergeer, I. Physical activity and mental health in children and adolescents: An updated
review of reviews and an analysis of causality. Psychol. Sport Exerc. 2019, 42, 146–155. [CrossRef] 3. Singh, A.; Uijtdewilligen, L.; Twisk, J.W.; van Mechelen, W.; Chinapaw, M.J. Physical activity and performance at school: A
systematic review of the literature including a methodological quality assessment. Arch. Pediatr. Adolesc. Med. 2012, 166, 49–55. [CrossRef] 4. Xu, F.; Adams, S.K.; Cohen, S.A.; Earp, J.E.; Graeney, M.L. Relationship between Physical Activity, Screen Time, and Sleep
Quantitiy and Quality in US Adolescents Aged 16–19. Int. J. Environ. Res. Public. Health 2019, 16, 1524. [CrossRef] [PubMed] 5. McMahon, E.M.; Corcoran, P.; O’Regan, G.; Keeley, H.; Cannon, M.; Carli, V.; Wasserman, C.; Hadlaczky, G.; Sarchiapone, M.;
Apter, A.; et al. Physical activity in European adolescents and associations with anxiety, depression and well-being. Eur. Child
Adolesc. Psychiatry 2017, 26, 111–122. [CrossRef] [PubMed] 6. Daley, A. School based physical activity in the United Kingdom: Can it create physically active adults? Quest 2002, 54, 21–33. [CrossRef] 7. Hallal, P.; Victora, C.; Azevedo, M.; Wells, J. Adolescent Physical Activity and Health: A systematic review. Sports Med. 2006, 36,
1019–1030. [CrossRef] 8. Telama, R.; Yang, X.; Lesikenen, E.; Kankaanpää, A.; Hirvensalo, M.; Tammelin, T.; Viikari, J.; Raitakari, O. Tracking of physical
activity from early childhood through youth into adulthood. Med. Sci. Sports Exerc. 2014, 46, 955–962. [CrossRef]
9. Biddle, S.J.H.; Mutrie, N. Psychology of Physical Activity: Determinants, Well-Being, and Interventions; Routledge: London, UK, 2007. activity from early childhood through youth into adulthood. Med. Sci. Sports Exerc. 2014, 46, 955–962. [CrossRef]
9. Biddle, S.J.H.; Mutrie, N. Psychology of Physical Activity: Determinants, Well-Being, and Interventions; Routledge: London, UK, 2007. y
y
g
y
p
9. Biddle, S.J.H.; Mutrie, N. Psychology of Physical Activity: Determinants, Well-Being, and Interventions; Routledge: London, UK, 2007. 10. World Heath Organization. Physical Activity. Available online: https://www.who.int/news-room/fact-sheets/detail/physical-
activity#:~{}:text=living%20with%20disability%3A-,should%20do%20at%20least%20150%E2%80%93300%20minutes%20of%
20moderate%2Dintensity,intensity%20activity%20throughout%20the%20week (accessed on 28 May 2021). 10. World Heath Organization. Physical Activity. Available online: https://www.who.int/news-room/fact-sheets/detail/physical-
activity#:~{}:text=living%20with%20disability%3A-,should%20do%20at%20least%20150%E2%80%93300%20minutes%20of% ate%2Dintensity,intensity%20activity%20throughout%20the%20week (accessed on 28 May 2021). 11. Hardy, L.; King, L.; Espinel, P.; Cosgrove, C.; Bauman, A. NSW Schools Physical Activity and Nutrition Survey (SPANS): Full Report;
NSW Ministry of Health: Sydney, Australia, 2010. References [CrossRef] y
32. Ntoumanis, N. A Self-Determination approach to the understanding of motivation in physical education. Br. J. Educ. Psychol. 2001, 71, 225–242. [CrossRef] 33. Standage, M.; Duda, J.L.; Pensgaard, A.M. The effect of competitive outcome and taks-involving, ego-involving, and co-operative
structures on the psychological well-being of individuals engaged in a co-ordination task. Motiv. Emot. 2005, 29, 41–68. [CrossRef]
34
Ferrer-Caja E ; Weiss M Predictors of intrinsic motivation among adolescent students in physical education Res Q Exerc Sport 33. Standage, M.; Duda, J.L.; Pensgaard, A.M. The effect of competitive outcome and taks-involving, ego
structures on the psychological well-being of individuals engaged in a co-ordination task. Motiv. Emo 33. Standage, M.; Duda, J.L.; Pensgaard, A.M. The effect of competitive outcome and taks-involving, ego-involving, and co-operative
structures on the psychological well-being of individuals engaged in a co-ordination task. Motiv. Emot. 2005, 29, 41–68. [CrossRef]
34. Ferrer-Caja, E.; Weiss, M. Predictors of intrinsic motivation among adolescent students in physical education. Res. Q. Exerc. Sport
2000, 71, 267–279. [CrossRef] structures on the psychological well being of individuals engaged in a co ordination task. Motiv. Emot. 2005, 29, 41 68. [CrossRef]
34. Ferrer-Caja, E.; Weiss, M. Predictors of intrinsic motivation among adolescent students in physical education. Res. Q. Exerc. Sport
2000, 71, 267–279. [CrossRef] 35. Ha, A.S.; Ng, J.Y. Autonomous Motivation Predicts 7-Day Physical Activity in Hong Kong Students. Appl. Psychol. Health Well
Being 2015, 7, 214–229. [CrossRef]
36
O
K B
S
i h J
L b
D R
N
J Y L
d l
C S lf d
i
d
i
i
d
h
i
l
i i
i
hild
d g J
y
y
y
g
g
pp
y
Being 2015, 7, 214–229. [CrossRef]
36
Owen K B ; Smith J ; Lubans D R ; Ng J Y; Lonsdale C Self-determined motivation and physical activity in children and Being 2015, 7, 214–229. [CrossRef]
36. Owen, K.B.; Smith, J.; Lubans, D.R.; Ng, J.Y.; Lonsdale, C. Self-determined motivation and physical activity in children and
adolescents: A systematic review and meta analysis Prev Med 2014 67 270 279 [CrossRef] [PubMed] 36. Owen, K.B.; Smith, J.; Lubans, D.R.; Ng, J.Y.; Lonsdale, C. Self-determined motivation and phys
adolescents: A systematic review and meta-analysis. Prev. Med. 2014, 67, 270–279. [CrossRef] [Pub 36. Owen, K.B.; Smith, J.; Lubans, D.R.; Ng, J.Y.; Lonsdale, C. Self-determined motivation and physical activity in children and
adolescents: A systematic review and meta-analysis. References Effects of gender,
activity type, class location and class composition on physical activity levels experienced during physical education classes in
British secondary schools: A pilot cross-sectional study. BMC Public Health 2020, 20, 1590. [CrossRef] [PubMed] y
p
y
[
] [
]
23. Erwin, H.E.; Stellino, M.B.; Beets, M.W.; Beighle, A.; Johnson, C.E. Physical Education Lesson Content and Teacher Style and
Elementary Students’ Motivation and Physical Activity Levels. J. Teach. Phys. Educ. 2013, 32, 321–334. [CrossRef] y
y
y
y
24. Mieziene, B.; Emeljanovas, A.; Putriute, V.; Novak, D. The Direct and Indirect Relationships Within the Extended Trans-contextual
Model for Moderate-to-vigorous Physical Activity. Front. Pediatr. 2021, 9, 666040. [CrossRef] 24. Mieziene, B.; Emeljanovas, A.; Putriute, V.; Novak, D. The Direct and Indirect Relationships W
Model for Moderate-to-vigorous Physical Activity. Front. Pediatr. 2021, 9, 666040. [CrossRef Int. J. Environ. Res. Public Health 2021, 18, 7457 15 of 17 15 of 17 25. Escriva-Boulley, G.; Tessier, D.; Ntoumanis, N.; Sarrazin, P. Need-supportive professional development in elementary school
physical education: Effects of a cluster-randomized control trial on teachers’ motivating style and student physical activity. Sport
Exerc. Perform. Psychol. 2018, 7, 218–234. [CrossRef] 26. Lonsdale, C.; Lester, A.; Owen, K.B.; White, R.L.; Peralta, L.; Kirwan, M.; Diallo, T.M.O.; Mader, A.J.; Bennie, A.; MacMillan,
F.; et al. An internet-supported school physical activity intervention in low socioeconomic status communities: Results from the
Activity and Motivation in Physical Education (AMPED) cluster randomised controlled trial. Br. J. Sports Med. 2019, 53, 341–347. [CrossRef] 27. Deci, E.; Ryan, R.M. The “what” and “why” of goal pursuits: Human needs and the self-determination of behavior. Psychol. Inq. 2000, 11, 227–268. [CrossRef] 28. Haerens, L.; Kirk, D.; Cardon, G.; De Bourdeaudhuij, I.; Vansteenkiste, M. Motivational profiles for secondary school physical
education and its relationship to the adoption of a physically active lifestyle among university students. Eur. Phys. Educ. Rev. 2010, 16, 117–139. [CrossRef] 29. Hagger, M.S.; Chatzisarantis, N.L.D.; Barkoukis, V.; Wang, C.K.J.; Baranowski, J. Perceived Autonomy Support in Physical
Education and Leisure-Time Physical Activity: A Cross-Cultural Evaluation of the Trans-Contextual Model. J. Educ. Psychol. 2005,
97, 376–390. [CrossRef] 30. Zhang, T.; Solmon, M.; Kosma, M.; Carson, R.; Gu, X. Need support, need satisfaction, intrinsic motivat
participation among middle school students. J. Teach. Phys. Educ. 2011, 30, 51–68. [CrossRef] 31. Ntoumanis, N. A prospective study of participation in optional school physical education using a selfdetermination theory
framework. J. Educ. Psychol. 2005, 97, 444–453. References Prev. Med. 2014, 67, 270–279. [CrossRef] [PubMed]
37. Reeve, J. Why teachers adopt a controlling motivating style toward students and how they can become more autonomy supportive. Educ. Psychol. 2009, 44, 159–175. [CrossRef] adolescents: A systematic review and meta analysis. Prev. Med. 2014, 67, 270 279. [CrossRef] [PubMed]
37. Reeve, J. Why teachers adopt a controlling motivating style toward students and how they can become more autonomy supportive. Educ. Psychol. 2009, 44, 159–175. [CrossRef] y
,
,
[
]
38. Reeve, J.; Jang, H.; Carrell, D.; Jeon, S.; Barch, J. Enhancing students’ engagement by increasing teachers’ autonomy support. Motiv. Emot. 2004, 28, 147–169. [CrossRef] 39. Patall, E.; Cooper, H.; Wynn, S. The effectiveness and relative importance of choice in the classroom. J. Educ. Psychol. 2010, 102,
896–915. [CrossRef] 40. Prusak, K.; Treasure, D.; Darst, P.; Pangrazi, R. The effects of choice on the motivation of adolescent girls in physical education. J. Teach. Phys. Educ. 2004, 23, 19–29. [CrossRef] imons, J.; Lens, W.; Sheldon, K.; Deci, E. Motivated learning, performance, and persistence: The synergistic
s and autonomy-support. J. Personal. Soc. Psychol. 2004, 87, 240–260. [CrossRef] y
41. Vansteenkiste, M.; Simons, J.; Lens, W.; Sheldon, K.; Deci, E. Motivated learning, performance, and pe
role of intrinsic goals and autonomy-support. J. Personal. Soc. Psychol. 2004, 87, 240–260. [CrossRef] 42. Jang, H.; Reeve, J.; Halusic, M. A new autonomy-supportive way of teaching that increases conceptual learning: Teaching in
students’ preferred ways. J. Exp. Educ. 2016, 84, 686–701. [CrossRef] p
y
J
p
[
]
43. Reeve, J.; Cheong, C. An interventionbased program of research on teachers’ motivating styles. Adv. Motiv. Achiev. 2014, 18,
297–343. 44. Jang, H.; Reeve, J.; Deci, E. Engaging students in learning activities: It is not autonomy support or structure but autonomy
support and structure. J. Educ. Psychol. 2010, 102, 588–600. [CrossRef] 45. Sierens, E.; Vansteenkiste, M.; Goossens, L.; Soenens, B.; Dochy, F. The synergistic relationship of perceived autonomy support
and structure in the prediction of self-regulated learning. Br. J. Educ. Psychol. 2009, 79, 57–68. [CrossRef] p
g
g
46. Vansteenkiste, M.; Sierens, E.; Goossens, L.; Soenens, B.; Dochy, F.; Mouratidis, A.; Beyers, W. Identifying configurations of
perceived teacher autonomy support and structure: Associations with self-regulated learning, motivation and problem behavior. Learn. Instr. 2012, 22, 431–439. [CrossRef] 47. Koka, A.; Hein, V. The effect of perceived teacher feedback on intrinsic motivation in physical education. Int. J. Sport Psychol. 2005, 36, 91–106. y
51.
Skinner, E.; Belmont, M. Motivation in the classroom: Reciprocal effects of teacher behavior and student engagement across the
school year. J. Educ. Psychol. 1993, 85, 571–581. [CrossRef] References Van den Berghe, L.; Vansteenkiste, M.; Cardon, G.; Kirk, D.; Haerens, L. Research on selfdetermination in
findings and proposals for future research. Phys. Educ. Sport Pedagog. 2014, 19, 97–121. [CrossRef] 60. Vasconcellos, D.; Parker, P.D.; Hilland, T.; Cinelli, R.; Owen, K.B.; Kapsal, N.; Lee, J.; Antczak, D.; Ntoumanis, N.; Ryan, R.M.; et al. Self-determination theory applied to physical education: A systematic review and meta-analysis. J. Educ. Psychol. 2020, 112,
1444–1469. [CrossRef] 61. De Meyer, J.; Tallir, I.; Soenens, B.; Vansteenkiste, M.; Speleers, L.; Aelterman, N.; Haerens, L. Rel
controlling teaching behavior and students’ motivation in physical education. J. Educ. Psychol. 2014, 10 61. De Meyer, J.; Tallir, I.; Soenens, B.; Vansteenkiste, M.; Speleers, L.; Aelterman, N.; Haerens, L. Relation between observed
controlling teaching behavior and students’ motivation in physical education. J. Educ. Psychol. 2014, 106, 541–554. [CrossRef]
62. Koka, A.; Tilga, H.; Kalajas-Tilga, H.; Hein, V.; Raudsepp, L. Perceived Controlling Behaviors of Physical Education Teachers and
Objectively Measured Leisure-Time Physical Activity in Adolescents. Int. J. Environ. Res. Public Health 2019, 16, 2709. [CrossRef]
[P bM d] 61. De Meyer, J.; Tallir, I.; Soenens, B.; Vansteenkiste, M.; Speleers, L.; Aelterman, N.; Haerens, L. Relation between observed
controlling teaching behavior and students’ motivation in physical education. J. Educ. Psychol. 2014, 106, 541–554. [CrossRef]
62
Koka A ; Tilga H ; Kalajas Tilga H ; Hein V; Raudsepp L Perceived Controlling Behaviors of Physical Education Teachers and 62. Koka, A.; Tilga, H.; Kalajas-Tilga, H.; Hein, V.; Raudsepp, L. Perceived Controlling Behaviors of Physical Education Teachers and
Objectively Measured Leisure-Time Physical Activity in Adolescents. Int. J. Environ. Res. Public Health 2019, 16, 2709. [CrossRef]
[PubMed] 63. Chatzisarantis, N.L.; Hagger, M.S. Effects of an intervention based on self-determination theory on self-reported leisure-time
physical activity participation. Psychol. Health 2009, 24, 29–48. [CrossRef] [PubMed] 64. Markland, D.; Tobin, V. A modification of the Behavioral Regulation in Exercise Questionnaire to i
amotivation. J. Sport Exerc. Psychol. 2004, 26, 191–196. [CrossRef] 65. Belmont, M.; Skinner, E.; Wellborn, J.; Connell, J. Teacher as Social Context: A Measure of Student Perceptions of Teacher Provision of
Involvement, Structure, and Autonomy Support; Technical Report; University of Rochester: Rochester, NY, USA, 1988. y
pp
p
y
66. Belmont, M.; Skinner, E.; Wellborn, J.; Connell, J. Teacher as Social Context: A Measure of Student Perceptions of Teacher Provision of
Involvement, Structure and Autonomy Support; Technical Report; University of Rochester: Rochester, NY, USA, 1992. 67. References Hambleton, R. Guidelines for adapting educational and psychological tests: A progress report. Eur. J. Psychol. Assess. 1994, 10,
229–244. 68. Reilly, J.J.; Penpraze, V.; Hislop, J.; Davies, G.; Grant, S.; Paton, J.Y. Objective measurement of physical activity and sedentary
behavior: Review with new data. Arch. Dis. Child. 2008, 93, 614–619. [CrossRef] [PubMed] 69. Trost, S.; Way, R.; Okely, A.D. Predictive validity of three Actigraph expenditure equations for chi
2006, 38, 380–387. [CrossRef] [PubMed] 69. Trost, S.; Way, R.; Okely, A.D. Predictive validity of three Actigraph expenditure equations for children. Med. Sci. Sports Exerc. 2006, 38, 380–387. [CrossRef] [PubMed]
70
Evenson K ; Cattelier D ; Gill K E Calibration of two objective measures of physical activity for children J Sports Sci 2008 26 69. Trost, S.; Way, R.; Okely, A.D. Predictive validity of three Actigraph expenditure equations for children. Med. Sci. Sports Exerc. 2006, 38, 380–387. [CrossRef] [PubMed]
70. Evenson, K.; Cattelier, D.; Gill, K.E. Calibration of two objective measures of physical activity for children. J. Sports Sci. 2008, 26, 2006, 38, 380–387. [CrossRef] [PubMed]
70. Evenson, K.; Cattelier, D.; Gill, K.E. Calibration of two objective measures of physical activity for children. J. Sports Sci. 2008, 26,
1557 1565 [CrossRef] 006,
, 380 38
[C oss e ] [
Me ]
70. Evenson, K.; Cattelier, D.; Gill, K.E. Calibration of two objective measures of physical activity for children. J. Sports Sci. 2008, 26,
1557–1565. [CrossRef] 70. Evenson, K.; Cattelier, D.; Gill, K.E. Calibration of two objective measures of physical activity for child
1557–1565. [CrossRef] 71. Muthén, L.; Muthén, B. Mplus User’s Guide, 8th ed.; StatModel: Los Angeles, CA, USA, 2017. 71. Muthén, L.; Muthén, B. Mplus User’s Guide, 8th ed.; StatModel: Los Angeles, CA, USA, 2017. Muthén, L.; Muthén, B. Mplus User’s Guide, 8th ed.; Stat 72. Hu, L.; Bentler, P. Cutoff criteria for fit indexes in covariance structure analysis: Conventional criteria versus new alternatives. Struct. Equ. Model. A Multidiscip. J. 1999, 6, 1–55. [CrossRef] 72. Hu, L.; Bentler, P. Cutoff criteria for fit indexes in covariance structure analysis: Conventional cr
Struct. Equ. Model. A Multidiscip. J. 1999, 6, 1–55. [CrossRef] q
p
73. Lüdtke, O.; Robitzsch, A.; Grund, S. Multiple imputation of missing data in multilevel designs: A
strategies. Psychol. Methods 2017, 1, 141–165. [CrossRef] g
y
74. Sinharay, S.; Stern, H.; Russel, D. The use of multiple imputations for the analysis of missing data. Psychol. References 48. Mouratidis, A.; Vansteenkiste, M.; Lens, W.; Sideridis, G. The motivating role of positive feedback in sport and physical education:
Evidence for a motivational model. J. Sport Exerc. Psychol. 2008, 30, 240–268. [CrossRef] p
y
49. Whitehead, J.; Fox, K. Student-centred physical education. Bull. Phys. Educ. 1983, 19, 21–30. p y
y
50. Soenens, B.; Sierens, E.; Vansteenkiste, M.; Dochy, F.; Goossens, L. Psychologically controlling teaching: Examining outcomes,
antecedents, and mediators. J. Educ. Psychol. 2012, 104, 108–120. [CrossRef] 51. Skinner, E.; Belmont, M. Motivation in the classroom: Reciprocal effects of teacher behavior and student engagement across the
school year. J. Educ. Psychol. 1993, 85, 571–581. [CrossRef] Int. J. Environ. Res. Public Health 2021, 18, 7457 16 of 17 16 of 17 52. Van den Berghe, L.; Cardon, G.; Tallir, I.; Kirk, D.; Haerens, L. Dynamics of needsupportive and need-thwarting teaching behavior:
The bidirectional relationship with student engagement and disengagement in the beginning of a lesson. Phys. Educ. Sport
Pedagog. 2016, 21, 653–670. [CrossRef] g g
53. Standage, M.; Gillison, F.B.; Ntoumanis, N.; Treasure, D.C. Predicting Students’ Physical Activity and Health-Related Well-Being:
A Prospective Cross-Domain Investigation of Motivation Across School Physical Education and Exercise Settings. J. Sport Exerc. Psychol. 2012, 34, 37–60. [CrossRef] [PubMed] y
54. Haerens, L.; Aelterman, N.; Vansteenkiste, M.; Soenens, B.; Van Petegem, S. Do perceived autonomy-supportive and controlling
teaching relate to physical education students’ motivational experiences through unique pathways? Distinguishing between the
bright and dark side of motivation. Psychol. Sport Exerc. 2015, 16, 25–36. [CrossRef] bright and dark side of motivation. Psychol. Sport E 55. Haerens, L.; Kirk, D.; Cardon, G.; Bourdeaudhuij, I.D. Toward the Development of a Pedagogical Model for Health-Based Physical
Education. Quest 2011, 63, 321–338. [CrossRef] 56. Taylor, I.M.; Ntoumanis, N.; Standage, M.; Spray, C. Motivational predictors of physical education students’ effort, exercise
intentions and leisure-time physical activity: A multilevel linear growth analysis. J. Sport Exerc. Psychol. 2010, 32, 99–120. [CrossRef] 57. Sanchez-Oliva, D.; Mouratidis, A.; Leo, F.M.; Chamorro, J.L.; Pulido-Gonzalez, J.J.; Garcia-Calvo, T. Understanding Physical
Activity Intentions in Physical Education Context: A multi-level Analysis from the Self-Determination Theory. Int. J. Environ. Res. Public Health 2020, 17, 799. [CrossRef] 58. Sparks, C.; Lonsdale, C.; Dimmock, J.; Jackson, B. An intervention to improve teachers’ interpersonally involving instructional
practices in high school physical education: Implications for student relatedness support and in-class experiences. J. Sport Exerc. Psychol. 2017, 39, 120–133. [CrossRef] 59. 77.
Lonsdale, C.; Sanders, T.; Parker, P.; Noetel, M.; Hartwig, T.; Vasconcellos, D.; Lee, J.; Antczak, D.; Kirwan, M.; Morgan, P.; et al.
Effect of a Scalable School-Based Intervention on Cardiorespiratory Fitness in Children A Cluster Randomized Clinical Trial.
JAMA Pediatr. 2021, 175, 680–688. [CrossRef] p y
p
y
y
,
,
[
]
80.
Sterne, J.A.C.; White, I.R.; Carlin, J.B.; Spratt, M.; Royston, P.; Kenward, M.G.; Wood, A.M.; Carpenter, J.R. Multiple imputation
for missing data in epidemiological and clinical research: Potential and pitfalls. BMJ 2009, 338, b2393. [CrossRef] [PubMed] ,
p
J
p
,
,
[
]
79.
Opstoel, K.; Chapelle, L.; Frans, J.P.; De Meester, A.; Haerens, L.; van Tartwijk, J.; De Martelaer, K. Persona
in physical education and sports: A review study. Eur. Phys. Educ. Rev. 2020, 26, 797–813. [CrossRef] J
,
,
[
]
78.
Rodrigues, F.; Teixeira, D.S.; Neiva, H.P.; Cid, L.; Monteiro, D. The bright and dark sides of motivation a
intention, and exercise persistence. Scand. J. Med. Sci. Sports 2020, 30, 787–800. [CrossRef] intention, and exercise persistence. Scand. J. Med. Sci. Sports 2020, 30, 787 800. [CrossRef]
79.
Opstoel, K.; Chapelle, L.; Frans, J.P.; De Meester, A.; Haerens, L.; van Tartwijk, J.; De Martelaer, K. Personal and social development
in physical education and sports: A review study. Eur. Phys. Educ. Rev. 2020, 26, 797–813. [CrossRef] ra, D.S.; Neiva, H.P.; Cid, L.; Monteiro, D. The bright and dark sides of motivation as predictors of enjoyment
ise persistence. Scand. J. Med. Sci. Sports 2020, 30, 787–800. [CrossRef] References Methods 2001, 6,
317–329. [CrossRef] 74. Sinharay, S.; Stern, H.; Russel, D. The use of multiple imputations for the analysis of missing data. Psychol. Methods 2001, 6,
317–329. [CrossRef] 75. Rubin, D.B. Multiple imputation for nonrespons in surveys. Wiley Online Libr. 1987, 519. [CrossRef 75. Rubin, D.B. Multiple imputation for nonrespons in surveys. Wiley Online Libr. 1987, 519. [CrossRef] 76. Hollis, J.L.; Sutherland, R.; Williams, A.J.; Campbell, E.; Nathan, N.; Wolfenden, L.; Morgan, P.J.; Lubans, D.R.; Gillham, K.;
Wiggers, J. A systematic review and meta-analysis of moderate-to-vigorous physical activity levels in secondary school physical
education lessons. Int. J. Behav. Nutr. Phys. Act. 2017, 14, 52. [CrossRef] [PubMed] 76. Hollis, J.L.; Sutherland, R.; Williams, A.J.; Campbell, E.; Nathan, N.; Wolfenden, L.; Morgan, P.J.; Lubans, D.R.; Gillham, K.;
Wiggers, J. A systematic review and meta-analysis of moderate-to-vigorous physical activity levels in secondary school physical
education lessons. Int. J. Behav. Nutr. Phys. Act. 2017, 14, 52. [CrossRef] [PubMed] Int. J. Environ. Res. Public Health 2021, 18, 7457 17 of 17 17 of 17
|
W2059724003.txt
|
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0069828&type=printable
|
en
|
Aberrant Proliferation in CXCR7+ Endothelial Cells via Degradation of the Retinoblastoma Protein
|
PloS one
| 2,013
|
cc-by
| 8,330
|
Aberrant Proliferation in CXCR7+ Endothelial Cells via
Degradation of the Retinoblastoma Protein
Jennifer E. Totonchy, Jessica M. Osborn, Sara Botto, Lisa Clepper, Ashlee V. Moses*
Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, United States of America
Abstract
Angiogenesis is a critical factor in the growth and dissemination of solid tumors. Indeed, tumor vasculature is abnormal and
contributes to the development and spread of malignancies by creating a hostile microenvironment. The alternative SDF-1/
CXCL12 receptor, CXCR7, is frequently and specifically expressed in tumor-associated vessels. In this study, we examine the
role of endothelium-expressed CXCR7 in tumor vascular dysfunction by specifically examining the contribution of CXCR7 to
endothelial cell (EC) proliferation. We demonstrate that CXCR7 expression is sufficient to drive post-confluent growth in EC
cultures. Further, we provide a novel mechanism for CXCR7-mediated proliferation via proteasomal degradation of the
tumor suppressor protein Rb. These findings identify a heretofore unappreciated role for CXCR7 in vascular dysfunction and
confirm this receptor as a plausible target for anti-tumor therapy.
Citation: Totonchy JE, Osborn JM, Botto S, Clepper L, Moses AV (2013) Aberrant Proliferation in CXCR7+ Endothelial Cells via Degradation of the Retinoblastoma
Protein. PLoS ONE 8(7): e69828. doi:10.1371/journal.pone.0069828
Editor: Ramani Ramchandran, Medical College of Wisconsin, United States of America
Received March 29, 2013; Accepted June 14, 2013; Published July 23, 2013
Copyright: ß 2013 Totonchy 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 a grant to Dr. Moses from the National Cancer Institute (grant 5R01CA099906-07) and the National Institutes of Health
Core Grant to ONPRC (8P510D011092-53). Dr. Vomaske was supported by fellowship funding from the National Institutes of Health (grant 5T32AI007472-17). 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: mosesa@ohsu.edu
designated CXCR7 [9]. Since its discovery as an alternative
receptor for SDF-1/CXCL12, a number of studies have explored
the expression of CXCR7 in tumors. CXCR7 is sporadically
expressed by tumor cells in renal [10], breast [11,12], lung [12],
liver [13], prostate [14] and central nervous system [15] cancers
and the implications of CXCR7 expression for malignant
progression are currently an area of intense investigation. EC
express very low levels of CXCR7 under normal physiological
conditions in vivo [12] and normal culture conditions in vitro [9],
but CXCR7 is induced in activated EC [9] suggesting that
CXCR7 may participate in the response of EC to physiological
stress. Interestingly, several studies have shown that tumorassociated EC display aberrant CXCR7 expression in a variety
of cancer models [11,16,17]. Indeed, one such study by Miao et.
al. demonstrated profound and highly specific expression of
CXCR7 in vessels associated with malignancies of the breast, lung,
liver, ovary, kidney and bladder, leading the authors to postulate
that CXCR7 might be a specific marker of tumor endothelium
[12]. Despite the fact that CXCR7 expression is extensively and
specifically observed on tumor-associated vasculature in both
primary tumors and metastases, the functional consequences of
CXCR7 expression in EC remain poorly understood.
Although CXCR7 expression has been linked to cellular
proliferation both in cancer models [9,12,13,17,18], and EC
cultures [19], the current literature fails to establish the
mechanisms by which CXCR7 influences cell division. In this
study, we investigate CXCR7-mediated proliferation in adult
primary lymphatic EC. We demonstrate that CXCR7+ EC
cultures display post-confluent proliferation, the extent of which
corresponds to their level of CXCR7 expression. We discover via a
protein microarray screen that CXCR7 influences the expression
Introduction
Angiogenesis is the process by which new vessels form from
existing vascular networks in both the blood and lymphatic
circulatory systems. This highly regulated process is critical for
wound healing and tissue regeneration but is co-opted in a variety
of pathogenic processes including angioproliferative diseases and
the growth of aberrant vasculature into tumors [1]. Endothelial
cells (EC) line all vessels and are key players in the angiogenic
process. In normal vessels, EC are long-lived, quiescent cells that
are highly dependent upon cell-cell and cell-substrate adhesion for
their survival and function. Angiogenesis requires both EC
migration into an angiogenic niche and EC proliferation in order
to form new vascular structures [2].
The vasculature that forms in the tumor microenvironment is
structurally and functionally abnormal compared to vessels formed
during normal wound healing. This vascular dysfunction is a direct
result of abnormalities in EC function and vessels formed by this
pathological process do not allow correct circulation within the
tumor tissue. The result is a hostile tumor microenvironment
characterized by abnormally high interstitial pressure, low pH,
poor oxygenation and poor immune surveillance. Tumor vascular
dysfunction exacerbates the development and spread of cancer by
selecting for tumor cells that can survive and proliferate under
these adverse conditions, thereby enhancing malignancy and
driving the development of metastases [3].
Chemokines and their receptors are important players in
pathological angiogenesis [4] as well as the migration and invasion
of tumor cells [5,6]. The chemokine SDF-1/CXCL12 and its
canonical receptor CXCR4 are among the most highly studied
chemokine/receptor pairs in cancer biology [7,8]. A second
receptor for SDF-1/CXCL12 was recently discovered and
PLOS ONE | www.plosone.org
1
July 2013 | Volume 8 | Issue 7 | e69828
Aberrant Proliferation of CXCR7+ Endothelial Cells
mented with 1% FBS, PSG and 37.5 mg/ml endothelial cell
growth supplement (ECGS, BD Biosystems 356006). Where
appropriate, infection medium was replaced with medium
containing drugs or neutralizing antibodies at 6 hours postinfection.
Indirect Immunofluorescence and Image Analysis - EC were plated on
collagen-coated coverslips (BD Biosystems 354089) and infected
with either Trans at MOI 100 only or Trans at MOI 100 and
CXCR7 at MOI 100. At 20 hours post-infection, cells were
washed once with phosphate buffered saline containing calcium
and magnesium (PBS+) and fixed in PBS+ containing 2%
paraformaldehyde (PFA). Coverslips were blocked for 15 min at
room temperature (RT) in PBS+0.2% saponin+2% normal goat
serum (NGS). All further incubations were performed in
PBS+0.2% saponin+0.2% NGS. Primary antibodies were diluted
1:200 and applied for 30 minutes at RT. Secondary antibodies
and 49,6-diamidino-2-phenylindole (DAPI) were diluted 1:1000
and applied for 30 minutes at RT. Coverslips were washed and
mounted on glass slides with FluoromountG (Southern Biotech,
0100-01). For the barrier formation studies, cultures were
trypsinized at 20 hours post-infection, counted and 2(10)5 cells
were replated in duplicate into 8-well Permanox chamber slides
(NUNC 1177445) coated with 1% gelatin, allowed to form a new
monolayer for a further 20 hours then fixed in PBS+ containing
2% PFA and 1% TritonX-100 for 15 minutes at RT. Coverslips
were then post-fixed for a further 5 minutes at RT in PBS+
containing 2% PFA only. Coverslips were blocked in PBS+ with
1% TritonX-100 and 2% NGS for 15 minutes at RT. All further
incubations were performed in PBS+ with 1% TritonX-100 and
0.2% NGS (Tx Wash). Antibody concentrations were the same as
above. Image acquisition was on a Deltavision real-time
deconvolution (DVRT) microscope (Applied Precision) using a
Photometrics CoolSNAP HQ camera. Image analysis was
performed using Softworx (Applied Precision). Unless otherwise
indicated, z-stacks with a 0.2 mm z-step size were taken at 60X
magnification. Stacks were subjected to deconvolution analysis
and 2–3 section projections were made superimposing representative z-planes to generate the final image.
of multiple proteins involved in cell cycle control, including the
tumor suppressor protein retinoblastoma (Rb). We verify that that
CXCR7+ EC cultures have reduced levels of Rb and that Rb
expression can be rescued by inhibiting the proteasome. We use
ligand neutralization, pharmacological receptor targeting and
receptor mutagenesis to establish that the loss of Rb in CXCR7+
EC requires CXCR7 ligands and that rescue of Rb expression is
associated with decreased proliferation. These results identify
CXCR7 as a mediator of aberrant proliferation in EC and
establish CXCR7 as a potential therapeutic target for pathological
angioproliferation in cancer.
Materials and Methods
Cell Lines and Reagents
Primary Human Adult Lymphatic and Blood Vascular Endothelial Cells (pLEC and pBEC, respectively) were commercially
obtained (Lonza) and maintained in EGM-2 medium (Lonza
#CC-3024) containing bullet kit growth supplements (Lonza
#CC-3124), 10% fetal bovine serum (FBS, Hyclone SH30396.03)
and Penicillin/Streptomycin/L-Glutamine (PSG, Hyclone
SV30082.01). All primary EC cultures were used between passage
4 and 10. MouseIgG1-anti-CXCR7 antibody (11G8) was provided
by Chemocentryx, Inc (Mountain View, CA), MouseIgG2b-antiCXCR7 antibody (clone 8F11, 331102), AlexaFluor647-conjugated mouseIgG1-anti-CXCR3 antibody (334903) and Mouse-IgG1
isotype control (401402) were from Biolegend. Mouse-IgG2b
(556654) and Pacific Blue Mouse–IgG2a (558118) isotype controls
were from BD Pharmingen. MouseIgG2a-anti-CD31/PECAM
antibody for IFA was from Thermo/Fisher (MA3100). Rabbitanti-HA (sc-805), Rabbit-IgG Isotype control (sc-2027) and HRPconjugated anti-mouse (sc-2306) anti-rabbit (sc-2305) were from
Santa Cruz Biotechnology. Rb antibody was from Cell Signaling
(9309) and GAPDH antibody was from Abcam (ab8245). AntimouseIgG2a-AlexaFluor488 (A21131), anti-mouseIgG1-AlexaFluor594 (A21125), anti-rabbit-AlexaFluor488 (A110088) and
Streptavidin-Pacific Blue (S11222) were from Invitrogen. HAHRP direct conjugate was from Roche (12013819011). Recombinant human SDF-1/CXCL12 (350-NS-050) and neutralizing
antibodies against SDF-1/CXCL12 (AF-310-NA) and ITAC/
CXCL11 (AF260) and biotinylated MouseIgG2a-anti-CXCR4
antibody (clone 12G5, FAB170B) were from R&D Systems. The
CXCR7 small molecule antagonist CCX733 was a generous gift
from Chemocentryx, Inc. Propidium Iodide was from Sigma
(P4170).
Flow Cytometry
Cells were dissociated with Cellstripper (Cellgro, 25-056-CI)
and resuspended in cold PBS+ containing 2% NGS and 0.1%
sodium azide (NaN3) (Surface Block) for 15 minutes on ice. Cells
were then incubated for 15 minutes on ice with Rabbit anti-HA
antibody diluted 1:100 in cold PBS+ containing 0.2% NGS and
0.1% NaN3 (Surface Wash) followed by 15 minutes on ice with
anti-rabbit Alexa488 secondary antibody at 1:1000 dilution and
1 mM propidium iodide (PI) in 100 ml Surface Wash. Analysis was
on a BD LSR2 flow cytometer. Live, non-necrotic cells were gated
based on scatter characteristics and negative PI staining.
Compensation settings were determined empirically for each
experiment on single color controls using BD CompBeads for
mouse antibodies (552843) and Flow cytometry protein A beads
for rabbit antibodies (Bangs Laboratories 553) and unstained cells
for PI.
CXCR7 Adenovirus Vectors
CXCR7-expressing vectors with an N-terminal HA tag were
constructed by subcloning the DNA fragment into pAdTet7. This
vector contains the tet-responsive enhancer within a minimal
CMV promoter followed by the SV40 late poly(A) cassette,
adenovirus E1A, and a single loxP site to increase recombination
frequency. Recombinant adenoviruses were produced by cotransfection of 293 cells expressing the Cre recombinase with
adenovirus DNA (Ad5-y5) that contains an E1A/E3-deleted
adenovirus genome and pAdtet7-HA-CXCR7 or pAdtet7-HACXCR7-D5. Recombinant adenoviruses were expanded on 293Cre cells, and the bulk stocks were titered on 293 cells by limiting
dilution. Expression was driven by co-infection with Ad-Trans
expressing the Tet-off transactivator.
CyQuant Proliferation Assay
EC in 96-well plates were infected as above with Trans and
CXCR7 at indicated doses. When applicable, drugs or inhibitors
were added at 6 hours post-infection. At 20 hours post-infection
cells were lysed in buffer containing CyQuant proliferation dye.
Lysates were transferred to white-walled 96-well plates (Costar
3903) and fluorescence was read on a Molecular Devices
Flexstation Plate Reader. All conditions were performed in at
Infection of EC with Adenovirus Vectors
Adenovirus infections were performed on confluent EC cultures
in endothelial SFM medium (endoSFM, Gibco 11111) supplePLOS ONE | www.plosone.org
2
July 2013 | Volume 8 | Issue 7 | e69828
Aberrant Proliferation of CXCR7+ Endothelial Cells
least 6 biological replicates per experiment. Individual experiments
were normalized to the average of negative control cultures and at
least two experimental replicates were averaged to achieve
statistical power. P-values were generated by Student’s T-test
using Microsoft Excel.
TACCCC-39. To perform the qPCR, 10 ng of cDNA (5 ul of
sample) were loaded on a 96-well optical plate together with 20 ul
of Power SYBR Green PCR Master Mix (ABI) containing the
appropriate set of primers, for a final volume of 25 ul. Evaluation
of primer and sample concentrations has been optimized for all the
targets. Amplification of the samples was performed on Real Time
PCR 7500 System (ABI), according to the manufacturer’s
instructions. Normalized relative gene expression levels were
calculated by applying the DDCT method, which compares the
expression of target genes in treated samples (Adenovirus-infected
cells) to the one in control samples (mock-infected cells). For the
purpose of this quantification, GAPDH was utilized as internal
control and the results were represented as change in the
expression level of each particular gene (fold change).
Antibody Microarray
pLEC were infected in duplicate with either Trans only at MOI
100 or Trans MOI 100+ CXCR7 at MOI 50 in EBM-2+ Bullet
Kit Supplements +1% FBS. At 18 hours post-infection cells were
starved in serum free M199 for 1 hour then stimulated for 10
minutes at 37uC with 50 ng/ml rhSDF-1/CXCL12. A subset of
cells were used to verify CXCR7 expression by flow cytometry
(FACS) as described above and duplicate samples were pooled.
Total cellular protein was extracted, biotinylated and hybridized
to PEX100 microarray according to the manufacturer’s instructions (Full Moon BioSystems, Sunnyvale, CA). Completed slides
were dried and scanned using a ScanArray Lite (Packard
Bioscience) scanner. Optical density of spots and background
subtraction was performed on the scanned images using TotalLab
software. Optical density ratios and sorting were performed in
Microsoft Excel.
Quantibody Antibody Array for Supernatant Cytokine
Analysis
pLEC in 3.5 cm dishes were infected as above with Trans at
MOI 200 or Trans+CXCR7 at MOI 100 and incubated for 20
hours at 37uC. At 20 hours post-infection, media was replaced
with 0.5 ml serum free M199 and incubated for 4 hours at 37uC.
After incubation supernatants were frozen in four 250 ml aliquots.
Cells were harvested and analyzed for CXCR7 transduction by
flow cytometry. Duplicate samples were collected from two
independent experiments. Quantibody arrays were stained
according to manufacturers instructions. Briefly, slides were
blocked in sample diluent provided for 30 minutes at RT,
cytokine standard curves were prepared and samples and
standards were hybridized to the array at RT for 2 hours followed
by 5X 5 minute washes. Detection antibody was hybridized to
slides for 2 hours at RT followed by 5X 5 minute washes. Cy3
streptavidin was added for 1 hour at RT, protected from light
followed by 5X 5 minute washes. The array slide was disassembled
and air dried. Scanning and analysis service was performed by
Ray Biotech.
Western Blot Analysis
Cells were lysed in 200 ml modified radioimmunoprecipitation
(RIPA) buffer (10 mM Tris pH 7.4, 150 mM NaCl, 1 mM
EDTA, 1%Triton-X-100, 1% Sodium Deoxycholate, 0.1% SDS)
containing protease inhibitors (Roche 11836145001) for 10
minutes on ice. Lysates were freeze-thawed once at 220uC and
protein was quantified by BCA protein assay (Pierce, 23225).
0.5 mg of total lysate was boiled for 5 minutes in 1X LDS protein
sample buffer containing reducing agent (Invitrogen, NP0009),
loaded on NuPAGE 4–12% Bis-Tris gradient protein gels
(Invitrogen, NP0335) and run in 1X NuPAGE MOPS buffer
(Invitrogen, NP0001). Protein was transferred to Immobilon-P
blotting membrane (Millipore, IPVH00010) and membranes were
blocked by drying overnight at RT. Membranes were rehydrated
in 2% ECL advance blocking buffer (Amersham, CPK1075) with
0.2% Tween-20 (Block) for 15 minutes. All subsequent incubations
were performed in Block. Rb primary antibody was at 1:2000
dilution and GAPDH primary antibody was at 1:50,000 dilution 1
hour at RT. HRP-conjugated secondary antibodies were diluted
1:40,000 and incubated for 20 minutes at RT. Blots were
developed using ECL Advance (Amersham, RPN2135) chemiluminescent reagent and autoradiography. For all experiments,
adenovirus transduction was verified by analysis of 0.2 mg of
unboiled total protein blotted as above with a direct conjugate
anti-HA-HRP. Densitometry analysis was performed on scanned
western blot results using TotalLab software.
Results
Adenovirus Expression System for CXCR7 in EC
In order to effectively study the ramifications of aberrant
CXCR7 expression in an EC culture system, we constructed a
Tet-inducible CXCR7-expressing adenovirus vector containing
the complete CXCR7 sequence fused to an N-terminal HAepitope tag. In this system, we achieve expression of CXCR7 via
co-infection of EC with CXCR7 adenovirus and a second
adenovirus vector expressing the tet-transactivator (hereafter
referred to as Trans). In all experiments, cells transduced with
Trans alone are used to control for nonspecific effects of
adenovirus infection. Indirect immunofluorescence (IFA) analysis
of HA-CXCR7-transduced EC demonstrate comparable staining
with either an HA probe or the CXCR7 monoclonal antibody
11G8 (Figure 1A). Interestingly, this IFA analysis reveals a
punctate intracellular staining pattern consistent with CXCR7
being primarily located in the secretory pathway and endosomes.
In order to determine whether adenovirus-expressed CXCR7 is
also displayed at the cell surface, we performed FACS analysis of
cultures transduced with increasing doses of CXCR7, gating
stringently on intact cells via propidium iodide exclusion. These
experiments revealed that CXCR7 is expressed on the surface of
adenovirus-transduced EC and that surface levels correlate with
adenovirus dose (Figure 1B). We chose to do our experiments in
primary human lymphatic EC (pLEC) because this lineage
displays more robust growth in static culture compared to primary
blood vascular lineage EC (pBEC) and has uniformly low levels of
Quantitative RT-PCR Analysis
Extraction of total RNA was performed on cell pellets using
miRNeasy Mini Kit (Qiagen), DNase I treatment (Qiagen) was
employed to degrade DNA from the RNA samples. Total cDNA
was produced by reverse transcribing 200 ng of RNA, using
SuperScript III First-Strand Synthesis System (Invitrogen). The
primers employed for the amplification of the target genes by
qPCR were the following: GAPDHF 59-GAAGGTGAAGGTCGGAGT-39, GAPDHR 59-GAAGATGGTGATGGGATTTC-39;
SDF-1 F 59-CTGTCACTGGCGACACGTAG -39, SDF-1 R 59TCCCATCCCACAGAGAGAAG-39;
CXCR7
F
59CTGCGTCCAACAATGAGACCT-39, CXCR7 R 59-CCGATCAGCCACTCCTTGA-39; ITAC-F 59-GTTCAAGGCTTCCCCATGTTC-39,
ITAC-R
59-CCACTTTCACTGCTTTPLOS ONE | www.plosone.org
3
July 2013 | Volume 8 | Issue 7 | e69828
Aberrant Proliferation of CXCR7+ Endothelial Cells
Figure 1. Adenovirus-transduced CXCR7+ EC display dose-dependent overproliferation. (A) pLEC were infected with Trans or
Trans+CXCR7 at MOI 100. At 20 hours post-infection coverslips were fixed and stained for the HA-tag (red), CXCR7 protein via 11G8 monoclonal
antibody (green) and DAPI. Images were taken at 60x magnification. White size bar indicates 30 mm. (B) pLEC were infected with Trans at MOI 50 or
Trans+CXCR7 at indicated doses. At 20 hours post-infection cells were stained live for the HA-tag and analyzed by flow cytometry. Necrotic cells were
excluded from the analysis via propidium iodide staining and scatter characteristics. Positive staining was compared to appropriate isotype control
(grey) and mean fluorescence intensity values were calculated for HA fluorescence (MFI) (C) Confluent pLEC cultures were infected with increasing
doses of Trans only or Trans+increasing doses of CXCR7. At 20 hours post-infection, cells were lysed in the presence of Cyquant. Fluorescence values
are normalized to uninfected controls. n = 24 from three independent experiments. * P = 0.01, ** P,0.003.
doi:10.1371/journal.pone.0069828.g001
baseline CXCR7 expression compared to primary umbilical vein
EC, in which we observe sporadic induction of CXCR7 in single
cells (data not shown). However, we have verified key findings of
the current study in pBEC (Figure S1) in order to verify that these
phenotypes are not specific to the lymphatic lineage.
was statistically significant at all doses, while increasing doses of
Trans alone did not result in significantly higher cell numbers
compared to uninfected controls (Figure 1C). Because these
cultures were quiescent prior to transduction, the proliferation
observed in these experiments represents significant, aberrant
post-confluent growth of EC as a result of CXCR7 expression.
Similar results were obtained in pBEC cultures (Figure S1A).
CXCR7+ EC are Hyperproliferative
In order to determine whether CXCR7 mediates aberrant
proliferation in EC cultures, we generated replication-quiescent
pLEC cultures by growing cells to confluence and maintaining
them at confluence for two days prior to initiating experiments.
Quiescent, contact-inhibited EC were then transduced with
increasing multiplicity of infection (MOI) of Trans only (0, 50,
100 or 200) or Trans at MOI 50 with increasing doses (MOI 0,
100, 200 or 300) of CXCR7 adenovirus. At 20 hours postinfection wells were lysed in the presence of CyQuant. We
observed that cultures transduced with CXCR7 displayed a dosedependent increase in overall cell numbers compared to uninfected or Trans-only controls. CXCR7-mediated overproliferation
PLOS ONE | www.plosone.org
CXCR7+ EC are not Contact Inhibited and Form
Abnormal Monolayers
In order to test whether post-confluent growth is associated with
a loss of contact inhibition in CXCR7+ EC, we infected
subconfluent pLEC with Trans only or Trans+CXCR7. At 20
hours post infection, cells were re-plated into smaller wells so that
cells would form a confluent monolayer without needing to
proliferate further. At 20 hours post-seeding (40 hours postinfection), wells were fixed and stained for CXCR7 and CD31/
PECAM. Examination of re-plated cultures by deconvolution
microscopy revealed a typical cobblestone monolayer formation
4
July 2013 | Volume 8 | Issue 7 | e69828
Aberrant Proliferation of CXCR7+ Endothelial Cells
tion of total Rb protein in CXCR7-expressing EC compared to
Trans controls (Figure 3A). Densitometry analysis of nine sample
sets from six independent experiments performed with CXCR7transduction at an MOI of 200 revealed that this phenotype is
reproducible with an average 2.860.3 fold decrease of total Rb
protein in CXCR7+ cultures compared to Trans controls. Similar
Rb degradation was observed in CXCR7-transduced pBEC
(Figure S1B). Others have shown that Rb degradation can occur
in cancer cells via a proteasome-mediated mechanism [21]. In
order to test whether the proteasome is responsible for CXCR7mediated Rb degradation, we performed similar experiments in
which DMSO vehicle or the proteasome inhibitor MG132 was
added to transduced cultures at 6 hours post-infection. Indeed, Rb
expression is restored in CXCR7+ EC treated with MG132,
demonstrating that Rb degradation in this system is mediated by
the proteasome (Figure 3B). Taken together, these results
demonstrate that CXCR7 expression in EC results in the
proteasomal degradation of the tumor suppressor protein Rb,
providing a potential mechanism for the aberrant proliferation
seen in CXCR7+ EC cultures.
with normal junctional CD31 staining in Trans controls. In
contrast, CXCR7-transduced cultures formed highly abnormal
monolayers with areas of multi-layered foci and low or absent
CD31 junctional staining (Figure 2A). Comparing the number of
nuclei per field in 40 random fields revealed that CXCR7+
cultures had significantly higher cell numbers per field, suggesting
that CXCR7+ cultures continue to proliferate even when plated at
confluence (Figure 2B). Taken together, these data reveal that
CXCR7 expression allows EC to grow in a non-contact inhibited
manner.
CXCR7+ EC Display Altered Levels of Critical Proliferation
Mediators
In order to identify potential mechanisms of CXCR7-mediated
proliferation we first sought to determine whether CXCR7
expression affects the expression and/or phosphorylation of
proteins involved in the regulation of cell division. We performed
identical antibody microarrays (Full Moon Systems PEX100) using
lysates from Trans or Trans+CXCR7 infected EC cultures and
compared the two samples to identify proteins specifically altered
in the presence of CXCR7. The complete list of altered expression
and phosphorylation hits is available as supporting documentation
(Table S1). Table 1 shows selected proteins altered by CXCR7
expression that are functionally associated with proliferation.
Importantly, multiple antibody spots demonstrated downregulation of the key tumor suppressor Retinoblastoma protein (Rb) in
CXCR7+ EC.
Expression of CXCR7 Ligands and EC Growth Factors are
not Significantly Altered in CXCR7+ EC
We next wanted to determine whether expression of the known
CXCR7 chemokine ligands SDF-1/CXCL12 and ITAC/
CXCL11 is altered in CXCR7-transduced EC cultures. In these
experiments we transduced pLEC with increasing doses of
CXCR7 adenovirus, harvested cells at 20 hours post-infection
and performed quantitative RT-PCR analysis for mRNA expression of CXCR7, SDF-1/CXCL12 and ITAC/CXCL11 (Table 2).
These results reveal that CXCR7 expression has no effect on
expression of SDF-1/CXCL12 transcripts. We observed a small
reproducible induction of ITAC/CXCL11 at higher doses of
CXCR7. We wanted to confirm these results by determining the
concentration of CXCR7 ligands in EC culture supernatants.
Additionally, we wanted to rule out the possibility that the
proliferation of CXCR7+ EC cultures was a result of indirect
induction of secreted growth factors. For these experiments, we
harvested supernatants at 20 hours post-infection from duplicate
experiments in which pLEC were transduced with Trans or
Trans+CXCR7. Cytokine levels in the supernatants were analyzed
using a custom QuantibodyH antibody array (Ray Biotech). We
found that transduction of EC with CXCR7 does not significantly
or reproducibly alter supernatant levels of any of the cytokines
assayed (Table 3). We did detect low levels of ITAC/CXCL11 in
some samples, consistent with our RT-PCR results. Although we
were unable to detect SDF-1/CXCL12 in the culture supernatants, SDF-1/CXCL12 is known to be highly cell-associated
through glycosaminoglycan interactions [22] and, as such, we
cannot rule out the presence of SDF-1/CXCL12 in these cultures.
Retinoblastoma Protein (Rb) Protein is Degraded in
CXCR7+ EC
The pocket protein family member Rb is a critical regulator of
cell cycle progression. Aberrant inhibition of Rb function is a
frequent occurrence in the course of human tumorigenesis [20].
Consistent with our microarray data, western blot analysis of
lysates from pLEC cultures revealed a dose-dependent degrada-
CXCR7-mediated Rb Degradation is Ligand-dependent
but not Ligand-specific
In order to determine whether Rb degradation in CXCR7+ EC
is mediated by CXCR7 ligands, we performed experiments in
which transduced pLEC cultures were treated with increasing
doses of neutralizing antibodies directed against the two CXCR7
ligands SDF-1/CXCL12 or ITAC/CXCL11. Western blot
analysis of cellular lysates revealed a dose-dependent rescue of
Rb expression with neutralization of either SDF-1/CXCL12
(Figure 4A) or ITAC/CXCL11 (Figure 4B). The finding that
SDF-1/CXCL12 neutralizing antibody abrogates CXCR7-mediated Rb degradation suggests that there is cell-associated SDF-1/
Figure 2. CXCR7+ EC are not contact inhibited. (A) pLEC were
infected with Trans only or Trans+CXCR7. At 20 hours post-infection
cells were trypsinized, counted and replated onto chamber slides at
confluence and allowed to attach for a further 20 hours. Resulting
monolayers were fixed and stained for DAPI (blue), CD31 (green), and
CXCR7 (red). (B) Nuclei were counted in 10 random fields from 2
independent wells from 2 independent experiments (n = 40, P,0.0001).
doi:10.1371/journal.pone.0069828.g002
PLOS ONE | www.plosone.org
5
July 2013 | Volume 8 | Issue 7 | e69828
Aberrant Proliferation of CXCR7+ Endothelial Cells
Table 1. Selected proliferation-related proteins displaying modified expression or phosphorylation in CXCR7+ EC.
Protein Name (antibody/phosphorylation site)
Expression Level (CXCR7/Trans)
GSK3a-b (Ab-216/279)
6.3
DAXX (Phospho-Ser668)
3.4
EGFR (Ab-1069)
2.2
p53 (Phospho-Thr81)
0.5
Stathmin 1(Ab-15)
0.5
p53 (Ab-18)
0.4
p53 (Ab-378)
0.4
Rb (Ab-780)
0.4
Rb (Ab-780)
0.4
Cyclin D3 (Ab-283)
0.4
Cyclin E1 (Phospho-Thr77))
0.4
Stathmin 1(Ab-37)
0.4
Rac1/cdc42 (Ab-71)
0.3
doi:10.1371/journal.pone.0069828.t001
CXCL12 present in pLEC cultures that was not detected in the
supernatant. These results demonstrate that CXCR7-mediated Rb
degradation requires CXCR7 ligand. Importantly, this phenotype
is not ligand-specific because rescue of Rb can be achieved by
neutralization of either CXCR7 ligand.
CXCR7 Transduction does not Affect Surface Expression
of CXCR3 and CXCR4
CXCR7 shares ligands with two other chemokine receptors;
SDF-1/CXCL12 binds to both CXCR7 and CXCR4 while
ITAC/CXCL11 binds to both CXCR7 and CXCR3 [9]. Indeed,
it has been hypothesized that CXCR7 is not a functional
chemokine receptor but a chemokine sink and that its primary
function is to alter the availability of ligands for these alternate
receptors [11,23,24]. This promiscuity makes receptor/ligand
interactions difficult to dissect in EC, which can express both
CXCR4 and CXCR3 [4,25]. Therefore, we wanted to rule out
participation of these alternate receptors in the ligand-dependent
degradation of Rb seen in CXCR7+ cultures. We performed
experiments in which we transduced pLEC with increasing
concentrations of CXCR7 adenovirus and detected surface
expression of CXCR7, CXCR3 and CXCR4 by flow cytometry
(Figure 5). We observed dose-dependent increases in CXCR7
expression as expected. However, we observed no CXCR4
staining above isotype control in any condition and although a
small number of CXCR3 positive EC were observed in these
experiments (4% 60.8 average from 8 samples in two experimental replicates), CXCR7 transduction did not alter CXCR3
levels. These results demonstrate that cell surface expression of
alternate receptors for CXCR7 ligands in pLEC cultures is very
Table 2. Fold changes in mRNA expression in CXCR7transduced EC compared to uninfected controls.
Figure 3. CXCR7 expression causes degradation of Rb in EC. (A)
pLEC cultures were infected with Trans only (0) or Trans+CXCR7 at MOI
50, 100 or 200. At 20 hours post-infection, cells were lysed and analyzed
by western blot for total Rb levels. Densitometry analysis was
performed on Rb blots wherein each sample was normalized to GAPDH
signal intensity and GAPDH-normalized fold decrease of Rb expression
compared Trans is displayed beneath each dose (B) pLEC cultures were
infected with Trans only or Trans+CXCR7. At 6 hours post-infection,
media was replaced with media containing DMSO vehicle or media
containing MG132 at 1 or 2.5 mM. At 20 hours post infection, cells were
lysed and analyzed by western blot for total Rb levels.
doi:10.1371/journal.pone.0069828.g003
PLOS ONE | www.plosone.org
CXCR7
SDF-1/CXCL12 ITAC/CXCL11
Trans
0.260.1
1.260.6
1.060.3
CXCR7 MOI 50
150.1619.9
0.860.4
1.060
CXCR7 MOI 100
578.9635
0.960.5
2.560.8
CXCR7 MOI 200
1114.96117.4
1.060.5
2.860.1
Average 6 standard error of two experimental replicates.
doi:10.1371/journal.pone.0069828.t002
6
July 2013 | Volume 8 | Issue 7 | e69828
Aberrant Proliferation of CXCR7+ Endothelial Cells
Table 3. Supernatant concentrations of selected cytokines in
Trans or CXCR7-transduced EC.
Experiment 1
Experiment 2
Trans
CXCR7
Trans
SDF-1/CXCL12
0.0
0.0
0.0
0.0
10.0
60,017
I-TAC/CXCL11
0.0
89.0
77.0
0.0
54.0
60,012
6ckine/CCL21
0.0
0.0
241.0
0.0
183.0
60,000
ANG-1
0.0
0.0
0.0
0.0
36.0
60,002
ANG-2
381471.0 465732.0 1447429.0 1162435.0138.0
EGF
786496.0 820226.0 9955.0
9158.0
158.0
60,005
ENA-78/CXCL5
180.0
212.0
0.0
0.0
110.0
60,006
HGF/SF
301.0
0.0
502.0
0.0
199.0
60,008
IL-8/CXCL8
310714.0 374540.0 146329.0 125787.0 137.0
60,009
IP-10/CXCL10
0.0
0.0
0.0
0.0
28.0
60,011
MIG/CXCL9
644.0
790.0
3569.0
1844.0
282.0
60,014
MIP-3b/CCL19
0.0
0.0
0.0
0.0
28.0
60,015
VEGF
0.0
141.0
0.0
0.0
119.0
60,018
VEGF-C
0.0
0.0
0.0
0.0
81.0
60,020
VEGF-D
0.0
0.0
0.0
0.0
37.0
60,021
CXCR7
LOD
MAX
60,003
Quantities are displayed in pg/ml.
LOD: Limit of Detection; MAX: maximum concentration of standard curve.
ANG: angiopoietin; EGF: epidermal growth factor; HGF/SF: hepatocyte growth
factor/scatter factor; VEGF: vascular endothelial growth factor.
doi:10.1371/journal.pone.0069828.t003
Figure 4. CXCR7-mediated Rb degradation requires ligand.
pLEC cultures were infected with Trans only or Trans+CXCR7. At 6 hours
post-infection, media was replaced with media only or media
containing (A) SDF-1/CXCL12 neutralizing antibody at 1.5, or 3.0 mg/
ml or (B) ITAC/CXCL11 neutralizing antibody at 0.5 or 1.0 mg/ml. At 20
hours post infection, cells were lysed and analyzed by western blot for
total Rb levels. Densitometry analysis was performed and fold change
values were calculated from GAPDH-normalized optical density ratios as
described for Figure 3. Bar graphs (bottom) represent the average fold
change at each condition for two independent experiments.
doi:10.1371/journal.pone.0069828.g004
low and is not affected by CXCR7 expression. Therefore, it is
unlikely that the significant gain-of-function proliferation and Rb
degradation phenotypes seen in CXCR7-transduced cultures is a
result of signaling from these alternate receptors.
Pharmacological Inhibition of CXCR7 Restores Rb
Expression and Prevents Overconfluent Growth
CXCR7 sequence in our existing CXCR7 adenovirus vector
(CXCR7-D5). The N-terminal HA-tag was retained to aid in
detection. Flow cytometry analysis of pLEC transduced with
CXCR7-D5 demonstrated that the modified protein is expressed
on the cell surface (Figure 7A). In contrast to wild-type (WT)
CXCR7 transduction, lysates from CXCR7-D5-transduced cultures displayed no degradation of Rb protein by western blot
analysis (Figure 7B). Moreover, CyQuant analysis of confluent
pLEC cultures transduced with increasing levels of CXCR7-D5
display decreased proliferation compared to CXCR7-WT
(Figure 7C). Taken together, these results indicate that the
proliferation phenotype associated with CXCR7-expression in
EC can be abrogated by expression of a CXCR7 mutant,
supporting our hypothesis that these phenotypes require interaction between CXCR7 and its chemokine ligands and further
demonstrating that the degradation of Rb corresponds to
proliferative capacity in these cultures.
In order to reinforce our hypothesis that CXCR7-mediated EC
proliferation and Rb degradation is a result of CXCR7 signaling,
we examined the effect of a small molecule inhibitor of CXCR7,
CCX733, on proliferation and Rb protein levels in CXCR7+ EC.
For these experiments, we transduced confluent pLEC cultures
with Trans or Trans+CXCR7. At 6 hours post-infection, we
added DMSO vehicle or increasing doses (10, 50 or 100 nM) of
CCX733. While the inhibitor was ineffective at 10 nM, treatment
with 50 nM CCX733 produced a statistically significant decrease
in the overproliferation seen in CXCR7+ EC cultures. The effect
was more pronounced at 100 nM, however we observed a low
level of cytotoxicity at this dose indicated by a decrease in cell
numbers in the control Trans cultures (Figure 6A). Similar
experiments in which we harvested total cellular lysates and
performed western blot analysis for Rb protein levels revealed a
partial rescue of Rb levels in cultures treated with CCX733
(Figure 6B). Therefore, pharmacological inhibition of CXCR7 can
prevent aberrant proliferation and Rb degradation in EC.
Moreover, these results show a direct correlation between Rb
levels and proliferative capacity in CXCR7+ EC.
Discussion
Since its identification as an alternate SDF-1/CXCL12 binding
receptor, CXCR7 has been the subject of intense study in the
cancer field. However, dissection of CXCR7 signaling and
function has proven difficult for several reasons. First and most
importantly, the promiscuity of CXCR7 ligands and the
widespread expression of CXCR4 and CXCR3 in tumor tissues
[6] makes the dissection of CXCR7-specific signaling particularly
Expression of a CXCR7 Mutant Rescues Rb and Displays
Lower Proliferation Levels
The N-terminal domain mediates high affinity chemokine
interaction for both CXC [26] and CC [27] chemokine receptors.
Therefore, we deleted five N-terminal amino acids from the
PLOS ONE | www.plosone.org
7
July 2013 | Volume 8 | Issue 7 | e69828
Aberrant Proliferation of CXCR7+ Endothelial Cells
Figure 5. CXCR7 transduction does not affect surface expression of CXCR3 and CXCR4. pLEC cultures were infected with Trans only or
Trans+CXCR7 at indicated doses. At 20 hours post-infection cells were harvested and stained by flow cytometry for CXCR7 via 8F11 monoclonal
antibody, CXCR4 and CXCR3. Necrotic cells were excluded from the analysis via propidium iodide staining and scatter characteristics. Positive staining
(black line) was compared to appropriate isotype control (grey fill) and positive populations were gated based on isotype control levels. Data is
representative of two experimental replicates.
doi:10.1371/journal.pone.0069828.g005
To our knowledge, all of the studies examining CXCR7
expression in tumor vasculature have used CD31/PECAM-1 as a
marker of EC. As such, the vessels represented could be blood
vascular, lymphatics or, most likely, both. Although we have
performed the majority of experiments in the current study using
primary lymphatic EC, we have shown that aberrant proliferation
and Rb degradation occurs in blood vascular lineage EC as well
(Figure S1). As such, the physiological implications of the current
study are generalizable to both the lymphatic and blood vascular
circulatory systems. The importance of tumor lymphatic vasculature to tumor immune surveillance [32] as well as the metastatic
spread of tumors to the lymph nodes [33,34] is well established.
challenging. Moreover, tumor cells can produce both SDF-1/
CXCL12 [5] and ITAC/CXCL11 [28,29], creating a complex
signaling background and making experiments with exogenous
chemokine ligand difficult to interpret. Third, it is clear from the
current lack of consensus in the CXCR7 literature that CXCR7
signaling is likely to be both cell-type specific and ligand-specific, a
phenomenon that has been described for other G-protein coupled
receptors (GPCRs) [30] and chemokine receptors [31]. The latter
challenge, in particular, necessitates careful examination of
CXCR7 function in the cell type of interest, because the biological
effects of CXCR7 expression and signaling are not necessarily
universal between tissue types.
PLOS ONE | www.plosone.org
8
July 2013 | Volume 8 | Issue 7 | e69828
Aberrant Proliferation of CXCR7+ Endothelial Cells
Figure 6. A small molecule inhibitor of CXCR7 prevents
overconfluent growth and restores Rb expression. (A) Confluent
pLEC cultures were infected with Trans only or Trans+CXCR7. At 6 hours
post-infection, media was replaced with media containing DMSO
vehicle control or CCX733 at 10 nM, 50 nM or 100 nM. At 20 hours
post-infection, cells were lysed in the presence of Cyquant. Flourescence values are normalized to Trans+DMSO control. n.10 from two
independent experiments. **P,0.01 (B) pLEC cultures were infected
and treated as described for (A). At 20 hours post-infection, cells were
lysed and analyzed by western blot for total Rb levels. Densitometry
analysis was performed and fold change values were calculated from
GAPDH-normalized optical density ratios as described for Figure 3.
doi:10.1371/journal.pone.0069828.g006
We believe that our current data supports further study into the
contribution of CXCR7 expression in tumor-associated lymphatic
vessels to tumor growth and metastasis.
Pathologically-induced CXCR7 has recently been shown to
drive proliferation of pulmonary microvascular EC in models of
pulmonary hypertension in vitro [35] and in vivo [19]. Moreover,
the latter study demonstrated that pharmacological inhibition of
CXCR7 could prevent vascular proliferation caused by chronic
hypoxia-induced pulmonary hypertension. While these results are
not necessarily translatable to tumor vascular dysfunction we
believe that, when taken together with our current study in
primary human EC and the wealth of histopathological data
showing that CXCR7 is highly expressed in tumor vasculature, the
potential of CXCR7 as an antiangiogenic target deserves further
study.
PLOS ONE | www.plosone.org
Figure 7. Expression of a CXCR7 mutant rescues Rb and
prevents aberrant proliferation. (A) pLEC cultures were transduced
with CXCR7 WT at MOI 200 or CXCR7-D5 at MOI 50. At 20 hours postinfection cells were stained for surface expression of the HA tag.
Propidium Iodide was used to exclude necrotic cells. (B) Total lysates
from pLEC cultures transduced as in (A) were harvested and analyzed by
western blot analysis for total Rb protein. (C) Confluent pLEC cultures
transduced with increasing doses of CXCR7-WT (MOI 50, 100, 200 or
300) or CXCR7-D5 (MOI 10, 20, 30 or 50). At 20 hours post-infection, cells
were lysed in the presence of Cyquant. Fluorescence values are
normalized to Trans only controls. n = 10. * P = 0.03, ** P = 0.001.
doi:10.1371/journal.pone.0069828.g007
9
July 2013 | Volume 8 | Issue 7 | e69828
Aberrant Proliferation of CXCR7+ Endothelial Cells
When CXCR7 was still the orphan GPCR known as RDC1,
our laboratory demonstrated that CXCR7 is highly upregulated in
EC infected with Kaposi Sarcoma Herpesvirus (KSHV) [36].
KSHV is the etiological agent of Kaposi Sarcoma (KS) an
angioproliferative tumor of the viscera, skin and mucosa in which
the tumor cell is of endothelial origin [37]. Importantly, in our
original study, knockdown of CXCR7 by RNA interference
abrogated the ability of KSHV to produce a transformed
phenotype in EC cultures, providing the first evidence that
aberrant expression of CXCR7 contributes to malignancy. To our
knowledge, KS is the only neoplasm studied to date that displays
uniformly high levels of CXCR7 on tumor cells, and we have
observed that levels of CXCR7 expression correlate with disease
progression (Moses et. al, unpublished observations). Results from
our current study provide CXCR7-mediated proliferation as a
potential mechanism for the growth of KS tumors and establish
CXCR7 as a potential target for the treatment of KS. Indeed, the
expression of CXCR7 in other angioproliferative neoplasms will
be of great interest in future studies.
There is significant evidence in the literature that CXCR7 alters
the function of CXCR4 either by direct interaction or manipulation of ligand availability [23,24,38]. Experiments employing
CXCR4 inhibitors would further strengthen the conclusion that
CXCR4 is not involved in the observed phenotypes. Unfortunately, two CXCR4 antagonists AMD3100 and TC14012 are
known agonists for CXCR7 [39,40] and, to our knowledge, the
other CXCR4 antagonists have not been tested for CXCR7
binding capacity. Therefore, we believe that the use of CXCR4
inhibitors would be uninterpretable in our EC system. We have
demonstrated that surface expression of both CXCR3 and
CXCR4 are very low in these cultures and are not altered by
CXCR7 expression (Figure 5), and we have utilized both a small
molecule inhibitor of CXCR7 and targeted mutagenesis of the
CXCR7 N-terminus to abrogate the observed phenotypes
(Figures 6 & 7). We believe that, taken together, the data
presented in the current study supports the conclusion that the
proliferative phenotypes observed in CXCR7+ EC are a direct
result of CXCR7 signaling and represent the most rigorous
demonstration thereof that is possible given the complexity of the
system and the tools currently available.
In the current study, we demonstrate that CXCR7 expression
causes the proteasome-mediated degradation of Rb protein in EC,
providing a specific cellular mechanism for CXCR7-mediated
proliferation. To our knowledge, this is the first demonstration of
CXCR7-mediated inhibition of a tumor suppressor pathway. The
Rb regulatory pathway is thought to be dysfunctional in most
human cancer [20]. Indeed, the function of Rb as a master
regulator of cellular proliferation was first appreciated when it was
shown to be the target of several viral oncogenes. Virus-mediated
inhibition of Rb function proceeds by a variety of mechanisms
including (1) direct phosphorylation of Rb, (2) steric inhibition of
Rb interactions with the E2F transcription factor and (3) targeting
of Rb protein for degradation [41,42]. These virus-mediated
oncogenic mechanisms provide clues to potential cellular mechanisms of Rb inactivation in uninfected malignant cells, some of
which have since been revealed. Overexpression of the E3
ubiquitin ligase MDM2 is one of the only cellular mechanisms
for degradation of Rb in cancer cells that has been characterized
to date [21], but the factors driving MDM2 overexpression in
cancer systems remain obscure. It will be interesting to determine
whether aberrant expression of CXCR7 in EC results in
overexpression or activation of MDM2 and whether MDM2
affects Rb expression in EC. Moreover, if the phenotype we
demonstrate is common and CXCR7 signaling causes degradation
of Rb in tumor cells in other cancer systems, the inhibition of
CXCR7 could be a powerful target for the treatment of malignant
cellular proliferation in general.
Although we have chosen to focus on Rb as a protein of interest
from our antibody microarray screen of CXCR7-modulated
proteins, we provide the complete list of proteins and phosphorylation sites found to be modified by CXCR7 expression as
supporting information (Table S1). In addition to identifying
additional proliferation-modulators affected by CXCR7 - including, notably, the tumor suppressor protein p53 (Table 1) – these
data also suggest that CXCR7 may participate in the control of
apoptosis and participate in the response of EC to environmental
stress. We anticipate that this data set will help further the studies
of researchers in multiple fields related to EC biology and CXCR7
signaling.
Supporting Information
CXCR7 expression in pBEC results in postconfluent proliferation and causes Rb degradation.
Confluent pBEC cultures were infected with Trans only or
Trans+CXCR7 at MOI 100. At 20 hours post-infection cells were
(A) lysed in the presence of CyQuant or (B) lysed and analyzed by
western blot for total Rb levels. Fluorescence values are
normalized to uninfected controls. n = 18 from three independent
experiments. *** P,0.001.
(PDF)
Figure S1
Table S1
(PDF)
Acknowledgments
The authors would like to thank Mark Penfold of Chemocentryx, Inc for
providing CXCR7 antibodies, the small molecule inhibitor CCX733 and
valuable advice.
Author Contributions
Conceived and designed the experiments: JET AVM. Performed the
experiments: JET JMO SB. Analyzed the data: JET AVM SB. Contributed
reagents/materials/analysis tools: LC. Wrote the paper: JET AVM SB.
References
6. Vandercappellen J, Van Damme J, Struyf S (2008) The role of CXC chemokines
and their receptors in cancer. Cancer Lett 267: 226–244. doi:10.1016/
j.canlet.2008.04.050.
7. Balkwill F (2004) The significance of cancer cell expression of the chemokine
receptor CXCR4. Semin Cancer Biol 14: 171–179. doi:10.1016/j.semcancer.2003.10.003.
8. Teicher BA, Fricker SP (2010) CXCL12 (SDF-1)/CXCR4 pathway in cancer.
Clin Cancer Res 16: 2927–2931. doi:10.1158/1078-0432.CCR-09-2329.
9. Burns JM, Summers BC, Wang Y, Melikian A, Berahovich R, et al. (2006) A
novel chemokine receptor for SDF-1 and I-TAC involved in cell survival, cell
adhesion, and tumor development. J Exp Med 203: 2201–2213. doi:10.1084/
jem.20052144.
1. Carmeliet P (2005) Angiogenesis in life, disease and medicine. Nature 438: 932–
936. doi:10.1038/nature04478.
2. Carmeliet P, Jain RK (2011) Molecular mechanisms and clinical applications of
angiogenesis. Nature 473: 298–307. doi:10.1038/nature10144.
3. Jain RK (2005) Normalization of Tumor Vasculature: An Emerging Concept in
Antiangiogenic Therapy. Science 307: 58–62. doi:10.1126/science.1104819.
4. Mehrad B, Keane MP, Strieter RM (2007) Chemokines as mediators of
angiogenesis. Thromb Haemost 97: 755–762.
5. Balkwill F (2004) Cancer and the chemokine network. Nat Rev Cancer 4: 540–
550. doi:10.1038/nrc1388.
PLOS ONE | www.plosone.org
10
July 2013 | Volume 8 | Issue 7 | e69828
Aberrant Proliferation of CXCR7+ Endothelial Cells
10. Gahan JC, Gosalbez M, Yates T, Young EE, Escudero DO, et al. (2012)
Chemokine and Chemokine Receptor Expression in Kidney Tumors: Molecular
Profiling of Histological Subtypes and Association With Metastasis. J Urol.
doi:10.1016/j.juro.2011.10.150.
11. Luker KE, Lewin SA, Mihalko LA, Schmidt BT, Winkler JS, et al. (2012)
Scavenging of CXCL12 by CXCR7 promotes tumor growth and metastasis of
CXCR4-positive breast cancer cells. Oncogene. doi:10.1038/onc.2011.633.
12. Miao Z, Luker KE, Summers BC, Berahovich R, Bhojani MS, et al. (2007)
CXCR7 (RDC1) promotes breast and lung tumor growth in vivo and is
expressed on tumor-associated vasculature. Proc Natl Acad Sci USA 104:
15735–15740. doi:10.1073/pnas.0610444104.
13. Zheng K, Li H-Y, Su X-L, Wang X-Y, Tian T, et al. (2010) Chemokine
receptor CXCR7 regulates the invasion, angiogenesis and tumor growth of
human hepatocellular carcinoma cells. J Exp Clin Cancer Res 29: 31.
doi:10.1186/1756-9966-29-31.
14. Sun X, Cheng G, Hao M, Zheng J, Zhou X, et al. (2010) CXCL12/CXCR4/
CXCR7 chemokine axis and cancer progression. Cancer Metastasis Rev 29:
709–722. doi:10.1007/s10555-010-9256-x.
15. Hattermann K, Held-Feindt J, Lucius R, Müerköster SS, Penfold MET, et al.
(2010) The chemokine receptor CXCR7 is highly expressed in human glioma
cells and mediates antiapoptotic effects. Cancer Res 70: 3299–3308.
doi:10.1158/0008-5472.CAN-09-3642.
16. Monnier J, Boissan M, L’helgoualc’h A, Lacombe M-L, Turlin B, et al. (2011)
CXCR7 is up-regulated in human and murine hepatocellular carcinoma and is
specifically expressed by endothelial cells. Eur J Cancer. doi:10.1016/
j.ejca.2011.06.044.
17. Würth R, Barbieri F, Bajetto A, Pattarozzi A, Gatti M, et al. (2011) Expression
of CXCR7 chemokine receptor in human meningioma cells and in intratumoral
microvasculature. J Neuroimmunol 234: 115–123. doi:10.1016/j.jneuroim.2011.01.006.
18. Singh RK, Lokeshwar BL (2011) The IL-8-regulated chemokine receptor
CXCR7 stimulates EGFR signaling to promote prostate cancer growth. Cancer
Res 71: 3268–3277. doi:10.1158/0008-5472.CAN-10–2769.
19. Sartina E, Suguihara C, Ramchandran S, Nwajei P, Rodriguez M, et al. (2012)
Antagonism of CXCR7 Attenuates Chronic Hypoxia-Induced Pulmonary
Hypertension. Pediatr Res 71: 682–688. doi:10.1038/pr.2012.30.
20. Classon M, Harlow E (2002) The retinoblastoma tumour suppressor in
development and cancer. Nat Rev Cancer 2: 910–917. doi:10.1038/nrc950.
21. Sdek P, Ying H, Chang DLF, Qiu W, Zheng H, et al. (2005) MDM2 Promotes
Proteasome-Dependent Ubiquitin-Independent Degradation of Retinoblastoma
Protein. Molecular Cell 20: 699–708. doi:10.1016/j.molcel.2005.10.017.
22. Murphy JW, Cho Y, Sachpatzidis A, Fan C, Hodsdon ME, et al. (2007)
Structural and functional basis of CXCL12 (stromal cell-derived factor-1 alpha)
binding to heparin. J Biol Chem 282: 10018–10027. doi:10.1074/
jbc.M608796200.
23. Levoye A, Balabanian K, Baleux F, Bachelerie F, Lagane B (2009) CXCR7
heterodimerizes with CXCR4 and regulates CXCL12-mediated G protein
signaling. Blood 113: 6085–6093. doi:10.1182/blood-2008-12-196618.
24. Naumann U, Cameroni E, Pruenster M, Mahabaleshwar H, Raz E, et al. (2010)
CXCR7 functions as a scavenger for CXCL12 and CXCL11. PLoS ONE 5:
e9175. doi:10.1371/journal.pone.0009175.
25. Teicher BA (2011) Antiangiogenic agents and targets: A perspective. Biochem
Pharmacol 81: 6–12. doi:10.1016/j.bcp.2010.09.023.
26. Ahuja SK, Lee JC, Murphy PM (1996) CXC chemokines bind to unique sets of
selectivity determinants that can function independently and are broadly
PLOS ONE | www.plosone.org
27.
28.
29.
30.
31.
32.
33.
34.
35.
36.
37.
38.
39.
40.
41.
42.
11
distributed on multiple domains of human interleukin-8 receptor B. Determinants of high affinity binding and receptor activation are distinct. J Biol Chem
271: 225–232.
Monteclaro FS, Charo IF (1996) The amino-terminal extracellular domain of
the MCP-1 receptor, but not the RANTES/MIP-1alpha receptor, confers
chemokine selectivity. Evidence for a two-step mechanism for MCP-1 receptor
activation. J Biol Chem 271: 19084–19092.
Furuya M, Yoneyama T, Miyagi E, Tanaka R, Nagahama K, et al. (2011)
Differential expression patterns of CXCR3 variants and corresponding CXC
chemokines in clear cell ovarian cancers and endometriosis. Gynecologic
Oncology 122: 648–655. doi:10.1016/j.ygyno.2011.05.034.
Furuya M, Suyama T, Usui H, Kasuya Y, Nishiyama M, et al. (2007) Upregulation of CXC chemokines and their receptors: implications for proinflammatory microenvironments of ovarian carcinomas and endometriosis.
Human Pathology 38: 1676–1687. doi:10.1016/j.humpath.2007.03.023.
Kelly E, Bailey CP, Henderson G (2008) Agonist-selective mechanisms of GPCR
desensitization. Br J Pharmacol 153 Suppl 1: S379–S388. doi:10.1038/
sj.bjp.0707604.
Vomaske J, Melnychuk RM, Smith PP, Powell J, Hall L, et al. (2009) Differential
ligand binding to a human cytomegalovirus chemokine receptor determines cell
type-specific motility. PLoS Pathog 5: e1000304. doi:10.1371/journal.ppat.1000304.
Lund AW, Swartz MA (2010) Role of lymphatic vessels in tumor immunity:
passive conduits or active participants? J Mammary Gland Biol Neoplasia 15:
341–352. doi:10.1007/s10911-010-9193-x.
Yin X, Truty J, Lawrence R, Johns SC, Srinivasan RS, et al. (2010) A critical
role for lymphatic endothelial heparan sulfate in lymph node metastasis. Mol
Cancer 9: 316. doi:10.1186/1476-4598-9-316.
Wang Y, Oliver G (2010) Current views on the function of the lymphatic
vasculature in health and disease. Genes Dev 24: 2115–2126. doi:10.1101/
gad.1955910.
Costello CM, McCullagh B, Howell K, Sands M, Belperio JA, et al. (2011) A
role for the CXCL12 receptor, CXCR7, in the pathogenesis of human
pulmonary vascular disease. Eur Respir J 39: –1424. doi:10.1183/
09031936.00044911.
Raggo C, Ruhl R, McAllister S, Koon H, Dezube BJ, et al. (2005) Novel cellular
genes essential for transformation of endothelial cells by Kaposi’s sarcomaassociated herpesvirus. Cancer Res 65: 5084–5095. doi:10.1158/00085472.CAN-04-2822.
Mesri EA, Cesarman E, Boshoff C (2010) Kaposi’s sarcoma and its associated
herpesvirus. Nat Rev Cancer 10: 707–719. doi:10.1038/nrc2888.
Thelen M, Thelen S (2008) CXCR7, CXCR4 and CXCL12: an eccentric trio?
J Neuroimmunol 198: 9–13. doi:10.1016/j.jneuroim.2008.04.020.
Kalatskaya I, Berchiche YA, Gravel S, Limberg BJ, Rosenbaum JS, et al. (2009)
AMD3100 is a CXCR7 ligand with allosteric agonist properties. Mol Pharmacol
75: 1240–1247. doi:10.1124/mol.108.053389.
Gravel S, Malouf C, Boulais PE, Berchiche YA, Oishi S, et al. (2010) The
peptidomimetic CXCR4 antagonist TC14012 recruits beta-arrestin to CXCR7:
roles of receptor domains. J Biol Chem 285: 37939–37943. doi:10.1074/
jbc.C110.147470.
Hume AJ, Kalejta RF (2009) Regulation of the retinoblastoma proteins by the
human herpesviruses. Cell Div 4: 1. doi:10.1186/1747-1028-4-1.
Felsani A, Mileo AM, Paggi MG (2006) Retinoblastoma family proteins as key
targets of the small DNA virus oncoproteins. Oncogene 25: 5277–5285.
doi:10.1038/sj.onc.1209621.
July 2013 | Volume 8 | Issue 7 | e69828
|
|
https://openalex.org/W3172511478
|
https://uca.hal.science/hal-03257033/document
|
English
| null |
Optimal deterministic and robust selection of electricity contracts
|
Journal of global optimization
| 2,021
|
cc-by
| 11,463
|
To cite this version: David Wu, Viet Hung Nguyen, Michel Minoux, Hai Tran. Optimal deterministic and robust selection
of electricity contracts. Journal of Global Optimization, 2021, 10.1007/s10898-021-01032-z. hal-
03257033 Optimal deterministic and robust selection of electricity
contracts David Wu, Viet Hung Nguyen, Michel Minoux, Hai Tran Distributed under a Creative Commons Attribution 4.0 International License HAL Id: hal-03257033
https://uca.hal.science/hal-03257033v1
Submitted on 10 Jun 2021 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 Journal of Global Optimization manuscript No. (will be inserted by the editor) Optimal deterministic and robust selection of electricity
contracts David Wu · Viet Hung Nguyen · Michel
Minoux · Hai Tran Received: date / Accepted: date Received: date / Accepted: date Abstract We address the Electricity Contract Selection Problem (ECSP), of find-
ing best parameters of an electricity contract for a client based on his/her past
records of electricity consumption over a fixed time period. The objective is to op-
timize the electricity bill composed by some fixed cost, the cost of the subscription
of the electricity contract and penalties due to overpowering when consumption
exceeds subscribed power. The ECSP can be formulated as a convex separable op-
timization problem subject to total order constraints. Due to this special structure,
ECSP is a special case of two well known classes of convex separable optimization
problems, namely the minimum network flow under convex separable cost and min-
imizing convex separable functions under chain constraints. Both classes are well
treated in the litterature and can be solved in polynomial time [1, 2, 5, 11, 13, 14]. In particular, the algorithm in [2] achieves the best theoretical time complexity
assuming that computing the objective function value at one specific point can be
done in constant time. However, when we work on a big amount of historic data
as in ECSP, the time required for evaluating the objective function cannot be as-
sumed to be O(1) anymore. In this paper, we propose a new algorithm for ECSP
which is specially designed to reduce the computational effort over large scale his-
torical data. We present numerical results showing that our algorithm outperforms
the algorithm in [2] when applied to consumption data of various types of clients. A robust version of ECSP based on a Seasonal and Trend decomposition approach David Wu
Sorbonne Universit´e, LIP6 CNRS UMR 7606, Paris, France
E-mail: david.wu@lip6.fr Viet Hung Nguyen
Universit´e Clermont Auvergne, LIMOS, CNRS UMR 6158, Aubi`ere, France
E-mail: vhnguyen@isima.fr
Corresponding author Michel Minoux
Sorbonne Universit´e, LIP6 CNRS UMR 7606, Paris, France
E-mail: michel.minoux@lip6.fr Hai Tran
Energisme SAS, Boulogne-Billancourt, France
E-mail: hai.tran@energisme.com 2 David Wu et al. for modelling consumption uncertainty is also investigated. The resulting worst-
case cost minimization problem is shown to be efficiently solvable using the same
algorithm as for deterministic ECSP. Keywords electricity contract, convex separable optimization, robust optimiza-
tion, active constraint set 1 Introduction Optimally selecting an energy contract is an important issue for many industrial
customers which have an electricity contract for each delivery point. Contracts
may need to fix the maximum of total energy consumption in kilowatt-hours and
the maximum of peak demand in kilowatt over a large period, typically one year. The electricity contract problem discussed in [6] can be formulated as a linear
program and solved as such in polynomial time. In the problem discussed in [6],
there is a fixed cost when the peak demand does not exceed the contract capacity
and some additional cost for excess demand. Combining the optimal energy contract selection problem with a lot sizing
problem by considering renewable energy sources has been investigated in [16]. Using a pricing based on the so-called ”subscribed power” tends to enforce
people to adapt their electricity consumption behaviour in order to match with
the subscription [18]. This subscribed power is based on billing the cost of the
electricity contract, the cost of some penalty of overpowering with respect to the
maximum peak demand defined in the contract and some other fixed costs. In this paper, we investigate an optimal electricity contract selection problem
(ECSP) based on subscribed power which is formulated as minimizing a convex
separable function subject to total order constraints. The problem is addressed
both in the deterministic case and in the case when consumption data are subject
to uncertainty. The paper is organized as follows. Section 2 presents the context
and proposes a formulation of the optimization problem considered in its determin-
istic version. Section 3 presents an efficient algorithm based on an active constraint
set approach to solve the optimal selection of electricity contracts. Section 4 inves-
tigates a robust version of the problem in which uncertainties on consumption are
taken into account. Section 5 presents a series of computational results obtained,
both for the deterministic case and for the robust version of the problem. Section
6 presents the main conclusions and some perspectives for future research. 2.1 Mathematical formulation of ECSP In France, ENEDIS is responsible for the management of 95% of the electricity
distribution network. The tariffs for using the electricity grid are referred to as
TURPE (see enedis.fr). Over the year, consumption periods are classified into several predefined cate-
gories, where each category may have it own consumption behaviour. Under the 5th
version of TURPE, denoted TURPE5, K = 5 categories are considered, namely:
winter peak hours (1), winter full hours (2), winter off-peak hours (3), summer 3 Optimal deterministic and robust selection of electricity contracts 3 full hours (4) and summer off-peak hours (5). Electricity used during peak hours
is billed at a higher rate than electricity used during off-peak hours, creating an
incentive for homeowners to reduce energy usage during peak hours. Let T be
the total number of 10 minute periods (e.g. T = 52560 for a year) and Ti the
total number of 10 minutes period in category i. Let M = {1, . . . , 12} be the set
of all months of the study period, and ∀i ∈{1, . . . , K}, Mi is the subset of M
corresponding to category i. For example, for the winter peak hours category with
i = 1, M1 = {1, 2, 12} which corresponds to the three months of winter. Each small
10 minute period t belongs to a category i and a month m ∈Mi, noted as t ∈Ti,m,
and for each t there is a required consumption level ct. Selecting an electricity contract defined by TURPE5 is to choose for each
category of consumption i a value of subscribed power xi ≥0 (in kW). The problem
of selecting a best contract thus consists in determining a K-dimensional non-
negative vector x = (x1, . . . , xK) minimizing the bill due by the consumer. For
each category i the corresponding subscribed power xi represents thresholds of
consumption, viewed as a commitment of maximum peak demand for each 10
minutes period. There is an annual cost for the subscription equal to P
i sixi (for given si > 0
in e /kW/year), this cost is an increasing linear function of x. Excess demand
of consumption, called overpowering, is allowed but in that case extra penalty
costs are due. The overpowering quantity for t is δt(xi) = max(0, ct-xi). 2.1 Mathematical formulation of ECSP For each
category i and month m ∈Mi, the penalty cost is pi
qP
t∈Ti,m δt(xi)2 (for given
pi > 0 in e /kWh), which is a decreasing function of xi. There is also some fixed
cost unrelated to subscribed power (e.g. consumption, transports and taxes) which
is not necessary to our analysis. The objective function of the problem is the total
annual cost F(x) defined as the sum of the annual costs Fi(xi) for the various
categories i ∈{1, ..., K} : Fi(xi) = sixi + pi
X
m∈Mi
s X
t∈Ti,m
δt(xi)2. (1) (1) (see Figure 1 for a graphical representation of a function Fi(xi)). (see Figure 1 for a graphical representation of a function Fi(xi)). Fig. 1: Objective function for category i: Fi(xi) Fig. 1: Objective function for category i: Fi(xi) 4 David Wu et al. In order to ensure the stability of the network load, TURPE5 imposes that
subscribed powers in high consumption categories (e.g. winter peak hours) must be
lower than subscribed powers in low consumption categories (e.g. summer off-peak
hours). This results into a series of K-1 constraints of the form ∀i < K, xi ≤xi+1,
defining a total order on the xi values. Let ci (resp.: ¯ci) be the smallest (resp.: greatest) value of consumed power
during the time slots in category i. Then we denote by c (resp.: ¯c) the smallest
(resp.: greatest) consumed power among the instance. Then the xi variables should
meet the bound constraints 0 ≤c ≤xi ≤¯c. Let C = ¯c −c + 1 be the number of
integer values among which the optimal solution is searched. This parameter C
together with the number of categories K will be useful for expressing the worst-
case time complexity of our algorithm. The ECSP can then be formulated as the following mathematical program P: P : min F(x) =
K
X
i=1
Fi(xi)
(2) (2) s.t. xi ≤xi+1,
1 ≤i ≤K-1,
(3)
c ≤xi ≤¯c,
1 ≤i ≤K,
(4) (3)
(4) (4) The constraints (3) are called the order constraints and the constraints (4) are the
bound constraints. A solution for P is a K-dimensional vector x = (x1, . . . , xK)T
satisfying the constraints (3) and (4). The objective function (2) is separable and
convex as stated in the following Proposition 1. Proposition 1 Each Fi is convex with respect to xi. Now, from the convexity of the Euclidean norm, it follows: λg1(¯x1) + (1-λ)g1(ˆx1)
... λgT (¯xT ) + (1-λ)gT (ˆxT )
≤λ
g1(¯x1)
... gT (¯xT )
+ (1-λ)
g1(ˆx1)
... gT (ˆxT ) In view of this, the following inequality is shown to hold: In view of this, the following inequality is shown to hold: g1(λ¯x1 + (1-λ)ˆx1)
... gT (λ¯xT + (1-λ)ˆxT )
≤λ
g1(¯x1)
... gT (¯xT )
+ (1-λ)
g1(ˆx1)
... gT (ˆxT ) and from this, we conclude that: and from this, we conclude that: v
u
u
t
T
X
i=1
gt(λ¯xi + (1-λ)ˆxi)2 ≤λ
v
u
u
t
T
X
i=1
gt(¯xi)2 + (1-λ)
v
u
u
t
T
X
i=1
gt(ˆxi)2, which proves the desires convexity property of G. which proves the desires convexity property of G. For each category i the subscription cost is linear in xi and the penalty cost
is of the form: piGi(xi) with Gi(xi) =
qPTi
i=1 gt(xi)2, where gt(xi) = δt(xi) is a
convex function of xi. Thus, for each category i, Fi is convex w.r.t. xi. ⊓⊔ 2.1 Mathematical formulation of ECSP Proof For all i ∈{1, . . . , T}, let gt(xi) be an univariate convex function such that
gt(xi) ≥0 for all xi ≥0. q For all x ∈IRT , let us denotes G(x) =
qPT
i=1 gt(xi)2 the Euclidean Norm (L2) For all x ∈IR , let us denotes G(x) =
qP
i=1 gt(xi)2 the Euclidean Norm (L2)
of
g1(x1)
... gT (xT )
i.e. G(x) =
g1(x1)
... gT (xT )
. Let ¯x =
¯x1.... ¯xT
≥0, ˆx =
ˆx1.... ˆxT
≥0 and λ ∈[0, 1]. ,
( )
qP
i=1 g (
)
of
g1(x1)
... gT (xT )
i.e. G(x) =
g1(x1)
... gT (xT )
. Let ¯x =
¯x1.... ¯xT
≥0, ˆx =
ˆx1.... ˆxT
≥0 and λ ∈[0, 1]. F
h
i
f
h
f
i
d
h
f of
From the convexity of the gt functions and the fact that the norm is a non
decreasing function on the set of non negative vectors, it holds:
g1(λ¯x1 + (1-λ)ˆx1) ≤λg1(¯x1) + (1-λ)g1(ˆx1)
... gT (λ¯xT + (1-λ)ˆxT ) ≤λgT (¯xT ) + (1-λ)gT (ˆxT ) Therefore: g1(λ¯x1 + (1-λ)ˆx1)
... gT (λ¯x1 + (1-λ)ˆx1)
≤
λg1(¯xT ) + (1-λ)g1(ˆxT )
... λgT (¯xT ) + (1-λ)gT (ˆxT ) Optimal deterministic and robust selection of electricity contracts 5 2.2 State of the art and motivation The ECSP can be reformulated as a minimum separable convex cost network
optimization problem in a graph featuring K nodes and 2K−2 arcs (see Appendix). Thus, in order to solve P, one might well consider applying some of the existing
solution procedures, in particular: – the algorithm proposed in [13, 14] which, in our case, would lead to a worst-case
complexity O(K3logC); – the algorithm proposed in [13, 14] which, in our case, would lead to a worst-case
complexity O(K3logC); – the algorithms proposed in [1] and in [11] which would lead to a worst-case
complexity O(K2log(K)log(KC)). – the algorithms proposed in [1] and in [11] which would lead to a worst-case
complexity O(K2log(K)log(KC)). For a survey of solution algorithms for convex cost network optimization problems
and related nonlinear optimization problems, we refer the reader to [9]. Note that
all the previous algorithms use various versions of minimum cost flow network
algorithms running on various specific types of graphs. Some of these graphs could
be of very big size (e.g. the number of the arcs could be KC in the graph con-
sidered in [1]) and the construction of these graphs is not taken into account in
the time complexity of algorithm. Moreover, the algorithms in [1] and [11] need
advanced data structures such as dynamic trees to achieve the time complexity
of O(K2log(K)log(KC)). Without them, the worst-case complexity would remain
O(K3logC). The ECSP also belongs to the class of convex separable function minimization
problems under total order constraints. This class of problem appears in the con-
text of isotonic regression which is a well-known problem in statistics. Given K 6 David Wu et al. data c1, . . . , cK, the Isotonic Regression Problem (IRP) consists in finding K val-
ues x1, . . . , xK minimizing the norm p distance between the solution and the data
subject to order constraints x1 ≤· · · ≤xK. Formally, it is formulated as follows: min
p
sX
i
(xi −ci)p
s.t. x1 ≤x2 ≤. . . ≤xK. s.t. x1 ≤x2 ≤. . . ≤xK. The generalized IRP is obtained when the objective function is replaced by any
convex separation function. One of the most efficient algorithms for solving generalized IRP has been proposed
by Ahuja and Orlin [2] under the name of ’Scaling PAV’. 2.2 State of the art and motivation Assuming that computing
(1) at any x in RK can be done in constant time O(1), its complexity is O(Klog(C)). In Scaling PAV, instead of calculating the exact optimal solution of each Fi(xi)
at each iteration, one only updates the intervals to which the optimal solution
should belong. The K intervals are all initially set equal to (c, ¯c) and reduced by
one half after each iteration. As new order constraints are successively detected
and saturated, the number of intervals is progressively decreased as variables are
fusioned. After log2( C
ϵ ) iterations, all the intervals have reduced length less than
ϵ, and an ϵ-optimal solution is found. Since, in each iteration, one works with a at
most K intervals, the worst-case time complexity of Scaling PAV is O(Klog(C)). p
y
g
(
g( ))
Obviously, the Scaling PAV algorithm could be applied to the ECSP addressed
here. However, in this context of application, the evaluation of the resulting com-
plexity has to be completely reconsidered, because careful examination reveals
that the computational effort required to compute each value Fi(xi) involved in
the objective function (2) cannot be assumed to be O(1). Indeed, from the ex-
pression given in (1), it is readily seen that computing Fi(xi) for any given value
of xi, requires O(N+(xi)) arithmetic operations, where N+(xi) is defined as the
number of time steps t in Ti such that ct > xi. Thus, for large values of xi (i.e. values close to max(ct, t ∈Ti), both N+(xi) and the computation time are reduced. By contrast, for smaller values of xi, N+(xi) can be of the same order of magni-
tude as |Ti|, the total number of time steps in the definition of Fi, thus leading
to possibly much bigger computation time. For further discussion and illustration
of this dependence of N+(xi) on xi, please refer to the forthcoming Section 3.2. Clearly, since |Ti| (the number of consumption data in the category i) can be much
larger than K, the number of decision variables, this parameter turns out to be a
key factor to be taken into account in the evaluation of an algorithm for solving
P. Thus, in the search for computational efficiency in the solution of ECSP, the
dependence of N+(xi) (a measure of the computational effort) with respect to xi
has to be taken into account. 3 Optim SP: an efficient algorithm based on an active constraint set
approach For k ∈{1, . . . , K-1}, let the kth order constraint denote the constraint xk ≤xk+1. For k ∈{0, . . . , K-1} let Pk denote the relaxation of the problem P where the last
K −1 −k order constraints are relaxed, i.e. the order constraints in Pk are only
the first k order constraints: Pk : min F(x)
s.t. xi ≤xi+1,
1 ≤i ≤k,
c ≤xi ≤¯c,
1 ≤i ≤K. 1 ≤i ≤k,
1 ≤i ≤K. Note that P0 is the relaxation of P without the order constraints and PK−1 is P
itself. More generally, for B ⊆{1, . . . , K −1}, let P(B) denote the relaxation of P where
all the order constraints are relaxed except those indexed in B: P(B) : min F(x)
s.t. xi ≤xi+1,
i ∈B,
c ≤xi ≤¯c,
1 ≤i ≤K. P(B) : min F(x)
s.t. xi ≤xi+1,
i ∈B,
c ≤xi ≤¯c,
1 ≤i ≤K. In addition, we denote P=(B) the restriction of P(B) where the order constraints
in B are set to equality: P=(B) : min F(x)
s.t. xi = xi+1,
i ∈B,
c ≤xi ≤¯c,
1 ≤i ≤K. Note that, if B = ∅, then P=(B) = P0. P=(B) : min F(x)
s.t. xi = xi+1,
c ≤xi ≤¯c P=(B) : min F(x)
s.t. xi = xi+1,
i ∈B,
c ≤xi ≤¯c,
1 ≤i ≤K. P=(B) : min F(x)
s.t. xi = xi+1, i ∈B, 1 ≤i ≤K. Note that, if B = ∅, then P=(B) = P0. Note that, if B = ∅, then P=(B) = P0. 2.2 State of the art and motivation In the present paper, we propose a special-purpose algorithm for solving ECSP
which will turn out to be practically more efficient than Scaling PAV, thanks to
a proper exploitation of the specific features of the problem pointed out above. The proposed algorithm, which will be called Optim SP, is based on the same
scheme of iterative active constraint set detection as Scaling PAV. However, its
implementation makes essential use of an extended asymmetric binary search pro-
cedure, thanks to which the computational effort required in each iteration to
minimize the relevant part of the objective function (2) can be significantly re-
duced, as compared with usual binary search. It is also worth mentioning here Optimal deterministic and robust selection of electricity contracts 7 Optimal deterministic and robust selection of electricity contracts that this possibility of resorting to this extended binary search procedure could
not be applied within the Scaling PAV algorithm for the following reason: when
running Scaling PAV, at any given step all the intervals must have the same length,
and this cannot be the case in case of using the proposed extended binary search. 3.1 Algorithm’s overview Optim SP initially solves P0 and then performs K-1 iterations thus solving suc-
cessively P1, P2, . . . , PK−1. For k = 0, . . . , K −1, let xk = (xk
1, . . . , xk
K)T denote
the optimal solution of Pk found by Optim SP and let Bk denote the set of the
indices of the active order constraints in Pk associated with xk, i.e. the order
constraints in Pk that xk satisfies at equality. At each iteration k = 1, . . . , K −1,
Optim SP sets B ←Bk−1 and x ←xk−1. Then Optim SP iteratively finds the
order constraint of greatest index i in Pk violated by x, updates B ←B ∪{i} and
finds a new x by solving P=(B). If no such index can be found then Optim SP sets
xk ←x and Bk ←B and terminates the iteration k. Optim SP can be formally
stated as Algorithm 1. David Wu et al. 8 Algorithm 1 Optim SP
1: Set B ←∅
2: Solve P=(B) and set x equal to the obtained optimal solution. 3: for k from 1 to K-1 do
4:
Set b ←True. 5:
repeat
6:
Find the greatest index 1 ≤i ≤k such that xi > xi+1. 7:
Set b ←False if such an index does not exist. 8:
if b=True then
9:
Set B ←B ∪{i}
10:
Solve P=(B) and update x. 11:
end if
12:
until b=False
13: end for
14: return x Algorithm 1 Optim SP 2: Solve P=(B) and set x equal to the obtained optimal solution. Algorithm 2 Ajustable binary search Algorithm 2 Ajustable binary search
1: function yopt ←A Search(FI(y), y, ¯y, a)
2:
ϵ ←0.1
3:
repeat
4:
ymid ←⌊(y + a ∗¯y)/(1 + a)⌋
5:
left cost ←FI(ymid −ϵ)
6:
right cost ←FI(ymid + ϵ)
7:
if left cost ≤right cost then
8:
¯y ←ymid
9:
a ←1
10:
else
11:
y ←ymid
12:
end if
13:
until y + 1 = ¯y
14:
yopt ←ymid
15:
return yopt
16: end function 3.2 Adjustable binary search for optimizing univariate convex functions F(x) 3.2 Adjustable binary search for optimizing univariate convex functions F(x) 3.2 Adjustable binary search for optimizing univariate convex functions F(x) Each step of Algorithm 1 requires the solution of a problem of univariate convex
function minimization over a given interval. To achieve this, we propose an ex-
tended binary search procedure called A Search, formally stated as Algorithm 2. A Search is an adjustable version of binary search which depends on the input
parameter a > 0. Thus, for given univariate convex function FI and an interval [y,
¯y] where I ⊂{1, . . . , K} and FI(y) = P
j∈I Fj(y), the function A Search returns: y
p
,
y
g
A Search is an adjustable version of binary search which depends on the input
parameter a > 0. Thus, for given univariate convex function FI and an interval [y,
¯y] where I ⊂{1, . . . , K} and FI(y) = P
j∈I Fj(y), the function A Search returns: yopt = argmin
y≤y≤¯y
y integer
FI(y). The adjustable binary search starts with a lower bound y and an upper bound
¯y. Until yopt is found, the algorithm computes the integer middle point ymid =
⌊(y+a ∗¯y)/(1 + a)⌋according to a parameter a, and computes objective values
left cost and right cost for the two neighbours at ymid-ϵ and ymid+ϵ, then it
updates either y or ¯y. Please note that the standard binary search procedure corresponds to the
choice of a = 1 in A Search. For this value of a, ymid is the middle of the interval Optimal deterministic and robust selection of electricity contracts 9 (y, ¯y). For a > 1, ymid is no longer the middle of the interval, and we refer to
this case as ‘asymmetric binary search’. The motivation behind the use of a > 1
stems from the observation that the computational effort O(N+
i (xi)) required to
compute the value of one (individual aggregated) component of the objective func-
tion as defined in (1) is strongly dependent on the value of the parameter xi. This
dependence is illustrated in Figure 3 on three typical examples of ECSP corre-
sponding to data sets D1 and D5, two of the data sets used in the computational
experiments discussed in Section 3 below. 3.2 Adjustable binary search for optimizing univariate convex functions F(x) More precisely, Figure 3(A) corresponds
to dataset D1 and i = 1; Figure 3(B) corresponds to data set D1 and i = 5; Figure
3(C) corresponds to data set D5 and i = 4. histogram (A)
histogram(B)
histogram (C)
N +
i (xi) for (A)
N +
i (xi) for (B)
N +
i (xi) for (C)
Fig. 3: Histograms and curves showing the dependence of N+
i (xi) on xi for three examples
which are part of the data sets D1 and D5 described in Section 5. g
(
)
N +
i (xi) for (A) N +
i (xi) for (B) N +
i (xi) for (A) Fig. 3: Histograms and curves showing the dependence of N+
i (xi) on xi for three examples
which are part of the data sets D1 and D5 described in Section 5. Note that when a > 1 does not allow anymore the binary search to continue
on the smaller subinterval on the right of ymid, we set the value of a to 1 (see
line 9 of Algorithm 2) and resume the last iterations with the standard symmetric
binary search. With this switch on the value of a, as our binary search scheme
performs at least as well as the symmetric binary search scheme on all iterations
except perhaps one, it can be checked that the number of iterations in A Search
is at most log2(¯y −y) + 1. 3.3 Solving P=(B) 3.3 Solving P=(B) To perform line 2 in Optim SP which consists in solving P=(∅), i.e. solving P0,
we call the A Search function for minimizing each Fi(x) for i = 1, . . . , K, i.e. xi
= A Search(Fi(x), ci, ¯ci, a). It easy to see that after execution of line 2, x is an
optimal solution of P=(B) with B = ∅. To perform line 2 in Optim SP which consists in solving P=(∅), i.e. solving P0,
we call the A Search function for minimizing each Fi(x) for i = 1, . . . , K, i.e. xi
= A Search(Fi(x), ci, ¯ci, a). It easy to see that after execution of line 2, x is an
optimal solution of P=(B) with B = ∅. We now explain the procedure corresponding to line 10 of Optim SP which
consists in solving P=(B) with B ̸= ∅. Let us suppose that we are in iteration
k (1 ≤k ≤K −1) and we are ready to execute line 10 after having added an 10 David Wu et al. index i to B in line 9. Let B′ = B \ {i}, i.e. the value of B before executing line
9. Let x′ be the optimal solution of P=(B′), i.e. the value of x before the line
10, we have then x′
i > x′
i+1. Let i and ¯i respectively denote the smallest and the
greatest indices of the block of consecutive indices in B which contains i. Let I =
{i, i + 1, . . . ,¯i,¯i + 1}. Line 10 is executed by just calling A Search(FI(x), x′
¯i, x′
i, a)
where FI(x) = P
j∈I Fj(x). This function call returns an integer value yopt and
the update of x (in line 10 of Algorithm 1) is done as follows: xj ←x′
j for j /∈I
and xj ←yopt for j ∈I. 3.4 Correctness of Optim SP Hence, by
Lemma 1, x is optimal for P. ⊓⊔ 3.4 Correctness of Optim SP A partition of the index set {1, 2, . . . , K} (of the variables) J = {J1, . . . , Jk} is
called a block partition if its elements are subsets (or blocks) of consecutive indices. Given an x ∈RK, x is conform to J if xi = xj for all i and j belonging to the
same block in J. The correctness of Optim SP is based on well-known results in
the literature. In particular, we quote here the following lemma (Lemma 2 in [2]
which uses results in [5]) appropriately restated to fit our context. Lemma 1 [2] If J = {J1, . . . , Jk} is a block partition of {1, 2, . . . , K} such that there
exists a x ∈RK conform to J which is also feasible for P then x is an optimal solution
for P. Then we can state: Theorem 1 The solution x output by Optim SP is optimal for P. Proof As we cannot find a greatest index 1 ≤i ≤K −1 such that xi > xi+1, x
is feasible for P. Let ¯B denote the last value of B after termination of Optim SP
then ¯B is the set of active constraints that x satisfies at equality. Let us build a
block partition J of {1, 2, . . . , K} from ¯B as follows: – For each of block of consecutive indices I in ¯B with i and ¯i as respectively the
smallest and the greatest indices in I, let us refer to {i, i + 1, . . . ,¯i,¯i + 1} as a
block in J. – For each of block of consecutive indices I in ¯B with i and ¯i as respectively the
smallest and the greatest indices in I, let us refer to {i, i + 1, . . . ,¯i,¯i + 1} as a
block in J. – For an index 1 ≤j ≤K, if neither j nor j −1 belongs to ¯B, then let us refer to {j} as a single block in J. It is then easy to see that x is a feasible solution of P conform to J. Hence, by
Lemma 1, x is optimal for P. ⊓⊔ It is then easy to see that x is a feasible solution of P conform to J. 3.5 Complexity of Optim SP Proposition 2 The worst-case time complexity of Optim SP is O(K2log(C)) pro-
vided that the evaluation of each Fi(x) at a specific point x can be done in O(1). Proof We can see that the worst case occurs when the set B in line 10 of Optim SP
contains successively 1, 2, . . . , K −1 elements and Optim SP calls K −1 times
A Search(FI(x), x′
¯i, x′
i, a) in line 10 with the sets I (as defined in Section 3.3)
containing successively 2, 3, . . . , K elements. Hence, the total number of times that
the functions Fi(x) (i = 1, . . . , k) are minimized in the executions of A Search Optimal deterministic and robust selection of electricity contracts 11 is K(K+1)
2
−1. We should also include the minimization of each Fi(x) in the K
calls of A Search for solving P0 at line 2 of Optim SP. Hence, overall there are
K(K+1)
2
−1 + K = K(K+3)
2
−1 minimizations of Fi(x) in the calls of A Search. In each minimization of Fi(x) by A Search, Fi(x) is evaluated at most log2(C) +
1 times as pointed out in Section 3.2. Hence, the number of evaluations of the
functions Fi(x) is O(K2 log(C)) in the worst case. ⊓⊔ 4 Optim SP for a robust version of the problem Now, if we consider input data as forecasted consumption, actual realisation of
electricity consumption can be anticipated to be different from the forecast. Indeed
the deviation from predicted consumption can create greater overpowering, the
consequence being to increase the electricity bill. In the sequel, we discuss a robust
version of the problem of optimal selection of electricity contract and show how it
can still be solved using Optim SP algorithm. 4.1 Modelling customer demand Customer demands are often represented as stochastic process based on influenc-
ing factors. Those influencing factors are often external condition (temperature,
climate...), physical characteristic of dwelling (type, age...), devices and occupants
(occupation and behaviour...), prices and subscriptions [3, 12, 21]. Works on light-
ning energy in large office building show that consumption can be accurately
simulated by considering occupant behaviour and seasonal variations, and can
be described using e.g. Poisson and Normal distribution [21]. The consumption
model is useful to predict consumption in the short-term (1 day), medium-term
(3 days), long-term (7 days) [19] and very long-term (1 year) [3]. Many works are
based on precise modelling of each device in household [10, 15, 17]. The authors
of [8] present an approach based on hidden Markov chains for the modelling and
statistical analysis of electric consumption curves. The ”Seasonal and Trend decomposition using Loess” (STL) method [7] de-
composes the consumption as: 4.2 Robust problem formulation We propose here to define a robust version of the problem using a concept of uncer-
tainty set similar to the one introduced in [4]. Following the latter, the uncertainty
set, corresponding to ν uncertain parameters µ1, . . . , µν, each taking bounded val-
ues between 0 and β, and having a very small probability of all simultaneously
taking their maximum value β, would typically be the polyhedron defined by the
inequalities 0 ≤µi ≤β and Pν
i=1 µi ≤Γβ, where Γβ is the so-called budget of
uncertainty. Increasing Γβ increases the range of possible scenarios against which
robustness is to be achieved, thus improving the robustness of the solutions ob-
tained but at the expense of increasing the solution cost. For each category i, let v = (v1, . . . , v|Ti|) be the variable vector of possible
deviations, where deviations typically are bounded as −bt ≤vt ≤bt. However, in
view of the max operator in the expression of the penalty cost, negative deviations
will not increase the objective function value. We consider that for a given category
i, all bt (t ∈Ti) are equal and we denote bi this common value. Finally, we consider
each deviation is bounded as 0 ≤vt ≤bi, where the value bi is chosen to be of the
same order of magnitude as the standard deviation σi (typically bi = r ∗σi with r
chosen between 2 and 3). In line with [4], denoting Bi the budget of uncertainty for category i, we al-
low a total deviation at most equal to Bi, thus the deviation v has to satisfy the
constraint: PTi
t=1 vt ≤Bi. As an indication about how to choose Bi, consider n re-
alisations of a random variable normally distributed with zero mean and standard
deviation σi. The sum of those n random realisations has a variance σ2 = nσ2
i , i.e. its standard deviation is σ = √nσi. In line with this remark, taking Vi to be an
integer value of the same order as √Ti, we define the uncertainty set Ui as: Ui = {v|0 ≤vt ≤bi, ∀t,
Ti
X
t=1
vt ≤Bi = Vibi}. For defining the robust version of the problem, the overpowering quantity for
period t is now δr
t (xi, vt) = max(0, (ct+vt)-xi), note that δr
t (xi, vt) = δt(xi −vt). raw data(t) = trend(t) + seasonal(t) + remainder(t). raw data(t) = trend(t) + seasonal(t) + remainder(t). The ’trend’ component corresponds to non-stationary long-term evolution of con-
sumption, the ’seasonal’ component corresponds to periodical evolution (e.g. pe-
riod = 1 week), and the remainder (or the residual) variation is what is left over
after fitting the model and will be viewed as a realisation of some random process. The ’trend’ component corresponds to non-stationary long-term evolution of con-
sumption, the ’seasonal’ component corresponds to periodical evolution (e.g. pe-
riod = 1 week), and the remainder (or the residual) variation is what is left over
after fitting the model and will be viewed as a realisation of some random process. In the following, consumption is viewed as a time series in which each sample
is collected every 10 minutes. For each category i, we apply the STL method to de-
compose the time series and the important parameter to characterize uncertainty
is taken to be the standard deviation σi of the remainder. Then for 10 minute pe-
riod t ∈{1, . . . , Ti} we will typically consider that consumption can deviate from
the trend + seasonal forecast by a value represented as an independent realisation
of the appropriate probability distribution. In Section 5 below, it will be assumed 12 David Wu et al. that the residuals are independent realizations of some known probabilistic dis-
tribution (typically a truncated normal distribution) with zero mean and known
standard deviation. 4.2 Robust problem formulation For given xi, the worst-case penalty cost for category i in the robust version of
the problem is obtained as the maximum value over the uncertainty set Ui of the
penalty cost function, which is defined as: Πr
i (xi) = max
v∈Ui
X
m
s X
t∈Ti,m
(δr
t (xi, vt))2. (5) (5) s
The objective function for the robust formulation is F r(x) = P
i F r
i (xi) =
P
i sixi + piΠr
i (xi) and the robust version of ECSP can be stated as: Pr : min F r(x)
s.t. xi ≤xi+1,
1 ≤i ≤K-1,
c ≤xi ≤
max
1≤i′≤K{ ¯
ci′ + bi′},
1 ≤i ≤K. Pr : min F r(x)
s.t. xi ≤xi+1,
1 ≤i ≤K-1,
c ≤xi ≤
max
1≤i′≤K{ ¯
ci′ + bi′},
1 ≤i ≤K. Pr : min F r(x) s.t. xi ≤xi+1, Optimal deterministic and robust selection of electricity contracts 13 We note that in the above formulation, the upper bound values on the variables
xi have been changed to take into account the possible increase of the maximum
value of consumption by bi for category i. Proposition 3 Each Πr
i (xi) is convex in xi. Proposition 3 Each Πr
i (xi) is convex in xi. Proof For any fixed v ∈Ui, we know from Proposition 1 that the function: X
m
s X
t∈Ti,m
(δr
t (xi, vt))2 X
m
s X
t∈Ti,m
(δr
t (xi, vt))2 is convex in xi. Now, since the maximum value in (5) is to be determined with
respect to the (finite) set of extreme points of Ui, Πr
i is recognized as the pointwise
maximum of a finite collection of functions, each of which is convex in xi. This
proves the claimed result. ⊓⊔ ⊓⊔ Corollary 1 Each F r
i is convex in xi, and hence Pr is a convex program. 4.3 Using Optim SP to solve the robust version of the problem Since it appears that the robust version of the optimum contract selection problem
has the same structure as the deterministic version, Optim SP algorithm turns out
to be readily applicable to the robust version of the optimum contract selection
problem. However in each call to A Search function, for a given category i and
a given value xi, whenever we have to evaluate the value F r
i (xi), we need now to
solve the sub-problem (5). Proposition 4 For a given xi, any optimal solution to the sub-problem (5) features
Vi components equal to bi, all the other components being 0. Proof For a category i, the objective of the sub-problem is to maximize a convex
function w.r.t. v, and it is a well-known fact that the maximum is reached at
an extreme point of the polyhedron representing the uncertainty set Ui. Now, we
just have to observe that, since Vi has been assumed to be an integer value, each
extreme point of the polyhedron Ui features exactly Vi non zero components equal
to their upper bound values bi. ⊓⊔ For the category i and given xi, according to proposition 4 the maximization
sub-problem (5) is solved when the Vi uncertain parameters that maximize the
objective function are found i.e. we need to find how to best dispatch those Vi
time slots over the months Mi. This optimum dispatch problem, (5) can be cast
into a Multiple-Choice Knapsack Problem (MCKP) with integer variables, which
according to [20] can be solved in worst-case time complexity O(N) (N = Vi ∗|Mi|
is the number of items). Let us explain how this MCKP is formulated. Let the variable zm,n = 1 if the algorithm assigns n ∈{0, . . . , Vi} deviations to
the month m ∈Mi, else zm,n = 0. Let T n
i,m denote the subset of t ∈Ti,m achieving
the n highest values of ct. Proposition 5 For a given category i and month m, if exactly n deviation parameters
vt, t ∈Ti,m, may take on their upper bound value bi, then the worst-case cost value for
month m is obtained when vt = bi, for all t ∈T n
i,m. 14 David Wu et al. Proof For a given category i and month m, the penalty cost function is maximized
by setting maximum deviations for period t with the highest nonzero δr
t values,
i.e. 4.3 Using Optim SP to solve the robust version of the problem exactly n deviation parameters may take on their upper bound value bi, then
the maximum cost value is obtained when vt = bi for all t ∈T n
i,m. ⊓⊔ According to proposition 5, when n parameters are set equal to their upper
bound bi the partial objective cost for month m is: γm,n =
s X
t∈T n
i,m
(δr
t (xi, bi))2 +
X
t∈Ti,m\T n
i,m
(δr
t (xi, 0))2. The MCKP to be solved in order to determine the worst-case cost is then: max
Mi
X
m=1
Vi
X
n=0
γm,n zm,n
s.t. Mi
X
m=1
Vi
X
n=0
n zm,n ≤Vi,
Vi
X
n=0
zm,n ≤1, ∀m,
zm,n ∈{0, 1}, ∀m∀n. MKCP:
max
Mi
X
m=1
Vi
X
n=0
γm,n zm,n
s.t. Mi
X
m=1
Vi
X
n=0
n zm,n ≤Vi,
Vi
X
n=0
zm,n ≤1, ∀m,
zm,n ∈{0, 1}, ∀m∀n. MKCP:
max
Mi
X
m=1
Vi
X
n=0
γm,n zm,n
s.t. Mi
X
m=1
Vi
X
n=0
n zm,n ≤Vi,
Vi
X
n=0
zm,n ≤1, ∀m,
zm,n ∈{0, 1}, ∀m∀n. MKCP: MKCP: zm,n ∈{0, 1}, ∀m∀n. Recall that Mi ⊆M and Vi is an integer value of the same order of magnitude
as √Ti (≤
√
T), thus for a given xi determining the optimal value of (5) takes
O(|M| ∗
√
T) worst-case time complexity. Therefore we can state: Proposition 6 The worst-case time complexity of Optim SP applied to the robust
version of the optimum contract selection problem is O(K2M
√
TlogC). 5.1 Experiments on the deterministic version of ECSP This section is devoted to a detailed computational study of the Optim SP algo-
rithm on a series of typical real instances of the ECSP problem. For each instance,
the evolution of CPU time as a function of the value chosen for the a parameter
is analyzed. The results obtained are also compared against those which would be
obtained by using the Scaling PAV algorithm on the same data. In our computational experiments, we consider 5 data sets referred to as D1 to D5. Each data set is defined by specifying the 52560 values of electricity consumption
of the customer under consideration, recorded in every 10-minute period along a
full year (2017). This set of values is decomposed into 5 subsets (time categories)
T1 to T5, and each Ti is in turn decomposed into several subsets (corresponding to
the relevant months during which consumption has been observed (these subsets
are denoted Ti,m for some m in M). Data set D1 corresponds to a big factory in
the food industry with subscribed power typically in the range 5000-7500 KW;
data set D2 corresponds to a company providing maintenance of transportation
equipment with subscribed power typically in the range 1500-2500 KW; data set Optimal deterministic and robust selection of electricity contracts 15 D1
D2
[c1, ..., cK]
[2269, 2056, 72, 1769, 1152]
[1430, 1242, 1189, 910, 358]
[ ¯c1, ..., ¯
cK]
[5536, 6732, 6667, 7539, 7189]
[2419, 2446, 2307, 1822, 1768]
x0
[5536, 6573, 6395, 6949, 6738]
[2419, 2425, 2254, 1730, 1691]
x∗
[5536, 6479, 6479, 6914, 6914]
[2317, 2317, 2317, 2317, 2317]
D3
D4
[c1, ..., cK]
[533, 284, 208, 183, 2]
[480, 193, 321, 375, 315]
[ ¯c1, ..., ¯
cK]
[1514, 1596, 1603, 1610, 1588]
[723, 737, 667, 722, 680]
x0
[1514, 1568, 1465, 1541, 1481]
[723, 736, 643, 700, 627]
x∗
[1514, 1526, 1526, 1533, 1533]
[711, 711, 711, 711, 711]
D5
[c1, ..., cK]
[735, 545, 664, 572, 665]
[ ¯c1, ..., ¯
cK]
[1302, 1464, 1818, 2292, 1594]
x0
[1302, 1449, 1238, 1716, 1449]
x∗
[1302, 1382, 1382, 1662, 1662]
Table 1: Main characteristics of the data sets D1, . . . , D5 Table 1: Main characteristics of the data sets D1, . . . 5.1 Experiments on the deterministic version of ECSP , D5 D3 corresponds to an industrial bakery with subscribed power typically in the
range 1000-1500 KW; D4 and D5 correspond to two big hotels with subscribed
power typically in the range 500-1500 KW. y
y
g
The main characteristics of each data set are shown in Table 1, namely: – for each time category, the minimum and maximum values of the ct values for
t ∈Ti ; – for each time category, the minimum and maximum values of the ct values for
t ∈Ti ; – for each time category i, the minimum value x0
i of Fi(xi), the component of
the objective function corresponding to time category i ; it is observed that in
all cases, the resulting 5 values do not meet the order constraints imposed in
ECSP; ;
– the five components x∗
1, . . . , x∗
5 of the optimum solution x∗to the ECSP
problem, which can be observed to satisfy the order constraints xi ≤xi+1
(i = 1, . . . , 4). Table 2 displays the computational results obtained with scaling PAV (first line
of the table labelled ’sPAV’) and Optim SP (in the following lines for values of
a ranging from 1 to 8) for the various instances corresponding to the data sets
D1 to D5. For each instance, the column labelled ‘#evalF’ provides the number
of calls to the A Search procedure; the column labelled ’Total N+’ provides the
the evaluation of the resulting total number of arithmetic operations as measured
using the N+
i (xi) values; the column labelled ‘cpu’ indicates the resulting total
cpu time (in milliseconds). All tests reported have been carried out using Python 3.6.8 on an environment
of 8-thread quad-core processor with 16 GB RAM and 2.8 GHz CPU running
Windows 10 (64 bits). (
)
The results shown in Table 2 suggest the following comments: The results shown in Table 2 suggest the following comments: – in all cases but D5, the Optim SP algorithm significantly outperforms Scal-
ing PAV in terms of CPU time for a chosen between 4 and 8, and the com-
parison remains favorable in the wider range 2 ≤a ≤8. For the data set D5,
conclusions are less clear, but one can observe that there are still two values of
a for which Optim SP outperforms Scaling PAV. (
)
– if, for each result shown in Table 2, one computes the ratio cpu/TotalN+, it
is observed that all values obtained typically range between 5e −4 and 7e −4,
which shows that cpu is, up to small fluctuations, proportional to TotalN+.
This confirms the relevance of our analysis based on the use of TotalN+ as a
measure of computational effort. Table 2: Computational results on the deterministic version of ECSP for the data sets D1, . . . ,
D5 5.1 Experiments on the deterministic version of ECSP – in most cases, it can be observed that there is a fairly wide range of values of a
for which Optim SP achieves improved efficiency as compared with one of the 16 David Wu et al. D1
D2
a
#evalF
Total N+
cpu
#evalF
Total N+
cpu
sPAV
130
113117
44
110
62766
28
1
192
103498
50
253
72739
34
2
174
39913
25
256
29724
15
3
172
18923
10
234
14463
8
4
167
11286
6
246
12082
8
5
166
7754
5
252
15993
9
6
183
5929
4
248
13183
8
7
168
4801
5
257
11984
7
8
169
4037
5
255
10989
7
D3
D4
a
#evalF
Total N+
cpu
#evalF
Total N+
cpu
sPAV
110
101162
38
90
93442
41
1
162
90373
44
199
77807
37
2
149
49375
24
171
34229
17
3
149
24729
11
169
18330
9
4
144
11882
6
164
9760
5
5
134
6426
4
162
6597
4
6
139
4248
3
159
22971
11
7
146
3434
3
160
20586
11
8
147
2977
2
174
19567
11
D5
a
#evalF
Total N+
cpu
sPAV
110
15022
7
1
167
23838
12
2
162
24938
12
3
155
14982
8
4
161
11746
6
5
157
9481
5
6
160
24505
13
7
167
22706
12
8
167
21914
11
Table 2: Computational results on the deterministic version of ECSP for the data sets D1, . . . ,
D5 best previously known algorithms for solving problems of minimizing a convex
separable function under order constraints. This shows that Optim SP features
a good deal of robustness with respect to the a parameter, and that the choice
of a particular value for the parameter a is not a critical issue: a practical
consequence of this is that a good value for a will be easily obtained on an
experimental basis, by observing the behavior of the Optim SP algorithm on
a sample of a few typical instances of the problem for a few values of a in the
range (2, 8). best previously known algorithms for solving problems of minimizing a convex
separable function under order constraints. 5.2.1 Analysis of uncertainties through STL decomposition 5.2.1 Analysis of uncertainties through STL decomposition Information on categories and values of the standard deviation (σi) of remainder
obtained by applying STL decomposition to the data set D1 are shown in table
3 (similar results would be observed for the other data sets). For example, the
winter peak hours cover three months from December to February and Ti = 1488
10-minute periods, and the standard deviation of remainder is σi = 116. Statistical tests on remainders reveal that they are uncorrelated, have zero
means and are normally distributed, then by considering a truncated normal dis-
tribution between −3σi and 3σi will give correct representation of deviation of the
consumption. In our experiments, the robust parameter bi is chosen to be 3 ∗σi
(r = 3), and we will use parameter corresponds to Bi = Vi ∗bi (with Vi = ⌊q∗√Ti⌋)
for different values of q ∈[0, 0.2, 0.5, 1]. Notice that for q = 0 the deterministic ver-
sion of the problem is obtained. For the summer off-peak hours, the different values
of q considered correspond to the values 0, 26, 65 and 130 for Vi. This section presents various computational experiments carried out on the robust
version of ECSP. This section presents various computational experiments carried out on the robust
version of ECSP. Optimal deterministic and robust selection of electricity contracts 17 Category
Months
ci
¯ci
Ti
⌊√Ti⌋
σi
Winter peak hours
Dec-Feb
2269
5536
1488
38
115
Winter full hours
Nov-Mar
2056
6732
8688
93
124
Winter off-peak hours
Nov-Mar
72
6667
11562
107
104
Summer full hours
Apr-Oct
1769
7539
13920
117
144
Summer off-peak hours
Apr-Oct
1152
7189
16902
130
134
Table 3: Information on remainder of STL decomposition applied the dataset D1 5.1 Experiments on the deterministic version of ECSP This shows that Optim SP features
a good deal of robustness with respect to the a parameter, and that the choice
of a particular value for the parameter a is not a critical issue: a practical
consequence of this is that a good value for a will be easily obtained on an
experimental basis, by observing the behavior of the Optim SP algorithm on
a sample of a few typical instances of the problem for a few values of a in the
range (2, 8). – if, for each result shown in Table 2, one computes the ratio cpu/TotalN+, it
is observed that all values obtained typically range between 5e −4 and 7e −4,
which shows that cpu is, up to small fluctuations, proportional to TotalN+. This confirms the relevance of our analysis based on the use of TotalN+ as a
measure of computational effort. Optimal deterministic and robust selection of electricity contracts 5.2.2 Numerical results concerning the robust version for the data set D1 Table 4 provides comparative information about the costs of various optimal or
sub-optimal solutions to both the deterministic version (q = 0) and the robust
version (q > 0) of ECSP for data set D1. Table 4 decomposes into three parts: – the first part of the table concerns the contract currently used by the company
(a big factory in the food industry), the corresponding solution (6200, 7000,
7000, 7300, 7300), is called the reference solution; the deterministic cost of this
reference solution, as well as its costs in terms of the robust objective function
for q = 0.2, 0.5, 1 are provided. – the first part of the table concerns the contract currently used by the company
(a big factory in the food industry), the corresponding solution (6200, 7000,
7000, 7300, 7300), is called the reference solution; the deterministic cost of this
reference solution, as well as its costs in terms of the robust objective function
for q = 0.2, 0.5, 1 are provided. – the second part concerns the optimal solutions to the deterministic ECSP (for
q = 0) and the robust versions of ECSP (for q = 0.2, 0.5, 1); p
p
(a) the deterministic cost 111296 of the optimal robust solution obtained for
q = 0.5 and q = 1, namely: (5881, 6837, 6837, 7341, 7341);
(b) for q = 0.2, 0.5, 1, the robust objective function values of the optimal
d t
i i ti
l ti
(5536 6479 6479 6914 6914) (a) the deterministic cost 111296 of the optimal robust solution obtained for
q = 0.5 and q = 1, namely: (5881, 6837, 6837, 7341, 7341); (b) for q = 0.2, 0.5, 1, the robust objective function values of the optimal
deterministic solution (5536, 6479, 6479, 6914, 6914). The results in Table 4 suggest the following comments: 18 David Wu et al. 5.2.2 Numerical results concerning the robust version for the data set D1 (iv) the cpu times required for solving the robust versions of ECSP are about
100 times more than for solving the deterministic version, however they
typically do not exceed two or three seconds, which is quite acceptable
from the point of view of practical applicability. (iv) the cpu times required for solving the robust versions of ECSP are about
100 times more than for solving the deterministic version, however they
typically do not exceed two or three seconds, which is quite acceptable
from the point of view of practical applicability. To conclude, let us point out that, in spite of the fact that the results in Table
4 only concern the instance D1, quite similar conclusions would be obtained by
analyzing the other data sets D2, . . . , D5. 5.2.2 Numerical results concerning the robust version for the data set D1 q
Subscribed Power (SP)
Cost
cpu
0
6200, 7000, 7000, 7300, 7300
112275
0.2
6200, 7000, 7000, 7300, 7300
114274
0.5
6200, 7000, 7000, 7300, 7300
114315
1
6200, 7000, 7000, 7300, 7300
114315
0
5536, 6479, 6479, 7316, 7316
107576
25
0.2
5881, 6837, 6837, 7287, 7287
113750
2235
0.5
5881, 6837, 6837, 7341, 7341
113771
2404
1
5881, 6837, 6837, 7341, 7341
113771
2755
0
5881, 6837, 6837, 7341, 7341
111296
0.2
5536, 6479, 6479, 6914, 6914
118212
0.5
5536, 6479, 6479, 6914, 6914
121448
1
5536, 6479, 6479, 6914, 6914
123161
Table 4: Comparing the costs of various solutions to the deterministic and robust versions of
ECSP for data set D1 Table 4: Comparing the costs of various solutions to the deterministic and robust versions of
ECSP for data set D1 (i) the comparison of the costs of the optimal solutions (part 2 of the table)
with the costs of the reference solution shows that the latter is suboptimal
in all cases: the difference is 4.2% for q = 0, 0.4% for q=0.2, and 0.5% for
q = 0.5 and q = 1. It is thus observed that the reference solution turns out
to be a fairly good approximation (to within 0.5% or so) of the optimal
robust solutions for all the (strictly positive) values of q considered. (
)
(ii) the comparison between the last three lines of part 2 and the last three
lines of part 3 shows the benefit provided by the optimal robust solution
over the optimal deterministic solution in the presence of uncertainty: when
q = 0.2, the optimal robust function value is 113750, whereas the robust
objective function value for the optimal deterministic solution is 118212,
showing that the former leads to an improvement in cos 3.8% over the
latter. The same comparison for q = 0.5 and q = 1 would lead to 6.3% and
7.6% improvement respectively. (iii) The comparison between the first line of part 2 of the table and the first
line of part 3 shows that the difference between the deterministic objective
function value of the optimal robust solution for q = 0.5 and q = 1, and the
optimal deterministic solution value (111296-107576= 3720) represents an
increase by 3.3%. This value can be interpreted as the price of robustness. 5.2.3 Computational efficiency of Optim SP on the Robust ECSP In addition to the results discussed in Section 5.2.2, we provide in Table 5 results
showing the computational efficiency of Optim SP applied to the robust version
of ECSP, in a form similar to Table 2. In these experiments, the value q = 0.5 has
been taken. The main comments suggested by the results shown in Table 5 are the
following: Optimal deterministic and robust selection of electricity contracts 19 – since the computational effort required to calculate the value of each component
of the objective function of the robust problem is significantly bigger than for
the deterministic case, it is all but surprising to observe significantly increased
cpu values. On average, they can be seen to be multiplied by a factor in the
range 50-100. – since the computational effort required to calculate the value of each component
of the objective function of the robust problem is significantly bigger than for
the deterministic case, it is all but surprising to observe significantly increased
cpu values. On average, they can be seen to be multiplied by a factor in the
range 50-100. – since the computational effort required to calculate the value of each component
of the objective function of the robust problem is significantly bigger than for
the deterministic case, it is all but surprising to observe significantly increased
cpu values. On average, they can be seen to be multiplied by a factor in the
range 50-100. – concerning the influence of varying the value of the a parameter in the range a =
1 to a = 8, a behavior similar to the one observed for the deterministic case can
be noticed: for all instances (except D5) Optim SP outperforms Scaling PAV
for a wide range of values for a. – the relationship between cpu and the Total N+ measure of computational ef-
fort, which was almost linear in the deterministic case, is more intricate in the
case of the robust ECSP; this is mainly due to the significant overhead induced
by the need of repeatedly solving the MCKP discussed in Section 4.3. Table 5: Computational results on the robust version of ECSP (q = 0.5) for the data sets D1,
. . . , D5. Acknowledgements This work was supported by Energisme SAS in supplying data and
validating the experiments. 6 Conclusion and future works This paper proposes an efficient polynomial-time algorithm based on an active
constraint set approach for the electricity contract selection problem (ECSP). This
problem is formulated as minimizing a convex separable function subject to total
order constraints. The computational results obtained show that the algorithm
features improved CPU time as compared with Scaling PAV [2], one of the best
existing methods for this problem. The robust version of the problem has also been investigated. The construction
of an uncertainty set representing realistic scenarios of deviation between realized
consumption and forecasted values has been proposed, based on the so-called Sea-
sonal and Trend decomposition method (STL). It has been shown that the robust
version of ECSP can be efficiently solved using the same algorithm as for the
deterministic version. However, taking uncertainty into account requires comput-
ing worst-case values of the objective function. The latter problem is reduced to
solving a multiple-choice knapsack problem, which is polynomially solvable. An interesting direction for future research will be to generalize the approach
of robustness. In the present paper, it has been assumed that each consumption
of a given category i can only deviate by a value bi which is the same for all the
time periods in the category. The next step is to have more detailed evaluation of
the σ values within each category, the standard deviation may be different from
one month to the next (e.g. the consumption of summer off-peak hours in June
may be quite different than the one in September). Another interesting subject
for future investigation would be to use more accurate stochastic models, possi-
bly capturing statistical dependence from one time instant to the next to better
represent uncertainties. 5.2.3 Computational efficiency of Optim SP on the Robust ECSP D1
D2
a
#evalF
Total N+
cpu
#evalF
Total N+
cpu
sPAV
130
5733875
3815
110
2781354
2363
1
198
4786268
4058
213
3537792
3271
2
173
1398527
2046
183
1067315
1803
3
181
490332
1534
180
461635
1578
4
173
223949
1401
176
302938
1406
5
170
130601
1254
176
178908
1362
6
182
82507
1327
196
324828
1559
7
175
55507
1267
185
274221
1457
8
172
50018
1255
183
243549
1472
D3
D4
a
#evalF
Total N+
cpu
#evalF
Total N+
cpu
sPAV
110
4399366
3024
100
3949268
2834
1
163
4121953
3512
201
3074664
2971
2
148
1900657
2237
184
949165
1832
3
152
570448
1413
174
295506
1387
4
151
202383
1282
174
129488
1325
5
143
106005
1099
172
76850
1279
6
144
64673
1076
175
56555
1290
7
139
45094
1036
177
916144
1747
8
145
39596
1065
185
864616
1757
D5
a
#evalF
Total N+
cpu
sPAV
110
539235
1115
1
171
825202
1695
2
160
171727
1273
3
156
643125
1472
4
156
432818
1388
5
161
355929
1398
6
166
1192940
1930
7
163
1078631
1810
8
167
997721
1773
Table 5: Computational results on the robust version of ECSP (q = 0.5) for the data sets D1,
. . . , D5. David Wu et al. 20 References 1. Ahuja, R.K., Hochbaum, D.S., Orlin, J.B.: Solving the Convex Cost Integer
Dual Network Flow Problem. Management Science 49(7), 950–964 (2003) 2. Ahuja, R.K., Orlin, J.B.: A Fast Scaling Algorithm for Minimizing Separable
Convex Functions Subject to Chain Constraints. Operations Research 49(5),
784–789 (2001) 3. Barbier, T.: Mod´elisation de la consommation ´electrique `a partir de grandes
masses de donn´ees pour la simulation des alternatives ´energ´etiques du futur. Ph.D. thesis, Universit´e de recherche Paris Sciences et Lettres PSL Research
University (2017) 4. Bertsimas, D., Sim, M.: The Price of Robustness. Operations Research 52(1),
35–53 (2004) 5. Best, M., Chakravarti, N., Ubhaya, V.: Minimizing separable convex functions
subject to simple chain constraints. SIAM Journal on Optimization 10, 658–
672 (2000) Optimal deterministic and robust selection of electricity contracts 21 6. Chen, C.Y., Liao, C.J.: A linear programming approach to the electricity con-
tract capacity problem. Applied Mathematical Modelling 35(8), 4077–4082
(2011) (
)
7. Cleveland, R.B., Cleveland, W.S., McRae, J.E., Terpenning, I.: STL: a
seasonal-trend decomposition. Journal of official statistics 6(1), 3–73 (1990) 8. Durand, J.B., Bozzi, L., Celeux, G., Derquenne, C.: Analyse de courbes de
consommation ´electrique par chaines de Markov cach´ees. Revue de statistique
appliqu´ee 52(4), 71–91 (2003) 9. Hochbaum, D.S.: Complexity and algorithms for convex network optimization
and other nonlinear problems. 4OR 3(3), 171–216 (2005) 10. Issi, F., Kaplan, O.: The Determination of Load Profiles and Power Consump-
tions of Home Appliances. Energies 11(3), 607 (2018) 11. Karzanov, A.V., McCormick, S.T.: Polynomial Methods for Separable Convex
Optimization in Unimodular Linear Spaces with Applications. SIAM Journal
on Computing 26(4), 1245–1275 (1997) ( )
(
)
12. Kavousian, A., Rajagopal, R., Fischer, M.: Determinants of residential elec-
tricity consumption: Using smart meter data to examine the effect of climate,
building characteristics, appliance stock, and occupants’ behavior. Energy 55,
184–194 (2013) 13. Minoux, M.: A polynomial algorithm for minimum quadratic cost flow prob-
lems. European Journal of Operational Research 18(3), 377–387 (1984) 14. Minoux, M.: Solving integer minimum cost flows with separable convex cost
objective polynomially. In: G. Gallo, C. Sandi (eds.) Netflow at Pisa, Math-
ematical Programming Studies, pp. 237–239. Springer, Berlin, Heidelberg
(1986) 15. Pipattanasomporn, M., Kuzlu, M., Rahman, S., Teklu, Y.: Load Profiles of
Selected Major Household Appliances and Their Demand Response Opportu-
nities. IEEE Transactions on Smart Grid 5(2), 742–750 (2014) 16. References Rodoplu, M., Arbaoui, T., Yalaoui, A.: Energy Contract Optimization for the
Single Item Lot Sizing Problem in a Flow-Shop Configuration and Multiple
Energy Sources. IFAC-PapersOnLine 51(11), 1089–1094 (2018) 17. Salerno, V., Rabbeni, G.: An Extreme Learning Machine Approach to Effective
Energy Disaggregation. Electronics 7(10), 235 (2018) 18. Sæle, H., Bremdal, B.A., Engan, T.T., Kristoffersen, V., Foosnæs, J.A.,
Nordal, T.E., Sletner, J.M.: Subscribed power–testing new power based net-
work tariffs stimulating for demand response. CIRED 2015, Paper 1085 (2015) 19. Tatsa, S.: Mod´elisation et pr´evision de la consommation horaire d’´electricit´e
au Qu´ebec: Comparaison de m´ethodes de s´eries temporelles. Master’s thesis,
Universit´e Laval (2014) (
)
20. Zemel, E.: An O(n) Algorithm for the Linear Multiple Choice Knapsack Prob-
lem and Related Problems. Inf. Process. Lett. 18(3), 123–128 (1984) 21. Zhou, X., Yan, D., Hong, T., Ren, X.: Data analysis and stochastic modeling
of lighting energy use in large office buildings in China. Energy and Buildings
86, 275–287 (2015) David Wu et al. 22 Appendix We state in this appendix the reformulation of P as a separable convex cost net-
work flow problem. The graph to be considered contains K nodes numbered 1, 2, . . . , K and a set
of 2K −1 arcs, decomposed into K ’primary arcs’ and K −1 ’secondary arcs’. – the set of primary arcs contains the K −1 arcs of the form (i, i + 1) for i =
1, . . . , K −1, together with a ’return arc’ (K, 1). The flow value xi on each of
these arcs (including xK for the return arc) has to meet the bound constraints
0 ≤xi ≤C (and 0 ≤xK ≤C) and the corresponding cost function is Fi (FK
for the return arc); these arcs (including xK for the return arc) has to meet the bound constraints
0 ≤xi ≤C (and 0 ≤xK ≤C) and the corresponding cost function is Fi (FK
for the return arc); – the set of secondary arcs is composed of K −1 arcs of the form (1, j) for
j = 2, . . . , K. The flow value sj on each of these arcs has to meet the bound
constraints 0 ≤sj ≤C, and the associated cost function is identically 0. Problem P then reduces to determining a minimum cost circulation on the above
graph. We observe that the flow values sj on the secondary arcs play the role of
slack variables for the constraints xj−1 ≤xj for j = 2, . . . , K.
|
https://openalex.org/W4308737042
|
https://www.nature.com/articles/s41598-022-22354-2.pdf
|
English
| null |
Volatile compounds of Bacillus pseudomycoides induce growth and drought tolerance in wheat (Triticum aestivum L.)
|
Scientific reports
| 2,022
|
cc-by
| 12,651
|
Volatile compounds of Bacillus
pseudomycoides induce growth
and drought tolerance in wheat
(Triticum aestivum L.)
OPEN 7Department of Biological Scienc
School of Science, Osaka University, Machikaneyama‑Cho 1‑1, Toyonaka, Osaka 560‑0043, Ja
malakhan_07@yahoo.com; saleh@ru.ac.bd Gobindo Kumar Paul1,4, Shafi Mahmud2, Amit Kumar Dutta3, Swagotom Sarkar4,
Aysha Akter Laboni4, Md. Shamim Hossain5, Abir Nagata6, Pranab Karmaker4,
Mamudul Hasan Razu4, Taheruzzaman Kazi6, Md. Salah Uddin1, Shahriar Zaman1,
Md Sayeedul Islam7, Mala Khan4* & Md. Abu Saleh1* The plant growth-boosting biofilm-forming bacteria Bacillus pseudomycoides is able to promote
growth and drought stress tolerance in wheat by suppressing the MYB gene, which synthesizes Myb
protein (TaMpc1-D4) through secreted volatile compounds. In the present study, Triticum aestivum
seeds were inoculated with five distinct bacterial strains. The growth, germination rate, root-shoot
length, RWC, and chlorophyll content of seedlings were investigated. Furthermore, the levels of
soluble sugars, proteins, H2O2, NO, cell death, and antioxidant enzymes (CAT, SOD, POD, and APX)
were observed throughout the growth stage. All of the results showed that B. pseudomycoides had a
substantially higher ability to form biofilm and promote these traits than the other strains. In terms
of molecular gene expression, B. pseudomycoides inoculation strongly expressed the Dreb1 gene
by silencing the expression of MYB gene through secreted volatile compounds. For identifying the
specific volatile compound that silenced the MYB gene, molecular docking with Myb protein was
performed. Out of 45 volatile compounds found, 2,6-ditert-butylcyclohexa-2,5-diene-1,4-dione and
3,5-ditert-butylphenol had a binding free energy of − 6.2 and − 6.5, Kcal/mol, respectively, which
predicted that these compounds could suppress this protein’s expression. In molecular dynamics
simulations, the RMSD, SASA, Rg, RMSF, and hydrogen bonding values found assured the docked
complexes’ binding stability. These findings suggest that these targeted compounds may be
suppressing Myb protein expression as well as the expression of Dreb1 and other drought response
genes in wheat. More research (field trial) into plant growth and drought stress is needed to support
the findings of this study. Abbreviations
RWC
Relative water content
H2O2
Hydrogen peroxide
NO
Nitric oxide
CAT
Catalase
SOD
Superoxide dismutase
POD
Peroxidases
APX
Ascorbate peroxidase
RMSD
Root-mean-square deviation 1Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi,
Rajshahi 6205, Bangladesh. 2Division of Genome Sciences and Cancer, The John Curtin School of Medical Research,
and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, ACT 2601,
Australia. 3Department of Microbiology, University of Rajshahi, Rajshahi 6205, Bangladesh. 4Bangladesh Reference
Institute for Chemical Measurements (BRiCM), Dhaka, Bangladesh. www.nature.com/scientificreports www.nature.com/scientificreports (2022) 12:19137
| https://doi.org/10.1038/s41598-022-22354-2
Volatile compounds o
pseudomycoides indu
and drought toleranc
(Triticum aestivum L. Gobindo Kumar Paul1,4, Shafi Mahmud2, Amit Kumar D
Aysha Akter Laboni4, Md. Shamim Hossain5, Abir Naga
Mamudul Hasan Razu4, Taheruzzaman Kazi6, Md. Sala
Md Sayeedul Islam7, Mala Khan4* & Md. Abu Saleh1*
The plant growth-boosting biofilm-forming bacteria Bacillus
growth and drought stress tolerance in wheat by suppressin
protein (TaMpc1-D4) through secreted volatile compounds. seeds were inoculated with five distinct bacterial strains. Th
length, RWC, and chlorophyll content of seedlings were inve
soluble sugars, proteins, H2O2, NO, cell death, and antioxid
were observed throughout the growth stage. All of the resu
substantially higher ability to form biofilm and promote the
of molecular gene expression, B. pseudomycoides inoculatio
by silencing the expression of MYB gene through secreted v
specific volatile compound that silenced the MYB gene, mol
performed. Out of 45 volatile compounds found, 2,6-ditert-b
3,5-ditert-butylphenol had a binding free energy of − 6.2 and
predicted that these compounds could suppress this protein
simulations, the RMSD, SASA, Rg, RMSF, and hydrogen bon
complexes’ binding stability. These findings suggest that th
suppressing Myb protein expression as well as the expressio
genes in wheat. More research (field trial) into plant growth
the findings of this study. Abbreviations
RWC
Relative water content
H2O2
Hydrogen peroxide
NO
Nitric oxide
CAT
Catalase
SOD
Superoxide dismutase
POD
Peroxidases
APX
Ascorbate peroxidase
RMSD
Root-mean-square deviation
OPEN
1Microbiology Laboratory, Department of Genetic Engineering
Rajshahi 6205, Bangladesh. 2Division of Genome Sciences and Can
and The Shine-Dalgarno Centre for RNA Innovation, The Austra
Australia. 3Department of Microbiology, University of Rajshahi, Raj
Institute for Chemical Measurements (BRiCM), Dhaka, Banglades
Engineering, Islamic University, Kushtia 7003, Bangladesh. 6Depa
School of Medicine, Osaka University, Suita 565‑0871, Japan. School of Science, Osaka University, Machikaneyama‑Cho 1‑1
malakhan_07@yahoo.com; saleh@ru.ac.bd Volatile compounds of Bacillus
pseudomycoides induce growth
and drought tolerance in wheat
(Triticum aestivum L.)
OPEN 2022) 12:19137
| https://doi.org/10.1038/s41598-022-22354-2
Volatile compounds of Bacillus
pseudomycoides induce growth
and drought tolerance in wheat
(Triticum aestivum L.)
Gobindo Kumar Paul1,4, Shafi Mahmud2, Amit Kumar Dutta3, Swagotom Sarkar4,
Aysha Akter Laboni4, Md. Shamim Hossain5, Abir Nagata6, Pranab Karmaker4,
Mamudul Hasan Razu4, Taheruzzaman Kazi6, Md. Salah Uddin1, Shahriar Zaman1,
Md Sayeedul Islam7, Mala Khan4* & Md. Abu Saleh1*
The plant growth-boosting biofilm-forming bacteria Bacillus pseudomycoides is able to pro
growth and drought stress tolerance in wheat by suppressing the MYB gene, which synthe
protein (TaMpc1-D4) through secreted volatile compounds. In the present study, Triticum a
seeds were inoculated with five distinct bacterial strains. The growth, germination rate, ro
length, RWC, and chlorophyll content of seedlings were investigated. Furthermore, the lev
soluble sugars, proteins, H2O2, NO, cell death, and antioxidant enzymes (CAT, SOD, POD,
were observed throughout the growth stage. All of the results showed that B. pseudomyco
substantially higher ability to form biofilm and promote these traits than the other strains
of molecular gene expression, B. pseudomycoides inoculation strongly expressed the Dreb1
by silencing the expression of MYB gene through secreted volatile compounds. For identify
specific volatile compound that silenced the MYB gene, molecular docking with Myb prote
performed. Out of 45 volatile compounds found, 2,6-ditert-butylcyclohexa-2,5-diene-1,4-d
3,5-ditert-butylphenol had a binding free energy of − 6.2 and − 6.5, Kcal/mol, respectively, w
predicted that these compounds could suppress this protein’s expression. In molecular dyn
simulations, the RMSD, SASA, Rg, RMSF, and hydrogen bonding values found assured the
complexes’ binding stability. These findings suggest that these targeted compounds may b
suppressing Myb protein expression as well as the expression of Dreb1 and other drought r
genes in wheat. More research (field trial) into plant growth and drought stress is needed t
the findings of this study. Abbreviations
RWC
Relative water content
H2O2
Hydrogen peroxide
NO
Nitric oxide
CAT
Catalase
SOD
Superoxide dismutase
POD
Peroxidases
APX
Ascorbate peroxidase
RMSD
Root-mean-square deviation
EN
1Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University
Rajshahi 6205, Bangladesh. 2Division of Genome Sciences and Cancer, The John Curtin School of Med
and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberr
Australia. 3Department of Microbiology, University of Rajshahi, Rajshahi 6205, Bangladesh. 4Banglade
Institute for Chemical Measurements (BRiCM), Dhaka, Bangladesh. 5Department of Biotechnology
Engineering, Islamic University, Kushtia 7003, Bangladesh. 6Department of Regenerative Dermatolo
School of Medicine, Osaka University, Suita 565‑0871, Japan. Volatile compounds of Bacillus
pseudomycoides induce growth
and drought tolerance in wheat
(Triticum aestivum L.)
OPEN 5Department of Biotechnology and Genetic
Engineering, Islamic University, Kushtia 7003, Bangladesh. 6Department of Regenerative Dermatology, Graduate
School of Medicine, Osaka University, Suita 565‑0871, Japan. 7Department of Biological Sciences, Graduate
School of Science, Osaka University, Machikaneyama‑Cho 1‑1, Toyonaka, Osaka 560‑0043, Japan. *email:
malakhan_07@yahoo.com; saleh@ru.ac.bd | https://doi.org/10.1038/s41598-022-22354-2 Scientific Reports | (2022) 12:19137 www.nature.com/scientificreports/ SASA
Solvent accessible surface area
Rg
Radius of gyration
RMSF
Root mean square fluctuation
ROS
Reactive oxygen species
PGPR
Plant-growth promoting rhizobacteria
VOCs
Volatile compounds
SEM
Scanning electron microscopy
GC–MS
Gas chromatography–mass spectrometry
IUPAC
International union of pure and applied chemistry
PEG
Polyethylene glycol
GR
Germination rate
GP
Germination potential
IG
Index of germination
LI
Length index
EDTA
Ethylenediamine tetraacetic acid
HbO2
Oxyhemoglobin
metHb
Methemoglobin
CBB
Coomassie brilliant blue
SPME
Solid phase microextraction
cDNA
Complementary DNA
RNA
Ribonucleic acid
RNase
Ribonuclease
PCR
Polymerase chain reaction
YASARA
Yet another scientific artificial reality application
NaCl
Sodium chloride
PME
Particle mesh Ewalds Triticum aestivum is the principal source of food for most of the world’s population including many American,
European, Australian, African, and some Asian countries1,2. It is the main component of foods such as bread,
biscuits, pasta, noodles, cakes, pizza, beer, and vodka, and contains carbohydrates (71%), protein (13%), water
(13%), fat (1.5%), and small amounts of phosphorus, niacin, and dietary fiber1,3. It is estimated that the world
population will exceed 8 billion in 2030, and ensuring food security for such a large population will be a major
issue for the agricultural sector due to water scarcity4. Future drought mitigation gains are critical if food demand
for the vast population is to be met5. Drought intensity is growing as a result of climate change and rising tem-
peratures around the world, causing agricultural crops to suffer6. In Bangladesh, for instance, most of the farmers
in the 13,000 sq. km Barind Tract land in the Districts of Rajshahi, Dinajpur, and Bogura face water scarcity.il q
j
jp
g
y
Some beneficial microorganisms influence plant metabolism to help plants survive from abiotic stress con-
ditions such as drought and salt stress7. Bacterial species in genera such as Bacillus, Enterobacter, Azospirillum,
Klebsiella, Pseudomonas, Arthobacter, and Serratia, among others, enrich growth by directly or indirectly sup-
plying nutrients8–10, while secretion of indole acetic acid and cytokinin-like phytohormones promotes root
area and surface proliferation11. Apart from this, cytokinins are also involved in the management of environ-
mental stresses by transfer signaling from root to shoot12. Volatile compounds of Bacillus
pseudomycoides induce growth
and drought tolerance in wheat
(Triticum aestivum L.)
OPEN Drought causes the production of reactive oxygen
species (ROS), which can harm numerous plant structures13, such as proteins and lipids, and cause nucleic acid
breakdown14. Plant cells include many antioxidant enzymes such as APX (ascorbate peroxidase), CAT (catalase),
SOD (superoxide dismutase), POD (peroxides), and GPX (glutathione peroxidase), which reduce free radical
H2O2 and superoxide O-
2 production during drought conditions and improve plant survival15,16. Under extreme
drought conditions, Plant-Growth Promoting Rhizobacteria (PGPR) improved an antioxidant CAT, implying
that it can reduce oxidative damage17.i g
Researchers have recently reported that bacterial biofilm formation on root hairs under drought conditions
may have a substantial positive impact on plants during high levels of drought stress18–20. Therefore, we chose five
bacterial strains (Bacillus pseudomycoides, Bacillus massilioanrexius, Bacillus thuringiensis, Serratia marcescens,
and Acinetobacter sp.), although only B. pseudomycoides has been shown to have potentially to produce biofilms
in dry conditions. Volatile compounds (VOCs) are organic molecules released by bacteria that mediate increased
biomass in plant roots, disease resistance, and abiotic stress tolerance19 and do not include any known plant
growth hormones20,21, but they do mediate plant endogenous auxin homeostasis and iron uptake20,22. g
y
p
g
p
Previous studies have found that over expression of the R2R3 MYB gene reduces drought tolerance and
has detrimental consequences in wheat under drought stress23. As a result, silencing of this gene may result in
increased drought tolerance. Molecular docking is a powerful method for identifying putative inhibitors based
on protein–ligand interactions, with molecular simulation used to validate the binding poses and orientations. To identify the best binding compounds regarding targeted protein active regions, homology modeling of myb
protein and volatile compounds were used for molecular docking. This technique is both cost- and time-effective
for understanding the relationship between proteins and ligands24,25. Many researchers are attempting to develop drought-tolerant wheat varieties that are both low-cost and
ecofriendly in response to global climate concerns26. The current study aimed to find environmentally friendly
bacterial strains that can form biofilms that aid in plant growth promotion. By possibly silencing the R2R3 MYB
gene and increasing the expression of Dreb1 genes in wheat, specific volatile compounds that might help with
drought stress tolerance could be identified. Scientific Reports | (2022) 12:19137 | https://doi.org/10.1038/s41598-022-22354-2 www.nature.com/scientificreports/ w.nature.com/scientificreports/
Figure 1. Germination parameters of wheat with five different bacterial inoculations. Results
M
h Morpho‑physiological characteristics. The Bp treatment had a germination rate of 88.8%, while Bm
had an 82.22% germination rate, Sm had a 74.44% germination rate, As had a 75.55% germination rate, Bt had a
71.11% germination rate, and the Control group a 71.11% germination rate (Fig. 1a and Fig. S1). Bp inoculation
demonstrated a higher germination rate when compared to other inoculations and controls. This inoculation
also considerably boosted germination potential (Fig. 1b), germination index (Fig. 1c), and vigor index (Fig. 1d). When compared to wheat control, Bp had considerably increased relative water content (Fig. 2a), average root
and shoot length (Fig. 2b and Fig. S2), plant height (Fig. 2c), root and shoot dry weight (Fig. 2d). In the case
of Bp, the relative water content in root was 94.90% and the shoot was 87.01% (Fig. 2a) where the average
root length and plant heights were 10.60 cm and 12.12 cm, respectively, whereas the control was 8.55 cm and
10.09 cm, respectively, after 10 days of inoculation (Fig. 2b). For average root-shoot dry weight, Bp was 0.048 g
and 0.082 g (Fig. 2d). Biochemical changes. In the biochemical analysis, total soluble sugar and protein content in the Bp inoc-
ulation were moderately higher than control plants, although these were lower in other inoculations. Sugar
concentration rose significantly in the root, averaging 6.20 mg g−1 and 5.08 mg g−1, respectively, in both Bp and
Bm inoculation compared to 3.81 mg g-1 in the control (Fig. 3a). For the Bp inoculation, the protein levels in
the root and shoot were 2.17 mg g−1 and 15.77 mg g−1, respectively, whereas the controls were 1.78 mg g−1 and
10.02 mg g−1 (Fig. 3b). Protein concentrations in the shoot, on the other hand, did not vary significantly. Fur-
thermore, Bp inoculation resulted in higher NO and H2O2 concentrations than the other inoculations, with NO
concentrations of 5.67 mg g−1 for the Bp inoculation and 4.89 mg g−1 for the control (Fig. 3c) and H2O2 concen-
tration for the Bp inoculation of 20.63 mg g−1 where the control was 13.56 mg g−1 (Fig. 3d). Chlorophyll, Fe, Zn, and cell death measurement. All treatments had different chlorophyll concen-
trations (chlorophyll a and b) (i.e., Bp: 36.83 mg/g and control: 25.98 mg/g) (Fig. 4a). As a result, the Bp treat-
ment likely had a higher photosynthetic capacity than the other inoculations. Volatile compounds of Bacillus
pseudomycoides induce growth
and drought tolerance in wheat
(Triticum aestivum L.)
OPEN Here, (a); indicates
germination rate, (b); indicates germination potential, (c); indicates germination index, and (d); indicates vigor
index of seeds. Different letters indicate significant differences between mean ± SD of replications (n = 3) at a
P < 0.05 significance level. Figure 1. Germination parameters of wheat with five different bacterial inoculations. Here, (a); indicates
germination rate, (b); indicates germination potential, (c); indicates germination index, and (d); indicates vigor
i d
f
d Diff
l
i di
i
ifi
diff
b
SD f
li
i
(
3) Figure 1. Germination parameters of wheat with five different bacterial inoculations. Here, (a); indicates
germination rate, (b); indicates germination potential, (c); indicates germination index, and (d); indicates vigor
index of seeds. Different letters indicate significant differences between mean ± SD of replications (n = 3) at a
P < 0.05 significance level. Results
M
h In the seeds that were treated with
Bp, Fe and Zn concentrations were dramatically raised in both root and shoots (Fig. 4c,d), while in other stains,
both Fe and Zn concentrations were identical with control plants (Fig. 4c,d). The percentage of cells that died is
also shown in Fig. 4b. https://doi.org/10.1038/s41598-022-22354-2 Scientific Reports | (2022) 12:19137 | www.nature.com/scientificreports/ Figure 2. Morpho-physiological characteristics of wheat. Here, (a); indicates RWC content, (b); indicates
root and shoot length, (c); indicates plant height and, (d); indicates root and shoot dry weight. Different letters
indicate significant differences between mean ± SD of replications (n = 3) at a P < 0.05 significance level. Figure 2. Morpho-physiological characteristics of wheat. Here, (a); indicates RWC content, (b); indicates
root and shoot length, (c); indicates plant height and, (d); indicates root and shoot dry weight. Different letters
indicate significant differences between mean ± SD of replications (n = 3) at a P < 0.05 significance level. Antioxidant (APX, SOD, and CAT) analysis. Antioxidant activity was considerably higher in the Bp
treatment but was only modestly increased in the other inoculations over the control. The highest levels of APX,
SOD, and CAT activity were observed in the Bp inoculation (Fig. 5). As a result, this Bp inoculation had better
antioxidant properties than other inoculations and controls. Antioxidant (APX, SOD, and CAT) analysis. Antioxidant activity was considerably higher in the Bp
treatment but was only modestly increased in the other inoculations over the control. The highest levels of APX,
SOD, and CAT activity were observed in the Bp inoculation (Fig. 5). As a result, this Bp inoculation had better
antioxidant properties than other inoculations and controls. Screening of biofilm production. The formation of biofilms is demonstrated in Fig. 6. In SEM screening,
biofilm was formed in Bp inoculated plant’s root hairs, but not in the control, Bm, Sm, As, and Bt inoculation
plants’ root hairs. Bp can form biofilms on wheat root hairs in drought conditions, which could assist plant
survival. Identification of volatile compounds produced by B. pseudomycoides. For B. pseudomycoides, 45
volatile compounds were found in the GC–MS analysis. IUPAC name, PubChem CID, canolic smile, molecular
weight and formula, retention time, area and height, and the GC–MS chromatogram are shown in Table S3 and
Fig. 7. Observation of morphology and survival rate. Results
M
h In the pots, plant survival rates were 83.33%, 66.67%,
58.33%, and 16.67% for Bp, Bm, Bt, and Sm, respectively, however, neither the control nor As had any surviving
plants after 15 days (Fig. S4 and Table S1). In the case of PEG treatment, Bp inoculation demonstrated the high-
est survival rates, 83.33%, where control was only 5% and other inoculations were less than 40% respectively,
at 15% PEG treatment after artificially inducing drought; however other strains showed less drought tolerance
than Bp (Table S2). Molecular expression. The extracted RNA showed two strong bands of 28S and 18S ribosomal RNA in 1%
agarose gel and no significant RNA degradation was observed (Fig. S5). The Real-time PCR analysis showed that
MYB3R and Dreb1 gene expression was comparatively similar in control, Bp, and Bm inoculation at 0-h drought
induction. After 24 h post-induction, MYB3R gene expression was increased in the control and Bm inocula-
tion but decreased in Bp inoculation, where Dreb1 gene was decreased in both control and Bm inoculation but
increased in Bp inoculation (Fig. 8). The Dreb1 gene was expressed considerably more in the Bp inoculation https://doi.org/10.1038/s41598-022-22354-2 Scientific Reports | (2022) 12:19137 | ww.nature.com/scientificreports/
Figure 3. Biochemical characterization of wheat root and soot treated with five different bacterial strains. Here,
(a), (b), (c), and (d) are indicating total soluble sugar, total soluble protein, NO concentration, and total soluble
H2O2, respectively in both root and shoot. Different letters indicate significant differences between mean ± SD of
replications (n = 3) at a P < 0.05 significance level. www.nature.com/scientificreports/ Figure 3. Biochemical characterization of wheat root and soot treated with five different bacterial strains. Here,
(a), (b), (c), and (d) are indicating total soluble sugar, total soluble protein, NO concentration, and total soluble
H2O2, respectively in both root and shoot. Different letters indicate significant differences between mean ± SD of
replications (n = 3) at a P < 0.05 significance level. than in the control but decreased in the Bm inoculation. In the case of Bp inoculation, Dreb1 gene was up regu-
lated with the down-regulation of MYB3R gene. Homology modeling. Using Phyre2 tools, the MYB gene from T. aestivum was modeled and run for short
dynamics for energy minimization processes. The structural stability and stiffness of the complex were inves-
tigated using the root mean square deviations of the C-alpha atoms from simulation trajectories over time. Results
M
h Because of their flexibility, the complexes exhibited a greater initial RMSD, as seen in Fig. 9c. However, after
2 ns, the MYB protein from wheat reached a steady state, and a lower degree of deviations was observed until
the simulation’s final periods. Ramachandran Plot analysis and ERRAT were used to further analyze the latest
snapshots from the molecular dynamics simulations. The MYB protein from wheat had 85.55% residues in the
allowed regions, 11.8% residues in the additional allowed regions, and 2.6% residues in the prohibited regions,
as seen in Fig. 9a. A high-quality model structure is defined as a modeled protein with 90% of residues in the
acceptable regions in Ramachandran plot assessments. The quality of the homology-modeled structure was also
determined to be 98.113 (Fig. 9b) via ERRAT, where a good model structure has an ERRAT score of 80. Finally,
the structures were used to perform molecular docking and simulations on the docked complex, as described
below. Molecular docking study. Two volatile compounds from B. pseudomycoides were investigated in this study
based on their lower binding energies. These ligand molecules, 2,6-ditert-butylcyclohexa-2,5-diene-1,4-dione
and 3,5-ditert-butylphenol, exhibited a higher binding affinity than other compounds. The binding energies of
these compounds were −6.2 and −6.5 kcal/mol, respectively, indicating that 3,5-ditert-butylphenol and the MYB
protein complex had higher binding energies than other compounds. The cartoon view, 3D view, and the surface
view of these docking complexes are shown in Fig. 10a–f. Two hydrogen, two pi-alkyl, and one pi-sulfur bond
was observed at Thr116, Leu117, Tyr168, Ala115, and Tyr168, respectively, stabilizing the 2,6-ditert-butylcy-
clohexa-2,5-diene-1,4-dione and MYB protein complex (Table 1 and Fig. 10b). Two hydrogen, two pi-alkyl, and
one pi-sulfur bond was formed at Thr116, Leu117, Tyr168, Ala115, and Tyr168, respectively, in the 3,5-ditert-
butylphenol and MYB protein complex (Table 1 and Fig. 10e). https://doi.org/10.1038/s41598-022-22354-2 Scientific Reports | (2022) 12:19137 | www.nature.com/scientificreports/ ww.nature.com/scientificreports/
Figure 4. Chlorophyll, cell death, and Fe-Zn concentration of wheat plant treated with five different bacterial
strains. Here, (a) indicates chlorophyll content in leaves, (b), (c), and (d) indicate cell death percentage, Fe
concentration, Zn concentration, respectively, in both root and shoot. Different letters indicate significant
differences between mean ± SD of replications (n = 3) at a P < 0.05 significance level. Figure 4. Chlorophyll, cell death, and Fe-Zn concentration of wheat plant treated with five different bacterial
strains. Results
M
h Here, (a) indicates chlorophyll content in leaves, (b), (c), and (d) indicate cell death percentage, Fe
concentration, Zn concentration, respectively, in both root and shoot. Different letters indicate significant
differences between mean ± SD of replications (n = 3) at a P < 0.05 significance level. Molecular dynamics. The goal of the molecular dynamics simulation was to understand the stable profile
of docked complexes as well as the flexible behavior of ligand–protein systems. The 2,6-ditert-butylcyclohexa-
2,5-diene-1,4-dione, and 3,5-ditert-butylphenol complexes showed reduced degrees of fluctuations over the sim-
ulation trajectories and hence demonstrated a stable mode during the simulation duration, as shown in Figs. 11
and 12. Furthermore, the complexes did not exceed 2.5 during the simulated timeframes, indicating that they are
stable. Furthermore, the solvent-accessible surface area (SASA) of the simulated complexes was investigated to
better understand the changes in the protein surface area, with a larger SASA indicating surface extension and a
lower SASA indicating the truncated nature of the protein.h g
p
The lesser degree of the complexes’ packing systems may be due to increased deviations at the initial points of
the complexes with MYB and 2, 6-ditert-butylcyclohexa-2,5-diene-1,4-dione and 3,5-ditert-butylphenol, as seen
in Fig. 13. As a result, after 70 ns, the SASA profiles of 2,6-ditert-butylcyclohexa-2,5-diene-1,4-dione complexes
were reduced, probably due to the compacted shape of the ligand interaction with the protein systems. The
degree of flexibility of the complexes is related to the radius gyration profile, with larger Rg descriptor deviations
indicating a dynamic nature and lower Rg descriptor deviations indicating stable and stiff conformations. The
2, 6-ditert-butylcyclohexa-2, 5-diene-1,4-dione complexes showed changes at numerous sites between 50 and
60 ns, indicating that they are more mobile. The simulated systems’ hydrogen bond patterning remained steady
along the simulation trajectories, indicating that the complexes were stable. The root means square fluctuations
of the simulated complexes also characterize the variations in amino acid residues in the simulating circum-
stances. According to Fig. 13, the complexes’ maximal residues had a lower RMSF of less than 2.5, indicating
that they were stable. https://doi.org/10.1038/s41598-022-22354-2 Scientific Reports | (2022) 12:19137 | ww.nature.com/scientificreports/
Figure 5. Antioxidant activity of wheat root and shoot treated with five different bacterial strains. Here, (a), (b),
and (c) are indicating CAT, APX, and POD activity, respectively in both root and shoot. Results
M
h Different letters indicate
significant differences between mean ± SD of replications (n = 3) at a P < 0.05 significance level. www.nature.com/scientificreports/ Figure 5. Antioxidant activity of wheat root and shoot treated with five different bacterial strains. Here, (a), (b),
and (c) are indicating CAT, APX, and POD activity, respectively in both root and shoot. Different letters indicate
significant differences between mean ± SD of replications (n = 3) at a P < 0.05 significance level. re 5. Antioxidant activity of wheat root and shoot treated with five different bacterial strains. Here, (a), (b),
c) are indicating CAT, APX, and POD activity, respectively in both root and shoot. Different letters indicate
fi
d ff
b
S
f
l
(
)
fi
l
l Figure 5. Antioxidant activity of wheat root and shoot treated with five different bacterial strains. Here, (a), (b),
and (c) are indicating CAT, APX, and POD activity, respectively in both root and shoot. Different letters indicate
significant differences between mean ± SD of replications (n = 3) at a P < 0.05 significance level. Figure 6. Screening Electron Microscopic observations visualizing biofilm in wheat root hairs treated with five
different bacterial stains. Biofilms were observed after 15 days of drought stress induction. Here, (a), (b), (c), (d),
(e), and (f) indicate control, Bp, Bm, Sm, As, and Bt inoculations, respectively. Figure 6. Screening Electron Microscopic observations visualizing biofilm in wheat root hairs treated with five
different bacterial stains. Biofilms were observed after 15 days of drought stress induction. Here, (a), (b), (c), (d),
(e), and (f) indicate control, Bp, Bm, Sm, As, and Bt inoculations, respectively. Scientific Reports | (2022) 12:19137 | https://doi.org/10.1038/s41598-022-22354-2 www.nature.com/scientificreports/ Discussion
Global population expansions and global climate change are both concerns that impact cultivated crops. As a
result, agricultural crops that can survive abiotic stresses are required around the world. Drought is a major abi-
Figure 7. GC–MS chromatogram of volatile compounds produced by B. pseudomycoides. Figure 8. Quantitative analysis of expression of Dreb1 and MYB3R gene in leaves of wheat plants grown
from seeds treated with Bp and Bm. Here, Bp and Bm indicate B. pseudomycoides and B. massilioanrexius,
respectively. Data were recorded after 24 h of drought stress induction. Here, * indicates significance at the
P = 0.05 level, and ** indicates significant at P = 0.01. Figure 7. GC–MS chromatogram of volatile compounds produced by B. pseudomycoides. Results
M
h Fi
7
GC MS h
t
f
l til
d
d
d b B p
d
id Figure 7. GC–MS chromatogram of volatile compounds produced by B. pseudomycoides. Figure 8. Quantitative analysis of expression of Dreb1 and MYB3R gene in leaves of wheat plants grown
from seeds treated with Bp and Bm. Here, Bp and Bm indicate B. pseudomycoides and B. massilioanrexius,
respectively. Data were recorded after 24 h of drought stress induction. Here, * indicates significance at the
P = 0.05 level, and ** indicates significant at P = 0.01. Figure 8. Quantitative analysis of expression of Dreb1 and MYB3R gene in leaves of wheat plants grown
from seeds treated with Bp and Bm. Here, Bp and Bm indicate B. pseudomycoides and B. massilioanrexius,
respectively. Data were recorded after 24 h of drought stress induction. Here, * indicates significance at the
P = 0.05 level, and ** indicates significant at P = 0.01. Discussion Global population expansions and global climate change are both concerns that impact cultivated crops. As a
result, agricultural crops that can survive abiotic stresses are required around the world. Drought is a major abi-
otic phenomenon that reduces plant development and growth, affecting agricultural demands. Although many
scientists believe that artificial gene transfer can be used to solve abiotic problems, there are many concerns
regarding this methodology. PGPR, on the other hand, can spontaneously transmit genes. As a result, many
scientists are attempting to use PGPR to further adapt drought-tolerant crop varieties. While this is not a novel
method, researchers have recently applied this technique to the global climate change dilemma under abiotic
stress circumstances. PGPR also reduces the use of chemical fertilizer by engaging in growth simulation. T. aestivum seeds germinate and grow faster after receiving beneficial bacterial inoculation27.f g
gt
gi
In our experiment, B. pseudomycoides inoculation was more effective than B. massilioanrexius, S. marces-
cens, B. turingiensis, and Acinetobacter sp. in terms of morphological growth, as measured by germination rate, Scientific Reports | (2022) 12:19137 | https://doi.org/10.1038/s41598-022-22354-2 www.nature.com/scientificreports/ entificreports/
Figure 9. The quality assessments for the model protein, (a) ERRAT, where there were 85.55% residues in
the allowed regions, (b) Ramachandran Plot assessment to validate structural quality, (c) root mean square
deviation from the C-alpha atoms of the modeled protein, where lower deviations were observed. Figure 9. The quality assessments for the model protein, (a) ERRAT, where there were 85.55% residues in
the allowed regions, (b) Ramachandran Plot assessment to validate structural quality, (c) root mean square
deviation from the C-alpha atoms of the modeled protein, where lower deviations were observed. potential, vigor index, potential, root-shoot length and number, and dry weight. Due to bacterial inoculation,
changes in biochemical levels, functions, and morphology of T. aestivum could be observed. The substantial
functional differences between the bacterial inoculation and control seeds were obvious throughout the entire
experiment. In the current study, we found that plants grown from B. pseudomycoides-inoculated seeds accumulated
considerably more dry weight, RWC, and chlorophyll content. Similar agronomic improvements have been
reported in the past with several bacterial inoculations28–30. Chlorophyll, a component of photosynthesis, has
been shown to contribute to sorghum yield (in drought conditions) or improve sorghum yield and transpiration
efficiency (in water-limited conditions)31–33. It has been observed that applying N2 to the seed surface improves
germination, which is consistent with our findings. B. Discussion pseudomycoides inoculation was found to be more effec-
tive in boosting germination than other strains, showing that B. pseudomycoides could be an efficient in seed
germination promoter. B. pseudomycoides inoculation in seeds resulted in an increase in total soluble protein and
sugar in the root and shoot, demonstrating that B. pseudomycoides is effective in boosting cell metabolism and
hence wheat plant growth and development. This observation is in line with prior wheat findings34. However,
NO is an important signaling molecule that is involved in plant germination, growth, pollen tube growth, root
organogenesis, flowering, physiology, biotic, abiotic, and developmental processes35–39, and in our study, NO
levels were not significantly affected in the root but significantly increased after B. pseudomycoides inoculation. gi
yf
gi
yt
p
y
In drought conditions, plant cells develop functional reactive oxygen species (ROS), whereas antioxidant
enzymes inhibit ROS generation and reactivity to environmental stresses. Antioxidant enzymes such as SOD,
CAT, and APX play a key role in reducing oxidative damage and ROS generation in plants, with CAT being the
most essential in H2O2 scavenging to prevent ROS formation41. According to our findings, CAT, SOD, and APX
activities increased in plants treated with B. pseudomycoides, but were lower in other bacterial treatments and
non-treated plants. Iron uptake by electrons is reduced when Fe 3 + is reduced to Fe 2 + at the cell surface40. We
also noticed that when B. pseudomycoides was inoculated, the concentrations of Fe and Zn in the root and shoot
increased dramatically. Taran, Nataliya, et al. 2017 showed that Cu, Zn-nanoparticles reduced the detrimental
effects of drought in wheat41. According to some studies, an adequate supply of Zn can modulate drought toler-
ance in crops like wheat, sunflower, tomato, and red cabbage42–44. So, inoculation with B. pseudomycoides may
also affect electron discharge, facilitating iron uptake in wheat plants.ii f
g
g
p
p
Under drought conditions, bacterial biofilm formation in plant root hairs is significant because it prevents
the dispersion of bacterial biologically active substance secretion, the products of which then accumulate on
the surface of the root to help plants absorb nutrients45. This biofilm formation encourages root-to-soil contact,
which allows plants to absorb more nutrients from the soil. In response to certain PGPR strains, wheat produces Scientific Reports | (2022) 12:19137 | https://doi.org/10.1038/s41598-022-22354-2 www.nature.com/scientificreports/ Figure 10. Discussion Docking simulation between MYB gene and 2,6-ditert-butylcyclohexa-2,5-diene-1,4-dione and
3,5-ditert-butylphenol, respectively, as a (a) cartoon view, (b) 3D view, (c) surface view of CID: 12,867 where (d)
is a cartoon view, (e) 3D view, (f) surface view of CID: 70,825. Figure 10. Docking simulation between MYB gene and 2,6-ditert-butylcyclohexa-2,5-diene-1,4-dione and
3,5-ditert-butylphenol, respectively, as a (a) cartoon view, (b) 3D view, (c) surface view of CID: 12,867 where (d)
is a cartoon view, (e) 3D view, (f) surface view of CID: 70,825. Table 1. The docking interactions of MYB gene and the top two ligand molecules in molecular docking. The interactions were found using Discovery Studio software, where A, PA, PS H, indicate the alkyl, pi-alkyl,
pi-sulfur, and hydrogen bond, respectively. Complex
Amino acid residues
Bond type
Distance (Å)
Docking energy (Kcal/mol)
MYB protein and 2,6-ditert-butylcyclohexa-2,5-di-
ene-1,4-dione
Thr116
H
2.24
−6.2
Leu117
H
2.25
Tyr168
PS
4.97
Tyr168
PA
5.49
Ala115
PA
3.92
MYB protein and 3,5-ditert-butylphenol
Thr116
H
2.03
−6.5
Leu117
H
2.80
Tyr168
PS
5.03
Tyr168
PA
5.25
Ala115
PA
3.96 Table 1. The docking interactions of MYB gene and the top two ligand molecules in molecular docking. The interactions were found using Discovery Studio software, where A, PA, PS H, indicate the alkyl, pi-alkyl,
pi-sulfur, and hydrogen bond, respectively. hygroscopic polysaccharide-type alginates that improve water status, while the bacterial alginates’ water-holding
capacity slowly depletes46–48. This cellular metabolic adjustment caused by B. pseudomycoides wheat treatment
adds to biofilm development, which reduces water loss. Flagella are required for the biofilm community to
approach and travel across the surface, according to the widely accepted theory of biofilm formation, which holds
that environmental cues start the process. Pili or LPSs, which are components of the outer membrane, mediate
the initial stages of attachment. The development of quorum-sensing signals is conducive to the formation of a
mature biofilm after the formation of micro colonies49. Surfactin was created during B. subtilis colonization50. This Surfactin contributes to the development of biofilms in plant root hair. It is known that Surfactin and other
lipopeptides generated by Bacillus spp. cause plants to develop systemic resistance. As a result, B. pseudomycoides’
alginate pathway may be responsible for drought tolerance. According to a recent study, several genes, including https://doi.org/10.1038/s41598-022-22354-2 Scientific Reports | (2022) 12:19137 | www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 11. Discussion The simulation snapshots of MYB gene and 2,6-ditert-butylcyclohexa-2,5-diene-1,4-dione
complexes acquired from the trajectories, where rigid profiles of the ligand–protein complex were observed in
the same binding pockets. The snapshots (a–c) were taken after 0, 50, and 100 ns intervals, respectively. Figure 11. The simulation snapshots of MYB gene and 2,6-ditert-butylcyclohexa-2,5-diene-1,4-dione
complexes acquired from the trajectories, where rigid profiles of the ligand–protein complex were observed in
the same binding pockets. The snapshots (a–c) were taken after 0, 50, and 100 ns intervals, respectively. DREB151, AtWRKY3052, TaASR153, and TaMYB30-B54, considerably improve wheat drought stress tolerance. We
chose DREB1 and MYB3R-1 genes expression after induced drought to illustrate wheat drought stress-related
genes expression. B. pseudomycoides has a significant ability to naturally express the DREB1 gene but a lessened
ability to express the MYB3R gene.i VOC released by PGPR bacteria have been shown to boost plant growth55, induce biofilm, and improve
disease resistance56, iron nutrition, and abiotic stress tolerance19,20. For instance, Pseudomonas chlororaphis also
produces 2,3-butanediol, a VOC that induces drought stress57. Homology modeling of myb protein and volatile
compounds were used for molecular docking to discover the best-binding compounds to active regions of the
targeted protein, MYB. Overexpression of myb reduces drought tolerance in transgenic Arabidopsis, as demon-
strated by a decreased germination rate, shorter root length, lower proline content, and impaired POD, SOD, and
CAT activities. Silencing myb expression in wheat enhanced antioxidant enzyme activity, proline content, and
RWC in addition to activating DREB1 and DREB31 stress-related genes. The myb gene was found to have a nega-
tive effect on drought tolerance genes58. Here, the VOC 2, 6-ditert-butylcyclohexa-2, 5-diene-1, 4-dione, and 3,
5-ditert-butylphenol were shown to suppress MYB gene expression in wheat, possibly enhancing drought stress.ii y p
pp
g
p
, p
y
g
g
Wheat seeds inoculated with five distinct bacterial strains, including B. pseudomycoides, showed significant
morphological improvement and chlorophyll content, leading to increased photosynthesis under normal and
drought conditions. This inoculation also revealed drought morphological adaptation, PEG treatment, biofilm
formation, and Dreb1 gene expression under drought conditions. B. pseudomycoides may also secrete several
volatile compounds, with the best results coming from in silico study on 2, 6-ditert-butylcyclohexa-2, 5-diene-1,
4-dione, and 3, 5-ditert-butylphenol. Binding stability was demonstrated in a molecular simulation of protein
and two volatile compounds. Sample collection.
h
( After treatment, 30 seeds were
placed in 90 mm petri dishes that had four layers of wet tissue papers at the bottom, and the dishes were placed
in a growth chamber set at 23 ± 2 °C and 50% humidity to monitor germination. After germination, the GR
(Germination Rate), GP (Germination potential), IG (Index of Germination), and LI (Length index) were also
calculated by the above reported method. After 10 days in petri dishes, plant growth was measured. Plants were
carefully removed from the tissue paper, and the roots were cleaned with tap water. The lengths of the roots and
shoots were measured and the number of roots tallied. Root‑shoot dry weights, ratio, and relative water content. The root and shoot dry weight measurements were
carried out according to Arshadullar and Zaidi 200760. The dry ratio was determined using the methods of Xu
et al., 201561. Five plants were randomly selected from each replication and rinsed with tap water to measure
both shoot and root dry weights. Then shoots were then cut at the base and dried for 4 days at 70 °C in an incu-
bator. The sample weights were determined using an electronic scale, and RWC (Relative Water Content) was
measured according to62. Biochemical characterization. Chlorophyll (a and b) determination. The total chlorophyll content
in leaves was measured according to Lichtenthaler and Wellburn 198363. In this case, young fresh leaves were
weighed and ground using a mortar and pestle in 90% methanol. Following grinding, the sample mixtures were
centrifuged at 12,000 rpm for 10 min and the supernatants transferred. Finally, the optical density was recorded
at 662 nm for chlorophyll a and 653 nm for chlorophyll b using a spectrophotometer (Analytic Gena, Germany),
and the total chlorophyll content was calculated as mg/g. Analysis of antioxidant enzymes (CAT, SOD, POD, and APX). CAT, SOD, POD, and APX activities were meas-
ured according to Verma and Dubey, 200364, Sun and Zigman, 197865, Yordanova et al. 199966, and Verma and
Dubey, 200364, respectively. In the case of all antioxidant activities, 0.3 g leaf and roots samples were crushed
separately in phosphate buffer (10 mL, 100 mM, and pH 7.0). Then, the homogenate samples were centrifuged
at 12,000 rpm for 12 min to separate the supernatant. Sample collection.
h
( For CAT activity, 2 mL of reaction mixtures contain-
ing potassium phosphate buffer (1.5 ml, 100 mM, pH 7.0), H2O2 (400 μl of 6%), and 100 μl leaf extract were
prepared. Then, the decrease in absorbance was recorded at 240 nm by using a UV–Vis spectrophotometer
(Analytic Gena, Germany). For SOD, reaction components were prepared by mixing sodium bicarbonate or
carbonate buffer (1.3 mL, 50 mM, pH 9.8), EDTA (100 µl, 0.1 mM), and Epinephrine (500 µl, 0.6 mM). Then,
adrenochrome formation was measured at 475 nm (Analytic Gena, Germany). In the case of APX, reaction
mixtures were prepared by using potassium phosphate buffer (1 mL of 100 mM, pH 7.0), ascorbic acid (500 μl of
0.2 mM), EDTA (100 μl of 0.2 mM), H2O2 (300 μl of 6%), and 100 μl of plant extract, and the decrease of absorb-
ance was recorded at 290 nm using a UV–VIS spectrophotometer (Analytic Gena, Germany) at 10 s intervals up
to 1 min. The specific activity of the enzyme was expressed as μmol min-1 (mg protein)-1. Determination of Fe and Zn concentration. The concentrations of Zn and Fe were determined according to
Kabir et al. 201767. For this, fresh plant tissues were washed with CaSO4 (1 mM) for 5 min and then thoroughly
washed with distilled water. After this, clean samples were dried in an incubator at 80 °C for 6 days. A total of
3 mL of HNO3 and 1 mL of H2O2 were added to each sample in the test tube and heated at 75 °C for 12 min. Zn and Fe concentrations were evaluated by Flame Atomic Absorption Spectroscopy, using a ASC-6100 auto
sampler and air-acetylene atomization gas mixture system (Model No.AA-6800, Shimadzu), where standard
solutions of Zn and Fe were separately prepared from their respective concentrations. Determination of H2O2, cell death, and NO. H2O2 was measured according to Alexieva et al. 200168, cell death
was determined according to Jacyn Baker and Mock, 199469, and NO was estimated according to Orozco-Cárde-
nas et al., 200270. In case of H2O2, fresh plant samples were separately homogenized in 0.1% Trichloroacetic acid
(TCA) and centrifuged at 10,000 rpm for 14 min. The supernatants were mixed with KI (1 M) and phosphate
buffer (10 mM, pH 7.0) then kept in the dark for 1 h, and the optical density (OD) of extracts were taken at
390 nm by spectrophotometer (Analytic Gena, Germany). Sample collection.
h
( Sample collection. Seed samples of T. aestivum (BARI gom-33) were collected from the Regional Wheat
Research Center (Bangladesh Agricultural Research Institute, Shyampur Rajshahi-6212) and transported to
the Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi,
Rajshahi, Bangladesh, for further analysis. Samples were treated with bacterial strains B. pseudomycoides (Bp),
B. massilioanrexius (Bm), B. thuringiensis (Bt), Serratia marcescens (Sm), and Acinetobacter sp. (As), which were
collected from this laboratory. We confirmed that all experiments related to plants (Seed samples of T. aestivum
(BARI gom-33)) were in accordance with the relevant guidelines and regulations. https://doi.org/10.1038/s41598-022-22354-2 Scientific Reports | (2022) 12:19137 | www.nature.com/scientificreports/ www.nature.com/scientificreports/ Figure 12. The simulation snapshots of MYB and 3,5-ditert-butylphenol complexes acquired from the
trajectories, where rigid profiles of the ligand–protein complex were observed in the same binding pockets. The
snapshots (a–c) were taken after 0, 50, and 100 ns intervals, respectively. Figure 12. The simulation snapshots of MYB and 3,5-ditert-butylphenol complexes acquired from the
trajectories, where rigid profiles of the ligand–protein complex were observed in the same binding pockets. The
snapshots (a–c) were taken after 0, 50, and 100 ns intervals, respectively. Figure 13. The molecular dynamics simulation. (a) Root mean square deviation of the two docked complexes,
(b) solvent accessible surface area, (c) radius of gyration, (d) hydrogen bond of the docked complexes, and (e)
root mean square fluctuation. Figure 13. The molecular dynamics simulation. (a) Root mean square deviation of the two docked complexes,
(b) solvent accessible surface area, (c) radius of gyration, (d) hydrogen bond of the docked complexes, and (e)
root mean square fluctuation. Scientific Reports | (2022) 12:19137 | https://doi.org/10.1038/s41598-022-22354-2 www.nature.com/scientificreports/ Seed inoculation. Seeds were inoculated with freshly cultured bacterium stains according to the method
described by Paul, et al. 202027. Briefly, seeds were soaked and washed with distilled water for 20 min and then
were sterilized with 70% (v/v) ethanol for 2.5 min. After washing thoroughly with distilled water, seeds were
placed in a conical flask and inoculated with 100 mL of concentrated fresh bacterial culture. Seeds treated with
the cultured medium alone were used as a control. After this, the conical flasks were placed on an orbital shaker
and shaken for 6 h at ambient temperature at 160 rpm. Morpho‑physiological characteristics. Germination parameters and plant growth. Germination pa-
rameters were screened following the method described by Zhou et al. 201659. Sample collection.
h
( Following centrifugation, the supernatants were
mixed with 0.2% anthrone reagent and incubated in a boiling water bath for 10 min. After cooling on ice, the
optical density OD was recorded at 620 nm (Analytic Gena, Germany). In the case of soluble protein, homog-
enized samples with 2 mM EDTA (Ethylenediamine Tetraacetic Acid), 50 mM Tris–HCl, pH 7.5 and 0.04% (v/v)
2-mercaptoethanol added were centrifuged at 12,000 rpm for 15 min at 25 °C. The supernatant was mixed with
1 mL CBB (Coomassie Brilliant Blue), and the optical density was determined at 595 nm using spectrophotom-
eter (Analytic Gena, Germany). Screening of volatile compounds. Volatile compounds were analyzed according to P. Fincheira et al., 201773. For
this, 20 mL of each bacterial culture was inoculated into 30 mL of LB liquid medium in a vial and incubated
at 30 °C for 6 days with constant shaking. The SPME fiber was then inserted into the headspace of the vial and
heated to 50 °C for 30 min. SPME fibers were desorbed at 220 °C for 5 min, and GC–MS was run for 25 min
using GC–MS, Shimadzu, with helium gas as the carrier. The column temperature was set to 35 °C for 3 min
before gradually increasing to 180 °C at a rate of 10 °C/min. After this, the temperature was increased to 240 °C
for 5 min, and the mass spectrometer was run in electron ionization mode at 70 Ev with a temperature of 220 °C
and a continuous scan from 50 to 500 m/z. The results were compared to the Mass Spectrum Library of the
NIST/EPA/NIH. Drought stress tolerance activity. Morphological stress observation. For drought stress analysis, eight
plants were selected in each treatment with three replications, and water was discontinued for 15 days to assess
vulnerability in pot conditions. After stress induction, discussed below, the plants were watered and given four
days to recover. The plants that were rescued were counted as survivors. PEG treatment. PEG (MW: 6000) was used to induce drought stress in wheat, with three treatments: control
(0% PEG), moderate drought stress (10% PEG), and severe drought stress (15% PEG). Every day, each petri dish
received a total of 10 doses of 350 mL PEG solution. The drought stress period lasted 12 days for each treatment. Screening of biofilm formation. Sample collection.
h
( After 15 days of artificial drought stress, plants were removed from the soil,
and roots were safely rinsed with tap water to remove adhering dirt. The roots were then split with scissors and
placed on a carbon tape before being coated by gold using a Sputter Coater 108 auto Cressington. Finally, the
samples were examined via a scanning electron microscope (JCM-6000 Plus (JEOL Japan) at various wave-
lengths for scanning biofilm. RNA isolation and gene expression analysis. RNA isolation and gene expression were analyzed by following
the method described by Rahman et al. 201874. Briefly, two genes, Dreb1 and MYB3R, were chosen for gene
expression analysis in leaves using quantitative reverse transcription PCR techniques. A total of 30 mg of leaves
were ground in liquid nitrogen using a mortar and pestle, and total RNA was extracted using Promega SV total
RNA isolation system. After DNase treatment, 1 μl extracted RNA of some samples was run in 1% agarose gel to
observe the level of RNA degradation. First-strand cDNA was produced using Promega, Reverse Transcription
systems, and the RNA extraction was confirmed by MoF buffer in agarose gel electrophoresis and quantified
by Nano drop. After this, RNase was used to clean the cDNA, and real-time PCR analysis was performed using
an Eco™ real-time PCR system controlled by Eco Software v 4.7.0 (Illumina. USA), with a program of 3 min at
95 °C, 40 cycles of 30 s at 94 °C, 15 s at 56 °C and 30 s at 72 °C. Expression was normalized using actin as an
internal control. Homology modeling. The crystal structure of the MYB-like domain-containing protein of T. aestivum had not
yet explored in the protein database (RCSBD). So, for further protein modeling and molecular docking study,
we used sequences from the UniPort database, MYB (UniProt ID: A0A3B6RJY9). The protein sequences’ fasta
format was extracted and entered into the Phyre2 web tools. The C chain of a specific DNA complex of the MYB
DNA-2 binding domain with cooperative recognition helices (PDB ID: 1MSE) was chosen as a template, with
confidence and percent identity of 100, and 56 for the MYB gene, respectively. The MYB model protein was
exposed to short molecular dynamics simulations (10 ns) for refinements and minimizations. Further valida-
tions were performed using the last snapshots from the simulation trajectories. ERRAT and Ramachandran Plot
analysis was used to further assess the reduced structures. Ligand preparation. Sample collection.
h
( For cell death determination, fresh samples were
incubated at 25 °C in 0.25% Evans blue solution for 16 min, then in 1.0 mL of 80% ethyl alcohol for 10 min, and
finally incubated in a water bath at 50 °C for 15 min. After this, the mixtures were centrifuged at 12,000 rpm
for 10 min. Then, the absorbance was measured at 600 nm (Analytic Gena, Germany) and the amount of cell
death calculated based on fresh weight. For NO determination, samples were homogenized in cooled NO buffer
(1 mL) and centrifuged at 10,000 rpm for 10 min. The supernatants were transferred to a 5 mM oxyhemoglobin
(HbO2) solution and incubated for 7 min at room temperature. Optical density was measured at 401 nm (Ana-
lytic Gena, Germany) to determine the conversion rate of oxyhemoglobin (HbO2) to methemoglobin (metHb),
which is an indicator of the presence of NO. https://doi.org/10.1038/s41598-022-22354-2 Scientific Reports | (2022) 12:19137 | www.nature.com/scientificreports/ Estimation of soluble sugar and protein. The total soluble sugar content of the plant samples was determined
using the method of M. Dubois, et al., 195671, and soluble protein content was determined using the Bradford
protein assay according to He, 201172. For soluble sugar, the fresh samples were homogenized in 90 °C hot aque-
ous ethanol (v/v 80%) and centrifuged at 12,000 rpm for 10 min. Following centrifugation, the supernatants were
mixed with 0.2% anthrone reagent and incubated in a boiling water bath for 10 min. After cooling on ice, the
optical density OD was recorded at 620 nm (Analytic Gena, Germany). In the case of soluble protein, homog-
enized samples with 2 mM EDTA (Ethylenediamine Tetraacetic Acid), 50 mM Tris–HCl, pH 7.5 and 0.04% (v/v)
2-mercaptoethanol added were centrifuged at 12,000 rpm for 15 min at 25 °C. The supernatant was mixed with
1 mL CBB (Coomassie Brilliant Blue), and the optical density was determined at 595 nm using spectrophotom-
eter (Analytic Gena, Germany). Estimation of soluble sugar and protein. The total soluble sugar content of the plant samples was determined
using the method of M. Dubois, et al., 195671, and soluble protein content was determined using the Bradford
protein assay according to He, 201172. For soluble sugar, the fresh samples were homogenized in 90 °C hot aque-
ous ethanol (v/v 80%) and centrifuged at 12,000 rpm for 10 min. Conclusion Wheat growth is enhanced by seed inoculation with B. pseudomycoides in a normal environment, with increased
of total soluble sugar, protein, chlorophyll concentrations, RWC, and root-shoot length. This inoculation can form
biofilm in drought stress, which supports morphological drought stress and expresses drought response genes. Molecular evidence revealed that B. pseudomycoides has a strong ability to spontaneously express the DREB1
gene but a weak ability to express the MYB gene. The overexpression of MYB gene suppresses the expression of
DREB1 gene. B. pseudomycoides secreted volatile compounds such as 2, 6-ditert-butyl cyclohex-2, 5-diene-1,
4-dione, and 3, 5-ditert-butylphenol, which had binding affinity and stability in molecular docking and simula-
tion. B. pseudomycoides, as well as 2, 6-ditert-butyl cyclohex-2, 5-diene-1, 4-dione, and 3, 5-ditert-butylphenol,
may enhance DREB1 gene expression by suppressing MYB gene under drought conditions. Microorganisms
may be able to help mitigate the detrimental effects of climate change on crop growth, according to the study. However, more investigation into the subject is required, as well as clarification of the protective method. www.nature.com/scientificreports/ ian algorithm, with the parameters set to 250 runs and 25,000,000 energy assessments for each cycle. The level
of thoroughness was set to 8. Finally, docking calculations were run in AutoDock Vina. The Discovery Studio
(version 3.0)80, and Pymol software was used (version 2.3)81 for binding interactions analysis. ian algorithm, with the parameters set to 250 runs and 25,000,000 energy assessments for each cycle. The level
of thoroughness was set to 8. Finally, docking calculations were run in AutoDock Vina. The Discovery Studio
(version 3.0)80, and Pymol software was used (version 2.3)81 for binding interactions analysis. Molecular dynamics simulation. The molecular dynamics simulation was performed by the YASARA dynam-
ics package using the AMBER14 force field82,83. The docked complexes were cleaned, optimized, and a hydrogen
bond networking system was used with a pH of 7.4, a temperature of 310 K, and a 0.9% NaCl concentration. A
TIP3P solvation model was used with periodic boundary conditions to produce a cubic simulations cell. Simu-
lated annealing methods were used to do fundamental energy minimization in steepest-gradient algorithms
(5000 cycles). Long-range electrostatic interactions were calculated by the Particle Mesh Ewalds (PME), with a
cut-off radius of 8.0 Å. The simulation cell was extended by 20 Å in each case from the complexes. The simula-
tions were run using a time step of 2.0 fs. The final simulation was run for 100 ns84, while adhering to constant
pressure and a Berendsen thermostat. The root mean square deviation, solvent accessible surface area, radius of
gyration, and hydrogen bonding were all calculated using simulated trajectories stored at 100 ps interval85–92. Statistical analysis. The experiment was performed using a CRBD (Complete Randomized Block Design)
with three replication of each biological sample. The DMRT (Duncan’s Multiple Range Test) was used to analyze
the significance of each group’s data at a P ≤ 0.05 level of significance in a one-way ANOVA in SPSS Statistics 26
software. Graph Pad Prism 8.0.2.263 was used for preparing all figures. Data availability All data generated or analyzed during this study are included in this published article and its supplementary
information files. Received: 10 May 2022; Accepted: 13 October 2022 Received: 10 May 2022; Accepted: 13 October 2022 References References
1. Shewry, P. R. & Hey, S. J. The contribution of wheat to human diet and health. Food Energy Secur. 4, 178–202 (2015). b l
l
h
(
)
k
f
f
l b l d
b l
h h
2. Kamran, A., Iqbal, M. & Spaner, D. Flowering time in wheat (Triticum aestivum L.): A key factor for global adaptability. Euphytica
197, 1–26 (2014). h
2. Kamran, A., Iqbal, M. & Spaner, D. Flowering time in wheat (Triticum aestivum L.): A key factor for global adaptability. Euphytica
197, 1–26 (2014). 3. Day, L., Augustin, M. A., Batey, I. L. & Wrigley, C. W. Wheat-gluten uses and industry needs. Trends Food Sci. Technol. 17, 82–90
(2006). 4. Smol, J. P. Climate change: A planet in flux. Nature https://doi.org/10.1038/483S12a (2012).f l
5. Flexas, J. et al. Diffusional conductances to CO2 as a target for increasing photosynthesis and photosynthetic water-use efficiency
Photosynth. Res. 117, 45–59 (2013). 6. Loutfy, N. et al. Changes in the water status and osmotic solute contents in response to drought and salicylic acid treatments in
four different cultivars of wheat (Triticum aestivum). J. Plant Res. https://doi.org/10.1007/s10265-011-0419-9 (2012). f
p
g
7. Bloemberg, G. V. & Lugtenberg, B. J. J. Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr. Opin
Plant Biol. https://doi.org/10.1016/S1369-5266(00)00183-7 (2001). p
g
8. Glick, B. R., Karaturovic, D. M. & Newell, P. C. A novel procedure for rapid isolation of plant growth promoting pseudomonads
Can. J. Microbiol. 41, 533–536 (1995).i 9. Okon, Y. & Labandera-Gonzalez, C. A. Agronomic applications of azospirillum: An evaluation of 20 years worldwide field inocula-
tion. Soil Biol. Biochem. 26, 1591–1601 (1994). (
)
0. Kloepper, J. W., Lifshitz, R. & Zablotowicz, R. M. Free-living bacterial inocula for enhancing crop productivity. Trends Biotechnol
7, 39–44 (1989). 1. Mantelin, S. & Touraine, B. Plant growth-promoting bacteria and nitrate availability: Impacts on root development and nitrate
uptake. J. Exp. Bot. 55, 27–34 (2004).h p
p
12. Hare, P. D., Cress, W. A. & Van Staden, J. The involvement of cytokinins in plant responses to environmental stress. Plant Growth
Regul. 23, 79–103 (1997).hi g
,
(
)
13. Nicholas Smirnof, F. The role of active oxygen in the response of plants to water deficit and desiccation. New Phytol. 125, 27–58
(1993). (
)
14. Nair, P. Agroecosystem management in the 21st century: It is time for a paradigm shift. J. Trop. Sample collection.
h
( The volatile compounds of B. pseudomycoides were derived through GC–MS analysis, and
the sdf format of 3D structures was retrieved from the PubChem database (http://www.pubchem.ncbi.nlm.nih.
gov/)75. The mmff94 force field was used to construct and optimize the structure of the ligands with the aid of
Avogadro software76. Molecular docking. Molecular docking is an important tool for identifying the best compounds to fit receptor
molecules based on docking energy. The Auto Dock Vina software package was used for performing molecular
docking. The ligands were converted to PDBQT format, and the grid box center was set to (X: 26.29 Å, Y:12.60 Å
Z:58.94 Å) and (X:50.33 Å, Y:67.27 Å, Z:59.25 Å), respectively77–79. Docking was performed using the Lamarck- https://doi.org/10.1038/s41598-022-22354-2 Scientific Reports | (2022) 12:19137 | www.nature.com/scientificreports/ www.nature.com/scientificreports/ www.nature.com/scientificreports/ 18. Ansari, F. A., Ahmad, I. & Pichtel, J. Growth stimulation and alleviation of salinity stress to wheat by the biofilm forming Bacillus
pumilus strain FAB10. Appl. Soil Ecol. 143, 45–54 (2019).hf p
pp
(
)
19. Liu, X. M. & Zhang, H. The effects of bacterial volatile emissions on plant abiotic stress tolerance. Front. Plant Sci. 6, 774 (20 hf
0. Farag, M. A., Zhang, H. & Ryu, C. M. Dynamic chemical communication between plants and bacteria through airborne signals
Induced resistance by bacterial volatiles. J. Chem. Ecol. 39, 1007–1018 (2013).f 20. Farag, M. A., Zhang, H. & Ryu, C. M. Dynamic chemical communication between plants and bacteria through airborne signals:
Induced resistance by bacterial volatiles. J. Chem. Ecol. 39, 1007–1018 (2013). 21 K
hi
C N M l
M & M ff i M E Ch
i
l di
it
f
i
bi l
l til
d th i
t
ti l f
l
t
th
d y
1. Kanchiswamy, C. N., Malnoy, M. & Maffei, M. E. Chemical diversity of microbial volatiles and their potential for plant growth and
productivity. Front. Plant Sci. 6, 151 (2015). p
y
(
)
22. Zhang, H. et al. Rhizobacterial volatile emissions regulate auxin homeostasis and cell expansion in Arabidopsis. Planta 226,
839–851 (2007).h (
)
3. Zheng, X. et al. The wheat GT factor TaGT2L1D negatively regulates drought tolerance and plant development. Sci. Rep. 6, 1–14
(2016).fifi (
)
24. Mahmud, S. et al. Efficacy of phytochemicals derived from avicennia officinalis for the management of covid-19: A combined in
silico and biochemical study. Molecules 26, 2210 (2021). y
(
)
25. Mahmud, S. et al. Molecular docking and dynamics study of natural compound for potential inhibition of main protease of SARS-
CoV-2. J. Biomol. Struct. Dyn. https://doi.org/10.1080/07391102.2020.1796808 (2020). y
p
g
6. Venkateswarlu, B. & Shanker, A. K. Climate change and agriculture: Adaptation and mitigation stategies. Indian J. Agron. 54
226–230 (2009).f 27. Paul, G. K. et al. Isolation and characterization of bacteria from two soil samples and their effect on wheat (Triticum aestivum l.)
growth promotion. J. Adv. Biotechnol. Exp. Ther. 3, 254–262 (2020). g
p
ph
8. Grobelak, A., Napora, A. & Kacprzak, M. Using plant growth-promoting rhizobacteria (PGPR) to improve plant growth. Ecol
Eng. 84, 22–28 (2015).f 9. Rajkumar, M. & Freitas, H. Effects of inoculation of plant-growth promoting bacteria on Ni uptake by Indian mustard. www.nature.com/scientificreports/ Effect of zinc and copper nanoparticles on drought resistance of wheat seedlings. Nanoscale Res. Lett. 12, 1–6 (2017). 42. Eslami, M., Dehghanzadeh, H., Jafarzade, M. & Aminian, R. The effect of zinc on yield and yield components of sunflower (Heli-
anthus annuus L.) under drought stress. Sci. J. Crop Sci. 3, 61–65 (2014). f
pp
p
g
g
(
)
2. Eslami, M., Dehghanzadeh, H., Jafarzade, M. & Aminian, R. The effect of zinc on yield and yield components of sunflower (Heli-
anthus annuus L.) under drought stress. Sci. J. Crop Sci. 3, 61–65 (2014).i f
42. Eslami, M., Dehghanzadeh, H., Jafarzade, M. & Aminian, R. The effect of zinc on yield
anthus annuus L.) under drought stress. Sci. J. Crop Sci. 3, 61–65 (2014).i g
3. Hajiboland, R. & Amirazad, H. Drought tolerance in Zn-deficient red cabbage (Brassica oleracea L. var. capitata f. rubra) plants
Hortic. Sci. 37, 88–98 (2010).t 4. Sadoogh, F. S., Shariatmadari, H., Khoshgoftarmanesh, A. H. & Mosaddeghi, M. R. Adjusted nutrition of tomato with potassium
and zinc in drought stress conditions induced by polyethylene glycol 6000 in hydroponic culture. J. Sci. Technol. Greenh. Cult
Isfahan Univ. Technol. 5, 67–81 (2014). 44. Sadoogh, F. S., Shariatmadari, H., Khoshgoftarmanesh, A. H. & Mosaddeghi, M. R. Adjusted nutrition of tomato with potassium
and zinc in drought stress conditions induced by polyethylene glycol 6000 in hydroponic culture. J. Sci. Technol. Greenh. Cult. Isfahan Univ. Technol. 5, 67–81 (2014). 45. Timmusk, S. et al. Drought-tolerance of wheat improved by rhizosphere bacteria from harsh environments: Enhanced biomass Isfahan Univ. Technol. 5, 67–81 (2014). 45. Timmusk, S. et al. Drought-tolerance of wheat improved by rhizosphere bacteria from harsh environments: Enhanced biomass
production and reduced emissions of stress volatiles. PLoS ONE https://doi.org/10.1371/journal.pone.0096086 (2014). f
5. Timmusk, S. et al. Drought-tolerance of wheat improved by rhizosphere bacteria from harsh environments: Enhanced biomas
production and reduced emissions of stress volatiles. PLoS ONE https://doi.org/10.1371/journal.pone.0096086 (2014).i p
p
g
j
p
46. Halverson, L. J. Role of Alginate in Bacterial Biofilms. 135–151 (2009) https://doi.org/10.1007/978-3-540-92679-5_6.i gi
g
47. Hay, I. D., Rehman, Z. U., Moradali, M. F., Wang, Y. & Rehm, B. H. A. Microbial alginate production, modification and its
tions. Microb. Biotechnol. 6, 637–650 (2013). 48. Donati, I. & Paoletti, S. Material Properties of Alginates. 1–53 (2009) https://doi.org/10.1007/978-3-540-92679-5_1.i 49. Rinaudi, L. V. & Giordano, W. An integrated view of biofilm formation in rhizobia. FEMS Microbiol. Lett. www.nature.com/scientificreports/ Bioresour
Technol. 99, 3491–3498 (2008).f 30. Viruel, E. et al. Inoculation of maize with phosphate solubilizing bacteria: Effect on plant growth and yield. J. Soil Sci. Plant Nutr. 14, 819–831 (2014).h 1. Haussmann, B. I. G. et al. QTL mapping of stay-green in two sorghum recombinant inbred populations. Theor. Appl. Genet. 106
133–142 (2002).l 2. Li, R. H., Guo, P. G., Michael, B., Stefania, G. & Salvatore, C. Evaluation of chlorophyll content and fluorescence parameters as
indicators of drought tolerance in barley. Agric. Sci. China 5(10), 751–757 (2006).l 33. Verma, V. et al. Mapping quantitative trait loci for flag leaf senescence as a yield determinant in winter wheat under optimal and
drought-stressed environments. Euphytica 135, 255–263 (2004). 34. Afzal, A. & Bano, A. Rhizobium and phosphate solubilizing bacteria improve the yield and phosphorus uptake in wheat (Triticum
aestivum). Int. J. Agric. Biol. 10, 85–88 (2008). g
5. Yu, M., Lamattina, L., Spoel, S. H. & Loake, G. J. Nitric oxide function in plant biology: A redox cue in deconvolution. New Phytol
202, 1142–1156 (2014). 36. Wendehenne, D. & Hancock, J. T. New frontiers in nitric oxide biology in plant. Plant Sci. 181, 507–508 (2011). . Wendehenne, D. & Hancock, J. T. New frontiers in nitric oxide b
k
T
d
l
h d
l
d D. & Hancock, J. T. New frontiers in nitric oxide biology in plant. P 37. Hancock, J. T. Nitric oxide in plant growth, development and stress physiology. Plant Cell Monogr. 6, 482 (2007). 38. Shehzadi, M. et al. Enhanced degradation of textile effluent in constructed wetland system using Typha domingensis and textile
effluent-degrading endophytic bacteria. Water Res. 58, 152–159 (2014). fl
g
g
p y
9. Glyanko, A. K. & Ischenko, A. A. Level nitric oxide (NO) and growth of roots of etiolated pea seedlings. Biol. Bull. 40(6), 533–538
(2013). 0. Cain, T. J. & Smith, A. T. Ferric iron reductases and their contribution to unicellular ferrous iron uptake. J. Inorg. Biochem. 218
111407 (2021).f 1. Taran, N. et al. Effect of zinc and copper nanoparticles on drought resistance of wheat seedlings. Nanoscale Res. Lett. 12, 1–6 (2017)
2 E l
i M D h h
d h H J f
d
M & A
i i
R Th
ff
t f i
i ld
d i ld
t
f
fl
(H li 41. Taran, N. et al. References Agric. 46, 1–12 (2008). g
y
g
y
gt
g
15. Simova-Stoilova, L., Demirevska, K., Petrova, T., Tsenov, N. & Feller, U. Antioxidative protection in wheat varieties under severe
recoverable drought at seedling stage. Plant, Soil Environ. 54, 529–536 (2008). g
g
g
6. Tobergte, D. R. & Curtis, S. Adherence of bacteria to hydrocarbons: A simple method for measuring cell-surface hydrophobicity
J. Chem. Inf. Model. 53, 1689–1699 (2013). J
f
(
)
17. Kohler, J., Hernández, J. A., Caravaca, F. & Roldán, A. Plant-growth-promoting rhizobacteria and arbuscular mycorrhizal fungi
modify alleviation biochemical mechanisms in water-stressed plants. Funct. Plant Biol. 35, 141–151 (2008). https://doi.org/10.1038/s41598-022-22354-2 Scientific Reports | (2022) 12:19137 | www.nature.com/scientificreports/ https://doi.org/10.1080/07391102.2019.1680440 (2019).i y
p
g
6. Uddin, M. Z. et al. Chemical profiles and pharmacological properties with in silico studies on elatostema papillosum wedd. Mol
ecules 26, 809 (2021). 87. Mahmud, S. et al. Virtual screening and molecular dynamics simulation study of plant-derived compounds to identify pote
inhibitors of main protease from SARS-CoV-2. Brief. Bioinform. https://doi.org/10.1093/bib/bbaa428 (2021). 88. Rakib, A. et al. A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that in
the main protease of SARS-CoV-2: An in silico investigation. Brief. Bioinform. https://doi.org/10.1093/bib/bbab045 (2021). p
g
f
f
p
g
89. Bappy, S. S. et al. Extensive immunoinformatics study for the prediction of novel peptide-based epitope vaccine with docking
confirmation against envelope protein of Chikungunya virus: A computational biology approach. J. Biomol. Struct. Dyn. https://
doi.org/10.1080/07391102.2020.1726815 (2020). g
(
)
0. Pramanik, S. K. et al. Fermentation optimization of cellulase production from sugarcane bagasse by Bacillus pseudomycoides and
molecular modeling study of cellulase. Curr. Res. Microb. Sci. 2, 100013 (2021). g
y
1. Chowdhury, K. H. et al. Drug repurposing approach against novel coronavirus disease (COVID-19) through virtual screening
targeting SARS-CoV-2 main protease. Biology (Basel) 10, 2 (2020). g
g
gy
92. Munia, M., Mahmud, S., Mohasin, M. & Kibria, K. M. K. In Silico design of an epitope-based vaccine against Choline binding
protein A of Streptococcus pneumoniae. Inform. Med. Unlocked https://doi.org/10.1016/j.imu.2021.100546 (2021). www.nature.com/scientificreports/ 3 Fi
h i
P P
d
M & Q i
A V l il
i
d
i
l
l
i
d p
g
He, F. Bradford protein assay. BIO-PROTOCOL (2011) https://doi p
g
2. He, F. Bradford protein assay. BIO-PROTOCOL (2011) https://doi.org/10.21769/bioprotoc.45. 3 Fincheira P Parada M & Quiroz A Volatile organic compounds stimulate plant growing and seed germination of Lactuca sativa p
g
72. He, F. Bradford protein assay. BIO-PROTOCOL (2011) https://doi.org/10.21769/bioprotoc.45. 3. Fincheira, P., Parada, M. & Quiroz, A. Volatile organic compounds stimulate plant growing and seed germination of Lactuca sativa
J. Soil Sci. Plant Nutr. 17, 853–867 (2017). 74. Rahman, M. M. et al. Mechanisms and signaling associated with LPDBD plasma mediated growth improvement in wheat
Rep. 8, 1–11 (2018). p
75. Kim, S. et al. PubChem substance and compound databases. Nucleic Acids Res. https://doi.org/10.1093/nar/gkv951 (2016). 76. Hanwell, M. D. et al. Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. J. Cheminfor
1–17 (2012).fi 77. Nguyen, N. T. et al. Autodock vina adopts more accurate binding poses but autodock4 forms better binding affinity. J. Chem. Inf. Model. 60, 204–211 (2020). 8. Jaghoori, M. M., Bleijlevens, B. & Olabarriaga, S. D. 1001 Ways to run AutoDock Vina for virtual screening. J. Comput. Aided. Mol
Des. 30, 237–249 (2016).fi 79. Trott, O. & Olson, A. J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient
optimization, and multithreading. J. Comput. Chem. NA-NA https://doi.org/10.1002/jcc.21334 (2009). 80. Gao, Y. D. & Huang, J. F. An extension strategy of discovery studio 2.0 for non-bonded interaction energy automatic calculation
at the residue level. Dongwuxue. Yanjiu. 32, 262–266 (2011). g
j
81. DeLano, L. W. PyMOL: An open-source molecular graphics tool. Ccp4 Newsl. Protein Crystallogr. 40(1), 82–94 (2002). d
bl
l
b
l
d
b
l
h d
l 82. Land, H. & Humble, M. S. YASARA: A tool to obtain structural guidance in biocatalytic investigations. Methods Mol. Bio
43–67 (2018). 83. Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. Development and testing of a general Amber force
Comput. Chem. 25, 1157–1174 (2004). p
84. Krieger, E. & Vriend, G. New ways to boost molecular dynamics simulations. J. Comput. Chem. 36, 996–1007 (2015). 85. Mahmud, S. et al. Exploring the potent inhibitors and binding modes of phospholipase A2 through in silico investigation. J. B
Struct. Dyn. www.nature.com/scientificreports/ 304, 1–11 (2010 50. Altaf, M. M. & Ahmad, I. Biofilm formation on plant surfaces by rhizobacteria: impact on plant growth and ecological signific
Handb. Microb. Bioresour. https://doi.org/10.1079/9781780645216.0081 (2016).i 51. Zhou, Y. et al. Overexpression of soybean DREB1 enhances drought stress tolerance of transgenic wheat in the field. J. Exp. Bot. 71, 1842–1857 (2020). 2. El-Esawi, M. A., Al-Ghamdi, A. A., Ali, H. M. & Ahmad, M. Overexpression of atWRKY30 transcription factor enhances hea
and drought stress tolerance in wheat (Triticum aestivum L.). Genes (Basel). 10, 163 (2019). 3. Hu, W. et al. TaASR1, a transcription factor gene in wheat, confers drought stress tolerance in transgenic tobacco. Plant, Cel
Environ. 36, 1449–1464 (2013). 54. Zhang, L. et al. A wheat R2R3-MYB gene, TaMYB30-B, improves drought stress tolerance in transgenic Arabidopsis. J. Exp. Bot. 63, 5873–5885 (2012).hf 55. Bailly, A. & Weisskopf, L. The modulating effect of bacterial volatiles on plant growth current knowledge and future challenges. Plant Signal. Behav. 7, 79–85 (2012).fi g
6. Bitas, V., Kim, H. S., Bennett, J. W. & Kang, S. Sniffing on microbes: Diverse roles of microbial volatile organic compounds in plan
health. Mol. Plant-Microbe Interact. 26, 835–843 (2013). 57. Cho, S. M., Kim, Y. H., Anderson, A. J. & Kim, Y. C. Nitric oxide and hydrogen peroxide production are involved in systemic
drought tolerance induced by 2R,3R-butanediol in Arabidopsis thaliana. Plant Pathol. J. 29, 427–434 (2013). l
h
l
l
d
h
l
b d
d
h 58. Li, X. et al. A wheat R2R3 MYB gene TaMpc1-D4 negatively regulates drought tolerance in transgenic Arabidopsis and wheat. Plant Sci. 299, 110613 (2020).f 9. Zhou, R. et al. Effects of atmospheric-pressure N2, He, Air, and O2 microplasmas on mung bean seed germination and seedling
growth. Sci. Rep. https://doi.org/10.1038/srep32603 (2016). 60. Arshadullar, M. & Zaidi, S. Role of total plant dry weight in the assesment of variation for salinity tolerance in Gossypium hirsutum. Sarhad J. Agric. 110, 600 (2007). https://doi.org/10.1038/s41598-022-22354-2 Scientific Reports | (2022) 12:19137 | Author contributions Conceptualization: M.A.S. and G.K.P.; methodology: M.A.S., G.K.P., S.M., A.K.D., S.S., A.A.L., M.S.H., P.K. and
M.H.R.; software: G.K.P. and S.M.; validation: M.A.S., M.S.U., S.Z., M.K., A.K.D. and M.S.I.; formal analysis:
G.K.P., S.M., A.K.D., S.S., A.N., T.K. and M.A.S.; investigation, M.A.S., G.K.P., S.M., and A.K.D.; resources:
M.A.S., M.K., M.S.U., and S.Z.; data curation: G.K.P., S.M., A.N., T.K.; writing—original draft preparation: G.K.P. and S.M.; writing—review and editing, G.K.P., S.M., M.A.S., M.K., M.S.U., S.Z., M.S.I.; visualization: M.A.S.,
M.K.; supervision: M.A.S. and M.K.; project administration: M.S.U., S.Z., M.S.I., M.A.S.; funding acquisition:
M.A.S., M.S.I. All authors have read and agreed to the published this version. Conceptualization: M.A.S. and G.K.P.; methodology: M.A.S., G.K.P., S.M., A.K.D., S.S., A.A.L., M.S.H., P.K. and
M.H.R.; software: G.K.P. and S.M.; validation: M.A.S., M.S.U., S.Z., M.K., A.K.D. and M.S.I.; formal analysis:
G.K.P., S.M., A.K.D., S.S., A.N., T.K. and M.A.S.; investigation, M.A.S., G.K.P., S.M., and A.K.D.; resources:
M.A.S., M.K., M.S.U., and S.Z.; data curation: G.K.P., S.M., A.N., T.K.; writing—original draft preparation: G.K.P. and S.M.; writing—review and editing, G.K.P., S.M., M.A.S., M.K., M.S.U., S.Z., M.S.I.; visualization: M.A.S.,
M.K.; supervision: M.A.S. and M.K.; project administration: M.S.U., S.Z., M.S.I., M.A.S.; funding acquisition:
M.A.S., M.S.I. All authors have read and agreed to the published this version. Fundingh g
The research was supported by the grant (5/52/R.U./Bio-16/2021-2022) provided by the University of Rajshahi,
Bangladesh. www.nature.com/scientificreports/ www.nature.com/scientificreports/ 61. Xu, W. et al. Drought stress condition increases root to shoot ratio via alteration of carbohydrate partitioning and enzymatic activity
in rice seedlings. Acta Physiol. Plant. https://doi.org/10.1007/s11738-014-1760-0 (2015).ii g
y
p
g
2. Weatherley, P. E. Studies in the water relations of the cotton plant: I. the field measurement of water deficits in leaves. New Phytol
49, 81–97 (1950).f ,
(
)
3. Lichtenthaler, H. K. & Wellburn, A. R. Determinations of total carotenoids and chlorophylls a and b of leaf extracts in different
solvents. Biochem. Soc. Trans. https://doi.org/10.1042/bst0110591 (1983). g
4. Verma, S. & Dubey, R. S. Lead toxicity induces lipid peroxidation and alters the activities of antioxidant enzymes in growing rice
plants. Plant Sci. https://doi.org/10.1016/S0168-9452(03)00022-0 (2003). plants. Plant Sci. https://doi.org/10.1016/S0168-9452(03)00022-0 (2003). 65. Sun, M. & Zigman, S. An improved spectrophotometric assay for superoxide dismutase based on epinephrine autoxidation. Anal. Bi
h
htt
//d i
/10 1016/0003 2697(78)90010 6 (1978) p
p
g
5. Sun, M. & Zigman, S. An improved spectrophotometric assay for superoxide dismutase based on epinephrine autoxidation. Anal
Biochem. https://doi.org/10.1016/0003-2697(78)90010-6 (1978).l p
g
(
)
(
)
66. Yordanova, R. Y., Christov, K. N. & Popova, L. P. Antioxidative enzymes in barley plants subjected to soil flooding. Environ. Exp. Bot. https://doi.org/10.1016/S0098-8472(03)00063-7 (2004). 67. Kabir, A. H., Hossain, M. M., Khatun, M. A., Sarkar, M. R. & Haider, S. A. Biochemical and molecular mechanisms associated
with zn deficiency tolerance and signaling in rice (Oryza sativa l.). J. Plant Interact. https://doi.org/10.1080/17429145.2017.13926
26 (2017). (
)
8. Alexieva, V., Sergiev, I., Mapelli, S. & Karanov, E. The effect of drought and ultraviolet radiation on growth and stress markers in
pea and wheat. Plant, Cell Environ. https://doi.org/10.1046/j.1365-3040.2001.00778.x (2001). p
p
g
j
69. Jacyn Baker, C. & Mock, N. M. An improved method for monitoring cell death in cell suspension and leaf disc assays using evans
blue. Plant Cell. Tissue Organ Cult. https://doi.org/10.1007/BF00037585 (1994). nt Cell. Tissue Organ Cult. https://doi.org/10.1007/BF00037585 (1 g
p
g
0. Orozco-Cárdenas, M. L. & Ryan, C. A. Nitric oxide negatively modulates wound signaling in tomato plants. Plant Physiol. 130
487–493 (2002). (
)
1. Dubois, M., Gilles, K. A., Hamilton, J. K., Rebers, P. A. & Smith, F. Colorimetric method for determination of sugars and related
substances. Anal. Chem. https://doi.org/10.1021/ac60111a017 (1956). p
g
72. He, F. Bradford protein assay. BIO-PROTOCOL (2011) https://doi.org/10.21769/bioprotoc.45. Competing interests h Competing interests
The authors declare no competing interests. p
g
The authors declare no competing interes Scientific Reports | (2022) 12:19137 | https://doi.org/10.1038/s41598-022-22354-2 www.nature.com/scientificreports/ Additional informationh Additional information
Supplementary Information The online version contains supplementary material available at https://doi.org/
10.1038/s41598-022-22354-2. Correspondence and requests for materials should be addressed to M.K. or M.S. 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
institutional affiliations. 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 Author(s) 2022 https://doi.org/10.1038/s41598-022-22354-2 Scientific Reports | (2022) 12:19137 |
|
https://openalex.org/W3154644038
|
https://zenodo.org/records/4729657/files/THE%20STALEMATE%20OF%20COMMUNITY%20POLICING%20IN%20SOUTH%20AFRICA.pdf
|
English
| null |
The stalemate of community policing in South Africa
|
Eureka, Social and Humanities./Eureka, Social and Humanities
| 2,021
|
cc-by
| 7,578
|
Original Research Article:
full paper Original Research Article:
full paper Original Research Article:
full paper Original Research Article:
full paper (2021), «EUREKA: Social and Humanities»
Number 2 THE STALEMATE OF COMMUNITY POLICING IN SOUTH
AFRICA Shaka Yesufu
Department of Research and Development
University of Limpopo
Turfloop, Sovenga, Republic of South Africa
Shakazulu17@yahoo.co.uk Abstract With the end of the apartheid regime in South Africa, new police service was needed to promote the transition to democracy. Community policing was introduced from the United Kingdom in the 1990s into South Africa as a channel to heal the wounds and
injustices of the past. Over Twenty-five years down the road, community policing in South Africa has made little or no impact on
the majority of South Africans who will openly admit that they do not attend their local community forums, because they simply do
not trust the police because of its oppressive past. It is a widely held view by several South Africans that the Police Service simply
cannot change overnight from being a very brutal force to become the protectors of citizen’s human rights. This research is a qual
itative study; whereby an extensive literature review was carried, exploring the issues and concepts related to community policing. The findings are that community policing has achieved its desired results. All citizens must go back to the drawing board again to
bring community policing back on track for the benefit of all citizens to whom the police serve and protect. The author argues that the
bitterness and divisions of the past must put be put to one side and that all citizens must co-create a country, where all South Africans
are proudly part of and allowed to make their contributions. Keywords: Barriers, Citizens, community policing forum, Police, Policing, South Africa. 1. Introduction For a better understanding, the article is separated into several parts. The first part
explores the meaning of community policing through international and South African perspec
tives by explaining what the research is all about, including the research aims. The second part
of the article is the development of the article part, which provides a prelude to the build-up
of exploring some of the obstacles to community policing in South Africa. The third part of
the article is the comparative analogy part using the community policing international best
practice model as a guide, providing the reader with several recommendations on how to put
community policing back on track in South Africa. While the final part of the article looks at
what the government, policymakers must do for community policing to be successfully imple
mented in South Africa. Community policing is a difficult concept to define as there is no single agreed defini
tion of it in the field of social sciences. However, common to all the definitions are words such
as “mutual understanding” vis-a-vis the relationship between the police and citizens. A work
ing community policing strategy requires the citizen to make contributions concerning the
needs of the community [1]. The rationale of community policing postulates that communities
can form an association with a common purpose and shared belief in one laudable goal of safe
ty and security. Community policing became the dominant model for policing in many coun
tries towards the end of the twentieth century – including the US, Australia, New Zealand, and
the Netherlands – and it is premised on greater interaction between the police and citizens [2]. Jerome Skolnick and David Bayley [3]. identified four elements of community policing
as follows: – police reciprocal characteristics. This means that police officers are put in a position, where they are forced to work in isola
tion or silos, detached from the community. To discourage this kind of aloofness, citizens are given
a platform to make both their meaningful and voluntary contributions to policing [3]: 61 Law (2021), «EUREKA: Social and Humanities»
Number 2 (2021), «EUREKA: Social and Humanities»
Number 2 Original Research Article:
full paper – area decentralisation of command. This type of decentralisation is imperative for efficiency and collaboration with the com
munity. The purpose of decentralisation is designed to create an enabling environment between the
police and the public [4]: – reorientation of patrols. Skolnick & Bayley [4] provide us with four possible reasons for supporting foot patrols
and a reduction in police emergency responses to crime in our communities. They argued that
foot patrols should be encouraged for the following reasons: (1) crime prevention; (2) main
tenance of order; (3) to generate neighbourhood goodwill; (4) to raise officers’ morale whilst
carrying out their duties: – civilianisation. Skolnick & Bayley [4] argue that the civilianisation of police departments is an opera
tional facilitating factor in building a community’s crime prevention strategy. Especially, when
civilians are recruited for urban cities, where community members are of predominate multicul
tural composition. The arguments, proposed by Skolnick and Bayley [4] above, can be translated
into the South African police context. The decentralisation of commands to local areas without
adequate structures to monitor the type of police service delivery has enabled an atmosphere of
corruption to thrive under the radar for many years. The South African Police Service’s decen
tralised command structures have made it possible for corruption to be institutionalised from
top to bottom in South Africa [5]; Within the last decade, two national police commissioners
have been sacked for corruption. In the United Kingdom, Brogden and Nihar [6] argued that
the deployment of community policing officers dates back 800 years, when such an officer was
called the “Tythingman” (literally one who collects tithes). They were considered to be commu
nity constables [7]. In 1829, Robert Peel, one of the founding fathers of British policing, coined
the phrase ‘policing by consent’, a notion that enabled the community to gain prominence. He
argued that modern-day policing needed the full support of citizens and that the police could not
function effectively without the support of the citizens [8]. Prevention of crime remains one of
the core foundations of policing in our communities today [9]. Police are friends of the citizens,
by winning their hearts and minds. In doing so, the police’s claim to ‘serve and protect’ us is
sustained and legitimised [10]. Original Research Article:
full paper (2021), «EUREKA: Social and Humanities»
Number 2 (2021), «EUREKA: Social and Humanities»
Number 2 and citizens can and should work together to identify and effectively solve community problems
Community Policing is a department-wide philosophy that requires department-wide acceptance
and implementation [17]. Community Policing calls for meaningful organizational change and re
structuring. Community Policing requires an improvement in the delivery of service to the com
munity [18]. Next, the author looks at community policing in South Africa. Community Policing in South Africa. Monique Marks [19] argues that the term ‘community policing’ became popular, because
it was found in the 1997 South African government policy document, published by the Depart
ment of Safety and Security. Marks [19] argues that Community Policing is a joint effort from
the police/citizens, coming together under one platform to set up crime prevention strategies that
work. The five components of community policing are found in the South African government
policy document of 1997 summarised as follows: – familiar and acceptable service, encapsulated in the provisioning of a professional police
i
h
i
i
i
d familiar and acceptable service, encaps
service that is responsive to community needs; service that is responsive to community needs; – professionalisation and partnership; – finding solutions to problems that cause crime; – accountability: law enforcement free from biases; – empowerment of communities/members to make meaningful contributions in their re
spective communities. – empowerment of communities/members to make meaningful contributions in their re
spective communities. The South African Government White Paper 1998. The South African Government White Paper 1998. This Paper defined crime prevention as: “all activities that reduce, deter or prevent the oc
currence of specific crimes, firstly by altering the environment, in which they occur, secondly by
changing the conditions, which are thought to cause them, and thirdly by providing a strong deter
rent in the form of an effective criminal justice system.” The Paper also specifically describes the new roles for the Community Police Forums in
South Africa as follows: The Paper also specifically describes the new roles for the Community Police Forums in
South Africa as follows: – cooperation with local government to jointly set crime prevention priorities; – locate flashpoints, criminal behaviours, and community crime activities; te flashpoints, criminal behaviours, and community – to assist in the formulation of crime prevention programmes. Community Police Forums in South Africa. The Interim Constitution Act 2000 of 1993 established the Community Police Forums. – area decentralisation of command. There are four key elements of community policing in the United Kingdom as follows:
– police consultative groups; There are four key elements of community policing in the United Kingdom as follows:
– police consultative groups; – community police officers in communities – predominantly foot patrols, popularly re
ferred to as the ‘bobby on the beat’; ferred to as the ‘bobby on the beat’; – community involvement in crime prevention strategies, such as Neighbourhood Watch
schemes; – membership of special constabulary – volunteer police officers (these are called reservists
in South Africa). A police service that does not work in partnership with members of the community will
not succeed, when it comes to crime information and investigation [11]. One can argue that, in the
absence of such a partnership, community policing was destined to fail from the onset or during
the introductory stage of it. Community policing cannot work well in a divided country, when
there is no spirit of cohesion [12]. A major objective of community policing is to establish an active
partnership between the Police and the community through which crime, service delivery, and
police-community relations can jointly be analyzed and appropriate solutions designed and imple
mented [13, 14]. Community Policing moves away from the incident-driven style of traditional policing by
following a more problem-oriented approach [15]. This means that reported crimes, complaints,
and telephone calls no longer serve as the primary determinants of how police resources should
be used. The police still react to individual complaints, but further, instead of merely waiting for
individual calls for service, the police – with the assistance of the community continuously identify
and try to solve recurring problems[16]. Community Policing is based on the premise that the police 62 Law (2021), «EUREKA: Social and Humanities»
Number 2 Original Research Article:
full paper 3. Result The author provided the readers with some of the identified barriers to community polic
ing in South Africa, the author thinks that until these barriers are removed, community policing
will achieve little or no progress. The identified barriers to community policing in South Africa
are as follows: a) importation of foreign police ideology and inability to fully transfer community policing
to the South African context [12]. Community policing is important because it is a key component of an export drive from
Western countries like UK and USA in the development of new policing structures in transitional
societies – those that might once have been described as ‘Third World’ (predominantly African
countries and the Indian sub-continent) or (optimistically) as ‘developing’ and are being forced by
economic and social exigencies (such as rising recorded crime rates) to construct new safety and
security agencies [6, 7]. The Western police consultants have been able to find a ‘niche’, to which
the Community can be sold and resold [11] Policing brands can be exported, sold, and profited according to market demand-pull fac
tors [20]. The author identifies that two factors are at play here. First, the host countries to the newly
introduced concept of community policing were not aware of how community policing works in
these foreign countries or how best to evaluate whether it works or not. The author hypothetically
provided the reader(s) with a scenario, where if any person is buying a new car, one expects the
car manual to be provided at the time of the sale. The author argues that, in looking at the South
African context today, both the exporters and importers of community policing failed to do their
research very well and did not take into consideration the needs of South Africans. Because South
Africa was very volatile in the 1990s, when community policing was imported from the West,
South Africans have not yet recovered from the racial hostilities of the apartheid era, exacerbated
by police brutality and political killings [21]. Second, one can safely argue that, from the beginning,
community policing was a very risky policing endeavour, hurriedly introduced by politicians, and
was bound to fail. The demographical, ecological, and social needs of the host nations were not
properly assessed [22]. 2. Materials and Methods This is a qualitative research, where the researcher carried out an extensive consultation,
relying on secondary data. Some of the data review processes included the following: books, jour
nals, official documents, media reports, and internet sources [20]. The use of secondary data as the
researcher understands it, is to avoid a time-consuming exercise, where the researcher is expected
to speak directly to several participants. The data, collected from the literature review, were ana
lysed into emerging themes relating to the research topic of community policing. The researcher
ensured that his results were clearly articulated and his findings were highlighted as a basis for
further research relating to community policing. (2021), «EUREKA: Social and Humanities»
Number 2 A Community Police Forum was defined as a group of citizens, coming together for a common
purpose, defined by both individual and collective safety. The functional roles for the CPFs are
as follows: – the provision of services to community members; – the evaluation of service delivery; assessing the service about local policing priorities; – to carry an appraisal of visible policing; – the selection and recruitment of law enforcement personnel; – the handling and investigation of complaints from members of the public; – the handling and investigation of complaints from – provision of protective services at gatherings; – patrolling for personal and business safety; – to bring offenders to justice. Objectives of the Community Police Forums in South Africa: – Promoting a partnership between the community and the service. – Supporting communication between the service and the community. – Providing effective service delivery nationwide. – Improving transparency in the service and accountability of the service to the community. – Promoting social problem identification and problem-solving by the service and the com
munity. (www.saps.gov.za). Aim of research. The research has three aims. First, the research was carried out to ex
plore and identify some of the persistent barriers to community policing in South Africa. Second, Aim of research. The research has three aims. First, the research was carried out to ex
plore and identify some of the persistent barriers to community policing in South Africa. Second, 63 Law (2021), «EUREKA: Social and Humanities»
Number 2 (2021), «EUREKA: Social and Humanities»
Number 2 Original Research Article:
full paper to draw a comparative international best-policing practice model, where community policing has
successfully implemented to the benefit of citizens. to draw a comparative international best-policing practice model, where community policing has
successfully implemented to the benefit of citizens. This research is designed to find some recommendations on how best community policing
must be implemented in South Africa. (2021), «EUREKA: Social and Humanities»
Number 2 Biko [27] described the police as: The philosophy behind the police action in this country seems to be based on both con
scious and unconscious revisitation of oppressive police history... ‘the white man, if not intel
lectually, at least in terms of power. White people, working through their vanguard – the South
African Police – have come to realise the truth of that golden maxim – if you cannot make a man
respect you, then make him fear you’ [27, p. 83]; c) negative media reports and police abuse of human rights. Over the years, the media have been highly diligent in exposing police brutality in
South Africa. Hardly a month passes in South Africa without police brutality being in the
spotlight, with incidents, such as the murder of Andries Tatane in Ficksburg in 2011, following
a poor service delivery protest, and the gruesome and horrific murder of Mido Macia, the Mo
zambican taxi driver, who was tied up and dragged along the road behind a police vehicle. The
author argues that this type of policing is barbaric and should have no place in any democratic
country. The South African Police have refused to relinquish the culture of violence, inherit
ed from the apartheid past. The orientation is that violence brings quick results, informed by
control and power; p
d) divided communities and social class. d) divided communities and social class. Because of its history of racial divisions, South Africa can be characterised by racial dif
ferences, social class differences, religious and cultural differences, sexual orientation differences,
and political differences [28]; e) xenophobic attacks on black African foreigners in South Africa. Within the last ten years, attacks on black foreigners have increased in South Africa. This
increase in xenophobic attacks and derogatory references has resulted in the construction of “oth
er” black Africa migrants, known as “Ama kwere Kwere”, meaning “people who speak in difficult
and incomprehensible languages”. The inferiorisation and construction of the ‘other’ have become
very popular amongst South Africans, in many cases leading to resentment, hostility, and physical
attacks, sometimes resulting in loss of lives and property. Black migrants from Mozambique, Ma
lawi, Zimbabwe, Congo, Nigeria, Somalia, Ethiopia, and Burundi have all been targeted during the
heightened state of xenophobia, witnessed in South Africa, especially in 2008, when xenophobic
incidents reached a shameful apogee. (2021), «EUREKA: Social and Humanities»
Number 2 Original Research Article:
full paper Original Research Article:
full paper (2021), «EUREKA: Social and Humanities»
Number 2 shacks and informal settlements, are blacks [24]. The author argues that, under the circumstances
highlighted above, community policing cannot grow in South Africa as long as economic inequal
ities, lack of trust, fear, and suspicion, and racial divisions in South Africa persist [25]. Most black
South Africans still see members of the South African Police Service as the oppressive appara
tus of the state and consequently do not trust the police [18]. The government of South Africa
and the police now need to work very hard to win the full support of South African citizens by
explaining to them the desired objectives of community policing. Until this message is delivered
effectively to the citizens of South Africa, community police forums will continue to experience
poor attendance [26]; shacks and informal settlements, are blacks [24]. The author argues that, under the circumstances
highlighted above, community policing cannot grow in South Africa as long as economic inequal
ities, lack of trust, fear, and suspicion, and racial divisions in South Africa persist [25]. Most black
South Africans still see members of the South African Police Service as the oppressive appara
tus of the state and consequently do not trust the police [18]. The government of South Africa
and the police now need to work very hard to win the full support of South African citizens by
explaining to them the desired objectives of community policing. Until this message is delivered
effectively to the citizens of South Africa, community police forums will continue to experience
poor attendance [26]; b) citizens’ lack of trust and confidence in the police. b) citizens’ lack of trust and confidence in the police. The researcher argues that South African citizens have every right not to trust the police, be
cause the police have a long and shameful history of using violence against them. Examples of the
South African Police chequered and shameful history, characterised by brutality, can be deduced
from the few out of some incidents as follows: The author argues that the death of Steve Biko at the hands of the police is just one of several
incidents of police brutality in South Africa. 3. Result For example, in South Africa, the importers of community policing may
have been motivated by the quest to realise the rainbow nation, made possible by the National Peace
Accord. The government of South Africa was put under pressure by the international community. It was hoped, that the creation of the rainbow nation would miraculously take away the pains of the
injustices of the past [17]. The author argues that it is very easy to say ‘let’s forget about the past and move on’; how
ever, the crucial, unanswered question is whether the South African government has put enough
psychological and economic support in place to cater to the needs of those South Africans, who
suffered both psychological and economic hardship during apartheid [23]. What we do know, how�
ever, is that most of the economically displaced and disempowered South African citizens, living in 64 Law Alexandra Police Station and CPF. Alexandra police station is located in the north-eastern township of Johannesburg. Alexandra
Township represents the opposite of Parkview. Alexandra is predominately black ‘native township’. Black South Africans were restricted to reside in townships under obnoxious laws like the Group Ar
eas Act of 1950, which divided cities and towns into segregated living. Millions of blacks, cloureds,
Indians were forcibly removed from their ancestral and original homes, because they were regarded
as trespassers in the country of birth. The apartheid successive regimes laid the foundation of some of
today’s inequalities that still permeates and divides us in South Africa today. The author argues that the
apartheid injustices of the past cannot be healed by 25 years of democratic rule in South Africa. The
healing process may take more than a century to heal properly. So long as the majority of blacks contin
ue to leave in abject poverty, hunger, and squalor, it is misleading to conclude that South Africans are all
united as one community, living in a rainbow nation. With the high unemployment rate amongst black
South Africans, trapped in informal settlements “Shacks”, made out of corrugated iron zinc houses. Community policing cannot be expected to be rolled out successfully under the bizarre economic and
disempowered circumstances our brothers and sisters have lived and continue to live in South Africa. Mottiar [30] argues that, due to the hallmark of apartheid, Alexandra township was not
properly catered. There are pieces of evidence of lack of access to necessities of life. One can argue
that little or no economic investments mean that a range of socio-economic challenges persists,
despite a decade of democracy in South Africa. Next, the author looks at the Brixton police station and its CPF. B i
P li
S
i
d CPF Brixton police station is located in the west of inner-city Johannesburg. The CPF was estab
lished in 1993 and has been notable for fundraising and the establishment of a victims center and
several drugs rehabilitation centers, set up by NGO’s. In short, the more funds communities can donate, the more likely they are to be well policed,
in comparison to poorer communities. Community policing becomes a pay-as-you-go system,
based on affordability. It is safer to reside in affluent communities because they can afford to fund
policing needs. This raises a crucial question: Who is supposed to fund policing – citizens or the
government? (2021), «EUREKA: Social and Humanities»
Number 2 Looking at the impact of social class on community policing in South Africa, Millicent
Maroga [29] shows us what it means to live in a country with different types of community polic
ing. Maroga [29] in her research, entitled Community policing and accountability at station level,
invites us to look at how the implementation of community policing differs from one community
to another depending on the community’s economic power and social class. In brief, she argues
that affluent neighbourhoods with financial strength spend more on resources to assist the police
to obtain a better partnership and security than marginalised communities who cannot afford to 65 Law (2021), «EUREKA: Social and Humanities»
Number 2 (2021), «EUREKA: Social and Humanities»
Number 2 Original Research Article:
full paper Number 2 purchase patrol vehicles. From her qualitative research into community policing in Parkview, Al
exandra, and Brixton police stations, the researcher provides brief descriptions of and a comparison
between these three separate police stations in Gauteng, Johannesburg, South Africa, where com
munity policing is operational. The Parkview Police Station and CPF. Parkview police station is located in the exclusive white and wealthy suburb about seven
kilometres north of Johannesburg. Parkview is described as one of the best-policed suburbs in
Gauteng. Members of the community use cell phone numbers of all members of the community as
a communication tool to warn members of the community of any criminal suspects in the area, or
that a crime has taken place or maybe about to occur. Police also send messages to residents from
computers at the police station, warning them about crime. Alexandra Police Station and CPF. Police use of discretionary powers is well documented by previous police researchers
in South Africa [12, 19, 31, 32]. High crime rates in South Africa. The National Crime Prevention Strategy 1996, one of the policy documents, setting the
agenda for community policing in South Africa, clearly explains the impact of crime…dependent
on the quality of the relationship between the police and community’ [33]. The author provides us
with some recent valuable insights using annual crime statistics, released by the SAPS, to show the
extent of crime in South Africa as follows: 1. House Breaking. 1. House Breaking. This remains the number one crime in South Africa. In 2019/2020 year alone, about
1.3 million incidences of housebreaking were reported to the police. This represented 5.8 %
of the households in South Africa. Below is a province by province breakdown as fol-
lows (Table 1). This remains the number one crime in South Africa. In 2019/2020 year alone, about
1.3 million incidences of housebreaking were reported to the police. This represented 5.8 %
of the households in South Africa. Below is a province by province breakdown as fol-
lows (Table 1). 66 Law Table 1
Crime rates in South Africa
Gauteng
336 358
6.81%
Kwazulu-Natal
195 599
6.5%
Western Cape
113 343
6.01%
Limpopo
70 066
4.41%
Mpumalanga
69 207
5.36%
Eastern Cape
67 786
4.06%
North West
59 678
4.95%
Free State
34 800
3.75%
Northern Cape
24 730
7.39%
Source: Stats sa, 2018/2019 What we can deduce from the above diagram is that Gauteng is the epic centre for house
breaking crime in South Africa. It can be argued, that good neighbourliness will go a long way to
deter housebreaking. There is a problem, when you reside in affluent suburbs, where your next-door
neighbour(s) ever hardly speak with you or know your name. This type of neighbourhood is more
vulnerable to housebreaking, because there is no community spirit or social cohesion. When one
becomes a victim of crime, your neighbours look at the other side and tell the police that they saw
nothing. The author writes us from his shared experiences having been a victim of housebreaking
a couple of times in South Africa. Criminals capitalise on lack of community social participation,
they easily prey on their target with relative ease. The stronger the community bonds, the much
harder it is for citizens to suffer housebreaking. In communities, where there are neighbourhood
watches, housebreaking is reduced to the barest minimum. One can argue that effective community
policing is needed in South Africa for citizen’s safety. As not all citizens can afford the luxury of
paying for private armed response security. (2021), «EUREKA: Social and Humanities»
Number 2 Original Research Article:
full paper Minaar [30] provides us with some of the reasons why community policing was abandoned
in South Africa. He argues that ‘this abandonment, with SAPS personnel strongly believing it
to be “too soft” for the tough crime conditions in South African townships, was also due in part
to several inherent constraints. At community policing, inception, personnel of SAPS were still
largely undertrained and under-skilled although not initially apparent, while still paying lip service
to a community-oriented approach (using all the appropriate terminology) the SAPS, as early as
the launch of the Community Safety Plan 1995, had already demonstrated – if one read between
the lines and observed the special operations, launched as part of this plan – “their intentions to
revert to more traditional methods to combat crime”…the implementation of Operation Sword and
Shield with its “return to basics” policing approach… Community policing per se, faded into the
background. Meanwhile, Marks [19] argues that ‘members of the SAPS have always been undermined by
members of the public whilst attending Community Police Forum meetings. They are opined that
they have to hold the police to account for every operational decision taken. In reality, we do know
that it is practically impossible for the police to dialogue with citizens always before operational
decisions are taken. These arrangements will cost lives on an unimaginable scale if allowed as a
standard procedure. The police is not a 9 am-5 pm everyday job. Certain split decisions have to be
taken sometimes to save lives, spontaneous decisions have to be taken using one’s discretion. The
infallibility of human beings places the onus on police management to be extra conscious when tak
en such decisions. Marks [33] argues that police officers, who have been witness to endless violent
crimes and come face to face with previously known suspects they have arrested in the past, are
underpaid. Policing is one of the most visible government organisation, found in most democratic
countries of the world [38]. It is necessary to clearly define what ‘community policing’ actually means in South Africa
for a better understanding of it. The desired benefits and roles and responsibilities of all stakehold
ers need to be clearly explained to all citizens. The police must re-evaluate their communication
mode and medium with the public. (2021), «EUREKA: Social and Humanities»
Number 2 The use of violence should be discouraged and replaced with
verbal communication skills to win the hearts and minds of South Africans. CPF attendance and
participation should be made mandatory for the police and citizens alike. Lack of attendance should
be reported to oversight committees and with a follow-up. Police in South Africa cannot police the
country effectively without the community partnering and supporting the police. Policy-makers
should facilitate more community consultative forums and participation between the police and
citizens [39]. The South Africa government must facilitate and encourage research-led policing. It
is necessary to examine why community policing failed in South Africa and what might be done to
make it work. The police service should be encouraged to open its doors to independent academic
researchers, as it is currently done in Australia, the UK, the USA, Canada, the Netherlands, and
New Zealand [40]. The author argues that there is more to be gained from such collaborative part
nerships with both researchers and research institutions. Finally, the contentious issue of the use
of firearms and public order control needs to be looked at as a matter of urgency, because some of
the current discontents arise from fatal shooting incidents and deaths of relatives in police custody. Community policing only works in countries with similar histories, demographics, and the same
social context [41–44]. Community policing was poorly implemented in South Africa. The expec�
tation that community policing was going to be waving a magic policing model to heal the wounds
of the apartheid past turned out to be wishful thinking [6, 12]. The historical antecedents and racial
injustices of the past governments in South Africa make it complicated for community police to
grow in South Africa. Community policing though was transferred from abroad [45], but did not
have the time to bear fruits and was not properly nurtured [46]; Hence its foundation in South Af
rica was shaking and not deeply rooted enough to realise its desired objectives. 1. House Breaking. The advantages of Community Policing includes: reduces the incidence of crime and fear
of victimization through more responsive and effective policing; increased community satisfaction
with the services, provided by the police and citizens through functional neighbourhood watches;
better coordination and allocation of responsibilities between the police and other criminal justice
and social service agencies; the support of the community for efforts, aimed at getting information,
supplementing or obtaining more police resources; the active participation of the community in
crime prevention; better appreciation of the constraints and problems, facing the police; prioriti
zation of services and the allocation of available resources to meet citizen’s list of safety priorities. 2. Home Robbery. 2. Home Robbery. In 2018/2019, about 260 000 home robberies were recorded, affecting 1 % of all households. The most common weapon, used to perpetrate the crime, were guns (54 %), Knives (47 %), About 12 000 murders were committed in South Afric 4. Car Hijacking: recorded about 32 000 for the same year. 5. Street robbery: for the same year stands at 580 000 [19, 34–37]. The author argues that, the more victims of crime, the lower citizens’ trust and confidence
in the police. We must return to the drawing board in South Africa to work out strategies, built on
crime prevention and community policing, to make our communities safer. Without the establishment of a working partnership between citizens and the police, the
desired goals of community policing will not be realised. South African Police Service structural defects. South African Police Service structural defects. Pelser [28]. identifies some challenges, faced by community police forums in South Africa. They are as follows: Pelser [28]. identifies some challenges, faced by community police forums in South Africa. They are as follows: – No consistent implementation and interpretation of community policing. – Members of CPFs and the SAPS continued to hold different expectations about the core
elements and objectives of community policing [29]. – Members of CPFs and the SAPS continued to hold diff
elements and objectives of community policing [29]. – Lack of full government support and allocated budget. 67 Law Law (2021), «EUREKA: Social and Humanities»
Number 2 Original Research Article:
full paper (2021), «EUREKA: Social and Humanities»
Number 2 (2021), «EUREKA: Social and Humanities»
Number 2 The author argues that we cannot comfortably talk about the implementation of community
policing, when some sections of society are feeling marginalised, discriminated against, perse
cuted, ostracised, and not protected equally in law, and when they perceive that they are not being
given equal opportunities to employment and the necessities of life. You will fully participate in
it. Police forces are tightly closed organisations, and very few people in the outside world clearly
understood police culture and the extent of its pervasiveness. In some countries, the police and the
public have become so detached from each other that in some communities the relationship has
broken down and been replaced by antagonism, resentment, and anger. Community policing cannot
thrive under these circumstances. Community policing is a philosophy that guides and informs
police management styles and operational strategies both internationally and in South Africa. It
focuses more on the establishment of police-community partnerships and a problem-solving ap
proach. The truth of the matter is that we have not got the implementation of community policing
right in South Africa. We must go back to the drawing board to correct our mistakes. References
[1] Palmiotto, M. J. (2015). Community Policing: A Police –Citizen Partnership. Police image and public expectations of the police
to decrease crime. London: Taylor Francis. References
[1] Palmiotto, M. J. (2015). Community Policing: A Police –Citizen Partnership. Police image and public expectations of the police
to decrease crime. London: Taylor Francis. Original Research Article:
full paper Original Research Article:
full paper References [2] Saureman, A., Ivkovic, S. K., Meyer, D.; Haberfield, M. (Ed). (2019). Exploring the reflection between support for community
policing and police integrity in South Africa. Springer, 11–137. doi: http://doi.org/10.1007/978-3-030-29065-8_5 [3] Skolnick, J., Bayley, D. (1986). The New Blue Line: Police Innovation in Six American Cities. New York: The Free Press, 246. [4] Carter, D.; Hoover, L. (Ed.) (1992). Community Alliance, in Police Management: Issues and Perspectives. Washington: Police
Executive Research Forum. [4] Carter, D.; Hoover, L. (Ed.) (1992). Community Alliance, in Police Management: Issues and Perspectives. Washington: Police
Executive Research Forum. [5] Trinkner, R., Tyler, T. R., Goff, P. A. (2016). Justice from within: The relations between a procedurally just organizational
climate and police organizational efficiency, endorsement of democratic policing, and officer well-being. Psychology, Public
Policy, and Law, 22 (2), 158–172. doi: http://doi.org/10.1037/law0000085 [5] Trinkner, R., Tyler, T. R., Goff, P. A. (2016). Justice from within: The relations between a procedurally just organizational
climate and police organizational efficiency, endorsement of democratic policing, and officer well-being. Psychology, Public
Policy, and Law, 22 (2), 158–172. doi: http://doi.org/10.1037/law0000085 [6] Brogden, M. Nijhar, P. (2005). Community Policing: National and international models and approaches. Devon: Willan Pub
lishing, 272. doi: http://doi.org/10.4324/9781843925798 [6] Brogden, M. Nijhar, P. (2005). Community Policing: National and international models and approaches. Devon: Willan Pub
lishing, 272. doi: http://doi.org/10.4324/9781843925798 [7] Kelling, G. L. (2019). Community Policing. Rightly Understood. New York: Springer. [7] Kelling, G. L. (2019). Community Policing. Rightly Understood. New York: Springer. ] Kelling, G. L. (2019). Community Policing. Rightly Un [8] Cossyleon, J. (2019). Community Policing. Chicago: Wiley & Sons Ltd. doi: http://doi.org/10.1002/9781118568446.eurs0058
[9] Ivkovic, S., Haberfeld, M. R. (Eds.) (2015). Studying Police Integrity. Police Integrity across the world. New York: Springer,
1–36. doi: http://doi.org/10.1007/978-1-4939-2279-6_1 [ ]
y
,
(
)
y
g
g
y
p
g
[9] Ivkovic, S., Haberfeld, M. R. (Eds.) (2015). Studying Police Integrity. Police Integrity across the world. New York: Springer,
1–36. doi: http://doi.org/10.1007/978-1-4939-2279-6_1 [9] Ivkovic, S., Haberfeld, M. R. (Eds.) (2015). Studying Police Integrity. Police Integrity across the world. New York: Springer,
1–36. doi: http://doi.org/10.1007/978-1-4939-2279-6_1 [10] Goetz, B. (2016). Community Policing and the Welfare State: The Problem of Institutional Solidarity. Paper Presented at the
Urban Affairs Association Annual Conference. [10] Goetz, B. (2016). Community Policing and the Welfare State: The Problem of Institutional Solidarity. Paper Presented at the
Urban Affairs Association Annual Conference. Goetz, B. (2016). 4. Conclusion Community policing is deeply rooted in the notion of partnership between police and the
community. It is designed to make the police responsive to the needs of the community. The closer
the police are to citizens, the more they will be able to deal with crime effectively. 68 Law References Community Policing and the Welfare State: The Problem of Institutional Solidarity. Paper Presen
U b
Aff i
A
i ti
A
l C
f Urban Affairs Association Annual Conference. [11] Marenin, O. (2018). Policing Change. Changing Police. International Perspectives. London: Taylor Francis. doi: http://
doi.org/10.4324/9781315861487 [11] Marenin, O. (2018). Policing Change. Changing Police. International Perspectives. London: Taylor Francis. doi: http://
doi.org/10.4324/9781315861487 [12] Yesufu, S. (2017). The Reality of Crime and Policing in the United Kingdom and South Africa, Reach Publishers. Cape Town. [13] Kelling, G. L. (2019) Community Policing. Rightly Understood. New York: Springer. [12] Yesufu, S. (2017). The Reality of Crime and Policing in the United Kingdom and South Africa, Reach Publishers. Cape Town. [13] Kelling, G. L. (2019) Community Policing. Rightly Understood. New York: Springer. [13] Kelling, G. L. (2019) Community Policing. Rightly Understood. New York: Springer. [14] Dias, R. A. (2016). Racism Creates Barrier to Effective Community Policing. Southern Illinois University Law Journal,
40 (3), 512–524. [14] Dias, R. A. (2016). Racism Creates Barrier to Effective Community Policing. Southern Illinois University Law Journal,
40 (3), 512–524. [15] Cummings, L. (2019). Study finds community policing improves attitudes towards the police. Yale News. [16] Tyler, T. R., Jackson, J., Mentovich, A. (2015). The Consequences of Being an Object of Suspicion: Potential Pitfalls of Proac
tive Police Contact. Journal of Empirical Legal Studies, 12 (4), 602–636. doi: http://doi.org/10.1111/jels.12086 [17] Public Sector Association (2018). Strategies to improve community policing. [18] Yesufu, S., Motsepe, L. L. (2020). Reflections on the Capacity of Policing Community Protests: A South Africa Perspective. International Journal of Social Sciences and Humanity Studies. [19] Marks, M. (1995). Community Policing, Human Rights and the Truth and Reconciliation Commission. Marks, M. (1995). Community Policing, Human Rights and [20] Presidential Task Force on 21st Century Policing (2015). Final Report of the President’s Task Force on 21st Century Policing. Office of the Community Oriented Policing Services. Washington. [21] Mummolo, J. (2018). Militarization fails to enhance police safety or reduce crime but may harm police reputation. Proceedings
of the National Academy of Sciences, 115 (37), 9181–9186. doi: http://doi.org/10.1073/pnas.1805161115 [22] Shjarback, J. A., Nix, J., Wolfe, S. E. (2017). The Ecological Structuring of Police Officers’ Perceptions of Citizen Cooperation. Crime & Delinquency, 64 (9), 1143–1170. doi: http://doi.org/10.1177/0011128717743779 69 Law (2021), «EUREKA: Social and Humanities»
Number 2 In Search of Safety: Police Transformations and Public Responses in South
130 (1), 259. [37] Minnaar, A. (2010). CRIMSA 2009 Conference Specia Edition No. 2. [37] Minnaar, A. (2010). CRIMSA 2009 Conference Specia Edition No. 2. [38] Yesufu, S. (2013). Police Corruption. A threat to South Africa democracy. Just Africa Journal, South Africa, All African
Criminal Justice Association. [39] Dunham, G., Alpert, G. P. (2001). Critical Issues in Policing: Contemporary Readings. Illinois: Waveland Pr [40] Dixon, B. (2000). Accountable Policing: A Four-Dimensional Analysis. South Africa Criminology Journal, 13 (1), 69–83. [40] Dixon, B. (2000). Accountable Policing: A Four-Dimensional Analysis. South Africa Criminology Journal, 13 (1), 69–83. [41] Friedman, W.; Rosenbaum, D. P. (Ed.) (1994). The Community Role in Community Policing. The Challenges of Community
Policing: Testing the Promises. Thousand Oaks: Sage Publications, 263–269. doi: http://doi.org/10.4135/9781483327006.n16
[42] Eck, J., Spelman, W. (1987). Problem-Oriented Policing in Newport News. Washington: National Institute of Justice and Police [41] Friedman, W.; Rosenbaum, D. P. (Ed.) (1994). The Community Role in Community Policing. The Challenges of Community
Policing: Testing the Promises. Thousand Oaks: Sage Publications, 263–269. doi: http://doi.org/10.4135/9781483327006.n16 [42] Eck, J., Spelman, W. (1987). Problem-Oriented Policing in Newport News. Washington: National Institute of
Executive Research Forum. 3] Minnaar, A. (2010). CRIMSA 2009 Conference Specia Edition No. 2. [43] Minnaar, A. (2010). CRIMSA 2009 Conference Specia Edition No. 2. [44] Malan, M.; Holm, T. T., Elde, E. B. (Eds.) (2001). Peacebuilding in Southern Africa: policing people in Mozambique and South
Africa. Peacebuilding and Police Reform. London: Frank Cass, 179–198. doi: http://doi.org/10.4324/9780203061855-14 [44] Malan, M.; Holm, T. T., Elde, E. B. (Eds.) (2001). Peacebuilding in Southern Africa: policing people in Mozambique and South
Africa. Peacebuilding and Police Reform. London: Frank Cass, 179–198. doi: http://doi.org/10.4324/9780203061855-14 [45] Steinberg, J. (2004). Monograph 110: Sector policing on the West Rand: Three case studies. [46] Brogden, M. (2002). Implanting Community Policing in South Africa: A failure of history of context and theory. Liverpool
Law Review, 24, 157–179. doi: http://doi.org/10.1023/a:1023937614261 © The Author(s) 2021
This is an open access article under the CC BY license
(http://creativecommons.org/licenses/by/4.0). © The Author(s) 202
This is an open access article under the CC BY licens
(http://creativecommons.org/licenses/by/4.0
Received date 24.02.2021
Accepted date 23.03.2021
Published date 31.03.2021 Received date 24.02.2021
Accepted date 23.03.2021
Published date 31.03.2021 Accepted date 23.03.2021 Published date 31.03.2021 How to cite. Yesufu, S. (2021). The stalemate of community policing in South Africa. (2021), «EUREKA: Social and Humanities»
Number 2 (2021), «EUREKA: Social and Humanities»
Number 2 Original Research Article:
full paper Original Research Article:
full paper Number 2 [23] Yesufu, S. (2020). Human Trafficking: A South African Perspective. Ebangi. Journal of Social Sciences and Humanities,
17 (6), 103–120. [23] Yesufu, S. (2020). Human Trafficking: A South African Perspective. Ebangi. Journal of Social Sciences and Humanities,
17 (6), 103–120. [24] Singh, S., Khan, S. (2020). Empowering Women in Blue Uniforms – Gender and Police in South Africa. Gender Questions,
7 (1), 15–30. doi: http://doi.org/10.25159/2412-8457/6769 [25] Qkalhekile, G and Ndelela, M. (2020) Crime in South Africa. Crime Law and Social Change, 1 (1), 1–19. [26] Beck, C., Rice, C. (2016). How Community Policing Can Work. Available at https://www.nytimes.com/2016/08/12/opinion/
how-community-policing-can-work.html Last accessed: 05.03.2021 [27] Biko, S. (2017). I write what I like. South Africa. Pan Macmillan. [27] Biko, S. (2017). I write what I like. South Africa. Pan Macmillan. ] Biko, S. (2017). I write what I like. South Africa. Pan M [28] Pelser, E. (1999) The Challenges of community Policing in South Africa. Occasional Paper No 42. Institute for Security Stud
ies (ISS). [29] Maroga, M. (2005). Community Policing and Accountability at Station Level. Center for the Study of Violence and Reconcil
iation (CSVR) Braamfontein. South Africa. [30] Singh, D. (2004). Violators and Victims: A Historical Review of Policing in South Africa after a Decade of
Criminological, 17 (3), 86–98. [31] Leggett, T. (2005) Just Another Miracle: A Decade of Crime and Justice in Democratic South Africa. Social Research,
72 (3), 581–604. [32] Minaar, A. (2008). Community Policing in a high crime transitional state: The case of South Africa since democratisation in
1994. 21st Annual ANZOC conference: National Convention Centre. Canberra. [32] Minaar, A. (2008). Community Policing in a high crime transitional state: The case of South Africa since democratisation in
1994. 21st Annual ANZOC conference: National Convention Centre. Canberra. [33] National Crime Prevention Strategy (NCPS) (1998) Republic of South Africa Gover [33] National Crime Prevention Strategy (NCPS) (1998) Republic of South Africa Government Press. [33] National Crime Prevention Strategy (NCPS) (1998) Republic of South Africa Government Press. [34] Crime Statistics South Africa. Available at: http://www.statssa.gov.za/?cat=26 [35] South African Police Service (SAPS). Available at: https://www.saps.gov.za/careers/careers.php [35] South African Police Service (SAPS). Available at: https://www.saps.gov.za/care [35] South African Police Service (SAPS). Available at: https://www.saps.gov.za/careers/careers.php [36] Gastrow, P. and Shaw, M. (2001). (2021), «EUREKA: Social and Humanities»
Number 2 EUREKA: Social and Humanities, 2, 61–70. doi: http://doi.org/10.21303/2504-5571.2021.001721 70 Law
|
https://openalex.org/W3000390490
|
https://ojs.ifes.edu.br/index.php/ric/article/download/415/368
|
Portuguese
| null |
PALAVRA CANTADA: A POTÊNCIA COMUNICATIVA, O ENCANTO ESTÉTICO E USO PEDAGÓGICO DO ACALANTO NA FORMAÇÃO DE LEITORES INFANTIS
|
Revista Ifes Ciência
| 2,019
|
cc-by
| 8,800
|
Artigo submetido em 03/08/2019, aceito em 01/09/2019 e publicado em 20/12/2019 Artigo submetido em 03/08/2019, aceito em 01/09/2019 e publicado em 20/12/2019 Resumo: O objetivo deste trabalho é investigar as características do subgênero textual acalanto dentro
do espectro de produções artísticas destinadas ao público infantil quanto à sua eficácia comunicativa,
ao seu encanto estético e ao seu uso pedagógico na formação de leitores e no processo de ensino e
aprendizagem, desde os primeiros anos de alfabetização. Para tal, serão analisados os recursos sonoros
e linguísticos operados na confecção das faixas do álbum “Canções de ninar”, do projeto Palavra
Cantada. Palavras-chave: Palavra cantada; acalanto; formação do leitor; semiótica. Abstract: This work seeks to investigate the characteristics of the textual subgenre acalanto within the
spectrum of artistic productions destined to the children regarding its communicative efficacy, its
aesthetic charm and its pedagogical use in the formation of teaching and learning process since the
first years of literacy. This study analyzes the sound and linguistic resources used in the making of the
tracks of the album “Canções de ninar”, by the project Palavra Cantada. Keywords: Sung word; acalanto; reader training; semiotics. sociais de leitura e escrita, a canção segue
com seu poder encantatório e sua eficácia
comunicativa, despertando, desde a mais
tenra
infância,
as
potencialidades
comunicacionais,
linguísticas,
sonoras,
dinamogênicas1, informativas e culturais 1 Inda [sic] estará certo a gente chamar uma música
de molenga, violenta, comoda [sic] porquê [sic]
certas
dinamogenias
fisiológicas
amolecem
o PALAVRA CANTADA: THE COMMUNICATIVE POWER, THE AESTHETIC
CHARM AND THE PEDAGOGICAL USE OF ACALANTO IN THE
FORMATION OF CHILDREN READERS Bruno Guedes Pinto1*
Ilioni Augusta da Costa2 1Instituto Federal do Espírito Santo. E-mail: guedespinto.bruno@gmail.com
2Instituto Federal do Espírito Santo. E-mail: ilionicosta@yahoo.com.br
*Autor para contato v.1 n.1 2019 63 dos participantes de seus espaços de
interação. O gênero textual é considerado,
inclusive, como uma ação de fala dentro de
um conjunto de diversas ações que
compõem um evento social, ou seja, “[...] os
gêneros textuais se apresentam como ações
sócio-discursivas para agir sobre o mundo e
dizer o mundo. Como ações sócio-
discursivas, os gêneros contribuem para
organizar as atividades comunicativas do
dia-a-dia” (CALAZANS, 2011, p. 02). Investigar
as
características
do
subgênero textual acalanto dentro do
espectro de produções artísticas destinadas
ao público infantil quanto à sua eficácia
comunicativa, ao seu encanto estético e ao
seu uso pedagógico na formação de leitores
e no processo de ensino e aprendizagem
desde os primeiros anos de alfabetização é o
ponto central deste trabalho. Fazer uma criança dormir, por
exemplo, é um evento, demanda de seus
integrantes várias ações para se atingir o
objetivo proposto (dentre elas, cobrir a
criança, acarinhá-la, apagar a luz do seu
quarto, afofar-lhe o travesseiro etc.). O
acalanto também é uma ação muito comum
a esse tipo de evento, mas difere das
demais, pois se constitui como um ato
levado a cabo por um (ou mais de um)
sistema(s) de representação (o linguístico, o
sonoro, o gestual etc.) (FALBO, 2010). Serão analisados os recursos sonoros
e linguísticos operados na confecção das
faixas do álbum “Canções de ninar”
(PERES; TATIT; 1994), do projeto Palavra
Cantada, para explorar a importância
pedagógica de operar um gênero textual
multimodal e dinamogênico como a canção. Mas o que é um gênero textual? 1 INTRODUÇÃO A canção é um gênero textual
multimodal que atravessa a história da
humanidade resistindo às tantas mudanças
na sensibilidade humana, nas instituições
sociais e nos contextos políticos (RUFINO,
2012). Por mais que a funcionalidade do
gênero tenha se adaptado às novas práticas 2 OS GÊNEROS TEXTUAIS: UM
BREVE PERCURSO Os gêneros textuais se caracterizam
por virtualmente compor um modelo
interativo de ordenamento cultural de (pelo
menos) um sistema de representação que
busca responder a uma demanda de
determinado
contexto
sócio-histórico-
interacional: sem demanda, de que serve
uma lista telefônica? Na sua gênese, a Teoria dos Gêneros
Textuais foi influenciada pelo materialismo
dialético e histórico, de Marx e Engels,
recuperando para os estudos linguísticos o
elo entre o texto, a situação enunciativa e o
contexto discursivo, afinal os gêneros são
definidos como “[...] tipos relativamente
estáveis de enunciados que se constituem
historicamente a partir das situações de
interação verbal. Esta afirmação parte da
ideia de que a língua é uma atividade social,
histórica e cognitiva” (CALAZANS, 2011,
p. 01). [Os
gêneros
textuais]
São
caracterizados mais por suas funções
comunicativas,
cognitivas
e
institucionais
do
que
por
suas
peculiaridades
linguísticas
e
estruturais. Possuem uma estrutura
formal não linear e, assim como
surgem,
podem
desaparecer
(CALAZANS, 2011, p. 02). O conceito de gêneros textuais põe
em destaque a importância das interações
psicossociais na formulação de modelos
comunicativos, culturais e sociocognitivos,
com estruturas textuais específicas, usados
para atender a funções sociais determinadas
por diretrizes culturais e contextuais de um
evento comunicativo (BAKHTIN, 2003). Apesar de os gêneros textuais serem
esses esquemas cognitivos e interativos pré-
estabelecidos culturalmente, ou nas palavras
do próprio Bakhtin “[...] situações típicas da
comunicação discursiva, a temas típicos, por
conseguinte, a alguns contatos típicos dos
significados das palavras com a realidade
concreta
em
circunstâncias
típicas”
(BAKHTIN, 2003, p. 293), eles ainda
guardam a possibilidade de inovação e organismo, regularisam [sic] o movimento dele ou o
impulsionam. Estas dinamogenias nos levam para
estados psicológicos equiparáveis a outros que já
tivemos na vida. Isto nos permite chamar um trecho
musical de tristonho, gracioso, elegante, apaixonado
etc. etc. Já com muito de metáfora e bastante de
convenção (ANDRADE, 1972, p. 41). v.1 n.1 2019 64 limítrofe (outro tipo de canção folclórica ou
ainda um exemplar de canção popular). criatividade, de maneira variável a depender
do gênero textual. Essa liberdade inventiva e não linear
de todo gênero textual é mais presente num
texto literário como o romance do que num
formulário cadastral, por exemplo; ambos
são gêneros textuais, mas o último é um
texto mais rígido, mais objetivo quanto à
sua função e obediente aos padrões culturais
historicamente mais estáveis, mais lineares
e menos dialógicos. 2 OS GÊNEROS TEXTUAIS: UM
BREVE PERCURSO Sempre que um evento social, com
as suas especificidades culturais, exige a
produção de uma forma específica de ação
envolvendo signos (linguísticos ou não), o
sujeito vai partir das convenções culturais
previamente estabelecidas para dar corpo ao
texto, definir as condições de dizer possíveis
ao contexto enunciativo e inserir a sua
produção e a si mesmo no continuum
político-discursivo do recorte social e
ideológico do qual faz parte: Como os gêneros textuais intervêm
diretamente nas relações interpessoais e/ou
institucionais, pode-se considerá-los uma
ação retórica de um sujeito da enunciação
dentro de um evento e que se constitui em
diálogo com a organização social com a
qual interage, interação pela qual se
constroem mutuamente – o ato de fala como
qualquer ato na vida se engendra enquanto é
engendrado. A canção, assim como o poema,
pertence ao campo literário. A canção
estaria no que Maingueneau (2005)
chama de discurso literário. Para o
autor, falar em discurso literário é
renunciar a um espaço consagrado,
pois as condições de dizer [grifo
nosso], ainda em referência ao autor,
atravessam o dito, que investe suas
próprias condições de enunciação
(RUFINO, 2012, p. 11-12). A canção, assim como o poema,
pertence ao campo literário. A canção
estaria no que Maingueneau (2005)
chama de discurso literário. Para o
autor, falar em discurso literário é
renunciar a um espaço consagrado,
pois as condições de dizer [grifo
nosso], ainda em referência ao autor,
atravessam o dito, que investe suas
próprias condições de enunciação
(RUFINO, 2012, p. 11-12). O fazer de uma ação enunciativa
como o acalanto exerce sua função ao
atingir um determinado objetivo, no caso,
fazer uma criança dormir. O objetivo
buscado pelo acalanto, por outro lado, está
marcado na estrutura desse gênero textual:
pragmaticamente, a situação enunciativa
exige um canto intimista, à capella, uma
melodia tematizante em tom médios, uma
performance acalentadora e acolhedora, o
que interage, cognitiva, dinamogênica e
culturalmente, com as demandas da situação
de enunciação, afinal “[...] todos os gêneros
têm uma forma e uma função, bem como
um estilo e um conteúdo, mas sua
determinação se dá basicamente pela função
e não pela forma” (MARCUSCHI, 2008, p. 150). A canção é um gênero textual
intersemiótico e isso é fundamental na sua
diferenciação de outros gêneros, apesar das
semelhanças que possui com o poema e a
música instrumental. 2 OS GÊNEROS TEXTUAIS: UM
BREVE PERCURSO Possui indissociável
relação entre palavra e som, entre texto
verbal e não verbal, sendo, nesse sentido,
preferencialmente analisável como uma
produção multimodal (COSTA, 2003). v.1 n.1 2019 65 político, etc. No processo de sua
formação
eles
incorporam
e
reelaboram diversos gêneros primários
(simples),
que
se
formaram
nas
condições da comunicação discursiva
imediata. Esses gêneros primários, que
integram
os
complexos,
aí
se
transformam e adquirem um caráter
especial: perdem o vínculo imediato
com a realidade concreta e os
enunciados reais alheios: por exemplo,
a réplica do diálogo cotidiano ou da
carta no romance, ao manterem a sua
forma e o significado cotidiano apenas
no plano do conteúdo romanesco,
integram a realidade concreta apenas
através do conjunto do romance, ou
seja, como acontecimento artístico-
literário e não da vida cotidiana
(BAKTHIN, 2003, p. 263). um som de altura definida, um canto não
existe sem voz, parece redundante, mas a
vocalidade do canto é fundamental para a
canção e possui traços distintivos da
oralidade e da fala, como se verá. O
arranjo
e
a
escolha
dos
instrumentos que compõem o canto e a
harmonia entre eles, o ritmo, os gêneros
musicais e sua construção sócio-histórica:
todos esses elementos são fundamentais à
sua produção e, consequentemente, a uma
análise da canção, mas, para se ter dimensão
da importância do canto na canção, o
semioticista Luiz Tatit (1986) se concentra
nas heranças entoativas que constroem as
melodias executadas pelo canto e que
conferem eficácia comunicativa e encanto
estético à canção quando compatibilizadas
com a interface linguística da obra. O
arranjo
e
a
escolha
dos
instrumentos que compõem o canto e a
harmonia entre eles, o ritmo, os gêneros
musicais e sua construção sócio-histórica:
todos esses elementos são fundamentais à
sua produção e, consequentemente, a uma
análise da canção, mas, para se ter dimensão
da importância do canto na canção, o
semioticista Luiz Tatit (1986) se concentra
nas heranças entoativas que constroem as
melodias executadas pelo canto e que
conferem eficácia comunicativa e encanto
estético à canção quando compatibilizadas
com a interface linguística da obra. A canção também é capaz de
reelaborar diversos gêneros primários, sem
dúvida o diálogo cotidiano é o gênero
primário
que
mais
é
apropriado
e
reformulado por ela: “[...] esta condição
[ação simulada onde alguém diz alguma
coisa de uma certa maneira a outro alguém],
por si só, já traz à canção um estatuto
popular, pois todos podem reconhecer
situações cotidianas de conversa [grifo
nosso]” (TATIT, 1986, p. 06). 2.1 O GÊNERO TEXTUAL CANÇÃO A canção é uma produção temporal
breve que envolve a cooperação de, pelo
menos, dois sistemas de representação, o
linguístico e o musical, por isso nenhuma
análise pode prescindir da relação entre
ambos. O acalanto, nesse exemplo, aparece
como um gênero textual mais ou menos
estável, mesmo que seja aberto a mudanças
estruturais e de estilo, esse gênero ainda
assim continuaria a ser um acalanto,
contanto que a função de fazer dormir se
mantenha (BAKHTIN, 2003). Caso o texto
esvaeça a funcionalidade do gênero textual,
provavelmente se atingirá uma produção de
natureza diversa que, obviamente, acarretará
numa
transmutação
para
um
gênero O canto é um elemento fundamental
na constituição da canção enquanto um
gênero textual, uma voz que cria um padrão
sonoro mais ou menos estável para entoar a
letra da canção. A canção pode ou não ser
acompanhada por instrumentos, como é o
caso das execuções à capella. O canto,
portanto, não é a produção e sustentação de v.1 n.1 2019 66 A cantora e psicanalista Marie-
France Castarède (apud FALBO, 2010)
associa o acalanto entoado pela mãe e seus
efeitos sobre a criança ao “sentimento
oceânico”, apontado por Freud como o
fundamento da religiosidade humana. O
acalanto seria “[...] paradigmático como
restituidor da sensação de plenitude do bebê
no ambiente do útero materno, perdida logo
após o nascimento” (FALBO, 2010, p. 221). robustecimento da reserva de mercado da
canção popular infantil, tantas vezes em
detrimento do caráter artístico da obra para
favorecimento de seu viés pedagógico,
moralizante
e
informativo
(COSTA;
GONZALEZ, 2014). Uma parcela expressiva da produção
musical hoje (fortemente presente nas
mídias tradicionais, as massivas) está
relacionada a resultados de pesquisas de
mercado e de análise comparativa de dados
de vendagem, tornando-se essa interferência
um fator importante na constituição do
gênero
canção
popular
atualmente
e,
especificamente, a canção popular infantil. Talvez seja essa, psicanaliticamente,
a fonte do encanto e do prazer que o canto
provoca no ser humano, uma restituição da
sensação de plenitude perdida, afinal o
acalanto e sua performance acalenta a
pulsação sinérgica entre ambos, orientada
pelo percurso vibratório, ondulatório da
canção da mãe para o bebê. A canção contém em si o gene da
transformação e da adaptação a novas
organizações sociais, situações enunciativas,
configurações
estruturais,
fatores
pragmáticos, estilos, conteúdos, tecnologias
etc. A história da canção entrelaça-se na
história do homem. Pode-se constatar a
capacidade de transição da funcionalidade
da canção, sem que, com isso, haja uma
transmutação
de
genericidade
(MARCUSCHI, 2008). Existem, no conjunto universo, três
tipos de canção: a folclórica, a erudita e a
popular. A canção popular possui maior
liberdade na execução do que a música
erudita, isso se deve ao fato de a canção
popular não estar ligada à notação musical,
à partitura. A canção popular geralmente
possui uma autoria conhecida, o que a
diferencia da canção folclórica, e é
multifacetada em gêneros musicais. Suas
obras movimentam um setor econômico
lucrativo do ramo do entretenimento e
sofrem com a influência do mercado mais
do que a canção erudita. Bakhtin
identifica
dois
grupos
distintos de gêneros textuais no vasto
universo
discursivo,
que
“[...]
compreenderia o conjunto de formações
discursivas de todos os tipos interagindo em
uma dada conjuntura” (COSTA, 2003, p. 13). Bakhtin
identifica
dois
grupos
distintos de gêneros textuais no vasto
universo
discursivo,
que
“[...]
compreenderia o conjunto de formações
discursivas de todos os tipos interagindo em
uma dada conjuntura” (COSTA, 2003, p. 13). O primeiro grupo é formado pelos
gêneros primários, são enunciados em
situações
comunicativas
rotineiras,
geralmente
esses
gêneros
atendem
a
necessidades
e/ou
desejos
interativos
imediatos, como o bilhete e o diálogo
cotidiano. Bakhtin, por outro lado, assim
define os gêneros secundários: Desde os tempos da invenção do
rádio até os dias de hoje, muita coisa mudou
para a história da canção, inclusive o
interesse do mercado financeiro. A canção
virou um produto comercial e como objeto
de consumo é tratada, estratificada em
nichos
mercadológicos,
como
vem
ocorrendo nas últimas décadas com o [...] surgem nas condições de um
convívio cultural mais complexo e
relativamente muito desenvolvido e
organizado
(predominantemente
o
escrito) – artístico, científico, sócio- v.1 n.1 2019 67 67 3 PARÂMETROS SEMIÓTICOS DA
CANÇÃO POPULAR BRASILEIRA também como ferramenta de tradução do
indizível: a voz” (FALBO, 2010, p. 221). Antes de articular a sua própria voz,
antes mesmo de compreender a estrutura
linguística formal do que lhe diz a mãe, a
voz do Outro, o bebê percebe no acalanto
algo ordenado, pleno, mas intraduzível: também como ferramenta de tradução do
indizível: a voz” (FALBO, 2010, p. 221). Antes de articular a sua própria voz,
antes mesmo de compreender a estrutura
linguística formal do que lhe diz a mãe, a
voz do Outro, o bebê percebe no acalanto
algo ordenado, pleno, mas intraduzível: A eficácia interativa da canção,
segundo Tatit (1986), se intensifica na
articulação e compatibilidade entre os
elementos do sistema de representação
linguístico e sonoro – a eficácia a que se
refere
o
autor
é
semiótica,
e
não
mercadológica. Na canção, o destinador-
locutor
(D.ºR
loc)
se
relaciona
interdependentemente com o destinatário-
ouvinte (D.ªRIO ouv) e dois “fazeres” são
postos em jogo. O destinador-locutor “[...]
faz com que o destinatário-ouvinte (D.ªRIO
ouv) deseje ouvir uma determinada canção”
(TATIT, 1986, p. 03). Levando em
consideração que o compositor faz uma
obra, um espaço de interação e expressão, e
o seu público faz uma audição, uma leitura
dela, os dois “fazeres” se completam e
podem ser organizados em um enunciado
sintáxico dos modalizadores intencionais: Quando a criança ainda não aprendeu a
falar, mas já percebeu que a linguagem
significa, a voz da mãe, com suas
melodias e seus toques, é pura música,
ou aquilo que depois continuaremos
para sempre a ouvir na música: uma
linguagem onde se percebe o horizonte
de um sentido que no entanto não se
discrimina em signos isolados, mas
que só se intui como uma globalidade
em
perpétuo
recuo,
não-verbal,
intraduzível, mas, à sua maneira,
transparente (WISNIK, 1989, p. 27). Castarède (apud FALBO, 2010) vê a
voz como “agente mediador” entre o corpo
e a linguagem. O grito do bebê é a
protovocalidade
humana,
ainda
muito
individual, mas já uma ação enunciativa de
qualquer maneira: 2.2 A CANÇÃO PELA PSICANÁLISE: O
ACALANTO Essa
sintonia
remonta
a
uma
situação anterior, um ordenamento de
pulsões
semelhante
ao
modelo
sociocognitivo e cultural do acalanto, como
assinala o crítico literário José Miguel
Wisnik: “O feto cresce no útero ao som do
coração da mãe, e as sensações rítmicas de
tensão e repouso, de contração e distensão
vêm a ser, antes de qualquer objeto, o traço
de inscrição das percepções” (WISNIK,
1989, p. 26). A boca é definida como instrumento
de satisfação de necessidades fisiológicas
como comer e beber, mas também como
fonte de prazer. A psicanalista Santaella
(2002) identifica que “[...] na fala está
inscrita a possibilidade [de prazer] do canto. Encantamento do canto: fala transmutada
em prazer” (SANTAELLA apud FALBO,
2010, p. 220). A voz é ainda mais que uma fonte de
prazer, é também uma “[...] ponte entre
corpo e linguagem, identidade e alteridade”
(FALBO, 2010, p. 221), é elemento
determinante na construção no ser humano
do seu “[...] estatuto de sujeito” (FALBO,
2010, p. 221). Até agora, no entanto, falou-se da
relação psicanalítica entre o bebê e a
recepção
dos
sons
do
mundo
e,
especificamente, da voz materna, mas logo
o bebê desenvolve a sua própria voz e esse
fato
é
também
basilar
no
“[...]
desenvolvimento da noção de Eu, que vai
possibilitar sua interação com o Outro”
(FALBO, 2010, p. 221). A origem dessa relação com a voz é
fundante e antiga, é um processo que se
inicia nos primeiros anos da infância. A
criança já ouve sons durante a gestação,
notadamente a voz da mãe, e é por meio da
audição, “[...] quando percebe as diferentes
freqüências sonoras (alturas), que [se]
constrói a noção de espaço no ser humano”
(FALBO, 2010, p. 221). É também por
meio da audição que o bebê é acalentado,
geralmente, pela voz da mãe, e por uma
performance que envolve mais do que
apenas o canto, mas todo um engajamento
afetivo, físico, corpóreo entre o bebê e a
mãe que o suspende e embala. Essa nova etapa no desenvolvimento
cognitivo e psicológico é um processo que
se inicia com o grito do recém-nascido. Ele,
mais do que um descontentamento, assinala
“[...] a descoberta de um novo meio de
expressão que passará a ser utilizado de
maneira cada vez mais deliberada e
articulada pelo indivíduo em linguagem”
(FALBO, 2010, p. 221). Esse meio de
expressão vai além do pragmatismo da
comunicação
para
“[...]
inscrever-se Sobre
isso
[interesse
cancional
específico: os achados na relação D.ºR loc/saber fazer/ D.ªRIO ouv/querer fazer/ Então a música
tem uma periodicidade que a fala não
tem. Na canção, essas duas instâncias,
a música e a fala, começam a trocar as
suas propriedades. Tem canções onde
a palavra recebe uma injeção de
regularidade musical [...] Ou seja, você
sabe, são aquelas melodias que são
feitas de pequenas células, módulos
geralmente de intervalos curtos que
tem uma certa geometria que vai
criando um rendilhado e vai apontando
para um lugar que você adivinha qual
é, você sabe pra onde vai essa melodia
quando ela começa esse desenho, e vai
indo, vai apontado, você sabe onde vai
dar. E são as melodias que tem mais
um apelo somático, a gente começa a
balançar junto com elas, a gente se
entrega a elas, porque elas estão
oferecendo o caminho e dizendo ‘eu
vou por aqui, vem junto!’, e a gente
vai com toda essa regularidade... Essas
canções
ele
[Tatit]
chama
de
tematizantes (WISNIK; PIEDADE;
MEHMARI; FIAMMENGHI, 2015). música
e
letra],
vou
falar
um
pouquinho do que diz o Luiz Tatit, que
diz o seguinte: a palavra, quando a
gente fala, ela não tem regularidade
rítmica, ela é irregular, o ritmo da fala
é irregular. Quando a gente fala,
também
a
gente
melodiza
pela
entoação, mas a entoação também é
irregular, ela não é estabilizada, não é
definida. Enquanto que na música, o
ritmo e a entoação, a melodia, ficam
estabilizadas em notas, em pulsos, em
tempo,
em
regularidades,
em
compassos, etecetera. Então a música
tem uma periodicidade que a fala não
tem. Na canção, essas duas instâncias,
a música e a fala, começam a trocar as
suas propriedades. Tem canções onde
a palavra recebe uma injeção de
regularidade musical [...] Ou seja, você
sabe, são aquelas melodias que são
feitas de pequenas células, módulos
geralmente de intervalos curtos que
tem uma certa geometria que vai
criando um rendilhado e vai apontando
para um lugar que você adivinha qual
é, você sabe pra onde vai essa melodia
quando ela começa esse desenho, e vai
indo, vai apontado, você sabe onde vai
dar. E são as melodias que tem mais
um apelo somático, a gente começa a
balançar junto com elas, a gente se
entrega a elas, porque elas estão
oferecendo o caminho e dizendo ‘eu
vou por aqui, vem junto!’, e a gente
vai com toda essa regularidade... Essas
canções
ele
[Tatit]
chama
de
tematizantes (WISNIK; PIEDADE;
MEHMARI; FIAMMENGHI, 2015). D.ºR loc/saber fazer/ D.ªRIO ouv/querer fazer/ A melodia mais se afasta da
entoação da fala, pois até a presença da voz
entra
nessa
dimensão
obsessiva
de
reiteração melódica. Há nesse parâmetro
melódico da canção uma supervalorização
do gênero musical, o texto linguístico fala
sobre o gênero executado, ele o exalta,
diretamente ou a um objeto-modal que o
represente, pois, de acordo com Tatit, a
exaltação é o correspondente textual da
tematização. A tematização é portadora de uma
persuasão somática e possui como fator
eufórico a sua empatia cognitiva com o
gênero musical. A periodicidade funciona
como um dispositivo de compatibilidade
entre a melodia e o texto, do ponto de vista
lógico (a periodicidade dos temas) e
sensitivo (as vibrações): “[...] o centro da
tensividade instala-se na ordenação regular
da articulação, na periodicidade dos acentos
e na configuração de saliências, muito bem
identificadas com o tema” (TATIT, 1995, p. 10). Outros recursos do texto linguístico das
canções tematizantes são as reiterações de
rima internas e externas, aliterações e
estímulos sensoriais de expressão. D.ºR loc/saber fazer/ D.ªRIO ouv/querer fazer/ onde o primeiro fazer (o do locutor)
corresponde a “compor” e o último fazer (o
do ouvinte) corresponde a “ouvir”, ou seja,
o destinador tem a competência modal de
provocar a volição do ouvinte em favor da
canção. Se o grito é a primeira expressão
afetiva, a voz vai lhe suceder,
introduzindo
fenômenos
sonoros
especificamente humanos, como as
vibrações harmônicas. Ela é mediadora
entre o corpo e a linguagem [...] A voz
é mediação, não apenas para o sujeito
em si mesmo, entre seu corpo e a
língua, mas com a voz do outro. Ela se
encarna em um ‘discurso vivo’, para
retomar a expressão de André Green. A fala levada pela voz é diferente do
pensamento, pois ela é resultado de
uma descarga motora. Falar de viva
voz
ao
outro
é
se
descarregar
(CASTARÈDE apud FALBO, 2010, p. 211). Tatit (1986) estabelece dentro da
música brasileira três parâmetros semióticos
para análise do gênero canção, com maior
atenção dada à melodia do canto popular. O
autor aponta a entoação da fala como celeiro
de frases e percursos melódicos para o canto
na canção brasileira, percebe ainda que
existem regularidades estruturais entre a
entoação da fala e a voz do canto e ordena a
canção brasileira em três critérios de
descrições
metalinguísticas
multimodais
mais
frequentes,
já
estabilizadas
e
rotinizadas, com processos de persuasão
particulares. Wisnik ainda se referenda
nesses critérios para falar da canção popular
brasileira: A
poética
vocal
da
canção,
midiatizada
ou
não,
traz
o
fascínio
psicanalítico oceânico, o prazer pelo canto e
pela reconstrução deste durante a audição e
a compreensão de aspectos de situações
interativas
e
sua
relação
com
as
organizações sociais enquanto condições
discursivas (FALBO, 2010). Sobre
isso
[interesse
cancional
específico: os achados na relação Sobre
isso
[interesse
cancional
específico: os achados na relação v.1 n.1 2019 68 ondulante etc.) manter o caráter tematizante
da canção. música
e
letra],
vou
falar
um
pouquinho do que diz o Luiz Tatit, que
diz o seguinte: a palavra, quando a
gente fala, ela não tem regularidade
rítmica, ela é irregular, o ritmo da fala
é irregular. Quando a gente fala,
também
a
gente
melodiza
pela
entoação, mas a entoação também é
irregular, ela não é estabilizada, não é
definida. Enquanto que na música, o
ritmo e a entoação, a melodia, ficam
estabilizadas em notas, em pulsos, em
tempo,
em
regularidades,
em
compassos, etecetera. v.1 n.1 2019 69 69 ser atualizados no caso do cancioneiro
popular infantojuvenil também. ser atualizados no caso do cancioneiro
popular infantojuvenil também. contato seja visto como uma espécie
de
“utilidade”
da
literatura. Se
pensarmos na escola, mais ainda:
afinal, a escola não se propõe a formar
indivíduos que saibam se expressar? (AZEVEDO, 2005, p. 38). Toda arte é simbólica. A literatura
enquanto "arte da palavra", poderá
perder seu valor de dialogar mais
profunda e abrangente com maior
número de receptores, não despertando
a reflexão e a criação que se devem
esperar de um texto artístico, se
pretender
privilegiar
o
caráter
educativo
ou
informativo
em
detrimento
do
literário. [...]
O
educador deve descobrir, para poder
transmitir,
que
a
leitura
é
o
estabelecimento de diálogos entre os
homens, no tempo e no espaço [...] Ler
é ver o mundo e, mais do que isso,
uma forma de reescrevê-lo, segundo o
mestre Paulo Freire (RIBEIRO, 2010,
p. 34). O discurso artístico “[…] transforma
o que é heterogêneo em homogêneo,
sintetiza e é capaz de unir ou estabelecer a
convivência entre elementos contraditórios”
(AZEVEDO, 2005, p. 29). E qual é o lugar
da canção infantil? Não terá esse nicho uma
particularidade formal em relação ao nicho
mais amplo da canção popular? Será que
apenas as relações de produção e a criação
de um nicho de consumidores de canção
infantil sustentam esse campo de fabulação? Ricardo Azevedo, pesquisador de
literatura infantil, destaca os estudos sobre
as cantigas trovadorescas do medievalista
Paul Zumthor para tratar dos “[...] índices
que caracterizariam os discursos orais,
proferidos em perfomance”, dos quais
participa a canção popular, inclusive a
infantil. Ele enumera três índices: Esse tipo de discurso, o artístico, o
literário, o poético, ainda segundo Azevedo
(2004), é fundamental para a formação do
sujeito do conhecimento. O conhecimento
analítico, científico, heterogêneo e objetivo
não deve ser a única preocupação da escola
e do educador. É importante reafirmar o
papel fundamental que o discurso poético
tem na formação humanista do discente, no
desenvolvimento de mecanismos empáticos
de relação com a alteridade e na inserção
cidadã dos sujeitos na vida social. [...]
1)
a
adaptabilidade
às
circunstâncias. Para
poder
se
comunicar, segundo Zumthor, o orador
costumava utilizar vocabulário público
e acessível e levar em conta o contexto
em que o discurso estava ocorrendo; 2)
a teatralidade. Um conjunto variado de
recursos como o lugar-comum, o tom
exagerado e hiperbólico; o uso de
redundâncias; o tom de confidência; as
brincadeiras com palavras (aliteração e
trocadilhos), as rimas e refrões;
recursos enfáticos como a reiteração, a
enumeração; repetições de palavras; o
uso da alegoria; metáforas; o estilo
coloquial etc., mas note-se, não para
fazer experiências formais com a
linguagem e, sim, com o intuito de
divertir, seduzir e prender a atenção do
ouvinte; 3) a concisão (AZEVEDO,
2005, p. 40-41). A literatura e outras fabulações
(como a canção) demonstram-se peças-
chave
do
processo
de
ensino
e
aprendizagem e na formação de leitores em
todos os níveis do ensino, apesar de
ocuparem espaços ainda periféricos nos
planos de ensino e no currículo básico. Nesse contexto, o discurso artístico deve
compor as formas de expressão dos alunos,
pois [...] o contato com textos subjetivos,
movidos a visões pessoais e não
consensuais, carregados de ficção e
poesia, que se permitem utilizar a
linguagem com liberdade, é outro
ponto instigante da literatura, seja ela
infantil ou outra. E já que vivemos em
tempos tão pragmáticos e objetivos
onde “tempo é dinheiro” e tudo precisa
ter uma função lógica, sugiro que tal [...] o contato com textos subjetivos,
movidos a visões pessoais e não
consensuais, carregados de ficção e
poesia, que se permitem utilizar a
linguagem com liberdade, é outro
ponto instigante da literatura, seja ela
infantil ou outra. E já que vivemos em
tempos tão pragmáticos e objetivos
onde “tempo é dinheiro” e tudo precisa
ter uma função lógica, sugiro que tal 4
A
ESCOLA
E
O
DISCURSO
ARTÍSTICO Cada parâmetro semiótico tem os
seus processos particulares de persuasão. A
tematização é um parâmetro que exerce a
sua persuasão por meio da reiteração
melódica, “[...] através dela, podemos
reconhecer o que já ouvimos e prever o que
ainda ouviremos” (TATIT, 1986, p. 47). A
reiteração garante maior independência
melódica, a linha melódica é tantas vezes
repetida que se tornam evidentes o seu
percurso, daí surgem os temas – todo esse
processo
se
chama
tematização. O
parâmetro musical mais importante na
tematização é a duração (pulso, ritmo),
apesar da importância do perfil melódico
(ascendente,
descendente,
pontilhado, O estudioso da literatura infanto-
juvenil Francisco Aurélio Ribeiro (2010)
defende posições sobre o papel da escola e
do educador na formação de leitores (leitura
aqui compreendida em sentido amplo, e não
apenas no tocante ao texto escrito) que são
relevantes ao debate sobre o lugar das
produções artísticas infantojuvenis – seja a
literatura (e a palavra escrita, como pontua
Ribeiro),
seja
a
canção
popular,
especificamente a infantil (e a palavra
cantada, como é proposto por este artigo). Ele
também
alerta
sobre
o
pragmatismo a que o mercado e a escola
condenam a arte da palavra destinada ao
público infantil, e seus apontamentos podem 5 ANÁLISE LÍTERO-MUSICAL
5.1 ANÁLISE DE ACALANTOS DO
ÁLBUM “CANÇÕES DE NINAR” (1994),
DE PALAVRA CANTADA 70
v.1 n.1 2019 70
v.1 n.1 2019 70
v.1 n.1 20 70 As cantigas de ninar que compõem a
primeira obra do projeto paulista que
acabou por se especializar em produção de
canções e espetáculos infantis são (quase)
todas inéditas. O projeto Palavra Cantada é
capitaneado por Paulo Tatit e Sandra Peres. das práticas cotidianas, das escatologias, da
sonoridade de versos inusitados e não
intelectivos etc.; tudo isso que está cheio de
graça, de ludismo, de brincadeira, de jogo,
de bobeira, é poesia e é humor também. O humor é um recurso que atrai a
atenção do destinatário-ouvinte. E, segundo
Leo Cunha, pesquisador da literatura
infantil, o humor em sentido amplo, não
apenas o do chiste, é uma valiosa tecnologia
educacional: O álbum “Canções
de Ninar”
(PERES; TATIT, 1994) é formado por
canções populares, algumas de autoria de
Paulo Tatit e Sandra Peres, outras são
assinadas pela dupla juntamente com
parceiros como Edith Derdyk, Ná Ozzetti,
Luiz e Zé Tatit, Akira Ueno, Neco Prates e
Zé Miguel Wisnik, além de obras de autoria
de
outros
compositores
como
Pedro
Mourão, Rodolfo Stroeter, Edgar Poças e
Hélio Ziskind ou até mesmo autores mais
consagrados
como
Arnaldo
Antunes,
Caetano Veloso, Cid Campos e Augusto de
Campos. Esse álbum foi vencedor do
Prêmio Sharp no ano de seu lançamento na
categoria de Melhor Disco Infantil daquele
ano. Mas é importante ressaltar que mesmo
um humor que não é claramente
crítico, ou politizado, mesmo o humor
que parece se limitar à brincadeira ou
aos jogos de linguagem tem sua
importância e seu valor, pois ele é
capaz de despertar no leitor o gosto
pelas palavras, o prazer de lidar de
forma lúdica com os sons, os ritmos, e
as formas das letras e palavras. Não
será surpresa se, por meio de um
poema como esse, a criança desconfiar
(se não tiver certeza) de que qualquer
texto pode esconder outros, pode trazer
a ideia nova, o pensamento novo
(CUNHA, 2005, p. 88). Os 22 acalantos enfeixados nesse
álbum renovam o repertório de berço, sem
fugir às características tradicionais desse
subgênero textual, tão marcadas pelas suas
manifestações folclóricas. A tematização no
nível musical se realiza no nível verbal de
modo a erigir um objeto que será
tematizado, processo que Tatit chama de
exaltação, por vezes iconizando elementos
relacionados
culturalmente
ao
gênero
musical executado. 5 ANÁLISE LÍTERO-MUSICAL
5.1 ANÁLISE DE ACALANTOS DO
ÁLBUM “CANÇÕES DE NINAR” (1994),
DE PALAVRA CANTADA Em Acalanto para você (Ná Ozzetti /
Neco Prates / Edith Derdyk), a tematização
da situação enunciativa do ato de acalentar
já se impõe no primeiro verso da canção,
“Eu canto pra você dormir”, em que a voz
lírica,
metalinguisticamente,
aborda
o
próprio
fazer
de
seu
exercício
comunicativo-pragmático. Outro ponto que promove a eficácia
desse acalanto é o humor presente no jogo
de palavras “negro céu” / “noite véu” na
mesma posição dentro da estrofe e da
melodia. Como aponta Cunha: O eu-lírico vai além, estabelece os
objetivos de seu ato de fala, o intuito de
fazer dormir, de organizar o mundo infantil
por meio da criação de uma regularidade
sonora que lhe passe a segurança da
previsibilidade musical e dinamogenênica
(“A Terra gira por um fio”). O eu-lírico vai além, estabelece os
objetivos de seu ato de fala, o intuito de
fazer dormir, de organizar o mundo infantil
por meio da criação de uma regularidade
sonora que lhe passe a segurança da
previsibilidade musical e dinamogenênica
(“A Terra gira por um fio”). Para a criança, a linguagem é um
"espaço" privilegiado para a apreensão
e compreensão do mundo. Por isso,
brincar com palavras é uma atividade
natural, que ela faz com prazer e por
prazer. Não é à toa que trava-línguas,
parlendas e outros jogos da tradição
oral são tão populares entre os
pequenos de todas as partes do mundo
(CUNHA, 2005, p. 81-82). A performance dedilhada do violão
na introdução segue acompanhando a voz
feminina que se estende até ser amparada
pela delicadeza de um piano – dois
instrumentos harmônicos, o primeiro um
instrumento de cordas muito presente na
música popular e o segundo, de cordas
percutidas e muito comum na música
erudita. O ordenamento do universo da
criança
está,
naqueles
sussurrados
momentos, por um fio – por um fio do
violão e do piano, por um fio de voz, por
uma linha melódica, pelas malhas de um
embalo. Esse
álbum
é
repleto
dessas
brincadeiras com as palavras. A canção de
ninar Carneirinho 1, 2, 3 (Paulo Tatit)
guarda uma brincadeira popular semelhante
à canção folclórica Um elefante incomoda
muita gente, brincadeira que consiste na
repetição sequenciada de números em uma
melodia tematizante com o acréscimo de
mais um número ao final da sequência. 5 ANÁLISE LÍTERO-MUSICAL
5.1 ANÁLISE DE ACALANTOS DO
ÁLBUM “CANÇÕES DE NINAR” (1994),
DE PALAVRA CANTADA No caso da canção de
ninar, I) a situação enunciativa própria do
acalanto é tematizada em diversas obras
desse subgênero, sejam folclóricas ou
populares; por vezes, no entanto, II) a
própria criança a que se destina ninar se
torna objeto da letra da canção; ou ainda é
III) a noite e sua afabilidade que é
tematizada no nível verbal. A situação enunciativa é tantas vezes
entoada e tematizada no álbum como
comprovam os versos da cantiga que abre o
disco, Vagarinho (Paulo Tatit / Edith
Derdyk): “Vagarinho, vagarinho / Fecha o
olho no seu ninho / E o sono vai chegar // E
o sono no escurinho / Vagarinho, vagarinho
/ Põe o mundo pra sonhar...”. Aqui tanto a melodia e o canto,
quanto a performance e o embalo, conjunto
de fatores que integram o ato de ninar uma
criança, são tematizados e a situação
enunciativa atravessa o vagar melódico para
manifestar-se
linguisticamente. Essa
linguagem informal, composta de reduções
e diminutivos estreita os laços afetivos que
se criam na situação enunciativa de
acalentar um bebê. Aliam-se ao processo de perseguição
obsessiva de um percurso melódico na
busca pela eficácia e pelo encanto das
canções de ninar, efeitos
de humor
provocados pelo esmero formal e pelo
trabalho com sons, letras, palavras, imagens,
conceitos etc. A descarga de prazer do jogo
de palavras, do jogo de ideias, da subversão As cordas mantêm uma regularidade
na execução e acompanham a formulação
de um tema melódico em uma performance
que conta com a presença das vozes da
dupla paulista, o que sugere a confluência
da voz paterna e materna no ato de 71
v.1 n.1 2019 v.1 n.1 2019 71 poeta investe na graça que surge da
sonoridade melodiosa, ou inusitada, das
palavras, muitas vezes até em detrimento do
sentido, ou seja, daquilo que é inteligível”
(CUNHA, 2005, p. 83). acalentar. Os ecos que se descolam das
cordas da guitarra e se propagam graças à
mesa de som “põem o mundo sonhar” com
suas sugestões oníricas, ainda mais quando
o teclado entra reproduzindo a percussão de
um vibrafone e sugerindo por meio do seu
som agudo e metálico imagens que
recuperem elementos noturnos em favor da
persuasão decantatória, como o brilho das
estrelas. v.1 n.1 2019 72 minha mão”), além de plasmar na forma da
execução a necessidade de quietude para se
atingir o relaxamento do sono (“Fique
calmo / Tranquilo"). Ela então descreve o momento de dormir
apenas usando o sentido da audição e assim
aquela situação, antes tão corriqueira, agora
ganha as asas da imaginação na mente da
criança que canta (“Parece um bicho… uma
/ Cobra… um sapo… sei lá, / Será que vai
mexer?…”) – e também excita a imaginação
daquela que a ouve, sem dúvida. Em Carneirinho 1,2,3, um velho
recurso para se conseguir dormir por meio
da contagem de carneirinhos é encenado
nesse acalanto, tangenciando a situação
enunciativa a que se dedica o eu-lírico. A criança também passa por um
processo de tematização no nível linguístico
desse subgênero multimodal. No acalanto
De ninar (Cid Campos / Augusto de
Campos), a repetição paralelística da
pergunta “E a criança o que faz?” ao final
de
cada
estrofe
tematiza
o
próprio
destinatário. Ela coloca a criança no centro
das analogias que desenvolve entre ela e
outros
seres
vivos,
animais
(peixe,
vagalume, pato, sapo e gato) e humanos em
funções sociais dentro do núcleo familiar,
papéis
possíveis
de
participarem
do
convívio da criança (a mamãe, o papai, o
vovô e a vovó). Em outras canções, como Boa noite
(Paulo Taitit e Zé Tatit) e Dorme (Arnaldo
Antunes), expressões ligadas ao ato de ninar
uma criança são repetidas obsessivamente
durante toda a execução, com justaposição
de timbres ou inserções de harmonizações
de coral. O
humor,
que
se
baseia
na
reinvenção do cotidiano, presente em Boa
noite, em Sono, preguiça e em Sono de Gibi
(Hélio Ziskind), se une à tematização na
tentativa de intensificar a eficácia e o
encanto comunicativo desses acalantos, pois
segundo Cunha, Aqui o humor vem também se aliar à
tematização. Nesse ponto, o humor emerge
do jogo com as ideias e os conceitos. A
imagem do peixe a nadar, vaga após vaga se
aproximando do sono do bebê no leito,
recria uma imagem oceânica, a do bebê que
descansa dentro d’água, no ventre da mãe. O poeta também pode perceber (ou
deixar aflorar) o humor que existe nas
situações mais banais, que a criança
encontra em seu dia-a-dia. 5 ANÁLISE LÍTERO-MUSICAL
5.1 ANÁLISE DE ACALANTOS DO
ÁLBUM “CANÇÕES DE NINAR” (1994),
DE PALAVRA CANTADA No
acalanto Lá vai alguém (Paulo Tatit / Zé
Miguel Wisnik) ocorre uma repetição do
termo “alguém” por diversas vezes, a ele se
unem outros termos de mesma terminação
(quem, ninguém, sem, porém, bem, além,
tem, vem), provocando entre os efeitos de
sentido o de estranhamento (Hein?) de
quem não sabe quem lá vem. Há momentos, como em Sono,
preguiça (Akira Ueno / Luiz Tatit), que a
situação enunciativa é descrita na fabulação
de uma encorajadora conversa informal
beira-berço entre quem nina e aquele que é
embalado: “Sono / Preguiça / Não tenha
medo não // Fique calmo / Tranquilo /
Pegue na minha mão // Sono / Preguiça /
Tudo isso é muito bom”. Na canção de ninar Chuva (Sandra
Peres / Paulo Tatit), esse jogo com a
sonoridade chega ao extremo. Na primeira
estrofe da canção (“A chuva cai faz ti lim /
O sapo coacha cha / O sino bate dim dom /
Eu canto la la la la”), a sua inteligibilidade
quase se parte em favor da musicalidade das
palavras e dos seus ecos, ou seja, “[...] o Sua performance possui os silêncios
que intervalam a execução do violão
ocupados pela duração constante dos
registros graves de outro violão, sugerindo
uma pulsação acelerada pelo medo a que o
eu-lírico se refere na letra. Com isso, o tom
de diálogo afetivo se reforça (“Pegue na 73
v.1 n.1 2019 v.1 n.1 2019 v.1 n.1 2019 73
v. 73 73 exercício
surgem
metáforas
surpreendentes, imagens inusitadas, e,
claro, divertidas (CUNHA, p. 85-86). A exaltação da “velha bossa nova”
resvala numa leitura que permite se refletir
sobre as dicotomias novo-velho, tradição-
inovação, e sobre os conflitos entre a
criança e o adulto – interpretação que fica
cada vez mais clara na canção devido à
performance, quando, ao final, é possível
ouvir bocejos do pai, vencido pela pequena,
que ainda por cima dança. Cunha se refere ainda ao humor
presente nas obras artísticas infantis que
“[...]
parodiam
ditados
populares,
provérbios, anúncios, ou outros textos. A
graça surge da subversão das expectativas,
da
desconstrução
dos
sentidos
já
estabelecidos” (CUNHA, 2005, p. 85). Em
“Canções de ninar”, a paródia ficou por
conta de Soneca (Rodolfo Stroeter / Edgar
Barbosa Poças) e o seu texto-base foi o
consagrado conto popular de tradição alemã
que foi compilado pelos Irmãos Grimm,
Branca de Neve e os sete anões, e,
especificamente, a canção Hi Ho, da
animação da Walt Disney de mesmo nome. Nessa canção de ninar, a tradição oral dos
contos infantis europeus encontra a tradição
oral das canções numeradas, já referidas
acima, o que enche de ludismo a recepção
desse acalanto. Na canção Meu anjo sim (Sandra
Peres / Zé Tatit), encontra-se operada
novamente
a
tematização
da
criança
enquanto objeto da canção. Ela aparece no
centro da exaltação do acalanto (“Dorme,
meu anjo lindo / Meu menino serafim”). Os
contornos delicados da performance desse
acalanto executada pelo piano remonta às
canções religiosas eruditas exatamente para
plasmar na forma angelical
a força
expressiva do destinatário tematizado. A
persuasão decantatória atrai o interlocutor
quando usa esse recurso, cuja inserção no
nível verbal o seduz afetivamente. Outra
tematização
linguística
comum aos acalantos é a exaltação da
afabilidade da noite. Na canção de ninar
Negro céu (Sandra Peres / Edith Derdyk), a
noite é o tema da letra e dela se destacam
suas características ligadas à leveza (véu),
beleza (luz do luar) e inefabilidade (noite do
além). A letra desbarata o medo da
escuridão e derruba o sol em favor dos
prazeres oníricos, a noite passa a ser um
convite ao sono (“Vai / Céu azul / Pro fim
do mundo // Vem / Noite do além”). Também no acalanto Pro nenê
nanar (Paulo Tatit / Zé Tatit), o eu-lírico
tematiza a criança no nível verbal. Atento, ele
percebe, em meio ao trivial, situações
de
espanto,
surpresa,
invenção,
elementos que são muito próprios ao
universo infantil, já que a criança ainda
está conhecendo e aprendendo as
coisas do mundo (CUNHA, 2005, p. 86). A mesma imagem parece se delinear
nos três versos da canção de Caetano
Veloso, Tudo, tudo, tudo (Tudo comer /
Tudo dormir / Tudo no fundo do mar). A
voz da performance, que, em meio a ecos,
sons sintetizados (efeito sonoro extraído do
disco Deserttracks de Michel Redolfi) e uma
marcação constante da percussão, balbucia a
melodia,
logo
torna-se
dobrada
(acompanhada por uma outra voz) e vai
abandonando no fluxo do registro apenas
“iscas” da letra. A repetição dos versos por
quatro vezes se incumbe de imergir o
interlocutor nesse sentimento oceânico,
além de remeter também ao sono das
espécies no caldo primordial: Na primeira canção de ninar referida
no parágrafo anterior, Boa noite, antes de
cada
monóstico,
encontram-se
falas
tipicamente dos adultos com as crianças,
falas da autoridade, falas da ordem, mas
muitas
delas
guardam
elementos
escatológicos que desmistificam o lirismo
desse subgênero musical e subvertem os
tabus do mundo dos mais velhos (“Garoto
que dá uma de bacana / Faz xixi, escova os
dentes / E já pra cama [...] Ih, e agora nenê
tá com cocô / E a mamãe já foi pra casa do
vovô”). O poeta (e por meio dele, o leitor)
enxerga e fala das coisas (ou pessoas,
ou situações) como se as estivesse
vendo
pela
primeira
vez. Deste No Sono de Gibi, o eu-lírico é uma
criança que reparte uma descoberta: “A luz
apaga / Parece que / A gente / Escuta mais”. Fica
claro o desespero da voz poética, ela sugere
um pai de uma menina recalcitrante em
dormir, “O que é que um pai pode fazer /
No meio da noite / Pro nenê nanar?”. A criança ao ser descrita (“Agora
está sequinha / Mamou toda a camomila”)
vai
deixando
claro
todas
as
ações
empreendidas pelo pai na expectativa de
fazer sua pequena pegar no sono (“Só falta
uma voltinha até a / Esquina”), nem mesmo
a alternativa metalinguística fica de fora do
evento de acalentar a filha (“Ouça essas
canções / Da tua fita de ninar”). A
performance
musical
desse
acalanto ressalta a inefabilidade da noite
pelos efeitos de sentido provocados pelo uso
de uma programação de sintetizadores que
sugere o som de um xilofone durante toda a
execução e pela voz feminina que se estende
em entoação melódica, com o uso da região
aguda de seu registro e a extensão das frases
melódicas. O coro, semelhante ao canto
tradicional da cultura japonesa, min'yō com
seus kakegoe (gritos que interseccionam a
melodia em formato coral), aponta “pro fim
do mundo” para onde vai o “céu azul” e de
onde vem a “noite do além”. A
tematização,
linguisticamente
representada pela exaltação da figura da
criança durante todo acalanto, também se
desdobra na exaltação do gênero musical
que embala a duração desse acalanto
(“Venha cá no colo / Pequenina tão
manhosa / Que eu te canto a velha bossa /
Nova”), tornando, por meio de uma
obsessão lítero-musical, a bossa nova tema
multimodal desse acalanto. 74
v.1 n.1 2019 74
v.1 n.1 2019 74
v.1 n.1 2019 74
v.1 n.1 20 74 infantil quanto à sua eficácia comunicativa,
ao seu encanto estético e ao seu uso
pedagógico na formação de leitores e no
processo de ensino e aprendizagem desde os
primeiros anos de alfabetização é o ponto
central deste trabalho. Outro acalanto que exalta a noite
como objeto temático que contemporiza
com a ideia de sono é Dorme em paz (Paulo
Tatit/Luis Tatit). A noite é tema no primeiro
verso das duas primeiras estrofes, entoada
exatamente no mesmo percurso melódico,
ansiada que é para o sono da criança – e da
mãe e do pai que ninam. Do de vista dos parâmetros musicais
semióticos,
é
possível
perceber
uma
predominância nesse subgênero cancional
da tematização, de reiteração de um tema e
a consequente harmonização da psiquê
infantil, aliados a recursos linguísticos de
exaltação de um objeto lírico. O papel das produções artísticas na
formação de leitores e cidadãos desde a
mais tenra infância, aproveitando de suas
inclinações psicanalíticas ao acalanto para
promover o contato com práticas sociais de
leitura, é importante ao processo de ensino e
aprendizagem. O contato infantil com esse
subgênero deve ser melhor explorado pela
escola e pelos educadores, além de ser
estimulado pelos familiares desde sempre. A figurativização aparece como outro
importante
parâmetro
musical
desse
subgênero, com menos ocorrências na obra
analisada, mas que, por meio de caminhos
melódicos
inconstantes,
próximos
da
entoação da fala, é possível uma interação
infantil com a paralinguagem de seus
sistemas linguísticos e as práticas sociais de
leitura e escrita. 6 CONCLUSÃO Este artigo apresentou a importância
das produções artísticas na formação de
leitores, aproveitando de suas inclinações
psicanalíticas ao acalanto para promover
desde a mais tenra infância o contato com
práticas sociais de leitura. Os recursos linguísticos descortinam a
presença de uma voz com quem o
destinatário-ouvinte
possa
manter
sentimentos de empatia ou que leva a
reflexões morais de situações cotidianas do
universo da criança. p
Por meio da análise da eficácia
comunicativa e do encanto estético da
canção de ninar, segundo os parâmetros
semióticos, aliados a recursos linguísticos
de exaltação e de humor em sentido amplo
nos acalantos presentes no álbum “Canções
de ninar”, do projeto Palavra Cantada, foi
possível observar como a canção (e,
especificamente, a canção infantil em seu
subgênero musical acalanto) possui a
pluralidade de níveis de linguagem para
estimular uma leitura híbrida e multimodal e
a capacidade de afetar dinamogenicamente
o interlocutor e, assim, instigá-lo ao
exercício mais constante da leitura, afinal,
apesar de aparentemente simples, a cultura e
a arte popular conseguem dar conta das
necessidades físicas e psicológicas das
crianças. Chega-se, portanto, a conclusão de o
gênero canção infantil em seu subgênero
acalanto é uma peça valiosa para a formação
pedagógica da criança, por meio da eficácia
comunicacional e do encanto estético, nos
níveis
cognitivos,
morais,
éticos,
dinamogênicos,
estéticos
e
lúdicos,
considerando-as
enquanto
leitoras
em
constante processo de alfabetização. v.1 n.1 2019 75 BAKHTIN, M. Os gêneros do discurso. In:
BAKHTIN, M. Estética da criação verbal. São. Paulo: Martins Fontes, 2003. p. 261-
306. CALAZANS, J. H. C. A criação de um
gênero textual a partir das relações onde,
quem e o que: espaço, sujeito e ideologia. In: Intercom, Recife, 2011. BAKHTIN, M. Os gêneros do discurso. In:
BAKHTIN, M. Estética da criação verbal. São. Paulo: Martins Fontes, 2003. p. 261-
306. n. 2,
2012. Disponível
em:<http://revistas.unincor.br/index.php/rec
orte/article/view/608/pdf>. Acesso em: 29
out. 2017. n. 2,
2012. Disponível
em:<http://revistas.unincor.br/index.php/rec
orte/article/view/608/pdf>. Acesso em: 29
out. 2017. n. TATIT, Luiz. A Canção, Eficácia e
Encanto. São Paulo: Atual Editora, 1986. CALAZANS, J. H. C. A criação de um
gênero textual a partir das relações onde,
quem e o que: espaço, sujeito e ideologia. In: Intercom, Recife, 2011. TATIT, Luiz. Análise semiótica através
das letras. 4. ed. São Paulo: Ateliê, 2001. TATIT, Luiz. O cancionista: composição
de canções no Brasil. São Paulo: EDUSP,
1995. COSTA, Nelson Barros da. Canção popular
e ensino da língua materna: o gênero canção
nos Parâmetros Curriculares de Língua
Portuguesa. In: Linguagem em (Dis)curso. Tubarão, 2003, p.9-36. WISNIK, José Miguel. O som e o sentido. Uma outra história das músicas. São Paulo,
Companhia das Letras, 1989. ______; GONZALEZ, B. N. A. C.. A
produção do discurso literomusical brasileiro
para crianças? Uma proposta de investigação
discursiva. In: Abralin em Cena Amazonas,
2014, Manaus. Abralin em Cena Amazonas. Manaus - AM: UEA edições, 2014. ______; PIEDADE, Acácio; MEHMARI,
André; FIAMMENGHI, Luiz Henrique. Mesa Redonda - A Canção Brasileira e a
Música Instrumental [Registo vídeo]. In:
Seminário
de
Improvisação
Musical
Brasileira. Florianópolis: Cinese Filmes,
2015. (1h52min). Disponível
em:
<https://www.youtube.com/watch?v=6BkN
ZqcRPsw&list=PLRJHFycO_yhhk7FfAjPs
SBb65nEv9WGdb&index=4>. Acesso em
21 dez. 2017. CUNHA, L. Poesia e humor para crianças. In: OLIVEIRA, Ieda de (Org.). O que é
qualidade em literatura infantil e juvenil
- Com a palavra, o escritor. São Paulo: DCI,
2005, p. 77-90. FALBO, C. V. R. A palavra em movimento:
algumas perspectivas teóricas para a análise
de canções no âmbito da música popular. In:
Per Musi, n. 22, Belo Horizonte: UFMG,
2010, p. 218-231. MARCUSCHI. L. A. Produção Textual,
Análise de Gêneros e Compreensão. São
Paulo: Parábola Editorial, 2008. PERES, Sandra e TATIT, Paulo. Canções
de ninar. Coleção Palavra Cantada. São
Paulo: Salamandra, 1994. Disponível em
<https://www.youtube.com/watch?v=1UrdP
DgWn08>. Acesso: 12 nov. 2018. RIBEIRO, Francisco Aurélio. "A literatura
infantojuvenil e sua utilização na escola. REFERÊNCIAS ANDRADE, Mário de. Ensaio sobre a
música brasileira. 3. ed. São Paulo:
Martins, 1972. AZEVEDO, Ricardo. Aspectos instigantes
da
literatura
infantil
e
juvenil. In:
OLIVEIRA, Ieda de (org.) O que é
qualidade em literatura infantil e juvenil
- Com a palavra o escritor, São Paulo, DCL,
2005, p. 25-46. AZEVEDO, Ricardo. Aspectos instigantes
da
literatura
infantil
e
juvenil. In:
OLIVEIRA, Ieda de (org.) O que é
qualidade em literatura infantil e juvenil
- Com a palavra o escritor, São Paulo, DCL,
2005, p. 25-46. As
características
do
subgênero
textual acalanto dentro do espectro de
produções artísticas destinadas ao público In:
Ensaios
de
leitura
e
literatura
infantojuvenil. Serra (ES): Editora Formar,
2010, p. 33-47. RUFINO, Janaína de Assis. As notas da
minha canção: considerações sobre o gênero
canção. Recorte – Revista Eletrônica, v. 9,
|
https://openalex.org/W3195157635
|
https://figshare.com/articles/journal_contribution/Towards_interoperable_blockchains_a_survey_on_the_role_of_smart_contracts_in_blockchain_interoperability/23003360/1/files/40754078.pdf
|
English
| null |
Towards Interoperable Blockchains: A Survey on the Role of Smart Contracts in Blockchain Interoperability
|
IEEE access
| 2,021
|
cc-by
| 15,856
|
Author Author
Khan, S, Muhammad Bilal Amin, Azar, AT, Aslam, S Khan, S, Muhammad Bilal Amin, Azar, AT, Aslam, S Is published in: 10.1109/ACCESS.2021.3106384 Is published in: 10.1109/ACCESS.2021.3106384 Bibliographic citation Khan, S; Amin, Muhammad Bilal; Azar, AT; Aslam, S (2021). Towards interoperable blockchains: a survey on
the role of smart contracts in blockchain interoperability. University Of Tasmania. Journal contribution. https://figshare.utas.edu.au/articles/journal_contribution/Towards_interoperable_blockchains_a_survey_on_the_ Khan, S; Amin, Muhammad Bilal; Azar, AT; Aslam, S (2021). Towards interoperable blockchains: a survey on
the role of smart contracts in blockchain interoperability. University Of Tasmania. Journal contribution. https://figshare.utas.edu.au/articles/journal_contribution/Towards_interoperable_blockchains_a_survey_on_the_ Copyright information This version of work is made accessible in the repository with the permission of the copyright holder/s under
the following, Downloaded from University of Tasmania Open Access Repository Downloaded from University of Tasmania Open Access Repository Please do not remove this coversheet as it contains citation and copyright information. Licence. Rights statement: This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0)
License. For more information, see https://creativecommons.org/licenses/by/4.0/ If you believe that this work infringes copyright, please email details to: oa.repository@utas. Title Title
Towards interoperable blockchains: a survey on the role of smart contracts in blockchain interoperability
Author Towards Interoperable Blockchains: A Survey
on the Role of Smart Contracts in
Blockchain Interoperability SAJJAD KHAN
1, MUHAMMAD BILAL AMIN
2,
AHMAD TAHER AZAR3,4, (Senior Member, IEEE),
AND SHERAZ ASLAM
5, (Member, IEEE)
1COMSATS University Islamabad, Islamabad 45550, Pakistan
2College of Sciences and Engineering, University of Tasmania, Hobart, TAS 7005, Australia
3College of Computer and Information Sciences, Prince Sultan University, Riyadh 11586, Saudi Arabia
4Faculty of Computers and Artificial Intelligence, Benha University, Benha 13518, Egypt
5Department of Electrical Engineering, Computer Engineering, and Informatics, Cyprus University of Technology, 3036 Limassol, Cyprus
Corresponding authors: Sajjad Khan (sajjadkhancui@gmail com) and Ahmad Taher Azar (aazar@psu edu sa) SAJJAD KHAN
1, MUHAMMAD BILAL AMIN
2,
AHMAD TAHER AZAR3,4, (Senior Member, IEEE),
AND SHERAZ ASLAM
5, (Member, IEEE)
1COMSATS University Islamabad, Islamabad 45550, Pakistan
2College of Sciences and Engineering, University of Tasmania, Hobart, TAS 7005, Australia
3College of Computer and Information Sciences, Prince Sultan University, Riyadh 11586, Saudi Arabia
4Faculty of Computers and Artificial Intelligence, Benha University, Benha 13518, Egypt
5Department of Electrical Engineering, Computer Engineering, and Informatics, Cyprus University of Technology, 3036 Limassol, Cyprus
Corresponding authors: Sajjad Khan (sajjadkhancui@gmail com) and Ahmad Taher Azar (aazar@psu edu sa) This work was supported by Prince Sultan University. ABSTRACT The slower than expected adoption rate of blockchain technology has highlighted that there
are barriers due to the diversity of its applications and its users. To overcome this limitation and take
full advantage of the novel technology, researchers from academia as well as industry are dedicated to
find different solutions, where two or more blockchains can interact with each other. As a result, several
interoperability solutions have presented themselves. To investigate the functionalities and underlying
mechanisms of interoperable blockchain solutions, researchers have conducted several surveys by discussing
the features and innovations of these methods. However, the existing surveys tend to focus on the architectural
description of the interoperability solutions and completely overlook the most promising aspect of blockchain
adaptability, namely the smart contract. This paper fills the gap by exploring the role of smart contracts
in blockchain interoperability solutions. Our research has classified the existing interoperability solutions
into three main categories: heterogeneous blockchains and homogeneous smart contracts, homogeneous
blockchains and homogeneous smart contracts, heterogeneous blockchains, and heterogeneous smart con-
tracts. To provide a systematic overview of the smart contracts used in blockchain interoperability, each
category is further divided into subcategories by identifying the functionalities of the smart contract used. Towards Interoperable Blockchains: A Survey
on the Role of Smart Contracts in
Blockchain Interoperability Based on our survey, a taxonomy is proposed to help classify the blockchain interoperability solutions. The interoperability solutions in each category are analyzed in-depth, and the results are presented in tabular
format to illustrate the characteristics of the interoperability solutions in a meaningful way. Finally, a number
of open issues and research directions are discussed to overcome the limitations and improve the performance
of blockchain interoperability. INDEX TERMS
Blockchain interoperability, smart contracts, chain code, cross chain transactions,
sidechains, decentralized applications, cryptocurrency, digital assets. INDEX TERMS
Blockchain interoperability, smart contracts, chain code, cross chain transactions,
sidechains, decentralized applications, cryptocurrency, digital assets. University of Tasmania Open Access Repository Library and Cultural Collections
University of Tasmania
Private Bag 3
Hobart, TAS 7005 Australia
E oa.repository@utas.edu.au CRICOS Provider Code 00586B | ABN 30 764 374 782
utas utas.edu.au Received August 10, 2021, accepted August 17, 2021, date of publication August 20, 2021, date of current version August 27, 2021. eceived August 10, 2021, accepted August 17, 2021, date of pu Digital Object Identifier 10.1109/ACCESS.2021.3106384 The associate editor coordinating the review of this manuscript and
approving it for publication was Mehedi Masud. under a Creative Commons Attribution 4.0 License. For more information, see https://creativecommons.org/licenses/by/4.0/
VOLUM I. INTRODUCTION When implemented
properly, smart-contract-based interoperability solutions or
cross-chain smart contracts can minimize the excess cost and
time required to develop an architecture-based interoperabil-
ity solution to a greater extent. The main contributions of this
paper are as follows. to work on Blockchain. As a result, a number of plat-
forms with smart contract capabilities have been developed
(e.g., Corda [3], Quorum [4] and Hyperledger Fabric [5],
etc.). Today, the blockchain domain is very rich. More-
over, due to its temper-resistance ledger with zero-knowledge
proof and smart contract capabilities in the decentralized
environment, it has gained attraction from various fields such
as cloud computing [6], Internet of Things (IoT) [7], [8],
energy domain [9], food supply chain [10] and education [11],
etc. The application of blockchain varies from cross domain
data sharing for industrial IoT [12], privacy preserving data
aggregation model in smart gird [13] and electronic health
records [14], etc. According to Gartner, the blockchain industry has poured
billions of dollars into research [15]. Both government
and private sector organizations are betting on the use of
blockchain technology. However, the growing interest in
this area is focusing on creating new types of Blockchains. Although these new blockchains are capable of meeting
the changing needs of users, they lack the ability to inter-
act or communicate with each other. Thus, if a user on
one blockchain wants to interact with another user on a
different blockchain, they must either have an account on
that blockchain or switch to the target blockchains. The
advantage of choosing a new blockchain over an existing
blockchain allows a user to take advantage of the advanced
features of modern technology. The disadvantage of choos-
ing a novel blockchain, on the other hand, involves security
risks due to the immaturity and security concerns of novel
blockchains [16]. In short, the ways in which two blockchains
can interact with each other remain unexplored. To solve the problem of blockchains’ inability to interact
and communicate with each other, Adam et al. proposed [17]
sidechains. ‘‘A sidechain refers to a secondary blockchain
that validates data from other blockchains’’. A pegged
sidechain refers to a blockchain that has the ability to import
and export digital property (i.e., coins, assets, etc.) from
other blockchains at an agreed-upon price or exchange rate. It allows the transfer of digital properties between the two
blockchains using a Simplified Payment Verification (SPV).1
Sidechains are independent blockchains. I. INTRODUCTION without mutual trust. However, the applications and use of
blockchains were limited only to the storage and transfer
of value of Bitcoin. With the development of competing
digital ledger technologies such as Ethereum [2], smart con-
tracts were introduced into the blockchain architecture. Smart
contracts transformed blockchains from a mere ledger to
a programmable machine. This opens the doors for many
individuals and organizations from academia and industry Blockchain has revolutionized the finance industry by intro-
ducing cryptocurrencies to the digital world [1]. It is the
core technology that enabled the transfer of cryptocurren-
cies by ensuring consistency in a decentralized environment The associate editor coordinating the review of this manuscript and
approving it for publication was Mehedi Masud. 116672 116672 116672 VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains tokens on the secondary chain using trusted or semi-trusted
intermediaries [19]. Since the introduction of smart contracts,
the applications of blockchains are no longer limited to token
creation and management, a number of platforms with smart
contract capabilities have emerged to connect blockchains. Some of the well-known solutions are Cosmos [20],
Polkadot [21], AION [22] that connects independent
blockchains using an intermediate chain, Tokrex [23], Block-
net [24], Agent chain [25], Komodo [26] using decentralized
exchanges, Scheid et al. [27] by developing a policy-based
framework, Testimonium [28] a validation relay on demand,
Zendoo [29] a sidechain capable of creating, communicat-
ing and integrating new sidechains with the main chain,
Ghaemi et al. [30] by developing a publisher/subscriber
architecture and Frauenthaler et al. [31] using a dynamic
framework to switch users from one blockchain to another
blockchain. Although all of these solutions aim to achieve
blockchain interoperability. There are significant trade-offs
between all existing solutions. Therefore, our goal in this
paper is to provide an overview of interoperability solutions. Although a number of authors have studied interoperability
approaches, their work focused on studying interoperability
from an architectural perspective, i.e., none of the existing
work studied the role of smart contracts in interconnecting
blockchains. Therefore, by studying the role of smart con-
tracts in interconnecting blockchains, interoperability can be
greatly improved. The main reason why smart-contract-based
interoperability will outperform architecture-based inter-
operability solutions is its ability to enforce contractual
terms in decentralized environments. 1It consists of block headers and cryptographic proof to show that a
particular output has been created. I. INTRODUCTION Each sidechain
has its own consensus mechanism and security protocols. Similarly, each blockchain is sovereign to implement its
own identity management and cryptographic algorithms [18]. Therefore, malicious attempts on one sidechain cannot
affect the performance of the main or parent blockchain
in the event of interoperation between the interacting
chains. p p
1) This study defined several areas through which inter-
operability between blockchains can be achieved. 2) This study provides an overview of solutions for inter-
operable blockchains by discussing the role of smart
contracts in blockchain interoperability. To the best of
our knowledge, this is the first study on the role of smart
contracts in blockchain interoperability. 3) A classification of interoperable blockchain solutions
is provided on the basis of blockchain type and
programming languages used to develop smart con-
tracts used in the interoperable blockchain solutions. A hierarchical taxonomy diagram is created in order
to help readers to explore the field of blockchain
interoperability. Although sidechains are emerging as promising solu-
tions, they are used for a specific use case, namely con-
necting the parent blockchain to a secondary blockchain
to exchange tokens by locking a certain set of tokens
on one chain and releasing the corresponding set of 4) For each category and subcategories, the correspond-
ing interoperability solution is analyzed. The in-depth
analysis of each solution is summarized in tables to
comprehensively present the results. 5) This study examined the main issues of each interoper-
ability solution and analyzed their implications with a
detailed discussion. VOLUME 9, 2021 116673 S. Khan et al.: Towards Interoperable Blockchains TABLE 1. Summary of the existing surveys. TABLE 1. Summary of the existing surveys. 6) Finally, open issues, challenges, and future directions
are discussed to enhance the performance of interoper-
ability solutions in the blockchain. 6) Finally, open issues, challenges, and future directions
are discussed to enhance the performance of interoper-
ability solutions in the blockchain. by studying the work done by the Token Atomic Swap
Technology (TAST) project. Moreover, the authors high-
lighted a number of open issues, challenges, and possi-
ble research directions. Schulte et al. [51] discussed token
transfer and smart contract interaction in cross-blockchain
transactions. The rest of this paper is organized as follows. A literature
review of the existing surveys is discussed in section II. The preliminary on smart contracts and programming lan-
guages are discussed in section III. I. INTRODUCTION Interoperability and the
various approaches through which interoperability between
blockchains can be achieved is discussed in section IV. Section V discusses the role of smart contracts in interop-
erability solutions. The future directions and challenges are
discussed in section VI. Lastly, section VII concludes the
paper. Koens et al. [43] assessed two of the renowned blockchain
interoperability solutions provided by Cosmos and Polkadot
using twelve key properties. Singh et al. [44] and Sandra [48]
surveyed interoperability solutions in sidechain technologies. Siris et al. [45] classified inter ledger approaches into six cat-
egories: atomic cross-chain transaction, bridging, sidechains,
the inter ledger protocols, transactions across a network, and
ledger of ledgers. In this work, the authors focused on how
the ledgers are interconnected. Moreover, an analysis is per-
formed on the exchange of values or assets, transaction cost,
complexity, scalability, and inter ledger trust mechanisms. Kannengießer et al. [46] categorized inter ledger approaches
into four categories: manual asset exchange, notary schemes,
relays, and hybrid solutions. Miraz et al. [47] classified
atomic cross-chain swaps into on-chain atomic swaps and
off-chain atomic swaps. In this work, the authors analyzed the
pros, cons, and key challenges associated with atomic cross-
chain swaps in cryptocurrencies. II. EXISTING SURVEYS This section discusses existing surveys on blockchain inter-
operability. Due to the novelty of this area, the number of
peer-reviewed articles is limited. Therefore, to give the reader
a clear idea of all the efforts done in this area, self publi-
cations are also included in this survey. A summary of the
existing surveys is given in table 1. In table 1, permission
type represents blockchain permissions such as public or
private blockchains. Blockchain type represents blockchain
type such as homogeneous or heterogeneous blockchains. Smart contract scripts represent if (or not) the existing surveys
discussed the smart contracts scripts or programming lan-
guages of the interacting blockchains. Arbitrary data shows if
(or not) the existing study review interoperability techniques
by considering data transfer across blockchains. Comparison
represents if (or not) the existing survey has performed any
comparison/analysis of the interoperability solutions. The
role of smart contracts shows if (or not) the authors discussed
the role of smart contracts in interoperability. Qasse et al. [49] classified interoperability into four cat-
egories namely sidechains, industrial solutions, smart con-
tracts, and blockchain routers. This work also discussed
inter-blockchain communication approaches. Vo et al. [50]
discussed interoperability solutions that support communi-
cation and interconnection between multi-chain architec-
ture. This work focused on the Internet of blockchains
and inter-blockchain communication between the interact-
ing blockchains. Belchior et al. [52] classified interoperabil-
ity solutions into three categories: cryptocurrency directed
approach, blockchain engines, and blockchain connectors. The cryptocurrency directed approach is further categorized
into sidechains, notary schemes, hashed time-locks, and
hybrid solutions. Similarly, the blockchain connectors are
further categorized into trusted relays, blockchain agnos-
tic protocols, blockchain of blockchains, and blockchain
migrators. Buterin [40] classified interoperability solutions into three
categories: notary schemes, sidechains/relays, and hash
locks. The author discussed that interoperability can be
achieved for portable assets, payment vs payment or payment
vs delivery methods, cross-chain assets, asset encumbrance,
and general cross-chain smart contracts. Borkowski et al. [41]
discussed atomic cross-chain transfer for token exchange
and user-issued assets. This work is extended in [42] 116674 116674 116674 VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains Table 1 summarizes the closely related surveys/reviews on
blockchain interoperability and reveals our survey’s novelty. The aforementioned surveys and review work either focus
on discussing the architectural aspects [40]–[52] or failed
to present a broad image of smart contracts in blockchain
interoperability. III. SMART CONTRACTS AND PROGRAMMING
LANGUAGES A smart contract is defined as a computer program that
enforces the promises agreed by the interacting parties in
the absence of trusted intermediaries. Though the concept of
smart contracts is relatively new, the idea was first introduced
by Szabo [32] in 1990. Back then, due to the unavailability of
technological requirements and decentralized network proto-
cols, the concept was only limited to theory. With the develop-
ment of the Ethereum ecosystem, the smart contract becomes
the key player to shape blockchains from a distributed ledgers
to programmable state machines by introducing the execution
of Decentralized Applications (dApps). The distinguishing
features that make smart contracts pertinent to many applica-
tions are built-in transparency and immutability. Like all other
transactions, smart contracts are stored in blockchains. More-
over, novel user requirements can easily be implemented by
deploying smart contracts. However, smart contracts mainte-
nance is different as compared to traditional computer soft-
ware because they cannot be altered once deployed, even by
the creator of the smart contracts [33]. A. IDENTITY MANAGEMENT It is likely that each blockchain has its own identity manage-
ment. However, when two or more blockchains are intercon-
nected. It is necessary to uniquely identify each user, transac-
tion or process in a cross-chain transaction while reading and
writing transactions or data from one blockchain to another
in order to ensure accountability. B. CRYPTOGRAPHIC MANAGEMENT In the case of cross-chain transactions or communication,
each blockchain will have different cryptographic/hash meth-
ods. Though intermediary chains facilitating cross-chain
transactions are tasked to resolve the cartographic hash of
each blockchain. For true interoperability, a cryptographic
management system must be developed to enable blockchains
to add users/transactions from other blockchains dynami-
cally. Such a cryptographic management system can grant
access to specific users temporarily. Smart contracts can be developed in a number of pro-
gramming languages. The most popular language for devel-
oping smart contracts is Solidity [34]. Solidity is an
object-oriented, Turing complete language developed by
the Ethereum platform to execute smart contracts on the
Ethereum Virtual Machine (EVM). Solidity smart contracts
can also be executed on Hyperledger Fabric [5] chains. IV. INTEROPERABILITY Generally, interoperability in computer science refers to ‘‘the
ability of computer systems or software to exchange and
make use of information’’. National Institute of Standards
and Technology (NIST) defined interoperability between
blockchains as: ‘‘an interoperable blockchain architecture
is a composition of distinguishable blockchain systems,
each representing a unique distributed data ledger, where
atomic transaction execution may span multiple heteroge-
neous blockchain systems, and where data recorded in one
blockchain is reachable, verifiable and referable by another
possibly foreign transaction in a semantically compatible
manner ’’ [39]. As blockchain is essentially a data structure,
in which transactions/records from various entities are stored
using the cryptographic mechanism with decentralized con-
sensus mechanism by means of a smart contract. This study
defined blockchain interoperability as follows: ‘‘The ability
of a distributed ledger to process transactions originated in
another distributed ledger with homogeneous/ heterogeneous
identity management, cryptographic management, consen-
sus mechanism, and smart contracts capabilities’’. Based on
the aforementioned definition, blockchain interoperability is
classified into four main areas. II. EXISTING SURVEYS For instance, some surveys only discussed
interoperability in permission-less blockchains and some are
discussing permissioned blockchains; on the other side, some
are reviewing only homogeneous blockchains and others are
discussing heterogeneous blockchains. Furthermore, none of
the existing surveys/reviews focused on the role of smart
contracts in blockchain interoperability. Our survey work is
therefore intrinsically different due to its broad view, along
with several features that are considered simultaneously. This
study presents a detailed overview of solutions for interoper-
able blockchains by discussing the role of smart contracts in
blockchain interoperability. To the best of our knowledge, this
is the first study on the role of smart contracts in blockchain
interoperability. Moreover, a classification of interoperable
blockchain solutions is provided on the basis of blockchain
type and programming languages used to develop smart con-
tracts used in the interoperable blockchain solutions. A hier-
archical taxonomy diagram is created in order to help readers
to explore the field of blockchain interoperability. Eventu-
ally, based on our comprehensive survey, this study outlines
various issues that still remain to be tackled and research
opportunities for the future. Similarly, Rootstock (RSK) [19] is a sidechain to Bitcoin
and compatible with Ethereum. General programming lan-
guages can also be used to design smart contracts for some
blockchains e.g., Hyperledger Fabric, Neo [35], Eos [36]
and Tendermint [37] supports smart contracts designed in
Go, Java, NodeJS, Python, and C++. Steller uses Javascript,
Golang, PHP, and python, however, the smart contracts of
Steller are not Turing complete. An overview of the program-
ming languages and smart contracts application development
platform is given in [38]. IV. INTEROPERABILITY D. CODE LEVEL INTEROPERABILITY Chain code/smart contracts are written in different lan-
guages. For true interoperability, a contract written in one
language can be scaled to other blockchain networks by
referencing their particular contract code. For this pur-
pose, a virtualization-based approach can be adopted. The
virtualization-based approach enables the execution of a
smart contract on multiple and heterogeneous blockchain
platforms by creating an abstraction layer over the underlying
blockchain. Furthermore, a user interface-based engine can
be developed to create smart contract workflows between
blockchains. This study focuses on code-level interoperabil-
ity between blockchains. An overview of all the interoperability solutions is given
in table 2. In table 2 privacy and security shows if (or not)
the authors considered any mechanism to ensure privacy and
security. Scalability shows if (or not) the proposed inter-
operability solution is scalable. Scalability in interoperable
blockchains can be vertical scalability or horizontal scalabil-
ity. We considered both the types and a detailed overview of
each type is given in the discussion. The degree of confidence
shows if (or not) the proposed solution considered a mecha-
nism to ensure that the transaction is added to the block by
following the longest chain. It refers to feedback mechanism
that a target blockchain used to inform the source blockchain. Feedback is usually given by waiting till a number of blocks
are confirmed on the main chain. It is used to avoid forks
in blockchain. Bidirectional transactions represent if (or not)
the interacting chains are able to send and receive transac-
tions from each other. The interacting blockchain shows the
details of blockchains for which the interoperability solu-
tion is achieved. Deployment mode shows the key player
(or mechanism) through which interoperability is achieved
between the interacting chains. Lastly, applications show the
scenarios in which the solution can be applied. Throughout
this paper, chain code (in Hyperledger blockchains) and smart
contracts are used interchangeably. Source chain represents a
blockchain where the transaction or smart contract is initiated
whereas target chain represents the blockchain where the
transaction terminates. V. ROLE OF SMART CONTRACTS IN BLOCKCHAIN
INTEROPERABILITY Today, the blockchain interoperability domain is very
rich. However, the number of peer-reviewed articles in this
area is limited. Therefore, self-published articles available
on public platforms such as arXiv and ResearchGate are
also included in this study. Moreover, the publicly available
whitepapers of the renowned interoperability solutions such
as Polkadot, Cosmos, Block Collider, and ICON republic,
etc. are also surveyed in this study. The search process
for the articles was conducted using google scholar. It is
worthy to mention that this survey does not cover all the
research articles in the blockchain interoperability area. This
study is focused to investigate the role of smart contracts in
blockchain interoperability solutions. Therefore, in this study
only those research articles were surveyed in which smart
contract is the main facilitator or key player in blockchain
interoperability. Although smart contracts have the potential to enhance
blockchain interoperability, no attention has been paid to
investigate the role of smart contracts in the interoperability
domain. One of the key advantages of achieving interoper-
ability in blockchains using smart contracts is that any peer
in the network can deploy a smart contract. Similarly, any
peer that agrees to the contractual clause of an existing smart
contract is also capable to execute it. As a result, a smart con-
tract can be reused. Smart contracts can call or invoke other
smart contracts using calls to fulfill a certain task, or inquire
about a past event. Typically, a smart contract can only be
invoked from the local chain. However, recent advancements
show that smart contracts on remote blockchains can also be
invoked by passing arbitrary data or machine level byte code
in the form of a transaction or Remote Procedure Call (RPC). A. HETEROGENEOUS BLOCKCHAINS AND
HOMOGENEOUS SMART CONTRACTS This subsection discusses interoperability solutions between
heterogeneous blockchains. Heterogeneous blockchains refer
to different blockchains e.g., Bitcoin, Ethereum and Hyper-
ledger, etc.). Whereas, homogeneous smart contracts refer to
smart contracts that are developed in the same programming
language e.g., Solidity, etc. C. CONSENSUS MECHANISMS Every blockchain has its own consensus algorithm. For inter-
operability, a case needs to be determined with an efficient VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains Creating a taxonomy implies grouping and classifying exist-
ing interoperability solutions into a compact representation,
allowing the exploration and comparison of different solution
designs. Similarly, it is difficult to evaluate if a taxonomy
is good, especially if the domain is emerging rapidly. It is
worth mentioning that there is not a hard rule in creating
the proposed taxonomy, as the interoperability solutions vary
on the basis of requirements and applications. The proposed
taxonomy is based on the existing work found in the lit-
erature. It simply aims to set the foundation of achieving
interoperability using smart contracts. algorithmic scheme such that either one consensus algorithm
can be scaled upon all the participating networks or a com-
patible mechanism for all the interacting blockchains can be
applied. 1) TIME LOCK CONTRACTS Herlihy [53] proposed an atomic swap protocol for assets
exchange across multiple blockchains. This protocol guar-
antees that if all interacting parties agree to the protocol,
then the exchange of assets occurs. If any of the parties
deviates from the protocol, then none of the parties incurs
losses. Furthermore, there is no incentive for deviation from
the protocol. The protocol can be seen as a directed graph In order to give the readers an intuitive view of our clas-
sification of the interoperability solutions in accordance with
the functionalities of the smart contracts, a high-level taxon-
omy of the interoperability solutions is provided in Figure 1. 116676 116676 VOLUME 9, 2021 VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains FIGURE 1. Taxonomy of smart contract based interoperability solutions in blockchains. FIGURE 1. Taxonomy of smart contract based interoperability solutions in blockchains. with a finite set of vertices and an ordered pair of arcs. The vertices represent the interacting parties, and the arcs
represent the exchange of assets. Atomic swap protocol uses
a Hashed Time Lock Contract (HTLC) to exchange assets in
order to assume the control of the other party assets temporar-
ily. A typical HTLC comprises hashed locks and keys. The
ownership of the assets changes upon receiving a matching
key before a certain time limit. However, if the matching
key is not received under the time limits, then the assets are
retained by the original owner. In this work, the presence of a
market-clearing service is assumed to enable communication
between the interacting parties to ensure consistency. The
protocol occurs in two phases. In the first phase, the protocol
is propagated in a leader-follower manner. In the second
phase, the interacting parties propagate the secrets via hash-
keys. The propagation terminates if the time limit expires or
all the secrets are unlocked. contract is locked on the source or target chain, only read
operations can be performed on that chain. It is assumed
that the source and target blockchains have the same vir-
tual machine to execute the smart contracts. Moreover, there
exists a procedure by which the source and target chain can
verify the state variables (such as Merkle-tree) of each other. Black et al. [55] proposed atomic loans. Atomic loans
can be implemented as an extension of atomic swaps. The
process is divided into four periods: loan, bidding, seizure,
and refund protocols. 3https://github.com/AtomicLoans; VOLUME 9, 2021 4https://github.com/crossclaim/xclaim-sol; 1) TIME LOCK CONTRACTS In this work, it is assumed that two
users residing on different chains communicate by means
of a communication protocol. When the users agree to the
terms of the loan such as the interest rate, repayment of
collateral, and liquidate the collateral (in the case of default),
the loan is issued and the terms are incorporated in a smart
contract. The authors highlighted a number of use cases to
ensure neither lender nor the borrower incurs losses. The loan
process requires blockchains with smart contract capabilities,
therefore this work is not compatible with some blockchains
such as bitcoin due to the limited functionality of scripting
language. Atomic loan is open-source.3 Fynn et al. [54] proposed atomic move. In this work,
the smart contract from the source blockchain migrates to the
target blockchain. Migration occurs in two steps. In the first
step, the state of the smart contract is locked on the source
chain. In the second step, the smart contract is recreated in
the target blockchain to execute transactions. When the smart 116677 VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains TABLE 2. Overview of interoperability solutions. Note: 1) P&S: Privacy and security, SC: Scalability, DoC: Degree of confidence, and BT: Bidirectional
transactions. TABLE 2. Overview of interoperability solutions. Note: 1) P&S: Privacy and security, SC: Scalability, DoC: Degree of confidence, and BT: Bidirectional
transactions. rability solutions. Note: 1) P&S: Privacy and security, SC: Scalability, DoC: Degree of confidence, and BT: Bidirectional VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains TABLE 2. (Continued.) Overview of interoperability solutions. Note: 1) P&S: Privacy and security, SC: Scalability, DoC: Degree of confidence,
and BT: Bidirectional transactions. TABLE 2. (Continued.) Overview of interoperability solutions. Note: 1) P&S: Privacy and security, SC: Scalability, DoC: Degree of confidence,
and BT: Bidirectional transactions. TABLE 2. (Continued.) Overview of interoperability solutions. Note: 1) P&S: Privacy and security, SC
and BT: Bidirectional transactions. Overview of interoperability solutions. Note: 1) P&S: Privacy and security, SC: Scalability, DoC: Degree of confidence,
ansactions S. Khan et al.: Towards Interoperable Blockchains TABLE 2. (Continued.) Overview of interoperability solutions. Note: 1) P&S: Privacy and security, SC: Scalability, DoC: Degree of confidence,
and BT: Bidirectional transactions. TABLE 2. (Continued.) Overview of interoperability solutions. Note: 1) P&S: Privacy and security, SC: Scalability, DoC: Degree of confidence,
and BT: Bidirectional transactions. rview of interoperability solutions. 1) TIME LOCK CONTRACTS Note: 1) P&S: Privacy and security, SC: Scalability, DoC: Degree of confidence,
actions s. Note: 1) P&S: Privacy and security, SC: Scalability, DoC: Degree of confidence, Zamyatin et al. [56] developed XCLAIM (cross-claim). XCLAIM is a cryptocurrency-backed approach for issu-
ing tokens on Ethereum. In such approaches, assets or
tokens on one blockchain are backed by cryptocurrencies on
another blockchain. This work used Bitcoin-backed tokens
on Ethereum. The primary objective of this work is to enforce
the correct issue, transfer/swap, and redeem operations on the
backing and issuing blockchains. In this work, all the opera-
tions are performed on a number of actors: requester, sender,
receiver, redeemer, vault, and smart contract. Requester locks
the cryptocurrencies on the backing blockchain. The sender
is used to shift ownership from one user to another on the
issuing blockchain. The receiver is assigned ownership of
the tokens. Redeemer destroys the corresponding tokens on
the backing blockchain. Vault is used to redeem requests
of the issuing blockchains on the backing blockchain. The
smart contract is used to issue as well as manage tokens
on the issuing blockchains. This work incorporates proof of punishment approach to enforce the correct behavior of
all the actors. Furthermore, collateral and publicly verifiable
audit logs are maintained on the backing as well as issu-
ing blockchains. In this work, P2PHK [57] transactions are
used on the backing blockchain. XCLAIM currently supports
Bitcoin-backed tokens on Ethereum. However, the authors
claim that the backing and issuing of blockchains can be
extended to other cryptocurrencies as well. The performance
of this work is evaluated in terms of execution cost for issuing,
transfer, and redeem protocols. This work claims to have
outperformed HTLCs by minimizing the execution cost and
the overall time. XCLAIM is open-source.4 4) OFF CHAIN SMART CONTRACTS Interoperability solution for a limited number of chains or
designated chains will only increase the number of isolated
chains rather than interconnecting chains. Interoperability
between independent chains can be accomplished using a
plug-in manner with generalized multi-chain communica-
tion and cross-chain transaction protocols. A key advantage
of [53] is that it can be extended to any model for assets
or service exchange. However, the model is vulnerable to
distributed denial of service attacks in the event if an adver-
sary repeatedly fails to complete the protocol. This results in
locking the assets of the interacting party and making him/her
unavailable to trade assets with other parties. Hosp et al. [61] proposed a Cryptographically secure
Off-chain Multi-asset Instant Transaction network (COMIT). COMIT allows instant transactions between blockchains
using off-chain smart contracts. It aims to develop a commu-
nication protocol so that nodes can communicate with each
other. COMIT network use payment channels and HTLCs
for assets exchange. The network comprises three entities:
users, businesses, and liquidity provider nodes. Users are
entities who acquire COMIT network services. Businesses
are the entities that upgrade their infrastructure to the COMIT
network. Liquidity provider nodes are the entities that have
accounts in multiple blockchains. They are market makers. Their job is to convert one blockchain asset to another by pro-
viding liquidity. The privacy-preserving protocols of COMIT
are under development at the time of writing. COMIT is
open-source.7 Ever since its emergence, the widespread adoption of
blockchain is confronted with scalability. Interoperability
has a huge impact on blockchain scalability. Scalability
in blockchains refers to two scenarios: i) higher transac-
tion processing capabilities and ii) interconnecting more
and more blockchain networks. The former is usually
referred to as vertical scalability whereas the latter is called
horizontal scalability. BTC relay [60] is not a scalable solu-
tion due to the underlying consensus mechanism in Bit-
coin blockchain. Moreover, the solution is only applicable to
Ethereum. In [54], smart contracts move according to client’s
request. As a result, smart contracts may end up in a repeated
back-and-forth cycle. To prevent this, once a smart contract
is moved from one blockchain to another blockchain. It is not
allowed to move to another blockchain for three days. In such 2) TRANSLATION PROTOCOL 2) TRANSLATION PROTOCOL Falazi et al. [58] developed Smart Contract Invocation Proto-
col (SCIP). SCIP is an interface that enables the interaction Falazi et al. [58] developed Smart Contract Invocation Proto-
col (SCIP). SCIP is an interface that enables the interaction 116680 VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains of smart contracts residing on different chains. The interface
acts as an intermediary and contains methods, roles, mes-
sages, and data formats of heterogeneous blockchains. It is
responsible to convert the data types and blockchain-specific
formats of one chain to the data and specific formats of other
chains. In this work, JSON schema is used to describe data
types and formats into text-based JSON. For conversion, first,
the abstract specification of data types and formats of the
interacting blockchains are generated. Afterward, an encod-
ing function generates the underlying inputs for the target
blockchain. For this purpose, one-to-one mapping rules are
defined for all the interacting blockchains and the interface is
responsible to invoke the desired method. Moreover, special
nodes (i.e., market nodes) are employed for decentralized
order matching. This work also supports offline trading. SCIP
is open-source5 and a prototype is implemented in [59] for
seafood supply chain using gateways. owned by individuals from the interacting chains or central-
ized exchanges. DCRM ensures that no individual or node
can take control of all the private keys or digital assets
via crypto-assets mapping. Its primary objective is to have
a management layer that is capable of interacting with all
the blockchains to overcome the inability of interaction or
transfer of digital assets or tokens. Fusion is open-source.8 6) GRAPHICAL APPROACH XChain [63] is a three-phase protocol designed for general
cross-chain transactions. The protocol is implemented in a
leader-follower manner. Leaders (i.e., feedback vertex set) are
a special set of nodes in the system. They are responsible for
the initiation of smart contracts. All other nodes are followers. In the first phase, smart contracts are created. In the second
phase, leaders release their secrets for propagation. In the
third step, the secret is relayed to the representative sources. The representative sources forward the collected secret to
the nodes who are responsible for propagating the secrets
throughout the network. This protocol ensures that all the
parties in a trade do not deviate. For this purpose, the leaders
wait to receive an incoming smart contract before releasing
the secrets for propagation. It is assumed that transactions
are assembled by market clearing services. This work uses
HTLCs for each party in the cross-chain transactions. 3) RELAY SMART CONTRACT BTC Relay [60] is a trustless Ethereum smart contract. It is
mainly used to verify or arbitrarily pass on Bitcoin transac-
tions. It can also be used to store or inspect Bitcoin block
headers stored in a smart contract. Nodes that submit block
headers to the BTC relay are known as Relayers. Relayers are
rewarded for submitting block headers. BTC relay is open-
source.6 5https://github.com/ghareeb-falazi;
6https://github.com/ethereum/btcrelay;
7https://github.com/comit-netwok 8https://github.com/FUSIONFoundation 5https://github.com/ghareeb-falazi;
6 5) TRADING SYSTEMS Fusion [62] is a crypto-financial platform where tokens from
various blockchains as well as centralized exchanges can be
traded using smart contracts. It aims to develop a bridge
where tokens from various chains are mapped in multi-token
smart contracts. Fusion use Distributed Control Rights Man-
agement (DCRM) to store the private keys of digital assets 8https://github.com/FUSIONFoundation 116681 VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains on the interacting blockchains have their own addresses
for cross-chain transactions. Moreover, the cross-chain sys-
tem is responsible for coordinating transactions, locking or
unlocking transactions, and providing notary nodes to mon-
itor transactions of the interacting system. A cross-chain
transaction between the interacting chains occurs in three
phases. First, assets on the interacting chains are locked using
a multi-signature address provided by the cross-chain system. Secondly, keys are negotiated between the interacting parties
on each chain using a notary from the cross-chain system. Keys are negotiated using the Diffie Hellman algorithm. Lastly, the transactions are processed and coordinated by the
notaries. Assets are swapped using time-out smart contracts
to ensure atomicity. Same smart contracts are used on the
interacting chains. a case, the clients from other blockchains repeatedly try their
transactions, and if the transaction is not successful, then the
client has to wait randomly. Blockchains were created to eliminate centralized third
parties with the distributed consensus mechanism such as
proof of work or proof of stake, etc. It is noteworthy that
decentralization is the key to success in the case of inter-
operable blockchain networks. However, the current interop-
erable solutions are moving towards centrality e.g., a fixed
number of validators in modified consensus mechanisms, etc. Other interoperability solutions that use vaults or any other
attestation services are also vulnerable to a single point of
failure. In [58], the gateway is responsible to formulate and
sign transactions on behalf of the client applications. As a
result, a bottleneck can occur at the gateway if the number of
transactions increases. Moreover, the increase in the number
of interacting blockchains may also degrade the performance
of the system. As the gateway is responsible for translation
using pre-defined rules. g
Sigwart et al. [65] discussed the verification process of
cross-chain transactions. In this work, clients constantly
pass block headers to the destination chain. To keep the
clients motivated for their participation in the submission
process, an incentive structure is proposed in [66]. 2) TRANSLATION PROTOCOL Abebe et al. [68] proposed architecture for data sharing
between interacting blockchains. The proposed architecture
comprises two autonomous chains. Relay service is incor-
porated on each chain to enable data sharing along with
verifiable proof. It is assumed that each blockchain is capable
to accept as well as verify data from the other chain. For
verification of the data, a policy is provided by the source
chain. Moreover, the target chain is capable to provide verifi-
able proof in accordance with the source chain demands. The
relay service on each blockchain communicates with each
other using a neutral protocol. Furthermore, the relay ser-
vice is capable of translating the network protocol messages
into the underlying network implementation using a set of
plug-in network drivers. A set of special system contracts are B. HOMOGENEOUS BLOCKCHAINS AND HOMOGENEOUS
SMART CONTRACTS This subsection discusses interoperability solutions between
homogeneous blockchains for which smart contracts are
either developed in the same programming language or a sim-
ilar execution/virtual environment is considered to execute
smart contracts. Homogeneous blockchains refer to similar
blockchains e.g., Ethereum and Ethereum classic, etc. 5) TRADING SYSTEMS When
a new header is submitted for verification, this work store
the information to track the branches of the main chain
and discard the remaining information. To verify a specific
transaction, clients request the destination chain about a
specific transaction. A smart contract is used to extract the
logged information of the block headers from the publicly
available transnational history. Furthermore, the hash of the
aforementioned information is calculated to verify a specific
transaction as valid or disputed. The steps used in cross-chain
transactions verification process for [65] are outlined in [67]. These steps are as follows: first, a specific number of tokens
on a chain can only be created if the source chain guarantees
that the same amount of token has been burned. Secondly,
the burning process cannot be faked. Third, for every burned
token on a source chain, the corresponding tokens can only be
created once on the destination chain. Lastly, it is not possible
to burn tokens on one chain unless the same amount of tokens
are recreated on the target chain. In this work, the authors also
discussed an optimization technique to minimize data storage
for cross-chain transactions. In interoperable blockchain solutions, cross-chain transac-
tions are charged from the users’ accounts in order to reward
the entities who partake in the process. In some cases, when
the cross-chain value is low, the transaction may end up
costly. Keeping in view the transaction fee and interest rates
and market fluctuations, the loan process in [55] may end up
very costly to the borrower. Some existing interoperable solutions use distributed
nodes in cross-chain transactions. To date, most of the exist-
ing work assumes honest behavior or ceasing collateral in
the event of dishonest behavior. What will happen if a node
or set of distributed nodes acts maliciously for a cross-chain
transaction with a cross-chain value more than the collateral
they submit? work in [56], relies on the performance of vaults. Similarly, [61] use liquidity provider nodes, whereas, [62] use
distributed nodes to hold private keys. In [63], if the graph is strongly connected, then the secrets
can be easily propagated throughout the network. However,
in the case of a weakly connected graph where every vertex
is not reachable by all other vertices, a follow-up mechanism
is required. Moreover, the timeout mechanism in an HTLC
must be carefully designed, as leaders may not be directly
reachable to the parties. 9 https://github.com/KyberNetwork/peace-relay;
10https://github.com/poanetwork/; 11https://github.com/liquidity-network/nocust-contracts-solidity; 4) OFF CHAIN SMART CONTRACTS Khalil et al. [71] developed NOCUST. It uses a challenge-
response mechanism for off-chain payments. The primary
objective of NOCUST is to improve throughput by process-
ing transactions on the sidechain without publishing on the
main chain. To process transactions on the sidechain, users
must on account on the main chain as well as a sidechain. Exchange occurs through an operator who acts as an inter-
mediary between the main and sidechain. Users communicate
with the off-chain operator to register and send tokens to the
recipient on the sidechain. In this work, after a pre-defined
time, checkpoints are incorporated to update the states of
all users on the main chain. Moreover, users can evaluate
the behavior of the operator by publishing challenges using
smart contracts. If the behavior of the operator is malicious,
users can penalize the operator and triggers the recovery
mechanism on the chain. This enables the user to recover
payment from the last validated checkpoint. The performance 1) TIME LOCK CONTRACTS Dai et al. [64] proposed a cross-chain transaction model. This model comprises three roles: individual blockchains,
users, and the cross-chain system. It is assumed that users VOLUME 9, 2021 116682 VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains of this work is evaluated in terms of gas consumption and
latency. NOCUST is open-source.11 incorporated for data sharing as well as enforcing network
rules. The governing bodies of the interacting chains are
responsible to initialize the metadata of the system contracts
to enable interoperability. Ye and Wu [72] presented Garou. Garou is an off-chain
token transfer protocol. It uses an election process to elect
a leader among the participants to execute off-chain trans-
actions. A new leader is elected at the beginning of each
epoch. The leader is elected on the basis of an arbitrary
hash function and the initial balance of the participants at
the beginning of each epoch. The leader is responsible to
keep a track of the initial balance and the total balance sent
or requested by the participants during an epoch. Moreover,
the leader is also responsible ensure that all participants
partake in a consensus mechanism regarding the initial state
of the next epoch and answer challenges posted by the partic-
ipants in the event of a dispute. To ensure that participants
didn’t lose their funds, all disputes are resolved using the
on-chain contract. The performance of this work is evaluated
in terms of throughput and latency. 3) RELAY SMART CONTRACTS Peace relay [69] is a smart contract that enables Ethereum
blockchain to interact and communicate with other Ethereum
chains such as Ethereum classic. Using the Peace relay, trans-
actions can be read as well as verified on Ethereum classic and
vice versa. Furthermore, it can also be used to verify account
balances. Peace relay is open-source.9 Proof of Authority (PoA) [70] is an autonomous net-
work that incorporates EVM-based blockchains. This project
aims to enhance the interoperability and transparency of the
blockchain ecosystem with the PoA consensus. It enables
cross-chain data as well as assets transfer using the PoA
TokenBridge. The main components of a TokenBridge are
Bridge Monitor (BM), user interface, Bridge Deployment
Playbooks BDP smart contracts (PDPSCs), and Arbitrary
Message Bridge (AMB). BM is used to check balance and
unprocessed events on the TokenBridge. BDPSCs keep a
record of the configurations as well as deployment of the
remote chains. The user interface enables cross-chain token
transfer. AMB enables data exchange between EVM-based
chains. The data exchanged using POA can be used to transfer
tokens, invoking a cross-chain smart contract, disseminate
token exchange rate to the target blockchain, and synchronize
smart contract states of the interacting chains. This work
depends on the correct behavior of validators. Therefore,
a number of fore-chosen validators are incorporated to par-
take in the consensus mechanism. POA is open-source.10 5) TRADING SYSTEM Wang et al. [73] proposed a cross-chain trading model for
joint operations of multi micro-grids. In this work, two
blockchains are incorporated with built-in P2P trading net-
works. These blockchains represent independent micro-grids
that trade power to an external network in the event of unbal-
anced electric power. Cross-chain trading occurs in six steps. First, the source chain identifies the requirements for trading
by writing the description and deadline in a smart contract. In the second step, the cross-chain trading requirements are
verified in the source chain using the local consensus mech-
anism. If the verification process succeeds, a smart contract
is deployed, and a request is forwarded to the target chain. Third, the request is verified by the target chain. In case of
successful verification, a smart contract is built and broadcast
to all the nodes. If the verification at the target chain fails,
the request is ignored. Afterward, the target chain has to
conclude the trading deal and send a response to the source
chain. In the next step, the source chain extracts the response
from the received message of the target chain and returns the
transaction keys upon the execution of the smart contracts. Lastly, the source and target chain broadcast their respective
certificate to the multi microgrid system. A key management
interoperable protocol is used for communication between
the interacting chains. This protocol uses the RSA algo-
rithm based on the Chinese reminder theorem. Moreover,
a special set of nodes in the system validates cross-chain
communication. 6) GRAPHICAL APPROACH Amiri et al. [74] proposed an asynchronous blockchain sys-
tem to support a set of distributed applications in a trustless
manner. The applications on the interacting blockchain main-
tain two sets of records, namely public and private records. These records are stored in a single data store. Private records VOLUME 9, 2021 116683 S. Khan et al.: Towards Interoperable Blockchains can be accessed and edited by the application itself whereas,
public records are visible as well as maintained by all the
applications. Similarly, each application maintains two types
of smart contracts, namely private and public smart contracts. Private smart contracts are used to implement internal trans-
actions whereas public smart contracts are used to implement
cross-chain transactions using a service layer agreement. Moreover, the public smart contract can be executed on all the
applications to enforce the terms of cross-chain transactions. The system comprises a special set of nodes called agents and
orderer nodes. Agent nodes are used to execute applications,
whereas orderer nodes are devoted to order cross-chain trans-
actions globally. In this work, the ledger is neither maintained
by the nodes nor applications. Instead, each application is
responsible to maintain a local view of the ledger in the
form of a directed acyclic graph. The blockchain system is
implemented in an execute-order-validate manner. cross-chain transactions. A cross-chain coordination contract
is deployed on the coordination blockchain. It enables the
sidechain to commit or discard the updates related to a
cross-chain transaction. A key feature of the coordination
contract is the Transaction Timeout Block Number (TTBN). TTBN is assigned by the coordination contract for all the
cross-chain transactions. If a cross-chain transaction does not
publish a commit message to the coordination blockchain
before TTBN is assigned. The corresponding transactions are
time-out. When the coordinating chain receives a cross-chain
transaction request, it has to check the status of the coor-
dination contract. The contract can either be in a locked or
unlocked state. If the contract is unlocked, the transaction
request is processed. If the contract is locked, then the trans-
action is ignored. A cross-chain transaction state represents
the state update of a transaction between commit or ignores
state in the coordination contract. Darisi et al. [77] proposed a token exchange mechanism
using a global exchange contract between the interacting
chains. The mechanism comprises two actors: token traders
and token owners. 7) DOUBLE SPENDING ATTACK Sai et al. [75] proposed a scheme to discourage attackers
who try to double-spend a transaction in cross-chains trans-
actions. It is assumed that a number of trustees exist in
the network. These trustees are responsible for cross-chain
transactions and hold sufficient funds on the interoperable
chains. Observers are employed in the network to endorse
transactions. A trustee only processes the transactions that
are endorsed by the observers. To discourage a double-spend
attack, observers and trustees initiate a smart contract. All
the observers submit their responses to the trustee. The deci-
sion is made on the basis of the majority of the responses
submitted to the trustee. If the outcome of an observer
does not match the majority of the responses, the observer
is considered malicious and penalized for his dishonest
response. Whereas all the other observers are rewarded. A game-theoretical analysis is performed to demonstrate that
the observers do not collude in a double-spending attack. Robinson et al. [78] proposed General Purpose Atomic
cross Chain Transactions (GPACT) for Ethereum based
blockchains. It is primarily used in the scenario when an
application needs to invoke a smart contract residing on
multiple blockchains. In this work, a cross-blockchain control
contract with instances deployed on all the interacting chains
is used to manage function calls. All the events emerging from
the control blockchain are trusted on the interacting chains. First, an application fetches the state of the smart contract
from a blockchain to determine the parameter value of the
remote functions. Afterward, a simulation of the contract
code is executed. The protocol starts with an application
calling the root blockchain. The root blockchain has a start
function that contains the entry points to the call graph. It registers the account that performs cross-chain transactions
of the interacting blockchains. Moreover, it registers other
parameters such as expected function values and cross-chain
transaction identifiers, etc. These parameters are included in
a start event and passed to the segment function. The segment
function is used to invoke a smart contract as part of the
cross-chain transaction. If the segment function executes suc-
cessfully, it returns a segment event containing a list of lock
contracts. The start event and signed segment event are passed
as parameters to the root functions. A root function indicates 6) GRAPHICAL APPROACH Token traders are user accounts who
trade tokens with the counterparty, whereas token owners
are user accounts who supply new tokens by deploying
smart contracts. In this work, the authors used two ways to
exchange tokens. In the first method, the interacting parties
register their tokens on the central exchange contract. After
registration, any of the interacting parties can initiate the
exchange. Once the exchange is completed, the interacting
parties un-register their tokens from the contract. In the sec-
ond method, the authors used oracles and atomic swaps for
token exchange. In this method, the central exchange contract
is also used to exchange trade price and hash secrets. 10) GENERAL INTEROPERABILITY Nissl et al. [79] proposed a framework to invoke smart
contracts on one blockchain from other blockchains. It is
assumed that users or smart contracts deployed on the source
as well as target blockchain are capable of sending and receiv-
ing a response from each other. A distributor and invocation
smart contract is deployed on the source and target chains,
respectively. Intermediaries (who are not part of the interact-
ing blockchains) are incorporated to forward calls between
the interacting chains. The proposed framework comprises
six phases: register, offer, execution, forwarding, verification,
and finalization phase. In the registration phase, the meta-
data of the aforementioned entities is saved by the caller
of the distribution contract. In the offer phase, an event is
announced on the source chain about the beginning of the
offer phase. Afterward, intermediaries with accounts on the
interacting chains are used to broke offers to the distribution
contract. In the execution phase, the intermediaries execute
the process of smart contract invocation on the target chain. To invoke a remote contract from a local chain, the desired
method along with its parameters to activate the smart con-
tract (e.g., the start gas, gas price, and the number of tokens)
are transferred to the target blockchain. In the forwarding
phase, the intermediaries selected are used to forward calls
between the interacting chains. Whereas, in the verification
phase, validators compare the data stored on the source chain
and target chain to ensure that the intermediaries have not
published incorrect data. Lastly, in the finalization phase,
the call to invoke a remote contract terminates by distributing
the reward among validators. A voting mechanism is used to
distribute the transaction reward or reimburse the transaction
cost. The performance of this work is evaluated in terms of
gas consumption. This framework is open source.13 Liu et al. [82] developed a Hyperservice that is a program-
ming platform. It enables the development and execution of
cross-chain applications. The core components of Hyperser-
vice are dApp clients, Verifiable Execution System (VESys),
Network Status blockchain (NSB), and Insurance Smart Con-
tracts (ISCs). DApp clients act as a gateway for the dApps
to interact with the Hyperservice platform. VESys is used to
compile and execute high-level programs in the dApps. NSB
provides the execution status of the dApps whereas, ISCs
ensure accountability. ISCs provide atomicity in a financial
transaction. 12https://github.com/ConsenSys/LTACFC;
13https://github.com/markusnissl/cross-chain-smartcontracts 14https://github.com/pantos-io/x-chain-smartcontracts
15https://github.com/HyperService-Consortium; 8) GLOBAL CONTRACTS Robinson et al. [76] developed a protocol for cross-chain
transactions in Ethereum based sidechains. In this work,
a cross-chain transaction comprises an originating transaction
and/or a subordinate transaction and subordinate view. The
originating transaction is Ethereum transactions that originate
in Ethereum blockchains, whereas subordinate transactions
or subordinate views are the transactions that result due
to originating transactions on sidechains. Every originating
transaction may or may not have a subordinate transaction
or subordinate views. The cross-chain transaction protocol
is based on multi-chain nodes, coordination blockchain, and
cross-chain coordination contracts. Multi-chain nodes rep-
resent a group of more than one node residing on different
chains. These nodes collaborate to enable cross-chain trans-
actions. Moreover, these nodes have validator nodes on each
sidechain to validate transactions. A coordination blockchain
can be any Ethereum blockchain such as Ethereum Mainnet,
etc. It has access to all the sidechains and coordinates the 116684 VOLUME 9, 2021 116684 VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains that all updates on the blockchain should either be committed
or discarded. Updates are discarded if an error message is
received in the segment event. A root function publishes a
root event upon successful execution. The root event along
with the segment event are passed as input parameters to
the signaling function. The signaling function is called if
an update needs to be committed or ignored on any of the
interacting blockchains. A signaling event is published upon
the successful execution of the signaling function, indicating
that smart contracts are unlocked. The performance of this
work is evaluated in terms of gas consumption and latency. GPACT is open-source.12 process. It is assumed that the interacting blockchains trust
each other to a certain level. Moreover, the participating
chains are capable of processing cross-chain transactions if
the counterpart presents valid proof. The performance of this
work is evaluated in terms of latency. Sigwart et al. [81] proposed RPCs invoke smart con-
tracts in target blockchain. RPCs are implemented in a
request-response paradigm. RPCProxy and RPCServer smart
contracts are deployed to initiate and verify the call requests
between the source and target chain. Off-chain clients resid-
ing on a different chain are used to forward the call requests
between the interacting chains. This model is open source.14 10) GENERAL INTEROPERABILITY Moreover, in the event of misbehavior from the
interacting parties, ISC is capable to revert all the finan-
cial transactions. To enable the execution of dApps across
different chains, Hyperservice uses a Unified State Model
(USM). USM unifies the interacting chains by providing a
virtualization layer. This enables the dApps to execute on any
chain regardless of the underlying blockchains implemen-
tations such as smart contracts, execution environment, and
consensus mechanism, etc. The proposed USM is developed
using Hyperservice programming Language (HSL). HSL is a
proprietary programming language developed by Hyperser-
vice platforms for writing cross-chain dApps. It also supports
smart contracts written in different languages. For this pur-
pose, a special program is written in HSL to abstract smart
contracts as interoperable entities. This work is evaluated
in terms of end-to-end execution latency and throughput. Hyperservice is open-source.15 11) DISCUSSION There is a need for a reward and punishment management
system for the validators or entities who assist cross-chain
transactions. With a fixed number of validators, if a validator
is punished by ceasing the funds only, the malicious validator
is still present in the system. A proper mechanism is required
to block such entities from participation in future transac-
tions. The work in [75] relies on the responses submitted by
observers. It is assumed that most of the responses submitted
are true. In the event, if two out of three observers collude
and initiate a secret smart contract with each other against Pillai et al. [80] proposed a cross-chain communication
model using transactions. In this work, a transaction refers
to a call that invokes a remote smart contract to perform
a certain task. The proposed model comprises two stages. In the first stage, information is retrieved by requesting blocks
from clients. In the second stage, the state of the blockchain
is updated using transactions, validation, and verification 116685 116685 VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains The promising feature of Block Collider is to enable the
invocation of smart contracts residing on one chain from a
remote chain and secure transactions in the absence of val-
idators or third-party intermediaries. Block Collider unifies
the recent most state of blocks from intermediary bridges
into the Block Collider multi-chain. Multi-chain transactions
are executed using incentive-based atomic swaps. A modified
version of Nakamoto consensus, i.e., proof of distance is used
to determine the next block. It is noteworthy that in Block
Collider, the number of transactions in the blocks is not fixed. Borderless [84] is a user interface that interacts with Block
Collider and enables the users to place as well as retrieve
trade orders in a human-readable format. Block Collider is
open-source.16 the third honest observer, then the honest observer can be
penalized. Though the game theoretical analysis shows that
it is in the best interest of the observer to remain honest to
the network. Observers may deviate if the transferring funds
are more than their deposited stakes. Similarly, [71] and [72]
relies on the performance of operators and leaders. Though
the behavior of the leaders and operators can be analyzed and
checkpoints are incorporated to recover the system from a
validated point. The malicious entities can still partake in the
validation process. 11) DISCUSSION Similarly, [73] and POA [70] use a special
set of validators. The work in [81] did not discuss the behavior
of off-chain clients to invoke smart contracts. The authors in [74] and [80] achieved promising results to
minimize latency. In [74], the same set of nodes are used for
local as well as cross-chain transactions. Therefore, increas-
ing the number of cross-chain transactions does not improve
performance. It is due to the reason that Fabric blockchain is
only capable to process a certain number of transactions with
a latency of 40ms. Similarly, [80] analyzed the performance
of the proposed work with a mother blockchain acting as
an intermediary to evaluate application latency. In practical
situations, the latency may vary for each application. Tian et al. [85] used intermediaries on the Ethereum test
net to exchange Bitcoins and Litcoins for Ethers. It is assumed
that the intermediaries are capable to support as well as verify
transactions on the interacting chains. Moreover, they are also
part of the validation committee and forwards transactions
between users of the interacting chains using smart contracts. g
g
ARK [86] is a blockchain capable of generating novel
blockchains on user demands. The ARK ecosystem com-
prises decentralized blockchains that are interoperable with
each other using ARK SmartBridge. The SmartBridge
enables the interacting blockchains to send data as well as
assets to each other. ARK uses two types of communica-
tion protocols, namely Protocol-specific SmartBridge and
Protocol-Agonostic SmartBridge. The former enables the
communication between ARK main net and the blockchains
that originate from the ARK core technology, whereas the
latter enables communication and token transfer between
heterogeneous blockchains such as Bitcoin and Ethereum,
etc. To enable communication between the interacting chains,
a special data section known as ‘‘Vender filed’’ is used. The
ARK Contract Execution Service (ACES) is a community
project that enables a two-way transfer of smart contracts
between ARK and Ethereum network. Data or assets are
exchanged using transactions. The data exchanged can be
used for hashing or invoking a smart contract on the tar-
get chains. Using a set of encoded listeners, ACES can be
applied to any chain to achieve interoperability. ARK is
open-source.17 The work in [76] and [77] use global smart contracts to
enable interoperability. Similarly, in [64], the cross-chain
system is responsible for coordinating transactions. 11) DISCUSSION A single
chain or smart contract handling numerous chains or transac-
tions are susceptible to a single point of failure. The work
in [78] is evaluated to read and write integer values from
one blockchain to another. Moreover, the performance of
this work may be confronted with latency as the successful
execution of the events depends on locking and unlocking
smart contracts of the chains. The
work
in
[79]
is
evaluated
for
permissioned
blockchains. This limits the applicability of the interoperabil-
ity solution to public chains. Moreover, intermediaries and
validators from various publish chains are unable to partake in
the validation process. The current implementation of [82] is
not fully atomic. Moreover, at this stage, the inter blockchain
communication protocol does not inform the smart contract
if an event terminates prematurely. The authors hope to
ensure atomicity by using stateless smart contracts. However,
this requires additional requirements such as decoupling the
consensus layer and using a trusted execution environment. Lu et al. [87] developed Wanchain. Wanchain is a trading
platform that enables interoperability by acting as a bridge
between the interacting chains. In this work, first, the users
from source and target blockchains have to register their
token/assets on Wanchain. Afterward, users of the interacting
blockchains are issued corresponding native coins (in the
form of smart contracts) on Wanchain for trading. Transac-
tions across the blockchains are accomplished using an asset
template and locked accounts. Wanchain uses a modified
proof of stake consensus algorithm with three types of nodes:
vouchers, storemen, and validators. Vouchers are responsible C. HETEROGENEOUS BLOCKCHAINS AND
HETEROGENEOUS SMART CONTRACTS This subsection discusses interoperability solutions between
heterogeneous blockchains (e.g., Ethereum, hyper-ledger,
and Bitcoin, etc.). Heterogeneous smart contracts refer to
the smart contracts that are developed in different pro-
gramming languages e.g., interoperability between different
blockchains using smart contracts developed in Solidity and
Java, etc. 16https://github.com/blockcollider
17https://github.com/ArkEcosystem 19https://github.com/quantnetwork
20https://github.com/cosmos 2) GENERAL INTEROPERABILITY ICON republic [88] is a trading platform that aims to connect
community-based independent blockchains. The core com-
ponents of ICON republic are community, Community Node
(C-Node), Community Representative (C-Rep), and citizen
nodes. Various blockchains such as Bitcoin and Ethereum,
etc. are considered as communities. C-Nodes are the build-
ing blocks of community. These nodes are responsible to
determine the policies and consensus mechanism of each
community. A C-Rep node represents their respective com-
munity inside the ICON republic ecosystem. A C-Rep node
is elected on the basis of ICON incentive and an artificial
intelligence-based scoring system. They act as validators in
the ICON republic. Nodes that generate transactions are cit-
izen nodes. Anyone can partake in the ICON republic as a
citizen node by using the dApps available in the ecosystem. The underlying blockchain that connects different communi-
ties is called NEXUS. NEXUS is a multi-channel blockchain. It comprises light clients who represent their respective com-
munities on the NEXUS chain. It acts as a decentralized
exchange to transfer tokens between the interacting chains. A blockchain transmission protocol is used for cross-chain
transactions. One of the key features of ICON republic is
the availability of a number of use cases and pre-developed
dApps for the participant nodes to use. Moreover, to accom-
modate the diverse need of various communities and users,
ICON use loopchain. Loopchain is an enterprise blockchain
with smart contract functionalities that can be customized
according to the operational needs of the communities. The
key feature of loopchain is the availability of a Smart Contract
On Reliable Environment (SCORE). SCORE enables the
deployment of smart contracts without a dedicated virtual
machine. ICON Republic is open-source.18 18https://github.com/icon-project 1) TRADING SYSTEMS Block Collider [83] aims to develop a multi-chain trad-
ing
platform
by
bridging
heterogeneous
blockchains. VOLUME 9, 2021 VOLUME 9, 2021 116686 S. Khan et al.: Towards Interoperable Blockchains communication as well as token and data transfers between
the interacting chains. For communication, Overledger uses
the two-phase commit protocol. Due to its layered approach,
Overledger can be used on top of any blockchain. The lay-
ers in Overledger are the transaction layer, messaging layer,
filtering & ordering layer, and application layer. The trans-
action layer is responsible for all the operations necessary to
reach a consensus on the interacting chains. The messaging
layer is used to retrieve transaction data or smart contracts. The filtering and ordering layer creates connections between
various messages on the messaging layer. Moreover, it is
also in-charge of validating the out-of-chain messages. The
application layer updates the state of applications. It is note-
worthy that, unlike other solutions, Overledger does not use
a blockchain to enable cross-chain interactions. It uses a
blockchain programming interface to enable interaction with
the underlying blockchain. Overledger is open-source.19 for providing proof of transaction, whereas storemen are
responsible for computing and merging the signature parts
of the locked accounts. The smooth operations of Wanchain
require storemen to stay online. The validators are responsi-
ble for validating the transactions on the Wanchain. However,
there is a chance of collusion among these nodes if the
gains of collusion exceed the participation cost. To preserve
privacy in cross-chain transactions, Wanchain uses a one-time
account with ring signatures to hide the identity of the smart
contract initiator. 3) BRIDGE CONTRACTS Kwon and Buchman [20] developed Cosmos network. Cos-
mos links isolated blockchains (also known as zones). The
primary zone in the cosmos network (i.e., the cosmos hub)
is a multi-asset blockchain capable of extending the net-
work to adapt to the advancements in novel blockchains. It allows instant transfer of tokens between zones securely. The exchange of tokens between zones does not require
liquidity exchange between the interacting zones. However,
token transfer among zones has to go through the cosmos
hub. Moreover, the hub maintains a record of the tokens
held by zones. Zones in cosmos networks communicate with
each other by using an inter-blockchains communication pro-
tocol. This protocol enables zones to identify the number
of transactions committed on the receiving chain. However,
the sender and receiver zones must be able to keep up with
the block header of one another. All the zones in the cosmos network use Tendermint
Byzantine fault tolerance algorithm. The algorithm is capable
of processing thousands of transactions in a span of one or
two seconds. A fixed number of validators validate the blocks
with respect to their voting power. If any of the validators act
maliciously, they are detected and penalized by the algorithm. As the cosmos network is a set of independent and isolated
blockchains. It allows the zones to employ their own gover-
nance system. The zones do not have to employ the policies
implemented in the cosmos hub. Similarly, the cosmos hub is
not responsible for committing and executing transactions of
the zones. Proprietary chains such as Bitcoin and Ethereum,
etc. can also be connected to the Cosmos network by means
of a dedicated zone known as Bridge-Zone. This requires the
bridge validators to have a tindermint powered blockchain
with a special application. A bridge-contract enables the
transfer of tokens to (and from) proprietary chains and the
Cosmos hub. Cosmos is open-source.20 Overledger [89] is a blockchain operating system capa-
ble of connecting heterogeneous as well as homogeneous
blockchains. It is capable of performing operations on mul-
tiple blockchains simultaneously using multi-chain applica-
tions. These multi-chain applications are capable of executing
smart contracts that are not dependent on a single blockchain. Coordination among multiple blockchains is achieved using
a special set of nodes called connectors. A connector can
be any entity or party with a minimum of one node on
each of the interacting chains. 3) BRIDGE CONTRACTS These nodes are in-charge of 116687 116687 VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains Wood [21] developed Polkadot. Polkadot is designed to
link parallel chains (also known as parachains) or data struc-
tures (not necessarily a blockchain). A relay chain adminis-
ters all the transactions between the parachains. A registry
is maintained in the relay chain to keep a record of the
parachains. To add or remove a parachain from the registry,
a referendum contract is placed. The network is maintained
by four participants, namely collators, validators, fishermen,
and nominators. Validators are selected using nominated
proof of stake. They are allowed to nominate other nodes to
validate blocks on their behalf. Nominators are stake-holding
parties. Their function in the network is to place risk capital. Risk capital refers to the funds invested in high-risk rewards. Collators assist validators in bringing forth authentic blocks. Fishermen can be thought of as bounty hunters. Their job is to
hunt bad actors who perform illegal actions and collect their
reward. For cross-chain transactions, input and output queues
are maintained at the parachains. Relay chain maintainers are
responsible to carry transactions from the source chain output
queue to the destination chain input queue. action, Wanchain incurs an overhead of creating a one-time
account. In [20] and [21], all the transactions and chains are
administered by the hub and relay chain. As the number of
connected chains increases, the network performance may
degrade because all the transactions are routed via a central
entity. Similarly, the cost of syncing all the chains will also
increase. In [20], the zones and Cosmos hub continuously
send messages to each other in order to be aware of each
other’s state. Whereas, in [21] parachains are able to spam
one another with transaction data. Currently, there is no mech-
anism to prevent parachains from spamming one another. In [86], the use of encoded listeners moves ACES towards
centrality. Similarly, in [83], a special set of nodes called
block rovers are incorporated to broadcast the recently mined
transactions in the interacting chains. Block rovers are remote
clients from the interacting chains. Overledger [89] can connect any chain regardless of the
underlying structure or technology. Similarly, ICON repub-
lic [88] use SCORE that does not require a dedicated virtual
machine. This makes the interoperability solution not limited
to a specific chain. 4) DISCUSSION A number of the existing solutions use native tokens of
their respective chain to enable cross-chain transactions,
i.e., off-chain transactions, trading platforms. To use the ser-
vices of these chains in cross-chain transactions, the interact-
ing users or blockchains must have an account and investment
for trading and transaction fee. Wanchain [87] issue native
tokens to the account holders of other chains by locking their
respective tokens. This requires a continuous flow of tokens
between the interacting chains. Moreover, for every trans- B. SCALABILITY Scalability is one of the major reasons due to which
the widespread adaptation of blockchains is slower than
expected. Though interoperability solutions are capable to
achieve horizontal scalability by integrating a number of
chains. Vertical scalability for cross-chain transactions is still
far from reality due to the underlying consensus and vali-
dations process of each chain. For cross-chain transactions,
one way to achieve vertical scalability is to have a dynamic
list of participants from both chains to validate cross-chain
transactions by suspending the local consensus mechanisms
in the interacting chains. VI. FUTURE DIRECTIONS AND CHALLENGES This section discusses the future directions and challenges
associated with blockchain interoperability. A. TYPES OF ASSETS EXCHANGED The existing solutions on blockchain interoperability mostly
focus on token or assets exchange between two or more
chains. In our opinion, there is a need for an interoperable
architecture that focuses on the exchange of data between
chains. Moreover, assets or tokens can be exchanged for ser-
vices as well. Data exchange can be used for many purposes
such as invoking smart contracts, verifying transactions, etc. Interoperable blockchain architecture with data sharing capa-
bilities will greatly improve blockchain interoperability. 21https://github.com/w3f/polkadot 3) BRIDGE CONTRACTS A Cross-Chain Communication protocol (XCMP) [90]
is proposed for the parachains to communicate. For two
parachains to communicate, they are required to have a chan-
nel. Moreover, a pair can only have two channels. XCMP is in
the development stage and a horizontal relay routed message
passing protocol exists among the parachains. However, this
protocol is resource intensive and stores all the messages
at the relay chain. Proprietary chains such as Bitcoin and
Ethereum, etc. can also be connected to the PolkaDot network
using the PolkaDot bridges. The bridge acts as a trust-free
gateway, allowing proprietary chains to post or route trans-
actions from (or to) PolkaDot network. PolkaDot ecosystem
consists of two types of bridges: bridge modules and bridge
contracts. The bridge module enables external chains to act
as a virtual parachain. Bridge contract is more like a bridge
module, however, unlike bridge modules, a bridge contract
functionality is limited to the parachains that support the
execution of smart contracts. The project supports building
bridges between PolkaDot ecosystem and proprietary chains. The future upgrades and changing user’s requirements in the
PolkaDot ecosystem are decided by the validators using ref-
erendum. PolkaDot is open-source 21 and its smart contracts
are written in WebAssembly (WASM) [91]. VI. FUTURE DIRECTIONS AND CHALLENGES C. PRIVACY AND SECURITY IN CROSS-CHAIN
TRANSACTIONS It is likely that all blockchains have their own mechanisms
to guarantee security and privacy. However, the fact that
there are always threats cannot be ignored. As in the case 116688 VOLUME 9, 2021 VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains of intermediary chains or forwarders who facilitate the inter-
acting chains, transaction anonymity and user identity can be
compromised. It is possible to breach the integrity of the inter-
acting chains by breaching the security of the intermediary
blockchain. Moreover, these facilitator chains between the
interacting chains are recording each transaction they forward
by means of their forwarders. Strict monitoring policies such
as force to forget must be applied on the interacting chains to
guarantee security and privacy in cross-chain transactions. [7] T. Sultana,
A. Almogren,
M. Akbar,
M. Zuair,
I. Ullah,
and
N. Javaid, ‘‘Data sharing system integrating access control mechanism
using blockchain-based smart contracts for IoT devices,’’ Appl. Sci.,
vol. 10, no. 2, p. 488, Jan. 2020. [8] S. Aslam, M. P. Michaelides, and H. Herodotou, ‘‘Internet of ships:
A survey on architectures, emerging applications, and challenges,’’ IEEE
Internet Things J., vol. 7, no. 10, pp. 9714–9727, Oct. 2020. [9] O. Samuel and N. Javaid, ‘‘A secure blockchain-based demurrage mecha-
nism for energy trading in smart communities,’’ Int. J. Energy Res., vol. 45,
no. 1, no. 2021, pp. 297–315. [10] A. Shahid, A. Almogren, N. Javaid, F. A. Al-Zahrani, M. Zuair, and
M. Alam, ‘‘Blockchain-based agri-food supply chain: A complete solu-
tion,’’ IEEE Access, vol. 8, pp. 69230–69243, 2020. VII. CONCLUSION The popularization of blockchain technology has disrupted
many application areas. There is high anticipation among
researchers that the true potential of this technology will
be revealed by achieving interoperability between isolated
blockchains. This paper discussed the role of smart con-
tracts in blockchain interoperability. The study shows that it
is possible to invoke a remote smart contract from a local
blockchain. Similarly, a virtualization-based approach can
also be used to achieve interoperability. Based on our sur-
vey, it is concluded that smart contract-based blockchain
interoperability solutions can be a potential game-changer
for the widespread adoption of blockchain technology. Unfortunately, there is a dearth of literature analyzing the
importance of smart contracts in blockchain interoperability
solutions. Hopefully, this study will serve as a foundation for
researchers working on smart contract based interoperable
blockchains. [16] X. Li, P. Jiang, T. Chen, X. Luo, and Q. Wen, ‘‘A survey on the security of
blockchain systems,’’ Future Gener. Comput. Syst., vol. 107, pp. 841–853,
Jun. 2020. [17] A. Back, M. Corallo, L. Dashjr, M. Friedenbach, G. Maxwell, A. Miller,
A. Poelstra, J. Timón, and P. Wuille. (2014). Enabling Blockchain
Innovations With Pegged Sidechains. [Online]. Available: http://www. opensciencereview.com/papers/123/enablingblockchain-innovations-
with-pegged-sidechains [18] B. Chandra Ghosh, V. Ramakrishna, C. Govindarajan, D. Behl,
D. Karunamoorthy, E. Abebe, and S. Chakraborty, ‘‘Decentralized cross-
network identity management for blockchain interoperation,’’ 2021,
arXiv:2104.03277. [Online]. Available: http://arxiv.org/abs/2104.03277 [19] S. D. Lerner, ‘‘RSK,’’ Tech. Rep., 2015. [20] J. Kwon and E. Buchman, ‘‘Cosmos whitepaper,’’ White Paper, 2019. [21] G. Wood, ‘‘Polkadot: Vision for a heterogeneous multi-chain framework,’’
White Paper, 2016. [22] M. Spoke, ‘‘Aion: Enabling the decentralized internet,’’ AION, White
Paper, Jul. 2017. [23] T. M. Mayer, C. Mai, and N. Jesse, ‘‘Tokrex: Meta-system for real-time
intra-and cross-chain swaps,’’ Tech. Rep., 2017. [24] A. Culwick
and
D. Metcalf. (2018). The
Blocknet
Design
Specification. [Online]. Available: https://www.blocknet.co/wp-content/
uploads/2018/04/whitepaper.pdf [25] D. Li, J. Liu, Z. Tang, Q. Wu, and Z. Guan, ‘‘AgentChain: A decentral-
ized cross-chain exchange system,’’ in Proc. 18th IEEE Int. Conf. Trust,
Secur. Privacy Comput. Commun./13th IEEE Int. Conf. Big Data Sci. Eng. (TrustCom/BigDataSE), Aug. 2019, pp. 491–498. ACKNOWLEDGMENT The authors would like to acknowledge the support of Prince
Sultan University for paying the Article Processing Charges
(APC) of this publication. [26] J. Lee, ‘‘Komodo: An advanced blockchain technology, focused on free-
dom,’’ Komodo Platform, Komodo, Tech. Rep., 2018. [27] E. Scheid, B. Rodrigues, and B. Stiller, ‘‘Toward a policy-based blockchain
agnostic framework,’’ in Proc. IFIP/IEEE Symp. Integr. Netw. Service
Manage. (IM), Apr. 2019, pp. 609–613. D. COMPATIBILITY AND RECOVERY MECHANISM [11] P. Bhaskar, C. K. Tiwari, and A. Joshi, ‘‘Blockchain in education manage-
ment: Present and future applications,’’ Interact. Technol. Smart Educ., to
be published. A blockchain interoperability solution must be compatible
with the existing as well as new chains. It is evident that in
the coming years the number of blockchains will increase. If the interoperable solutions are not compatible with the
novel solutions, they may not survive in the long run. More-
over, none of the existing solutions discussed their recovery
mechanism in the event of a failure. [12] P. Singh, M. Masud, M. S. Hossain, and A. Kaur, ‘‘Cross-domain secure
data sharing using blockchain for industrial IoT,’’ J. Parallel Distrib. Comput., vol. 156, pp. 176–184, Oct. 2021. [13] P. Singh, M. Masud, M. S. Hossain, and A. Kaur, ‘‘Blockchain and homo-
morphic encryption-based privacy-preserving data aggregation model in
smart grid,’’ Comput. Electr. Eng., vol. 93, Jul. 2021, Art. no. 107209. mart grid,’’ Comput. Electr. Eng., vol. 93, Jul. 2021, Art. no. 107 [14] S. Tanwar, K. Parekh, and R. Evans, ‘‘Blockchain-based electronic health-
care record system for healthcare 4.0 applications,’’ J. Inf. Secur. Appl.,
vol. 50, Feb. 2020, Art. no. 102407. [15] Gartner. Accessed: Jan. 26, 2021. [Online]. Available: https://www. gartner.com/en REFERENCES Available: https://www.poa.network/ pp
[46] N. Kannengießer, M. Pfister, M. Greulich, S. Lins, and A. Sunyaev,
‘‘Bridges between islands: Cross-chain technology for distributed ledger
technology,’’ in Proc. 53rd Hawaii Int. Conf. Syst. Sci., 2020, pp. 1–10. [71] R. Khalil, A. Gervais, and G. Felley, ‘‘NOCUST-a non-custodial 2nd-layer
financial intermediary,’’ IACR Cryptol. ePrint Arch., Tech. Rep., 2018,
p. 642. [47] M. H. Miraz and D. C. Donald, ‘‘Atomic cross-chain swaps: Development,
trajectory and potential of non-monetary digital token swap facilities,’’
Ann. Emerg. Technol. Comput., vol. 3, no. 1, pp. 42–50, Jan. 2019. p
[72] Y. Ye and W. Wu, ‘‘Garou: An efficient and secure off-blockchain
multi-party payment hub,’’ 2020, arXiv:2010.07555. [Online]. Available:
http://arxiv.org/abs/2010.07555 g
p
pp
[48] S. Johnson, P. Robinson, and J. Brainard, ‘‘Sidechains and interoper-
ability,’’ 2019, arXiv:1903.04077. [Online]. Available: http://arxiv.org/
abs/1903.04077 [73] L. Wang, J. Wu, R. Yuan, D. Zhang, J. Liu, S. Jiang, Y. Zhang, and
M. Li, ‘‘Dynamic adaptive cross-chain trading mode for multi-microgrid
joint operation,’’ Sensors, vol. 20, no. 21, p. 6096, Oct. 2020. [49] I. A. Qasse, M. Abu Talib, and Q. Nasir, ‘‘Inter blockchain communication:
A survey,’’ in Proc. ArabWIC 6th Annu. Int. Conf. Res. Track, 2019,
pp. 1–6. j
p
p
[74] M. J. Amiri, D. Agrawal, and A. El Abbadi, ‘‘CAPER: A cross-application
permissioned blockchain,’’ Proc. VLDB Endowment, vol. 12, no. 11,
pp. 1385–1398, 2019. [50] H. Tam Vo, Z. Wang, D. Karunamoorthy, J. Wagner, E. Abebe, and
M. Mohania, ‘‘Internet of blockchains: Techniques and challenges ahead,’’
in Proc. IEEE Int. Conf. Internet Things (iThings) IEEE Green Comput. Commun. (GreenCom) IEEE Cyber, Phys. Social Comput. (CPSCom)
IEEE Smart Data (SmartData), Jul. 2018, pp. 1574–1581. [75] K. Sai and D. Tipper, ‘‘Disincentivizing double spend attacks across inter-
operable blockchains,’’ in Proc. 1st IEEE Int. Conf. Trust, Privacy Secur. Intell. Syst. Appl. (TPS-ISA), Dec. 2019, pp. 36–45. IEEE Smart Data (SmartData), Jul. 2018, pp. 1574–1581. y
pp
pp
[76] P. Robinson, D. Hyland-Wood, R. Saltini, S. Johnson, and J. Brainard,
‘‘Atomic crosschain transactions for ethereum private sidechains,’’ 2019,
arXiv:1904.12079. [Online]. Available: http://arxiv.org/abs/1904.12079 [51] S. Schulte, M. Sigwart, P. Frauenthaler, and M. Borkowski, ‘‘Towards
blockchain interoperability,’’ in Proc. Int. Conf. Bus. Process Manage. Cham, Switzerland: Springer, 2019, pp. 3–10. [77] M. Darisi, J. Savla, M. Shirole, and S. Bhirud, ‘‘STEM: Secure token
exchange mechanisms,’’ in Proc. Int. Conf. Adv. Cyber Secur. Singapore:
Springer, 2019, pp. 206–219. [52] R. Belchior, A. Vasconcelos, S. Guerreiro, and M. REFERENCES [1] S. Nakamoto, ‘‘Re: Bitcoin P2P e-cash paper,’’ in The Cryptography
Mailing List. 2008. [28] P. Frauenthaler, M. Sigwart, C. Spanring, and S. Schulte, ‘‘Testimonium:
A cost-efficient blockchain relay,’’ 2020, arXiv:2002.12837. [Online]. Available: http://arxiv.org/abs/2002.12837 [2] V. Buterin. (2016). What is Ethereum?. Accessed: Feb. 28, 2021. [Online]. Available: http://www.ethdocs.org/en/latest/introduction/what-
is-ethereum.html [29] A. Garoffolo, D. Kaidalov, and R. Oliynykov, ‘‘Zendoo: A zk-
SNARK verifiable cross-chain transfer protocol enabling decoupled and
decentralized sidechains,’’ 2020, arXiv:2002.01847. [Online]. Available:
http://arxiv.org/abs/2002.01847 [3] R. G. Brown, J. Carlyle, I. Grigg, and M. Hearn, ‘‘Corda: An introduction,’’
R3 CEV, vol. 1, p. 15, Aug. 2016. [4] Quorum. Accessed: Feb. 27, 2021. [Online]. Available: https://github.com/
ConsenSys/quorum/wiki [30] S. Ghaemi, S. Rouhani, R. Belchior, R. S. Cruz, H. Khazaei, and P. Musilek,
‘‘A pub-sub architecture to promote blockchain interoperability,’’ 2021,
arXiv:2101.12331. [Online]. Available: http://arxiv.org/abs/2101.12331 [5] C. Cachin, ‘‘Architecture of the hyperledger blockchain fabric,’’ in Proc. Workshop Distrib. Cryptocurrencies Consensus Ledgers, 2016, vol. 310,
no. 4, pp. 1–4. [31] P. Frauenthaler,
M. Borkowski,
and
S. Schulte,
‘‘A
framework
for
blockchain
interoperability
and
runtime
selection,’’
2019,
arXiv:1905.07014. [Online]. Available: http://arxiv.org/abs/1905.07014 [6] K. Gai, J. Guo, L. Zhu, and S. Yu, ‘‘Blockchain meets cloud computing:
A survey,’’ IEEE Commun. Surveys Tuts., vol. 22, no. 3, pp. 2009–2030,
3rd Quart., 2020. [32] N. Szabo, ‘‘Formalizing and securing relationships on public networks,’’
1st Monday, vol. 2, no. 9, Sep. 1997. VOLUME 9, 2021 116689 S. Khan et al.: Towards Interoperable Blockchains [33] J. Chen, X. Xia, D. Lo, J. Grundy, and X. Yang, ‘‘Maintaining smart
contracts on ethereum: Issues, techniques, and future challenges,’’ 2020,
arXiv:2007.00286. [Online]. Available: http://arxiv.org/abs/2007.00286 [59] G. Falazi, A. Lamparelli, U. Breitenbuecher, F. Daniel, and F. Leymann,
‘‘Unified integration of smart contracts through service orientation,’’ IEEE
Softw., vol. 37, no. 5, pp. 60–66, Sep. 2020. [34] Solidity Programming Language. Accessed: Mar. 1, 2021. [Online]. Avail-
able: https://docs.soliditylang.org/en/v0.7.4/ [60] BTC Relay. Accessed: Dec. 2, 2020. [Online]. Available: http://btcrelay. org// p
y
g
g
[35] Neo
Whitepaper. Accessed:
Mar. 1,
2021. [Online]. Available:
https://docs.neo.org/docs/en-us/ g
[61] COMIT Project. Accessed: Dec. 6, 2020. [Online]. Available: https://
comit.network/docs/comit-protocol/comit-projects/ p
g
[36] IO, EOS, Technical White Paper. Accessed: Mar. 1, 2021. [Online]. Avail-
able: https://github.com/EOSIO/Documentation p
p
j
[62] A Cryptofinance Platform. Accessed: Dec. 2, 2020. [Online]. Available:
https://uploads-ssl.webflow.com/Whitepaper.pdf [37] J. Kwon, ‘‘Tendermint: Consensus without mining,’’ Draft V. 0.6, Fall,
vol. 1, no. 11, 2014. [63] N. Shadab, F. Houshmand, and M. Lesani, ‘‘Cross-chain transactions,’’
in Proc. REFERENCES IEEE Int. Conf. Blockchain Cryptocurrency (ICBC), May 2020,
pp. 1–9. [38] S. Rouhani and R. Deters, ‘‘Security, performance, and applica-
tions of smart contracts: A systematic survey,’’ IEEE Access, vol. 7,
pp. 50759–50779, 2019. [64] B. Dai, S. Jiang, M. Zhu, M. Lu, D. Li, and C. Li, ‘‘Research and implemen-
tation of cross-chain transaction model based on improved hash-locking,’’
in Proc. Int. Conf. Blockchain Trustworthy Syst. Singapore: Springer, 2020,
pp. 218–230. pp
[39] D. Yaga,
P. Mell,
N. Roby,
and
K. Scarfone,
‘‘Blockchain
technology overview,’’ 2019, arXiv:1906.11078. [Online]. Available:
http://arxiv.org/abs/1906.11078 pp
[65] M. Sigwart, P. Frauenthaler, T. Hukkinen, and S. Schulte, ‘‘Towards cross-
blockchain transaction verifications,’’ Tech. Rep., 2019. [Online]. Avail-
able: http://www.infosys.tuwien.ac.at/tast p
g
[40] V. Buterin, ‘‘Chain interoperability,’’ R3 Research Paper, 2016. [41] M. Borkowski, D. McDonald, C. Ritzer, and S. Schulte, ‘‘Towards atomic
cross-chain token transfers: State of the art and open questions within tast,’’
Distrib. Syst. Group TU Wien (Technische Universität Wien), Vienna,
Austria, Tech. Rep., 2018. [66] M. Sigwart, P. Frauenthaler, C. Spanring, and S. Schulte, ‘‘Prepar-
ing simplified payment verifications for cross-blockchain token trans-
fers,’’ Tech. Rep., 2019. [Online]. Available: https://dsg.tuwien.ac.at/
projects/tast [42] M. Borkowski, P. Frauenthaler, M. Sigwart, T. Hukkinen, O. Hladký, and
S. Schulte, Cross-Blockchain Technologies: Review, State of the Art, and
Outlook. 2019, pp. 1–5. p
j
[67] P. Frauenthaler, M. Sigwart, C. Spanring, and S. Schulte, ‘‘Leveraging
blockchain relays for cross-chain token transfers,’’ Gas, vol. 300, p. 600,
Mar. 2020. pp
[43] T. Koens and E. Poll, ‘‘Assessing interoperability solutions for distributed
ledgers,’’ Pervas. Mobile Comput., vol. 59, Oct. 2019, Art. no. 101079. [68] E. Abebe, D. Behl, C. Govindarajan, Y. Hu, D. Karunamoorthy,
P. Novotny, V. Pandit, V. Ramakrishna, and C. Vecchiola, ‘‘Enabling
enterprise blockchain interoperability with trusted data transfer (indus-
try track),’’ in Proc. 20th Int. Middleware Conf. Ind. Track, Dec. 2019,
pp. 29–35. [44] A. Singh, K. Click, R. M. Parizi, Q. Zhang, A. Dehghantanha, and
K.-K.-R. Choo, ‘‘Sidechain technologies in blockchain networks: An
examination and state-of-the-art review,’’ J. Netw. Comput. Appl., vol. 149,
Jan. 2020, Art. no. 102471. [45] V. A. Siris, P. Nikander, S. Voulgaris, N. Fotiou, D. Lagutin, and
G. C. Polyzos,
‘‘Interledger
approaches,’’
IEEE
Access,
vol. 7,
pp. 89948–89966, 2019. pp
[69] Peace Relay. Accessed: Nov. 2, 2020. [Online]. Available: https://
peacerelay.io/ [70] I. Barinov, V. Baranov, and P. Khahulin. Proof of Authority Network. Accessed: Nov. 2, 2020. [Online]. REFERENCES Correia, ‘‘A survey
on blockchain interoperability: Past, present, and future trends,’’ 2020,
arXiv:2005.14282. [Online]. Available: http://arxiv.org/abs/2005.14282 [78] P. Robinson and R. Ramesh, ‘‘General purpose atomic crosschain trans-
actions,’’ 2020, arXiv:2011.12783. [Online]. Available: http://arxiv.org/
abs/2011.12783 p
g
[53] M. Herlihy, ‘‘Atomic cross-chain swaps,’’ in Proc. ACM Symp. Princ. Distrib. Comput., Jul. 2018, pp. 245–254. [54] E. Fynn, A. Bessani, and F. Pedone, ‘‘Smart contracts on the move,’’ in
Proc. 50th Annu. IEEE/IFIP Int. Conf. Dependable Syst. Netw. (DSN),
Jun. 2020, pp. 233–244. [79] M. Nissl, E. Sallinger, S. Schulte, and M. Borkowski, ‘‘Towards cross-
blockchain smart contracts,’’ 2020, arXiv:2010.07352. [Online]. Avail-
able: http://arxiv.org/abs/2010.07352 [55] M. Black,
T. Liu,
and
T. Cai,
‘‘Atomic
loans:
Cryptocurrency
debt
instruments,’’
2019,
arXiv:1901.05117. [Online]. Available:
http://arxiv.org/abs/1901.05117 p
g
[80] B. Pillai, K. Biswas, and V. Muthukkumarasamy, ‘‘Cross-chain interoper-
ability among blockchain-based systems using transactions,’’ Knowl. Eng. Rev., vol. 35, 2020. [56] A. Zamyatin, D. Harz, J. Lind, P. Panayiotou, A. Gervais, and
W. Knottenbelt, ‘‘XCLAIM: Trustless, interoperable, cryptocurrency-
backed assets,’’ in Proc. IEEE Symp. Secur. Privacy (SP), May 2019,
pp. 193–210. [81] M. Sigwart, P. Frauenthaler, C. Spanring, and S. Schulte. Towards Cross-
Blockchain Smart Contracts. Accessed: Feb. 27, 2021. [Online]. Available:
https://dsg.tuwien.ac.at/index.html [82] Z. Liu, Y. Xiang, J. Shi, P. Gao, H. Wang, X. Xiao, B. Wen, and
Y.-C. Hu, ‘‘Hyperservice: Interoperability and programmability across het-
erogeneous blockchains,’’ in Proc. ACM SIGSAC Conf. Comput. Commun. Secur., 2019, pp. 549–566. pp
[57] P2PHK Transactions. Accessed: Dec. 21, 2020. [Online]. Available:
https://en.bitcoinwiki.org/wiki/Pay-to-Pubkey-Hash [58] G. FalaziEmail, U. Breitenbücher, F. Daniel, A. Lamparelli, F. Leymann,
and V. Yussupov, ‘‘Smart contract invocation protocol (SCIP): A protocol
for the uniform integration of heterogeneous blockchain smart contracts,’’
in Proc. Int. Conf. Adv. Inf. Syst. Eng. Cham, Switzerland: Springer, 2020,
pp. 134–149. pp
[83] D. K. Bhavani. Block Collider an Ultimate Unifier for Crypto. Accessed:
Nov. 21, 2020. [Online]. Available: https://www.blockcollider.org/ p
g
[84] What is Borderless?. Accessed: Nov. 21, 2020. [Online]. Available:
https://docs.blockcollider.org/docs/ 116690 VOLUME 9, 2021 S. Khan et al.: Towards Interoperable Blockchains [85] H. Tian, K. Xue, S. Li, J. Xu, J. Liu, and J. Zhao, ‘‘Enabling cross-chain
transactions: A decentralized cryptocurrency exchange protocol,’’ 2020,
arXiv:2005.03199. [Online]. Available: http://arxiv.org/abs/2005.03199 AHMAD TAHER AZAR (Senior Member, IEEE)
received the M.Sc. and Ph.D. degrees from the
Faculty of Engineering, Cairo University, Egypt,
in 2006 and 2009, respectively. He is currently a
Research Professor with Prince Sultan University,
Riyadh, Saudi Arabia. REFERENCES He is also an Associate Pro-
fessor with the Faculty of Computers and Artificial
Intelligence, Benha University, Egypt. He worked
in the areas of control theory and its applica-
tions, process control, chaos control and synchro-
nization, nonlinear control, robust control, and computational intelligence. He served as an Associate Editor for the IEEE TRANSACTIONS ON NEURAL
NETWORKS AND LEARNING SYSTEMS, from 2013 to 2017, and ISA Transactions
(Elsevier), from 2018 to 2020. He is the Editor-in-Chief of the Interna-
tional Journal of System Dynamics Applications (IJSDA) (IGI Global, USA)
and the International Journal of Intelligent Engineering Informatics (IJIEI)
(Inderscience Publishers, Olney, U.K.). He is currently an Associate Editor
of the IEEE SYSTEMS JOURNAL. [86] ARK Public Network, Point Click Blockchain. Accessed: Nov. 23, 2020. [Online]. Available: https://ark.io/Whitepaper.pdf p
p p
p
[87] L. Jack, B. Yang, Z. Liang, Y. Zhang, D. Shi, E. Swartz, and L. Lu,
‘‘Wanchain,’’ Tech. Rep., 2017. [88] ICON:
Hyper
Connect
the
World,
ICON
Foundation. Accessed:
Nov. 23, 2020. [Online]. Available: https://icon.foundation/?lang=en [89] G. Verdian, P. Tasca, C. Paterson, and G. Mondelli, Quant Overledger
Whitepaper. Accessed: Feb. 28, 2021. [Online]. Available: https://uploads- [89] G. Verdian, P. Tasca, C. Paterson, and G. Mondelli, Quant Overledger
Whitepaper. Accessed: Feb. 28, 2021. [Online]. Available: https://uploads-
ssl.webflow.com/Quant_Overledger_Whitepaper_2019.pdf [90] PolkaDot
XCMP. Accessed:
Nov. 23,
2020. [Online]. Available:
https://wiki.polkadot.network/docs/en/ [91] W3C, Web Assembly. Accessed: Nov. 23, 2020. [Online]. Available:
https://webassembly.org/ SAJJAD KHAN received the B.S. degree in com-
puter science from the University of Peshawar,
in 2012, and the M.S. degree in computer science
from COMSATS University Islamabad, Pakistan,
in 2019. He is currently pursuing the Ph.D. degree
in computer science. His research interests include
blockchain interoperability, distributed comput-
ing, optimization, and scheduling and forecasting
using machine learning/deep learning techniques. SHERAZ ASLAM (Member, IEEE) received the
B.S. degree in computer science from Bahauddin
Zakariya University (BZU), Multan, Pakistan,
in 2015, and the M.S. degree in computer science
with a specialization in energy optimization in
the smart grid from COMSATS University Islam-
abad(CUI), Islamabad, Pakistan, in 2018. He is
currently pursuing the Ph.D. degree with the DICL
Research Laboratory, Cyprus University of Tech-
nology (CUT), Limassol, Cyprus, under the super-
vision of Dr. H. Herodotou. During his M.S. degree, he worked as a Research
Associate with Dr. N. Javaid at CUT. REFERENCES He has authored more than 50 research
publications in ISI-indexed international journals and conferences such as the
IEEE INTERNET OF THINGS (IoT) JOURNAL, Renewable and Sustainable Energy
Reviews, IEEE ACCESS, Electrical Power System Research, and Energies. He is also a part of European Union funded research project named as
STEAM. His research interests include data analytics, generative adversar-
ial networks, network security, wireless networks, smart grid, and cloud
computing. He also served as a TPC member and an invited reviewer for
international journals and conferences. MUHAMMAD BILAL AMIN received the M.S. degree from
DePaul University, Chicago, IL,
USA, in 2006, and the Ph.D. degree from Kyung
Hee University, South Korea, in 2015. He is cur-
rently a Korea Research Fellow and a Lecturer
with the Department of ICT, University of Tas-
mania, Australia. He has an experience of more
than ten years in the software industry, working for
Fortune 500 companies in USA. He is an author of
more than 50 publications. His research interests
include blockchain, distributed systems, software engineering and architec-
ture, and performance-based cloud applications. 116691 VOLUME 9, 2021
|
https://openalex.org/W4313435619
|
https://jurnal.stikesmus.ac.id/index.php/avicenna/article/download/590/395
|
Indonesian
| null |
PENGARUH TEH DAUN KELOR (Moringa oleifera L) TERHADAP PENINGKATAN KADAR HEMOGLOBIN PENDERITA ANEMIA
|
Avicenna
| 2,022
|
cc-by-sa
| 5,311
|
Andrias Priyas Hastuti1, Ajeng Novita Sari2
1,2Politeknik Santo Paulus Surakarta
ajengpolsapa@gmail.com Andrias Priyas Hastuti1, Ajeng Novita Sari2
1,2Politeknik Santo Paulus Surakarta
ajengpolsapa@gmail.com ABSTRAK Latar Belakang : Anemia merupakan penurunan kadar hemoglobin dalam darah
yang menyebabkan kadar oksigen dalan tubuh tidak tercukupi. Pencegahan dan
pengobatan anemia dapat dilakukan dengan pemberian suplemen dan konsumsi
makanan yang mengandung zat besi. Salah satunya dengan menggunakan daun
kelor (Moringa oleifera L.) dikarenakan mengandung kadar zat besi sebesar 28,2
mg dalam 100 gram daun kelor segar. Tujuan: Penelitian ini bertujuan untuk mengetahui efektivitas pemberian teh
daun kelor terhadap kadar hemoglobin pada wanita usia produktif penderita
anemia. Metode : Penelitian ini merupakan studi korelasi dengan pendekatan Quasi-
eksperimen research. Pemeriksaan kadar Hb menggunakan metode POCT dengan
spesimen darah kapiler. Teknik sampling yang digunakan adalah purposive
sampling. Jumlah responden 141 yang dibagi menjadi 3 kelompok yaitu
kelompok teh daun kelor, kelompok tablet Fe dan kelompok kapsul gelatin selama
21 hari. Uji statistika yang digunakan yaitu uji Repeated Measure Anova, uji
Friedman dan uji Independent sample T-Test. Hasil : Pada kelompok teh daun kelor mengalami rerata peningkatan sebesar 1,3
g/dl, kelopok tablet fe mengalami rerata peningkatan sebesar1,6 g/dl, dan
kelompok kapsul gelatin mengalami peningkatan sebesar 0,4 g/dl. Lama waktu
yang dibutuhkan teh daun kelor dalam meningkatkan kadar Hb dalam tubuh
selama kurang lebih 2 minggu. Simpulan : Penelitian menunjukkan bahwa pada ketiga kelompok mengalami
peningkatan sebelum dan sesudah pengonsumsian 0,005 (p<0,05). Kata kunci : Teh daun kelor, anemia, haemoglobin Kata kunci : Teh daun kelor, anemia, haemoglobin PENGARUH TEH DAUN KELOR (Moringa oleifera L) TERHADAP
PENINGKATAN KADAR HEMOGLOBIN PENDERITA ANEMIA The Effect Of Moringa Leaf Tea (Moringa Oleifera L) To The Increasing
Hemoglobin Levels In Anemia Patients Available online at https://jurnal.stikesmus.ac.id/index.php/avicenna
Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) Available online at https://jurnal.stikesmus.ac.id/index.php/avicenna
Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 27 ABSTRACT Background : Anemia is a decrease in blood hemoglobin levels with insufficient
oxygen levels. Prevention and treatment of anemia is carried out by
supplementing and consuming foods that contain iron, such as Moringa leaves
(Moringa oleifera L.) because there is 28.2 mg of iron in 100 grams of fresh
Moringa leaves. Research Puprose : To determine the effectiveness of Moringa leaf tea on
hemoglobin levels of women of productive age who are anemic. Methods : Correlational research with Quasi-experimental research approach. Examination of Hb levels using the POCT method of capillary blood specimens. 10.36419/avicenna.v5i1.590 28 Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 28
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) sampling by purposive sampling. The number of respondents was 141 people
divided into 3 groups, namely the Moringa leaf tea group, the Fe tablet group and
the gelatin capsule group for 21 days. The statistical test is the Repeated Measure
Anova test, Friedman test and the Independent sample T-Test test. Results : Moringa leaf tea group increased by an average of 1.3 g/dl, Fe tablet sampling by purposive sampling. The number of respondents was 141 people
divided into 3 groups, namely the Moringa leaf tea group, the Fe tablet group and
the gelatin capsule group for 21 days. The statistical test is the Repeated Measure
Anova test, Friedman test and the Independent sample T-Test test. Results : Moringa leaf tea group increased by an average of 1.3 g/dl, Fe tablet
group increased by an average of 1.6 g/dl, and gelatin capsule group increased
by an average of 0.4 g/dl. The length of time for Moringa leaf tea to increase Hb
levels in the body is ± 2 weeks. C
l
i
l
h
d
h
h
i
d b f
d
f Results : Moringa leaf tea group increased by an average of 1.3 g/dl, Fe tablet
group increased by an average of 1.6 g/dl, and gelatin capsule group increased
by an average of 0.4 g/dl. The length of time for Moringa leaf tea to increase Hb
levels in the body is ± 2 weeks. Conclusion : Results showed the three groups increased before and after
consumption by 0.005 (p<0.05). Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 28
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) PENDAHULUAN Maret 2022 (27 - 36) 29
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) 29 Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 36) 29
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) ,
(
)
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) Menurut Yulianti et al., (2016) . Satu kantong teh daun kelor berisi 2,5 gram
serbuk daun kelor kering. Untuk tujuan sumber antioksidan, anti-inflamasi dan
nutrisi yang tinggi, konsumsi teh daun kelor dapat dilakukan sehari dua kali, yaitu
pada pagi dan sore hari. Cara konsumsinya cukup diseduh menggunakan air panas
sebanyak 250 ml, ditunggu hingga larutan berubah warna dan siap dikonsumsi
dalam keadaan hangat (Pratiwi & Nurjanna, 2019). METODE Penelitian ini merupakan studi korelasi dengan pendekatan Quasi-eksperim
research. Rancangan penelitian ini menggunakan metode pra eksperimen yaitu
one group pretes postest, yaitu rancangan penelitian yang dilakukan observasi
pertama (pretest) yang dilakukan sebelum pemberian teh daun kelor, kemudian
dilakukan observasi kedua (postest) dengan tujuan memungkinkan menguji
perubahan-perubahan yang terjadi setelah adanya eksperimen yang melibatkan
satu kelompok subjek, yaitu kadar Hb wanita usia subur setelah diberikan teh
daun kelor. Populasi dalam penelitian ini adalah Seluruh wanita usia subur yang
menderita anemia di Kelurahan Trangsan sebanyak 221 orang. Jumlah sampel
didapatkan 141 responden dengan teknik purposive sampling sehingga setiap
kelompok terdiri dari 47 responden. Waktu penelitian dimulai bulan April 2021
sampai bulan Juli 2021 dilakukan secara door to door di Kelurahan Trangsan,
Gatak, Sukoharjo. Responden penelitian berjumlah 141 orang, dibagi menjadi 3
kelompok yaitu kelompok teh daun kelor, kelompok kontrol positif tablet Fe dan
kelompok kontrol negatif kapsul gelatin selama 21 hari. Cara pengonsumsian
sediaan teh daun kelor dengan diseduh menggunakan air matang dan hangat,
perendaman kantung teh juga tidak boleh terlalu lama. Hal ini dikarenakan
menyebabkan teh menjadi lebih kental dan merusak rasa. Teh dikonsumsi dengan
takaran 2 kali per hari selama 21 hari. Kelompok control positif tablet fe
merupakan pemberian tablet fe 30 mg dengan dosis 1 kali sehari selama 21 hari. Sedangkan kelompok control negative dilakukan dengan pemberian kapsul
kosong yang merupakan kapsul gelatin kepada kelompok placebo dengan dosis 1
tablet per hari selama 21 hari. Pemeriksaan sampel menggunakan metode POCT
(Point of Care Testing) yaitu pemeriksaan kadar Hb yang dilakukan menggunakan
alat teknologi elektrokimia dengan penambahan enzim pada stik test yang akan
dibaca oleh alat dengan cepat, pemeriksaan ini dilakukan setiap 1 minggu sekali. Uji statistika yang digunakan yaitu uji Repeated Measure Anova, uji Friedman
dan uji Independent sample T-Test. Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online)
HASIL DAN PEMBAHASAN
Hasil
Tabel 1 Distribusi Frekuensi Karakteristik Responden
Kriteria
Frekuensi
Presentase (%)
Umur
16-25
62
44.0
26-35
56
39.7
36-45
23
16.3 Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online)
HASIL DAN PEMBAHASAN
Hasil
Tabel 1 Distribusi Frekuensi Karakteristik Responden
Kriteria
Frekuensi
Presentase (%)
Umur
16-25
62
44.0
26-35
56
39.7
36-45
23
16.3 HASIL DAN PEMBAHASAN PENDAHULUAN Anemia merupakan penurunan kadar hemoglobin atau jumlah sel darah
merah dalam darah yang menyebabkan kadar oksigen dalam tubuh tidak tercukupi
(Arulprakash & Umaiorubahan, 2018). Berdasarkan data Riskesdas (2013) faktor
risiko kejadian anemia pada wanita usia produktif di Kecamatan Gatak Sukoharjo
sebesar 37%. Wanita usia produktif merupakan kelompok yang rentan terkena
anemia defisiensi besi karena kurangnya asupan zat besi yang dipengaruhi pola
konsumsi, peningkatan kebutuhan tubuh akibat infeksi, penyakit kronis, hamil,
menstruasi dan faktor sosial ekonomi. Salah satu cara pencegahan dan pengobatan anemia dapat menggunakan
daun kelor (Moringa oleifera L.) dikarenakan dalam 100 gram daun kelor segar
memiliki kandungan zat besi sebesar 28,29 mg, ini setara dengan kandungan zat
besi pada tablet Fe yang sebesar 30 mg dalam satu tablet. WHO bahkan
menganjurkan konsumsi daun kelor untuk mencukupi kadar zat besi dalam tubuh,
terutama penderita anemia defisiensi besi. Berbagai penelitian membuktikan
efektivitas pemberian daun kelor dalam berbagai sediaan sebagai terapi penderita
anemia. Daun kelor mengandung zat besi (Fe) yang cukup tinggi. Zat besi dalam
daun kelor dapat membantu proses pembentukan sel darah merah sehingga dapat
meningkatkan kadar hemoglobin di dalam darah. Menurut Fauziandri (2019),
suplemen ekstrak daun kelor dalam bentuk kapsul dengan dosis dinilai lebih
efisien dalam mencegah anemia dan dapat mempertahan kadar Hb normal
(mencegah anemia). Gejala anemia pada umumnya yaitu pucat (pada bibir, gusi,
mata, kuku, telapak tangan), tubuh yang cepat lelah, jantung berdetak kencang
pada saat melakukan suatu aktivitas yang ringan, pusing, nyeri pada dada, tangan
dan kaki dingin serta mata berkunang-kunang (Zidni et al., 2018). Konsumsi daun kelor dapat dilakukan melalui berbagai cara. Selain
dikonsumsi dalam bentuk segar, daun kelor dapat dibuat berbagai macam sediaan
yang bertujuan untuk meningkatkan kadar Hb, misalnya dikeringkan dan dibuat
menjadi teh atau kapsul atau dibuat menjadi tepung dan digunakan untuk
membuat olahan lainnya. Setiap sediaan memiliki kemampuan yang berbeda
dalam meningkatkan kadar Hb, tergantung jenis perlakuan, lama atau durasi dan
karakteristik responden penelitian. Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) vicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) Avicenna : Journal of Health Research, Vol 5 No 1. Hasil Maret 2022 (27 - 36) 30
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) 30 Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) Pendidikan Terakhir
SMP
12
8.3
SMA/SMK
82
58.3
D4/SI
45
33.3
S2
2
1.4
Jumlah
141
100 Tabel 2 Data Kadar Hb Pada Setiap Kelompok
Waktu
Teh Daun Kelor
Tablet Fe
Kapsul Gelatin
Mean ±
SD
Min
Max
Mean ±
SD
Min
Max
Mean ±
SD
Min
Max
Minggu 0
10,93±0,3
63
10,1
11,5
10,90±0,3
16
10,3
11,5
11,05±0,
379
10,3
11,8
Minggu 1
11,27±1,3
07
10.7
11.9
11,20±0.2
27
10,5
11,7
11,24±0,
295
10,5
11,7
Minggu 2
11,78±0,4
04
11.0
12.7
12,04±0,4
65
11,0
12,8
11,27±0,
278
10,5
11,8
Minggu 3
12,20±0,5
00
11.3
13.4
12,51±0,5
43
11,3
13,5
11,46±0,
316
10,3
11,9
Rerata
peningkatan
Kadar Hb
1,3 g/dl
1,6 g/dl
0,4 g/dl Tabel 2 Data Kadar Hb Pada Setiap Kelompok Tabel 3 Uji Normalitas Kadar Hb Pada Setiap Kelompok Perlakuan Tabel 3 Uji Normalitas Kadar Hb Pada Setiap Kelompok Perlakuan
Waktu
Teh Daun Kelor
Tablet Fe
Kapsul Gelatin
Statistic
Df
Sig
Statistic
df
Sig
Statistic
df
Sig
Minggu 0
0,965
47
0,177
0,959
47
0,101
0,967
47
0,208
Minggu 1
0,966
47
0,179
0,972
47
0,310
0,957
47
0,080
Minggu 2
0,974
47
0,375
0,962
47
0,134
0,960
47
0,104
Minggu 3
0,964
47
0,160
0,978
47
0,530
0,915
47
0,002*
Keterangan : * Data terdistribusi tidak normal (p<0,05) Keterangan : * Data terdistribusi tidak normal (p<0,05) Data dari uji normalitas shapiro-wilk diperoleh hasil kadar Hb pada setiap
kelompok perlakuan dengan nilai signifikasi p>0,05 Tabel 4 Hasil Uji Repeated Measure Anova Antar Kelompok Perlakuan Teh
Daun Kelor Dan Tablet Fe
keterangan : *Terdapat beda nyata (p<0,05)
Kelompok
p-Value
Sig. (2-tailed)
Teh Daun Kelor
0,000*
p<0,05
Tablet Fe
0,000*
p<0,05 Tabel 4 Hasil Uji Repeated Measure Anova Antar Kelompok Perlakuan Teh
Daun Kelor Dan Tablet Fe keterangan : *Terdapat beda nyata (p<0,05) Kelompok perlakuan yang diberi teh daun kelor dan tablet Fe terdistribusi normal Kelompok perlakuan yang diberi teh daun kelor dan tablet Fe terdistribusi normal
sehingga dilanjutkan dengan uji repeated measures anova karena dapat menguji
perbedaan dari tiga kelompok uji yang saling berpasangan. Hasil Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 30
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia)
Tabel 2 Data Kadar Hb Pada Setiap Kelompok
Waktu
Teh Daun Kelor
Tablet Fe
Kapsul Gelatin
Mean ±
SD
Min
Max
Mean ±
SD
Min
Max
Mean ±
SD
Min
Max
Minggu 0
10,93±0,3
63
10,1
11,5
10,90±0,3
16
10,3
11,5
11,05±0,
379
10,3
11,8
Minggu 1
11,27±1,3
07
10.7
11.9
11,20±0.2
27
10,5
11,7
11,24±0,
295
10,5
11,7
Minggu 2
11,78±0,4
04
11.0
12.7
12,04±0,4
65
11,0
12,8
11,27±0,
278
10,5
11,8
Minggu 3
12,20±0,5
00
11.3
13.4
12,51±0,5
43
11,3
13,5
11,46±0,
316
10,3
11,9
Rerata
peningkatan
Kadar Hb
1,3 g/dl
1,6 g/dl
0,4 g/dl
Tabel 3 Uji Normalitas Kadar Hb Pada Setiap Kelompok Perlakuan
Pendidikan Terakhir
SMP
12
8.3
SMA/SMK
82
58.3
D4/SI
45
33.3
S2
2
1.4
Jumlah
141
100 Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 30
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) Avicenna : Journal of Health Research, Vol 5 No 1. Hasil (2-tailed)
Kelompok Teh
0,000*
P<0,05
Kelompok Kapsul
0,000*
P<0,05 Tabel 8 Perbedaan Kadar Hb Kelompok Kontrol Positif Dan Kelompok Kontrol Negatif ngan : *Terdapat beda nyata (p<0,05) Tabel 6-7 uji independent sampel T-Test untuk mengetahui perbedaan
kadar Hb dua kelompok yang tidak berpasangan. Nilai p value < 0,05
menunjukkan adanya perbedaan kadar Hb pada kedua kelompok perlakuan. Hasil Nilai p (p value) <
0,05 menunjukkan terdapat beda nyata rata-rata kadar Hb antara kelompok
perlakuan teh daun kelor dan tablet Fe. Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 31
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) 31 Tabel 5 Hasil Uji Friedman Kelompok Perlakuan Kontrol Negatif (Kontrol
Negatif)
Keterangan : *Terdapat beda nyata (p<0,05)
Kelompok
p-Value
Sig. (2-tailed)
Kapsul Gelatin
0,001*
p<0,05 Tabel 5 Hasil Uji Friedman Kelompok Perlakuan Kontrol Negatif (Kontrol
Negatif) g
p
y
p
Data yang tidak berdistrisbusi normal pada kelompok kontrol negatif
sehingga dilanjutkan uji friedman. Nilai p<0,05 menujukkan ada beda nyata
kadar Hb. Tabel 6 Perbedaan Kadar Hb Kelompok Perlakuan Teh Daun Kelor Dan Tablet Fe
(Kelompok Kontrol Positif). Keterangan : *Terdapat beda nyata (p<0,05)
Kelompok
p-Value
Sig. (2-tailed)
Kelompok Teh
0,005*
P<0,05
Kelompok Fe
0,005*
P<0,05 Tabel 6 Perbedaan Kadar Hb Kelompok Perlakuan Teh Daun Kelor Dan Tablet Fe
(Kelompok Kontrol Positif). Tabel 7 Perbedaan Kadar Hb Kelompok Perlakuan Teh Daun Kelor Dan Kapsul
Gelatin (Kelompok Kontrol Negatif)
Keterangan : *Terdapat beda nyata (p<0,05)
Tabel 8 Perbedaan Kadar Hb Kelompok Kontrol Positif Dan Kelompok Kontrol Negatif
Keterangan : *Terdapat beda nyata (p<0,05)
Tabel 6-7 uji independent sampel T-Test untuk mengetahui perbedaan
kadar Hb dua kelompok yang tidak berpasangan. Nilai p value < 0,05
menunjukkan adanya perbedaan kadar Hb pada kedua kelompok perlakuan. Pembahasan
H
il
k
k d
h
l bi
d
b l 3 did
k
k d
Kelompok
p-Value
Sig. (2-tailed)
Kelompok Teh
0,000*
P<0,05
Kelompok Kapsul
0,000*
P<0,05
Kelompok
p-Value
Sig. (2-tailed)
Kelompok Teh
0,000*
P<0,05
Kelompok Kapsul
0,000*
P<0,05 Tabel 7 Perbedaan Kadar Hb Kelompok Perlakuan Teh Daun Kelor Dan Kapsul
Gelatin (Kelompok Kontrol Negatif)
Keterangan : *Terdapat beda nyata (p<0,05)
Kelompok
p-Value
Sig. (2-tailed)
Kelompok Teh
0,000*
P<0,05
Kelompok Kapsul
0,000*
P<0,05 Tabel 7 Perbedaan Kadar Hb Kelompok Perlakuan Teh Daun Kelor Dan Kapsul
Gelatin (Kelompok Kontrol Negatif) Tabel 8 Perbedaan Kadar Hb Kelompok Kontrol Positif Dan Kelompok Kontrol Negatif
Keterangan : *Terdapat beda nyata (p<0,05)
Kelompok
p-Value
Sig. Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 31
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) Pembahasan Hasil pengukuran kadar hemoglobin pada tabel 3 didapatkan rerata kadar
Hb minggu 0 (sebelum konsumsi teh) yaitu 10,9 g/d. Sedangkan rerata kadar Hb
konsumsi teh kelor minggu ke 3 (setelah konsumsi teh) yaitu 12,20 g/dl. Kadar
Hb pada kelompok teh mengalami kenaikan 1,3 g/dl. Hal ini membuktikan bahwa
pada kelompok perlakuan yang mengonsumsi teh daun kelor dapat meningkatkan
kadar hemoglobin dalam darah. Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) 32 Pada kelompok tablet fe kadar Hb minggu 0 (sebelum konsumsi tablet fe)
yaitu 10,9 g/d. Sedangkan rerata kadar Hb konsumsi tablet fe minggu ke 3
(setelah konsumsi tablet fe) yaitu 12,51 g/dl. Kadar Hb pada kelompok tablet fe
mengalami kenaikan 1,6 g/dl. Rerata peningkatan kadar Hb kelompok perlakuan
yang mengonsumsi tablet Fe dari minggu ke 0 samapi minggu ke 3 sangat
signifikan dibandingkan pada kelompok yang mengonsumsi teh kelor. Hal ini
mungkin disebabkan karena menggunakan sediaan daun kelor yang telah
mengalami proses lebih lanjut, yaitu pengeringan yang mungkin dapat
menurunkan kandungan zat Fe di dalamnya. Daun kelor segar mengandung zat
besi sebesar 54,92 mg dalam 1 kg daun basah (BPPOM, 2014) Sedangkan
menurut Isnainy (2020) teh daun kelor mengandung Fe sebesar 11,41 mg% pada
daun kering. Konsumsi teh daun kelor tidak disertai dengan pemberian vitamin C. Menurut Fauziandri (2019) pemberian vitamin C bersamaan dengan suplementasi
zat besi memberikan pengaruh terhadap status zat besi dengan meningkatkan
absorpsinya. Hal ini sejalan dengan penelitian Anisa, et al (2019) untuk
membantu peningkatan penyerapan zat besi dalam tubuh , suplementasi perlu
dikombinasi dengan makronutrien lain seperti vitamin C. g
p
Pada kelompok kontrol negatif yang diberi kapsul gelatin juga
menunjukkan kenaikan kadar Hb setiap minggunya. Kapsul gelatin terbuat dari
gelatin dan tidak memiliki kandungan zat apapun, selain itu kapsul gelatin mudah
terurai dalam air panas dan asam lambung. Adanya peningkatan kadar
hemoglobin pada kelompok kapsul gelatin dapat dipengaruhi oleh gelatin
umumnya terbuat dari kolagen babi, sapi, serta unggas dan ikan yang kaya akan
protein. Hasil penelitian Isnainy (2020) menunjukkan adanya pengaruh pemberian
asupan protein yang cukup terhadap kadar hemoglobin dan menemukan pola
hubungan yang positif dimana semakin banyak konsumsi protein semakin tinggi
kadar hemoglobin (setiap penambahan 1 g protein, kadar hemoglobin bertambah
0,009 g/dL). Sari (2018) menemukan terdapat hubungan antara asupan protein dan
kadar hemoglobin pada remaja putri. Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) Pembahasan Pola konsumsi keseharian probandus yang
mengandung zat besi seperti sayur bayam, brokoli, kentang, daging, ikan sarden,
kerang, kacang merah, dan kacang kedelai. Kandungan zat besi yang tinggi
terdapat pada sayuran yang berwarna hujau gelap seperti bayam, kangkung dan
lembayung. Kulit kentang memiliki kandungan vitamin C dan zat besi yang cukup
tinggi. Menurut penelitian Zidni,et al (2018) kandungan zat besi pada daging
sebesar 2,8 mg dalam 100 gram bahan, ikan sarden mengandung zat besi sebesar
1 mg. Kerang memiliki kandungan zat besi yang sangat tinggi, menurut penelitian
Andaruni,et al (2018) kandungan zat besi dalam 100 gram kerang mencapai 644,7
mg. Menurut Indriani, et al. (2019) kandungan zat besi pada kacang kedelai
sebesar 11,39 mg dalam 100 gram dan kacang merah sebesar 50 mg zat besi
dalam 10 gram kacang merah yang sudah diolah. beberapa makanan hewani dan
nabati yang dikonsumsi oleh responden pada waktu penelitian berlangsung
kerang, sayuran berwarna hijau gelap (bayam) dan kacang merah memiliki
persentase tertinggi dalam menaikkan kadar hemoglobin dalam tubuh. Pada kelompok perlakuan, rerata kenaikan kadar Hb sebesar 0,34 mg/dL
(minggu 1), 0,85 mg/dL (minggu ke-2) dan 1,27 mg/dL (minggu ke 3). Sedangkan
pada kelompok kontrol positif yang diberi tablet Fe, rerata kenaikan kadar Hb nya Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 33
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 33
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) 33 lebih besar, yaitu 0,3 mg/dL (minggu ke 1), 1,14 mg/dL (mingu ke-2) dan 1,61
mg/dL (minggu ke 3). Menurut penelitian Azkiah,et al (2021) kadar Hb rerata
dapat mengalami kenaikan sekitar 2,752 g/dl dalam 2 minggu apabila dilakukan
terapi zat besi secara rutin, selain itu pola konsumsi yang mengandung zat besi
juga mempengaruhi peningkatan kadar Hb dalam darah. Dalam penelitian ini,
faktor-faktor yang dapat mempengaruhi peningkatan kadar hemoglobin dalam
darah antara lain pengetahuan. Responden dalam penelitian ini telah menerima
edukasi tentang anemia dan upaya pencegahan anemia bersamaan dengan
penandatangan informed consent sehingga mereka konsisten minum teh daun
kelor/tablet Fe/kapsul gelatin sesuai dengan kelompok perlakuan. Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) Pembahasan Maret 2022 (27 - 36) 34
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 34
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) 34 (sebelum konsumsi tablet fe) yaitu 10,9 g/d. Sedangkan rerata kadar Hb konsumsi
tablet fe minggu ke 3 (setelah konsumsi tablet fe) yaitu 12,51 g/dl. Kadar Hb pada
kelompok tablet fe mengalami kenaikan 1,6 g/dl. Rerata peningkatan kadar Hb
kelompok perlakuan yang mengonsumsi tablet fe dari minggu ke 0 samapi
minggu ke 3 sangat signifikan dibandingkan pada kelompok yang mengonsumsi
teh kelor. Berdasarkan penelitian Indriana, et al (2017) pemberian tablet darah
masih menjadi prioritas paling utama dalam menanggulangi kejadian anemia pada
remaja. Selain itu remaja juga dianjurkan untuk memenuhi kebutuhan zat besi. Kekurangan zat besi pada remaja dapat mempengaruhi kesehatan seperti
gangguan konsentrasi belajar, penurunan daya tahan tubuh. Salah satu upaya yang
dapat dilakukan untuk mencegah anemia pada remaja putri selain mengkonsumsi
tablet penambah darah adalah memanfaatkan tanaman lokal seperti daun kelor
karena memiliki kandungan zat besi dan vitamin yang cukup tinggi (Yulianti et
al., 2016). Pada kelompok kapsul gelatin kadar Hb minggu 0 (sebelum konsumsi
kapsul) yaitu 11,05 g/d. Sedangkan rerata kadar Hb minggu ke 3 (setelah
konsumsi kapsul) yaitu 11,46 g/dl. Kadar Hb pada kelompok kapsul gelatin
mengalami kenaikan 0,4 g/dl. Rerata peningkatan kadar Hb pada kelompok kapsul
tidak tinggi, dikarenakan probandus tidak mengonsumsi teh kelor dan tablet
penambah darah. Akan tetapi adanya kenaikan kadar Hb pada kelompok kapsul
gelatin karena konsumsi keseharian probandus yang mengandung zat besi. Dapat
dilihat bahwa ke 3 kelompok mengalami kenaikan akan tetapi responden yang
mengkonsumsi tablet fe mempunyai rerata kadar Hb lebih tinggi dari pada
responden yang mengkonsumsi teh dan kapsul gelatin dan responden yang
mengkonsumsi teh mempunyai rerata kadar Hb lebih tinggi dari pada responden
yang mengkonsumsi kapsul gelatin. Pada hasil uji Independent T-Test pada ke 3 kelompok didapatkan
p<0,05) yang berarti ada perbedaan kadar Hb yang signifikan antara kelompok teh
daun kelor, kelompok tablet fe dan kelompok kapsul gelatin. Penelitian yang
dilakukan di Balai Penelitian Rempah dan Obat pada tahun 2014 menunjukan
hasil bahwa 1 kg daun kelor menghasilkan kandungan fe sebanyak 54,92 mg. Pembahasan Maka dari hasil tersebut dapat disimpulkan bahwa daun kelor dapat menjadi
alternatif sumber zat besi (Fauziandri, 2019). Menurut penelitian Pratiwi &
Nurjanna (2019), pemberian teh daun kelor pada remaja putri dianggap memiliki
efektifitas yang cukup tinggi, hal ini dikarenakan terdapat peningkatan kadar
hemoglobin. Daun kelor berguna bagi penderita anemia baik dalam dosis rendah
dan relatif tinggi. Kadar Hb yang cukup dapat membantu keteraturan siklus
menstruasi pada remaja putri. Pembahasan Pengetahuan
pasien yang kurang terkait obat, meningkatkan risiko pasien untuk tidak
patuh menjalankan terapinya sehingga dapat meningkatkan anemia (Adawiyani,
2014). Karakteristik tingkat pendidikan responden sebagian besar merupakan
lulusan SMA sehingga memiliki tingkat pengetahuan dan pemahaman yang baik
tentang anemia. Tingkat pendidikan dapat mendasari sikap dalam menyerap
dan mengubah sistem informasi tentang kesehatan. Semakin tinggi tingkat
pendidikan seseorang makin realitas cara berpikirnya serta makin luas
ruang lingkup cara berpikirnya termasuk pengetahuan tentang anemia (Sulfianti,
2021). Menstruasi dan lama waktu menstruasi. Seluruh probandus dalam
penelitian ini merupakan wanita usia subur yang mengalami menstruasi teratur
setiap bulannya. Karena lama penelitian dilaksanakan selama 21 hari, dalam
rentang itu dimungkinkan ada probandus yang mengalami menstruasi sehingga
berpengaruh terhadap kadar Hb dalam darahnya. Lamanya proses menstruasi akan
mempengaruhi jumlah sel darah merah di dalam tubuh, semakin lama proses
menstruasi maka semakin banyak darah yang keluar sehingga menyebabkan
anemia (Basith et al., 2017). Status gizi. Responden yang memiliki status gizi
normal, mereka dapat terkena anemia apabila kebiasaan makan mereka tidak
seimbang seperti jarang mengkonsumsi sayur-sayuran dan bisa juga disebabkan
apabila sering memakan makanan yang mengandung karbohidrat dan lemak saja
tidak diimbangi dengan mengkonsumsi makanan yang mengandung mineral,
protein, dan vitamin (Basith et al., 2017). Tingkat ekonomi. Orang yang memiliki
tingkat ekonomi yang rendah lebih memilih jenis makanan yang berorientasi pada
karbohidrat dibandingkan protein, vitamin dan mineral. Hal ini dikarenakan
makanan yang mengandung karbohidrat lebih murah dibandingkan yang lain. Responden dalam penelitian ini merupakan kelompok masyarakat dengan tingkat
ekonomi menengah, sehingga konsumsi karbohidrat, lemak dan protein dalam
makanan sehari-sehari seimbang. Sejalan dengan penelitian Pratiwi & Nurjana (2019) dimana pemberian teh
daun kelor pada remaja putri dianggap memiliki efektifitas yang cukup tinggi, hal
ini dikarenakan terdapat peningkatan kadar hemoglobin. Daun kelor berguna bagi
penderita anemia baik dalam dosis rendah dan relatif tinggi. Kadar Hb yang cukup
dapat membantu keteraturan siklus menstruasi pada remaja putri. Ini sejalan
dengan penelitian Fitriyaa & Wijayanti (2020) yang menyatakan bahwa hasil uji
Paired T test didapatkan nilai p value sebesar (0,000), karena nilai p = 0,000< 0,05
(α = 5%), sehingga dapat disimpulkan bahwa ada pengaruh pemberian teh daun
kelor terhadap kenaikan kadar Hb. Pada kelompok tablet fe kadar Hb minggu 0 Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) Avicenna : Journal of Health Research, Vol 5 No 1. Saran Berdasarkan hasil penelitian “pengaruh teh daun kelor (Moringa oleifera L.)
terhadap peningkatan kadar hemoglobin penderita anemia” peneliti memberikan
saran untuk peneliti selanjutnya dapat melakukan penelitian dengan treatment
daun kelor yang dibuat menjadi variasi olahan dan melihat pengaruhnya terhadap
peningkatan kadar Hb penderita anemia. Bagi masyarakat untuk mencegahan
anemia, sebaiknya daun kelor dikonsumsi dalam bentuk segar, diikuti dengan
konsumsi makanan yang banyak mengandung vitamin C. Simpulan Berdasarkan analisa terhadap hasil penelitian, baik secara deskriptif maupun
analisis data statistik didapatkan kesimpulan bahwa pemberian teh daun kelor
cukup efektif terhadap kadar Hb pada wanita penderita anemia tetapi tablet Fe
lebih efektif digunakan, terdapat perbedaan kadar Hb pada penderita anemia yang
diberi suplementasi teh daun kelor, tablet Fe dan kapsul gelatin. Rerata kenaikan Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) 35 Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 35
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 35
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) kadar Hb pada kelompok yang diberi tablet Fe lebih tinggi dibandingkan
kelompok yang diberi teh daun kelor (1,6 g/dL vs 1,3 g/dL), lama waktu yang
dibutuhkan oleh teh daun kelor untuk meningkatkan kadar hemoglobin yaitu
kurang lebih 2 minggu. DAFTAR PUSTAKA Adawiyani, R. 2014. Pengaruh pemberian booklet anemia terhadap pengetahuan,
kepatuhan minum tablet tambah darah dan kadar hemoglobin ibu hamil. Calyptra. 2(2): 1-20. Andaruni, R., Qamariah, N., & Nurbaety, B. 2018. Efektivitas Pemberian Tablet
Zat Besi (Fe), Vitamin C Dan Jus Buah Jambu Biji Terhadap Peningkatan
Kadar Hemoglobin (Hb) Remaja Putri Di Universitas Muhammadiyah
Mataram. Midwifery Journal. 3(2): 104-107. Anisa, N., Wahyuni, S., Rahayu, S., Choirunnisa, A., & Martanti, L. E. 2019,
August. Effect of Moringa Leaves and Vitamin C Capsule Combinations in
Increaseing Hemoglobin Levels of Young Women with Anemia. In
Proceedings of the International Conference on Applied Science and Health. 4: 565-570). Arulprakash, N., & Umaiorubahan, M. 2018. Causes of delayed arrival with acute
ischemic stroke beyond the window period of thrombolysis. Journal of
family medicine and primary care. 7(6): 1248. Azkiyah, S. Z., Rahmaniyah, D. N. K., Istiana, I., & Wafiyah, I. 2021. Pengaruh
Pemberian Vitamin C terhadap Absorpsi Besi (Fe) pada Mencit (Mus
musculus) Anemia dengan Induksi Natrium Nitrit. Jurnal Farmasi Tinctura,
2(2): 79-86. Badan Pengawas Obat dan Makanan Republik Indonesia (BPOM RI). 2014. Peraturan Kepala Badan Pengawas Obat dan Makanan Republik Indonesia
Nomor 17 Tahun 2014 tentang Perubahan atas Peraturan Peraturan Kepala
Badan Pengawas Obat dan Makanan Nomor HK.03.1.23.07.11.6662 Tahun
2011. Jakarta: Badan Pengawas Obat dan Makanan Republik Indonesia. Basith, A., Agustina, R., & Diani, N. 2017. Faktor-faktor yang berhubungan
dengan kejadian anemia pada remaja putri. Dunia Keperawatan: Jurnal
Keperawatan dan Kesehatan. 5(1): 1-10. Fauziandri, E. N. 2019. Efektifitas Ekstrak Daun Kelor Terhadap Peningkatan
Kadar Hemoglobin Pada Remaja Putri. Jurnal Kesehatan Karya Husada. 7(2): 24–29. Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online) Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 36
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) 36 Fitriyaa, M., & Wijayanti, W. 2020. Upaya Peningkatan Kadar Hemoglobin
Melalui Suplemen Tepung Daun Kelor Pada Remaja Putri. Proceeding of
The
URECOL,
86–94. http://repository.urecol.org/index.php/proceeding/article/view/1022 Indriana, R. 2017. Hubungan Tingkat Kecukupan Fe, Vitamin B9, Dan Vitamin
B12 Dengan Kadar Hemoglobin Anak Usia 11 Tahun Ssekolah Dasar Negeri
02 Pedurungan Kidul Semarang. Journal of Chemical Information and
Modeling. 53(9): 1689–1699. Indriani, L., Zaddana, C., Nurdin, N. M., & Sitinjak, J. S. M. 2019. Avicenna : Journal of Health Research, Vol 5 No 1. Maret 2022 (27 - 36) 36
Andriyas Priyas Hastuti, Ajeng Novita Sari (Pengaruh Teh Daun Kelor (Moringa oleifera L)
Terhadap Peningkatan Kadar Hemoglobin Penderita Anemia) DAFTAR PUSTAKA Pengaruh
Pemberian Edukasi Gizi dan Kapsul Serbuk Daun Kelor (Moringa oleifera
L.) terhadap Kenaikan Kadar Hemoglobin Remaja Putri di Universitas
Pakuan. Media Pharmaceutica Indonesiana (MPI). 2(4): 200. Isnainy, U. C. A. S., Arianti, L., & Rosalia, D. 2020. Pengaruh Konsumsi Ekstrak
Daun Kelor Dan Madu Terhadap Peningkatan Hb Ibu Hamil Di Wilayah
Kerja Puskesmas Way Halim Kota Bandar Lampung. Malahayati Nursing
Journal. 2(1): 57-67. Kemenkes RI. 2013. Riset Kesehatan Dasar; RISKESDAS. Jakarta: Balitbang
Kemenkes RI Pratiwi, W. R., & Nurjanna. 2019. Efek Pemberian Teh Daun Kelor ( Moringa
Oleifera Tea ) Dan Tablet Tambah Darah Terhadap Peningkatan Kadar
Hemoglobin Pada Remaja Anemia di Kabupaten Sidrap. Jurnal Antara
Kebidanan. 2(4): 101–111. Sari, A. A., & Muwahkidah, S. K. M. (2018). Hubungan Asupan Protein dan Zat
Besi Dengan Kadar Hemoglobin Remaja Putri di SMA N 1 Weru Sukoharjo
(Doctoral dissertation, Universitas Muhammadiyah Surakarta). Sulfianti, S. 2021. Faktor-Faktor yang Mempengaruhi Anemia pada Ibu Hamil di
UPT Puskesmas Ajangale. Bina Generasi: Jurnal Kesehatan. 13(1): 39-49. Yulianti, H., Hadju, V., & Alasiry, E. 2016. Pengaruh ekstrak daun kelor terhadap
peningkatan kadar hemoglobin pada remaja putri di SMU Muhammadiyah
Kupang. JST Kesehatan. 6(3): 399–404. p
g
Zidni, I., Waryana, W., Sitasari, A., Sitasari, A., & Aritonang, I. 2018. Media
Aplikasi Mobile “Stop Anemia” Terhadap Pengetahuan Tentang Anemia
Dan Sikap Dalam Mencegah Anemia Pada Remaja Putri. Poltekkes
Kemenkes
Yogyakarta. 11–30. PhD
Thesis. http://eprints.poltekkesjogja.ac.id/545/ Copyright © 2022, Avicenna : Journal of Health Research
ISSN 2615-6458 (print) | ISSN 2615-6466 (online)
|
https://openalex.org/W4220708914
|
https://zenodo.org/records/6132552/files/v4n1p126-137.pdf
|
English
| null |
The Role of Brand Reputation on Customer Retention of Social Media Users
|
Zenodo (CERN European Organization for Nuclear Research)
| 2,022
|
cc-by
| 5,267
|
1Master of Management Student, Faculty of Economics, Jakarta State University. E-mail:arcvaputra@gmail.com
2Lecturer of the Faculty of Economics, Jakarta State University
3Lecturer of the Faculty of Economics, Jakarta State University Abstract This study analyzes the effect of brand reputation on customer loyalty,
customer satisfaction, and customer commitment and its impact on
customer retention on TikTok users in Jakarta. This research was
conducted in October-December 2021. The research method used was
a quantitative method. In this study, the authors conducted an
exploratory factor analysis test to determine the level of validity of
each research indicator. Meanwhile, to test the reliability using
Cronbach's Alpha value. In this study, the authors also used the
Structural Equation Modeling analysis test using the AMOS application. The sample in this study amounted to 313 respondents. The results of
the validity and reliability tests show that all research indicators meet
the specified standards. From the research results, it is known that
brand reputation has a positive effect on customer loyalty, customer
satisfaction, and customer commitment. Customer loyalty and
customer satisfaction do not have a positive effect on customer
retention. Meanwhile, customer commitment has a positive effect on
customer retention. Brand reputation;
customer loyalty;
customer
satisfaction;
Customer
commitment;
customer retention The International Journal of Social Sciences World Growingscholar Publisher The Role of Brand Reputation on Customer Retention
of Social Media Users
Agus Putra1, Usep Suhud2, Agung Wahyu Handaru3
Article history:
Received November, 30 2022, Accepted: February, 02 2022; Displayed Online: February 18, 2022; Published: June 30, 2022 1. Introduction Technological developments are progressing very rapidly in various parts of the world. Communication capabilities and technological advances develop over time and undergo
fundamental changes compared to the previous era. The internet is a combination of technology
and computational science that are interrelated by linking satellites in the dissemination of
information. The influence seen in the development of the internet is seen in developments in
society (Comer, 2019). y (
)
Social media is an autonomous system which is transmitted through communication
technology and social environment. Social media is growing rapidly in developing and developed 126 countries as the integration of media and the internet continues to occur(Schroeder, 2018). With
the presence of the internet, social media is growing with the emergence of various available social
media platforms. TikTok is one of the fastest growing social media platforms and is one of the
social media platforms originating from China. Along with the influence of TikTok, which has
experienced ups and downs, TikTok has to face various problems it faces. This certainly affects the
company's image or brand reputation. According to Dijkmans(2015), brand reputation is an
invisible asset for a company that is very valuable and difficult to control in an era that is already
based on today's technology world. Massive developments have led to the growth of brand
reputation which must also be considered properly so as not to create a negative stigma in society. People who understand the importance of brand reputation in an institution certainly make it a
reason to use or take advantage of the various products or services provided by the company. The growing customer trust, loyalty or loyalty from customers is another aspect that cannot
be ruled out in determining customer retention for a product. According to Yang and
Peterson(2004), customer loyalty becomes important in determining the purchase and use of the
company's products. Customer loyalty is something that must be improved in order to help
maintain the product for continued use by customers in the future. Based on research conducted
by Ting(2016), it can be shown that customer satisfaction can also determine the sustainability of
the company's products in retaining its customers. Customers will feel satisfied if the products and
services provided by the company fall into the product category that are purchased or used
continuously. This results in positive and significant results on customer satisfaction in an effort
to continue using the products provided. 1. Introduction In addition to trust, loyalty, and customer satisfaction in an effort to determine the continuity
of product use, customer commitment in using the product can also be one of the other factors. Customer commitment is one of the main keys in measuring the ability to find loyal customers and
use the product continuously. This causes different commitments with various aspects in order to
cause high customer retention in the use of the product(Harrison-Walker, 2001). The higher trust
in the company's reputation and the various aspects that follow in it cause customers to show their
retention in using the products and services provided. This is what causes the development of
customer retention in determining the continuity of product use. Customers will use the products
and services provided with effective marketing activities. This ongoing customer retention can
lead to effective marketing(Appiah-Adu, 1999). TikTok as one of the social media that provides the possibility to influence user interest and
develop customer retention. Therefore, to determine the effect of the relationship between brand
reputation and customer retention on TikTok users, the authors are interested in conducting a
study entitled "The role of brand reputation on customer retention in social media users in
Jakarta". The Role of Brand Reputation on Customer Retention of Social Media Users
(A Putra; U Suhud; AW Handaru) 2. Research methods The research method that the author uses is a quantitative method. The research subjects are
users of the Tikok application in Jakarta. The object under study is the TikTok application. While
the research period is 3 months from October to December 2021. In this study, the scope of
research determined by the researcher is regarding the effect of brand reputation on customer
loyalty, customer satisfaction, and customer commitment and its impact on customer retention. This research was conducted in Jakarta, Indonesia. The choice of the city of Jakarta was based on
the large number of users of the TikTok application in Jakarta. 128 The International Journal of Social Sciences World The number of samples taken in this population is estimated at 313 samples by considering
the number of samples in previous studies. This is based on the consideration of samples that can
provide high accuracy results. So the authors took a sample of 313 research studies. The number of samples taken in this population is estimated at 313 samples by considering
the number of samples in previous studies. This is based on the consideration of samples that can
provide high accuracy results. So the authors took a sample of 313 research studies. p
g
y
p
In this study, the authors calculated the EFA or exploratory factor analysis to determine the
level of validity of each research indicator. By Hair(2018), the loading factor for 313 samples is
0.40. So it is hoped that it will get a better validity value. While the instrument reliability test is a follow-up process after carrying out the validity of
the instrument. A reliable instrument is an instrument which, if used several times to measure the
same object, will produce the same data. Reliability relates to the stability and consistency of the
measuring instrument. By Hair(2018), an instrument can be said to be reliable if there is a
sequence of Cronbach's Alpha values. The value of the level of reliability is indicated from zero to
one. With a standard of reliability that is above 0.7. In this study, researchers used Structural
Equation Modeling data analysis with the AMOS application. q
g
y
pp
Figure 1. Research Model
The picture above shows that the research model adapted to the relationship between
variables resulted in the formulation of a hypothesis. So there are six hypotheses that form the
basis of this research. 2. Research methods So that this research model produces hypotheses that will be tested further. Figure 1. Research Model Figure 1. Research Model Figure 1. Research Model Figure 1. Research Model The picture above shows that the research model adapted to the relationship between
variables resulted in the formulation of a hypothesis. So there are six hypotheses that form the
basis of this research. So that this research model produces hypotheses that will be tested further. The picture above shows that the research model adapted to the relationship between
variables resulted in the formulation of a hypothesis. So there are six hypotheses that form the
basis of this research. So that this research model produces hypotheses that will be tested further. Table 1. Profile of Respondents Respondent Analysis The research that the author conducted shows that there were 321 respondents who filled
out the online survey that the author had distributed to obtain research results. However, there
were eight respondents who did not meet the requirements in this study. So the respondents who
can continue filling out the survey until the end of the survey questions and are declared valid as
respondents to the author's research are 313 respondents or equivalent to 97.51% of respondents
from 321 respondents. Meanwhile, a number of eight respondents or 2.49% of respondents were
declared invalid or could not be used as a reference to continue answering research questions. This study produced a variety of respondents, but based on the table below, it can be seen that
there are balanced results regarding the gender of the respondents. Table 1. Profile of Respondents Table 1. Profile of Respondents Vol. 4 No. 1, January-June 2022, pages: 126~137 TIJOSSW Demographics
Demographics
Frequency
Percentage
Valid
Percentage
Cumulative
Percentage
Gender
Man
158
50.5
50.5
50.5
Woman
155
49.5
49.5
100.0
Age
17-24 years old
172
55.0
55.0
55.0
25-35 years old
140
44.7
44.7
99.7
36-45 years old
1
0.3
0.3
100.0
45 years old
0
0
0
100.0
Education
<high school
5
1.6
1.6
1.6
high school
140
44.7
44.7
46.3
Diploma
8
2.6
2.6
48.9
Bachelor
159
50.8
50.8
99.7
Master/Doctoral
1
0.3
0.3
100.0
Work
Work
187
59.7
59.7
59.7
Not yet working
103
32.9
32.9
92.7
Own your own
business
16
5.1
5.1
97.8
Does not work
7
2.2
2.2
100.0
Marital status
Not married yet
260
83.1
83.1
83.1
Marry
52
16.6
16.6
99.7
Spouse died
1
0.3
0.3
100.0
Separated/divorced
0
0
0
100.0
Total
313
100
100 Based on the answers given by respondents to the research results, there are various answers
to each question. The author found that the level of trust in TikTok is quite high with the
percentage of those who answered agreeing to reach 68.7% or 215 respondents agreeing that
TikTok is a trustworthy application. What is quite interesting is that there are male respondents
or 118 out of 215 respondents who agree that TikTok is a trustworthy application. This shows that
male respondents have a high level of trust compared to female respondents. Strong competition in social media turns out to be an interesting thing in this study. The Role of Brand Reputation on Customer Retention of Social Media Users
(A Putra; U Suhud; AW Handaru) Respondent Analysis Where
only 74 people or 23.6% of respondents answered agree and strongly agree to prioritize TikTok
over other similar applications. A total of 205 respondents or 65.5% of respondents felt somewhat
agree in answering this question. This shows that the competition between social media is quite
high in attracting users. Similar results are also seen in the indicator that notices that users will say positive things
about TikTok to others. Only 37.4% or 114 respondents agreed while 114 respondents or 37.1%
other respondents answered somewhat agree. This shows that the majority of respondents are in
between agree and disagree in their positive confession to tell TikTok to others. The Role of Brand Reputation on Customer Retention of Social Media Users
(A Putra; U Suhud; AW Handaru) 130 The International Journal of Social Sciences World This study shows that 65.5% of respondents or 205 respondents answered agree and strongly
agree that they will continue to use TikTok. The product made by TikTok succeeded in convincing
respondents to believe that they would continue to use it and only 5 respondents or 1.6%
disagreed and strongly disagreed with the statement. Vol. 4 No. 1, January-June 2022, pages: 126~137 Validity test Validity testing is carried out to determine the research indicators have a strong level of
validity. Based on the results of the validity test with SPSS in Table 2, the results of the validity test
are obtained according to the calculation with a loading factor of 0.40 and the number of samples
is 313(Hair et al., 2018). Table 2. Validity Test Results
Brand Reputation
BR1 TikTok is a trustworthy app
0.813
BR2 TikTok has a good reputation
0.579
BR3 TikTok makes a good product
0.716
BR4 TikTok is a reliable app
0.791
BR5 I know how TikTok looks
0.554
Customer Loyalty
CL1 I will recommend TikTok to others
0.754
CL2 I will prioritize TikTok over other similar apps
0.683
CL3 I will say positive things about TikTok to other people 0.791
CL4 I will continue to use TikTok
0.735
CL5 I will continue to use TikTok in the future
0.582
Customer Satisfaction
CS1 I am satisfied with TikTok service
0.771
CS2 TikTok provides the best service
0.682
TikTok CS3 delivers the expected service
0.734
CS4 I am happy with TikTok service
0.718
CS5 I am very satisfied with my experience using TikTok
0.677
Customer Commitment
CC1 TikTok maintains good relationship with users
0.655
CC2 I get a sense of belonging when I use TikTok
0.701
CC3 I have good emotions while using TikTok
0.948
CC4 I'm proud to be a TikTok user
0.860
CC5 I care about the future success of TikTok
0.827 Table 2. Validity Test Results Customer Retention
CR1 I will recommend TikTok to others
0.768
CR2 I will continue to use TikTok in the future
0.559
CR3 I will still choose TikTok over similar apps
0.645
CR4 I will use TikTok over and over
0.668
CR5 I will recommend TikTok to my close relatives
0.769 Based on the results of the table above, each indicator on the variable is declared valid because
it has a value above the loading factor of 0.4. This shows that the research indicators are declared
valid. Reliability Test Reliability test was conducted to determine the level of reliability of the 25 questions with a
standard Cronbach Alpha value > 0.7. Table 3. Reliability Results of 25 items
Case Processing Summary
N
%
Cases
Valid
313
100.0
Excluded
0
.0
Total
313
100.0
Cronbach's Alpha
N of items
0.926
25
Table 3 shows the reliability of 313 respondents, namely 100% of respondents filled in
completely in the case processing summary table. In addition, the reliability statistics table shows
that all question items with a total of 25 questions show a Cronbach Alpha score at a value of 0.926,
which is above the Cronbach Alpha value limit > 0.7. So that it can be stated that all of the question
items are reliable. Table 3. Reliability Results of 25 items
Case Processing Summary
N
%
Cases
Valid
313
100.0
Excluded
0
.0
Total
313
100.0
Cronbach's Alpha
N of items
0.926
25 Table 3. Reliability Results of 25 items
Case Processing Summary
N
%
Cases
Valid
313
100.0
Excluded
0
.0
Total
313
100.0
Cronbach's Alpha
N of items
0.926
25
Table 3 shows the reliability of 313 respondents, namely 100% of respondents filled in
completely in the case processing summary table. In addition, the reliability statistics table shows
that all question items with a total of 25 questions show a Cronbach Alpha score at a value of 0.926,
which is above the Cronbach Alpha value limit > 0.7. So that it can be stated that all of the question
items are reliable. Table 3 shows the reliability of 313 respondents, namely 100% of respondents filled in
completely in the case processing summary table. In addition, the reliability statistics table shows
that all question items with a total of 25 questions show a Cronbach Alpha score at a value of 0.926,
which is above the Cronbach Alpha value limit > 0.7. So that it can be stated that all of the question
items are reliable. Table 3 shows the reliability of 313 respondents, namely 100% of respondents filled in
completely in the case processing summary table. In addition, the reliability statistics table shows
that all question items with a total of 25 questions show a Cronbach Alpha score at a value of 0.926,
which is above the Cronbach Alpha value limit > 0.7. So that it can be stated that all of the question
items are reliable. In Table 5 it can be seen that the overall estimated value has met the standard and the model
can be declared fit. Based on the standard values that have been determined, the results of the
Goodness of Fit analysis are as follows: Reliability Test The Role of Brand Reputation on Customer Retention of Social Media Users
(A Putra; U Suhud; AW Handaru)
Table 4. Variable Reliability
Cronbach's Alpha N of Items
Brand Reputation
0.711
5
Customer Loyalty
0.754
5
Customer Satisfaction
0.738
5
Customer Commitment
0.720
5
Customer Retention
0.712
5 The Role of Brand Reputation on Customer Retention of Social Media Users
(A Putra; U Suhud; AW Handaru) 132 The International Journal of Social Sciences World The reliability table for each variable shows a number above Cronbach's Alpha which is 0.7. All variables show a reliable number value. So this can result in all questionnaire items declared
reliable. In this study, the author analyzed the data using Structural Equation Modeling using the
AMOS application. By using AMOS, the authors modify the indications on the modification indices. After reducing the indicators, the authors modeled the research model with the remaining
indicators according to the following figure: Figure 2. Research fit model
The output on the Fit model has met the requirements that have been determined through the
CFA, namely the P value > 0.05 and CMIN/DF 2.00 as shown in the following table: Figure 2. Research fit model Figure 2. Research fit model Figure 2. Research fit model The output on the Fit model has met the requirements that have been determined through the
CFA, namely the P value > 0.05 and CMIN/DF 2.00 as shown in the following table: The output on the Fit model has met the requirements that have been determined through the
CFA, namely the P value > 0.05 and CMIN/DF 2.00 as shown in the following table: Table 5. Results of CMIN Model Fit
Model
NPAR
CMIN
DF
P
CMIN/DF
Default model
27
48,817
39
0.135
1.252
Saturated model
66
0
0
Independence model
11
1205.089
55
0
21,911 In Table 5 it can be seen that the overall estimated value has met the standard and the model
can be declared fit. Based on the standard values that have been determined, the results of the
Goodness of Fit analysis are as follows: Vol. 4 No. 1, January-June 2022, pages: 126~137 Table 6. Reliability Test Goodness of Fit Analisis Analysis Results
GOF size
Limit Value
Mark
Decision
CMIN/DF
< 2.00
1.252
Good Fit
Goodness of Fit Index (GFI)
0.90
0.973
Good Fit
Root Mean Square (RMR)
0.05
0.028
Good Fit
Root Mean Square Error of Approximation(RMSEA)
0.05
0.028
Close Fit
Normal Fit Index(NFI)
0.90
0.959
Good Fit
Adjust Goodness of Fit Index(AGFI)
0.90
0.954
Good Fit
Incremental Fit Index (IFI)
0.90
0.992
Good Fit
Comparative Fit Index(CFI)
0.90
0.991
Good Fit
Tucker Lewis Index(TLI)
0.90
0.988
Good Fit Table 6. Goodness of Fit Analisis Analysis Results With the fit conditions for each standard and because all the requirements are met for each
standard, the research model is declared good fit for the overall assessment standard. With the fit conditions for each standard and because all the requirements are met for each
standard, the research model is declared good fit for the overall assessment standard. The Role of Brand Reputation on Customer Retention of Social Media Users The Role of Brand Reputation on Customer Retention of Social Media Users
(A Putra; U Suhud; AW Handaru) (A Putra; U Suhud; AW Handaru) Hypothesis testing The hypothesis has a significance value using a standard value of CR > 1.96 and a P value <
0.05, while the strength of the influence can be seen in the estimation table based on Generalized
Least Squares Estimates which is seen in the following table. Table 7. Hypothesis Test Results
Ha
Hypothesis
Estimate
SE
CR
P
Description
H1 BR
→
CL
1.151
0.124
9,260
***
Received
H2 BR
→
CS
0.884
0.084
10,490
***
Received
H3 BR
→
CC
1,456
0.118
12,338
***
Received
H4
CL
→
CR
0.191
0.201
0.949
0.342
Rejected
H5
CS
→
CR
0.145
0.134
1.077
0.281
Rejected
H6
CC
→
CR
0.212
0.090
2,367
0.018
Received Based on table 7 above, it can be concluded that the first hypothesis is that brand reputation
has a positive and significant effect on customer loyalty. This is in accordance with previous
studies(Bontis et al., 2007; Yee & Faziharudean, 2010)which states that brand reputation has an 134 The International Journal of Social Sciences World influence on customer loyalty. This study shows that brand reputation is very important in
determining customer loyalty in using the product. A good reputation of a company will result in
high customer loyalty as well. So this study shows the reputation of the company will affect the
level of loyalty. influence on customer loyalty. This study shows that brand reputation is very important in
determining customer loyalty in using the product. A good reputation of a company will result in
high customer loyalty as well. So this study shows the reputation of the company will affect the
level of loyalty. y
y
The next hypothesis shows that brand reputation has a positive and significant effect on
customer satisfaction. This is in line with previous studies(Gul, 2014; Le-Hoang, 2020; Sengupta
et al., 2014). Overall provides an explanation that the positive significance is seen in the influence
of brand reputation on customer satisfaction. This is also what causes the author's research to
make brand reputation a factor influencing customer satisfaction. In the end, it will result in a good
brand reputation that can result in customer satisfaction in using social media. The third hypothesis is that brand reputation has a positive and significant effect on customer
commitment. This is in accordance with previous studies(Lai, 2019; Su et al., 2016)which shows
that there is a positive significant influence of brand reputation on customer satisfaction. Hypothesis testing So that
brand reputation has a positive effect on customer commitment. This shows that the reputation of
a social media brand will lead to a strong commitment of its users as well. The fourth hypothesis shows that customer loyalty has no positive effect on customer
retention. This result contradicts the research conducted by previous research(Danish et al., 2015;
Lay, 2018). This study did not produce positive and significant results regarding the effect of
customer loyalty on customer retention. So that customer loyalty does not have a significant effect
on customer retention. This shows that user loyalty does not necessarily affect the ability to
survive in using social media. The fifth hypothesis shows that customer satisfaction does not have a positive effect on
customer retention. This result is also contrary to research conducted by previous studies(Ali et
al., 2010; Darzi & Bhat, 2018; Lay, 2018; Nazir et al., 2016; Sari et al., 2018; Simarmata et al., 2017). This study shows that there is no significant effect of customer satisfaction on customer retention. This shows that user satisfaction which still tends to be lacking does not result in the user's ability
to survive in using social media. The sixth hypothesis shows that customer commitment has a positive effect on customer
retention. This research is in accordance with what was done by previous research(Boohene et al.,
2013; Moghadam, 2013). This shows that there is a significant effect of customer commitment on
customer retention. So that it can be seen that the relationship increases in the committed
relationship made by social media users. This causes the ability to survive using the media has also
increased. 4. Conclusion Based on the research that has been done by the author, it shows that the results of the
hypothesis are very diverse. The first hypothesis is that brand reputation has a positive and
significant effect on customer loyalty. This results in the influence of a good reputation will result
in the loyalty of social media users to use it. While the second hypothesis is that brand reputation
has a positive and significant effect on customer satisfaction. This shows that a good reputation on
a brand will result in satisfaction of the social media users. Vol. 4 No. 1, January-June 2022, pages: 126~137 TIJOSSW The third hypothesis is that brand reputation has a positive and significant effect on customer
commitment. This shows that there is a positive influence on the reputation of a brand on the
commitment of social media users. While the fourth hypothesis shows that customer loyalty has
no positive and significant effect on customer retention. This results in customer satisfaction does
not necessarily affect the survival ability of a social media user in using it. The same thing happened with the results of the fifth hypothesis, namely that customer
satisfaction had no positive and significant effect on customer retention. So it can be seen that user
satisfaction does not necessarily lead to the ability to survive in using social media. While the sixth
hypothesis, namely customer commitment has a positive and significant effect on customer
retention. This results in a positive influence on user commitment in determining the survival
ability of social media users. The Role of Brand Reputation on Customer Retention of Social Media Users
(A Putra; U Suhud; AW Handaru) Acknowledgements Thank you to the journal editor who has proposed double-blind reviewers, and therefore, this
manuscript has been reviewed and accepted. 136 The International Journal of Social Sciences World Bibliography Ali, JF, Ali, I., Rehman, K., Yilmaz, AK, & Safwan, N. (2010). Determinants of consumer retention in
cellular industry of Pakistan. African Journal of Business Management, 4(12), 2402–2408. Ali, JF, Ali, I., Rehman, K., Yilmaz, AK, & Safwan, N. (2010). Determinants of consumer retention in
cellular industry of Pakistan. African Journal of Business Management, 4(12), 2402–2408. Appiah-Adu, K. (1999). Marketing effectiveness and customer retention in the service sector. Service
Industries Journal, 19(3), 26–41. https://doi.org/10.1080/02642069900000028 Appiah-Adu, K. (1999). Marketing effectiveness and customer retention in the service sector. Service
Industries Journal, 19(3), 26–41. https://doi.org/10.1080/02642069900000028 Bontis, N., Booker, LD, & Serenko, A. (2007). The mediating effect of organizational reputation on
customer loyalty and service recommendation in the banking industry. Management Decisions,
45(9), 1426–1445. https://doi.org/10.1108/00251740710828681 ( )
p //
g/
/
Boohene, R., Agyapong, GKQ, & Gonu, E. (2013). Factors influencing the retention of customers of
Ghana commercial bank within the Agona Swedru Municipality. International Journal of
Marketing Studies, 5(4). https://doi.org/10.5539/ijms.v5n4p82 Comer, DE (2019). The internet book: Everything you need to know about computer networking and
how the internet works (5th ed.). Florida: CRC Press. Danish, RW, Ahmad, F., Ateeq, A., Yasir Ali, H., & Afzal Humayon, A. (2015). Factors affecting customer
retention in telecom sector of Pakistan. American Journal of Marketing Research, 1(2), 28–36. Darzi, MA, & Bhat, SA (2018). Personnel capability and customer satisfaction as predictors of
customer retention in the banking sector: A mediated-moderation study. International Journal
of Bank Marketing, 36(4), 663–679. https://doi.org/10.1108/IJBM-04-2017-0074 g,
( ),
p //
g/
/ J
Dijkmans, C., Kerkhof, P., & Beukeboom, CJ (2015). A stage to engage: Social media use and corporate
reputation. Tourism Management, 47, 58–67. https://doi.org/10.1016/j.tourman.2014.09.005
Gul, R. (2014). The relationship between reputation, customer satisfaction, trust, and loyalty. Journal Dijkmans, C., Kerkhof, P., & Beukeboom, CJ (2015). A stage to engage: Social media use and corporate
reputation. Tourism Management, 47, 58–67. https://doi.org/10.1016/j.tourman.2014.09.005 Gul, R. (2014). The relationship between reputation, customer satisfaction, trust, and loyalty. Journal
of
Public
Administration
and
Governance,
4(3),
368–387. https://doi.org/10.5296/jpag.v4i3.6678 Hair, JF, Black, WC, Babin, BJ, & Anderson, RE (2018). Multivariate Data Analysis (8th ed.). Hampshire:
Pearson. https://doi.org/10.1002/9781119409137.ch4 Harrison-Walker, LJ (2001). The measurement of word-of-mouth communication and an
investigation of service quality and customer commitment as potential antecedents. Journal of
Service Research, 4(1), 60–75. Harrison-Walker, LJ (2001). The measurement of word-of-mouth communication and an
investigation of service quality and customer commitment as potential antecedents. Journal of
Service Research, 4(1), 60–75. Bibliography ( )
Lai, IKW (2019). Hotel image and reputation on building customer loyalty: An empirical study in
Macau. Journal
of
Hospitality
and
Tourism
Management,
38(1),
111–121. https://doi.org/10.1016/j.jhtm.2019.01.003 Lai, IKW (2019). Hotel image and reputation on building customer loyalty: An empirical study in
Macau. Journal
of
Hospitality
and
Tourism
Management,
38(1),
111–121. https://doi.org/10.1016/j.jhtm.2019.01.003 p //
g/
/j j
Lay, E. (2018). Factors affecting customer retention in the banking sector (Study on BRI customers in
East Nusa Tenggara, Indonesia). 10(12), 31–41. Le-Hoang, PV (2020). Factors affect customer satisfaction: The case of cargo delivery services. Independent
Journal
of
Management
&
Production,
11(4),
1342–1356. https://doi.org/10.14807/ijmp.v11i4.1103 Le-Hoang, PV (2020). Factors affect customer satisfaction: The case of cargo delivery services. Independent
Journal
of
Management
&
Production,
11(4),
1342–1356. https://doi.org/10.14807/ijmp.v11i4.1103 g
Moghadam, M. (2013). Determinants of customer retention: Offering a model to the banking industry. Journal of Applied Business and Finance Researches, 2(3), 76–81. Moghadam, M. (2013). Determinants of customer retention: Offering a model to the banking industry. Journal of Applied Business and Finance Researches, 2(3), 76–81. Nazir, B., Ali, M., & Jamil, M. (2016). The impact of brand image on the customer retention: A mediating
role of customer satisfaction in Pakistan. International Journal of Business and Management
Invention, 5(3), 56–61. Nazir, B., Ali, M., & Jamil, M. (2016). The impact of brand image on the customer retention: A mediating
role of customer satisfaction in Pakistan. International Journal of Business and Management
Invention, 5(3), 56–61. ( )
Sari, SW, Sunaryo, & Mugiono. (2018). The effect of service quality on customer retention through
commitment and satisfaction as mediation variables in Java Eating Houses. Journal of Applied
Management, 16(4), 593–604. ( )
Sari, SW, Sunaryo, & Mugiono. (2018). The effect of service quality on customer retention through
commitment and satisfaction as mediation variables in Java Eating Houses. Journal of Applied
Management, 16(4), 593–604. Vol. 4 No. 1, January-June 2022, pages: 126~137 TIJOSSW Schroeder, R. (2018). Social Theory after the Internet: Media, Technology and Globalization (1st ed.). London: UCL Press. Sengupta, AS, Balaji, MS, & Krishnan, BC (2014). How customers cope with service failure? A study of
brand reputation and customer satisfaction. Journal of Business Research, 68(3), 665–674. https://doi.org/10.1016/j.jbusres.2014.08.005 Simarmata, J., Keke, Y., Veronica, Silalahi, SA, & Benkova, E. (2017). How to establish customer trust
and retention in a highly competitive airline business. Polish Journal of Management Studies,
16(1), 202–214. The Role of Brand Reputation on Customer Retention of Social Media Users
(A Putra; U Suhud; AW Handaru) Schroeder, R. (2018). Social Theory after the Internet: Media, Technology and Globalization (1st ed.).
London: UCL Press. Bibliography https://doi.org/10.17512/pjms.2017.16.1.17 Su, L., Swanson, SR, Chinchanachokchai, S., Hsu, MK, & Chen, X. (2016). Reputation and intentions: The
role of satisfaction, identification, and commitment. Journal of Business Research, 69(9), 3261–
3269. https://doi.org/10.1016/j.jbusres.2016.02.023 Ting, OS, Ariff, MSM, Zakuan, N., Sulaiman, Z., & Saman, MZM (2016). E-service quality, e-satisfaction
and e-loyalty of online shoppers in business to consumer market; evidence form Malaysia. IOP
Conference Series: Materials Science and Engineering, 131(1). https://doi.org/10.1088/1757-
899X/131/1/012012 Yang, Z., & Peterson, RT (2004). Customer perceived value, satisfaction, and loyalty: The role of
switching
costs. Psychology
and
Marketing,
21(10),
799–822. https://doi.org/10.1002/mar.20030 Yee, BY, & Faziharudean, TM (2010). Factors affecting customer loyalty of using internet banking in
Malaysia. Journal
of
Electronic
Banking
Systems,
2010,
1–22. https://doi.org/10.5171/2010.592297 Yee, BY, & Faziharudean, TM (2010). Factors affecting customer loyalty of using internet banking in
Malaysia. Journal
of
Electronic
Banking
Systems,
2010,
1–22. https://doi.org/10.5171/2010.592297
|
https://openalex.org/W2944813678
|
https://europepmc.org/articles/pmc6818181?pdf=render
|
English
| null |
Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name
|
Genomics, Proteomics & Bioinformatics/Genomics, proteomics and bioinformatics
| 2,019
|
cc-by
| 10,651
|
Warburg Effects in Cancer and Normal
Proliferating Cells: Two Tales of the Same Name Huiyan Sun 1,2,3,a, Liang Chen 4,b, Sha Cao 3,5,c, Yanchun Liang 2,6,d, Huiyan Sun 1,2,3,a, Liang Chen 4,b, Sha Cao 3,5,c, Yanchun Liang 2,6,d, Ying Xu 1,2,3,*,e 1 The China-Japan Union Hospital, Jilin University, Changchun 130033, China 1 The China-Japan Union Hospital, Jilin University, Changchun 130033, China
2 MOE Key Laboratory of Symbolic Computation and Knowledge Engineering, College of Computer Science and Technology,
Jilin University, Changchun 130012, China
3 Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics,
University of Georgia, Athens, GA 30602, USA
4 Faculty of Health Sciences, University of Macau, Taipa, Macau SAR 999078, China
5 Department of Biostatistics, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
6 Zhuhai Laboratory of MOE Key Laboratory of Symbolic Computation and Knowledge Engineering, Zhuhai College of
Jilin University, Zhuhai 519041, China p
p
,
y,
g
,
2 MOE Key Laboratory of Symbolic Computation and Knowledge Engineering, College of Computer Science and Technology,
Jilin University, Changchun 130012, China Faculty of Health Sciences, University of Macau, Taipa, Macau SAR 999078, China Department of Biostatistics, School of Medicine, Indiana University, Indianapolis, IN 46202, USA 6 Zhuhai Laboratory of MOE Key Laboratory of Symbolic Computation and Knowledge Engineering, Z
Jilin University, Zhuhai 519041, China Received 18 July 2018; revised 19 November 2018; accepted 21 December 2018
Available online 7 May 2019 Handled by Jun Yu KEYWORDS
Cancer;
Warburg effect;
Fenton reaction;
Cell proliferation;
pH homeostasis KEYWORDS
Cancer;
Warburg effect;
Fenton reaction;
Cell proliferation;
pH homeostasis Abstract
It has been observed that both cancer tissue cells and normal proliferating cells (NPCs)
have the Warburg effect. Our goal here is to demonstrate that they do this for different reasons. To
accomplish this, we have analyzed the transcriptomic data of over 7000 cancer and control tissues of
14 cancer types in TCGA and data of five NPC types in GEO. Our analyses reveal that NPCs accu-
mulate large quantities of ATPs produced by the respiration process before starting the Warburg
effect, to raise the intracellular pH from 6.8 to 7.2 and to prepare for cell division energetically. Once cell cycle starts, the cells start to rely on glycolysis for ATP generation followed by ATP
hydrolysis and lactic acid release, to maintain the elevated intracellular pH as needed by cell divi-
sion since together the three processes are pH neutral. Genomics Proteomics Bioinformatics 17 (2019) 273–286 Genomics Proteomics Bioinformatics 17 (2019) 273–286 Genomics Proteomics Bioinformatics Abstract
It has been observed that both cancer tissue cells and normal proliferating cells (NPCs)
have the Warburg effect. Our goal here is to demonstrate that they do this for different reasons. To
accomplish this, we have analyzed the transcriptomic data of over 7000 cancer and control tissues of
14 cancer types in TCGA and data of five NPC types in GEO. Our analyses reveal that NPCs accu-
mulate large quantities of ATPs produced by the respiration process before starting the Warburg
effect, to raise the intracellular pH from 6.8 to 7.2 and to prepare for cell division energetically.
Once cell cycle starts, the cells start to rely on glycolysis for ATP generation followed by ATP
hydrolysis and lactic acid release, to maintain the elevated intracellular pH as needed by cell divi-
sion since together the three processes are pH neutral. The cells go back to the normal respiration-
based ATP production once the cell division phase ends. In comparison, cancer cells have reached
their intracellular pH at 7.4 from top down as multiple acid-loading transporters are up-regulated https://doi.org/10.1016/j.gpb.2018.12.006
1672-0229 2019 The Authors. Published by Elsevier B.V. and Science Press on behalf of Beijing Institute of Genomics, Chinese Academy of Sciences, and
Genetics Society of China.
This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Introduction Fenton reactions result from
local iron accumulation and elevated H2O2 concentration
due to increased local populations of innate immune cells,
specifically neutrophil and macrophages. We predict that can-
cer cells of all the 14 cancer types examined have such reac-
tions persistently using superoxide (O
2 ), produced by local
innate immune cells and the host cells’ mitochondria, as the
key reducing element of Fe
3+. We have further shown that
OH produced by such reactions would ultimately overwhelm
the cytosolic pH buffer, and hence drive up the intracellular
pH. As response, various processes are induced to acidify the
intracellular space to maintain the acid-base homeostasis [16]. We have predicted that glycolytic ATP synthesis represents
a key responding process for acidifying the intracellular pH,
since
glycolytic
ATP
synthesis
is
pH
neutral,
while
respiration-based ATP production consumes one proton per
ATP and hydrolysis of any ATP releases one proton [17]. That
is, synthesis of each glycolytic ATP releases one net proton
when it is consumed while a respiration-synthesized ATP will
be neutral when the ATP is hydrolyzed. In addition, it is also
known that the level of glycolysis correlates strongly with the
level of the predicted cytosolic Fenton reaction [16]. In contrast, NPCs generate ATPs through the respiration
pathway and accumulate ATPs before cell proliferation. NPCs
will partially switch to glycolytic ATP production when suffi-
ciently large numbers of ATPs are intracellularly accumulated,
hence driving up the intracellular pH as well as preparing for
cell division energetically. During proliferation, consumption
of an ATP leads to the release of a proton, coupled with the
lactate generated from pyruvate at the end of glycolysis. There-
fore, serving two purposes, that is, to maintain the raised pH
level needed for proliferation and replenish each consumed
ATP. We have approached this problem from the perspective of
intracellular acid-base homeostasis. It is known that healthy
human epithelial cells have a mildly acidic intracellular pH
at 6.8 and a basic extracellular pH at 7.2, while cancer cells
have reversed these pH levels with intracellular pH at 7.2–7.4
[14] and extracellular pH at 6.6–6.8 [15]. Introduction metabolic processes that continuously produce alkaline mole-
cules, since that the gradient-driven lactic acid exporters can-
not accomplish the reversal between the intracellular and
extracellular pH levels, at least not by the transporters alone. Otto Warburg published his seminal paper in 1927 on the
observation that cancer cells tend to allocate substantial frac-
tions of glucose to glycolytic ATP production followed by lac-
tate generation rather than by the TCA cycle and the
respiration chain regardless of the O2 level, which is referred
to as the Warburg effect [1] and serves as the basis for PET/
CT based cancer detection. This observation has perplexed
generations of cancer researchers, since the respiration path-
way is considerably more efficient for ATP generation than
glycolysis, with the former producing 36 ATPs and the latter
producing 2 ATPs per glucose. Multiple hypotheses have been
put forward about why cancer cells do this as follows. (1) Can-
cer cells may have dysfunctional mitochondria, which was later
proved to be incorrect [2–4]. (2) The glycolytic pathway is fas-
ter than the respiration pathway for synthesizing the same
number of ATPs from glucose, hence selected to support the
rapid cell proliferation in cancer [5]; but this view is challenged
as ATP is shown to be not a rate-limiting factor in cancer pro-
liferation [6]. (3) Cancer cells have reduced mitochondrial
activities due to hypoxia, partially because of the increased
generation of reactive oxygen species (ROS) [7] and nitric
oxide production [8]; however, cancer cells are known to have
respiration activities across different cancer types and high
levels of such activities are reported in some cancers [9]. (4)
Cancer cells are lack of NAD+, hence using the conversion
of pyruvate to lactate for NAD+ production [5], which was
argued against since most of the relevant carbons were
excreted, hence there is no net NAD+ production [10]. And
(5) Warburg effect is a common characteristic of all proliferat-
ing cells, including cancer cells and NPCs [5]. While other
hypotheses are largely considered as unacceptable [11], the last
one has gained popularity in the past few years [12,13], which
we address here. We have recently predicted [16], through mining cancer
tissue transcriptomic data and mathematical modeling, that
cancer cells have Fenton reactions: Fe
2+ + H2O2 ? Fe
3+ +
OH + OH in their cytosol. Introduction To understand how
cancer cells have reversed the intracellular and extracellular
pH levels, we have examined the gene expression levels of all
H+, OH and HCO3
related plasma-membrane transporters
across 14 cancer types, which include all the cancer types in
the TCGA database with sufficiently large numbers (at least
10) of cancer tissues. To our surprise, we note that all cancer
cells consistently up-regulate the expressions of multiple acid-
loading transporters and repress the expressions of most
acid-extruding transporters except for the lactic acid exporters
throughout the progression of the cancers examined. This
strongly suggests that there must be some unidentified Warburg Effects in Cancer and Normal
Proliferating Cells: Two Tales of the Same Name The cells go back to the normal respiration-
based ATP production once the cell division phase ends. In comparison, cancer cells have reached
their intracellular pH at 7.4 from top down as multiple acid-loading transporters are up-regulated * Corresponding author. E-mail: xyn@uga.edu (Xu Y). a ORCID: 0000-0002-4664-7147. b ORCID: 0000-0001-6644-477X. c ORCID: 0000-0002-8645-848X. d ORCID: 0000-0002-1147-3968. e ORCID: 0000-0002-7856-3343. Peer review under responsibility of B
https://doi.org/10.1016/j.gpb.2018.12.0
1672-0229 2019 The Authors. Publis
Genetics Society of China. This is an open access article under the * Corresponding author. E-mail: xyn@uga.edu (Xu Y). a ORCID: 0000-0002-4664-7147. b ORCID: 0000-0001-6644-477X. c ORCID: 0000-0002-8645-848X. d ORCID: 0000-0002-1147-3968. e ORCID: 0000-0002-7856-3343. b ORCID: 0000-0001-6644-477X. c ORCID: 0000-0002-8645-848X. d ORCID: 0000-0002-1147-3968. e ORCID: 0000-0002-7856-3343. 0000 0002 7856 3343. nder responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. https://doi.org/10.1016/j.gpb.2018.12.006 018.12.006
. Published by Elsevier B.V. and Science Press on behalf of Beijing Institute of Genomics, Chinese Academy of Sciences, and https://doi.org/10.1016/j.gpb.2018.12.006
1672-0229 2019 The Authors. Published by Elsevier B.V. and Science Press on behalf of Beijing Institute of Genomics, Chinese Academy of Sciences, and
Genetics Society of China. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). https://doi.org/10.1016/j.gpb.2018.12.006
1672-0229 2019 The Authors. Published by Elsevier B.V. and Science Press on behalf of Beijing Institute of Genomics, C
Genetics Society of China. 274 Genomics Proteomics Bioinformatics 17 (2019) 273–286 and most acid-extruding ones except for lactic acid exporters are repressed. Cancer cells use
continuous glycolysis for ATP production as way to acidify the intracellular space since the lactic
acid secretion is decoupled from glycolysis-based ATP generation and is pH balanced by increased
expressions of acid-loading transporters. Co-expression analyses suggest that lactic acid secretion is
regulated by external, non-pH related signals. Overall, our data strongly suggest that the two cell
types have the Warburg effect for very different reasons. and most acid-extruding ones except for lactic acid exporters are repressed. Cancer cells use
continuous glycolysis for ATP production as way to acidify the intracellular space since the lactic
acid secretion is decoupled from glycolysis-based ATP generation and is pH balanced by increased
expressions of acid-loading transporters. Co-expression analyses suggest that lactic acid secretion is
regulated by external, non-pH related signals. Warburg Effects in Cancer and Normal
Proliferating Cells: Two Tales of the Same Name Overall, our data strongly suggest that the two cell
types have the Warburg effect for very different reasons. Acid-extruding transporter genes (ii) the proportion of the glycolytic flux via pyruvate kinase
(PK, encoded by PKM) into the TCA cycle via pyruvate
dehydrogenase (PDH, encoded by PDHB) decreases in can-
cer tissues (and activated NPC cells) in comparison to con-
trols. Here, we use the normalized expression of PDHB
against that of PKM as an approximation to the fraction
of the metabolic efflux out of PK into the TCA cycle via
PDH. Among the four groups of acid-extruding transporter genes,
SLC4A4/9 are down-regulated or show no changes in their
expressions across all cancer types except for PRAD with
SLC4A4 being up-regulated. In comparison, these genes show
no changes or are up-regulated in their expressions in all the
activated NPCs vs. the controls except for iPSC and effector
T cell, in which SLC4A4 and SLC4A9 are down-regulated,
respectively. We note that the expression of LDHA is up-regulated in the
cancer tissues of all 14 cancer types examined except for LIHC
(Figure S1). In addition, the expression of either SLC16A1 or
SLC16A3 is up-regulated in the cancer tissues of all 14 cancer
types except for COAD (see Materials and Methods for defini-
tion), which is known to have weak Warburg effect and hence
generally not detected via PET/CT. In addition, the relative
ratio of PDHB/PKM decreases in cancer tissues across differ-
ent stages in comparison to the controls. Similarly, we found
increased expression of SLC16A1 and LDHA (or LDHB) in
all the five NPC types (Figure S2). However, the relative
PDHB/PKM ratio is reduced only in CD4+ T cells and effec-
tor T cells but remains comparable in the other three cell types
in comparison to the matched controls. Hence, we predict that
all the cancer types and the NPCs under consideration have
the Warburg effect. For SLC9A2, 3, 4, 9, they are mostly down-regulated in
cancer vs. controls, mostly by SLC9A9 and SLC9A2, while
majority of these genes show no changes in their expressions
in the activated NPCs vs. controls. SLC26A9 is predominantly down-regulated in cancer, and
has no change in NPCs. The only group of genes considered here has the same
behaviors between cancer vs. NPCs is SLC16A1/3, with their
expressions up-regulated in both cancer and the activated
NPCs. In sum, expressions of the acid-loading transporter genes are
largely up-regulated, whereas expressions of the acid-extruding
transporter genes are down-regulated in cancer vs. controls
except for SLC16A1/3. Opposite behaviors of pH-related transporters in cancer vs. NPCs We have examined the gene expression levels of all the selected
pH-related plasma-membrane transporters in cancer and in
NPCs (see Materials and methods). We now go through the
key differences between the expression patterns of these genes
in groups in cancer vs. NPCs, with the detailed comparisons
given in Figure 1. Note that in the following, the first three
groups of genes are acid-loading transporter genes, and the
next four are acid-extruding ones. A natural question would be: how can cancer cells maintain
a basic intracellular pH when they are continuously acidified
by powerful transporters? First, we posit that SLC16A1/3
are not the reason since they are driven by proton gradients,
hence impossible for them to reverse the intracellular and
extracellular pH. More importantly, there are numerous up-
regulated acid-loading transporters with comparable expres-
sion levels (Figure 1), and multiple such transporters have
higher Vmax values than SLC16A1/3. For instance, the Vmax
of V-ATPase is 3–4 orders of magnitude higher (40 nmol/
min/mg) [20] than that of SLC16A1/3 (63.0 pmol/min/mg)
[21]. These data indicate that the acidification rate is substan-
tially higher than the alkalinization rate by these transporters. Acid-extruding transporter genes For the acid-loading transporter genes,
NPCs generally show the opposite gene-expression patterns to
those in cancer while the acid-extruding transporters mostly
show no changes in their expressions. Hence we conclude that
cancer cells use the transporters under consideration to acidify
their intracellular pH while NPCs alkalinize it. Given that both
cancer and NPCs have comparable intracellular pH level
[14,19], we infer that cancer cells reach their pH level from
above while NPCs get there from below. Warburg effects in cancer vs. in activated NPC samples We have used the following criteria to determine if a cancer
tissue (and a NPC sample) has the Warburg effect: (i)
Expressions of the genes encoding lactate dehydrogenase
unit A or B, LDHA or LDHB, and of the genes encoding
the main lactic acid exporters, SLC16A1 or SLC16A3, are
considerably up-regulated (fold change >2) in cancer tissue
(and activated NPC cells) in comparison to the controls; and 275 Sun H et al / Warburg Effects in Cancer vs. Normal Proliferating Cells Acid-extruding transporter genes Acid-loading transporter genes Among the acid-loading transporter genes, the expressions of
SLC4A1AP, SLC4A2, and SLC4A3 are up-regulated or
remain unaltered in cancer tissues vs. controls across most of
the 14 cancer types. In comparison, the expressions of these
genes are mostly down-regulated or remain unchanged across
all the NPCs except for SLC4A1AP, which is up-regulated in
iPSC. Actually cancer tissue cells are known to utilize a number of
other metabolic processes to acidify their intracellular space. These include: (i) diffusion of fatty acids from blood circula-
tion into cancer cells, hence acidifying the intracellular space
since their pKa values are approximately 4.5 [22], lower than
the intracellular pH; (ii) diffusion of NH3 out of cancer cells
into blood circulation [23], thus making the intracellular pH
more acidic, knowing that its pKa is 9.26 [22]; (iii) biosynthesis
and deployment of large quantities of sialic acids and ganglio-
sides [24], making the intracellular pH more acidic [25]; and
(iv) glycolytic ATP production (see the next section). The expression of SLC26A6 is up-regulated or remains the
same in 11 of the 14 cancer types except for COAD, KIRC,
and KIRP. In comparison, the expression of SLC26A6 is not
changed in the activated NPC samples vs. controls except for
the iPSC samples. For the ATP6V genes, we have considered the expressions
of ATP6V0B and ATP6V0C since their protein products are
known to be localized in plasma membrane and have the same
expression by definition. Table S1 shows the subcellular loca-
tions for the ATP6V0 protein products predicted by Gene-
cards [18], and Table S2 gives the predicted ATP6V0B
expressions in both cancers and NPCs. We can see from the
table that the gene is up-regulated across all cancer types
except for KIRC and KIRP; and it has no change or is
down-regulated in its expressions across all the NPC samples
in the activated state vs. the control. All these data strongly suggest one possibility that there are
unknown metabolic processes that continuously produce alka-
line molecules inside cancer cells, which may have triggered all
the above processes to continuously acidify the intracellular
space to keep the cells viable. Genomics Proteomics Bioinformatics 17 (2019) 273–286 276 gure 1
Heatmaps for differential expressions of the selected transporter genes
he first zone is for acid-loading transporters, the second for acid-extruding transporters, and the last for lactate acid ext
ansporters. Fenton reactions in cancer cells and their impact on intracellular
pH acid-loading transporter genes and simultaneously negatively
with those of the acid-extruding ones for each cancer type. Table S5 lists the pathways enriched by such genes for each
cancer type, with the detailed enrichment procedure given
in File S1. Functional analyses reveal that these pathways lar-
gely fall into four categories: (1) cell proliferation and devel-
opment; (2) macromolecular damages and degradation; (3)
immune activities; and (4) stress response. These results point
to the possibility that the behaviors of the transporters might
be relevant to cytosolic Fenton reactions since as we previ-
ously shown [16] and outlined in the previous section that
(i) Fenton reactions are the results of immune response to
persistent irritations at the disease sites; and (ii) cytosolic
Fenton reactions damage intracellular macromolecules by
their OH, and drive cell division by the persistent nucleotide
synthesis induced as response to continuous production of
OH [16]. We have recently build a computational model based on gene
expression data of cancer vs. control tissues of all the 14 cancer
types examined in this study, to demonstrate that all cancer tis-
sue cells have Fenton reactions in their cytosol [16]. We outline
the general idea of the study, for readers’ convenience. It has been widely observed that cancer tends to be associ-
ated with chronic inflammation [26], which will give rise to ele-
vated H2O2 level [27]. In addition, it has also been widely noted
that cancer tends to have local accumulation of iron [28]. The
combination of the two will result in an inorganic chemical
reaction,
called
Fenton
reaction:
Fe
2+ + H2O2 ? Fe
3+ +
OH + OH. Multiple authors have reported the observation
of Fenton reactions in cancer across numerous cancer types
[28,29]. In our previous study, we have predicted that cancer
cells generally use superoxide (O
2 ) as the reducing molecule
to convert Fe
3+ to Fe
2+, produced predominantly by local
innate immune cells including neutrophil and macrophages
[16]. This will lead to persistent Fenton reaction, which can
be rewritten as Furthermore analyses have revealed that these transporter
genes indeed strongly correlate genes/pathways used to define
cytosolic Fenton reactions as detailed in Table S6 and Figure 2. Fenton reactions in cancer cells and their impact on intracellular
pH Specifically, as shown in Figure 2, the expressions of protea-
some (PSM) genes, one of the three gene groups used to define
Fenton reaction (see later discussion of this section) positively
correlate with those of the acid-loading transporter genes and
negatively correlate with those of the acid-extruding trans-
porter genes across all 14 cancer types. By these and the above
paragraph, we predict the behaviors of these transporters are
related to the OH produced by Fenton reactions. In contrast,
the above correlations do not exist for NPC samples, as
detailed in Table S7. O
2 þ H2O2 ! OH þ OH þ O2 (also known as Haber-Weiss reaction) with Fe2+ as the cata-
lyst and not consumed, where Fe2+ could be in iron-sulfur
clusters or labile-iron pool [30]. Essentially, the reaction con-
tinuously produce OH and OH, fueled by O
2 and H2O2 gen-
erated predominantly by local immune cells and catalyzed
intracellular Fe2+. Interestingly, the correlation between PKM and SLC16A1
in cancers is considerably weaker than it in NPCs as shown
in Figure 3A and Figure S3, hence suggesting that the role of
SLC16A1 might be different from the other pH-related
transporters. Knowing that OH can only be produced intracellularly by
Fenton reactions when cells are not exposed to radiation [31],
we have predicted if a cell harbors Fenton reaction in its cyto-
sol if the quantities on two sides of the above chemical reaction
strongly correlate with each other, given the level of Fe2+,
specifically between [OH vs: ½H2O2; ½O
2 and ½Fe2þ, where
[X] represents the quantity of X. The rationale is that (1) we
have observed that each of these quantities can be reliably esti-
mated using the expressions of selected genes; and (2) the level
of correlation between the two sides is highly consistent with
the level of Fenton reaction [16]. File S1 and Table S3 show
the statistical correlation between the two sides for all the can-
cer tissues of the 14 cancer types considered in our study [16]. Based on the data, we predict that all the cancer tissues have
Fenton reactions in their cytosol. We now show statistically that glycolytic ATP production
is also relevant to cytosolic Fenton reactions. Fenton reactions in cancer cells and their impact on intracellular
pH To accomplish
this, we have calculated correlations between the level of gly-
colytic ATP production as reflected by the expression of
PKM and (i) the level of protein damage as reflected by the
expression of the PSM genes, (ii) the level of iron uptake rep-
resented by the expressions of TFRC (transferrin receptor) and
TFR2, and (iii) the intracellular H2O2 level reflected by the
expressions of TXN (thioredoxin), TXN2, GCLC (glutamate-
cysteine ligase catalyst) and GCLM, respectively, with detailed
results shown in Figure 3B. Note that the three groups of genes
(i–iii) are used for establishing cytosolic Fenton reactions [16]. Hence, we conclude that the level of glycolytic ATP produc-
tion strongly correlates with the level of Fenton reaction. In addition, we have also shown that Fenton reaction-
produced OH can overwhelm the cytosolic pH buffer within
a relatively short amount of time [16]. Then a range of pro-
cesses is triggered to acidify the intracellular space, including
the transporters under study, thus keeping its pH from becom-
ing too high, since changes in intracellular pH can alter the
whole biochemistry in a fundamental manner. In comparison,
we predict that the activated NPCs have no or slight Fenton
reactions based on data given in Table S4. To see how glycolytic ATP production may be relevant to
cytosolic pH, we note that the production of an ATP by respi-
ration: ADP3 + HPO4
2 ? ATP4 + OH consumes one
proton,
while
ATP
generation
by
glycolysis:
glucose +
2ADP3 + 2HPO4
2 ? 2 lactate + 2 ATP4 is pH neutral
[17]. And
hydrolysis
of
any
ATP:
ATP4 + H2O ? ADP3 + HPO4
2 + H+ releases one proton. Hence, we con-
clude that glycolytic ATP production generates one net H+ for
ATP when the ATP is hydrolyzed while in comparison, respi-
ration based ATP production is pH neutral when the ATP is
consumed. Acid-loading transporter genes Gene expression levels are indicated with FPKM presented as log2FC, with log2FC > 0.6 for up-regulated gen
g2FC < 0.6 for down-regulated genes. FC, fold change. 76
Genomics Proteomics Bioinformatics 17 (2019) 273–286 Figure 1
Heatmaps for differential expressions of the selected transporter genes
The first zone is for acid-loading transporters, the second for acid-extruding transporters, and the last for lactate acid extruding
transporters. Gene expression levels are indicated with FPKM presented as log2FC, with log2FC > 0.6 for up-regulated genes and
log2FC < 0.6 for down-regulated genes. FC, fold change. ferential expressions of the selected transporter genes Figure 1
Heatmaps for differential expressions of the selected transporter genes
The first zone is for acid-loading transporters, the second for acid-extruding transporters, and the last for lactate acid extruding
transporters. Gene expression levels are indicated with FPKM presented as log2FC, with log2FC > 0.6 for up-regulated genes and
log2FC < 0.6 for down-regulated genes. FC, fold change. Sun H et al / Warburg Effects in Cancer vs. Normal Proliferating Cells 277 Increased glycolytic ATP production is a response to cytosolic
Fenton reactions Normal Proliferating Cells 279 We find that the most enriched pathways are involved in the
biological processes related to immune system, cell cycle, and
response to stress (Figure 4) hence suggesting that the secre
fore, we conclude that lactic acid secretion by SLC16A1 is
most likely not related to intracellular pH homeostasis, instead
it serves a protective role for cancer
Figure 3
Correlations between Fenton reaction level and ATP production genes
A. Correlation between PKM and one acid-loading and two acid-extruding transporter genes: SLC4A3, SLC4A4, and SLC9A9,
SLC16A1, and SLC16A3. ‘‘” represents the lack of the significant correlation. B. Pearson correlation between glycolytic ATP
production genes (PKM and PGK1) and genes reflecting the levels of cytosolic Fenton reactions (proteasome genes, iron uptake genes and
H2O2 related genes in Table S6) in cancer. Figure 3
Correlations between Fenton reaction level and ATP production genes g
p
g
A. Correlation between PKM and one acid-loading and two acid-extruding transporter genes: SLC4A3, SLC4A4, and SLC9A9,
SLC16A1, and SLC16A3. ‘‘” represents the lack of the significant correlation. B. Pearson correlation between glycolytic ATP
production genes (PKM and PGK1) and genes reflecting the levels of cytosolic Fenton reactions (proteasome genes, iron uptake genes and
H2O2 related genes in Table S6) in cancer. fore, we conclude that lactic acid secretion by SLC16A1 is
most likely not related to intracellular pH homeostasis, instead
it serves a protective role for cancer. We find that the most enriched pathways are involved in the
biological processes related to immune system, cell cycle, and
response to stress (Figure 4), hence suggesting that the secre-
tion of the lactic acid might be regulated by external signals. This observation is consistent with previous studies suggesting
that expression of SLC16A1 is regulated by hypoxia [32], hya-
luronic acid receptor CD44 [33], and local stromal cells [33] in
cancer. Increased glycolytic ATP production is a response to cytosolic
Fenton reactions To pin down the possible reasons for the observed behaviors of
the transporters in the first Results section, we searched for
genes whose expressions correlate positively with those of the By integrating all the above results, we predict that gly-
colytic ATP biosynthesis is a cellular response to the persistent Genomics Proteomics Bioinformatics 17 (2019) 273–286 278 OH production by cytosolic Fenton reactions across all 14
cancer types. remain viable? To address this issue, we have conducted co
lation analyses between the expression levels of SLC16A1
Figure 2
Co-expression of proteasome (PSM) genes and acid-loading or acid-extruding transporter genes in 14 cancer types and NP
Co-expression was measured using Pearson correlation coefficient. The positive and negative correlations are indicated in green and b
respectively, with the size of each square representing the correlation level. Proteasome genes is given in Table S6. 278
Genomics Proteomics Bioinformatics 17 (2019) 273–286 Figure 2
Co-expression of proteasome (PSM) genes and acid-loading or acid-extruding transporter genes in 14 cancer types and NPCs
Co-expression was measured using Pearson correlation coefficient. The positive and negative correlations are indicated in green and black,
respectively, with the size of each square representing the correlation level. Proteasome genes is given in Table S6. Figure 2
Co-expression of proteasome (PSM) genes and acid-loading or acid-extruding transporter genes in 14 cancer types and NPCs
Co-expression was measured using Pearson correlation coefficient. The positive and negative correlations are indicated in green and black,
respectively, with the size of each square representing the correlation level. Proteasome genes is given in Table S6. OH production by cytosolic Fenton reactions across all 14
cancer types. remain viable? To address this issue, we have conducted corre-
lation analyses between the expression levels of SLC16A1 and
all the up-regulated genes in each cancer type, followed by
pathway-enrichment analyses of these genes. We have then
examined the 100 most enriched pathways in each cancer type. One puzzling issue remains: why do cancer cells secrete lac-
tic acids (lactate + proton) when they face a major challenge
to keep the intracellular pH from becoming too alkaline to Sun H et al / Warburg Effects in Cancer vs. Glycolytic ATP synthesis maintains the elevated intracellular
pH during NPC proliferation To understand the functional roles of glycolytic ATP produc-
tion followed by lactic acid secretion in NPCs, we have per-
formed correlation analyses between the expressions of PKM Previous studies have suggested that lactic acids might serve
protective roles in cancer against attacks by T cells [34]. There- Genomics Proteomics Bioinformatics 17 (2019) 273–286 Genomics Proteomics Bioinformatics 17 (2019) 273–286 280 Figure 4
The most commonly enriched pathways by genes strongly correlated with SLC16A1 across the 14 cancer types
The length of a bar represents the number of cancer types where the pathway is enriched with genes whose expression strongly correlates
with the expression of SLC16A1. Figure 4
The most commonly enriched pathways by genes strongly correlated with SLC16A1 across the 14 cancer types
The length of a bar represents the number of cancer types where the pathway is enriched with genes whose expression strongly correlates Figure 4
The most commonly enriched pathways by genes strongly correlated with SLC16A1 across the 14 cancer types
The length of a bar represents the number of cancer types where the pathway is enriched with genes whose expression strongly correlates
with the expression of SLC16A1. and genes related to the predicted cytosolic Fenton reaction on
the NPC data. The analyses revealed that unlike cancer cells,
no or very little correlation between expressions of glycolytic
ATP production (PKM gene) and the Fenton reaction-
defining genes, namely proteasome, iron uptake, and H2O2
genes in NPCs, as shown in Figure S3, hence suggesting that
the reason for glycolytic ATP production in NPCs is different
from that in cancers. poses: (1) maintaining the intracellular pH and (2) replenishing
the consumed ATP. Again, it is worthy reemphasizing that the
proton released along with lactate is NOT from glycolysis,
instead, from hydrolysis of an ATP previously generated by
respiration. While this has not been demonstrated for normal human
proliferating cells, we hypothesize that they basically follow
a similar process to maintain a pH level needed for cell prolif-
eration through glycolytic ATP production followed by lactic
acid secretion. To provide supporting evidence, we have con-
ducted a co-expression analysis between SLC16A1 and all
the up-regulated genes in each set of NPC samples, followed
by pathway enrichment analyses. We find that majority of
the enriched pathways are growth or development related. Glycolytic ATP synthesis maintains the elevated intracellular
pH during NPC proliferation Moreover, over two thirds of the pathways that are most com-
monly shared by different NPCs are also growth or develop-
ment related (Table S8), hence suggesting our prediction that
the cellular roles of SLC16A1 is different in cancer and in
NPCs. To probe why NPCs utilize glycolysis to produce ATP dur-
ing their proliferating phase, we first review how unicellular
organisms such as Escherichia coli and yeast control their cell
cycle. It has been well established that in E. coli, nutrients are
first used towards ATP production via the respiration process. This process switches largely to nucleotide and nucleotide-
sugar syntheses once the cellular ATP concentration rises to
a certain level, as result of that ATP production rate is higher
than that of ATP consumption. Clearly, this will lead to
increased
cellular
concentrations
of
nucleotides
and
nucleotide-sugar. It has been established that the cellular
nucleotide-sugar concentration serves as the cue for cell cycle
progression in E. coli [35] and Bacillus subtilis [36]. Hence when
the cell cycle starts, the cells already have substantial levels of
ATP accumulated needed for cell division. While we do not have experimental data to directly sup-
port the prediction that increased intracellular pH is essential
to human cell proliferation, there are data that indirectly sup-
port our prediction. Specifically, we have analyzed a gene
expression dataset (GSE77239) that was generated in an
study aimed to examine the effect of inhibiting an acid-
extruding pump in endothelial cells [39]. We have found that
the expression levels of cell proliferation and glycolytic genes
were reduced when the cells were treated by the inhibitor of
the pump (Table S9). The accumulation of the respiration-synthesized ATP also
leads to an increase in the intracellular pH, as needed for the
proliferation phase [37]. The reason is that respiration-based
ATP biosynthesis consumes one proton per ATP, hence driv-
ing the pH up when the ATPs are accumulated. Since cell pro-
liferation requires an elevated intracellular pH (from 6.8 to
7.2–7.4 [38]), cells must alter its way of ATP synthesis as other-
wise the consumption of each ATP will release one H+, hence
decreasing the pH. We predict that this is the reason that
NPCs switch to glycolytic ATP production when cell prolifer-
ation starts. Details follow. Recall that the synthesis of each
glycolytic ATP is pH neutral and produces on lactate [17]. Glycolytic ATP synthesis maintains the elevated intracellular
pH during NPC proliferation When the respiration based ATP is consumed for cell prolifer-
ation, one H+ is generated. Now cells release this proton along
with the lactate in the form of lactic acid. This serves two pur- We have also studied the time-course data in one of the
NPC datasets, GSE11292 for regulatory T cells and effector
T cells. The dataset contains gene-expression data of the cells
collected every 20 min at 19 time points starting from time
zero. We have specifically examined genes involved in the res-
piratory chain, glycolysis, lactic acid secretion, and the gene,
PRKAA1, involved in AMP degradation, whose expression
level is known to be proportional to the intracellular ATP level
[40], as shown in Figure 5. We find that the expression levels of Sun H et al / Warburg Effects in Cancer vs. Normal Proliferating Cells 281 Figure 5
Time-specific expression data of key genes involved in Warburg effect, electron transport chain and nucleotide synthesis pathways
in GSE11292
The left panel shows the expression levels of PKM, SLC16A1, NDUFS2, SDHD, UQCRFS1, and COX10, four representative genes for
electron transport chain Complex I, II, III and IV, respectively, where the time course data with 18 time points are grouped into six
segments with each containing three consecutive points and Ti represents the ith segment, 0 i 5. The right panel shows the expression
levels of PPAT, GART, PRPS2, and HPRT1 (blue), key genes in nucleotide synthesis pathways, as well as the expression level of PRKAA. Figure 5
Time-specific expression data of key genes involved in Warburg effect, electron transport chain and nucleotide synthesis pathways
in GSE11292
The left panel shows the expression levels of PKM, SLC16A1, NDUFS2, SDHD, UQCRFS1, and COX10, four representative genes for
electron transport chain Complex I, II, III and IV, respectively, where the time course data with 18 time points are grouped into six
segments with each containing three consecutive points and Ti represents the ith segment, 0 i 5. Glycolytic ATP synthesis maintains the elevated intracellular
pH during NPC proliferation The right panel shows the expression Figure 5
Time-specific expression data of key genes involved in Warburg effect, electron transport chain and
in GSE11292 Figure 5
Time-specific expression data of key genes involved in Warburg effect, electron transport chain and nucleotide synthesis pathways
in GSE11292 Figure 5
Time-specific expression data of key genes involved in Warburg effect, electron transport chain and nucleotide synthesis pathways The left panel shows the expression levels of PKM, SLC16A1, NDUFS2, SDHD, UQCRFS1, and COX10, four representative genes for
electron transport chain Complex I, II, III and IV, respectively, where the time course data with 18 time points are grouped into six
segments with each containing three consecutive points and Ti represents the ith segment, 0 i 5. The right panel shows the expression
levels of PPAT, GART, PRPS2, and HPRT1 (blue), key genes in nucleotide synthesis pathways, as well as the expression level of PRKAA. the respiratory chain genes decrease continuously while the
expressions of glycolytic ATP synthesis genes increase. In the
meantime, the intracellular ATP concentration with the
expression of PRKAA1 as a readout reaches and stays at a
high level and then gradually goes down starting at time T3
This observation is consistent with our model, namely, that
(i) cell proliferation starts at a point when the intracellular
ATP concentration reaches a high level; and (ii) the cells
increase glycolytic ATP production and reduces respiration-
based ATP synthesis during proliferation. Highly similar pat-
terns are observed in other similar cases, as detailed in
Figure S4. 6 109nucleotides in human genome and it takes approxi-
mately five ATPs to synthesize one nucleotide on average,
we predict that a cell must accumulate at least the number of
ATPs needed to synthesize 4.7% (143/3000) of a human
DNA to raise the pH from 6.8 to 7.4. Figure 6 summarizes the key differences between the War-
burg effects in cancer cells vs. NPCs. Based on all the analyses,
we predict that while both normal proliferating cells and can-
cer cells have the Warburg effect, they do it for fundamentally
different reasons. Discussion It is noteworthy that unlike E. coli, respiratory ATPs are
generated in mitochondria rather than in cytosol. Since cytoso-
lic proton movement into mitochondria via the ATP synthase
(or UCP transporters) is driven by proton gradient [41], we
postulate that the increased mitochondrial pH would lead to
increased cytosolic pH. Several papers suggest that the Warburg effect is a common
characteristic of all proliferating cells, including cancer and
normal proliferating cells. Our comparative analyses of gene
expression data between cancer tissue cells and NPCs provide
strong evidence that they do this for fundamentally different
reasons. Specifically, cancer cells do this mainly to produce
net protons for neutralizing OH that is generated persistently
by cytosolic Fenton reactions, whereas NPCs do this to main-
tain the elevated cytosolic pH needed for the optimal perfor-
mance of the ribosomal proteins [37]. Moreover, cancer cells
secrete lactic acids largely independent of lactate generation
and they do this probably for protecting cancer cells from
destruction by immune cells. To estimate the number of respiratory ATPs that need to be
accumulated to raise the intracellular pH from 6.8 to 7.4 (pH
value needed for cell proliferation) in a normal human cell, we
have calculated the number of protons needed to make such a
change. Here we assume that the volume of the cell is 100 lm3,
based on human cell data [42]. For the intracellular pH to
change from 6.8 to 7.4, the concentration of the H+ needs
to change from 106.8 to 107.4. Assuming that the pH buffer-
ing coefficient of the cell is 2 105 for this pH range [43], the
number of protons needed to make such a change is calculated
as, To avoid possible noises introduced by non-cancerous cells,
we have selected in our analyses cancer tissue samples that are
predicted to contain cancer cells with high purity. However,
the results derived using such samples are essentially the same
with the results derived from all samples of the 14 caner types
in TCGA without this selection. 106:8 107:4
100 2 105 10
15 6:02 1023
ffi1:43 109 where 6:02 1023 is the Asogadro constant. Hence, it takes
approximately 1:43 109 protons, hence this number of ATPs
to make the desired pH change. Knowing that there are where 6:02 1023 is the Asogadro constant. Discussion Hence, it takes
approximately 1:43 109 protons, hence this number of ATPs
to make the desired pH change. Knowing that there are While our analyses provide generally consistent results
across the 14 cancer types, we notice that kidney cancers tend
to show different characteristics in maintaining their cytosolic Genomics Proteomics Bioinformatics 17 (2019) 273–286 282 Figure 6
Schematic illustration of the key differences between the Warburg effects in cancer cells vs. NPCs
A. Warburg effects in cancer. B. Warburg effects in normal proliferating cells. 282
Genomics Proteomics Bioinformatics 17 (2019) 273 286 Figure 6
Schematic illustration of the key differences between the Warburg effects in cancer cells vs. NPCs
A. Warburg effects in cancer. B. Warburg effects in normal proliferating cells. information derived from gene-expression data with detailed
chemistry properties of cells such as pH may offer a novel
approach to tackle complex diseases like cancer, hence poten-
tially leading to deeper understanding about cancer formation
and development. acid-base homeostasis from other cancers, suggesting that fur-
ther studies are needed. We have also examined the protein abundances of the up-
regulated genes in our model in the relevant cancer types
(when available) from the Human Protein Atlas, and found
that virtually all the highly up-regulated genes also have signif-
icant increase in protein abundance in the same cancer types if
such data are available, hence indicating that our gene-
expression based analyses are as valid as protein abundance
based analyses if they were available. Selection of pH-related transporter genes The family of sodium-proton exchangers consists of nine
SLC9A genes, which generally exchange extracellular Na+
for intracellular H+ (or NH4
+), hence acid extruders [54]. The following five SLC9A genes are not considered for differ-
ent reasons in our study. SLC9A1 and A7 can be localized to
at least three subcellular compartments [55]. SLC9A8 is local-
ized only in Golgi. SLC9A5 is not expressed in any samples
studied here. SLC9A6 is predominantly expressed in endosome
[56]. This leaves SLC9A2, 3, 4, 9 for further analyses. Table 1 summarizes the sample information for both cancer
and NPC data used in this study. The original information of
the cancer samples collected from TCGA before selection is
given in Table S10 and Figure S5. The expression levels of all genes in all cancer samples of
each type form a bimodal distribution (Figure S6), where the
first peak (from left to right) represents genes that are not
expressed and the second peak is for the expressed genes. For each cancer type, genes with expression values lower than
or equal to the lowest point of the valley between the two
peaks is considered as not expressed. The same criteria apply
to the controls as well as the NPC samples from GEO. Among the SLC26 anion exchangers, only
six may
exchange Cl for HCO3
, namely SLC26A3–4, 6–7, 9, 11
[57]. SLC26A3 and A4 are not expressed in majority of the tis-
sue types under study, hence not considered. SLC26A7 is Table 1
Samples of cancer tissues of 14 types and of five NPC types Table 1
Samples of cancer tissues of 14 types and of five NPC types
Type
No. of cancer/activated samples
No. Selection of pH-related transporter genes cancer and (not necessarily paired) control samples, with gene
expression levels indicated using normalized FPKM (with log2
transformation). We examined all the genes in the transporter families, includ-
ing
bicarbonate
transporters,
sodium-proton
exchangers,
anion exchangers, V-ATPase, lactic acid transporters, Ca2+-
ATPase, and K+/H+ ATPase. A few transporters localized
in plasma membrane were considered as reliable acid-loading
or acid-extruding transporters. Details follow. The purity of cancer tissue samples was predicted using five
programs, namely ESTIMATE, ABSOLUTE, LUMP, IHC,
and CPE [45]. Cancer tissue samples with the highest purity
for each cancer type were selected, based on consensus results
by the five methods. The detailed information about how tis-
sue purity is assessed is given in File S1. The family of bicarbonate-transporter genes consists of ele-
ven SLC4 genes. SLC4A1, 2, 3 are known to exchange extra-
cellular Cl for intracellular HCO [52], hence serving as acid
loaders; and SLC4A4-10 tend to cotransport extracellular
Na+ and HCO3
into cells [53], hence acid extruders. It is
known that SLC4A11 does not transport bicarbonate, hence
not considered; and SLC4A6 has not been identified yet. Out
of the remaining ones, SLC4A8 and A10 are not expressed
in any samples, cancer or control. SLC4A1 and SLC4A5 are
each expressed in only one tissue type: 4A1 in kidney and
4A5 in thyroid. SLC4A7 tends to be located in focal adhesion
sites, in addition to plasma membrane, making their interpre-
tation challenging. Hence, we do not consider any of these
SLC4 transporters, which leaves SLC4A1AP (an adaptor pro-
tein of SLC4A1), A2, A3 as acid loaders, and SLC4A4 and A9
as acid extruders. In
addition,
143
samples
of
five
NPC
types
with
microarray-based gene expression data were selected from
the
GEO
[46]. These
include
activated
CD4+
T
cells
(GSE60235, GPL570) [47], induced pluripotent stem cell
(GSE25970,
GPL3921)
[48],
re-epithelialization
cells
(GSE28914,
GPL570)
[49],
activated
regulatory
T
cells
(GSE11292,
GPL570),
and
activated
effector
T
cell
(GSE11292) [50]. Each dataset consists of gene-expression data
for both activated and inactive cell, used as controls. These
cells are good representatives among proliferating noncancer-
ous human cells, with the related datasets representing good
qualities among all the relevant datasets in GEO. For a gene
with multiple probes, we chose the probe having the highest
average expression level to represent its expression. MAS5 in
the R package ‘‘affy” [51] was used to normalize the gene
expression data. Data processing and normalization Overall, the discovery made in this study offers a novel
angle to examine cancer from the perspective of acid-base
homeostasis. Our unique way in connecting coarse-grained We have used RNA-seq data of 1612 samples covering 14 can-
cer types from the TCGA database [44], each having at least 13 Sun H et al / Warburg Effects in Cancer vs. Normal Proliferating Cells 283 Note: *represents a case where all the cancer samples of the cancer type in TCGA are used instead those with predicted high purity since some of the
programs do not apply to the data format of the cancer type. Identification of differentially-expressed genes mainly a chloride channel, which exchanges Cl for a range of
intracellular anions [58], hence not considered. SLC26A11 can
be localized to five subcellular compartments, hence too non-
specific and not considered. This leaves two genes in our study:
SLC26A6 and A9. Interestingly, while both transporters
exchange Cl for an anion, including HCO3
, they facilitate
Cl flux in the opposite directions, namely SLC26A6 moving
extracellular Cl into cells [59] and A9 moving intracellular
Cl out [60]. mainly a chloride channel, which exchanges Cl for a range of
intracellular anions [58], hence not considered. SLC26A11 can
be localized to five subcellular compartments, hence too non-
specific and not considered. This leaves two genes in our study:
SLC26A6 and A9. Interestingly, while both transporters
exchange Cl for an anion, including HCO3
, they facilitate
Cl flux in the opposite directions, namely SLC26A6 moving
extracellular Cl into cells [59] and A9 moving intracellular
Cl out [60]. We have applied Wilcoxon signed-rank test for cancer samples
vs. matching controls and NPCs vs. controls to identify
differentially- expressed genes (DEGs). A gene is considered
to be significantly differentially expressed if the difference in
its expression is at least 1.3-fold between cancer (or NPCs)
and their relevant control samples (FC > 1.3), with the false
discovery rate <0.01. The ATP6V genes encoding the V-ATPase complex tend to
have multiple subcellular locations. Considering that only
those localized to plasma membrane are relevant to our study,
we have developed a computational method to de-convolute
the observed expressions of the ATP6V genes to tease out
the portions of these genes whose protein products are local-
ized in the plasma membrane (see File S1). Table S2 lists the
estimated average expression levels of the ATP6V genes whose
protein products are localized in plasma membrane across dif-
ferent cell types. The authors declare no potential conflicts of interest. The authors declare no potential conflicts of interest. Authors’ contributions YX, HS, and YL designed the project; HS, LC, and SC per-
formed the study; HS and LC analyzed the data; YX and
HS wrote the paper. All authors read and approved the final
manuscript. ð1Þ wheree g
ð Þ is the expression of gene g; PC1 and PC2 are the first
and second PCs of the expression of the gene set in the given
samples; and {big are regression parameters. If PC1 and PC2
fail to explain at least 75% of the data variance, we use the fol-
lowing procedure to assess the statistical significance of the
detected correlation between the gene g and the set of M genes. First, we calculate the Pearson correlations between g and each
of the N genes in the human genome (N = 20,000) as the back-
ground; and then we conduct a multiple-hypothesis test using
the false discovery rate control, to select n genes from N to
achieve statistical significance for each correlation with g
(P < 0.01). The P value for the correlation is calculated as: wheree g
ð Þ is the expression of gene g; PC1 and PC2 are the first
and second PCs of the expression of the gene set in the given
samples; and {big are regression parameters. If PC1 and PC2
fail to explain at least 75% of the data variance, we use the fol-
lowing procedure to assess the statistical significance of the
detected correlation between the gene g and the set of M genes. First, we calculate the Pearson correlations between g and each
of the N genes in the human genome (N = 20,000) as the back-
ground; and then we conduct a multiple-hypothesis test using
the false discovery rate control, to select n genes from N to
achieve statistical significance for each correlation with g
(P < 0.01). The P value for the correlation is calculated as: Supplementary data to this article can be found online at
https://doi.org/10.1016/j.gpb.2018.12.006. Calculation of correlation and statistical significance The authors thank funding support from Georgia Research
Alliance, the National Natural Science Foundation of China
(Grant
Nos. 61472158,
61572228,
and
61572227),
the
Premier-Discipline Enhancement Scheme supported by Zhuhai
Government
and
Premier
Key-Discipline
Enhancement
Scheme supported by Guangdong Government, China. To calculate the correlation between the expression of a given
gene g and a set of M genes in a sample set, we choose the first
two principle components (PCs) to represent the gene set if
they can explain at least 75% of the data variance. A linear
regression model was constructed as shown below. e g
ð Þ b1PC1 þ b2PC2 þ b0
ð1Þ Selection of pH-related transporter genes of control samples
Bladder urothelial carcinoma (BLCA)
94
19
Breast invasive carcinoma (BRCA)
153
113
Colon adenocarcinoma (COAD)
55
41
Esophageal carcinoma (ESCA)
184*
13
Head and Neck squamous cell carcinoma (HNSC)
79
44
Kidney chromophobe (KICH)
34
25
Kidney renal clear cell carcinoma (KIRC)
91
72
Kidney renal papillary cell carcinoma (KIRP)
38
32
Liver hepatocellular carcinoma (LIHC)
65
50
Lung adenocarcinoma (LUAD)
92
59
Lung squamous cell carcinoma (LUSC)
59
51
Prostate adenocarcinoma (PRAD)
133
52
Stomach adenocarcinoma (STAD)
238*
33
Thyroid carcinoma (THCA)
56
59
Activated CD4 + T cells (GSE60235)
15
15
Activated effector T cells (GSE11292)
32
6
Activated regulatory T cells (GSE11292)
32
6
Induced pluripotent stem cell (GSE25970)
12
6
Re-epithelizing skin cells (GSE28914)
11
8
Note: *represents a case where all the cancer samples of the cancer type in TCGA are used instead those with predicted high purity since some of the
programs do not apply to the data format of the cancer type. Note: *represents a case where all the cancer samples of the cancer type in TCGA are used instead those with predicted high purity since some of the
programs do not apply to the data format of the cancer type. Genomics Proteomics Bioinformatics 17 (2019) 273–286 284 Competing interests Both lactic acid transporter genes, SLC16A1 and A3, are
included in our analyses. Neither the Ca2+-ATPase (encoded
by the ATP2B1-4 genes) nor the K+/H+ ATPase (encoded
by the ATP4A, B genes) is particularly informative, hence we
did not include them in our analyses. Supplementary material e g
ð Þ b1PC1 þ b2PC2 þ b0 References [40] Gault VA, Harriott P, Flatt PR, O’Harte FP. Cyclic AMP
production and insulin releasing activity of synthetic fragment
peptides of glucose-dependent insulinotropic polypeptide. Biosci
Rep 2002;22:523–8. [19] Zieve PD, Haghshenass M, Krevans JR. Intracellular pH of the
human lymphocyte. Am J Physiol 1967;212:1099–102. [20] Sun-Wada GH, Tabata H, Kawamura N. Selective assembly of V-
ATPase subunit isoforms in mouse kidney. J Bioenerg Biomembr
2005;37:415–8. [41] Jagendorf AT, Uribe E. ATP formation caused by acid-base
transition of spinach chloroplasts. Proc Natl Acad Sci U S A
1966;55:170–7. [21] Majumdar S, Gunda S, Pal D, Mitra AK. Functional activity of a
monocarboxylate transporter, MCT1, in the human retinal
pigmented
epithelium
cell
line,
ARPE-19. Mol
Pharm
2005;2:109–17. [42] Li Q, Rycaj K, Chen X, Tang DG. Cancer stem cells and cell size:
a causal link? Semin Cancer Biol 2015;35:191–9. [43] Saleh AM, Rombola G, Batlle DC. Intracellular H+ buffering
power and its dependency on intracellular pH. Kidney Int
1991;39:282–8. [22] Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K,
Va´ zquezfresno R, et al. HMDB 4.0: the human metabolome
database for 2018. Nucleic Acids Res 2017;46:D608–17. [44] Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger
BA, Ellrott K, et al. The cancer genome atlas pan-cancer analysis
project. Nat Genet 2013;45:1113–20. [23] Spinelli JB, Yoon H, Ringel AE, Jeanfavre S, Clish CB, Haigis
MC. Metabolic recycling of ammonia via glutamate dehydroge-
nase supports breast cancer biomass. Science 2017;358:941–6. [45] Aran D, Sirota M, Butte AJ. Systematic pan-cancer analysis of
tumour purity. Nat Commun 2015;6:8971. [24] Bu¨ ll C, Stoel MA, den Brok MH, Adema GJ. Sialic acids sweeten
a tumor’s life. Cancer Res 2014;74:3199–204. [46] Edgar R, Domrachev M, Lash AE. Gene expression omnibus:
NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002;30:207–10. [25] Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler
IM, et al. The MetaCyc database of metabolic pathways and
enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2016;44:D471–80. [47] Ye CJ, Feng T, Kwon HK, Raj T, Wilson MT, Asinovski N, et al. Intersection of population variation and autoimmunity genetics in
human T cell activation. Science 2014;345:1254665. [26] Yongzhong W, Smitha A, Meitzler JL, Doroshow JH. Molecular
mechanisms underlying chronic inflammation-associated cancers. Cancer Lett 2014;345:164–73. [48] Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD,
et al. References The Warburg effect: how does it benefit
cancer cells? Trends Biochem Sci 2016;41:211–8. [34] Fischer K, Hoffmann P, Voelkl S, Meidenbauer N, Ammer J,
Edinger M, et al. Inhibitory effect of tumor cell-derived lactic acid
on human T cells. Blood 2007;109:3812–9. [12] Shaw RJ, Kosmatka M, Bardeesy N, Hurley RL, Witters LA,
DePinho RA, et al. The tumor suppressor LKB1 kinase directly
activates
AMP-activated
kinase
and
regulates apoptosis in
response
to
energy
stress. Proc
Natl
Acad
Sci
U
S
A
2004;101:3329–35. [35] Monahan LG, Hajduk IV, Blaber SP, Charles IG, Harry EJ. Coordinating bacterial cell division with nutrient availability: a
role for glycolysis. MBio 2014;5:e00935–1014. [13] Lum JJ, Bauer DE, Kong M, Harris MH, Li C, Lindsten T, et al. Growth factor regulation of autophagy and cell survival in the
absence of apoptosis. Cell 2005;120:237–48. [36] Monahan LG, Harry EJ. You are what you eat: metabolic control
of Bacterial division. Trends Microbiol 2016;24:181–9. [14] Damaghi M, Wojtkowiak JW, Gillies RJ. pH sensing and
regulation in cancer. Front Physiol 2013;4:370. [37] Johansson M, Ieong KW, Trobro S, Strazewski P, Aqvist J,
Pavlov MY, et al. pH-sensitivity of the ribosomal peptidyl transfer
reaction dependent on the identity of the A-site aminoacyl-tRNA. Proc Natl Acad Sci U S A 2011;108:79–84. [15] Silva AS, Yunes JA, Gillies RJ, Gatenby RA. The potential role
of systemic buffers in reducing intratumoral extracellular pH and
acid-mediated invasion. Cancer Res 2009;69:2677–84. [38] Kruse CR, Singh M, Targosinski S, Sinha I, Sorensen JA,
Eriksson E, et al. The effect of pH on cell viability, cell migration,
cell proliferation, wound closure, and wound reepithelialization:
in vitro and in vivo study. Wound Repair Regen 2017;25:
260–9. [16] Sun H, Zhang C, Cao S, Sheng T, Dong N, Xu Y. Fenton
Reactions Drive Nucleotide and ATP Syntheses in Cancer. J Mol
Cell Biol 2018;10:448–59. [17] Swietach P, Vaughan-Jones RD, Harris AL, Hulikova A. The
chemistry, physiology and pathology of pH in cancer. Philos
Trans R Soc Lond B Biol Sci 2014;369:20130099. [39] Costarelli L, Giacconi R, Malavolta M, Basso A, Piacenza F,
Provinciali M, et al. Different transcriptional profiling between
senescent and non-senescent human coronary artery endothelial
cells (HCAECs) by Omeprazole and Lansoprazole treatment. Biogerontology 2017;18:217–36. [18] Campbell DB, Sutcliffe JS, Ebert PJ, Militerni R, Bravaccio C,
Trillo S, et al. A genetic variant that disrupts MET transcription is
associated
with
autism. Proc
Natl
Acad
Sci
U
S
A
2006;103:16834–9. References [1] Warburg
O. On
the
origin
of
cancer
cells. Science
1956;123:309–14. [2] Weinhouse S. The Warburg hypothesis fifty years later. Z
Krebsforsch Klin Onkol Cancer Res Clin Oncol 1976;87:115–26. [3] Fantin VR, St-Pierre J, Leder P. Attenuation of LDH-A
expression uncovers a link between glycolysis, mitochondrial
physiology, and tumor maintenance. Cancer Cell 2006;9:425–34. P ¼ 1
X
m1
i¼0
M
i
NM
ni
N
n
ð2Þ P ¼ 1
X
m1
i¼0
M
i
NM
ni
N
n
[4] Moreno-Sanchez R, Rodriguez-Enriquez S, Marin-Hernandez A,
Saavedra
E. Energy
metabolism
in
tumor
cells. FEBS
J
2007;274:1393–418. ð2Þ where m is the number of genes in the union of the n- and M-
gene sets. For two gene sets GS1 and GS2 and their gene
expression matrices M1 and M2 (across samples), we first cal-
culate their principal curves [61] to capture the nonlinear vari-
ance within matrices M1 and M2. We then project each sample
of M1 or M2 onto the corresponding principal curve, denoted
as DP1 and DP2, respectively. Pearson’s correlation coefficient
(PCC) between DP1 and DP2 is then calculated to indicate the
correlation between the two gene sets and the relevant p-value. R package ‘‘pathifier” was applied to calculate the principal
curve of the gene expression matrix. [5] Vander Heiden MG, Cantley LC, Thompson CB. Understanding
the Warburg effect: the metabolic requirements of cell prolifera-
tion. Science 2009;324:1029–33. [6] Locasale JW, Cantley LC. Metabolic flux and the regulation of
mammalian cell growth. Cell Metab 2011;14:443–51. [7] Murphy MP. How mitochondria produce reactive oxygen species. Biochem J 2009;417:1–13. [8] Brown GC, Borutaite V. Inhibition of mitochondrial respiratory
complex I by nitric oxide, peroxynitrite and S-nitrosothiols. Biochim Biophys Acta 2004;1658:44–9. [9] Viale A, Corti D, Draetta GF. Tumors and mitochondrial
respiration: a neglected connection. Cancer Res 2015;75:3687–91. Sun H et al / Warburg Effects in Cancer vs. Normal Proliferating Cells 285 hypoxia through a HIF-1alpha-dependent mechanism. J Biol
Chem 2006;281:9030–7. hypoxia through a HIF-1alpha-dependent mechanism. J Biol
Chem 2006;281:9030–7. [10] Lunt SY, Vander Heiden MG. Aerobic glycolysis: meeting the
metabolic requirements of cell proliferation. Annu Rev Cell Dev
Biol 2011;27:441–64. [33] Perez-Escuredo J, Van Hee VF, Sboarina M, Falces J, Payen VL,
Pellerin L, et al. Monocarboxylate transporters in the brain and in
cancer. Biochim Biophys Acta 2016;1863:2481–97. [11] Liberti MV, Locasale JW. References Reference maps of human ES and iPS cell variation enable
high-throughput characterization of pluripotent cell lines. Cell
2011;144:439–52. [27] Mittal M, Siddiqui MR, Tran K, Reddy SP, Malik AB. Reactive
oxygen species in inflammation and tissue injury. Antioxid Redox
Signal 2014;20:1126–67. [49] Nuutila K, Siltanen A, Peura M, Bizik J, Kaartinen I, Kuokkanen
H, et al. Human skin transcriptome during superficial cutaneous
wound healing. Wound Repair Regen 2012;20:830–9. [28] Torti SV, Torti FM. Iron and cancer: more ore to be mined. Nat
Rev Cancer 2013;13:342–55. [29] Toyokuni S. Role of iron in carcinogenesis: cancer as a ferrotoxic
disease. Cancer Sci 2009;100:9–16. [50] He F, Chen H, Probst-Kepper M, Geffers R, Eifes S, Del Sol A,
et al. PLAU inferred from a correlation network is critical for
suppressor
function
of
regulatory
T
cells. Mol
Syst
Biol
2012;8:624. [30] Kruszewski M. Labile iron pool: the main determinant of cellular
response to oxidative stress. Mutat Res 2003;531:81–92. [51] Gautier L, Cope L, Bolstad BM, Irizarry RA. affy–analysis of
Affymetrix GeneChip data at the probe level. Bioinformatics
2004;20:307–15. [31] Li WP, Su CH, Chang YC, Lin YJ, Yeh CS. Ultrasound-induced
reactive oxygen species mediated therapy and imaging using a
fenton
reaction
activable
polymersome. ACS
Nano
2016;10:2017–27. [52] Romero MF, Chen AP, Parker MD, Boron WF. The SLC4 family
of
bicarbonate
(HCO3
)
transporters. Mol
Aspects
Med
2013;34:159–82. [32] Ullah MS, Davies AJ, Halestrap AP. The plasma membrane
lactate transporter MCT4, but not MCT1, is up-regulated by [61] Drier Y, Sheffer M, Domany E. Pathway-based personalized
analysis of cancer. Proc Natl Acad Sci U S A 2013;110:6388–93. Genomics Proteomics Bioinformatics 17 (2019) 273–286 286 Genomics Proteomics Bioinformatics 17 (2019) 273–286 [58] Kim KX, Sanneman JD, Kim HM, Harbidge DG, Xu J,
Soleimani M, et al. Slc26a7 chloride channel activity and
localization in mouse Reissner’s membrane epithelium. PLoS
One 2014;9:e97191. [53] Wang CZ, Yano H, Nagashima K, Seino S. The Na+-driven Cl/
HCO3
exchanger. Cloning, tissue distribution, and functional
characterization. J Biol Chem 2000;275:35486–90. [54] Donowitz M, Ming Tse C, Fuster D. SLC9/NHE gene family, a
plasma membrane and organellar family of Na+/H+ exchangers. Mol Aspects Med 2013;34:236–51. [59] Chernova MN, Jiang L, Friedman DJ, Darman RB, Lohi H, Kere
J, et al. Functional comparison of mouse slc26a6 anion exchanger
with human SLC26A6 polypeptide variants: differences in anion
selectivity,
regulation,
and
electrogenicity. J
Biol
Chem
2005;280:8564–80. [55] Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D. GeneCards:
integrating information about genes, proteins and diseases. Trends Genet 1997;13:163. [60] Anagnostopoulou P, Riederer B, Duerr J, Michel S, Binia A,
Agrawal R, et al. SLC26A9-mediated chloride secretion prevents
mucus
obstruction
in
airway
inflammation. J
Clin
Invest
2012;122:3629–34. [56] Xinhan L, Matsushita M, Numaza M, Taguchi A, Mitsui K,
Kanazawa H. Na+/H+ exchanger isoform 6 (NHE6/SLC9A6) is
involved in clathrin-dependent endocytosis of transferrin. Am J
Physiol Cell Physiol 2011;301:C1431–44. [61] Drier Y, Sheffer M, Domany E. Pathway-based personalized
analysis of cancer. Proc Natl Acad Sci U S A 2013;110:6388–93. [57] Alper SL, Sharma AK. The SLC26 gene family of anion
transporters and channels. Mol Aspects Med 2013;34:494–515.
|
https://openalex.org/W2903149528
|
http://repo.unand.ac.id/19726/1/artikel%20shinta.pdf
|
English
| null |
The Effect of Therapeutic Group Therapy to Mother’s Knowledge about Cognitive and Psychosocial of Preschool-age Children
|
International journal of research in nursing
| 2,018
|
cc-by
| 3,895
|
The Effect of Therapeutic Group Therapy to Mother’s
Knowledge about Cognitive and Psychosocial of Preschool-age
Children Shinta Dewi Kasih Bratha, Meri Neherta and Dewi Eka Putri Shinta Dewi Kasih Bratha, Meri Neherta and Dewi Eka Putri Faculty of Nursing, Andalas University, Limau Manis Padang. Indonesia Abstract: A non-optimal growth might affect the mental development of
children. Mental development disorder’s children around the world were
classified as high. To prevent that situation it was required a consant
stimulation from the mother. Providing stimulation was supported by
mother's knowledge about children growth and development so that
stimulation could be given according to the growth stage. Therapeutic
group therapy was one of the altematives that provide knowledge to the
mother in doing a developmental stimulation according to the children's
age. The purpose of this research was to determine the effect of therapeutic
group therapy on rnother’s knowledge in providing a cognitive and
psychosocial developmental stimulation of preschool-age children. This
research used "Quasi-experiment pre-post test control group” with
therapeutic Group Therapy intervention of preschool-age children (3-4
years). The result of this research obtained that the cognitive aspect of
mother's knowledge was 0,070 (p value>0,05) which implied that there was
no difference between intervention and control group. Whereas in the
psychosocial aspect it was found that knowledge of mother was 0,460 (p
value> 0,05) which meant that there was no difference between
intervention and control group. With the providing of this therapy, it was
expected to improve the development of preschoolers. especially on the
cognitive and psychosocial aspects. Article history
Received: 22-05-2018
Revised: 29-06-2018
Accepted: 10-07-2018 Corresponding Author:
Shinta Dewi Kasih Bratha
Faculty of Nursing, Andalas
University, Limau Manis
Padang. Indonesia
Email: shintadkb@qmail.com Group
Therapy,
Mother's
Knowledge, Group
Therapy,
Mother's
Knowledge, Keywords:
Therapeutic
Developmental Stimulation © 2018 Shinta Dewi Kasih Bratha, Meri Neherta and Dewi Eka Putri. This open access article is distributed under a Creative
Commons Attribution (CC-BY) 3.0 license. International Journal of Research in Nursing International Journal of Research in Nursing Introduction Therapeutic group therapy of preschoolers consists of
five sessions which are the evaluation of preschoolers
development and stimulation of fine and gross motor, the
stimulation of cognitive and language development, the
stimulation of emotional and personality development,
the stimulation of moral, religious and psychosocial
development and the evaluation of child development. Therapeutic group therapy can educate and improve the
potential of members and improve the quality of the
group in handling problems both individually and in
groups (Enns et al., 2016). Meanwhile, in Indonesia, Istiana (2015) has done a
therapeutic group therapy toward school-age children
which has an impact on the mental development of
these children. Therapeutic group therapy also gives an
influence on the mental development of adolescents as
has been done by Maryatun (2014) in Banjarmasin. From all the research about therapeutic group therapy
conducted in Indonesia, researchers assume that this is
the best alternative to observe mother's knowledge in
stimulating cognitive development and psychosocial
within preschoolers. y
Based on the results of Feil's research (2017) in
America, obtained that 75% of mothers have no
knowledge about children development in accordance
with their age. Mothers are not able to provide
appropriate
stimulation
with
aspects
of
child
development. So that, the child development is handed
over thoroughly to school or another educational place
(Feil et al., 2017). Stimulation is also obtained from
Early Childhood Education and Development (ECED)
which is presented by teachers, but it is limited due to the
unbalanced number of teachers and children. Therefore, it
should be extended by a continual stimulation of the
mother at home (Cameron et al., 2017). The problem that
is still encountered by the mother in providing
development stimulus is that the mother provides
excessive stimulation only on the elements of cognitive
development so that she does not allow the children to
play outside the home (Spielfogel et al., 2011). The efforts to improve the quality and develop the
potencies of children, in line with the establishment of
Padang Panjang City, West Sumatra which began to
concentrate on nurturing the younger generation. Early
childhood education in Padang Panjang City is the
primary alternative for parents in nurturing preschoolers. However, the stimulation is not optimal for each child
because the children presence is only around 3-4 hours a
day and the number of teachers that are disproportionate
to the number of pupils. Introduction children with mental health problems during 1994-2011
and countries in Asia have 10-20% of children and
adolescents who have experienced mental health
problems (Nikolaev et al., 2016). The high number of
mental health disorders within preschoolers can be
handled by increasing the stimulation of growth and
development in children (Years, 2014). In Indonesia, out
of 1000 children aged 4-15 years, 140 children experience
mental and emotional problems (Riskesdas, 2013). a community-based mental health care approach that not
only focuses on mental disorders but also to improve the
quality of life of healthy communities (Years, 2014). The services of psychiatric nursing can be provided in
the form of intervention and therapy for individuals,
families and groups. A variety of therapies can be given
by the nurses such as family therapy, supportive and
therapeutic group therapy. Therapeutic group therapy is an alternative in this
situation. Therapeutic group therapy is a promotive
action to enhance child development to be optimal so as
to limit the appearance of mental health problems
(Nugter and Engelsbel, 2015). Therapeutic group therapy
is applied to a proper group which is suitable for the
development of age to increase the potential for gaining
an optimal growth. p
Prevention efforts of mental health problems can be
done by stimulating the growth and development of
healthy children, so it can maintain the mental health
status of the child (Years, 2014). A mother must be able
to provide stimulus for her children and the most
efficient is at the age of 24-48 months (Kim et al., 2017). According to Hurlock, at the age of 3 to 4 years, physical
maturity occurs in the brain and the nervous system that
can improve motoric skills. If the maturity of the brain is
accompanied by appropriate stimulation, it will produce
optimal development of the child (Kim et al., 2017). The
stimulation presentation should be supported by mother's
knowledge about child growth so that the stimulation can
be given accordance with the stage of development
(Conference and Psychology, 2012). According to
Murphy (2017), the process of giving this stimulation
can also not be arbitrary because only four kinds of
stimuli that will be saved by the child, those are the first
being recorded, the more reliable, more enjoyable and
that lasted continuously. Introduction development in children. The process of development
that is not working optimally will lead to disturbance and
affect the mental development of children. Mental
development disorders among children around the world
classified as high, such as in the United States reaching
12-16%, Thailand 24%, Argentina 22% and Indonesia
13-18%. The
prevalence
of
children's
mental
development disorder in Indonesia tends to increase in
the last 6 years (Cameron et al., 2017). Preschoolers (3-6 years old) is a critical period that
has a profound effect concerning the success of the
growth and development process that must be
accomplished by adults (Shoshani et al., 2017). This
growth can be observed in seven aspects; motoric,
cognitive, language, emotional, personality, religious
and moral character as well as psychosocial. Cognitive
development during preschoolers plays an important role
because children will be able to evaluate the
consequence of an event or age-related change in mental
activities (Hapsari, 2016). According to Erikson,
psychosocial development during preschoolers is better
known as initiative versus guilt. Initiatives are used to
possess and pursue various goals and also to suppress or
delay a goal. Objectives that must be restrained will
bring about a sense of guilt or sin (Xing et al., 2017). This psychosocial aspect will influence other aspects of Non-optimal development can lead to mental health
problems. Some cases of psychiatric problems occur due
to the lack of attention and stimulation of the parents that
are given during childhood. In China, it is recorded that
75% of the perpetrators of violent acts in adulthood is
caused by the lack of parents' attention during their
childhood (Balseviciene et al., 2014). Meanwhile, many
teenagers in Australia do criminal acts, free sex and
become bullies at their school (Mills et al., 2013). In the
United States, it is reported that there are around 13-20% Shinta Dewi Kasih Bratha et al. / International Journal of Research in Nursing 2018, ■■■ (■): ■■■.■■■
DOI: 10.3844/ijrnsp.2018.■■■.■■■ children with mental health problems during 1994-2011
and countries in Asia have 10-20% of children and
adolescents who have experienced mental health
problems (Nikolaev et al., 2016). The high number of
mental health disorders within preschoolers can be
handled by increasing the stimulation of growth and
development in children (Years, 2014). In Indonesia, out
of 1000 children aged 4-15 years, 140 children experience
mental and emotional problems (Riskesdas, 2013). Research Design Quasi-experimental pre-post test control group was
used as a research design with an intervention of
Therapeutic Group Therapy on preschoolers. This
research was conducted to observe the variety of
mother's
knowledge
in
giving
stimulation
of
development within 3 to 4 year-olds children before and
after therapy in Padang Panjang City. Table 1 represents mothers' knowledge in providing
stimulation of cognitive and psychosocial development
of preschoolers before therapy in intervention and
control groups. Based on the table, it was obtained that
the average of mothers' knowledge about cognitive
aspect in the intervention group was 2,68 and 3,15 in the
control group. Based on the result of the statistical test of
cognitive aspect obtained p-value <0,05 which meant
there was a difference of mothers' knowledge in
intervention and control group. If we observed from the
psychosocial aspects, it was found that the average
knowledge of mothers in the intervention group was 4.30
and 5.78 in the control group. Based on the result of the
statistical test, mother's knowledge in psychosocial
aspect was found that p-value <0,05 so that there was no
difference between intervention and control group. Method boys in the intervention group. While in the control
group, there was 19 girls and 21 boys. In the intervention
group, there were 26 mothers who did not work and 14
mothers who were working. Meanwhile, in the control
group, there were 17 mothers who did not work and 23
mothers were working. Based on statistical results, both
groups were homogeneous. Research Sample Random cluster sampling was used in this research to
collect samples and obtained 40 respondents for the
intervention group and 40 respondents for control group
with inclusion criteria: (1) Willing to be the respondent,
(2) Have 3-4 years old children in Padang Panjang City
(3) Willing to follow therapy from beginning to end of
session, (4) Able to read-write.. Reseacrh Ethics Before collecting the data, researchers first followed
the ethical test at the Faculty of Medicine of Andalas
University Padang. Then the researchers requested written
consent from the participants, including the explanation of
the research and conducted a voluntary commitment from
the participants. Participants had the option to accept or
reject and all personal information was kept confidential. In addition, the researchers also conducted expert tests
before doing the research. The researchers administered
the research approval and prepared the enumerator (for
data collecting) who had been willing to assist in pre and
post data-collecting activities. After preparing the data
collector, the researchers determined the research location
in West Padang Panjang as the control group and East
Padang Panjang as the intervention group. One
intervention group consisted of 5 respondents (mother and
child). The intervention was conducted in 5 sessions in 3
meetings for duration 1 month. g
p
Table 2 illustrates the analysis of mothers' knowledge
before and after therapeutic group therapy in the
intervention group. It was obtained a score of 0.051 (p
value> 0.05) which meant that there were no differences
in the cognitive aspects before and after therapy. Whereas in psychosocial aspect, obtained a score of
0,027 (p-value <0,05) which meant there was a
significant difference in mothers' knowledge within the
intervention group before and after therapy. While the
analysis of mothers' knowledge before and after therapy
in the control group, obtained that mothers' knowledge
on cognitive aspect was 0,183 (p value> 0,05) which
meant that there was no difference between before and
after. In the psychosocial aspect, mothers' knowledge in
control group was 0.323 (p value> 0,05) which meant
that there was no difference before and after. Table 3 shows mother's knowledge of cognitive
aspect in giving stimulation after therapeutic group
therapy. Obtained a score of 0,070 (p value> 0,05) which
meant that there was no difference between intervention
and control group. Whereas in the psychosocial aspect, it
was found that mothers' knowledge was 0,460 (p value>
0,05) which meant that there was no difference between
intervention and control group. Introduction This inspired the researchers to
conduct a research to provide therapeutic group therapy
regarding mother's knowledge and ability about the
mental development of preschoolers in Padang Panjang
City. The purpose of this research was to determine the
effect of therapeutic group therapy regarding mother's
knowledge in providing stimulation of cognitive and
psychosocial development of preschoolers. To overcome this circumstance, it is required the role
of nurses who can help mothers in implementing
knowledge to stimulate children for their optimal
development. Nursing
services
in
the
form
of
Community of Mental Health Nursing (CMHN) that
should exist in the Public Health Center (Puskesmas) are
demanded to provide knowledge to the mother in
stimulating child development (Damayanti, 2010). Nurses as a part of the health services need to implement ■■ Shinta Dewi Kasih Bratha et al. / International Journal of Research in Nursing 2018, ■■■ (■): ■■■.■■■
DOI: 10.3844/ijrnsp.2018.■■■.■■■ Shinta Dewi Kasih Bratha et al. / International Journal of Research in Nursing 2018, ■■■ (■): ■■■.■■■
DOI: 10.3844/ijrnsp.2018.■■■.■■■ Shinta Dewi Kasih Bratha et al. / International Journal of Research in Nursing 2018, ■■■ (■): ■■■.■■■
DOI: 10.3844/ijrnsp.2018.■■■.■■■ Discussion The differences in mothers' knowledge after therapy
in both intervention and control groups did not have any
significant change. In the intervention group, there is an
increase in mother's knowledge regarding psychosocial
aspects. This occurs because, before the therapy,
respondents do not know about the psychosocial aspects. Even the researchers get many questions when giving
therapy in psychosocial aspects. Starting from a child's
ability to help with simple homework, playing with
household appliances and enjoy playing with peers with
gender-based games, visiting neighbors, friends or
relatives without parents, making family albums, playing
creatively with friends, playing selling and shopping are
the stimulation on psychosocial aspects (Hapsari, 2016). This has led to significant changes before and after
treatment. Through the presenting of stimuli can support
the participants during the learning process (Bhinnety,
2012). As more stimulus is given, it enhances a person in
some way. The method of therapy given in this
intervention is a very suitable stimulation during the
adult learning process (Ur and Govt, 2016). Therapeutic group therapy is a promotive action to
enhance child development to be optimal so as to
prevent the appearance of mental health problems. This
therapy allows participants to share their experiences and
help each other to solve problems, including to
anticipate upcoming problems by training effective
ways to control stress (Nugter and Engelsbel, 2015). Therapeutic group therapy also intends to develop the
ability of members and mutually strengthening to form
an adaptive behavior (Damayanti, 2010). This research
also
performs
aforementioned. However,
unlike
previous therapy, the researchers only set small groups
which consist of 3 to 5 people for each group. It
intended to let the researchers focus on every person
and surely teach all aspects for each respondent. There was no significant change in the control group. Actually, mothers' knowledge in the control group may
increase through pre-test and post-test because the
questions in the tests are the evaluation that must be
completed by the respondent. The questions can remind
the respondents about everything they are supposed to
know
regarding
aspects
of
development
within
preschoolers. In the learning process of an adult, people
will believe in a new knowledge if they feel the necessity. Consequently, there will be a learning process that is
formed by the individual itself. There is no significant difference in the cognitive
aspect. This happens because some mothers brought
non-preschoolers during the therapy. Results From the demographic data, it was found that the
respondents were preschoolers in their 3 and 4 years old. In the intervention group, there were 25 children in their
3 years old and 15 children aged 4 years. Whereas, in the
intervention group there were 22 children aged 3 years
and 18 children aged 4 years. There were 22 girls and 18 Table 1: Analysis of mothers' knowledge in giving stimulation of preschoolers development before therapy on intervention and
control group
Development dimensions
Group
N
Mean
SD
P-Value
Cognitive
Intervention
40
2,68
1,207
0,041
Control
40
3,15
0,802
Psychosocial
Intervention
40
4,30
1,814
0,000
Control
40
5,78
1,074 ■■ Shinta Dewi Kasih Bratha et al. / International Journal of Research in Nursing 2018, ■■■ (■): ■■■.■■■
DOI: 10.3844/ijrnsp.2018.■■■.■■■ Shinta Dewi Kasih Bratha et al. / Intern
DOI: 10.3844/ijrnsp.2018.■■■.■■■ Table 3: Analysis of mothers' knowledge in giving stimulation of preschoolers development after therapy on intervention and
control group
Development Dimensions
Group
N
Mean
SD
P-Value
Cognitive
Intervention
40
2,85
1,099
0,81
Control
40
3,22
0,768
Psychosocial
Intervention
40
4,60
1,707
0,000
Control
40
5,80
1,091 respondents would split (Damayanti, 2010). The
researchers suggest that during this therapy, the
respondents do not bring other toddlers so that they can
concentrate on the therapy. Acknowledgment Hapsari, I.I., 2016. Psikologi perkembangan anak. Indeks: Jakarta. This is a non-grant sponsored research. Istiana, D., 2015. Terapi kelompok terapeutik anak
dengan
orang
tua
dan
guru
meningkatkan
perkembangan mental anak usia sekolah. Discussion Consequently, the
researchers unable to concentrate even though they had
tried to focus on each individual. However, the
characteristic of Indonesian society who have more
toddlers in a family presents a particular challenge for
the researchers. A noisy environmental factor can affect
the outcome of the therapy because it can interrupt the
absorption
of
information
(Gwinner,
2016). An
unbalanced quantity of groups might disrupt the
implementation of therapy because the concentration of The improving of mothers' knowledge in the therapy
group indicates the importance of providing therapeutic
therapy groups for preschoolers to enhance children
development according to their age. However, in providing
this therapy, the researchers should concentrate on each
respondent in order to optimize the results of this research. ■■ Shinta Dewi Kasih Bratha et al. / International Journal of Research in Nursing 2018, ■■■ (■): ■■■.■■■
DOI: 10.3844/ijrnsp.2018.■■■.■■■ Shinta Dewi Kasih Bratha et al. / International Journal of Research in Nursing 2018, ■■■ (■): ■■■.■■■
DOI: 10.3844/ijrnsp.2018.■■■.■■■ In the presenting of therapeutic group therapy, it can
be concluded that the improvement of mothers'
knowledge can happen if there is a conducive
environment, high curiosity from the respondent and
active cooperation of the participants. When conducting
the
therapy,
researchers
should
anticipate
the
surroundings and encourage the respondents about the
importance of this therapy for the development of
preschoolers. Thus, it can enhance the knowledge of
mothers
or
respondents
in
giving
development
stimulation toward preschoolers, especially on cognitive
and psychosocial aspects. Bhinnety, M., 2012. Struktur dan Proses Memori. Social
Sci. Med., 16: 74-88. Cameron, X.J.L., K.L. Eagleson, N.A. Fox, T.K. Hensch
and X. Levitt, 2017. Social origins of developmental
risk for mental and physical illness. J. Neurosci., 37:
10783-10791. DOI: 10.1523/JNEUROSCI.1822-17.2017 Conference, I. and E. Psychology, 2012. Relationship
Between Parent’s Spiritual Intelligence, level of
education and children’s mental health, 69(Iceepsy). pp: 2114-2118. Damayanti, R., 2010. Pengaruh Terapi Kelompok
Terapeutik
terhadap
Kemampuan
Ibu
dalam
Memberikan Stimulasi Perkembangan Inisiatif Anak
Usia Prasekolah di Kelurahan Kedaung Bandar
Lampung 2010. Conclusion There was no change regarding mothers' knowledge
in the cognitive aspect before and after therapeutic group
therapy in the intervention and control group. Meanwhile,
there was a meaningful change of the psychosocial aspects
within the intervention group. And there were significant
differences before and after therapeutic group therapy in
the intervention and control group. With this therapy, it
was expected to improve the development of preschoolers,
especially on the cognitive and psychosocial aspects. Suggestions for next researchers, optimize the granting of
therapy
and
suggest
participants
only
to
bring
preschoolers, where a conducive environment makes
participants focus on receiving therapy. Enns, J., M. Holmqvist, P. Wener, G. Halas and A. Schultz et al., 2016. Mapping interventions that
promote mental health in the General Population: A
scoping review of reviews. Preventive Medicine. DOI: 10.1016/j.ypmed.2016.02.022 Feil, E.G., A. Frey, H.M. Walker, J.W. Small and J.R. Seeley et al., 2017. The efficacy of a home-school
intervention for preschoolers with challenging
behaviors: A randomized controlled trial of
preschool first step to success. J. Early Intervention,
36: 151-170. DOI: 10.1177/1053815114566090 Gwinner, K., 2016. Arts, therapy and health: Three
stakeholder viewpoints related to young people’s
mental health and wellbeing in Australia. Arts
Psychotherapy. DOI: 10.1016/j.aip.2016.05.016 Ethics This study has been reviewed by the ethical
committee of Faculty of Medicine no 127/KEP/FK/2018
and meet all the requirements of intervention study. Mills, R., J. Scott, R. Alati, M.O. Callaghan and J.M. Najman et al., 2013. Child abuse and neglect child
maltreatment and adolescent mental health problems
in a large birth cohort ଝ. Child Abuse Neglect, 37:
292-302. DOI: 10.1016/j.chiabu.2012.11.008 Author’s Contributions Shinta Dewi Kasih Bratha: Developed and finalized
the manuscript. Kim, M.H., L. Shimomaeda, R.J. Giuliano and E.A. Skowron,
2017. Experimental
child
intergenerational associations in executive function
between mothers and children in the context of
risk. J. Experimental Child Psychology, 164: 1-15. DOI: 10.1016/j.jecp.2017.07.002 Meri Neherta: Supervised and provided feedback
for the manuscript. Dewi Eka Putri: Supervised and provided feedback
for the manuscript. Maryatun,
2014. Pengaruh
terapi
kelompok
terapeutik terhadap perkembangan remaja di
panti
sosial
marsudi
putra
dharmapala
inderalaya. J. Srivijaya Nursing, 1: 12-20. References Balseviciene, B., L. Sinkariova and S. Andrusaityte,
2014. Do Green spaces matter? The associations
between parenting stress, child mental health
problems and green spaces. Procedia – Social
Behavioral Sci., 140: 511-516. Nikolaev, E.L., E.A. Baranova and S.A. Petunova, 2016. Mental Health Problems in young children: The
role of mother’s coping and parenting styles and
characteristics of family functioning. Procedia -
Social Behavioral Sci., 233: 94-99. DOI: 10.1016/j.sbspro.2016.10.152 DOI: 10.1016/j.sbspro.2014.04.462 ■■ Shinta Dewi Kasih Bratha et al. / International Journal of Research in Nursing 2018, ■■■ (■): ■■■.■■■
DOI: 10.3844/ijrnsp.2018.■■■.■■■ Notoadmodjo, Soekidjo. (2012). Promosi Kesehatan dan
Perilaku Kesehatan. Rineka Cipta Jakarta. Spielfogel, J.E., S.J. Leathers, E. Christian and L.S. Mcmeel,
2011. Parent
management
training,
relationships with agency staff and child mental
health: Urban foster parents’ perspectives. Children
Youth Services Review, 33: 2366-2374. DOI: 10.1016/j.childyouth.2011.08.008 Nugter, M.A. and F. Engelsbel, 2015. Outcomes of
FLEXIBLE
Assertive
Community
Treatment
(FACT) Implementation: A prospective real life
study. Community Mental Health J., 52: 898-907. DOI: 10.1007/s10597-015-9831-2 Ur, A. and R. Govt, 2016. Mothers’ Knowledge about
Child Development. Riskesdas, 2013. Badan Statistik Indonesia. Xing, S., X. Gao, X. Song, M. Archer and D. Zhao et al.,
2017. Chinese Preschool Children’s Socioemotional
Development: The effects of maternal and paternal
psychological control. Front. Psychol., 8: 1-9. DOI: 10 3389/fpsyg 2017 01818 Shoshani, A., M. Slone and L.E. Prino, 2017. Positive
education for young children: Effects of a positive
psychology intervention for preschool children on
subjective well being and learning behaviors. Front. Psychol., 8: 1-11. DOI: 10.3389/fpsyg.2017.01866 Years, I., 2014. Promoting Early Childhood Mental Health. ■■
|
https://openalex.org/W2624499583
|
https://www.nature.com/articles/s41598-017-03239-1.pdf
|
English
| null |
Multimode quantum states with single photons carrying orbital angular momentum
|
Scientific reports
| 2,017
|
cc-by
| 6,502
|
Multimode quantum states with
single photons carrying orbital
angular momentum Received: 16 January 2017
Accepted: 20 April 2017
Published: xx xx xxxx Received: 16 January 2017
Accepted: 20 April 2017
Published: xx xx xxxx Xin-Bing Song1, Shi-Yao Fu2, Xiong Zhang1, Zhen-Wei Yang1, Qiang Zeng1, Chunqing Gao2 &
Xiangdong Zhang1 Xin-Bing Song1, Shi-Yao Fu2, Xiong Zhang1, Zhen-Wei Yang1, Qiang Zeng1, Chunqing Gao2 &
Xiangdong Zhang1 We propose and experimentally demonstrate a scheme for generating multimode quantum states
with single photons carrying orbital angular momentum (OAM). Various quantum states have been
realized by superposing multiple OAM modes of single photons in two possible paths. These quantum
states exhibit NOON-like “super-resolving” interference behavior for the multiple OAM modes of
single photons. Compared with the NOON states using many photons, these states are not only easily
prepared, but also robust to photon losses. They may find potential applications in quantum optical
communication and recognizing defects or objects. The method to identify a particular kind of defect
has been demonstrated both theoretically and experimentally. Quantum entanglement plays a key role in quantum information processing such as quantum teleportation,
quantum cryptographic, quantum metrology and parallel computing1–11. One kind of multiphoton entangled
states, known as NOON states, are a particularly useful class of states11–16. They contain N indistinguishable par-
ticles in an equal-weighted superposition of all being in one of two possible modes w and v, which are expressed
as
|
〉
+ |
〉
N
N
(
, 0
0,
)
w v
w v
1
2
,
, , and can be used to obtain a high measurement precision that scales as N. Many
schemes for the generation of NOON-states have been proposed theoretically12–18. However, experimentally, it is
extremely challenging. So far, NOON states with only a few photons or particles have been reported experimen-
tally19–26. In addition, N-photon entangled states become increasingly sensitive to losses as N grows27, 28. In the
presence of losses or other types of noise, no two-mode quantum state can beat the standard limit by more than
just a constant factor in the limit of large N29. Multimode quantum states with
single photons carrying orbital
angular momentum +
−
(
)
1
1
R
q
L
q
1
2
,
2
,2 ,
b
diff j
g
Recently, single-photon NOON-like quantum states
+
−
(
)
1
1
R
q
L
q
1
2
,
2
,2 , superpositions of eigenstates of
light with opposite total angular momentum quantum numbers at different polarization modes (right- and
left-circular), have been proposed and demonstrated experimentally30. Such states in the single-photon regime
can be exploited to measure rotation angles with a precision scaling up to m times the square root of the number
of probes used. Although these states are also affected by angular momentum decoherence such as noises, com-
pared with the N-photon NOON states, the OAM scheme still shows some advantages for the ultra-sensitive
angular measurement, because every photon in this regime is disentangled from all others and hence the loss of a
photon does not affect the overall phase coherence30. pf
p
Inspired by the above studies, in this work we propose a kind of new NOON-like quantum states based on
single photons with orbital angular momentum (OAM)31–33. We call them multimode NOON-like states. In our
scheme, multiple OAM modes of single photons have been used to superpose in two possible paths and various
NOON-like quantum states can be realized. When the multiple modes degenerate into single modes, our scheme
is the same to that in ref. 30. Because the transmission capacity of information can be increased by adding modes,
in the past few years many investigations have been done to increase the number of modes in various multiplexers
for optical communications34–36. Since various multimode NOON-like states can be generated by our scheme, it
is expected to have potential applications in optical communications. www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports Results and Discussion The state of an incident single photon can be written as Ψ = L
in
, where
=
∑
L
c l
D L
p p p
1
( )
describes an equivalent OAM mode, D L
( ) is a coefficient for normalization, and cp is the prob-
ability amplitude of the eigen-mode lp with p being the topological charge. The single photon with such a vortex
charge can be obtained by the diffraction of a specially designed hologram37, 38. After a beam splitter (BS) and a
phase difference φ, the incident state of the single photon turns to be: ϕ
| 〉
=
|
〉+
|
〉
φ
L
e
L
1
2
(
, 0
0,
),
(1)
La b
a b
i
a b
,
,
, (1) where
=
L
L
, 0
0
a b
a
b
,
and
=
L
L
0,
0
a b
a
b
,
. L a ( L b) represents the OAM L mode corresponding to the
path mode a b
( ), and 0 is an empty mode. The state described by Eq. (1) indicates a photon with a superposition
of the OAM mode L either in one path or the other. Similar to the relation between the phase and photon number
in NOON states, here the phase φ is sensitive to OAM eigen-modes. So, Eq. (1) can be further written as ∑
ϕ
=
∑
+
θ
(
)
c
c
l
e
l
1
2
, 0
0,
,
(2)
La b
p
p
p
p
p
a b
ip
pa b
,
2
,
, (2) where θ
p is the phase for the OAM eigen-mode lp, and θ is an angular. Because of orthogonality
δ
〈
〉=
l l
p q
pq,
where δ is Kronecker function, we can obtain the probability to get the photon without mode discrimination: where θ
p is the phase for the OAM eigen-mode lp, and θ is an angular. Because of orthogonality
δ
〈
〉=
l l
p q
pq,
where δ is Kronecker function, we can obtain the probability to get the photon without mode discrimination: ∑
θ
=
∑
+
. Results and Discussion Experiment demonstration of multimode NOON-like states. We consider that a single photon with
OAMs impinges into a Mach-Zehnder (MZ) interferometer as shown on the top of Fig. 1. The two paths are 1Beijing Key Laboratory of Nanophotonics & Ultrafine Optoelectronic Systems, School of Physics, Beijing Institute
of Technology, Beijing, 100081, China. 2School of Opto-Electronics, Beijing Institute of Technology, Beijing, 100081,
China. Correspondence and requests for materials should be addressed to X.Z. (email: zhangxd@bit.edu.cn) Scientific Reports | 7: 3601 | DOI:10.1038/s41598-017-03239-1 1 1 www.nature.com/scientificreports/ Figure 1. The probability P to get the photon by a detector on an output of the interferometer. (a) The result for
an equivalent mode L composed of equal weighted superposition of l7 and l8. (b) The result for a mode
composed of eigen modes from 1 to 100 with weighting factors
=
−
c
p
101
p
. (c) The result for a mode
composed of equal weighted OAM eigenmodes from 1 to 100. The inset is the magnification of the box area. (d)
The result for a mode composed of all prime number modes between 1 and 100 with equal weight. Scheme to
test NOON states is shown on top of the figure. Ψ in describes a single photon state with superposition OAMs. BS: beam splitter; M: mirror. Figure 1. The probability P to get the photon by a detector on an output of the interferometer. (a) The result for
an equivalent mode L composed of equal weighted superposition of l7 and l8. (b) The result for a mode
composed of eigen modes from 1 to 100 with weighting factors
=
−
c
p
101
p
. (c) The result for a mode
composed of equal weighted OAM eigenmodes from 1 to 100. The inset is the magnification of the box area. (d)
The result for a mode composed of all prime number modes between 1 and 100 with equal weight. Scheme to
test NOON states is shown on top of the figure. Ψ in describes a single photon state with superposition OAMs. BS: beam splitter; M: mirror. denoted by modes a and b, respectively. Results and Discussion 1(b), a cluster of oscillation appears in such
a case, which is shown in the inset of Fig. 1(c). It is interesting that the noise-like pattern as shown in Fig. 1(d) can
also be produced, if we choose all prime number of OAM modes between 1 and 100 with the same weight. Recent
experiments have shown that the OAM with
<
l
300
p
can be well modulated41, 42. In fact, within such a range, very
rich multimode NOON-like states can be constructed.hh The above theoretical scheme can be realized by the experimental setup as shown on the top of Fig. 2. The
scheme consists of two parts: Mode generation and State analysis. The single photon source is provided by the
signal photons of entangled photon pairs which are produced through spontaneous parametric down conversion
process in a ×
×
mm
5
5
3
type-I phase matching beta-barium-borate crystal (BBO). The crystal is pumped by
the second harmonic of a Ti:sapphire picoseconds laser (Tsunami, Spectral Physics) with center wavelength
390 nm, and repetition rate 80 MHz. The signal photons are collected into a single mode fiber and projected onto
a spatial light modulator (SLM) to gain OAM modes, then pass through an interferometer to reach detector Ds. The idle photons are detected by Di as a trigger. Both the signal and idler photons are spectrally filtered by inter-
ference filters with 10 nm bandwidth centered at 780 nm before arriving at single-photon detectors (Perkin-Elmer
SPCMAQR-14). A time window of 5 ns is chosen to capture coincidence counting, and the coincidence rates are
recorded as experimental data. Here we take
=
+
. L
l
l
2 5
1
5 and
=
+
+
. L
l
l
l
2 5
1
2
6 as examples to show how this setup can generate multi-
mode NOON-like states. The choice of these examples is only to facilitate the realization of the experiment with-
out losing generality. First, we manipulate the SLM to generate single photons with OAM modes. Dp1 will be
rotated in the up path and Dp2 is fixed in the low path to compensate path difference. The experimental results for
the coincidence counting (circle dots) are shown in Fig. 2(a) and (b) under the condition of pump power 50 mW. The error bars demonstrate experimental statistical deviation. Results and Discussion p
c
c
l
1
2
1
cos(
)
(3)
p
p
p
p
p
2
2 (3) Such a result originates from the superposition of multiple OAM modes, the mode amplitude cp can be taken
as arbitrary value by controlling a specially designed hologram, which is different from the single mode case
described in ref. 30. In addition, a superposition of one photon without the OAM in two paths has been discussed
in the previous investigations39, 40, which is different from the present case with multiple OAM modes. According
to the present design, we can obtain various NOON-like quantum states. For example, if we take two OAM modes
l7 (
=
p
7) and l8 (
=
p
8), that is
=
+
L
l
l
(
)
1
2
7
8 , the output NOON-like states exhibit beat wave-like pattern as
shown in Fig. 1(a). If
= ∑
−
∑
−
=
=
L
p l
p
(101
) /
(101
)
p
p
p
1
100
1
100
2 is taken, comb-like pattern appears as shown in
Fig. 1(b). Furthermore, if we modulate the weighting factor equaled, that is
=
∑=
L
l
p
p
1
100
1
100
, we still get a Scientific Reports | 7: 3601 | DOI:10.1038/s41598-017-03239-1 2 www.nature.com/scientificreports/ Figure 2. Experimental setup and results for multimode NOON states. SMF: single mode fiber; Col: collimator;
SLM: spatial light modulator; AM: absorbing material; BS1,2: beam splitter; DP1,2: Dove prism; M1,2: mirror; Di,s:
detector. (a) and (b) show the results for
=
+
. L
l
l
2 5
1
5 and
=
+
+
. L
l
l
l
2 5
1
2
6, respectively. The round dots
and solid lines represent the experimental results and theoretical fitting, respectively. Figure 2. Experimental setup and results for multimode NOON states. SMF: single mode fiber; Col: collimator;
SLM: spatial light modulator; AM: absorbing material; BS1,2: beam splitter; DP1,2: Dove prism; M1,2: mirror; Di,s:
detector. (a) and (b) show the results for
=
+
. L
l
l
2 5
1
5 and
=
+
+
. L
l
l
l
2 5
1
2
6, respectively. The round dots
and solid lines represent the experimental results and theoretical fitting, respectively. comb-like pattern as shown in Fig. 1(c). Comparing it with that in Fig. Results and Discussion Under the same
conditions as in (a), the results for =
l
1, 2, 3, 4 are shown in (b), (c), (d) and (e), respectively. The round dots
and solid lines represent the experimental and theoretical results, respectively. circle dots represent the experimental results and the solid lines are corresponding normalized theoretical results. The l-fold improvement for the angular measurement precision is observed clearly. For the scheme in ref. 30, the stability of interferometer is not needed and a polarization measurement gives
information on a physical rotation of the reference frame by using a single mode OAM state. However, in the
present scheme the stability of interferometer is very important, the generation of multimode quantum states
depends directly on it. Based on such a scheme, various multimode quantum states can be realized. Because these
quantum states can exhibit NOON-like “super-resolving” interference behavior, they are expected to have some
special applications, such as recognition of complex defects or objects. Recognition of spiral defects with single photons. The multiphoton NOON states are usually used to
obtain high-precision phase measurements. The present multimode NOON-like quantum states we have con-
structed can not only be applied to this aspect, but we believe they can be applied to optical communication to
improve the efficiency of information transfer because of multiple modes involved. Especially, it can be applied to
recognition of complex spiral defects or objects. In general, defects always exist in real materials. How to identify
defects is an important issue. There are various types of defects, in which the spiral (screw) defects are also very
common in the process of fabricating microstructures. The characteristics of these defects have been described in
refs 43 and 44. In the following, we discuss how to identify the spiral defects by using these states. When the pho-
ton is incident on the material with the defect, the scattered light will be affected by the defect. If the defect can
destroy the photons of certain modes (say q) with a probability ηq, that is, the operator of destroying process can
be described by
η
−∑
l
l
1
q q q
q , when the material with a defect is put in one path (say the up path) of the inter-
ferometer on the top of Fig. 2, Eq. Results and Discussion For all plots, error bars are calculated directly from
experimental data by repeating measurement, and the instability of interferometer under the finite experimental
condition is the key factor. Figure 2(a) corresponds to the case with
=
+
. L
l
l
2 5
1
5(
=
c
1
1
and
=
. c
2 5
5
), and
Fig. 2(b) to that with
=
+
+
. L
l
l
l
2 5
1
2
6 (
=
=
c
c
1
1
2
and
=
. c
2 5
6
). The solid lines in Fig. 2(a) and (b) are the
corresponding theoretical results as depicted by Eq. (3). It is seen clearly that the agreements between the exper-
imental measurements and theoretical results are very well. In fact, if we only take one OAM mode such as the
topological charge l, our results naturally degenerate into the single mode case. In such a case, Eq. (1) can be
written as: ϕ
|
〉
=
|
〉
+
|
〉
. θ
l
l
e
l
1
2
( , 0
0,
)
(4)
a b
a b
il
a b
,
,
, (4) The probability to get the photon in one output port is expressed as The probability to get the photon in one output port is expressed as θ
=
+
. P
l
1
2
[1
cos( )]
(5) (5) The single-photon NOON-like quantum states with the single OAM mode have been analyzed in ref. 30. The
present method is different from them where the polarization degree of freedom (DOF) is replaced by the path
DOF. However, the results are similar. The experimental result for =
l
0 is shown in Fig. 3(a) as a calibration. Under the same conditions, the measured results for =
l
1, 2, 3, 4 are given in Fig. 3(b)–(e), respectively. The Scientific Reports | 7: 3601 | DOI:10.1038/s41598-017-03239-1 3 www.nature.com/scientificreports/ tificreports/
Figure 3. Experimental results for NOON-like states. (a) The experimental result for =
l
0. Under the same
conditions as in (a), the results for =
l
1, 2, 3, 4 are shown in (b), (c), (d) and (e), respectively. The round dots
and solid lines represent the experimental and theoretical results, respectively. Figure 3. Experimental results for NOON-like states. (a) The experimental result for =
l
0. Results and Discussion The top pattern shows the incident multimode NOON states. The middle one is the output pattern when
the defect is introduced. The bottom one shows the difference between the above two. The left column displays
results for the situation of equal weighted superposition by l7 and l8. (a) Is the result when l7 and l8 are both
included, and it is the same as Fig. 1(a). (b) Is the result when the mode l8 is broken. (c) Shows the difference
between (a) and (b). The right column shows results for the situation of the mode composed of all prime
number modes between 1 and 100 with the equal weight. (d) Is the result when all prime modes are included,
and it is the same as Fig. 1(d). (e) Is the result when the mode l2 is broken. (f) Shows the difference between (a)
and (c). Figure 4. Theoretical results for defect recognition. The center column shows the progress of defect recognition
sketch. The top pattern shows the incident multimode NOON states. The middle one is the output pattern when
the defect is introduced. The bottom one shows the difference between the above two. The left column displays
results for the situation of equal weighted superposition by l7 and l8. (a) Is the result when l7 and l8 are both
included, and it is the same as Fig. 1(a). (b) Is the result when the mode l8 is broken. (c) Shows the difference
between (a) and (b). The right column shows results for the situation of the mode composed of all prime
number modes between 1 and 100 with the equal weight. (d) Is the result when all prime modes are included,
and it is the same as Fig. 1(d). (e) Is the result when the mode l2 is broken. (f) Shows the difference between (a)
and (c). Figure 5. Experimental results for recognition. The left column describes results for the incident NOON state
with
=
+
. L
l
l
2 5
1
5. (a) Is the result when the iris is open and it is part of Fig. 2(a). (b) Is the result when the iris
is partly closed to block the mode l5. (c) Shows the difference between (a) and (b). The right column shows
results for the incident NOON state with
=
+
+
. L
l
l
l
2 5
1
2
6. Results and Discussion (2) becomes ∑
∑
ϕ
η
=
∑
+
−
θ
θ
(
)
c
c
l
e
l
c
e
l
1
2
, 0
0,
0,
,
(6)
L a b
p
p
p
p
p
a b
ip
p a b
q
q q
iq
q a b
,
2
,
,
, (6) where the last term in Eq. (6) represents the effect of the defect. Here we assume that the introduction of defects
does not affect the coherent superposition, thus, Eq. (6) is still described with a pure state. In such a case, the
corresponding probability is ∑
∑
θ
η
η
η
θ
=
∑
+
+
−
−
. P
c
c
l
c
l
1
2
[1
cos(
)]
1
2
[
2
2
cos(
)]
(7)
b
p
p
p
p
p
q
q
q
q
q
q
2
2
2
2hf (7) We perform the experiments with and without the defect, separately. The difference of the output signals is
expressed as We perform the experiments with and without the defect, separately. The difference of the output signals is
expressed as
∑
η
η
η
θ
= −
∑
−
−
. ( )
P
c
c
l
1
4
2
2
cos
(8)
p
p
q
q
q
q
q
q
2
2
2 (8) From Eq. (8), we can get the information of the defect. In the middle column of Fig. 4, we show the defect
recognition process vividly. The top pattern shows the multimode NOON-like state and the middle one describes
the output result when the defect is introduced. From the difference between them, we can obtain the information
of the defect as shown by the bottom pattern. In the left column of Fig. 4, a concrete example is given. In such a
case, the incident multimode NOON-like state is taken as the beat wave-like pattern (
=
+
L
l
l
(
)
1
2
7
8 ) as shown
in Fig. 1(a). The output pattern is given in Fig. 4(b), which describes the interference result of the unaffected mode Scientific Reports | 7: 3601 | DOI:10.1038/s41598-017-03239-1 4 www.nature.com/scientificreports/ Figure 4. Theoretical results for defect recognition. The center column shows the progress of defect recognition
sketch. Results and Discussion (d) Is the result when the iris is open and it is part
of Fig. 2(b). (e) Is the result when the iris is partly closed to block the mode l6. (f) Shows the difference between
(d) and (e). The round dots and solid lines represent the experimental and theoretical results, respectively. Figure 5. Experimental results for recognition. The left column describes results for the incident NOON state
with
=
+
. L
l
l
2 5
1
5. (a) Is the result when the iris is open and it is part of Fig. 2(a). (b) Is the result when the iris
is partly closed to block the mode l5. (c) Shows the difference between (a) and (b). The right column shows
results for the incident NOON state with
=
+
+
. L
l
l
l
2 5
1
2
6. (d) Is the result when the iris is open and it is part
of Fig. 2(b). (e) Is the result when the iris is partly closed to block the mode l6. (f) Shows the difference between
(d) and (e). The round dots and solid lines represent the experimental and theoretical results, respectively. l8. The difference between them (
−
P
Pb) is the defect state l7, which has been shown in Fig. 4(c). If we take the
defect mode l2, and the noise-like multimode NOON-like state (Fig. 1(d)) as the incident state, similar recogni-
tion process has also been demonstrated, which is shown in the right column of Fig. 4.h p
g
g
The defect recognition process can be performed by the experimental setup as shown on the top of Fig. 2. In
the experiment, based on the partially space separation of different modes, we use an iris to mimic the defect. This
scheme is universally valid for all kinds of OAM modes, but here we just take two examples. One is that the inci-
dent multimode NOON state is taken as that described in Fig. 2(a) (
=
+
. L
l
l
2 5
1
5), the iris is set to block the
photons with an OAM mode l5, and the results are shown in Fig. 5(a), (b) and (c). The other is that the multimode
NOON state described in Fig. 2(b) (
=
+
+
. Results and Discussion L
l
l
l
2 5
1
2
6) has been used as the incident state, the iris is partly The defect recognition process can be performed by the experimental setup as shown on the top of Fig. 2. In
the experiment, based on the partially space separation of different modes, we use an iris to mimic the defect. This
scheme is universally valid for all kinds of OAM modes, but here we just take two examples. One is that the inci-
dent multimode NOON state is taken as that described in Fig. 2(a) (
=
+
. L
l
l
2 5
1
5), the iris is set to block the
photons with an OAM mode l5, and the results are shown in Fig. 5(a), (b) and (c). The other is that the multimode
NOON state described in Fig. 2(b) (
=
+
+
. L
l
l
l
2 5
1
2
6) has been used as the incident state, the iris is partly Scientific Reports | 7: 3601 | DOI:10.1038/s41598-017-03239-1 5 www.nature.com/scientificreports/ closed to block the mode l6, and the corresponding results are given in Fig. 5(d), (e) and (f). In the experiment, we
modulate the weights of l5 and l6 bigger than others to make the experiment easier. The round dots and solid lines
represent the experimental and theoretical results, respectively. The agreement between the theoretical results and
experimental measurements is observed again. We have to point out that the pinhole is unable to discriminate
two adjacent modes, here we only provide a demonstration of the principle. j
y p
p
p
It is worth noting that the sensing processes shown in Figs 4 and 5 work only if the defect objects are present
in the querying light. In fact, if the objects are not in the querying light, we can measure the scattered fields of the
defect objects as the output signals. In such a case, it is directly related to the quantum radar45, 46. In recent years,
quantum illumination and radar without OAM photons have been discussed in detail45, 46. For the case with OAM
photons, the discussions will be given elsewhere. At end, we would like to point out that the present scheme is
also applicable to the case of classical OAM beam although the above discussions only focused on quantum states
with single photons carrying OAM. Conclusions In summary, we have demonstrated both theoretically and experimentally the generation of multimode
NOON-like quantum states using the superposition of OAM multiple modes of single photons in two possi-
ble paths. Various NOON-like quantum states have been realized, which is able to return to the single mode
case when one OAM mode is taken30. This means that NOON-like quantum states with required modes can
be designed according to our scheme. Compared with the NOON states using many photons, these states are
not only easily prepared, but also robust to photon losses. Thus, the difficulty using many photons can also be
avoided. We anticipate that potential applications of the present scheme in optical communications can improve
the efficiency of information transfer. It is also anticipated to have important applications in recognition of defects
or objects. Based on these NOON-like quantum states, we have also demonstrated both theoretically and exper-
imentally recognition of the particular kind of defect. References 1. Nielsen, M. A. & Chuang, I. L. Quantum Computation and Quantum Information. Cambridge University Press (2000). 2. Bennett, C. H. & DiVincenzo, D. P. Quantum information and computation. Nature 404, 247 (2000). 1. Nielsen, M. A. & Chuang, I. L. Quantum Computation and Quantum Information. Cambridge University Press (2000
2. Bennett, C. H. & DiVincenzo, D. P. Quantum information and computation. Nature 404, 247 (2000). Q
p
(
)
3. Horodecki, R., Horodecki, P., Horodecki, M. & Horodecki, K. Quantum entanglement. Rev. Mod. Phys. 81, 865 (2009). g
y
4. Pan, J.-W. et al. Multiphoton entanglement and interferometry. Rev. Mod. Phys. 84, 777 (2012). p
g
y
y
5. Gisin, N., Ribordy, G., Tittel, W. & Zbinden, H. Quantum cryptography. Rev. Mod. Phys. 74, 145 (2002). y
yp g p y
y
6. Giovannetti, V., Lloyd, S. & Maccone, L. Quantum metrology. Phys. Rev. Lett. 96, 010401 (2006). ovannetti, V., Lloyd, S. & Maccone, L. Quantum metrology. Phys. R 7. DiVincenzo, D. P. Quantum computation. Science 270, 255 (1995). p
(
)
8. Spagnolo, N. et al. Phase estimation via quantum interferometry for noisy detectors. Phys. Rev. Lett. 108, 233602 (2012). h
ll
b
l
‘
’ f
l
(
) agnolo, N. et al. Phase estimation via quantum interferometry for n 9. Roos, C. F., Chwalla, M., Kim, K., Riebe, M. & Blatt, R. ‘Designer atoms’ for quantum metrology. Nature 443, 316 (20 10. Lee, H., Kok, P. & Dowling, J. P. A quantum Rosetta stone for interferometry. J. Mod. Opt. 49, 2325 (2002). g
y
p
11. Lee, S.-Y., Lee, C.-W., Lee, J. & Nha, H. Quantum phase estimation using path-symmetric entangled states. Sci. R
k
f
l
d
l
ffi
l 11. Lee, S.-Y., Lee, C.-W., Lee, J. & Nha, H. Quantum phase estimat 11. Lee, S.-Y., Lee, C.-W., Lee, J. & Nha, H. Quantum phase estimation using path-symmetric entangled states. Sci. Rep. 6, 30306 (2
12 Lee H Kok P Cerf N J & Dowling J P Linear optics and projective measurements alone suffice to create large photon num W., Lee, J. & Nha, H. Quantum phase estimation using path-symme 11. Lee, S.-Y., Lee, C.-W., Lee, J. & Nha, H. Quantum phase estimation using path-symmetric entangled states. Sci. Rep. 6, 30306 (2016
12. Lee, H., Kok, P., Cerf, N. J. & Dowling, J. P. References Linear optics and projective measurements alone suffice to create large-photon-numb
th
t
l
t Ph
R
A 65 030101 (2002) 11. Lee, S.-Y., Lee, C.-W., Lee, J. & Nha, H. Quantum phase estimation using path-symmetric entangled states. Sci. Rep. 6, 30306 (2
12. Lee, H., Kok, P., Cerf, N. J. & Dowling, J. P. Linear optics and projective measurements alone suffice to create large-photon-nu
path entanglement. Phys. Rev. A 65, 030101 (2002). p
g
y
3. Kok, P., Lee, H. & Dowling, J. P. Creation of large-photon-number path entanglement conditioned on photodetection. Phys. Rev. A
65, 052104 (2002). 4. Kok, P., Braunstein, S. L. & Dowling, J. P. Quantum lithography, entanglement and Heisenberg-limited parameter estimation. J. Opt
B: Quantum Semiclass. Opt. 6, 811 (2004). p
15. Dowling, J. P. Quantum optical metrology – the lowdown on high-N00N states. Contemp. Phys. 49, 125 (2008) p
15. Dowling, J. P. Quantum optical metrology – the lowd ntum optical metrology – the lowdown on high-N00N states. Cont tional generation of N-photon entangled states of light. Phys. Rev. A 16. Fiurášek, J. Conditional generation of N-photon entangled stat g
p
g
g
y
17. Hofmann, H. F. & Ono, T. High-photon-number path entanglement in the interference of spontaneously down-converted 17. Hofmann, H. F. & Ono, T. High-photon-number path entanglement in the interference of spontaneously down-converted photon
pairs with coherent laser light Phys Rev A 76, 031806 (2007) 17. Hofmann, H. F. & Ono, T. High-photon-number path entangl
pairs with coherent laser light. Phys. Rev. A 76, 031806 (2007). 7. Hofmann, H. F. & Ono, T. High-photon-number path entanglement in the interference of spontaneously down-converted photo
pairs with coherent laser light. Phys. Rev. A 76, 031806 (2007). h
d
d
d l
f
h
(
) 17. Hofmann, H. F. & Ono, T. High photon number path entangle
pairs with coherent laser light. Phys. Rev. A 76, 031806 (2007). pairs with coherent laser light. Phys. Rev. A 76, 031806 (2007). 18. Lee, S.-Y. & Nha, H. Second-order superposition operations via 19. Mitchell, M. W., Lundeen, J. S. & Steinberg, A. M. Super-resolving phase measurements with a multiphoton entangled state. Nature
429, 161 (2004). 20. Walther, P. et al. De Broglie wavelength of a non-local four-pho g
g
21. Nagata, T., Okamoto, R., O’Brien, J. L., Sasaki, K. & Takeuchi, S. Beating the Standard Quantum Limit with Four-Entangled Photons. Science 316, 726 (2007). . References Chen, H. et al. Integrated cladding-pumped multicore few-mode erbium-doped fibre amplifier for space-divisionmultiplexed
communications. Nat. Photon 10, 529–532 (2016). 37. Bazhenov, V. Y., Vasnetsov, M. V. & Soskin, M. S. Laser beams with screw dislocations in their wavefronts. JETP Lett 5
38 L
h J D
i M R C
ti l J & P d
tt M J V t
k
t i li ht N
J Ph
7 55 (2005) 7. Bazhenov, V. Y., Vasnetsov, M. V. & Soskin, M. S. Laser beams with screw dislocations in their wavefronts. JETP Lett 52, 429 (1990)
8. Leach, J., Dennis, M. R., Courtial, J. & Padgett, M. J. Vortex knots in light. New J. Phys. 7, 55 (2005). 37. Bazhenov, V. Y., Vasnetsov, M. V. & Soskin, M. S. Laser beams with screw dislocations in their wavefronts. JE , J ,
,
,
, J
g
,
J
g
J
y
,
(
)
39. Lvovsky, A. I. & Mlynek, J. Quantum-Optical Catalysis: Generating Nonclassical States of Light by Means of Linear Optics. Phys. Rev. Lett. 88, 250401 (2002). ime-Reversal and Super-Resolving Phase Measurements. Phys. Rev Resch, K. J. et al. Time-Reversal and Super-Resolving Phase Measur
h
h
h J
p
g
y
(
)
41. Jesacher, A., Furhapter, S., Maurer, C., Bernet, S. & Ritsch-Marte, M. Holographic optical tweezers for object manipulations at an
air-liquid surface. Opt. Express 14, 6342 (2006). 41. Jesacher, A., Furhapter, S., Maurer, C., Bernet, S. & Ritsch-Marte, M. Holographic optical tweezer
air-liquid surface. Opt. Express 14, 6342 (2006). p
p
. Fickler, R. et al. Quantum Entanglement of High Angular Momen g
g
g
43. Nicolau, Y. F., Dupuy, M. & Rolland, G. Extended structural defects in α-Hgl2 single crystals. Journal of materials science-Materials
in electronics 4, 129–172 (1993).t 4. Godinho, M. H., Almeida, P. L. & Figueirinhas, J. L. From Cellulosic Based Liquid Crystalline Sheared Solutions to 1D and 2D Sof
Materials. Materials 7, 4601–4627 (2014). 45. Jiang, K., Lee, H., Gerry, C. C. & Dowling, J. P. Super-resolving quantum radar: Coherent-state sources with homodyne detection
suffice to beat the diffraction limit. J. Appl. Phys. 114, 193102 (2013). fif
pp
y
46. Ball Philip Focus: Quantum Mechanics Could Improve Radar. Physics 8, 18 (2015). fif
46. Ball Philip Focus: Quantum Mechanics Could Improve Radar. Physics 8, 18 (2015). Acknowledgements Author Contributionsh The work was performed by X.S. In performing the work, X.S. got the help of S.F., X.Z., Z.Y., Q.Z. and C.G. The
dea and physical analysis are given by X.Z. All authors reviewed the manuscript. Acknowledgements g
This work is supported by the National Natural Science Foundation of China (Grants Nos 11574031 and
1421001). g
This work is supported by the National Natural Science Foundation of China (Grants Nos 11574031 and
61421001). References Afek, I., Ambar, O. & Silberberg, Y. High-NOON States by Mixin 23. Israel, Y., Rosen, S. & Silberberg, Y. Supersensitive Polarization Microscopy Using NOON States of Light. Phys. Rev. Lett. 112, 1
(2014). . Leibfried, D. et al. Creation of a six-atom ‘Schrödinger cat’ state. N D. et al. Creation of a six-atom ‘Schrödinger cat’ state. Nature 438, 63 g
(
)
25. Jones, J. A. et al. Magnetic Field Sensing Beyond the Standard Quantum Limit Using 10-Spin NOON States. Science 324, 1166
(2009).h 25. Jones, J. A. et al. Magnetic Field Sensing Beyond the Standard Quantum Limit Using 10-Sp
(2009).h 6. Kim, H., Park, H. S. & Choi, S.-K. Three-photon N00N states generated by photon subtraction from double photon pairs. Optic
Express 17, 19720 (2009). p
(
)
27. Dorner, U. et al. Optimal Quantum Phase Estimation. Phys. Rev. Lett. 102, 040403 (2009). p
27. Dorner, U. et al. Optimal Quantum Phase Estimation. Phys. Rev. Lett. 102, 040403 (2009). y
8. Kacprowicz, M., Demkowicz-Dobrzański, R., Wasilewski, W., Banaszek, K. & Walmsley, I. A. Experimental quantum-enhanced
estimation of a lossy phase shift. Nat. Photon 4, 357 (2010). 28. Kacprowicz, M., Demkowicz-Dobrzański, R., Wasilewski, W., Banaszek, K. & Walmsley, I. A
estimation of a lossy phase shift. Nat. Photon 4, 357 (2010). t
29. Demkowicz-Dobrzanski, R., Kolodynski, J. & Guta, M. The elusive Heisenberg limit in quantum-enhanced metrology. Nat. Commun. 3, 1063 (2012). 30. D’Ambrosio, V. et al. Photonic polarization gears for ultra-sensitive angular measurements. Nat. Commun. 4, 2432 (2013). ll
b
d
b
l
l
f l h
d h
f 31. Allen, L., Beijersbergen, M. W., Spreeuw, R. J. C. & Woerdman, J. P. Orbital angular momentum of light and the transformation of
Laguerre-Gaussian laser modes. Phys. Rev. A 45, 8185 (1992). g
y
32. Mair, A., Vaziri, A., Weihs, G. & Zeilinger, A. Entanglement of the orbital angular momentum states of photons. Nature 412, 313
(2001). (
)
33. Yao, A. M. & Padgett, M. J. Orbital angular momentum: origins, behavior and applications. Adv. Opt. Photonics 3, 161 (2011). g
g
g
pp
p
34. van Uden, R. G. H. et al. Ultra-high-density spatial division multiplexing with a few-mode multicore fibre. Nat. Photon 8, 865–870
(2014).i 35. Richardson, D. J., Fini, J. M. & Nelson, L. E. Space-division multiplexing in optical fibres. Nat. Photon 7, 354–362 (2013). Scientific Reports | 7: 3601 | DOI:10.1038/s41598-017-03239-1 6 www.nature.com/scientificreports/ 6. Scientific Reports | 7: 3601 | DOI:10.1038/s41598-017-03239-1 Additional Informationh Competing Interests: The authors declare that they have no competing interests. Competing Interests: The authors declare that they have no competing interests. ublisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and
nstitutional affiliations. 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 Cre-
ative Commons license, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the
material. If material is not included in the article’s Creative Commons license and your intended use is not per-
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/. Scientific Reports | 7: 3601 | DOI:10.1038/s41598-017-03239-1 7
|
https://openalex.org/W3206814265
|
http://ir.unimas.my/id/eprint/37112/1/melioidosis-1.pdf
|
English
| null |
Fine-needle aspiration to improve diagnosis of melioidosis of the head and neck in children: a study from Sarawak, Malaysia
|
BMC infectious diseases
| 2,021
|
cc-by
| 839
|
Fine‑needle aspiration to improve diagnosis
of melioidosis of the head and neck in children:
a study from Sarawak, Malaysia Anand Mohan1,2, Yuwana Podin2* , Da‑Wei Liew1, Jeevithaa Mahendra Kumar1, Peter Sie‑Teck Lau1,
Yee‑Yen Tan1, Yi‑Pinn Tai1, Ranveer Singh Gill3, Ram Shanmugam3, Su‑Lin Chien4, Lee‑See Tan4,
Nurul Asiah Mat Sani4, Kamilah Manan5 and Mong‑How Ooi2,6 Abstract Background: Melioidosis, the infection caused by Burkholderia pseudomallei, is associated with a high case fatality
rate, due in part to difficulties in clinical recognition and diagnostic confirmation of the disease. Although head and
neck involvement is common in children, specific disease manifestations differ between geographic regions. The aim
of this study was to provide a detailed description of melioidosis of the head and neck among children in Sarawak,
Malaysia, and determine if fine-needle aspiration of suspected head or neck lesions could improve melioidosis
diagnosis. Methods: We conducted a retrospective descriptive study of all children aged < 12 years with culture-confirmed
melioidosis presenting with head and neck manifestations and admitted to Bintulu Hospital in Sarawak, Malaysia,
from January 2011 until December 2020. Fine-needle aspiration of head and neck lesions suspected to be due to
melioidosis with inoculation in blood culture bottles (FNA + BCB) was used from the beginning of 2016. Results: Of 34 children with culture-confirmed melioidosis, 20 (59%) had an infection involving one or more sites in
the head and neck. Of these, 17 (85%) were diagnosed in or after 2016. Cervical lymph nodes were the most common
organ or site affected, involved in 19 (95%) children. Clinical presentations of B. pseudomallei lymph node infections
were highly variable. Five (25%) children had salivary gland involvement. Lacrimal gland involvement (dacryocystitis)
and skin or soft tissue infection (scalp abscess) were less frequent. B. pseudomallei was isolated from the head or neck
using FNA + BCB in 15 (75%) children and by standard culture methods of direct plating of pus on agar following inci‑
sion and drainage in only 2 (10%) children. B. pseudomallei was isolated from non-head or neck specimens or blood in
3 (15%) children. Conclusions: Manifestations of pediatric head and neck melioidosis in Sarawak, Malaysia, differ from those of other
regions. Fine-needle aspiration, mainly of affected cervical lymph nodes, facilitates B. pseudomallei detection and
enables confirmation of melioidosis infections. Keywords: Melioidosis, Children, Head and neck, Lymph nodes, Diagnosis, Malaysia Mohan et al. BMC Infect Dis (2021) 21:1069
https://doi.org/10.1186/s12879-021-06754-9 Open Access © The Author(s) 2021. 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://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Background Melioidosis, the infection caused by the environmental
saprophyte Burkholderia pseudomallei, is associated with
a high case fatality rate [1, 2]. This is due partly to the
extensive intrinsic antibiotic resistance of the organism *Correspondence: pyuwana@unimas.my
2 Institute of Health and Community Medicine, Universiti Malaysia
Sarawak, Kota Samarahan, Sarawak, Malaysia
Full list of author information is available at the end of the article *Correspondence: pyuwana@unimas.my
2 Institute of Health and Community Medicine, Universiti Malaysia
Sarawak, Kota Samarahan, Sarawak, Malaysia
Full list of author information is available at the end of the article *Correspondence: pyuwana@unimas.my
2 Institute of Health and Community Medicine, Universiti Malaysia
Sarawak, Kota Samarahan, Sarawak, Malaysia
Full list of author information is available at the end of the article © The Author(s) 2021. 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://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
|
https://openalex.org/W3016591737
|
https://publishup.uni-potsdam.de/files/47194/pmnr1034.pdf
|
Latin
| null |
Convergence Rate of the Modified Landweber Method for Solving Inverse Potential Problems
|
Mathematics
| 2,020
|
cc-by
| 10,712
|
Mathematisch-Naturwissenschaftliche Fakultät Mathematisch-Naturwissenschaftliche Fakultät Mathematisch-Naturwissenschaftliche Fakultät Pornsarp Pornsawad | Parada Sungcharoen | Christine Böckmann Received: 25 March 2020; Accepted: 10 April 2020; Published: 16 April 2020 Abstract: In this paper, we present the convergence rate analysis of the modified Landweber method
under logarithmic source condition for nonlinear ill-posed problems. The regularization parameter
is chosen according to the discrepancy principle. The reconstructions of the shape of an unknown
domain for an inverse potential problem by using the modified Landweber method are exhibited. Keywords: nonlinear operator; regularization; modified Landweber method; discrepancy principle;
logarithmic source condition Article Pornsarp Pornsawad 1,2,*,†
, Parada Sungcharoen 1,2,† and Christine Böckmann 3,†
1
Department of Mathematics, Faculty of Science, Silpakorn University, 6 Rachamakka Nai Rd.,
Nakhon Pathom 73000, Thailand
2
Centre of Excellence in Mathematics, Mahidol University, Rama 6 Rd., Bangkok 10400, Thailand;
parada_pame@hotmail.com
3
Institut für Mathematik, Universität Potsdam, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam OT Golm,
Germany; bockmann@uni-potsdam.de
*
Correspondence: pornsawad_p@silpakorn.edu; Tel.: +66-34-245-320
†
These authors contributed equally to this work. *
Correspondence: pornsawad_p@silpakorn.edu; Tel.: +66-34-245-320 †
These authors contributed equally to this work. mathematics mathematics Convergence Rate of the Modified
Landweber Method for Solving Inverse
Potential Problems Suggested citation referring to the original publication:
Mathematics 8(2020) 4, 608
DOI https://doi.org/10.3390/math8040608
ISSN (online) 2227-7390 Suggested citation referring to the original publication:
Mathematics 8(2020) 4, 608
DOI https://doi.org/10.3390/math8040608
ISSN (online) 2227-7390 Postprint archived at the Institutional Repository of the Potsdam University in:
Postprints der Universität Potsdam
Mathematisch-Naturwissenschaftliche Reihe ; 1034
ISSN 1866-8372
https://nbn-resolving.org/urn:nbn:de:kobv:517-opus4-471942
DOI https://doi.org/10.25932/publishup-47194 1. Introduction Later, a second-order
asymptotic regularization for the linear problem Ax = y was investigated in Zhang and Hofmann [8],
where the optimal order is obtained under the Hölder type source condition and a conventional
discrepancy principle as well as a total energy discrepancy principle. Recently, the study of modified
asymptotic regularization is reported in Pornsawad et al. [6] where the term ¯x −xδ(t), xδ(0) = ¯x,
is included to the method proposed by Tautenhahn [7], i.e., ˙xδ(t) = F′(xδ(t))∗[yδ −F(xδ(t))] −(xδ(t) −¯x),
0 < t ≤T. (5) (5) A discrete version analogue to Equation (5) is successfully developed in Pornsawad and Böckmann [9],
where the whole family of Runge–Kutta methods is applied and one obtaines an optimal convergence
rate under Hölder-type sourcewise condition if the Fréchet derivative is properly scaled and locally
Lipschitz continuous. A discrete version analogue to Equation (5) is successfully developed in Pornsawad and Böckmann [9],
where the whole family of Runge–Kutta methods is applied and one obtaines an optimal convergence
rate under Hölder-type sourcewise condition if the Fréchet derivative is properly scaled and locally
Lipschitz continuous. It is well known that, for many applications such as the inverse potential problem and the inverse
scattering problem [5], the Hölder type source condition in general is not fulfilled even if a solution is
very smooth. It is applicable only for mildly ill-posed problems [1,10,11]. Therefore, the convergence
rate analysis of an explicit Euler method presented by xδ
n+1 = xδ
n + F′(xδ
n)∗(yδ −F(xδ
n)) −αn(xδ
n −x0)
(6) (6) is considered in this article under the logarithmic source condition in Equation (7) and the properly
scaled Fréchet derivative ∥F′(x+)∥≤1. The method in Equation (6) is a particular method of the
iterative Runge–Kutta-type method [9], where τn = α−1
n
is the relaxation parameter obtained by
discretization of conventional asymptotic regularization [7]. We define f = fp,
fp(λ) :=
( ln e
λ
−p
for 0 < λ ≤1
0
for λ = 0
(7) (7) with p > 0 and the usual sourcewise representation x+ −x0 = f
F′(x+)∗F′(x+)
w,
w ∈X
(8) (8) where ∥w∥is sufficiently small. The method in Equation (6) is also known as the modified Landweber
method [12] which has the rate O(
√
δ) under the Hölder-type source condition and general discrepancy
principle. 1. Introduction An inverse potential problem consists in determining the shape of an unknown domain D form
measurements of the Neumann boundary values of u on ∂Ω, where the solution u of the homogeneous
Dirichlet problem fulfills ∆u = χD
in
ΩR \ ∂D,
(1)
u = 0
on
∂ΩR
(2) (1) (1)
(2) (2) where χD is the characteristic function of the domain D ⊂ΩR = {x ∈R2 : |x| < R}. This inverse
problem is a nonlinear severely ill-posed problem; see [1,2]. If a classical difference method is used
for solving the inverse problem, the errors can grow exponentially fast as the mesh size goes to
zero. Many regularizing methods are adopted to provide a stable solution of inverse potential
problems, e.g., a second-degree method with frozen derivatives [3], level set regularization [4],
the iteratively regularized Gauss–Newton method [5] and Levenberg–Marquardt method [1]. In this
work, we consider a discrete version analoguous to the modified asymptotic regularization proposed
by Pornsawad et al. [6] to recover the starlike shape of the unknown domain D. In a general setting, an inverse potential problem can be formulated via a nonlinear
operator equation F(x) = y,
(3) (3) where y is the normal derivative of u on the boundary, ∂u
∂ν |∂ΩR, ν is the outer normal vector on ∂ΩR,
the operator F : D (F) ⊆X →Y is a nonlinear operator on domain D (F) ⊂X, X and Y are Hilbert
spaces, and the unknown x includes the information of the domain D ⊂ΩR. For convenience in tics 2020, 8, 608; doi:10.3390/math8040608
www.mdpi.com/journal/mathematics Mathematics 2020, 8, 608; doi:10.3390/math8040608 2 of 22 Mathematics 2020, 8, 608 this article, the indices of inner products ⟨·, ·⟩and norms ∥· ∥are neglected but they can always be
identified from the context in which they appear. Due to the nonlinearity of Equation (3), we assume
all over that Equation (3) has a solution x+ which needs not to be unique. We have the disturbed data
yδ with yδ −y
≤δ
(4) (4) where δ > 0 is a noise level. If one solves Equation (3) by traditional numerical method, high oscillating
solutions may occur. Thus, one needs a regularization to minimize the approximation and data error. One well-known continuous regularization is Showalter’s method or asymptotic regularization [7],
where an approximate solution is obtained by solving an initial value problem. 1. Introduction The convergence rate analysis under the logarithmic source condition in Equation (7) has
been successfully studied by Hohage [5] for the iteratively regularized Gauss–Newton method and
by Deuflhard et al. [13] for Landweber’s iteration. Current studies of source condition may be found,
e.g., in Romanov et al. [11], Bakushinsky et al. [14], Schuster et al. [15] and Albani et al. [16]. The purpose of this work is to present the convergence rate analysis of the iterative scheme
of Equation (6) under the logarithmic source condition in Equation (7) with 1 ≤p ≤2 and
to recover the shape of an unknown domain D for an inverse potential problem (Equations (1) 3 of 22 Mathematics 2020, 8, 608 and (2)). Thus, in Section 2, a preliminary result is prepared. As usual, the Fr´echet derivative
of F needs to be scaled. Furthermore, we assume a nonlinearity condition of F in a ball
Bρ(x0) = {x ∈X : ∥x −x0∥≤ρ}, ρ > 0, which is given in Assumption 1. It is well known that,
without the additional assumption on the nonlinear operator, the convergence rate cannot be provided. The following assumption has been used in many works [5,17], i.e., there exists a bounded linear
operator R : Y →Y and Q : X →Y such that F′( ˜x) = R( ˜x, x)F′(x) + Q( ˜x, x)
∥I −R( ˜x, x)∥≤CR
∥Q( ˜x, x)∥≤CQ∥F′(x†)( ˜x −x)∥ with nonnegative constants CR and CQ. However a weaker condition will be used in this work. This will be shown in Assumption 1. In Section 3, the convergence rate of the modified Landweber
method under the logarithmic source condition is presented. Application of the modified Landweber
method to an inverse potential problem is provided in Section 4. 2. Preliminary Results In this section, preliminary results are prepared to provide the convergence analysis of the
modified Landweber method. Lemma 1. Let A be a linear operator with ∥A∥≤1. For n ∈N with n > 1, e0 := f (λ)w with f given by
Equation (7) and p > 0, there exist positive constants c1 and c2 such that n−1
∏
i=0
(1 −αi)(I −A∗A)ne0
≤c1(ln(n + e))−p∥w∥
(9) (9) and A
n−1
∏
i=0
(1 −αi)(I −A∗A)ne0
≤c2(n + 1)−1/2(ln(n + e))−p∥w∥
(10) (10) ≤1, i = 0, 1, 2, . . . , n. Proof. By spectral theory and Equations (7), (A1), and (A2), we have Proof. By spectral theory and Equations (7), (A1), and (A2), we have n−1
∏
i=0
(1 −αi)(I −A∗A)ne0
≤
n−1
∏
i=0
(1 −αi)∥(I −A∗A)n f (A∗A)∥∥w∥
≤
sup
λ∈(0,1]
|(1 −λ)n(1 −ln λ)−p|∥w∥
≤
c1(ln(n + e))−p∥w∥ (11) for some constant c1 > 0. Similary, spectral theory and Equations (7), (A3), and (A4) provides A
n−1
∏
i=0
(1 −αi)(I −A∗A)ne0
≤
n−1
∏
i=0
(1 −αi)∥(I −A∗A)n(A∗A)1/2 f (A∗A)∥∥w∥
≤
sup
λ∈(0,1]
|(1 −λ)nλ1/2(1 −ln λ)−p|∥w∥
≤
c2(n + 1)−1/2(ln(n + e))−p∥w∥
(12) (12) for some constant c2 > 0. for some constant c2 > 0. for some constant c2 > 0. 4 of 22 Mathematics 2020, 8, 608 Proposition 1. Let A be a linear operator with ∥A∥≤1. For n ∈N with n > 1, e0 := f (λ)w with f given
by Equation (7) and p = 2ψ, for some ψ ∈[1/2, 1], there exist positive constants ˜c1 and ˜c2 such that Proposition 1. Let A be a linear operator with ∥A∥≤1. For n ∈N with n > 1, e0 := f (λ)w with f given
by Equation (7) and p = 2ψ, for some ψ ∈[1/2, 1], there exist positive constants ˜c1 and ˜c2 such that n−1
∑
j=0
αn−j−1(I −A∗A)j
j
∏
i=1
(1 −αn−i)e0
≤˜c1(ln(n + e))−p∥w∥
(13) (13) and and
∥A
n−1
∑
j=0
αn−j−1(I −A∗A)j
j
∏
i=1
(1 −αn−i)e0∥≤˜c2(n + 1)−1/2(ln(n + e))−p∥w∥
(14)
for αi = 1
2(i + l0)−ψ, i = 0, 1, 2, . . . , n and l0 ≥2. ∥A
n−1
∑
j=0
αn−j−1(I −A∗A)j
j
∏
i=1
(1 −αn−i)e0∥≤˜c2(n + 1)−1/2(ln(n + e))−p∥w∥
(14) (14) for αi = 1
2(i + l0)−ψ, i = 0, 1, 2, . . . , n and l0 ≥2. Proof. 2. Preliminary Results We will prove by induction that, for some c ∈R
, the inequality k−1
∑
j=0
αn−j−1(I −A∗A)j
j
∏
i=1
(1 −αn−i)e0
≤c(ln(k + e))−p∥w∥
(15) (15) j=0
i=1
is true. Note that p
ψ = 2 ≤
ln 2
ln(ln(1 + e)) and l0 ≥2 provide
p
ψ ln(ln(1 + e)) ≤ln 2 ≤ln l0 ≤ln(l0 + n −1). is true. Note that p
ψ = 2 ≤
ln 2
ln(ln(1 + e)) and l0 ≥2 provide
p l (l (1 + )) ≤l 2 ≤l l ≤l (l +
1) true. Note that p
ψ = 2 ≤
ln 2
ln(ln(1 + e)) and l0 ≥2 provide p
ψ ln(ln(1 + e)) ≤ln 2 ≤ln l0 ≤ln(l0 + n −1). (ln(1 + e))−p ≥(l0 + n −1)−ψ. Using Equation (7), we have
∥αn−1(I −A∗A)0e0∥
≤
1
2(n −1 + l0)−ψ sup
λ∈(0,1]
|(1 −ln λ)−p|∥w∥
≤
1
2(ln(1 + e))−p∥w∥. Thus, Equation (15) holds for k = 1. Next, we assume that Equation (15) holds for k −1 < n for some
constant c. Applying Lemma 1, we obtain Thus, Equation (15) holds for k = 1. Next, we assume that Equation (15) holds for k −1 < n for some
constant c. Applying Lemma 1, we obtain Thus, Equation (15) holds for k = 1. Next, we assume that Equation (15) holds for k −1 < n for some
constant c. Applying Lemma 1, we obtain k
∑
j=0
αn−j−1(I −A∗A)j
j
∏
i=1
(1 −αn−i)e0
≤
k−1
∑
j=0
αn−j−1(I −A∗A)j
j
∏
i=1
(1 −αn−i)e0
+
αn−k−1(I −A∗A)k
k
∏
i=1
(1 −αn−i)e0
≤
c(ln(k + e))−p∥w∥+ 1
2(n −k −1 + l0)−ψ
(I −A∗A)k f (A∗A)w
≤
c(ln(k + e))−p∥w∥+ c1
2 (n −k −1 + l0)−ψ(ln(k + e))−p∥w∥. (16) (16) By Figure 1, we observe that By Figure 1, we observe that By Figure 1, we observe that By Figure 1, we observe that 1
2(n −k −1 + l0)−ψ(ln(k + e))−p ≤(ln(k + 1 + e))−p. 5 of 22 Mathematics 2020, 8, 608 Figure 1. Plot of (ln(k + 1 + e))−p and 1
2(n −k −1 + l0)−ψ(ln(k + e))−p with n = 1000, l0 = 10,
and (left) ψ = 1 and (right) ψ = 0.5. 2. Preliminary Results Moreover, in Figure 2, the graph of
ln(k + 1 + e)
ln(k + e)
!p
+ 1 has a maximum at k = 1 and p = 2 and
the maximum value is
ln(2 + e)
ln(1 + e)
!2
+ 1 = 2.3956. Thus, Equation (16) becomes
k
∑
j=0
αn−j−1(I −A∗A)j
j
∏
i=1
(1 −αn−i)e0
≤
max{c, c1}(ln(k + 1 + e))−p∥w∥
(ln(k + e))−p
(ln(k + 1 + e))−p + 1
≤
˜c1(ln(k + 1 + e))−p∥w∥ Moreover, in Figure 2, the graph of
ln(k + 1 + e)
ln(k + e)
!p
+ 1 has a maximum at k = 1 and p = 2 and
the maximum value is
ln(2 + e)
ln(1 + e)
!2
+ 1 = 2.3956. Thus, Equation (16) becomes Moreover, in Figure 2, the graph of
ln(k + 1 + e)
ln(k + e)
!p
+ 1 has a maximum at k = 1 and p = 2 and
2 Moreover, in Figure 2, the graph of
ln(k + 1 + e)
ln(k + e)
!p
+ 1 has a maximum at k = 1 and p = 2 and
the maximum value is
ln(2 + e)
ln(1 + e)
!2
+ 1 = 2.3956. Thus, Equation (16) becomes k
∑
j=0
αn−j−1(I −A∗A)j
j
∏
i=1
(1 −αn−i)e0
≤
max{c, c1}(ln(k + 1 + e))−p∥w∥
(ln(k + e))−p
(ln(k + 1 + e))−p + 1
≤
˜c1(ln(k + 1 + e))−p∥w∥ for some constant ˜c1. Thus, the induction is complete. for some constant ˜c1. Thus, the induction is complete. for some constant ˜c1. Thus, the induction is complete. Figure 2. Plot of
ln(k + 1 + e)
ln(k + e)
!p
+ 1. We prove Equation (14) by induction in the same manner as Equation (13). We prove Equation (14) by induction in the same manner as Equation (13). ematics 2020, 8, 608
6 of 22 Mathematics 2020, 8, 608 6 of 22 Assumption 1. There exist positive constants cL, cR, and cr and linear bounded operator Rx : Y →Y such
that, for x ∈Bρ(x0), the following condition holds Assumption 1. 2. Preliminary Results There exist positive constants cL, cR, and cr and linear bounded operator Rx : Y →Y such
that, for x ∈Bρ(x0), the following condition holds F′(x) = RxF′(x+)
(17)
∥Rx −I∥≤cL
x −x+
(18)
|∥Rx∥−∥I∥| ≥cR
(19)
∥Rx∥≤cr
(20) F′(x) = RxF′(x+)
(17)
∥Rx −I∥≤cL
x −x+
(18)
|∥Rx∥−∥I∥| ≥cR
(19)
∥Rx∥≤cr
(20) (17)
(18) (17) (20) where x+ is the exact solution of Equation (3). where x+ is the exact solution of Equation (3). where x+ is the exact solution of Equation (3). Lemma 2. Let the Assumption 1 be assumed. Then, we have Lemma 2. Let the Assumption 1 be assumed. Then, we have Lemma 2. Let the Assumption 1 be assumed. Then, we have (1 −αn)I −R∗
xδn
≤1
2KR ∥en∥
(21) (1 −αn)I −R∗
xδn
≤1
2KR ∥en∥
(21) (21) for some constant KR > 0 with en = x+ −xδ
n. for some constant KR > 0 with en = x+ −xδ
n. for some constant KR > 0 with en = x+ −xδ
n. Proof. We note that the reverse triangle inequality and Equation (19) guarantee the estimates Proof. We note that the reverse triangle inequality and Equation (19) guarantee the estimates 1 ≤
∥Rx −I∥
|∥Rx∥−∥I∥| ≤c−1
R ∥Rx −I∥
(22) 1 ≤
∥Rx −I∥
|∥Rx∥−∥I∥| ≤c−1
R ∥Rx −I∥
(22)
and (22) and ∥I + R∗
x∥≤
1
|∥Rx∥−∥I∥| × ∥I −R∗
x∥∥I + R∗
x∥≤c−1
R ∥I −R∗
x∥∥I + R∗
x∥. (23) (23) Using the estimates in Equations (18), (20), (22), and (23) and the triangle inequality, we now have (1 −αn)I −R∗
xδn
=
1
2
h
(1 −(1 + αn))(I + R∗
xδn)
i
+ 1
2
h
(1 + (1 −αn))(I −R∗
xδn)
i
≤1
2
h
αnc−1
R
I + R∗
xδn
+ |2 −αn|
i
I −R∗
xδn
≤1
2KR ∥en∥ stant KR =
h
αnc−1
R (∥I∥+ cr) + |2 −αn|
i
cL. with the positive constant KR =
h
αnc−1
R (∥I∥+ cr) + |2 −αn|
i
cL. with the positive constant KR =
h
αnc−1
R (∥I∥+ cr) + |2 −αn|
i
cL. Proposition 2. Let the conditions in Equations (17) and (18) in Assumption 1 be true. Then, F(xδ
n) −F(x+) −F′(x+)(xδ
n −x+)
≤1
2cL ∥en∥∥Ken∥
(24) (24) for x ∈Bρ(x0) with K = F′(x+) and en = x+ −xδ
n. Proof. 2. Preliminary Results Define
wt = x+ + t(xδ
n −x+) as 0 ≤t ≤1. Using the mean value theorem with
Equations (17) and (18), we obtain Proof. Define
wt = x+ + t(xδ
n −x+) as 0 ≤t ≤1. Using the mean value theorem with
Equations (17) and (18), we obtain F(xδ
n) −F(x+) −F′(x+)(xδ
n −x+)
=
R 1
0
F′(x+ + t(xδ
n −x+)) −F′(x+)
(xδ
n −x+)dt
≤R 1
0 ∥Rwt −I∥
F′(x+)(xδ
n −x+)
dt
≤1
2cL ∥en∥∥Ken∥. (25) F(xδ
n) −F(x+) −F′(x+)(xδ
n −x+)
=
R 1
0
F′(x+ + t(xδ
n −x+)) −F′(x+)
(xδ
n −x+)dt
≤R 1
0 ∥Rwt −I∥
F′(x+)(xδ
n −x+)
dt
≤1
2cL ∥en∥∥Ken∥. (25) (25) Mathematics 2020, 8, 608 7 of 22 3. Convergence Analysis 8 of 22 Mathematics 2020, 8, 608 Since en := x+ −xδ
n and K := F′(x+), we present en as Since en := x+ −xδ
n and K := F′(x+), we present en as en+1 = (1 −αn)en + F′(xδ
n)∗(F(xδ
n) −yδ) −αn(x0 −x+)
= (1 −αn)(I −K∗K)en + (1 −αn)K∗Ken + F′(xδ
n)∗(F(xδ
n) −yδ) −αn(x0 −x+)
= (1 −αn)(I −K∗K)en + (1 −αn)K∗h
F(xδ
n) −F(x+) −K(xδ
n −x+)
i
+
h
K∗−F′(xδ
n)∗i
yδ −F(xδ
n)
−αnK∗(yδ −F(xδ
n)) + (1 −αn)K∗(y −yδ)
−αn(x0 −x+) = (1 −αn)(I −K∗K)en + (1 −αn)K∗h
F(xδ
n) −F(x+) −K(xδ
n −x+)
i
+
h
K∗−K∗R∗
xδn
i
yδ −F(xδ
n)
−αnK∗(yδ −F(xδ
n)) + (1 −αn)K∗(y −yδ)
−αn(x0 −x+) = (1 −αn)(I −K∗K)en + (1 −αn)K∗h
F(xδ
n) −F(x+) −K(xδ
n −x+)
i
+ K∗h
(1 −αn)I −R∗
xδn
i
yδ −F(xδ
n)
+ (1 −αn)K∗(y −yδ)
−αn(x0 −x+). (30) −αn(x0 −x+). (30) writting Equation (30), we have Rewritting Equation (30), we have Rewritting Equation (30), we have Rewritting Equation (30), we have en+1 = (1 −αn)(I −K∗K)en + (1 −αn)K∗(y −yδ) −αn(x0 −x+) + K∗zn
(31) (31) where zn = (1 −αn)(F(xδ
n) −F(x+) −K(xδ
n −x+)) + [(1 −αn)I −R∗
xδn](yδ −F(xδ
n)). By recurrence and Equation (31), we obtain the closed expression for the error en =
"
n−1
∏
i=0
(1 −αi)(I −K∗K)n +
n−1
∑
j=0
αn−j−1(I −K∗K)j
j
∏
i=1
(1 −αn−i)
#
e0
+
"
n
∑
j=1
(I −K∗K)j−1
j
∏
i=1
(1 −αn−i)
#
K∗(y −yδ)
+
n−1
∑
j=0
n−1
∏
i=n−j
(1 −αi)(I −K∗K)jK∗zn−j−1. (3 en =
"
n−1
∏
i=0
(1 −αi)(I −K∗K)n +
n−1
∑
j=0
αn−j−1(I −K∗K)j
j
∏
i=1
(1 −αn−i)
#
e0
+
"
n
∑
j=1
(I −K∗K)j−1
j
∏
i=1
(1 −αn−i)
#
K∗(y −yδ)
1
1 "
i=0
j=0
i=1
#
+
"
n
∑
j=1
(I −K∗K)j−1
j
∏
i=1
(1 −αn−i)
#
K∗(y −yδ)
+
n−1
∑
j=0
n−1
∏
i=n−j
(1 −αi)(I −K∗K)jK∗zn−j−1. (32) +
n−1
∑
j=0
n−1
∏
i=n−j
(1 −αi)(I −K∗K)jK∗zn−j−1. 3. Convergence Analysis To investigate the convergence rate of the modified Landweber method under the logarithmic
source condition, we choose the regularization parameter n according to the generalized discrepancy
principle, i.e., the iteration is stopped after N = N(yδ,δ) steps with yδ −F(xδ
N)
≤τδ <
yδ −F(xδ
n)
,
0 ≤n < N
(26) (26) where τ > 2−η
1−η is a positive number. In addition to the discrepancy principle, F satisfies the local
property in the open ball Bρ(x0) of radius ρ around x0 where τ > 2−η
1−η is a positive number. In addition to the discrepancy principle, F satisfies the local
property in the open ball Bρ(x0) of radius ρ around x0 F(x) −F( ˜x) −F′(x)(x −˜x)
≤η ∥F(x) −F( ˜x)∥,
η < 1
2
(27) (27) with x, ˜x ∈Bρ(x0) ⊂D (F). Utilizing the triangle inequality yields
1
1 + η
F′(x)(x −˜x)
≤∥F(x) −F( ˜x)∥≤
1
1 −η
F′(x)(x −˜x)
(28) with x, ˜x ∈Bρ(x0) ⊂D (F). Utilizing the triangle inequality yields 1
1 + η
F′(x)(x −˜x)
≤∥F(x) −F( ˜x)∥≤
1
1 −η
F′(x)(x −˜x)
(28) (28) to ensure at least local convergence to a solution x+ of Equation (3) in B ρ
2 (x0). Theorem 1. Assume that the problem in Equation (3) has a solution x+ in B ρ
2 (x0), yδ fulfills Equation (4),
and F satisfies Equations (17) and (18). Assume that the Fr´echet derivative of F is scaled such that ∥F′(x)∥≤1
for x ∈B ρ
2 (x0). Furthermore, assume that the source condition in Equations (7) and (8) is fulfilled and that the
modified Landweber method is stopped according to Equation (26). If ∥w∥is sufficiently small, then there exists
a constant K2 depending only on p and ∥w∥with ∥en∥≤K2(ln n)−p
(29) (29) and and and yδ −F(xδ
n)
≤4K2(n + 1)−1/2(ln n)−p. Proof. We give the abbreviation en := x+ −xδ
n for the error of the nth iteration xδ
n of Equation (6) and
K := F′(x+). We can rewrite Equation ( 6) into the form Proof. We give the abbreviation en := x+ −xδ
n for the error of the nth iteration xδ
n of Equation (6) and
K := F′(x+). We can rewrite Equation ( 6) into the form x+ −xδ
n+1 = (1 −αn)(x+ −xδ
n) + F′(xδ
n)∗(F(xδ
n) −yδ) −αn(x0 −x+). 3. Convergence Analysis (32) (32) Moreover, it holds Ken =
"
K
n−1
∏
i=0
(1 −αi)(I −K∗K)n + K
n−1
∑
j=0
αn−j−1(I −K∗K)j
j
∏
i=1
(1 −αn−i)
#
e0
+ K
"
n
∑
j=1
(I −K∗K)j−1
j
∏
i=1
(1 −αn−i)
#
K∗(y −yδ)
+ K
n−1
∑
j=0
n−1
∏
i=n−j
(1 −αi)(I −K∗K)jK∗zn−j−1. + K
n−1
∑
j=0
n−1
∏
i=n−j
(1 −αi)(I −K∗K)jK∗zn−j−1. (33) (33) Next, for 0 ≤n < N, using the discrepancy principle, triangle inequality, Equation (28), and τ > 2−η
1−η ,
we get yδ −F(xδ
n)
≤2
yδ −F(xδ
n)
−τδ ≤2
y −F(xδ
n)
≤
2
1 −η ∥Ken∥. (34) (34) Mathematics 2020, 8, 608 9 of 22 Using Lemma 2, Proposition 2, and Equation (34), we obtain Using Lemma 2, Proposition 2, and Equation (34), we obtain ∥zn∥≤(1 −αn)
F(xδ
n) −F(x+) −K(xδ
n −x+)
+
(1 −αn)I −R∗
xδn
yδ −F(xδ
n)
≤1
2(1 −αn) ∥en∥∥Ken∥cL + 1
2KR ∥en∥(
2
1 −η ) ∥Ken∥
≤ˆc1 ∥Ken∥∥en∥ (35) where ˆc1 = cL
2 + KR
1−η , and we use the fact that 1 −αn ≤1. where ˆc1 = cL
2 + KR
1−η , and we use the fact that 1 −αn ≤1. It holds that ∥en∥is decreasing independently of the source condition for 0 ≤n < N; see
Proposition 2.2 in Scherzer [12]. 2
1
η
It holds that ∥en∥is decreasing independently of the source condition for 0 ≤n < N; see
Proposition 2.2 in Scherzer [12]. Next, we show by induction that ∥en∥≤bK2(ln(n + e))−p
(36) ∥en∥≤bK2(ln(n + e))−p (36) and and ∥Ken∥≤bK2(n + 1)−1/2(ln(n + e))−p
(37) (37) hold for all 0 ≤n < N with bK2 being a positive constant which does not depend on n. It is obvious for
n = 0. Assuming that Equations (36) and (37) are true for all k with 0 ≤k < n < N, we have to show
that Equations (36) and (37) are true for all k = n. We rewrite Equation (32) as follow ∥en∥
≤
n−1
∏
i=0
(1 −αi)(I −K∗K)ne0
+
n−1
∑
j=0
αn−j−1(I −K∗K)j
j
∏
i=1
(1 −αn−i)]e0
+
n
∑
j=1
(I −K∗K)j−1
j
∏
i=1
(1 −αn−i)K∗(y −yδ)
+
n−1
∑
j=0
n−1
∏
i=n−j
(1 −αi)(I −K∗K)jK∗zn−j−1
. 3. Convergence Analysis (38) (38) By assumption ∥K∥
≤
1 (see, e.g., Louis [18] or Vainikko and Veterennikov [19] cited
in Hanke et al. [20]), we have By assumption ∥K∥
≤
1 (see, e.g., Louis [18] or Vainikko and Veterennikov [19] cited
in Hanke et al. [20]), we have n−1
∑
k=0
(I −K∗K)kK∗
≤√
n,
d n−1
∑
k=0
(I −K∗K)kK∗
≤√
n, n−1
∑
k=0
(I −K∗K)kK∗
≤√
n, ∑
k=0
(I −K∗K)kK∗
≤√
n,
and
(I −K∗K)jK∗
≤(j + 1)−1/2, j ≥1. k=0
and
(I −K∗K)jK∗
≤(j + 1)−1/2, j ≥1. and
(I
K∗K)jK∗
≤(j + 1)−1/2 j ≥1 and (I −K∗K)jK∗
≤(j + 1)−1/2, j ≥1. Consequently, Consequently, n
∑
j=1
(I −K∗K)j−1
j
∏
i=1
(1 −αn−i)K∗(y −yδ)
≤
n
∑
j=1
(I −K∗K)j−1K∗
y −yδ
≤
√
nδ (39) tics 2020, 8, 608
10 of 22 10 of 22 Mathematics 2020, 8, 608 and and n−1
∑
j=0
n−1
∏
i=n−j
(1 −αi)(I −K∗K)jK∗zn−j−1
≤
n−1
∑
j=0
(I −K∗K)jK∗
zn−j−1
≤
n−1
∑
j=0
(j + 1)−1/2∥
zn−j−1
. (40) (40) Using Lemma 1 for n > 1, Proposition 1, and Equations (39) and (40) to Equation (38), we obtain n > 1, Proposition 1, and Equations (39) and (40) to Equation (38), we obtain ∥en∥
≤
c1(ln(n + e))−p∥w∥+ ˜c1(ln(n + e))−p∥w∥+ √
nδ
+
n−1
∑
j=0
(j + 1)−1/2
zn−j−1
. (41) ∥en∥
≤
c1(ln(n + e))−p∥w∥+ ˜c1(ln(n + e))−p∥w∥+ √
nδ
1 ∥n∥
1(
(
))
∥∥
1(
(
))
∥∥
√
+
n−1
∑
j=0
(j + 1)−1/2
zn−j−1
. (41) (41) Then, using Equation (35) to estimate the last term of Equation (41), we obtain n−1
∑
j=0
(j + 1)−1/2
zn−j−1
≤ˆc1
n−1
∑
j=0
(j + 1)−1/2
Ken−j−1
en−j−1
. (42) (42) We apply the assumption of the induction in Equations (36) and (37) into Equation (42): n−1
∑
j=0
(j + 1)−1/2
zn−j−1
≤ˆc1
n−1
∑
j=0
(j + 1)−1/2
Ken−j−1
en−j−1
≤ˆc1 bK2
2
n−1
∑
j=0
(j + 1)−1/2(n −j)−1/2(ln(n −j −1 + e))−2p
= ˆc1 bK2
2
n−1
∑
j=0
j + 1
n + 1
−1/2 n −j
n + 1
−1/2
(ln(n −j −1 + e))−2p
1
n + 1
. 3. Convergence Analysis (43) j
0
= ˆc1 bK2
2
n−1
∑
j=0
j + 1
n + 1
−1/2 n −j
n + 1
−1/2
(ln(n −j −1 + e))−2p
1
n + 1
. (43) (43) Rewritting Equation (43), we have Rewritting Equation (43), we have Rewritting Equation (43), we have n−1
∑
j=0
(j + 1)−1/2
zn−j−1
= ˆc1 bK2
2(ln(n + e))−2p
n−1
∑
j=0
j + 1
n + 1
−1/2 n −j
n + 1
−1/2
1
n + 1
ln(n + e)
ln(n −j −1 + e)
2p
≤ˆc1 bK2
2(ln(n + e))−p
n−1
∑
j=0
j + 1
n + 1
−1/2 n −j
n + 1
−1/2
1
n + 1
ln(n + e)
ln(n −j −1 + e)
2p
. (44) j
= ˆc1 bK2
2(ln(n + e))−2p
n−1
∑
j=0
j + 1
n + 1
−1/2 n −j
n + 1
−1/2
1
n + 1
ln(n + e)
ln(n −j −1 + e)
2p
≤ˆc1 bK2
2(ln(n + e))−p
n−1
∑
j=0
j + 1
n + 1
−1/2 n −j
n + 1
−1/2
1
n + 1
ln(n + e)
ln(n −j −1 + e)
2p
. (44) (44) The next idea is similar to the proof of Lemma A.5 in Deuflhard et al. [13]. Firstly,
n −j ≥1 provides The next idea is similar to the proof of Lemma A.5 in Deuflhard et al. [13]. Firstly,
n −j ≥1 provides ln
n + 1
n −j −1 + e
ln(n −j −1 + e) ≥ln
n + 1
n −j −1 + e
. 3. Convergence Analysis 11 of 22 Mathematics 2020, 8, 608 For 0 ≤j ≤n −1, the properties of the logarithm provide For 0 ≤j ≤n −1, the properties of the logarithm provide For 0 ≤j ≤n −1, the properties of the logarithm provide For 0 ≤j ≤n −1, the properties of the logarithm provide ln(n + e)
ln(n −j −1 + e)
=
ln(n + e)
ln(n + 1)
1 +
ln
n+1
n−j−1+e
ln(n −j −1 + e)
ln(n + e)
ln(n −j −1 + e)
=
ln(n + e)
ln(n + 1)
1 +
ln
n+1
n−j−1+e
ln(n −j −1 + e)
≤
E
1 + ln
n + 1
n −j −1 + e
(45) ≤
E
1 + ln
n + 1
n −j −1 + e
(45) (45) with a generic constant E < 2 which does not depend on n ≥1. Accordingly, Equation (44) can be estimated as follows: with a generic constant E < 2 which does not depend on n ≥1. Accordingly, Equation (44) can be estimated as follows: n−1
∑
j=0
(j + 1)−1/2
zn−j−1
≤ˆc1E2p bK2
2(ln(n + e))−p
n−1
∑
j=0
j + 1
n + 1
−1/2 n −j
n + 1
−1/2
1
n + 1
1 + ln
n + 1
n −j −1 + e
2p
≤ˆc1E2p bK2
2(ln(n + e))−p
n−1
∑
j=0
j + 1
n + 1
−1/2 n −j
n + 1
−1/2
1
n + 1
1 −ln
n −j
n + 1
2p
. (46) (46) The last summation is bounded since, with s :=
1
2(n+1), the integral The last summation is bounded since, with s :=
1
2(n+1), the integral Z 1−s
s
x−1/2(1 −x)−1/2(1 −ln(1 −x))2pdx is bounded from above by a positive constant Ep independently of n. Substituting the above estimation
into Equation (41) yields is bounded from above by a positive constant Ep independently of n. 3. Convergence Analysis Substituting the above estimation
into Equation (41) yields ∥en∥
≤
c1(ln(n + e))−p∥w∥+ ˜c1(ln(n + e))−p∥w∥+ √
nδ
+cp bK2
2(ln(n + e))−p
=
[(c1 + ˜c1)∥w∥+ cp bK2
2](ln(n + e))−p + √
nδ
(47) (47) =
[(c1 + c1)∥w∥+ cpK2](ln(n + e))
+ √
nδ
(47)
with cp = ˆc1E2pEp. with cp = ˆc1E2pEp. with cp = ˆc1E2pEp. p
p
Similarly, Equation (33) can be rewritten as Similarly, Equation (33) can be rewritten as ∥Ken∥
≤
K
n−1
∏
i=0
(1 −αi)(I −K∗K)ne0
+
K
n−1
∑
j=0
αn−j−1(I −K∗K)j
j
∏
i=1
(1 −αn−i)e0
+
K
n
∑
j=1
(I −K∗K)j−1
j
∏
i=1
(1 −αn−i)K∗(y −yδ)
+
K
n−1
∑
j=0
n−1
∏
i=n−j
(1 −αi)(I −K∗K)jK∗zn−j−1
. (48) (48) By assumption ∥K∥
≤
1 (see, e.g., Louis [18] or Vainikko and Veterennikov [19] cited
in Hanke et al. [20]), we have By assumption ∥K∥
≤
1 (see, e.g., Louis [18] or Vainikko and Veterennikov [19] cited
in Hanke et al. [20]), we have (I −KK∗)jKK∗
≤(j + 1)−1 (I −KK∗)jKK∗
≤(j + 1)−1
d (I −KK∗)jKK∗
≤(j + 1)−1 and and K
n−1
∑
k=0
(I −K∗K)kK∗
≤∥I −(I −KK∗)n∥≤1. K
n−1
∑
k=0
(I −K∗K)kK∗
≤∥I −(I −KK∗)n∥≤1. ematics 2020, 8, 608
12 of 2 8, 608
12 of 22 12 of 22 Mathematics 2020, 8, 608 Consequently, K
n
∑
j=1
(I −K∗K)j−1
j
∏
i=1
(1 −αn−i)K∗(y −yδ)
≤
I −(I −KK∗)k
δ ≤δ
(49) (49) and K
n−1
∑
j=0
n−1
∏
i=n−j
(1 −αi)(I −K∗K)jK∗zn−j−1
≤
n−1
∑
j=0
(j + 1)−1
zn−j−1
. (50) (50) Lemma 1 for n > 1 and Proposition 1 and applying Equations (49) and (50) to Equation (48), Using Lemma 1 for n > 1 and Proposition 1 and applying Equations (49) and (50) to Equation (48),
we get ∥Ken∥
≤
c2(n + 1)−1/2(ln(n + e))−p∥w∥+ ˜c2(n + 1)−1/2(ln(n + e))−p∥w∥
+δ +
n−1
∑
j=0
(j + 1)−1
zn−j−1
. 3. Convergence Analysis (51) ∥Ken∥
≤
c2(n + 1)−1/2(ln(n + e))−p∥w∥+ ˜c2(n + 1)−1/2(ln(n + e))−p∥w∥
n−1 (51) We may estimate the last term of Equation (51) by using Equations (35) and (45) and the fact that
(ln(n + e))−p ≤1 as follows: We may estimate the last term of Equation (51) by using Equations (35) and (45) and the fact that
(ln(n + e))−p ≤1 as follows: n−1
∑
j=0
(j + 1)−1
zn−j−1
≤
ˆc1
n−1
∑
j=0
(j + 1)−1
Ken−j−1
en−j−1
≤
ˆc1 bK2
2
n−1
∑
j=0
(j + 1)−1(n −j)−1/2(ln(n −j −1 + e))−2p n−1
∑
j=0
(j + 1)−1
zn−j−1
≤
ˆc1
n−1
∑
j=0
(j + 1)−1
Ken−j−1
en−j−1
≤
ˆc1 bK2
2
n−1
∑
j=0
(j + 1)−1(n −j)−1/2(ln(n −j −1 + e))−2p
=
ˆc1 bK2
2(n + 1)−1/2(ln(n + e))−p
×
n−1
∑
j=0
j + 1
n + 1
−1 n −j
n + 1
−1/2
ln(n + e)
ln(n −j −1 + e)
2p
(ln(n + e))−p
1
n + 1
≤
ˆc1E bK2
2(n + 1)−1/2(ln(n + e))−p
×
n−1
∑
j=0
j + 1
n + 1
−1 n −j
n + 1
−1/2
1 −ln
n −j
n + 1
2p
1
n + 1. (52) =
ˆc1 bK2
2(n + 1)−1/2(ln(n + e))−p
×
n−1
∑
j=0
j + 1
n + 1
−1 n −j
n + 1
−1/2
ln(n + e)
ln(n −j −1 + e)
2p
(ln(n + e))−p
1
n + 1
≤
ˆc1E bK2
2(n + 1)−1/2(ln(n + e))−p
×
n−1
∑
j=0
j + 1
n + 1
−1 n −j
n + 1
−1/2
1 −ln
n −j
n + 1
2p
1
n + 1. ( =
ˆc1 bK2
2(n + 1)−1/2(ln(n + e))−p
×
n−1
∑
j=0
j + 1
n + 1
−1 n −j
n + 1
−1/2
ln(n + e)
ln(n −j −1 + e)
2p
(ln(n + e))−p
1
n + 1 ≤
c1EK2
2(n + 1)
1/2(ln(n + e))
p
×
n−1
∑
j=0
j + 1
n + 1
−1 n −j
n + 1
−1/2
1 −ln
n −j
n + 1
2p
1
n + 1. 3. Convergence Analysis (52) (52) The last summation is bounded because, with s :=
1
2(n+1), the integral Z 1−s
s
x−1(1 −x)−1/2(1 −ln(1 −x))2pdx ≤eEp
(53) (53) with a positive constant eEp independently of n. Substituting above information into (51) yield with a positive constant eEp independently of n. Substituting above information into (51) yields ∥Ken∥
≤
c2(n + 1)−1/2(ln(n + e))−p∥w∥+ ˜c2(n + 1)−1/2(ln(n + e))−p∥w∥
+δ + ˜cp bK2
2(n + 1)−1/2(ln(n + e))−p
≤
h
(c2 + ˜c2) ∥w∥+ ˜cp bK2
2
i
(n + 1)−1/2(ln(n + e))−p + δ
(54) (54) with ˜cp = ˆc1E2p eEp. Setting c∗:= max{c1 + ˜c1, c2 + ˜c2}, Equations (47) and (54) become
∥en∥
≤
h
c∗∥w∥+ cp bK2
2
i
(ln(n + e))−p + √
nδ
(55) c1 + ˜c1, c2 + ˜c2}, Equations (47) and (54) become
∥en∥
≤
h
c∗∥w∥+ cp bK2
2
i
(ln(n + e))−p + √
nδ
(55) 1
1, 2
2},
q
(
)
(
)
∥en∥
≤
h
c∗∥w∥+ cp bK2
2
i
(ln(n + e))−p + √
nδ
(55) (55) 13 of 22 13 of 22 Mathematics 2020, 8, 608 and ∥Ken∥
≤
h
c∗∥w∥+ ˜cp bK2
2
i
(n + 1)−1/2(ln(n + e))−p + δ. (56) (56) Because of Equations (26) and (28) we have Because of Equations (26) and (28) we have τδ ≤
yδ −F(xδ
n)
≤δ +
1
1 −η ∥Ken∥ τδ ≤
yδ −F(xδ
n)
≤δ +
1
1 −η ∥Ken∥ Moreover, (1 −η)(τ −1)δ ≤∥Ken∥≤
h
c∗∥w∥+ ˜cp bK2
2
i
(n + 1)−1/2(ln(n + e))−p + δ. (57) (57) > 2−η
1−η , we have Θ = (1 −η)(τ −1) −1 > 0. We can rewrite Equation (57) as follows: 2−η
1−η , we have Θ = (1 −η)(τ −1) −1 > 0. We can rewrite Equation (57) as follows: δ ≤1
Θ
h
c∗∥w∥+ ˜cp bK2
2
i
(n + 1)−1/2(ln(n + e))−p. (58) (58) Applying Equation (58) to Equation (55), we get Applying Equation (58) to Equation (55), we get Applying Equation (58) to Equation (55), we get Applying Equation (58) to Equation (55), we get ∥en∥
≤
1 + 1
Θ
h
c∗∥w∥+ ˆcp bK2
2
i
(ln(n + e))−p
(59) (59) with ˆcp = max{cp, ˜cp}. with ˆcp = max{cp, ˜cp}. 3. Convergence Analysis In similar manner, Equation (56) can be written as p
p
p
In similar manner, Equation (56) can be written as ∥Ken∥
≤
1 + 1
Θ
h
c∗∥w∥+ ˜cp bK2
2
i
(n + 1)−1/2(ln(n + e))−p. (60) (60) Finally, we select ∥w∥such that
1 + 1
Θ
h
c∗∥w∥+ ˜cp bK2
2
i
≤K2. This is always possible for sufficiently
small ∥w∥, [13]. Therefore, the induction is completed. Using Equation (36), we have Finally, we select ∥w∥such that
1 + 1
Θ
h
c∗∥w∥+ ˜cp bK2
2
i
≤K2. This is always possible for sufficiently
small ∥w∥, [13]. Therefore, the induction is completed. Using Equation (36), we have ∥en∥≤bK2
ln n
ln(n + e)
p
(ln n)−p ≤K2(ln n)−p
(61) (61) and similarly, by using Equation (34), we have and similarly, by using Equation (34), we have yδ −F(xδ
n)
≤
2
1 −η K2(n + 1)−1/2
ln n
ln(n + e)
p
(ln n)−p ≤4K2(n + 1)−1/2(ln n)−p. Thus, the assertion is obtained. Thus, the assertion is obtained. Thus, the assertion is obtained. Theorem 2. Under the assumptions of Theorem 1 and 1 ≤p ≤2, we have Theorem 2. Under the assumptions of Theorem 1 and 1 ≤p ≤2, we have
N1/2(ln N)p ≤c
δ N1/2(ln N)p ≤c
δ and and x+ −xδ
N
≤C(−ln δ)−p 14 of 22 Mathematics 2020, 8, 608 Proof. We recall Equation (32) and e0 = x+ −x0 = f (K∗K)w selected from a source condition in
Equation (7). Therefore, en =
"
n−1
∏
i=0
(1 −αi)(I −K∗K)n +
n−1
∑
j=0
αn−j−1(I −K∗K)j
j
∏
i=1
(1 −αn−i)
#
f (K∗K)w
+
n
∑
j=1
(I −K∗K)j−1
j
∏
i=1
(1 −αn−i)K∗(y −yδ)
+
n−1
∑
j=0
n−1
∏
i=n−j
(1 −αi)(I −K∗K)jK∗zn−j−1. 3. Convergence Analysis Then, eN = f (K∗K)wN +
"
N
∑
j=1
(I −K∗K)j−1
j
∏
i=1
(1 −αN−i)K∗
#
(y −yδ)
(62) eN = f (K∗K)wN +
"
N
∑
j=1
(I −K∗K)j−1
j
∏
i=1
(1 −αN−i)K∗
#
(y −yδ)
(62) (62) where wN =
"
N−1
∏
i=0
(1 −αi)(I −K∗K)N +
N−1
∑
j=0
αN−j−1(I −K∗K)j
j
∏
i=1
(1 −αN−i)
#
w
+
N−1
∑
j=0
N−1
∏
i=N−j
(1 −αi)(I −K∗K)j ef (K∗K)ezN−j−1 wN =
"
N−1
∏
i=0
(1 −αi)(I −K∗K)N +
N−1
∑
j=0
αN−j−1(I −K∗K)j
j
∏
i=1
(1 −αN−i)
#
w with
ezN−j−1
=
zN−j−1
, j = 0, 1, 2, . . . , N −1
and ef (K∗K) := R 1
0 λ1/2(1 −ln λ)pdEλ. with
ezN−j−1
=
zN−j−1
, j = 0, 1, 2, . . . , N −1
and ef (K∗K) := R 1
0 λ1/2(1 −ln λ)pdEλ. f (
)
R
0
(
)
λ
Applying Equation (A4) with q = −p, we have f (
)
R
0
(
)
λ
Applying Equation (A4) with q = −p, we have f (
)
R
0
(
)
Applying Equation (A4) with q = −p, we have (I −K∗K)j ef (K∗K)
≤
c3(j + 1)−1/2(ln(j + 1))p
(63) (63) for some constant c3 > 0. Using Equation (A9) by setting N −1 = k, we have N−1
∑
j=0
(j + 1)−1/2(ln(j + 1))p(N −j)−1/2(ln(N −j −1 + e))−2p
=
k−1
∑
j=0
(j + 1)−1/2(ln(j + 1))p(k + 1 −j)−1/2(ln(k −j + e))−2p
+(k + 1)−1/2(ln(k + 1))p
≤
D + (N)−1/2(ln N)p. (64) N−1
∑
j=0
(j + 1)−1/2(ln(j + 1))p(N −j)−1/2(ln(N −j −1 + e))−2p
=
k−1
∑
j=0
(j + 1)−1/2(ln(j + 1))p(k + 1 −j)−1/2(ln(k −j + e))−2p
+(k + 1)−1/2(ln(k + 1))p
≤
D + (N)−1/2(ln N)p. ≤
D + (N)−1/2(ln N)p. (64) (64) 15 of 22 Mathematics 2020, 8, 608 From Equations (35), (36), (37), (63), and (64), we obtain N = c2
6(−ln δ)−2p
δ2 From Equations (35), (36), (37), (63), and (64), we obtain From Equations (35), (36), (37), (63), and (64), we obtain ∥wN∥
≤
N−1
∏
i=0
(1 −αi)(I −K∗K)Nw
+
N−1
∑
j=0
αN−j−1
j
∏
i=1
(1 −αN−i)
(I −K∗K)jw
+
N−1
∑
j=0
N−1
∏
i=N−j
(1 −αi)
(I −K∗K)j ef (K∗K)
ezN−j−1
≤
(N + 1) ∥w∥+ c2
N−1
∑
j=0
(j + 1)−1/2(ln(j + 1))p
ezN−j−1
≤
(N + 1) ∥w∥+ ˆc1c2
N−1
∑
j=0
(j + 1)−1/2(ln(j + 1))p
KeN−j−1
eN−j−1
≤
(N + 1) ∥w∥
+c2 ˆc1 bK2
2
N−1
∑
j=0
(j + 1)−1/2(ln(j + 1))p(N −j)−1/2(ln(N −j −1 + e))−2p
≤
(N + 1) ∥w∥+ D + (N)−1/2(ln N)p. (65) From Equation (62) we conclude that From Equation (62) we conclude that From Equation (62) we conclude that ∥eN∥≤∥f (K∗K)wN∥+
N−1
∑
k=0
(I −K∗K)kK∗
δ ≤∥f (K∗K)wN∥+
√
Nδ. From Equation (A8) in Lemma A2 and Equation (29) for some c4 > 0, we have
∥f (K∗K)wN∥
≤
c4(−ln δ)−p h
(N + 1) ∥w∥+ D + (N)−1/2(ln N)pi
. Thus From Equation (A8) in Lemma A2 and Equation (29) for some c4 > 0, we have
∥f (K∗K)wN∥
≤
c4(−ln δ)−p h
(N + 1) ∥w∥+ D + (N)−1/2(ln N)pi From Equation (A8) in Lemma A2 and Equation (29) for some c4 > 0, we have
∥f (K∗K)wN∥
≤
c4(−ln δ)−p h
(N + 1) ∥w∥+ D + (N)−1/2(ln N)pi
. Thus, on (A8) in Lemma A2 and Equation (29) for some c4 > 0, we have
∥f (K∗K)wN∥
≤
c4(−ln δ)−p h
(N + 1) ∥w∥+ D + (N)−1/2(ln N)pi
. ∥eN∥
≤
c4(−ln δ)−p h
(N + 1) ∥w∥+ D + (N)−1/2(ln N)pi
+
√
Nδ. (66) (66) We apply Equation (58); then, (N + 1)1/2(ln(N + e))p ≤
1
Θδ
h
c∗∥w∥+ ˜cp bK2
2
i
= c5
δ or or (N + 1)(ln(N + e))2p ≤c2
5
δ2 (N + 1)(ln(N + e))2p ≤c2
5
δ2 for some positive c5. By the fact that N(ln N)2p ≤(N + 1)(ln(N + e))2p ≤c2
5
δ2
(67) N(ln N)2p ≤(N + 1)(ln(N + e))2p ≤c2
5
δ2 (67) we have N(ln N)2p ≤c2
5
δ2 . By Lemma A4, we have
N = c2
6(−ln δ)−2p
δ2
(68) N(ln N)2p ≤c2
5
δ2 . From Equations (35), (36), (37), (63), and (64), we obtain By Lemma A4, we have N = c2
6(−ln δ)−2p
δ2 N = c2
6(−ln δ)−2p
δ2
(68) (68) 16 of 22 Mathematics 2020, 8, 608 Applying Equation (68) to Equation (66), we get Applying Equation (68) to Equation (66), we get Applying Equation (68) to Equation (66), we get ∥eN∥
≤
c4(−ln δ)−p h
(N + 1) ∥w∥+ D + (N)−1/2(ln N)pi
+c6(−ln δ)−p
=
(−ln δ)−p
c4
h
(N + 1) ∥w∥+ D + (N)−1/2(ln N)pi
+ c6
. For 1 ≤p ≤2, we know that N−1/2(ln N)p ≤c7 for some c7 > 0; see Figure 3. Figure 3. Graph of y = N−1/2(ln N)p for 1 ≤p ≤2. Figure 3. Graph of y = N−1/2(ln N)p for 1 ≤p ≤2. Thus, the assertion can be obtained. 4. Application to an Inverse Potential Problem It is well known that an inverse potential problem is severely ill-posed. It is the problem of
determining the shape of an unknown domain D from measurements of the Neumann boundary
values of u on ∂ΩR where the solution u fulfills Equations (1) and (2). In this work, Assumption 2.1 for
the inverse potential problem cannot be presented. It fails even in the case of two concentric circles [2]. However, if we implement the method by representing the curve with a collocation basis, as will be
seen in Proposition 3, the Fréchet derivative is reformulated. Without the verification of Assumption 1,
we show a quite good performance of an approximated potential. q
g
p
pp
p
The nonlinear operator for an inverse potential problem is defined in the following form [F(x)] (t) =
1
4πR
Z 2π
0
x2(s)ds +
∞
∑
i=1
1
πRi+1(i + 2)
Z 2π
0
xi+2(s) cos(is)ds cos(it)
∞
1
Z 2π [F(x)] (t) =
1
4πR
Z 2π
0
x2(s)ds +
∞
∑
i=1
1
πRi+1(i + 2)
Z 2π
0
xi+2(s) cos(is)ds cos(it)
+
∞
∑
i=1
1
πRi+1(i + 2)
Z 2π
0
xi+2(s) sin(is)ds sin(it)
(69) (69) where F : L2[0, 2π] →L2[0, 2π]. Moreover, the Fréchet derivative of the operator F is
F′(x)h
(t) =
1
2πR
Z 2π
0
x(s)h(s)ds
+
∞
∑
i=1
1
πRi+1
Z 2π
0
xi+1(s)h(s) cos(is)ds cos(it)
+
Z 2π
0
xi+1(s)h(s) sin(is)ds sin(it)
,
(70) (70) 17 of 22 Mathematics 2020, 8, 608 See Reference [1] for more details. In the presented work, we use R = 1 and x0 = δx+(s). Since X = L2[0, 2π] and Y = L2[0, 2π], we discretized [0, 2π] into m intervals with the grid points
0 = t0, t1, . . . , tm = 2π and 0
=
s0, s1, . . . , sm
=
2π. Note that Xm
=
span
n
ϕ(m)
j
o
and
Ym = span
n
ψ(m)
j
o
, where the sets
n
ϕ(m)
1
. . . ϕ(m)
m
o
and
n
ψ(m)
1
. . . ψ(m)
m
o
are orthogonal bases. 4. Application to an Inverse Potential Problem The orthogonal bases are defined with respect to the step length h(m) := 2π/m, m ∈N by the
piecewise continuous function with ϕ(m)
j
(s) = 1 for s ∈[sj−1, sj] , ψ(m)
j
(t) = 1 for t ∈[tj−1, tj], and
with ϕ(m)
j
(s) = 0, ψ(m)
j
(t) = 0 otherwise. The result in the next proposition provides the formula for
the calculation of xδ
n+1. Proposition 3. Let xδ
n(s) = ∑m
j=1 u(m)
j
ϕ(m)
j
(s), xδ
n+1(s) = ∑m
j=1 v(m)
j
ϕ(m)
j
(s), x0 = ∑m
j=1 z(m)
j
ϕ(m)
j
(s) The
coefficient vector V(m) is given by Proposition 3. Let xδ
n(s) = ∑m
j=1 u(m)
j
ϕ(m)
j
(s), xδ
n+1(s) = ∑m
j=1 v(m)
j
ϕ(m)
j
(s), x0 = ∑m
j=1 z(m)
j
ϕ(m)
j
(s) The
coefficient vector V(m) is given by v(m)
r
= (1 −αn)u(m)
r
+
1
h(m) qr + αnz(m)
r
(71) (71) for r = 1, . . . , m, where qr = h(m)
m
∑
k=1
"
yδ
k(tk) −C −
∞
∑
i=1
(Dki + Eki)
# "
h(m)
4π (xδ
n(sr−1) + xδ
n(sr))
+
∞
∑
i=1
h(m)
2π Air cos(itk) + h(m)
2π Bir sin(itk)
!#
, Air = (xδ
n(sr−1))i+1 cos(sr−1) + (xδ
n(sr))i+1 cos(isr),
Bir = (xδ
n(sr−1))i+1 sin(sr−1) + (xδ
n(sr))i+1 sin(isr),
C = h
4π
m
∑
l=1
u(m)
l
2
,
Dki =
h(m)
π(i + 2)
m
∑
l=1
u(m)
l
i+2
cos(isl) cos(itk)
Eki =
h(m)
π(i + 2)
m
∑
l=1
u(m)
l
i+2
sin(isl) sin(itk). C = h
4π
m
∑
l=1
u(m)
l
2
,
Dki =
h(m)
π(i + 2)
m
∑
l=1
u(m)
l
i+2
cos(isl) cos(itk)
Eki =
h(m)
π(i + 2)
m
∑
l=1
u(m)
l
i+2
sin(isl) sin(itk). and and z(m)
r
= h
2 (x0(sr−1) + x0(sr)) . Proof. The idea of the proof is analogous to Proposition 5 in Reference [21]. Proof. The idea of the proof is analogous to Proposition 5 in Reference [21]. The numerical examples for recovering the potential x+ are demonstrated in Figures 4–6. We obtain data yδ by solving the direct problem for the test curves. The program was written in
MATLAB2018a. The results are demonstrated in Figures 4 and 5 for the first test curve x+ = 5+sin(3s)
6
and in Figure 6 for the second test curve x+ = 1 −sin(s). For both examples, the number of basis
functions is 65 and the number of equidistant grid points is 200. In Figure 4, αn = 1
2(100 + n)−0.9,
δ = 0.01, and τ = 120 provide the error 0.4197 with the residual norm 1.0792 after 8 iterations for
imax = 3 and the error 0.3911 with the residual norm 1.1171 after 8 iterations for imax = 6. In Figure 5,
αn = 1
2(100 + n)−0.9, δ = 0.001, and τ = 1100 provide the error 0.6282 with the residual error 1.0607
after 8 iterations for imax = 3 and the error 0.5869 with the residual norm 1.0993 after 8 iterations for
imax = 6. For the second example, αn = 1
2(1000 + n)−0.9, δ = 0.01, and τ = 3000 provide the error 0.5720 18 of 22 18 of 22 Mathematics 2020, 8, 608 with the residual norm 28.2597 after 13 iterations and αn = 1
2(1000 + n)−0.9, δ = 0.001, and τ = 1700
provide the error 0.5925 with the residual norm 15.4140 after 14 iterations. Figures 4, 5b,d, and 6b show
that the curve of ln
x+ −xδ
n
lies below a straight line with slope −p as suggested by Equation (29). (a)
(b)
(c)
(d)
Figure 4. The polar plot shows the exact solution (dot line) and the computed solution (solid line)
for (a) imax = 3 and (c) imax = 6 with δ = 0.01. In (a) the thin curve is an initial value. In (c) the thin
curves are the curve of xδn for n = 1, . . . , 8. The error ∥x+ −xδn∥versus the logarithm of the number of
iteration step using a double logarithm scale for (b) imax = 3 and (d) imax = 6 are shown. The initial
value is x0= 0.1 + 1
5 sin(3s) . The parameter αn in Equation (71) is 1
2(100 + n)−0.9. Proof. The idea of the proof is analogous to Proposition 5 in Reference [21]. (b) (a)
(c) (a) (d) (c) (d) Figure 4. The polar plot shows the exact solution (dot line) and the computed solution (solid line)
for (a) imax = 3 and (c) imax = 6 with δ = 0.01. In (a) the thin curve is an initial value. In (c) the thin
curves are the curve of xδn for n = 1, . . . , 8. The error ∥x+ −xδn∥versus the logarithm of the number of
iteration step using a double logarithm scale for (b) imax = 3 and (d) imax = 6 are shown. The initial
value is x0= 0.1 + 1
5 sin(3s) . The parameter αn in Equation (71) is 1
2(100 + n)−0.9. 19 of 22 Mathematics 2020, 8, 608 (a)
(b)
(c)
(d)
Figure 5. The polar plot shows the exact solution (dot line) and the computed solution (solid line) for
(a) imax = 3 and (c) imax = 6 with δ = 0.001. The error ∥x+ −xδn∥versus the logarithm of the number
of iteration step using a double logarithm scale for (b) imax = 3 and (d) imax = 6 are shown. The initial
value is x0= 0.1 + 1
5 sin(3s) . The parameter αn in Equation (71) is 1
2(100 + n)−0.9. (a) (b) (a)
(c) (a) (b) (d) (c) (d) Figure 5. The polar plot shows the exact solution (dot line) and the computed solution (solid line) for
(a) imax = 3 and (c) imax = 6 with δ = 0.001. The error ∥x+ −xδn∥versus the logarithm of the number
of iteration step using a double logarithm scale for (b) imax = 3 and (d) imax = 6 are shown. The initial
value is x0= 0.1 + 1
5 sin(3s) . The parameter αn in Equation (71) is 1
2(100 + n)−0.9. (a) (a)
(b)
Figure 6. Cont. (b) (b) Figure 6. Cont. 20 of 22 Mathematics 2020, 8, 608 (c) (c)
(d)
Figure 6. (a) The polar plot shows the exact solution (dot line) and the computed solution (solid line)
for example 2 with (a,b) δ = 0.01 and (c,d) 0.001. In (a), the thin curve is an initial value. The error
∥x+ −xδn∥versus the logarithm of the number of iteration step using a double logarithm scale is
shown in (b) and (d). The initial value is x0= 1.6 −sin(s) . Proof. The idea of the proof is analogous to Proposition 5 in Reference [21]. The parameter αn in Equation (71) is
1
2(1000 + n)−0.9. C
l
i (d) (c) (d) Figure 6. (a) The polar plot shows the exact solution (dot line) and the computed solution (solid line)
for example 2 with (a,b) δ = 0.01 and (c,d) 0.001. In (a), the thin curve is an initial value. The error
∥x+ −xδn∥versus the logarithm of the number of iteration step using a double logarithm scale is
shown in (b) and (d). The initial value is x0= 1.6 −sin(s) . The parameter αn in Equation (71) is
1
2(1000 + n)−0.9. 5. Conclusions In this article, we show that the rate O((−ln δ)−p) of the modified Landweber method in
Equation (6) under the logarithmic source condition in Equation (7) with 1 ≤p ≤2 is obtained. The regularization parameter was chosen according to the discrepancy principle. The linearity
properties in Equations (17) and (18) of the nonlinear operator are needed although the verification
for the inverse potential problem is not possible [2]. The test examples are used to illustrate the
results in Theorem 1. For the modified Landweber regularization, the initial guess x0 is an important
information. With a good choice of initial guess, the shapes of the unknown domains D are quite good
reconstructions. The curves in Figures 4, 5b,d, and 6b confirm the result in Theorem 1, where the curve
of ln
x+ −xδ
n
lies below a straight line with slope −p. Author Contributions: The authors P.P., P.S., and C.B. carried out jointly this research work and drafted the
manuscript together. All the authors validated the article and read the final version. All authors have read and
agreed to the published version of the manuscript. Funding: This work was supported by the Faculty of Science of Silpakorn University under the grant number
SRF-JRG-2561-07 and by Centre of Excellence in Mathematics of Mahidol University.. Acknowledgments: This work was supported by the Faculty of Science of Silpakorn University under the grant
number SRF-JRG-2561-07 and by Centre of Excellence in Mathematics of Mahidol University. The authors would
like to thank the reviewers for valuable hints and improvements. Conflicts of Interest: The authors declare no conflict of interest Conflicts of Interest: The authors declare no conflict of interest Appendix A Appendix A t al. [13]. Let p > 0 and k ∈N0. The real-valued function
ˆf (λ) = (1 −λ)k(ln e
λ)−p
(A1) Lemma A1. Similar to Deuflhard et al. [13]. Let p > 0 and k ∈N0. The real-valued function
ˆf (λ) = (1 −λ)k(ln e
λ)−p
(A1) Lemma A1. Similar to Deuflhard et al. [13]. Let p > 0 and k ∈N0. The real-valued function Lemma A1. Similar to Deuflhard et al. [13]. Let p > 0 and k ∈N0. The real-valued function
ˆf (λ) = (1 −λ)k(ln e
λ)−p
(A1) ˆf (λ) = (1 −λ)k(ln e
λ)−p
(A1) (A1) defined on [0, 1] satisfies
ˆf (λ) ≤C(ln(k + e))−p
(A2) ˆf (λ) ≤C(ln(k + e))−p
(A2) (A2) with C independent of k. Moreover, for each q ∈R, the real-valued function with C independent of k. Moreover, for each q ∈R, the real-valued function ˆg(λ) = (1 −λ)kλ1/2
ln e
λ
−q
(A3) ˆg(λ) = (1 −λ)kλ1/2
ln e
λ
−q ˆg(λ) = (1 −λ)kλ1/2
ln e
λ
−q (A3) 21 of 22 21 of 22 Mathematics 2020, 8, 608 defined on [0, 1] satisfies defined on [0, 1] satisfies ˆg(λ) ≤C(k + 1)−1/2(ln(k + e))−q ≤C(k + 1)−1/2(ln(k + 1))−q
(A4) (A4) with C independent of k. with C independent of k. of. Following the proof of Deuflhard et al. [13] for 1 ≤b, we have Proof. Following the proof of Deuflhard et al. [13] for 1 ≤b, we have ˆf (k−b) =
1 −1
kb
k
1 −b ln 1
k
−p
≤(ln(k + e))−p
(A5) (A5) for k ≥k0. Therefore, for any λ ∈[0, 1] (independent of k), we have ˆf (λ) ≤C(ln(k + e))−p. Similarly,
for a > 1, we have for k ≥k0. Therefore, for any λ ∈[0, 1] (independent of k), we have ˆf (λ) ≤C(ln(k + e))−p. Similarly,
for a > 1, we have ˆg2(λ) ≤
1 −1
ka
2k
k−1 (1 + a ln k)−2q ≤(k + 1)−1(ln(k + e))−2q. (A6)
ollows that ˆg(λ) ≤C(k + 1)−1/2(ln(k + e))−q ˆg2(λ) ≤
1 −1
ka
2k
k−1 (1 + a ln k)−2q ≤(k + 1)−1(ln(k + e))−2q. (A6) (A6) Therefore, it follows that ˆg(λ) ≤C(k + 1)−1/2(ln(k + e))−q Lemma A2 ([13]). Let p ≥1, C > 0 and δ > 0 be sufficiently small such that 1 ≥(−ln(δC))−2p ≥δ. Let
1 Lemma A2 ([13]). Appendix A Let p ≥1, C > 0 and δ > 0 be sufficiently small such that 1 ≥(−ln(δC))−2p ≥δ. Let Lemma A2 ([13]). Let p ≥1, C > 0 and δ > 0 be sufficiently small such that 1 ≥(−ln(δC))−2p ≥δ. Let Lemma A2 ([13]). Let p ≥1, C > 0 and δ > 0 be sufficiently small such that 1 ≥(−ln(δC))
2p ≥δ. Let
Z 1
0 exp(−((1 −ln(λ))−2p)−1/(2p))(1 −ln(λ))−2p ∥dEλw∥2 = Cδ2. (A7) Z 1
0 exp(−((1 −ln(λ))−2p)−1/(2p))(1 −ln(λ))−2p ∥dEλw∥2 = Cδ2. Z 1
0 exp(−((1 −ln(λ))−2p)−1/(2p))(1 −ln(λ))−2p ∥dEλw∥2 = Cδ2. (A7) (A7) Then, Then, Z 1
0 (1 −ln(λ))−2p ∥dEλw∥2 ≤C(−ln δ)−2p
(A8) Z 1
0 (1 −ln(λ))−2p ∥dEλw∥2 ≤C(−ln δ)−2p
(A8)
. ,
Z 1
0 (1 −ln(λ))−2p ∥dEλw∥2 ≤C(−ln δ)−2p
(A8)
with a generic constant C. (A8) with a generic constant C. Lemma A3 ([13]). Let p ≥1, k ∈N, k ≥2. Then, there exists a constant D, which is independent of k,
such that Lemma A3 ([13]). Let p ≥1, k ∈N, k ≥2. Then, there exists a constant D, which is independent of k,
such that k−1
∑
j=0
j + 1
k + 1
−1/2 k −j
k + 1
−1/2
1
k + 1
ln(k + 2)
ln(k −j + 1)
2p! ≤D
(ln(k + 2))−p
k−1
∑
j=0
j + 1
k + 1
−1 k −j
k + 1
−1/2
1
k + 1
ln(k + 2)
ln(k −j + 1)
2p
≤D. Moreover, there exists a constant D (independent of k) such that Moreover, there exists a constant D (independent of k) such that k−1
∑
j=0
(j + 1)−1/2(ln(j + 1))p(k −j + 1)−1/2(ln(k −j + 1))−2p ≤D. (A9) (A9) Lemma A4 ([13]). Let ˆk be a solution of Lemma A4 ([13]). Let ˆk be a solution of
k(ln k)2p = C
δ2 . (A10)
Then, ˆk satisfies
ˆk = O
(−ln δ)−2p
δ2
. (A11) k(ln k)2p = C
δ2 . (A10) k(ln k)2p = C
δ2 . (A10) Then, ˆk satisfies ˆk = O
(−ln δ)−2p
δ2
. (A11) (A11) 22 of 22 Mathematics 2020, 8, 608 References 1. B¨ockmann, C.; Kammanee, A.; Braunß, A. Logarithmic convergence rate of Levenberg–Marquardt method
with application to an inverse potential problem. J. Inv. Ill-Posed Probl. 2011, 19, 345–367. [CrossRef] 1. B¨ockmann, C.; Kammanee, A.; Braunß, A. Logarithmic convergence rate of Levenberg–Marquardt method
with application to an inverse potential problem. J. Inv. Ill-Posed Probl. 2011, 19, 345–367. [CrossRef] 2. Hettlich, F.; Rundell, W. Iterative methods for the reconstruction of an inverse potential problem. Inverse Probl. 1996, 12, 251–266. [CrossRef] 2. Hettlich, F.; Rundell, W. Iterative methods for the reconstruction of an inverse potential problem. Inverse Probl. 1996, 12, 251–266. [CrossRef] 3. Hettlich, F.; Rundell, W. A second degree method for nonlinear inverse problems. SIAM J. Numer. Anal. 1999, 37, 587–620. [CrossRef] 3. Hettlich, F.; Rundell, W. A second degree method for nonlinear inverse problems. SIAM J. Numer. Anal. 1999, 37, 587–620. [CrossRef] . Van den Doel, K.; Ascher, U. On level set regularization for highly ill-posed distributed parameter estima
problems. J. Comput. Phys. 2006, 216, 707–723. [CrossRef] . Hohage, T. Logarithmic convergence rates of the iteratively regularized Gauss—Newton method fo
inverse potential and an inverse scattering problem. Inverse Probl. 1997, 13, 1279. [CrossRef] 6. Pornsawad, P.; Sapsakul, N.; Böckmann, C. A modified asymptotical regularization of nonlinear ill-posed
problems. Mathematics 2019, 7, 419. [CrossRef] 6. Pornsawad, P.; Sapsakul, N.; Böckmann, C. A modified asymptotical regularization of nonlinear ill-posed
problems. Mathematics 2019, 7, 419. [CrossRef] 7. Tautenhahn, U. On the asymptotical regularization of nonlinear ill-posed problems. Inverse Probl. 1994,
10, 1405–1418. [CrossRef] 7. Tautenhahn, U. On the asymptotical regularization of nonlinear ill-posed problems. Inverse Probl. 1994,
10, 1405–1418. [CrossRef] 8. Zhang, Y.; Hofmann, B. On the second order asymptotical regularization of linear ill-posed inverse problems. Appl. Anal. 2018. [CrossRef] 8. Zhang, Y.; Hofmann, B. On the second order asymptotical regularization of linear ill-posed inverse problems. Appl. Anal. 2018. [CrossRef] 9. Pornsawad, P.; Böckmann, C. Modified iterative Runge-Kutta-type methods for nonlinear ill-posed problems. Numer. Funct. Anal. Optim. 2016, 37, 1562–1589. [CrossRef] 10. Mahale, P.; Nair, M. Tikhonov regularization of nonlinear ill-posed equations under general source condition. J. Inv. Ill-Posed Probl. 2007, 15, 813–829. [CrossRef] 11. Romanov, V.; Kabanikhin, S.; Anikonov, Y.; Bukhgeim, A. Ill-Posed and Inverse Problems: Dedicated
to Academician Mikhail Mikhailovich Lavrentiev on the Occasion of his 70th Birthday; De Gruyter: Berlin,
Germany, 2018. 12. Scherzer, O. A modified Landweber iteration for solving parameter estimation problems. Appl. Math. Optim. 1998, 38, 45–68. [CrossRef] 13. References Deuflhard, P.; Engl, W.; Scherzer, O. A convergence analysis of iterative methods for the solution of nonlinear
ill-posed problems under affinely invariant conditions. Inverse Probl. 1998, 14, 1081–1106. [CrossRef] 14. Bakushinsky, A.; Kokurin, M.; Kokurin, M. Regularization Algorithms for Ill-Posed Problems; Inverse and
Ill-Posed Problems Series; De Gruyter: Berlin, Germany, 2018. 15. Schuster, T.; Kaltenbacher, B.; Hofmann, B.; Kazimierski, K. Regularization Methods in Banach Spaces; Radon
Series on Computational and Applied Mathematics; De Gruyter: Berlin, Germany, 2012. 16. Albani, V.; Elbau, P.; de Hoop, M.V.; Scherzer, O. Optimal convergence rates results for linear inverseproblems
in Hilbert spaces. Numer. Funct. Anal. Optim. 2016, 37, 521–540. [CrossRef] [PubMed] 17. Kaltenbacher, B.; Neubauer, A.; Scherzer, O. Iterative Regularization Methods for Nonlinear Ill-Posed Problems;
De Gruyter: Berlin, Germany; Boston, MA, USA, 2008. 18. Louis, A.K. Inverse und Schlecht Gestellte Probleme; Teubner Studienbücher Mathematik, B. G. Teubner:
Stuttgart, Germany, 1989. 9. Vainikko, G.; Veterennikov, A.Y. Iteration Procedures in Ill-Posed Problems; Nauka: Moscow, Russia, 1986 20. Hanke, M.; Neubauer, A.; Scherzer, O. A convergence analysis of the Landweber iteration for nonlinear
ill-posed problems. Numer. Math. 1995, 72, 21–37. [CrossRef] p
p
21. B¨ockmann, C.; Pornsawad, P. Iterative Runge-Kutta-type methods for nonlinear ill-posed problems. Inverse Probl. 2008, 24, 025002. [CrossRef] c⃝2020 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 (http://creativecommons.org/licenses/by/4.0/).
|
https://openalex.org/W4213346186
|
https://www.mdpi.com/2073-4352/12/2/302/pdf?version=1645442568
|
English
| null |
Effect of Fineness and Heat Treatment on the Pozzolanic Activity of Natural Volcanic Ash for Its Utilization as Supplementary Cementitious Materials
|
Crystals
| 2,022
|
cc-by
| 10,252
|
llah Khan 1,*
, Muhammad Nasir Amin 1,*
, Muhammad Usman 2
, Muhammad Imran 3,
4
1 1
Department of Civil and Environmental Engineering, College of Engineering, King Faisal University (KFU),
P.O. Box 380, Al-Hofuf, Al-Ahsa 31982, Saudi Arabia; fshalabi@kfu.edu.sa 2
Interdisciplinary Research Center for Hydrogen and Energy Storage (IRC-HES), King Fahd University of
Petroleum & Minerals (KFUPM), Dhahran, Eastern Province 31261, Saudi Arabia;
muhammadu@kfupm.edu.sa p
3
School of Civil and Environmental Engineering (SCEE), National University of Sciences & Technology (NUST),
Islamabad 44000, Pakistan; imran.nice@nust.edu.pk p
4
Department of Chemical Engineering, College of Engineering, King Faisal University (KFU), P.O. Box 380,
Al-Hofuf, Al-Ahsa 31982, Saudi Arabia; malfaiad@kfu.edu.sa *
Correspondence: kkhan@kfu.edu.sa (K.K.); mgadir@kfu.edu.sa (M.N.A.); Tel.: +966-13-589-5408 (K.K.);
Fax: +966-13-581-7068 (K.K.) Abstract: The aim of this study was to investigate the influence of fineness and heat-treatment on the
pozzolanic and engineering properties of volcanic ash. To this end, two different fineness levels of
volcanic ash, ultra-fine (VAF) and fine (VA), without and after heat treatment at different temperatures
(VA550, VA650, and VA750), were partially substituted for cement. In addition to the control (100%
cement), five binary mortar mixes, each containing 20% of the different types of volcanic ash (VAF and
VA; heat-treated and not), were prepared. First, X-ray fluorescence (XRF), X-ray powder diffraction
(XRD), particle size analysis, and modified Chappelle tests were used to characterize the material. All mortar mixes were then tested for compressive strength development, water absorption, and
apparent porosity. Finally, the microstructure of each of the mixes was evaluated by performing XRD,
thermogravimetric analysis (TGA), and Fourier transform infrared spectroscopy (FTIR) analyses on
paste samples at 91 days post-formation. The XRD and Chappelle reactivity results revealed increased
pozzolanic reactivity with increasing volcanic ash fineness. In contrast, heat treatment adversely
affected the pozzolanic reactivity of the volcanic ash due to the formation of crystalline phases at
high temperatures. The mortars containing VAF20 (VAF, no heat, at 20%) showed slightly improved
compressive strength (69.6 MPa) than the control (68.1 MPa) and all other binary mixes (66.7, 63.5,
64.2, and 63.9 MPa for VA20, VA20-550, VA20-650, and VA20-750, respectively) at 91 days. The mortar
containing VAF20 demonstrated the lowest level of water absorption (9.3%) and apparent porosity
(19.1%) of all mixes, including the control. The XRD results for the paste samples show that both VA
and VAF showed the least intensity of portlandite phase, as compared to the control and other binary
mixes. llah Khan 1,*
, Muhammad Nasir Amin 1,*
, Muhammad Usman 2
, Muhammad Imran 3,
4
1 TGA results also show that binary mixes of VA and VAF have a reduced amount of portlandite,
resulting in the densification of the mixes’ microstructures. With the addition of VAF, there is a
significant shift in the FTIR band from 980 to 992 cm−1, which causes the formation of additional
C–S–H gels that lead to the densification of the paste matrix. These results demonstrate that VAF
exhibits high pozzolanic reactivity, making it suitable for use as a natural pozzolan that can partially
substitute cement in the production of strong, durable, and environmentally friendly concrete. crystals crystals Effect of Fineness and Heat Treatment on the Pozzolanic
Activity of Natural Volcanic Ash for Its Utilization as
Supplementary Cementitious Materials han 1,*
, Muhammad Nasir Amin 1,*
, Muhammad Usman 2
, Muhammad Imran 3,
i d 4
d
i
l
Sh l bi 1 Kaffayatullah Khan 1,*
, Muhammad Nasir Amin 1,*
, Muhammad Usman 2
, Muhammad Imran 3,
Majdi Adel Al-Faiad 4
and Faisal I. Shalabi 1 1. Introduction A significant amount of natural resources is consumed by buildings and infrastructure,
creating an ongoing sustainability challenge. Concrete is the second most consumed
material on the planet, after water. In 2006, it was estimated that about 25 billion tons of
concrete are produced annually worldwide [1–5]. The production of cement peaked in 2016
at 4 billion tons, which indicates the huge amount of greenhouse gases being released into
the atmosphere along with the enormous amount of water and aggregates that are utilized
in making concrete. Global cement production accounts for around 7% of total carbon
dioxide emissions. In order to produce 1000 kg of cement, 4–7 GJ of energy is required,
which releases 800–1000 kg of carbon dioxide gas into the atmosphere. CO2 emissions
contribute to climate change and global warming [6–11]. The demand for low-carbon
concrete for climate change mitigation and adaptation increases daily. In order to reduce the high energy demands and the increased carbon footprint,
researchers have suggested multiple techniques, such as carbon capturing and utiliza-
tion, clinker reduction, alternate fuel sources and modifications in cement manufacturing,
etc. [12–14]. It is most effective to replace clinker, the major source of CO2 emissions in
cement production, with alternate materials that have pozzolanic properties or cementi-
tious properties. A wide range of pozzolans and auxiliary cementitious materials (SCM),
including fly ash, silica fume, electric arc furnace slag, rice husk ash, wheat straw ash
and natural pozzolans [15–22], etc., are used for cement substitution, which helps reduce
clinker production and emission of CO2. The impact of SCMs on the future cement industry
will be determined by many factors, including the availability of SCMs, their production
efficiency, and cost-effectiveness. Fly ash and slag production is currently estimated at 500
and 300 million tons, respectively [23]. Due to limited supplies, it is usually not possible to
reduce CO2 emissions further with SCMs, such as ground granulated blast furnace slag or
fly ash from coal incineration [24] Therefore, there is an urgent need to investigate new ce-
ment substitutes to reduce the CO2 emissions produced by the concrete industry. Naturally
occurring pozzolanic materials, such as volcanic ash, volcanic pumice, and calcined clay,
which are available in mass amounts, can be used as an alternative to meet the needs of the
concrete industry. Construction in the Kingdom of Saudi Arabia (KSA) has gained pace during the last
two decades.
Citation: Khan, K.; Amin, M.N.;
Usman, M.; Imran, M.; Al-Faiad,
M.A.; Shalabi, F.I. Effect of Fineness
and Heat Treatment on the
Pozzolanic Activity of Natural
Volcanic Ash for Its Utilization as
Supplementary Cementitious
Materials. Crystals 2022, 12, 302. https://doi.org/10.3390/cryst12020302 Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
published maps and institutional affil-
iations. Copyright:
© 2022 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/). Keywords: volcanic ash; heat treatment; mortar; compressive strength; X-ray powder diffraction;
thermogravimetric analysis; Fourier transform infrared spectroscopy analysis https://www.mdpi.com/journal/crystals Crystals 2022, 12, 302. https://doi.org/10.3390/cryst12020302 Crystals 2022, 12, 302 2 of 19 1. Introduction KSA has one of the world’s highest per capita cement consumption rates,
with production estimated at 42.2 million tons in 2019 [25]. In order to meet the local
concrete industry’s needs, KSA imports a huge amount of SCMs, such as FA, GGBFS, and
SF. Recently, natural volcanic pozzolans found in Western KSA, have been identified as
a promising partial cement replacement material. A large portion of the basaltic flows in
the west of KSA formed millions of years ago. These areas are known as Harrat [26]. The
western part of Saudi Arabia is home to several big and small Harrats, spread out over
a vast area of km2 [27]. Both Harrat Rahat and Kishb contain 644 and 163 scoria cones,
respectively [28,29]. A total of 327 scoria cones have been found in Harrat Khaybar, Ithnayn,
and Kura [30–32]. Scoria has lightweight particles of between 2 and 32 mm in size, with a
reddish or black appearance. Scientists have extensively studied the pozzolanic properties
of such deposits, finding that the vast majority of samples show pozzolanic activity. The
researchers concluded that scoria samples could possibly be used as cement substitutes in
concrete [33,34]. Volcanic ash from locally available natural sources can be used as a partial
substitute for Portland cement in the production of strong and durable concrete. p
g
Several studies have been performed to investigate the role of natural volcanic ash on
the mechanical and microstructural properties of mortar and concrete [35–41] Researchers
have documented the significant technical benefits of partially substituting OPC with NP,
but they also noted that the early age strength (7 and 28 days) of concrete mixtures using
volcanic ash as a substitute for different percentages of cement in the cement mixtures, was
lower than that of control samples. In accordance with Moufti et al. [35], finely pulverized
scoria passed through a 45 mm sieve with a 10% mass content has a compressive strength
comparable to control samples. Sabtan et al. [36] concluded that all samples from the Crystals 2022, 12, 302 3 of 19 3 of 19 Harrat region demonstrate pozzolanic behavior and meet Italian requirements. A study
by Khan et al. [37] reported that when 15% of natural pozzolans were substituted by
cement, the finely ground pozzolans had a lower compressive strength at all ages, as
compared to controls. According to Patil et al. 1. Introduction [40], volcanic ash substitutions of up to 30%
of the mass of OPC led to increased vascularity and porosity of the cementitious matrix. Fadala et al. [42] reported that a 10% substitution of volcanic ash in cement resulted in
a minor reduction in strength compared to control samples. Meanwhile, 20% and 30%
substitutions of volcanic ash in cement led to significant reductions in strength, at all
ages, as compared to control samples. Research studies have shown that volcanic ash
has low reactivity, which contributes to delays in the development of strength and other
durability characteristics. Therefore, it is imperative that volcanic ash be improved in
order to increase its reactivity and ultimately improve its strength and durability. Previous
research studies have demonstrated that natural pozzolans can be improved by utilizing
mechanical, chemical, and thermal techniques [43–49]. The aim of this study was to determine the influence of fineness and heat treatment
of volcanic ash used as a partial replacement for cement to produce a high-performance
sustainable mortar. Initially, the ground volcanic ash was passed through sieves No. 450
and 625 to obtain fine volcanic ash (VA) and ultra-fine volcanic ash (VAF). Then, VA was
exposed to different elevated temperatures (550, 650, and 750 ◦C) in a kiln to examine
the impact of heat treatment on the pozzolanic properties of VA. Chemical composition
analyses, using XRF analysis, particle size analysis, X-ray diffraction analysis (XRD), and
modified Chapelle reactivity was performed on both ground (VA, VAF) and heat-treated
volcanic ash (VA550, VA650, and VA750). In the second phase, mortar samples were
prepared for a control mix and five binary mixes containing 20% volcanic ash (VA, VAF,
VA550, VA650, and VA750) as a replacement for cement as shown in Figure 1. Mechanical
properties, such as compressive strength (7, 28, and 91 days), water absorption (WA), and
apparent porosity (AP) (91 days) were investigated for all of the mortar mixes. Finally,
a microstructural investigation of the mixes using XRD, TGA, and FTIR analyses was
conducted on the paste samples. Figure 1. Schematic presentation of the use of volcanic ash for mortar cubes applications. Figure 1. Schematic presentation of the use of volcanic ash for mortar cubes applications. 2. Materials and Methods
2.1. Materials Ordinary Portland cement I corresponding to ASTM C150 Type I was used as the
major binding material [50]. The main binder material had a specific gravity of 3.15 g/cm3
and a Blaine fineness of 344 m2/kg. The volcanic ash used in this study was obtained
from the western part of the Kingdom of Saudi Arabia. Raw volcanic ash in aggregate
form was obtained from a quarry located at Harrat Rahat, Medina province, Saudi Arabia. Crystals 2022, 12, 302 4 of 19 The volcanic ash was ground and passed through sieves no. 450 and 625. Sieving was
performed to produce VA and VAF to evaluate the effect of fineness on its engineering
properties. The volcanic ash passed through sieve no. 450 (VA) was heated at three different
temperatures (550, 650, and 750 ◦C) in order to determine the effect of heat treatment on
the mechanical and microstructural properties (Figure 2). An electrical muffle furnace was
used to calcine fine volcanic ash (VA) at temperatures of 550 ◦C, 650 ◦C, and 750 ◦C for two
hours, and then to allow the ash to air-cool abruptly. The elemental composition of OPC
and volcanic ash can be found in Table 1. Figure 2. The materials used in this study, in powder form: cement (C); fine volcanic ash (VA); ultra-
fine volcanic ash (VAF); and VA at 550 ◦C (VA550), VA at 650 ◦C (VA650), and VA at 750 ◦C (VA750). Table 1. Physical and chemical composition of cement and volcanic ash. Figure 2. The materials used in this study, in powder form: cement (C); fine volcanic ash (VA); ultra-
fine volcanic ash (VAF); and VA at 550 ◦C (VA550), VA at 650 ◦C (VA650), and VA at 750 ◦C (VA750). Figure 2. The materials used in this study, in powder form: cement (C); fine volcanic ash (VA); ultra
fine volcanic ash (VAF); and VA at 550 ◦C (VA550), VA at 650 ◦C (VA650), and VA at 750 ◦C (VA750). Figure 2. The materials used in this study, in powder form: cement (C); fine volcanic ash (VA); ultra-
fine volcanic ash (VAF); and VA at 550 ◦C (VA550), VA at 650 ◦C (VA650), and VA at 750 ◦C (VA750). Table 1. Physical and chemical composition of cement and volcanic ash. Table 1. Physical and chemical composition of cement and volcanic ash. 2. Materials and Methods
2.1. Materials C
VA
VAF
Physical Properties
Specific gravity (g/cm3)
3.15
2.64
Fineness (m2/kg)
(Blain)
344
-
-
Fineness (m2/cc)
(Microtrac S3500)
0.5670
0.816 (<38 µ)
1.194 (<20 µ)
Chemical properties (oxides, % by weight)
SiO2
20.9
46.4
Al2O3
5.18
14.4
Fe2O3
3.04
12.8
(SiO2 + Al2O3 + Fe2O3) *
-
73.6
CaO
63.9
8.80
MgO
1.65
8.30
Na2O
0.10
3.80
K2O
0.52
1.90
SO3
2.61
0.80
LOI **
2.51
2.80 Crystals 2022, 12, 302 5 of 19 Table 1. Cont. C
VA
VAF
Physical Properties
Compounds (%)
C2S
52.1
-
C3S
19.6
-
C3A
8.17
-
C4AF
8.81
-
* ASTM C618-15; ** LOI = loss on ignition. Table 1. Cont. Figure 3 shows the particle size analysis curves using laser diffraction techniques for
C, VA, and VAF. The particle size analysis indicates that both VA and VAF are finer than
the control, cement samples. X-ray diffraction analyses (Figure 4) were performed on the
raw sample of VA and again once it had been heated to three different temperatures (550,
650, and 750 ◦C) to investigate how heat treatment impacts the morphology and phases
of the samples. Commercially available desert sand was used as a fine aggregate with a
fineness modulus of 2.54 and met the standard code provisions esp. EN 196-1: 2016 and
ISO 679: 2009 [51,52]. According to ASTM C125, the fineness modulus should be between
2.3 and 3.1 [53]. Figure 3. Particle size distribution curves of cement, fine volcanic ash, and ultra-fine volcanic ash. Figure 3. Particle size distribution curves of cement, fine volcanic ash, and ultra-fine volcanic ash. Crystals 2022, 12, 302 6 of 19 Figure 4. XRD patterns of fine volcanic ash (VA) before and after heat treatment at different temperatures. 2.2. Mix Proportions and Test Methods Figure 4. XRD patterns of fine volcanic ash (VA) before and after heat treatment at different temperatures. Figure 4. XRD patterns of fine volcanic ash (VA) before and after heat treatment at different temperatures. 2.2. Mix Proportions and Test Methods Figure 4. XRD patterns of fine volcanic ash (VA) before and after heat treatment at different temperatures. 2.2. Mix Proportions and Test Methods
2.2.1. Mix Proportions 2.2.1. Mix Proportions A total of 72 samples with different mix proportions were cast including the control
sample which contained 100% cement as a binder. The different mix proportions in Table 2
show that fine and ultra-fine (VA, VAF) and heat-treated (VA550, VA650, VA750) volcanic
ashes were used as a 20% replacement in cement to investigate its effects as a cement
substitute in mortar. A 20% substitution of volcanic ash (VA20, VAF20, VA20-550, VA20-650,
and VA20-750) along with 80% cement as a binder in terms of quantity, was used in this
study. Different mix IDs represent the composition of the constituent binders e.g., VA20
represents 80% of C and 20% of VA, whereas VA20-550 represents 80% of C and 20% of VA
exposed to 550 ◦C, etc. Compressive strength tests were conducted on 50 mm3 samples after
curing for 7, 28, and 91 days. Water absorption capacity and porosity were simultaneously
calculated on 50 mm3 samples after 91 days of curing. For all tests, three samples were
tested and an average was taken as the final result. The water to binder ratio in the mortar
was maintained in accordance with standard code provisions (ASTM C109) [54]. Table 2. Mixture proportions of mortar (w/cm = 0.40; cm:s = 1:1.36). Table 2. Mixture proportions of mortar (w/cm = 0.40; cm:s = 1:1.36). Batch Quantities (g) for Nine 50-mm3 Mortar Specimens
Mix ID
Water
(w)
Cement
(c)
VA
VAF
Sand
(s)
Control Mortar
(CM)
440
1100
0
0
1500
20% VA
(VA20)
440
880
220
0
1500
20% VAF
(VAF20)
440
880
0
220
1500
20% VA550
(VA20-550)
440
880
220
0
1500
20% VA650
(VA20-650)
440
880
220
0
1500
20% VA750
(VA20-750)
440
880
220
0
1500 Batch Quantities (g) for Nine 50-mm3 Mortar Specimens Crystals 2022, 12, 302 7 of 19 7 of 19 2.2.2. Mixing and Testing for Compressive Strength of Mortar Cubes A three-speed Hobart mixer was used to mix the constituents of mortar according to
ASTM C305 [55]. Initially, the binder and water were mixed for 30 s at a low speed. The
sand was then added while the mixing speed was kept constant. Then, the mixer speed was
increased to an intermediate level, and stirring continued for 30 s. The mixing was stopped
for 90 s and was then resumed at a medium speed for 60 s in the final stage. 2.3. Modified Chappelle Test to Evalute the Reactivity of Pozzolanic Materials The reactivity of pozzolans can be evaluated chemically by using a Chapelle activity
test. The test adhered to the NF P 18-531 standard, as follows Figure 5): 2 g of CaO was
mixed with 1 g of pozzolanic material, together with 250 mL of deionized water in an
Erlenmeyer flask. The flask was placed in a hot water bath with a shaker at 90 ± 5 ◦C for
16 ± 2 h. The solution was then cooled to room temperature; 250 mL of sucrose solution
(240 g/L) were added to the flasks and mixed for 15 min. The solution was then filtered
and 25 mL of the filtrate was tittered with 0.1 M HCl solution using phenolphthalein as
indicator. Chapelle activity was calculated by: mg CaO per gram o f material = (28)(2)(2)Fc(v3m3 −v2)
m4m3m2
(1) (1) m2 = grams of pozzolanic material; m3 = grams of CaO mixed with pozzolanic material;
m4 = grams of CaO in the blank test; v2 = milliliters of HCl 0.1M consumed by the sample
solution; v3 = milliliters of HCl 0.1 M consumed by the blank solution; Fc = correction factor
of HCl 0.1 M standard solution. 2.2.1. Mix Proportions Total mixing
time for the whole process was 4 min, using the same Hobart mixer for each mixture. A
constant flow of between (15–115%) was maintained (ASTM C1467) for all mixes by adding
a naphthalene sulphonate-based superplasticizer. Based on the mixer’s capacity, mixing
was performed in order to cast twelve 50 mm3 samples for each mix. Immediately after
mixing, casting took place. The fresh mortar was filled in two layers into a 50 mm3 steel
mold which had been oiled on the inside. Roding was performed after each layer was
filled, in accordance with the ASTM C109 code [54]. To test compressive strength (7, 28,
and 91 days) and porosity and water absorption (91 days), 12 samples of each mix were
cast (Table 2). After casting, the samples were covered by plastic sheets to prevent any
loss of water. Samples were demolded after 24 h and kept in a water tank to cure until the
testing age. The cured mortar cubes were taken from the curing tanks after completing the required
curing duration and were subsequently tested for compressive strength. Testing was
carried out in accordance with the relevant ASTM C109 codes. A universal testing machine
(UTM) was used for testing the mortar samples. The UTM had a capacity of 300 kN
and the rate of strain was maintained as 1 mm/min. A data logger was attached to the
transducers and strain gauges which recorded all the readings automatically. The peak
strength was calculated as the ratio of the maximum load at failure, to the area of the
sample (here 2500 mm2). Water absorption capacity and apparent porosity were calculated
as per ASTM C 948-81 [56]. For all testing, the average value of three samples was taken as
the final reading. 2.3. Modified Chappelle Test to Evalute the Reactivity of Pozzolanic Materials 2.4.1. X-ray Diffraction (XRD) Analysis The crystal structure of the samples was determined via Rigaku CuKα radiation using
a bench top Mini Flex X-ray diffraction (mini-XRD) instrument. The patterns were measured
from 2θ = 5 up to 80◦with a step size and scan speed of 0.02 and 2◦per minute, separately. XRD analysis was performed to determine the distinct phases prevalent in the VA paste
and to obtain an indication of the reactivity potential of the mixture. This technique was
required to understand the crystalline or pozzolanic behavior of the materials. Analysis of Pastes Containing Pozzolanic Materials The microstructural investigation, such as X-ray diffraction analysis, Fourier transform
infrared spectroscopy analysis, and thermogravimetric analysis was performed on the
cement pastes samples. A detailed description of each technique is discussed below. Crystals 2022, 12, 302 8 of 19 8 of 19 Figure 5. Illustration of the several steps performed to determine Chappelle activity. (a) Samples and
blank placed in the water bath; (b) mixing after adding sucrose solution; (c) filtration of the samples;
and (d) The filtrated sample. Figure 5. Illustration of the several steps performed to determine Chappelle activity. (a) Samples and
blank placed in the water bath; (b) mixing after adding sucrose solution; (c) filtration of the samples;
and (d) The filtrated sample. 2.4.2. Thermogravimetric Analysis (TGA) In addition, thermogravimetric analysis (TGA) was performed on the samples using a
Mettler Toledo instrument at a temperature ranging from 25 to 800 ◦C with a heating rate
of 10 ◦C min−1. All thermogravimetric experiments were conducted under air. Through
TGA, the distinct phases in cement paste were determined and the extent of pozzolanic
reaction was measured by measuring the consumption of the CH phase. 2.4.3. Fourier Transform Infrared Spectroscopy (FTIR) Analysis 2.4.3. Fourier Transform Infrared Spectroscopy (FTIR) Analysis FTIR (Fourier transform infrared spectroscopy, Nicolet NEXUS-FTIR-670 spectrometer)
was used to identify vibrations. FTIR was performed using a sample (0.22 vol%) and KBr
(50 mg) mixed into a wafer and placed into a self-made cell. A spectrum was then recorded. Cement paste samples were analyzed with FTIR in order to determine any changes in the
spectra which indicated that the mineralogical arrangement had changed. Crystals 2022, 12, 302 9 of 19 3.2. Chappelle Reactivity Test 3.2. Chappelle Reactivity Test Chapelle reactivity is used to measure the amount of CaO consumed by pozzolans; a
greater value of Chapelle reactivity indicates better pozzolanic reactivity of a given sample. According to the test results presented in Table 3, the VAF sample demonstrated the highest
level of reactivity among the samples. These results indicate that the particle size of the
material can greatly affect its reactivity with CaO. In addition, both VA and VAF exhibited
better pozzolanic reactivity compared to the heat-treated VA (VA550, VA650, and VA750). Furthermore, VA samples exposed to high temperatures (VA650 and VA750) showed the
lowest Chapelle reactivity values. The reduction in pozzolanic reactivity can be attributed
to the formation of crystalline phases at high temperatures. The Chappelle test results
are also in agreement with those from the XRD analysis and the other tests conducted in
this study. Table 3. Chappelle test results of VA, VAF, and heat-treated VA550, VA650, and VA750 according to
NF P 18-531. Materials
Chappelle Activity (mg CaO/g Sample)
VA
821.51
VAF
844.32
VA550
808.75
VA650
792.80
VA750
800.29 Table 3. Chappelle test results of VA, VAF, and heat-treated VA550, VA650, and VA750 according to
NF P 18-531. 3.3. Influence of Fineness and Heat-Treatment on Strength, Porosity, and Water Absorption Figure 7 shows a comparison of the compressive strength test results of the control
mortar (CM) and the binary mortar containing 20% VAF, both before (VA20) and after heat
treatment at 550 ◦C (VA20-550), 650 ◦C (VA20-650), and 750 ◦C (VA20-750). As compared to
the control, the compressive strength of VA20 decreased at all ages. However, the intensity
of the strength reduction was significantly reduced at later ages, where a comparable
91-day strength was observed to that of CM. Moreover, due to increasing fineness, a slight
increase in strength was observed for VAF20 as compared to VA20. However, despite
increased fineness, the compressive strength of VAF20 remained lower than that of CM
at all ages, except at 91 days, where a slightly higher strength, as compared to CM, was
observed. An improved later age strength for both VA20 and VAF20 is attributed to the
delayed pozzolanic action of VA. Similar results were reported by other researchers where
the strength of mortar at early ages (7 or 28 days) was reduced due to adding 20% fly
ash or 20% waste glass sludge as a replacement of cement [34,60]. 3.1. Material Characterisations by XRF and XRD Analysis 3.1. Material Characterisations by XRF and XRD Analysis Table 1 shows the chemical composition of raw volcanic ash determined by XRF
analysis. Silica (SiO2), Alumina (Al2O3), Iron oxide (Fe2O3), Calcium oxide (CaO), and
Magnesia (MgO) are the major elements present in VA. In terms of weight content, silica
has the highest value (47.02 wt.%). The sum of SiO2, Al2O3, and Fe2O3 is around 70%,
which shows that VA fulfills the minimum requirements set by ASTM C618-15 [57] for
natural pozzolans. p
The XRD analysis of the raw volcanic ash (VA, VAF) and the heat-treated volcanic ash
(VA550, VA650, and VA750) are shown in Figure 4. An XRD pattern of the raw volcanic
ash showed significant amounts of amorphous glass. Figure 4 shows a broad pozzolanic
hump of around 21◦to 38◦with few distinct crystalline peaks. The peaks in the volcanic
ash sample became sharper and more intense when heated at different temperatures. Moreover, new crystal phases evolved, such as hematite, ilmenite, parasite, etc., which
changed the color of VA from black to deep red. Many factors could have contributed to
this transformation, including the recrystallization of minerals, oxidation of iron oxides,
and a transformation into hematite. By increasing the heating temperature, the peaks on
the XRD scale became sharper, indicating a further crystallization of hematite and other
minerals phases, which ultimately led to a decrease in the amorphous phases. FTIR analysis (Figure 6) shows the infrared spectrum of the raw volcanic ash (VA,
VAF) and the heat-treated volcanic ash (VA550, VA650, and VA750). It is believed that the
bands located between 920 and 990 cm−1 are caused by the stretching of the Si–O–Al bonds. Quartz minerals possess a vibration mode of Si–O at 558 cm−1. Water molecules vibrate in
the O–H mode around 3324 cm−1 [58,59]. The IR bands show that the relative intensity of
the Si–O–Si band is higher in the raw volcanic ash (VA) as compared to the heat-treated
volcanic ashes. The results further demonstrate that Si–O–Si for VA is more broad and wide
as compared to the heat-treated sample, which shows the availability of a high amount of
amorphous silica present in the sample. The results of this FTIR analysis are consistent
with the XRD analysis. Figure 6. FTIR intensities for untreated VA and heat-treated VA at 550, 650, and 750 ◦C. Figure 6. FTIR intensities for untreated VA and heat-treated VA at 550, 650, and 750 ◦C. 3.1. Material Characterisations by XRF and XRD Analysis Crystals 2022, 12, 302 10 of 19 3.2. Chappelle Reactivity Test However, at later ages
(91 days), similar to the findings of the current study, a comparable strength to that of the
control mortar was observed in these studies. Unlike the positive influence of increased
fineness, the negative impact of heat treatment on strength was observed in all mortar mixes
(VA20-550, VA20-650, VA20-750), especially at later ages. For instance, the compressive
strength of mortar mixes containing heat-treated VA, slightly decreased as compared to
untreated VA at all ages (28 and 91 days), except at early ages (7 days). This decrease in the
strength of mortar containing the heat-treated VA is due to the transformation of the nature
of VA from amorphous to crystalline. However, at early ages, a slight rise in strength occurs
due to an improvement in the cementitious potential of VA following heat treatment. The
closeness of the strength test results, irrespective of aging, among all mortars containing
treated VA, demonstrates an insignificant effect of increasing heat treatment temperatures. Therefore, the current results suggest that mechanical treatment of VA alone should be used
to obtain an optimized fineness and the best strength potential and that heat treatment
should not be used, to avoid compromising strength potentials. 11 of 19 11 of 19 Crystals 2022, 12, 302 Figure 7. Comparison of compressive strength development between control and mortar containing
VAF, and heat-treated and untreated VA. Figure 7. Comparison of compressive strength development between control and mortar containing
VAF, and heat-treated and untreated VA. Like compressive strength, very similar trends of water absorption and apparent
porosity were observed among all mortars (Figure 8), which indirectly validates the strength
results. For instance, a slight increase in WA and AP values was observed for VA20 as
compared to CM, while VAF20 exhibited lower values as compared to both CM and VA20
due to its decreased particle sizes, which ultimately would lead to better packing and filling
abilities along with improved pozzolanic action. Once again, a negative impact of heat
treatment was also observed for WA and AP among mortars containing heat-treated VA. The results show that WA and AP values for mortars containing heated-treated VA were
higher as compared to mortar containing untreated VA or CM. This ultimately validates
the lower strength results of mortar having treated VA. 3.4. X-ray Diffraction of Cement Pastes Containing Pozzolanic Materials Figure 9 shows the XRD analysis peak results for paste samples of control and binary
mixes containing 20% volcanic ashes (VA, VAF, VA550, VA650, and VA750) as a replacement
for cement. Pozzolans contain amorphous and glassy silica which forms calcium silicate
hydrate (CSH) when it reacts with portlandite (Ca(OH)2). During the pozzolanic reaction,
the pozzolans combine with the portlandite phase in the cement matrix and produce
additional C–S–H gels, which mainly contribute toward strength development. Therefore,
the depletion of the portlandite phase in cement paste can be used to determine the
pozzolanic potential of cement substitutes [61,62]. A comparison of the XRD patterns of
the cement pastes from the mixes was conducted for their peak Ca(OH)2 intensity, which
corresponded to 18.02◦two-theta at 91 days, as shown in Figure 9. Crystals 2022, 12, 302 12 of 19 12 of 19 Figure 8. Comparison of (a) water absorption, (b) apparent porosity results between control, an
mortar containing VAF, and heat-treated and untreated VA after 91 days of standard curing. Figure 8. Comparison of (a) water absorption, (b) apparent porosity results between control, and
mortar containing VAF, and heat-treated and untreated VA after 91 days of standard curing. Crystals 2022, 12, 302 13 of 19 13 of 19 Crystals 2022, 12, x FOR PEER REVIEW
14 of 20
Figure 9. Comparison of XRD peaks between the control mortar (CM) paste and pastes containing
different volcanic ashes at 91 days. Figure 9. Comparison of XRD peaks between the control mortar (CM) paste and pastes co
different volcanic ashes at 91 days. Figure 9 Comparison of XRD peaks between the control mortar (CM) paste and pastes contai Figure 9. Comparison of XRD peaks between the control mortar (CM) paste and pastes containing
different volcanic ashes at 91 days
Figure 9. Comparison of XRD peaks between the control mortar (CM) paste and pastes containing
different volcanic ashes at 91 days. Crystals 2022, 12, 302 14 of 19 The intensity of Ca(OH)2 for the control sample is the highest among all other samples. The high amount of cement present in the control samples led to hydration, resulting
in the formation of a significant amount of Ca(OH)2 in the samples. The XRD results
also demonstrate that the VAF samples showed the least amount of the portlandite phase
as compared to all other samples. 3.4. X-ray Diffraction of Cement Pastes Containing Pozzolanic Materials This indicates that VAF possesses better pozzolanic
reactivity, due to the presence of amorphous silica, which consumes the portlandite phases
to form additional CSH phases. However, the cement paste samples containing heat-
treated volcanic ash (VA550, VA650, and VA750) had a high intensity of Ca(OH)2, which is
indicative of low reactivity due to the formation of a crystalline phase at high temperatures. Among all blended samples, the VA750 sample showed the highest level of Ca(OH)2,
indicating the presence of a large number of crystalline phase. 3.5. Thermo Gravimetric Analysis (TGA) of Cement Pastes Containing Pozzolanic Materials Thermogravimetric analysis was used to measure the amount of Ca(OH)2 in the
cement paste samples due to the weight loss that occurred between 400 ◦C and 500 ◦C after
thermal decomposition [63,64]. The thermogravimetric analysis was performed on the
paste samples, including control mixes (C) and the binary mixes (VA, VAF, VA550, VA650,
and VA750) at 91 days age, as shown in the Figure 10. Figure 10. TGA results for control mortar (CM) paste and pastes containing different volcanic ashes
at 91 days. Figure 10. TGA results for control mortar (CM) paste and pastes containing different volcanic ashes
at 91 days. The TGA results shows that the control mix (CM) demonstrated the greatest amount
of portlandite (C–H), when compared to the other mixes. The binary mix with 20% VAF,
recorded the least amount of portlandite phase among the mixes. This significant reduction
is attributed to the high reactivity of the very fine amorphous silica in the VAF sample,
causing greater consumption of the C–H phase to form additional C–S–H phases in the
paste matrix. Further, the VA sample also exhibits a better reduction of the portlandite (C–H)
phase, which is attributed to an amorphous silica present in the VA sample. However, the Crystals 2022, 12, 302 15 of 19 heat-treated samples (VA550, VA650, and VA750) exhibited a lower reduction of portlandite,
indicating low reactivity of these materials due to the development of a crystalline phase at
high temperatures. 3.6. Fourier Transform Infrared Spectroscopy (FTIR) Analysis of Cement Pastes Containing
Pozzolanic Materials IR bands are visible at the same location in all paste samples, but at varying intensities,
as shown in Figure 11. This is primarily attributed to the formation of the C–S–H and C–H
phases. Si–O bonds in the C–S–H phase are responsible for the peaks between 900 cm−1
and 1100 cm−1 [65]. The IR bands show that the relative intensity of the Si–O band is
higher in VAF as compared to the other binary mixes and the control sample. The Si–O
band in the VAF samples is broad and shifts toward a high wavelength (992 cm−1), which
indicates high silica polymerization, which is ultimately responsible for the maximum
number of high-density C–S–H phases. The formation of high-density C–S–H phases causes
densification of the micro and pore structure, resulting in better mechanical performance. 3.5. Thermo Gravimetric Analysis (TGA) of Cement Pastes Containing Pozzolanic Materials In
addition, the VA sample showed a slight increase in the intensity of Si–O bands (984 cm−1)
as compared to the control sample, which is an indication of the low pozzolanic reactivity
of VA as compared to VAF. The heat-treated volcanic ashes (VA550, VA650, and VA750)
showed a decrease in the intensity of the Si–O band, which indicates poor pozzolanic
reactivity, which leads to the formation of low density C–S–H phases and ultimately affect
its engineering performance. Figure 11. FTIR intensities for control mortar (CM) paste and pastes containing different volcanic
ashes at 91 days. Figure 11. FTIR intensities for control mortar (CM) paste and pastes containing different volcanic
ashes at 91 days. In all the samples tested, the peak at 3645 cm−1 shows the presence of free OH groups,
indicating the existence of the portlandite phase [66]. The peak at 3645 cm−1 is wide and
more visible in the control sample. For the binary mixes, this peak became smaller which
indicates pozzolanic reactivity of the volcanic ashes by utilizing Ca(OH)2. The portlandite
peak is very small for VA, and is especially so in the VAF sample, as compared to the
other blended samples, which show better reactivity of fine and ultra-fine volcanic ash, Crystals 2022, 12, 302 16 of 19 which ultimately lead to the formation of a more refined microstructure, resulting in better
mechanical performance. which ultimately lead to the formation of a more refined microstructure, resulting in better
mechanical performance. 4. Conclusions The purpose of the current study was to evaluate the impact of fineness and heat
treatment on the performance of natural volcanic ash, used as a cement substitute to
produce a sustainable and high-performance mortar. Along with the control (100% cement),
five binary mixes of volcanic ash (VA, VAF, VA550, VA650, and VA750) were selected. The
effect of fineness and heat-treatment on the mechanical properties (compressive strengths,
WA, and AP) was examined. Furthermore, XRD, FTIR, and TGA analyses were conducted
to investigate the effect of volcanic ash on the microstructure of the cemented paste. g
The results of this study led to the following conclusions: •
The X-ray diffraction and Chapelle reactivity results indicate that pozzolanic reactivity
increases with fineness. Therefore, ultra-fine volcanic ash (VAF) showed highest value
of Chapelle reactivity due to the availability of very fine amorphous silica. Heat-treated
volcanic ashes (VA-550, VA-650 and VA-750), on the other hand, had comparatively
reduced pozzolanic reactivity due to the crystallization of the existing phases and the
formation of new crystalline phases, when exposed to high temperatures. y
p
p
g
p
•
An improvement in compressive strength was observed in a mortar containing 20%
VAF (69.6 MPa) due to increasing the fineness of VA, as compared to CM (68.1 MPa),
especially at 91 days. The above results were validated by VAF20 being shown to have
the lowest WA (9.3%) and AP (19.1%) capacity at 91 days among all mixes. Moreover,
the negative impact of heat treatment on VA (at 550, 650, and 750 ◦C) was observed in
terms of strength. The strength of the mortar containing heat-treated VA was slightly
reduced (63.5, 64.2 and 63.9 MPa for VA20-550, VA20-650, and VA20-750, respectively)
as compared to the control (68.1 MPa) or untreated VA (66.7 MPa). This is attributed
to the change of the amorphous nature of the VA into crystalline, due to the heat
treatment. The current findings suggest that grinding VA to increase its fineness is the
most effective and viable approach to achieving optimal engineering performance. X-ray diffraction analysis results on the paste samples showed that the binary mixes
with 20% VAF (VAF20) significantly reduced the intensity of calcium hydroxide due
to its better pozzolanic behavior as compared to the other mixes. This resulted in
the better pozzolanic reactivity of VAF in the paste matrix. Author Contributions: K.K. and M.N.A. contributed to the design of this research project. K.K.,
M.N.A. and M.U. contributed to performing the experiments starting with the collection of all 4. Conclusions The mixes having heat-
treated volcanic ashes (VA20-550, VA20-650, and VA20-750) showed high intensities
of portlandite peaks, which indicates that these volcanic ashes have low reactivity;
therefore, they do not significantly contribute to the improvement of micro and pore
structure. TGA analysis also showed that the portlandite phase is significantly reduced
in binary mixes containing fine and ultra-fine volcanic ashes (VA20 and VAF20), as
compared to the other mixes (including the control mix). This indicates the superior
pozzolanic property of the fine amorphous silica present in these samples. On the
other hand, heat-treated samples (VA20-550, VA20-650, and VA20-750) showed a high
amount of portlandite phase among all binary mixes, due to its low reactivity, as was
also shown by the XRD results and the results of the Chappelle reactivity test. y
pp
y
FTIR analysis results showed a shift in the Si–O–Si band with the addition of fine
and heat-treated volcanic ashes in the binary mixes. This shift (980 to 992 cm−1) was
more pronounced in the binary mix containing VAF, which indicates the presence of a
large number of high-density C–S–H phases, causing densification of the micro and
pore structure of the paste mix. In addition, the portlandite peaks (3640 cm−1) are
significantly reduced in VA20 and VAF20 mixes, as compared to other binary mixes,
which shows the superior reactivity of fine VA, that ultimately results in the formation
of more C–S–H phases, causing densification of paste matrix. FTIR analysis results showed a shift in the Si–O–Si band with the addition of fine
and heat-treated volcanic ashes in the binary mixes. This shift (980 to 992 cm−1) was
more pronounced in the binary mix containing VAF, which indicates the presence of a
large number of high-density C–S–H phases, causing densification of the micro and
pore structure of the paste mix. In addition, the portlandite peaks (3640 cm−1) are
significantly reduced in VA20 and VAF20 mixes, as compared to other binary mixes,
which shows the superior reactivity of fine VA, that ultimately results in the formation
of more C–S–H phases, causing densification of paste matrix. Author Contributions: K.K. and M.N.A. contributed to the design of this research project. K.K. M.N.A. and M.U. contributed to performing the experiments starting with the collection of all Crystals 2022, 12, 302 17 of 19 17 of 19 materials, sieving VA to obtain desired fineness, mixing, casting, demolding, curing of mortar cubes. K.K. 4. Conclusions performed the compressive strength tests on mortar cubes and measured water absorption and
porosity at different ages. M.A.A.-F. performed the Chapple reactivity test. M.I. and M.U. supported
in the particle size analysis and the XRD, TGA, FTIR analyses of materials and pastes. All authors
(K.K., M.N.A., M.U., M.I., M.A.A.-F. and F.I.S.) contributed to the preparation of the initial draft of
this manuscript. K.K. and M.N.A. critically analyzed and discussed the results of this research and
prepared the final draft of this manuscript. At the revision stage, K.K. and M.N.A. contributed to
the revision and prepared the final revised manuscript. All authors have read and agreed to the
published version of the manuscript. Funding: The Deanship of Scientific Research (DSR) at King Faisal University (KFU) financially
supported this research through its Nasher Track “Grant Number 216010”. Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable. Informed Consent Statement: Not applicable. Data Availability Statement: All the data utilized in current research are available on a reasonable
request from the corresponding author. Data Availability Statement: All the data utilized in current research are available on a reasonable
request from the corresponding author. Acknowledgments: This research was supported by the Deanship of Scientific Research (DSR) at
King Faisal University (KFU), through Nasher Track Grant Number 216010. The authors wish to
express their gratitude for the financial support that made this study possible. The authors also
extend their appreciation to Department of Civil Engineering at King Faisal University, Saudia Arabia
for providing its lab facilities to conduct the required experimental tasks. Conflicts of Interest: The authors declare no conflict of interest. The founding sponsors 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 Comparative sustainability assessment of binary blended concretes usin
i i
M
i l (SCM )
d O di
P
l
d C
(OPC) J Cl
P
d 2019 220 445 459 [C 10. Rahla, K.M.; Mateus, R.; Bragança, L. Comparative sustainability assessment of binary blended con
Cementitious Materials (SCMs) and Ordinary Portland Cement (OPC). J. Clean. Prod. 2019, 220, 445 y
11. Amin, M.N.; Khan, K.; Saleem, M.U.; Khurram, N.; Niazi, M.U.K. Aging and Curing Temperature Effects on Compressive
Strength of Mortar Containing Lime Stone Quarry Dust and Industrial Granite Sludge. Materials 2017, 10, 642. [CrossRef]
[PubMed] 12. Habert, G.; Miller, S.A.; John, V.M.; Provis, J.L.; Favier, A.; Horvath, A.; Scrivener, K.L. Environmental imp
strategies in the cement and concrete industries. Nat. Rev. Earth Environ. 2020, 1, 559–573. [CrossRef] ,
;
,
; J
,
;
, J
;
,
;
,
;
,
p
ategies in the cement and concrete industries. Nat. Rev. Earth Environ. 2020, 1, 559–573. [CrossRef] g
13. Garba, M.D.; Usman, M.; Khan, S.; Shehzad, F.; Galadima, A.; Ehsan, M.F.; Ghanem, A.S.; Humayun, M. CO2 towards fuels: A
review of catalytic conversion of carbon dioxide to hydrocarbons. J. Environ. Chem. Eng. 2021, 9, 104756. [CrossRef] g
13. Garba, M.D.; Usman, M.; Khan, S.; Shehzad, F.; Galadima, A.; Ehsan, M.F.; Ghanem, A.S.; Humayun, M. CO2 towards fuels: A 13. Garba, M.D.; Usman, M.; Khan, S.; Shehzad, F.; Galadima, A.; Ehsan, M.F.; Ghanem, A.S.; Humayu
review of catalytic conversion of carbon dioxide to hydrocarbons. J. Environ. Chem. Eng. 2021, 9, 10 review of catalytic conversion of carbon dioxide to hydrocarbons. J. Environ. Chem. Eng. 2021, 9, 104756. [CrossRef]
14. Muhammad, U.; Naseem, I.; Tayyaba, N.; Neelam, Z.; Aisha, A.; Mahmoud, M.A.; Ahmad, G.; Aasif, H. Advanced strategies in
M t l O
i F
k f
CO C
t
d S
ti
Ch
R
2021 [C
R f] y
y
g
14. Muhammad, U.; Naseem, I.; Tayyaba, N.; Neelam, Z.; Aisha, A.; Mahmoud, M.A.; Ahmad, G.; Aasif, H. Advanced strategies in
Metal-Organic Frameworks for CO2 Capture and Separation. Chem. Rec. 2021. [CrossRef] 14. Muhammad, U.; Naseem, I.; Tayyaba, N.; Neelam, Z.; Aisha, A.; Mahmoud, M.A.; Ahmad,
Metal-Organic Frameworks for CO2 Capture and Separation. Chem. Rec. 2021. [CrossRef] uhammad, U.; Naseem, I.; Tayyaba, N.; Neelam, Z.; Aisha, A.; Mahmoud, M.A.; Ahmad, G.; Aasif, H. Adv
etal-Organic Frameworks for CO2 Capture and Separation. Chem. Rec. 2021. References 1. Yang, K.H.; Jung, Y.B.; Cho, M.S.; Tae, S.H. Effect of supplementary cementitious materials on reduction of CO2 emissions from
Concrete. In Handbook of Low Carbon Concrete, 1st ed.; Butterworth-Heinemann: Oxford, UK, 2017; pp. 89–110. 2. Klee, H. The Cement Sustainability Initiative: Recycling Concrete-Summary; World Business Council for Sustainable Development
(WBCSD): Geneva, Switzerland, 2009. 3. Abergel, T.; Dean, B.; Dulac, J. Global status report 2017: Towards a zero-emission, efficient, and resilient buildings and
construction sector. U. N. Environ. Program. 2017, 48, 1–48. g
4. IEA-WBCSD, Cement Technology Roadmap 2009—Carbon Emissions Reductions up to 2050. Availa
org/publications/freepublications/publication/Cement.pdf (accessed on 25 January 2022). g
nt Technology Roadmap 2009—Carbon Emissions Reductions up to 2050. Available online: https://www.iea
eepublications/publication/Cement.pdf (accessed on 25 January 2022). g/p
/
p
/p
/
p
(
J
y
)
5. Coffetti, D.; Crotti, E.; Gazzaniga, G.; Carrara, M.; Pastore, T.; Coppola, L. Pathways towards sustainable concrete. Cem. Concr. Res. 2022, 154, 106718. [CrossRef] 5. Coffetti, D.; Crotti, E.; Gazzaniga, G.; Carrara, M.; Pastore, T.; Coppola, L. Pathways towards susta
Res. 2022, 154, 106718. [CrossRef] tti, E.; Gazzaniga, G.; Carrara, M.; Pastore, T.; Coppola, L. Pathways towards sustainable concrete. Cem. Co
06718. [CrossRef] 6. Emmanuel, H.; Marine, S.; Gondia, S.S.; Clément, B.; Aymen, J.; Samuel, C. The impact of future power generation on cement
demand: An international and regional assessment based on climate scenarios. Int. Econ. 2020, 163, 114–133. 7. Ozbay, E.; Erdemir, M.; Durmu¸s, H.I. Utilization and efficiency of ground granulated blast furnace slag on concrete properties—A
review. Constr. Build. Mater. 2016, 105, 423–434. [CrossRef] 8. Abolhasani, A.; Samali, B.; Dehestani, M.; Libre, N.A. Effect of rice husk ash on mechanical properties, fracture energy, brittleness
and aging of calcium aluminate cement concrete. Structures 2021, 36, 140–152. [CrossRef] 9. Qudoos, A.; Kim, H.G.; Atta-ur-Rehman; Jeon, I.K.; Ryou, J.-S. Influence of the particle size of wheat straw ash on the microstruc-
ture of the interfacial transition zone. Powder Technol. 2019, 352, 453–461. [CrossRef] 9. Qudoos, A.; Kim, H.G.; Atta ur Rehman; Jeon, I.K.; Ryou, J. S. Influence of the particle size of whe
ture of the interfacial transition zone. Powder Technol. 2019, 352, 453–461. [CrossRef] teus, R.; Bragança, L. Comparative sustainability assessment of binary blended concretes using Supplemen hla, K.M.; Mateus, R.; Bragança, L. References In Proceedings of the Second Intern 23. Mehta, P.K. Sustainable cements and concrete for the climate change era—A review. In Proceedings
C
f
S
t i
bl C
t
ti
M t i l
d T h
l
i
U i
ità P lit
i
d ll M
h
A 23. Mehta, P.K. Sustainable cements and concrete for the climate change era—A review. In Proceedin
Conference on Sustainable Construction Materials and Technologies; Università Politecnica delle Marche 23. Mehta, P.K. Sustainable cements and concrete for the climate change era
A review. In Proceedings o
Conference on Sustainable Construction Materials and Technologies; Università Politecnica delle Marche: A Conference on Sustainable Construction Materials and Technologies; Università Politecnica delle Marche: Anco f
g
y
24. Scrivener, K.L.; John, V.M.; Gartner, E.M. Eco-efficient cements: Potential, economically viable solutions for a low-CO2 cement-
based materials industry. Cem. Concr. Res. 2016, 114, 2–26. [CrossRef] y
25. Cembureau. Activity Report 2020 of The European Cement Association; Cembureau: Bruxelles, Belgium, 2020. 26. Camp, V.E.; Roobol, M.J. The Arabian continental alkali basalt province: Part 1. Evolution of Harr
Arabia. Bull. Geol. Soc. Am. 1989, 101, 71–95. [CrossRef] 27. Roobol, M.J.; Pint, J.J.; Al-Shanti, M.A.; Al-Juaid, A.J.; Al-Amoudi, S.A.; Pint, S.; Al-Eisa, A.M.; Allam, F.; Al-Sulaimani, G.S.;
Banakhar, A.S. Preliminary Survey for Lavatube Caves on Harrat Kishb. In Open-File Report SGS-OF-2002-3; Saudi Geological
Survey: Jeddah, Saudi Arabia, 2002. y J
28. Camp, V.E.; Roobol, M.J.; Hooper, P.R. The Arabian continental alkali basalt province: Part III, Ev
Kingdom of Saudi Arabia. Bull. Geol. Soc. Am. 1992, 104, 379–396. [CrossRef] obol, M.J.; Hooper, P.R. The Arabian continental alkali basalt province: Part III, Evolution of Harrat Ki
di Arabia. Bull. Geol. Soc. Am. 1992, 104, 379–396. [CrossRef] Kingdom of Saudi Arabia. Bull. Geol. Soc. Am. 1992, 104, 379–396. [CrossRef]
29. Camp, V.E.; Roobol, M.J.; Hooper, P.R. The Arabian continental alkali basalt province: Part II. Evolution of Harrats Khaybar,
Ithnayn and Kura, Kingdom of Saudi Arabia. Bull. Geol. Soc. Am. 1991, 103, 363–391. [CrossRef] 29. Camp, V.E.; Roobol, M.J.; Hooper, P.R. The Arabian continental alkali basalt province: Part II. Evolu
Ithnayn and Kura, Kingdom of Saudi Arabia. Bull. Geol. Soc. Am. 1991, 103, 363–391. [CrossRef] 30. Al-Nakhebi, Z.; Laurent, D. Prospecting for Pozzolan in Midwest Harrat Rahat. In Open-File Report BRGM-OF-05-15; Saudi
Arabian Deputy Ministry for Mineral Resources: Jeddah, Saudi Arabia, 1985. p
y
y
31. Sabbahi, A.A. References Geology and Resources of Basalt Quarry Site Kishb-12, Southern Harrat Kishb. In Open File Report SGS-OF-2002-1;
Saudi Geological Survey: Jeddah, Saudi Arabia, 2002. 32. Kurdi, H.H. Geology and Resources of Basalt Quarry site Kishb-13, Southern Harrat Kishb. In Open File Report SGSOF-2002-4;
Saudi Geological Survey: Jeddah, Saudi Arabia, 2002. g
y
33. Khan, K.; Amin, M.N.; Saleem, M.U.; Qureshi, H.J.; Al-Faiad, M.A.; Qadir, M.G. Effect of Fineness of Basaltic Volcanic Ash on
Pozzolanic Reactivity, ASR Expansion and Drying Shrinkage of Blended Cement Mortars. Materials 2019, 12, 2603. [CrossRef] 33. Khan, K.; Amin, M.N.; Saleem, M.U.; Qureshi, H.J.; Al-Faiad, M.A.; Qadir, M.G. Effect of Fineness of Basaltic Volcanic Ash on
Pozzolanic Reactivity, ASR Expansion and Drying Shrinkage of Blended Cement Mortars. Materials 2019, 12, 2603. [CrossRef]
34. Khan, K.; Amin, M.N. Influence of fineness of volcanic ash and its blends with quarry dust and slag on compressive strength of
mortar under different curing temperatures Constr Build Mater 2017 154 514 528 [CrossRef] 34. Khan, K.; Amin, M.N. Influence of fineness of volcanic ash and its blends with quarry dust and slag on
mortar under different curing temperatures. Constr. Build. Mater. 2017, 154, 514–528. [CrossRef] 35. Moufti, M.R.; Sabtan, A.A.; El-Mahdy, O.R.; Shehata, W.M. Assessment of the industrial utilization of scoria materials in central
Harrat Rahat, Kingdom of Saudi Arabia. Eng. Geol. 2000, 57, 155–162. [CrossRef] g
36. Sabtan, A.A.; Shehata, W.M. Evaluation of engineering properties of scoria in central Harrat Rahat, Kingdom of Saudi Arabia. Bull. Eng. Geol. Env. 2000, 59, 219–225. [CrossRef] 37. Khan, M.I.; Alhozaimy, A.M. Properties of natural pozzolan and its potential utilization in environmental friendly concrete. Can. J. Civ. Eng. 2011, 38, 71–78. [CrossRef] 38. Al-Chaar, G.K.; Alkadi, M.; Asteris, P.G. Natural pozzolan as a partial substitute for cement in concrete. Open Constr. Build. Technol. J. 2013, 7, 33–42. [CrossRef] 39. Celik, K.; Jackson, M.D.; Mancio, M.; Meral, C.; Emwas, A.-H.; Mehta, P.K.; Monteiro, P.J.M. High-volume natural volcanic
pozzolan and limestone powder as partial replacements for portland cement in self-compacting and sustainable concrete. Cem. Concr. Compos. 2014, 45, 136–147. [CrossRef] 40. Kupwade-Patil, K.; Al-Aibani, A.F.; Abdulsalam, M.F.; Mao, C.; Bumajdad, A.; Palkovic, S.D.; Buyukozturk, O. Microstructure of
cement paste with natural pozzolanic volcanic ash and Portland cement at different stages of curing. Constr. Build. Mater. 2016,
113, 423–441. [CrossRef] 41. References [CrossRef] g
p
p
15. Khotbehsara, M.M.; Mohseni, E.; Yazdi, M.A.; Sarker, P.; Ranjbar, M.M. Effect of nano-CuO and fly ash on the properties of
self-compacting mortar. Constr. Build. Mater. 2015, 94, 758–766. [CrossRef] 15. Khotbehsara, M.M.; Mohseni, E.; Yazdi, M.A.; Sarker, P.; Ranjbar, M.M. E
self-compacting mortar. Constr. Build. Mater. 2015, 94, 758–766. [CrossRef] Crystals 2022, 12, 302 18 of 19 18 of 19 16. Mazloom, M.; Ramezanianpour, A.A.; Brooks, J.J. Effect of silica fume on mechanical properties of high-strength concrete. Cem. Concr. Compos. 2004, 26, 347–357. [CrossRef] p
17. Amin, M.N.; Khan, K.; Saleem, M.U.; Khurram, N.; Niazi, M.U.K. Influence of mechanically activated electric arc furnace slag on
compressive strength of mortars incorporating curing moisture and temperature effects. Sustainability 2017, 9, 1178. [CrossRef] 18. Khan, K.; Ullah, M.F.; Shahzada, K.; Amin, M.N.; Bibi, T.; Wahab, N.; Aljaafari, A. Effective use of micro-silica extracted from
rice husk ash for the production of high-performance and sustainable cement mortar. Constr. Build. Mater. 2020, 258, 119589. [CrossRef] [
]
19. Amin, M.N.; Murtaza, T.; Shahzada, K.; Khan, K.; Adil, M. Pozzolanic Potential and Mechanical Performance of Wheat Straw Ash
Incorporated Sustainable Concrete. Sustainability 2019, 11, 519. [CrossRef] p
y
20. Játiva, A.; Ruales, E.; Etxeberria, M. Volcanic Ash as a Sustainable Binder Material: An Extensive Review. Materials 2021, 14, 1302. [CrossRef] [PubMed] 21. Pang, L.; Liu, Z.; Wang, D.; An, M. Review on the Application of Supplementary Cementitious Materials in Self-Compacting
Concrete. Crystals 2022, 12, 180. [CrossRef] y
22. Wang, Q.; Ma, Y.; Wang, F.; Shi, Z.; You, H.; Tian, Y.; Liu, Y.; Hu, Z.; Song, H.; Wang, D.; et al. Experimen y
22. Wang, Q.; Ma, Y.; Wang, F.; Shi, Z.; You, H.; Tian, Y.; Liu, Y.; Hu, Z.; Song, H.; Wang, D.; et al. Experimental Study on Carbonation
Durability of Kaolin Strengthened with Slag Portland Cement. Materials 2022, 15, 1240. [CrossRef] 22. Wang, Q.; Ma, Y.; Wang, F.; Shi, Z.; You, H.; Tian, Y.; Liu, Y.; Hu, Z.; Song, H.; Wang, D.; et al. Experimental Study on Carbonation
Durability of Kaolin Strengthened with Slag Portland Cement. Materials 2022, 15, 1240. [CrossRef] g, Q ;
,
;
g,
;
,
;
,
;
,
;
,
;
,
;
g,
;
g,
;
p
Durability of Kaolin Strengthened with Slag Portland Cement. Materials 2022, 15, 1240. [CrossRef] Sustainable cements and concrete for the climate change era—A review. References g
y
53. American Society for Testing and Materials. Standard Terminology Relating to Concrete and Concrete Agg
www.astm.org (accessed on 10 January 2022). r Testing and Materials. Standard Terminology Relating to Concrete and Concrete Aggregates. Available online
ssed on 10 January 2022). 54. American Society for Testing and Materials. Standard Test Method for Compressive Strength of Hydraulic Cement Mortars (Using 2-in
or 50-mm. Cube Specimens). Available online: www.astm.org (accessed on 10 January 2022). p
g (
y
)
55. Standard Practice for Mechanical Mixing of Hydraulic Cement Pastes and Mortars of Plastic Consistency. ASTM International:
West Conshohocken, PA, USA, 2014. Available online: www.astm.org (accessed on 10 January 2022). g (
J
y
)
56. Standard Test Method for Dry and Wet Bulk Density, Water Absorption, and Apparent Porosity of Thin Sections of Glass-Fiber
Reinforced Concrete. Available online: www.astm.org (accessed on 10 January 2022). [CrossRef] g
y
56. Standard Test Method for Dry and Wet Bulk Density, Water Absorption, and Apparent Porosity of Th
Reinforced Concrete Available online: www astm org (accessed on 10 January 2022) [CrossRef] g
y
Standard Test Method for Dry and Wet Bulk Density, Water Absorption, and Apparent Porosity of Thin S 56. Standard Test Method for Dry and Wet Bulk Density, Water Absorption, and Apparent Porosity of Th
Reinforced Concrete. Available online: www.astm.org (accessed on 10 January 2022). [CrossRef] einforced Concrete. Available online: www.astm.org (accessed on 10 January 2022). [CrossRef] 57. Standard Specification for Coal Fly Ash and Raw or Calcined Natural Pozzolan for Use in Concrete. Available online: http:
//www.astm.org (accessed on 10 January 2022). g
y
58. Beleuk à Moungam, L.M.; Lemougna, P.N.; Kaze, R.C.; Mohamed, H.; Deutou Nemaleu, J.G.; Billong, N.; Kamseu, E.; Mvondo-Ze,
A.D.; Kenfack, I.T. Synthesis of Volcanic Ash-based Porous Inorganic Polymers Using Biomass as Pore Inducing Agent: Phase
Evolution and Descriptive Microstructure. Silicon 2021, 1–14. [CrossRef] 59. Metekong, J.V.S.; Kaze, C.R.; Deutou, J.G.; Venyite, P.; Nana, A.; Kamseu, E.; Melo, U.C.; Tatietse, T.T. Evaluation of performances
of volcanic-ash-laterite based blended geopolymer concretes: Mechanical properties and durability. J. Build. Eng. 2020, 34, 101935. [CrossRef] 60. Kim, J.; Yi, C.; Zi, G. Waste glass sludge as a partial cement replacement in mortar. Constr. Build. Mater. 2015, 75, 242–246. [CrossRef] 61. Chindaprasirt, P.; Jaturapitakkul, C.; Sinsiri, T. Effect of fly ash fineness on microstructure of blended cement paste. Constr. Build. Mater. 2007, 21, 1534–1541. [CrossRef] 62. References Letelier, V.; Ortega, J.M.; Tremiño, R.M.; Henriquéz-Jara, B.I.; Fustos, I.; Real-Herraiz, T.; Moriconi, G.; Climent, M.Á.; Sánchez, I. The Use of Volcanic Powder as a Cement Replacement for the Development of Sustainable Mortars. Appl. Sci. 2020, 10, 1460. [CrossRef] [
]
42. Al-Fadala, J.S.; Chakkamalayath, S.; Al-Bahar, A.; Al-Aibani, S. Ahmed. Significance of performance based specifications in the
qualification and characterization of blended cement using volcanic ash. Constr. Build. Mater. 2017, 144, 532–540. [CrossRef] Crystals 2022, 12, 302 19 of 19 19 of 19 43. Charkhi, A.; Kazemian, H.; Kazemeini, M. Optimized experimental design for natural clinoptilolite zeolite ball milling to produce
nano powders. Powder Technol. 2010, 203, 389–396. [CrossRef] p
44. Usman, M.; Zhu, J.; Chuiyang, K.; Arslan, M.T.; Khan, A.; Galadima, A.; Muraza, O. Propene Adsorption-Chemisorption
Behaviors on H-SAPO-34 Zeolite Catalysts at Different Temperatures. Catalysts 2019, 9, 919. [CrossRef] 45. Saamiya, S.; Raissa, D.F.; Maria, C.G.J. Calcining natural zeolites to improve their effect on cementitious mixture workability. Cem. Concr. Res. 2016, 85, 102–110. 46. Moussa, H.; Larbi, K.; Martin, C.; Pierre, C. Evaluation and improvement of pozzolanic activity of andesite for its use in
eco-efficient cement. Constr. Build. Mater. 2013, 47, 1268–1277. 47. Kucukyıldırım, E.; Uzal, B. Characteristics of calcined natural zeolites for use in high-performance pozzolan blended cements. Constr. Build. Mater. 2014, 73, 229–234. [CrossRef] 47. Kucukyıldırım, E.; Uzal, B. Characteristics of calcined natural zeolites for use in high-performance pozzolan blended cements. Constr. Build. Mater. 2014, 73, 229–234. [CrossRef]
48
Alaettin K ; Zeynep S Effect of heat treatment on pozzolanic activity of volcanic pumice used as cementitious material Cem p, S. Effect of heat treatment on pozzolanic activity of volcanic pumice used as cementitious material. Cem
57, 128–132. 48. Alaettin, K.; Zeynep, S. Effect of heat treatment on pozzolanic activity of volcanic pumice used as cem
Concr. Compos. 2015, 57, 128–132. p
49. Burris, L.E.; Juenger, M.C.G. Milling as a pretreatment method for increasing the reactivity of natural zeolites for use as
supplementary cementitious materials. Cem. Concr. Compos. 2016, 65, 163–170. [CrossRef] 50. American Society for Testing and Materials. Standard Specification for Portland Cement. Available online: www.astm.org (accessed
on 10 January 2022). 51. Methods of Testing Cement—Part 1: Determination of Strength. European Committee for Standardization. Available online:
https://standards.cen.eu. (accessed on 10 January 2022). p
y
52. Cement—Test Methods—Determination of Strength. International Organization for Standardization: Geneva, Switzerland, 2009. Available online: https://www.iso.org/standard/45568.html. (accessed on 10 January 2022). References Altwair, N.M.; Azmi, M.; Johari, M.; Fuad, S.; Hashim, S. Strength activity index and microstructural characteristics of treated
palm oil fuel ash. Int. J. Civil Environ. Eng. 2011, 11, 100–107. .R.; Stevens, L.A.; Rigby, S.P. Effects of high-pressure/temperature curing on reactive powder concrete
ation. Constr. Build. Mater. 2016, 105, 554–562. [CrossRef] 63. Helmi, M.; Hall, M.R.; Stevens, L.A.; Rigby, S.P. Effects of high-pressure/temperature curing on r
microstructure formation. Constr. Build. Mater. 2016, 105, 554–562. [CrossRef] 64. Scrivener, K.; Snellings, R.; Lothenbach, B. A Practical Guide to Microstructural Analysis of Cementitious Materials; CRC Press: Boca
Raton, FL, USA, 2016. ,
,
,
65. Yu, P.; Kirkpatrick, R.J.; Poe, B.; McMillan, P.F.; Cong, X. Structure of calcium silicate hydrate (C–S–H): Near-, Mid-, and
Far-infrared spectroscopy. J. Am. Ceram. Soc. 1999, 82, 742–748. [CrossRef] p
py
66. Hughes, T.L.; Methven, C.M.; Jones, T.G.; Pelham, S.E.; Fletcher, P.; Hall, C. Determining cement composition by Fourier transform
infrared spectroscopy. Adv. Cem. Based Mater. 1995, 2, 91–104. [CrossRef]
|
https://openalex.org/W2933898568
|
https://www.repository.cam.ac.uk/bitstream/1810/326060/2/41386_2020_Article_780.pdf
|
English
| null |
Synaptic control of DNA-methylation involves activity-dependent degradation of DNMT3a1 in the nucleus
|
bioRxiv (Cold Spring Harbor Laboratory)
| 2,019
|
cc-by
| 13,355
|
1RG Neuroplasticity, Leibniz Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany; 2Center for Behavioral Brain Sciences, Otto von Guericke University, 39120
Magdeburg, Germany; 3Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke University, Leipziger Str. 44, Haus 91, 39120 Magdeburg,
Germany; 4Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 Osaka, Japan; 5Department of Nutritional Sciences, Faculty of Nutritional Sciences,
Nakamura Gakuen University, Fukuoka, Japan; 6Laboratory of Organic Chemistry, Institute for Protein Research, Osaka University, Suita, Japan; 7Center for Twin Research,
Graduate School of Medicine, Osaka University, Suita, Japan; 8NeuroCure Clinical Research Center & Department of Neuropsychiatry at Department of Psychiatry and
Psychotherapy, Charité-Universitätsmedizin Berlin, Virchowweg 6, Charitéplatz 1, 10117 Berlin, Germany; 9Leibniz Group ‘Dendritic Organelles and Synaptic Function’, ZMNH,
20251 Hamburg, Germany and 10German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
Correspondence: Michael R. Kreutz (Kreutz@lin-magdeburg.de)
11Present address: UK Dementia Research Institute at the University of Cambridge, Island Research Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge
CB2 0AH, UK www.nature.com/npp ARTICLE
OPEN
Synaptic control of DNA methylation involves activity-
dependent degradation of DNMT3A1 in the nucleus Gonca Bayraktar
1,11, PingAn Yuanxiang
1, Alessandro D. Confettura1, Guilherme M. Gomes
1,2, Syed A. Raza3, Oliver Stork2,3,
Shoji Tajima4, Isao Suetake
5,6,7, Anna Karpova1,2, Ferah Yildirim8 and Michael R. Kreutz
1,2,9,10 DNA methylation is a crucial epigenetic mark for activity-dependent gene expression in neurons. Very little is known about how
synaptic signals impact promoter methylation in neuronal nuclei. In this study we show that protein levels of the principal de novo
DNA-methyltransferase in neurons, DNMT3A1, are tightly controlled by activation of N-methyl-D-aspartate receptors (NMDAR)
containing the GluN2A subunit. Interestingly, synaptic NMDARs drive degradation of the methyltransferase in a neddylation-
dependent manner. Inhibition of neddylation, the conjugation of the small ubiquitin-like protein NEDD8 to lysine residues,
interrupts degradation of DNMT3A1. This results in deficits in promoter methylation of activity-dependent genes, as well as synaptic
plasticity and memory formation. In turn, the underlying molecular pathway is triggered by the induction of synaptic plasticity and
in response to object location learning. Collectively, the data show that plasticity-relevant signals from GluN2A-containing NMDARs
control activity-dependent DNA-methylation involved in memory formation. Neuropsychopharmacology (2020) 45:2120–2130; https://doi.org/10.1038/s41386-020-0780-2 Received: 2 February 2020 Revised: 16 July 2020 Accepted: 20 July 2020
Published online: 29 July 2020 ch Institute at the University of Cambridge, Island Research Building, Cambridge Biomedical Campus, University of Cambridge, Cambridg INTRODUCTION
d l b l de novo DNA methyltransferase in the brain and plays a
documented
role
in
activity-dependent
DNA
methylation
[15, 16]. Impaired spatial learning and memory, as well as
attenuated CA1 long-term potentiation (LTP), have been reported
following a forebrain specific DNMT gene knockout in principal
neurons [16, 17]. It is widely believed that rapid and reversible DNA methylation is
essential for the stability of long-term memory but very little is
known about how synaptic signals can induce changes in DNA
methylation to elicit enduring alterations in plasticity-related gene
expression [1–6]. In addition, aberrant DNA methylation has been
implicated in neuropsychiatric diseases, including schizophrenia,
bipolar, and major depressive disorders [1, 7, 8]. N-methyl-D-
aspartate receptors (NMDAR) signaling to the nucleus is instru-
mental for learning and memory formation and is altered in
schizophrenia as well as other neuropsychiatric disorders [9, 10]. However, a mechanistic link between NMDAR signaling and DNA
methylation is currently missing. It is nowadays widely accepted that memory consolidation
as well as synaptic plasticity not only rely on de novo protein
synthesis but also protein degradation [18–20]. Proteasomal
degradation of proteins in neurons has been studied mainly in
the context of ubiquitylation and sumoylation, whereas neddy-
lation, the attachment of the small ubiquitin-like peptide neural
precursor cell-expressed developmentally down-regulated gene
8 (NEDD8) has not been thoroughly investigated. Here we
show that activation of synaptic GluN2A-containing NMDARs
drives the neddylation-dependent proteasomal degradation
of the principal de novo DNA-methyltransferase in the adult
brain DNMT3A1. Collectively, the data point to a mechanism
that allows for the synaptic control of nuclear DNMT3A1
protein levels thereby creating a time window for reduced
de novo DNA methylation at a subset of target genes. This
signaling pathway highlights how synapse-to-nucleus signaling
might directly impact on DNA methylation and memory
consolidation. Compelling evidence exists for learning-induced de novo DNA
methylation with several studies showing the importance of active
DNA methylation as well as demethylation particularly in the
hippocampus during memory consolidation [1, 11–13]. One of the
target genes is the brain-derived neurotrophic factor (BDNF),
which undergoes promoter-specific DNA demethylation in the
CA1 region of the hippocampus during memory consolidation
[14]. The underlying signaling machinery in this process is also not
well understood. It is fundamentally unclear how synaptic signals
conveyed to the nucleus impact mechanisms of DNA methylation
and demethylation of the Bdnf promoter. 11Present address: UK Dementia Research Institute at the University of Cambridge, Island Research Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge
CB2 0AH UK METHODS Cell culture and drug treatments Cell culture and drug treatments g
Rat cortices and hippocampi were dissected from embryonic day
18 rats (Sprague Dawley). Cells were plated in a density of 30.000
cells per 18 mm coverslip, grown in 1 ml of neurobasal medium
(NB, Gibco) supplemented with B27 medium. Primary neurons
were kept in Neurobasal medium (NB/GIBCO/Life Technologies)
supplemented with B27 (GIBCO/Life Technologies), L-glutamine
(GIBCO/Life
Technologies)
and
penicillin/streptomycin
(PAA
Laboratories, Pasching, Austria). On day 4 after plating cortical
neurons were treated with 5 μM cytosine D-arabino-furanoside
(Sigma-Aldrich)
in
order
to
prevent
proliferation
of
non-
neuronal cells. Hippocampal neurons were treated for 10 min, 1 h, 3 h or 6 h at
DIV 14–15 with the following drugs: Bicuculline methiodide
(50 μM, Tocris, Bristol, UK), 4-aminopyridine (4AP, 2.5 mM, Sigma-
Aldrich, St. Louis, MO), MG132 (30 μM, AG Scientific), lactacystin
(15 μM,
Sigma-Aldrich,
St. Louis,
MO),
carfilzomib
(100 nM,
UBPBio), NVP-AAM007 (50 nM, Novartis), APV (20 μM, Calbiochem),
ifenprodil (10 μM, Tocris, Bristol, UK), nifedipine (10 μM, Santa
Cruz), KN93 (5 μM, Tocris, Bristol, UK) and MLN4924 (5 nM, Cayman
Chemicals, Hamburg, Germany). Hippocampal neurons were
treated for 3, 5 or 10 min with 100 μM N-methyl-D-aspartic acid
(NMDA, Sigma-Aldrich, St. Louis, MO). Cortical neurons were
seeded in T-75 flasks (Thermo Scientific, Rockford, USA). They were
fed with the same neuron chow and proliferation of non-neuronal
cells was arrested by the addition of 1 μM cytosine arabinoside
(Sigma-Aldrich, St. Louis, MO) at DIV 5. Cortical neurons were
treated with 1 μM tetrodotoxin (TTX, Alomone Labs, Jerusalem,
Israel) for 12 h, media was washed-out and Bic/4AP were applied
for 6 h at 21 DIV. HEK293T cells were cultured in DMEM media
supported by fetal bovine serum. In all graphs depicting
quantitative immunocytochemistry, the numbers for each experi-
mental group indicate the number of analyzed neurons derived
from at least two or three independent culture preparations,
where from each culture preparation at least 2 culture wells are
included in the study. Percent methylation at single CpG sites in Bdnf IV promoter was
determined using the bisulfite sequencing method. For this
genomic DNA (gDNA) was extracted from 21 DIV cultured cortical
neurons treated with Bic/4AP for 6 h or neurons that did not
receive any treatment. The extraction was performed using
Chargeswitch DNA extraction kit, as described above. 200 ng of
gDNA was used for bisulfite conversion (EZ DNA methylation-
gold, Zymo Research). INTRODUCTION
d l b l DNMT3A1 is the major Received: 2 February 2020 Revised: 16 July 2020 Accepted: 20 July 2020
Published online: 29 July 2020 © The Author(s) 2020 Synaptic control of DNA methylation involves activity-dependent. . . G Bayraktar et al. 2121 sonicator (Picoruptor, Diagenode, Seraing, Belgium) with 30 s on
and 90 s off cycles using 1.5 ml Bioruptor microtubes. The
efficiency of the sonication was established by running the
fragmented DNA samples on agarose gels, which confirmed the
accumulation of fragmented DNA to be mainly within a range of
200–600 bp. Afterward MeDIP experiments were carried out
using the MagMeDIP kit (Diagenode, Seraing, Belgium) following
the user guide with ~750 ng fragmented DNA as starting
material. The methylation levels were assessed by qPCR and
evaluated using the formula given in the user guide for
both kits. The forward primer used in the OneStepqMethyl-Kit
was 5′-TATGACAGCTCACGTCAAGG-3′ and reverse primer was
5′-CCTTCAGTGAGAAGCTCCAT-3′, containing three methylation-
sensitive restriction enzyme sites. The forward primer used in
the MeDIP-qPCR study for BDNF promoter IV was 5′-GCATGC
AATGCCCTGGAACGG-3′ and the reverse primer was 5′-GAG
GGCTCCACGCTGCCTTG-3′, and forward primer for BDNF pro-
moter I 5′-TACCTGGCGACAGGGAAATC-3′ and reverse primer 5′-
GCGCCCTAGCACAAAAAGTT-3′. sonicator (Picoruptor, Diagenode, Seraing, Belgium) with 30 s on
and 90 s off cycles using 1.5 ml Bioruptor microtubes. The
efficiency of the sonication was established by running the
fragmented DNA samples on agarose gels, which confirmed the
accumulation of fragmented DNA to be mainly within a range of
200–600 bp. Afterward MeDIP experiments were carried out
using the MagMeDIP kit (Diagenode, Seraing, Belgium) following
the user guide with ~750 ng fragmented DNA as starting
material. The methylation levels were assessed by qPCR and
evaluated using the formula given in the user guide for
both kits. The forward primer used in the OneStepqMethyl-Kit
was 5′-TATGACAGCTCACGTCAAGG-3′ and reverse primer was
5′-CCTTCAGTGAGAAGCTCCAT-3′, containing three methylation-
sensitive restriction enzyme sites. The forward primer used in
the MeDIP-qPCR study for BDNF promoter IV was 5′-GCATGC
AATGCCCTGGAACGG-3′ and the reverse primer was 5′-GAG
GGCTCCACGCTGCCTTG-3′, and forward primer for BDNF pro-
moter I 5′-TACCTGGCGACAGGGAAATC-3′ and reverse primer 5′-
GCGCCCTAGCACAAAAAGTT-3′. METHODS To amplify the region of interest 1 to 2 μl of
bisulfite-converted DNA was run in a PCR using specific primers
spanning 19 CGs. Bisulfite sequencing primer sequences used to
assess CpG methylation levels of the rat Bdnf promoter IV were:
Forward 1–5′-TTTATAAAGTATGTAATGTTTTGGAA-3′, Forward 2–5′-
AGTTAGTATGAAATTTTTTAGTTTTTGTT-3′, Reverse 1–5′-TTCAATA
AAAAACTCCATTTAATCTA-3′, Reverse 2–5′-TATCAAAATAAACATCA
AAACAACTAC-3′. The sequencing was performed on the MiSeq
with a 600 cycle v3 kit, generating 300 base pair end reads. Mapping of the reads and methylation level extractions were
performed using Bismark [21]. Average methylation rate of each
CpG site was quantified using the methylKit R package [22]. The
groups were compared using a Chi-square test and the correction
applied was the false discovery rate (FDR) [23]. Neuropsychopharmacology (2020) 45:2120 – 2130 Experimental animals p
Neurons for primary cell cultures and slices for electrophysiology
experiments were prepared from brains of Sprague Dawley
(Janvier, France) or Wistar rats (Animal facilities of the Leibniz
Institute of Neurobiology, Magdeburg, Germany). Male C57BL/6J
(10–13 weeks old) mice were used for behavioral experiments
(Charles River/Animal facilities of the Leibniz Institute of
Neurobiology, Magdeburg, Germany). GluRε1 (GluN2A) knock-
out (KO) mice were obtained from RIKEN Japan (RBRC01813). Animals were housed in groups of up to 5 in individually
ventilated cages (IVCs, Green line system, Tecniplast) under
controlled environmental conditions (22 °C ± 2 °C, 55% ± 10%
humidity, 12 h light/dark cycle, with lights on at 06:00). Food and
water were available ad libitum. All procedures and animal care
were consented and performed under established standards of
the German federal state of Sachsen-Anhalt, Germany in
agreement with the European Communities Council Directive
(2010/63/EU) and approved by the local authorities of Sachsen-
Anhalt/Germany/Regierungspräsidium
Halle
Sachsen-Anhalt/
Germany. Quantitative real time-PCR
14 DIV hippocampal neurons were treated with 50 μM bicucul-
line methiodide and 2.5 mM 4AP with or without 5 nM MLN4924
for 6 h. DMSO was used as a sham control. Following the
treatment, neurons were immediately harvested in lysis buffer
and total RNA was isolated (RNeasy plus mini kit, Qiagen,
Valencia,
CA,
USA). 50
nanograms
of
RNA
were
reverse
transcribed using random nonamers (Sigma-Aldrich, St. Louis,
MO, USA) according to the manufacturer’s instructions (Sensi-
script, Qiagen). BDNF exon IV and glyceraldehyde 3-phosphate
dehydrogenase (GAPDH) mRNA (as a reference gene) were
amplified using the iScript RT-PCR iQ SYBR Green Supermix
(BIORAD, Hercules, CA, USA) in a real-time quantitative PCR
(qPCR) detection system (LC480, Roche, Basel, Switzerland) using
the following primers: Bdnf exon IV forward 5′-GCAGCTGCCTT
GATGTTTAC-3′
and
reverse
5′-CCGTGGACGTTTGCTTCTTTC-3′;
Dnmt3a1 forward 5′- CCCTCAGATCTGCTACCCAA-3′ and reverse
5′-TGCTCTGGAGGCTTCTGGTG-3′; Dnmt3a2 forward 5′-CTCACAC
CTGAGCTGTACTGCAGAG-3′ and reverse 5′-CTCCACCTTCTGGG
ACTCCCCAGAG-3′; Gapdh forward 5′-TGCTGAGTATGTCGTGGAG-
3′ and 5′-ACCCAGAAGACTGTGGATGG-3′; Gapdh reverse 5′-
GTCTTCTGAGTGGCAGTGAT-3′ and 5′-CACATTGGGGGTAGGAAC
AC-3′. Each sample reaction was run in duplicate and Ct values of
the reference genes from the samples were subjected to Grubbs’
outlier test (http://www.graphpad.com/quickcalcs/Grubbs1.cfm). The relative expression levels were analyzed using the 2−ΔΔCt
method with normalization relative to GAPDH. Methylation analysis Horejsi Lab, Prague, Czech Republic),
pcDNA3-myc3-CUL4B (gift from Yue Xiong, Addgene plasmid
#19922), pcDNA3-myc3-NEDD8 (gift from Yue Xiong, Addgene
plasmid #19943), pcDNA3-HA-NEDD8 (gift from Edward Yeh,
Addgene plasmid #18711), CUL1, CUL2, CUL3, CUL4A, CUL4B,
CUL5 and CUL7 in pcDNA3-myc3 backbone (which were a gift
from Yue Xiong, Addgene plasmid #19896, #19892, #19893,
#19951, #19922, #19895, #20695 respectively). The vector for the
expression
of
constitutively
active
CaMKIV
with
a
nuclear
localization signal (eGFP-CaMKIV-3xNLS) and dominant negative
CaMKIV are were kindly provided by Dr. Gina Turrigiano (Waltham,
USA) [24, 25]. The shRNA constructs to knock down human
DNMT3A1/3A2 and scrambled controls were hDNMT3A shRNA,
pSMP-DNMT3A1 and pSMP-Luc (a gift from George Daley,
Addgene plasmid #36380, Addgene plasmid #36394, respectively). shRNA targeting, ratDNMT3A and scrambled control were cloned
into pZ-off vector with the following sequences: 5′-CCCAAGGT
CAAGGAGATCA-3′ and 5′-GCTTCGCGCCGTAGTCTTA-3′, respec-
tively. shRNA targeting rat-Nedd8, human-Nedd8 and scrambled
control were cloned into pSuper vector with the following
sequences: 5′-GCGGCTCATCTACAGTGGCAA-3′, 5′-GAGGCTCATC
TACAGTGGCAA-3′,
5′-CTTCGCGCCGTAGTCTTA-3′,
respectively. The target shRNA sequence that efficiently knocked down rat-
CaMKIV was 5′-CTAAGAAGCGGCTGACTAC-3′. Confocal laser scanning microscopy and image analysis
The SP5 CLSM system (Leica-Microsystems, Mannheim, Germany)
equipped with Diode (405 nm) and Argon (488, 561, and 633 nm)
laser lines was used for quantitative immunocytochemistry. Z-
stack images of neurons were taken using the ×63 oil-immersion
objective (Leica, Mannheim, Germany). Confocal images of triple-
stained neurons were taken with Plan Apo ×63 oil NA 1.4 objective
lenses. All images were acquired sequentially to avoid crosstalk
between channels. The acquisition parameters were kept the
same for all scans. Regions of interest (ROI) were drawn around
nuclei, as delineated by DAPI staining. These ROI were then
applied to a corresponding image of antibody staining from which
the mean average intensity was collected to determine nuclear
immunoreactivity levels using Image J software (NIH, Rasband, W. S., ImageJ, U. S. National Institutes of Health, Bethesda, Maryland,
USA, http://imagej.nih.gov/ij/, 1997–2014). The total number of dendritic spines per 20 μm secondary
dendrites of the primary hippocampal neurons, which received
5 nM or 1 μM MLN4924 treatment at basal conditions or with
synaptic stimulation using Bic/4AP were counted based on the
Homer1 staining. The total synapse number per 20 μm secondary
dendrites of the primary hippocampal neurons following Cul4B
knockdown were counted based on the colocalization of Homer1
and Synaptophysin1. Surface expression of GluN2A was evaluated
in primary hippocampal neurons following the knockdown
of Cul4B. Methylation analysis Methylation analysis y
y
DNA from CA1 was extracted using Chargeswitch DNA extrac-
tion kit from Invitrogen (Carlsbad, CA, USA) according to the
instructor’s manual. Methylation-sensitive restriction enzyme-
dependent methylation analysis was performed using OneStep
q-Methyl Kit (Zymo, Irvine, CA, USA) following the instructions
given in the manual using 20 ng DNA for each sample. For methylated DNA immunoprecipitation (MeDIP) experiments,
the extracted DNA was then subjected to fragmentation via a Neuropsychopharmacology (2020) 45:2120 – 2130 Synaptic control of DNA methylation involves activity-dependent. . . G Bayraktar et al. G Bayraktar et al. 2122 Instruments) and anesthesia was maintained with 1.5% isofluor-
ane using gas anesthesia system (Rothacher Medical GmbH.,
Switzerland). After craniotomy, 10 μl NanoFil microsyringes (World
Precision Instruments) containing 33G injection needles were
lowered into the dorsal CA1 area under stereotactic guidance with
the coordinates anterioposterior (AP) −2.0 mm, mediolateral (ML)
± 1.5 mm from Bregma and dorsoventral (DV) −0.14 mm from
brain surface. Each animal received 1.5 μl/hemisphere bilateral
infusion of drug (MLN4924) while (saline with respective volume
of DMSO) as sham control, at an infusion rate of 0.5 μl/min. Immunocytochemistry
Following drug treatment, cells were fixed either in methanol or in
4% paraformaldehyde (PFA) and immunostaining was performed
with primary antibodies specific for the DNMT3AN-terminus,
CUL4B (Proteintech, catalog #12916-1-AP), GFAP (Synaptic Sys-
tems, catalog #173011), HOMER1 (Synaptic Systems, catalog
#160011),
NEDD8
(Proteintech,
catalog
#16777-1-AP),
MAP2
(Sigma-Aldrich,
catalog
#M4403),
5meCytosine
(Calbiochem,
catalog #MABE146, clone 33D3), Synaptophysin1 (Synaptic Sys-
tems, catalog #101004); secondary antibodies anti-rabbit/mouse-
Alexa Fluor 488/568 linked (Molecular Probes Europe BV, Leiden,
The Netherlands), anti-rabbit/mouse-CyTM5-conjugated (Dianova,
Hamburg, Germany) and DAPI (Sigma-Aldrich, catalog #D9564). Live immunostaining was performed for the detection of the
surface expression of the GluN2A subunit of NMDARs. To this end,
the GluN2A antibody (Alomone Labs, #AGC-002) was applied in
cell media for 20 min, then cells were fixed and staining was
performed as outlined above. Overexpression and knockdown experiments Overexpression and knockdown experiments Overexpression and knockdown experiments
The overexpression experiments in HEK-293T cells were per-
formed
using
the
following
constructs:
C2-eGFP-hDNMT3A
(Clontech, subcloned from pcDNA3/Myc-DNMT3A1, which was a
gift from Arthur Riggs, Addgene plasmid #35521), C2-eGFP-
hDNMT3A2 (Clontech, subcloned from pcDNA3/Myc-DNMT3A2,
which was a gift from Arthur Riggs, Addgene plasmid #36941), pK-
MYC-C3 (gift from V. Methylation analysis Acute hippocampal slice preparation and electrophysiology
Hippocampi from 8 weeks old male Wistar rats (House strain, LIN,
Magdeburg) were cut using a vibratome (LeicaVT1000S, Nussloch,
Germany) into 350 μm thick slices. The hippocampal slices were
incubated for 2 h in carbogenated (95% O2–5%CO2) artificial
cerebrospinal fluid (ACSF, containing in mM: 110 NaCl, 2.5 KCl, 2.5
CaCl2·2H2O, 1.5 MgSO4·7H2O, 1.24 KH2PO4, 10 glucose, 27.4
NaHCO3, having a pH of 7.3) at room temperature. Then slices
were transferred into a recording chamber (at 31 ± 1 °C). Field
excitatory postsynaptic potentials (fEPSPs) were evoked by
stimulation of CA1 Schaffer-collateral fibers with metal electrodes. fESPSs were recorded with ACSF filled glass capillary microelec-
trodes (3–5 MΩ) and amplified by an extracellular amplifier (EXT-
02B, npi, Germany) and digitized at a sample frequency of 5 kHz
by Digidata 1401 plus AD/DA converter (CED, England). Stimula-
tion strength was adjusted to 30% – 40% of the maximum fEPSP-
slope values. Single stimuli were applied every 30 s (at 0.0333 Hz)
and were averaged every 3 min. After a 30 min stable baseline
recording, MLN4924 was applied into the bath. 30 min later, late-
long term potentiation (L-LTP) was induced by tetanization
consisting of three 1 s stimulus trains at 100 Hz with a 6 min
inter-train interval where the width of the single stimulus was
0.1 ms. MLN4924 was dissolved in DMSO and diluted in ACSF at
final concentration (5 μM, or 50 nM) applied 30 min before the first
tetanus. Data are represented as mean ± SEM. Fluorescent microscopy and image analysis
The number of dendrites crossing each circle was counted manually. Studies of GluN2A knockdown on hippocampal primary hippocam-
pal neurons were also carried out using Zeiss Axio Imager A2
fluorescent microscope (Zeiss, Jena, Germany) with Cool Snap EZ
camera (Visitron System) and MetaMorph Imaging software (MDS
Analytical Technologies). Up to 3 coverslips were treated individually
and processed per group. The same exposure time and intensity
were taken for each coverslip among the different groups. Upon
background subtraction using Fiji software, images of fluorescent
positive puncta were measured along secondary dendrites, right
after the branching point. The synaptic immunofluorescence
intensities were assessed in a region of 400 nm × 400 nm square
set by the mask in the channel for Homer1, a synaptic marker. The mask was created semi-automatically using Openview software. Object location memory Tissue collection and analysis j
y
Object location memory was performed in a square arena (50 × 50 ×
50 cm) under mild light conditions. Briefly, the task consisted of a
habituation session, training and test. During habituation, animals
were allowed to explore the empty arena for 20 min. Twenty-four
hours later, a training session took place, where animals were free to
explore a pair of similar objects (made of plastic mounting bricks),
placed in the arena, for 20 min. A test session was performed 6 h
after training, where one of the objects was placed in a new
position, and again, animals were free to explore the two objects for
20 min. All three sessions were video-recorded and behavior was
analyzed offline using ANY-maze software (ANY-mazeTM Video
Tracking System, version 4.50, Stoelting Co. Wood Dale, USA). Exploration was recorded only when the animal touched or reached
the object with the nose at a distance of less than 2 cm. The time
mice spent exploring the objects was recorded, and the discrimina-
tion index was then calculated, taking into account the difference of
time spent exploring the new and familiar position ([(Tnovel –
Tfamiliar)/(Tnovel + Tfamiliar)] × 100). An experimenter blind to
treatment conducted the experiment and analyzed the data. Chambers and objects were thoroughly cleaned with 10% ethanol
before and after each animal was tested. y
After the LTP recordings, only the potentiated CA1 region of the
Hippocampus was collected from the acute slices. The tissue was
either subjected to RNA or DNA extraction for transcription or
promoter methylation analysis, respectively, or for total protein
extraction for western blotting. For the experiments investigating
learning-dependent DNMT3A1 degradation, mice were sacrificed
3 or 6 h after training and the CA1 region of the hippocampus was
dissected. Bilateral intrahippocampal MLN4924 (7.5 pmol/site) or
saline infusions were performed immediately after training. Immunoprecipitation experiments p
p
p
Endogenous IP experiments were performed from cultured rat
cortical neurons. 50 μl dynabeads Protein G (ThermoFischer
Scientific, Waltham, MA, USA) were blocked using albumin from
chicken egg white (Sigma-Aldrich, St. Louis, MO, USA), while
rocking for 30 min. Then, the dynabeads protein G were incubated
with 2–3 μg of rabbit polyclonal anti-CUL4B antibody (Proteintech,
catalog #20882-1-AP), while gently rotating for 2 h at 4 °C. Nuclear
protein extracts were then incubated with antibody-bound-
protein G dynabeads overnight at 4 °C. Object location memory The next day, following
several washes with ice-cold TBS-T, the samples were eluted using
4× Laemmli sample buffer. p
Heterologous co-immunoprecipitation (het-coIP) experiments
were performed in HEK-293T cells. Transfection of HEK-293T
cells was performed with constructs pcDNA3-myc3-CUL4B, C2-
eGFP-hDNMT3A, and pK-MYC-C3. 3 h prior to harvesting the
cells, either the proteasome inhibitor MG132 (30 μM) or DMSO
as sham control was applied to the cells. 24 h after transfection
cells were harvested. In the het-coIP experiment in which the
effect of neddylation was studied, transfections were performed
using the constructs pcDNA3-myc3-CUL4B, C2-eGFP-hDNMT3A,
pK-MYC-C3, and myc3-NEDD8. 24 h after transfection HEK-T cells
were treated with NEDD8-activating enzyme inhibitor MLN4924
(94 nM) or DMSO as sham control for 24 h. MG132 application
was done as mentioned above. Cell lysate extracts were
incubated with the anti-GFP microbeads (MiltenyiBiotec GmbH,
Gladbach, Germany) for 1 h. Eluted samples were run on SDS-
PAGE. Statistical analysis
The data were analyzed by one-way ANOVA and unpaired one/two-
tailed Student’s t-test. Two-way ANOVA followed by Bonferroni’s
post-hoc test was employed to compare means from multiple
groups. Quantitative real-time PCR data were subjected to Grubbs’
outlier test and analyzed by either unpaired two-tailed Student’s
t-test or two-way ANOVA, which was followed by Bonferroni’s post
hoc test, where applicable. The Mann Whitney U-test was used to
compare the Averaged field potentials (300 – 360 min) between two
groups of differentially treated slices. Error bars present S.E.M. except
when otherwise stated. Statistical analyses were performed in
GraphPad (GraphPad Software, Inc., La Jolla, USA). Methylation analysis The intensities of the puncta positive for GluN2A were measured at
points of co-localization with Homer1; values were normalized to
mean of the control and plotted. Intrahippocampal injections
Mice were anesthetized with 5% isofluorane in O2/N2O mixture. Mice were placed in a stereotaxic frame (World Precision Neuropsychopharmacology (2020) 45:2120 – 2130 Synaptic control of DNA methylation involves activity-dependent. . . G Bayraktar et al. 2123 RESULTS Synaptic activity controls levels of DNMT3A1 in neuronal nuclei
DNMT3A1 is the major de novo DNA methyltransferase expressed
in the adult brain [15]. In addressing the cellular localization of this
enzyme using an antibody that recognizes an N-terminal region
[26] specific for DNMT3A1 (Fig. S1A–D), we found a prominent
nuclear localization in hippocampal primary neurons and much
fainter staining hardly above background in astrocytes (Fig. 1a),
indicating that DNMT3A1 is mainly expressed in neurons. This
finding prompted us to ask next whether synaptic activity might
regulate nuclear DNMT3A1 protein levels. When we induced burst
firing of excitatory synapses in hippocampal primary neurons with
the
GABA-A
receptor
antagonist
bicuculline
(Bic)
and
the
potassium channel blocker 4-amino-pyridine (4AP), we observed
a prominent reduction in the nuclear immunofluorescence of
DNMT3A1 (Fig. 1b, c), a finding that was confirmed by quantitative
immunoblot analysis of cell lysates from cortical primary neurons
(Fig. 1d–f). Enhancing excitatory activity for 10 min with Bic/4AP
was sufficient to reduce DNMT3A1 immunofluorescence for 3 h
following stimulation (Fig. 1g, h), while excitotoxicity, elicited with
bath application of 100 µM NMDA for 10 min, a protocol that
results in extrasynaptic NMDAR activation and delayed cell death,
had no effect [27]. Of note, the reduction of DNMT3A1 protein
levels lasted at least for 24 h and returned back to baseline
expression only after 72 h (Fig. S1E–J). Western blot analysis Western blot analysis y
Total homogenates were prepared from mouse and rat brain or
cultured cortical neurons by performing the lysis in 10 mM Tris/
HCl pH 7.5, 0.5% TritonX, and a protease inhibitor cocktail
(Roche, catalog #04693116001) containing TBS. 4× Laemmli
buffer was added to produce a final dilution of 1.5×. Following
10 min-incubation at 95 °C, samples were ready for protein
analysis. HEK-293T cells were harvested in TBS, which contained
the protease inhibitor cocktail. Cells were lysed in 1% Triton-X
containing lysis buffer; centrifuged for 30 min at 21,000 rpm
and the supernatant fraction was collected. Protein estimation
was performed either by amidoblack or BCA assay (Thermo
Scientific). Western blots were then performed using 4–20%
gradient polyacrylamide gels. The following antibodies were
used in this study: DNMT3AN (1:2000) and DNMT3A-mid
(1:2000), CUL4B (1:1000, Proteintech, catalog #12916-1-AP),
NEDD8 (1:1000, Proteintech, catalog #16777-1-AP), FK1 (1:1000,
Enzo, catalog #BML-PW8805), β-Actin (1:2000, Sigma-Aldrich,
catalog #A5441), myc-tag (1:1000, Cell Signaling, catalog #2276),
and horseradish peroxidase-coupled goat anti mouse/rabbit
IgG-HRP linked secondary antibodies (1:20000, Jackson Immu-
noresearch Laboratories, catalog #115035003 and #111035003,
respectively). Quantification of immunoblots was done with
ImageJ software (NIH, Maryland, USA). Integrated density values
were evaluated for the analysis. When necessary, data from
individual experiments performed at different time points were
normalized to respective controls and pooled together with
other data sets. Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 4 0
255
Bic/4AP
basal
h
6
h
3
h
1
DNMT3A1
DNMT3A1
DAPI MAP2
DAPI MAP2
B C
1h
3h
6h
basal
Bic/4AP
n.s. ***
**
25
25
24
26
27
30
nuclear DNMT3A1 IF (% of control)
0
50
100
150
200 B 0
255
DNMT3A1
DNMT3A1
DNMT3A1
DAPI,MAP2
DAPI, GFAP
DAPI, MAP2
DAPI, GFAP
ROI 1
ROI 2
ROI 1
ROI 2
A A F
0
50
100
150
200
TTX, 18h
TTX 12h +
Bic/4AP, 6h
Dnmt3a1 IR (normalized to actin)
*
7
8 H
nuclear Dnmt3a1 IF (% of control)
***
**
basal
Bic/4AP,
3h
NMDA,
10min
20
21
20
22
Bic/4AP,
10min
0
50
100
150
200 E
TTX
anti-Actin
Bic/4AP
anti-Dnmt3a-1
kDa
40
130 G
DNMT3A1
basal
Bic/4AP 3h
DAPI MAP2
DAPI MAP2
DNMT3A1
NMDA 10min
Bic/4AP 10min
0
255 H D
Time Line
TTX18h
↑↓
wash out
TTX12h
Bic/4AP
6h
WB
&
ICC G F
) D E Fig. 1
Synaptic activity regulates DNMT3A1 protein levels in neurons. a Nuclear DNMT3A1 immunofluorescence is prominent in MAP2-
positive neurons but much less in GFAP-positive astrocytes at 15 DIV hippocampal cultures. Scale bars are 20 μm. b, c Downregulation of
DNMT3A1 protein levels in 14–15 DIV hippocampal primary neurons following treatment with Bic/4AP for 1 h, 3 h or 6 h as evidenced by
quantitative immunocytochemistry. Scale bar is 20 μm. Unpaired Student’s t-test **p < 0.01, ***p < 0.001. d–f DNMT3a1 protein levels are
decreased following the removal of tonic inhibition in DIV 21 cortical neurons. β-Actin was used as an internal control for normalization. Student’s t-test *p < 0.05. g, h Hippocampal neurons were treated with Bic/4AP for 10 min or 3 h. Media from 10 min-long treated neurons was
washed out and cells were kept for 3 h before fixation. Both treatments were equally effective to reduce nuclear DNMT3A1
immunofluorescence. Application of 100 μM NMDA for 10 min had no effect. Unpaired Student’s t-test **p < 0.01, ***p < 0.001. Error bars
present S.E.M. Sample numbers for each experimental group indicate neurons from three different culture preparations. Potential mediators of DNMT3A1 degradation are members of
the family of Cullin proteins [32]. Cullin family members combine
with RING proteins to form Cullin-RING E3 ubiquitin ligases [33]
and neddylation is a prerequisite for their activation in the
nucleus. Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 Neddylation has been studied only recently in neurons
[34, 35] and the subcellular distribution of NEDD8 in neurons
has not been determined yet. We found that NEDD8 is
abundantly localized in the nucleus of hippocampal primary
neurons,
whereas immunofluorescence
intensity
was
much
weaker at synapses (Fig. 3a). We observed heterologous co-
immunoprecipitation of DNMT3A1 with CUL4B, CUL1, CUL3,
CUL4, CUL7, but not with CUL2 and CUL5 from HEK293T cell
lysates (Fig. S4A). In addition, we found that poly-ubiquitination
of DNMT3A1 was elevated following forced expression of CUL4B
in HEK293T cells (Fig. S4B, D), which was chosen as an example
because of its abundance in the brain. Conversely, shRNA-based
CUL4B protein knockdown resulted in reduced DNMT3A1 poly-
ubiquitination (Fig. S4E). The neddylation inhibitor MLN4924 se-
lectively inhibits the NEDD8-Activating-Enzyme (NAE) at very low
concentrations [36]. Accordingly, poly-ubiquitination of immuno-
precipitated DNMT3A1 was reduced in cells that were subjected
to MLN4924 treatment (Fig. S4F). Moreover, neddylated CUL4B
was co-immunoprecipitated with DNMT3A1 (Fig. S4G). application of the antagonist NVP-AAM077, which mainly targets
di-heteromeric GluN2A-containing NMDARs [28] in low doses,
completely prevented degradation as evidenced by quantitative
immunocytochemistry (Fig. 2c, d) and immunoblotting (Fig. 2e, f). In addition, shRNA-induced protein knockdown (Fig. S2A, B) of
GluN2A confirmed a requirement for NMDARs specifically contain-
ing this subunit to elicit degradation of DNMT3A1 (Fig. 2h, i),
whereas application of the GluN2B antagonist ifenprodil had no
effect (Fig. 2j, k). Co-application of the L-type Ca2+-channel
blocker nifedipine (Fig. S2C, D) or the CaMKII and CaMKIV inhibitor
KN93 to the stimulation buffer also hindered nuclear DNMT3A1
degradation (Fig. S2E, F). Likewise, CaMKIV shRNA knockdown
clearly reduced DNMT3A1 degradation in response to enhanced
synaptic activity (Fig. S2G–I). Similarly, nuclear overexpression of a
dominant negative form of CaMKIV reduced activity-dependent
degradation, whereas constitutively active CaMKIV [19, 20] had the
opposite effect (Fig. S2J–L). Taken together, these experiments
indicate that brief activation of synaptic GluN2A-containing
NMDARs is a potent stimulus to control DNMT3A1 protein levels
in the nucleus and that synaptic control probably involves the
induction of backpropagating dendritic action potentials and
nuclear calcium waves which in turn activate CaMKIV, upstream of
DNTM3A1 downregulation. application of the antagonist NVP-AAM077, which mainly targets
di-heteromeric GluN2A-containing NMDARs [28] in low doses,
completely prevented degradation as evidenced by quantitative
immunocytochemistry (Fig. 2c, d) and immunoblotting (Fig. 2e, f). In addition, shRNA-induced protein knockdown (Fig. Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 The activity-dependent degradation of DNMT3A1 was blocked in
the presence of the competitive NMDAR antagonist 2-amino-5-
phosphonopentanoic acid (APV) (Fig. 2a, b). Interestingly, the Neuropsychopharmacology (2020) 45:2120 – 2130 Synaptic control of DNA methylation involves activity-dependent. . . G Bayraktar et al. 2124 0
255
DNMT3A1
DNMT3A1
DNMT3A1
DAPI,MAP2
DAPI, GFAP
DAPI, MAP2
DAPI, GFAP
ROI 1
ROI 2
ROI 1
ROI 2
A
0
255
Bic/4AP
basal
h
6
h
3
h
1
DNMT3A1
DNMT3A1
DAPI MAP2
DAPI MAP2
B
C
1h
3h
6h
basal
Bic/4AP
n.s. ***
**
25
25
24
26
27
30
nuclear DNMT3A1 IF (% of control)
0
50
100
150
200
E
D
F
Time Line
TTX18h
↑↓
wash out
TTX12h
Bic/4AP
6h
WB
&
ICC
0
50
100
150
200
TTX, 18h
TTX 12h +
Bic/4AP, 6h
Dnmt3a1 IR (normalized to actin)
*
G
H
DNMT3A1
basal
Bic/4AP 3h
DAPI MAP2
DAPI MAP2
DNMT3A1
NMDA 10min
Bic/4AP 10min
nuclear Dnmt3a1 IF (% of control)
***
**
basal
Bic/4AP,
3h
NMDA,
10min
20
21
20
22
Bic/4AP,
10min
0
50
100
150
200
7
8
0
255
TTX
anti-Actin
Bic/4AP
anti-Dnmt3a-1
kDa
40
130
Fig. 1
Synaptic activity regulates DNMT3A1 protein levels in neurons. a Nuclear DNMT3A1 immunofluorescence is prominent in MAP2-
positive neurons but much less in GFAP-positive astrocytes at 15 DIV hippocampal cultures. Scale bars are 20 μm. b, c Downregulation of
DNMT3A1 protein levels in 14–15 DIV hippocampal primary neurons following treatment with Bic/4AP for 1 h, 3 h or 6 h as evidenced by
quantitative immunocytochemistry. Scale bar is 20 μm. Unpaired Student’s t-test **p < 0.01, ***p < 0.001. d–f DNMT3a1 protein levels are
decreased following the removal of tonic inhibition in DIV 21 cortical neurons. β-Actin was used as an internal control for normalization. Student’s t-test *p < 0.05. g, h Hippocampal neurons were treated with Bic/4AP for 10 min or 3 h. Media from 10 min-long treated neurons was
washed out and cells were kept for 3 h before fixation. Both treatments were equally effective to reduce nuclear DNMT3A1
immunofluorescence. Application of 100 μM NMDA for 10 min had no effect. Unpaired Student’s t-test **p < 0.01, ***p < 0.001. Error bars
present S.E.M. Sample numbers for each experimental group indicate neurons from three different culture preparations. Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 21 C
D
NVP-AAM077
control
Bic/4AP
basal
DNMT3A1
DNMT3A1
DAPI MAP2
DAPI MAP2
nuclear DNMT3A1 IF (% of control)
***
Untreated
29
31
0
50
100
150
200
0
255
basal
077,
G
n s 55
B
0
50
100
150
200
APV
Untreated
31
31
41
40
nuclear DNMT3A1 IF (% of control)
***
n.s. basal
Bic/4AP
0
F 0
255
B
Bic/4-AP
MT3A1
DNMT3A1
DAPI MAP2
0
50
100
150
200
APV
Untreated
31
31
41
40
nuclear DNMT3A1 IF (% of control)
***
n.s. basal
Bic/4AP
0
F A D C C A B G E F E
Lysis
6 h Bic/4AP
basal / no treatment
6 h NVP (50nM)+Bic/4AP
Hippocampal neurons 14 DIV
Timeline
WB G
basal
Bic/4AP 6 h
NVP-AAM077+ Bic/4AP 6 h
0
50
100
150
n.s. **
*
DNMT3A1 IR
(normalized to actin) kDa
NVP-AAM077,
Bic/4AP 6h
basal
F
Bic/4AP 6h
anti-DNMT3A1
anti-Actin
130
40 H I
Dnmt3a1
DAPI, MAP2
transfection
shRNA GluN2A
shScrambled
H
shScrambled
Bic/4AP
basal
0
255
shRNA GluN2A I
Dnmt3a1
DAPI, MAP2
transfection
shRNA GluN2A
shScrambled
0
50
100
150
200
34
39
38
32
***
shScrambled
shRNA
GluN2A
nuclear DNMT3A1 IF (% of control)
n.s. H
shScrambled
Bic/4AP
basal
basal
Bic/4AP
0
255
Ifenprodil
control
b
DAPI MAP2
J
shRNA GluN2A
anti Actin Ifenprodil
***
***
nuclear DNMT3A1 IF (% of control)
31
35
31
35
0
50
100
150
200
Untreated
K
5
basal
Bic/4AP Ifenprodil
control
Bic/4AP
basal
DNMT3A1
DNMT3A1
DAPI MAP2
DAPI MAP2
J
Ifenprodil
***
***
nuclear DNMT3A1 IF (% of control)
31
35
31
35
0
50
100
150
200
Untreated
K
0
255
basal
Bic/4AP I
0
50
100
150
200
34
39
38
32
***
shScrambled
shRNA
GluN2A
nuclear DNMT3A1 IF (% of control)
n.s. basal
Bic/4AP J Fig. 2
GluN2A-dependent NMDAR signaling regulates nuclear DNMT3A1 protein levels in 14–15 DIV hippocampal primary neurons. a, b
Treatment with the NMDAR antagonist APV (20 μM) prevented the reduction in the nuclear levels of DNMT3A1 following synaptic stimulation
by Bic/4AP for 6 h. c, d Treatment with the GluN2A inhibitor NVP-AAM077 (50 nM) prevented the reduction in the nuclear levels of DNMT3A1
following synaptic stimulation by Bic/4AP for 6 h. Two-way ANOVA followed by Bonferroni’s post hoc test. e Timeline view of hippocampal
neuron treatment by Bic/4AP for 6 h with or without NVP-AAM077. Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 In addition, 5meC
immunocytochemistry revealed that no gross quantitative altera-
tions in global DNA methylation occur following sustained
stimulation of synaptic GluN2A-containing NMDARs (Fig. 3e, g). However, enhanced synaptic activity resulted in rapidly increased
neddylation of CUL4B (Fig. 3h, i), whereas shRNA knockdown of
NEDD8 (Fig. S5C–E) prevented activity-dependent degradation of
DNMT3A1 (Fig. 3j, k). Collectively, the biochemical, pharmacolo-
gical and shRNA knockdown experiments show that synaptic
activation of GluN2A-containing NMDARs will drive neddylation of
Cullin-ligases in the nucleus, which is a prerequisite for DNMT3A1
degradation. even a high dose of MLN4924 (1 µM) did not alter the total
number of spines (Fig. S5A, B) as it was reported previously with a
higher concentration and long-term treatment [34, 35]. Moreover,
we observed that nuclear NEDD8 staining intensity was not
altered following Bic/4AP treatment (Fig. 3e, f), which excludes the
possibility that activity-dependent nucleocytoplasmic shuttling of
NEDD8 contributes to DNMT3A1 degradation. In addition, 5meC
immunocytochemistry revealed that no gross quantitative altera-
tions in global DNA methylation occur following sustained
stimulation of synaptic GluN2A-containing NMDARs (Fig. 3e, g). However, enhanced synaptic activity resulted in rapidly increased
neddylation of CUL4B (Fig. 3h, i), whereas shRNA knockdown of
NEDD8 (Fig. S5C–E) prevented activity-dependent degradation of
DNMT3A1 (Fig. 3j, k). Collectively, the biochemical, pharmacolo-
gical and shRNA knockdown experiments show that synaptic
activation of GluN2A-containing NMDARs will drive neddylation of
Cullin-ligases in the nucleus, which is a prerequisite for DNMT3A1
degradation. downregulation of DNMT3A1 protein levels within 6 h in the
potentiated CA1 region following tetanization of the slices (Fig. 4b,
c). Moreover, the expression of late-LTP is neddylation-sensitive
and
field
excitatory
postsynaptic
potentiation
slope
values
returned to baseline within three hours when the slices were
treated
with
the
NEDD8
inhibitor
MLN4924
like
reported
previously [37] (Fig. 4d–f). p
y
g
We subsequently investigated whether following the induction
of LTP signaling of GluN2A-containing NMDARs to the nucleus is
crucial in neddylation-dependent degradation of DNMT3A1. Interestingly, DNMT3A1 protein levels were already clearly higher
in hippocampal tissue homogenates of GluN2A knockout mice as
compared to wild-type controls (Fig. 4g, h). GluN2A knockout mice
show reportedly impaired hippocampal LTP [38] but a stronger
tetanic stimulation rescues this impairment and the saturation
level of LTP remains unaltered [39]. We could replicate these
published findings (Fig. Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 S2A, B) of
GluN2A confirmed a requirement for NMDARs specifically contain-
ing this subunit to elicit degradation of DNMT3A1 (Fig. 2h, i),
whereas application of the GluN2B antagonist ifenprodil had no
effect (Fig. 2j, k). Co-application of the L-type Ca2+-channel
blocker nifedipine (Fig. S2C, D) or the CaMKII and CaMKIV inhibitor
KN93 to the stimulation buffer also hindered nuclear DNMT3A1
degradation (Fig. S2E, F). Likewise, CaMKIV shRNA knockdown
clearly reduced DNMT3A1 degradation in response to enhanced
synaptic activity (Fig. S2G–I). Similarly, nuclear overexpression of a
dominant negative form of CaMKIV reduced activity-dependent
degradation, whereas constitutively active CaMKIV [19, 20] had the
opposite effect (Fig. S2J–L). Taken together, these experiments
indicate that brief activation of synaptic GluN2A-containing
NMDARs is a potent stimulus to control DNMT3A1 protein levels
in the nucleus and that synaptic control probably involves the
induction of backpropagating dendritic action potentials and
nuclear calcium waves which in turn activate CaMKIV, upstream of
DNTM3A1 downregulation. Following this, we asked whether neddylation of Cullins might
be involved in controlling activity-dependent DNMT3A1 protea-
somal degradation in neurons. With co-immunoprecipitation
experiments on endogenous proteins extracted from cortical
primary neurons using a CUL4B specific antibody as pars pro toto
we revealed that neuronal CUL4B and DNMT3A1 might be in one
complex in vivo (Fig. 3b). Acute treatment of hippocampal primary
neurons with concentrations of MLN4924 as low as 5 nM
prevented DNMT3A1 degradation (Fig. 3c, d). Of note, acute
treatment of primary neurons for 6 h with either a low (5 nM) or Proteasomal degradation of DNMT3A1 requires neddylation
We next examined which mechanisms might contribute to
DNMT3A1 downregulation and found that the proteasome
inhibitors MG132, lactacystin or carfilzomib, which all operate
via different mechanisms [29–31], completely abolished the effect
of GluN2A stimulation (Fig. S3A–F). Since we found no con-
comitant alteration of Dnmt3a1 mRNA levels (Fig. S3G-I), these
data suggest that proteasomal degradation controls the protein
levels of the enzyme in an activity-dependent manner. Neuropsychopharmacology (2020) 45:2120 – 2130 Synaptic control of DNA methylation involves activity-dependent. . . G Bayraktar et al. 2125 D
nuclear DNMT3A1 IF (% of control)
NVP-
AAM077
***
n.s. Untreated
29
31
30
39
0
50
100
150
200
55
basal
Bic/4AP
2125 A
0
255
control
APV
B
Bic/4-AP
basal
DNMT3A1
DNMT3A1
DAPI MAP2
DAPI MAP2
0
50
100
150
200
APV
Untreated
31
31
41
40
nuclear DNMT3A1 IF (% of control)
***
n.s. Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 f, g Quantitative immunoblotting revealed the inhibition of DNMT3A1
degradation by the use of NVP-AAM077. One-sample t-test is performed while the hypothetical value is set to 100. h, i shRNA-based
knockdown of GluN2A in the presence of synaptic stimulation by Bic/4AP for 6 h prevented the DNMT3A1 degradation. j, k Treatment with
the GluN2B subunit inhibitor ifenprodil (10 μM) in the presence of synaptic stimulation with Bic/4AP for 6 h did not prevent the reduction in
the nuclear levels of Dnmt3A1. Scale bars, 20 μm. Two-way ANOVA followed by Bonferroni’s post hoc test. ***p < 0.001, n.s. not significant. Error bars present S.E.M. Sample numbers for each experimental group indicate neurons from three different culture preparations. even a high dose of MLN4924 (1 µM) did not alter the total
number of spines (Fig. S5A, B) as it was reported previously with a
higher concentration and long-term treatment [34, 35]. Moreover,
we observed that nuclear NEDD8 staining intensity was not
altered following Bic/4AP treatment (Fig. 3e, f), which excludes the
possibility that activity-dependent nucleocytoplasmic shuttling of
NEDD8 contributes to DNMT3A1 degradation. In addition, 5meC
immunocytochemistry revealed that no gross quantitative altera-
tions in global DNA methylation occur following sustained
stimulation of synaptic GluN2A-containing NMDARs (Fig. 3e, g). However, enhanced synaptic activity resulted in rapidly increased
neddylation of CUL4B (Fig. 3h, i), whereas shRNA knockdown of
NEDD8 (Fig. S5C–E) prevented activity-dependent degradation of
DNMT3A1 (Fig. 3j, k). Collectively, the biochemical, pharmacolo-
gical and shRNA knockdown experiments show that synaptic
activation of GluN2A-containing NMDARs will drive neddylation of
Cullin-ligases in the nucleus, which is a prerequisite for DNMT3A1
degradation. Synaptic plasticity inducing stimuli elicit DNMT3A1 degradation in
a GluN2A-dependent manner
We then addressed whether induction of NMDAR-dependent LTP,
a form of plasticity that is considered to be a cellular model of
learning and memory, impacts nuclear DNMT3A1 protein levels. When we induced LTP in the hippocampus with high-frequency
stimulation of Schaffer-collaterals (Fig. 4a), we found a significant
Neuropsychopharmacology (2020) 45:2120 – 2130 even a high dose of MLN4924 (1 µM) did not alter the total
number of spines (Fig. S5A, B) as it was reported previously with a
higher concentration and long-term treatment [34, 35]. Moreover,
we observed that nuclear NEDD8 staining intensity was not
altered following Bic/4AP treatment (Fig. 3e, f), which excludes the
possibility that activity-dependent nucleocytoplasmic shuttling of
NEDD8 contributes to DNMT3A1 degradation. Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 C
D
NVP-AAM077
control
Bic/4AP
basal
DNMT3A1
DNMT3A1
DAPI MAP2
DAPI MAP2
nuclear DNMT3A1 IF (% of control)
NVP-
AAM077
***
n.s. Untreated
29
31
30
39
0
50
100
150
200
0
255
I
Dnmt3a1
DAPI, MAP2
transfection
shRNA GluN2A
shScrambled
0
50
100
150
200
34
39
38
32
***
shScrambled
shRNA
GluN2A
nuclear DNMT3A1 IF (% of control)
n.s. H
shScrambled
Bic/4AP
basal
basal
Bic/4AP
0
255
Ifenprodil
control
Bic/4AP
basal
DNMT3A1
DNMT3A1
DAPI MAP2
DAPI MAP2
J
Ifenprodil
***
***
nuclear DNMT3A1 IF (% of control)
31
35
31
35
0
50
100
150
200
Untreated
K
0
255
basal
Bic/4AP
basal
Bic/4AP
shRNA GluN2A
basal
Bic/4AP
kDa
NVP-AAM077,
Bic/4AP 6h
basal
E
F
Bic/4AP 6h
anti-DNMT3A1
anti-Actin
Lysis
6 h Bic/4AP
basal / no treatment
6 h NVP (50nM)+Bic/4AP
Hippocampal neurons 14 DIV
Timeline
WB
G
basal
Bic/4AP 6 h
NVP-AAM077+ Bic/4AP 6 h
0
50
100
150
n.s. **
*
DNMT3A1 IR
(normalized to actin)
130
40
Fig. 2
GluN2A-dependent NMDAR signaling regulates nuclear DNMT3A1 protein levels in 14–15 DIV hippocampal primary neurons. a, b
Treatment with the NMDAR antagonist APV (20 μM) prevented the reduction in the nuclear levels of DNMT3A1 following synaptic stimulation
by Bic/4AP for 6 h. c, d Treatment with the GluN2A inhibitor NVP-AAM077 (50 nM) prevented the reduction in the nuclear levels of DNMT3A1
ollowing synaptic stimulation by Bic/4AP for 6 h. Two-way ANOVA followed by Bonferroni’s post hoc test. e Timeline view of hippocampal
neuron treatment by Bic/4AP for 6 h with or without NVP-AAM077. f, g Quantitative immunoblotting revealed the inhibition of DNMT3A1
degradation by the use of NVP-AAM077. One-sample t-test is performed while the hypothetical value is set to 100. h, i shRNA-based
knockdown of GluN2A in the presence of synaptic stimulation by Bic/4AP for 6 h prevented the DNMT3A1 degradation. j, k Treatment with
he GluN2B subunit inhibitor ifenprodil (10 μM) in the presence of synaptic stimulation with Bic/4AP for 6 h did not prevent the reduction in
he nuclear levels of Dnmt3A1. Scale bars, 20 μm. Two-way ANOVA followed by Bonferroni’s post hoc test. ***p < 0.001, n.s. not significant. Error bars present S.E.M. Sample numbers for each experimental group indicate neurons from three different culture preparations. Neuropsychopharmacology (2020) 45:2120 – 2130 Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 S6A, C) and found that despite the
induction of LTP with a stronger protocol no reduction in nuclear
DNMT3A1 protein levels like in wild-type mice was detectable
(Fig. 4i–l). Notably, while we observed a negative correlation
between the strength of LTP and the magnitude of DNMT3A1
degradation in wild-type control animals (Fig. S7D) no correlation
was seen in GluN2A -/- mice despite recovered LTP. Thus, GluN2A
signaling in synaptic plasticity and not the induction of LTP as
such is instrumental in controlling nuclear protein levels of
DNMT3A1. Synaptic plasticity inducing stimuli elicit DNMT3A1 degradation in
a GluN2A-dependent manner We then addressed whether induction of NMDAR-dependent LTP,
a form of plasticity that is considered to be a cellular model of
learning and memory, impacts nuclear DNMT3A1 protein levels. When we induced LTP in the hippocampus with high-frequency
stimulation of Schaffer-collaterals (Fig. 4a), we found a significant Neuropsychopharmacology (2020) 45:2120 – 2130 Synaptic control of DNA methylation involves activity-dependent. . . G Bayraktar et al. 2126 Fig. 3
DNMT3A1 degradation is a neddylation-dependent process. a NEDD8 is abundantly expressed in the nucleus of 16 DIV hippocamp
neurons whereas weaker staining was observed at synapses. Scale bar 20 μm (top panel), 5 μm (lower panel). b Immunoprecipitation of CUL4
protein from nuclear extracts of cortical primary neurons (top panel) results in co-precipitation of DNMT3A1 (lower panel, indicated with a
arrow). c, d Hippocampal primary neurons were treated with Bic/4AP for 6 h in the presence or absence of MLN4924 (5 nM). Scale bars, 20 μm
Quantitative immunocytochemistry revealed that blocking neddylation prevents DNMT3A1 degradation. e Representative immunofluore
cence images of nuclear NEDD8 and total cytosine methylation (5meC) at basal conditions or after treatment with Bic/4AP for 6 h. Scale bar
20 μm. f, g Upon synaptic activation nuclear NEDD8 and 5meC levels remained unchanged. Unpaired Student’s t-test. n.s. not significant. h
CUL4B was immunoprecipitated from nuclear extracts of primary cortical neurons and neddylated CUL4B was quantified. Following 10 min
synaptic stimulation, the amount of neddylated CUL4B was increased. Unpaired Student’s t-test **p < 0.01. j, k shRNA knockdown of NEDD8
hippocampal primary neurons reduced DNMT3A1 degradation following 10 min-long Bic/4AP treatment and fixation of cells 3 h aft
washout of the drug-containing-media. Two-way ANOVA followed by Bonferroni’s post-hoc test. ***p < 0.001, scale bar, 20 μm. Error ba
present S.E.M. Sample numbers for each experimental group indicate neurons from three different culture preparations. Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 6 Fig. 3
DNMT3A1 degradation is a neddylation-dependent process. a NEDD8 is abundantly expressed in the nucleus of 16 DIV hippocampal
neurons whereas weaker staining was observed at synapses. Scale bar 20 μm (top panel), 5 μm (lower panel). b Immunoprecipitation of CUL4B
protein from nuclear extracts of cortical primary neurons (top panel) results in co-precipitation of DNMT3A1 (lower panel, indicated with an
arrow). c, d Hippocampal primary neurons were treated with Bic/4AP for 6 h in the presence or absence of MLN4924 (5 nM). Scale bars, 20 μm. Quantitative immunocytochemistry revealed that blocking neddylation prevents DNMT3A1 degradation. e Representative immunofluores-
cence images of nuclear NEDD8 and total cytosine methylation (5meC) at basal conditions or after treatment with Bic/4AP for 6 h. Scale bar is
20 μm. f, g Upon synaptic activation nuclear NEDD8 and 5meC levels remained unchanged. Unpaired Student’s t-test. n.s. not significant. h, i
CUL4B was immunoprecipitated from nuclear extracts of primary cortical neurons and neddylated CUL4B was quantified. Following 10 min of
synaptic stimulation, the amount of neddylated CUL4B was increased. Unpaired Student’s t-test **p < 0.01. j, k shRNA knockdown of NEDD8 in
hippocampal primary neurons reduced DNMT3A1 degradation following 10 min-long Bic/4AP treatment and fixation of cells 3 h after
washout of the drug-containing-media. Two-way ANOVA followed by Bonferroni’s post-hoc test. ***p < 0.001, scale bar, 20 μm. Error bars
present S.E.M. Sample numbers for each experimental group indicate neurons from three different culture preparations. Neddylation facilitates Bdnf gene expression
In the adult brain, BDNF has principal functions in synaptic
plasticity, learning, and memory [40]. Bdnf gene expression is
controlled by eight promoters [41] and among those, particularly
promoter IV activity is strongly stimulated by the calcium influx
through synaptic NMDARs [14, 42]. DNA methylation of the Bdnf IV
promoter has been studied previously also in the context of
neuropsychiatric disorders [43, 44]. We could replicate these
findings and profiled the changes in DNA methylation levels
following neuronal activity by the 6 h-long Bic/4AP treatment with
bisulfite sequencing that cover the 19 CGs in Bdnf IV gene
promoter (Fig. S7A). We, therefore, chose Bdnf IV gene expression
to test whether neddylation and activity-dependent degradation
of DNMT3A1 might impact DNA methylation of promoters of
plasticity-related genes and corresponding gene expression. Neuropsychopharmacology (2020) 45:2120 – 2130 Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 Quantitative real-time PCR experiments first revealed that Bdnf
IV mRNA expression is increased by enhanced synaptic activity in
primary hippocampal neurons and this increase in transcript levels was significantly lower in the presence of MLN4924 (Fig. S7B). Comparable results were obtained in acute hippocampal slices
following
high-frequency
stimulation
of
Schaffer-collaterals
(Fig. S7C) and importantly, the LTP-induced increase in Bdnf IV
transcript levels was reduced in the presence of the NEDD8-
inhibitor (Fig. S7C). We next addressed whether increased Bdnf IV mRNA produc-
tion was correlated with the demethylation of the Bdnf IV
promoter in acute slices following LTP induction, as predicted by
the degradation of DNMT3A1. First, methylation specific restric-
tion enzyme analysis was performed using primers that span the
Bdnf IV promoter sequence possessing three different restriction
sites (Fig. S7G). Tetanized CA1 samples revealed a reduction in
Bdnf IV promoter methylation, whereas increased promoter
methylation was observed for the group that received high-
frequency
stimulation
while
being
treated
with
MLN4924
(Fig. S7D). A subsequent series of MeDIP-qPCR experiments
were performed using tetanized CA1 tissue samples following Neuropsychopharmacology (2020) 45:2120 – 2130 Synaptic control of DNA methylation involves activity-dependent. . . G Bayraktar et al. 2127 21 Fig. 4
The NEDD8 inhibitor MLN4924 impairs LTP in rat hippocampal slices and degradation of DNMT3A1 upon LTP induction is absent
in GluN2A knock out mice. a Schematic presentation of LTP induction by high-frequency stimulation in acute CA1 hippocampal slices. Only
the potentiated CA1 region was dissected from individual hippocampal slices 6 h following LTP recordings. Representative traces from
recordings at the time points indicated under control and treatment conditions. b, c DNMT3A1 levels are reduced 6 h after LTP induction and
neddylation inhibition prevented the degradation of Dnmt3A1. β-Actin was used as an internal control for normalization. Two-way ANOVA
followed by Bonferroni’s post hoc test. **p < 0.01, *p < 0.05. d Averaged fEPSP slopes of the last hour following LTP induction showed
significantly reduced LTP in MLN4924 (50 nM) treated slices in comparison to slices treated by DMSO. Mann–Whitney U-Test ***p < 0.001. e Application of MLN4924 for 6 h induces significantly impaired LTP as compared to controls. *p < 0.05 and **p < 0.01. f Baseline recordings
revealed no alterations. g, h GluN2A knockout (KO) mice show higher DNMT3A1 protein levels in the CA1 region of the hippocampus
compared to the age-matched wild type (WT) control mice. Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 unpaired Student’s t-test **p < 0.01. i–l Quantitative immunoblotting either from
the CA1 of WT (i, j) or GluN2A KO (k, l) mice revealed no reduction in the GluN2A KO mice following 3 h of LTP recordings unlike reduction
seen in the WT control mice tissue. Unpaired Student’s t-test. *p < 0.05, n.s. not significant. Error bars present S.E.M. Sample numbers for each
experimental group indicate potentiated pooled CA1 slices from at least three different recordings or mice used per group. 21 Fig. 4
The NEDD8 inhibitor MLN4924 impairs LTP in rat hippocampal slices and degradation of DNMT3A1 upon LTP induction is absent
in GluN2A knock out mice. a Schematic presentation of LTP induction by high-frequency stimulation in acute CA1 hippocampal slices. Only
the potentiated CA1 region was dissected from individual hippocampal slices 6 h following LTP recordings. Representative traces from
recordings at the time points indicated under control and treatment conditions. b, c DNMT3A1 levels are reduced 6 h after LTP induction and
neddylation inhibition prevented the degradation of Dnmt3A1. β-Actin was used as an internal control for normalization. Two-way ANOVA
followed by Bonferroni’s post hoc test. **p < 0.01, *p < 0.05. d Averaged fEPSP slopes of the last hour following LTP induction showed
significantly reduced LTP in MLN4924 (50 nM) treated slices in comparison to slices treated by DMSO. Mann–Whitney U-Test ***p < 0.001. e Application of MLN4924 for 6 h induces significantly impaired LTP as compared to controls. *p < 0.05 and **p < 0.01. f Baseline recordings
revealed no alterations. g, h GluN2A knockout (KO) mice show higher DNMT3A1 protein levels in the CA1 region of the hippocampus
compared to the age-matched wild type (WT) control mice. unpaired Student’s t-test **p < 0.01. i–l Quantitative immunoblotting either from
the CA1 of WT (i, j) or GluN2A KO (k, l) mice revealed no reduction in the GluN2A KO mice following 3 h of LTP recordings unlike reduction
seen in the WT control mice tissue. Unpaired Student’s t-test. *p < 0.05, n.s. not significant. Error bars present S.E.M. Sample numbers for each
experimental group indicate potentiated pooled CA1 slices from at least three different recordings or mice used per group. into CA1 immediately after object location learning (Fig. Synaptic GluN2A-containing NMDARs drive the degradation of
nuclear DNMT3A1 5f)
resulted in a disturbance of object location memory, as indicated
by profoundly reduced discrimination of novel and familiar object
locations when compared to mice that received vehicle infusion
(Fig. 5g). Interestingly, the learning impairment in MLN4924
treated mice was associated with the prevention of DNMT3A1
degradation (Fig. 5h, i). Protein levels were significantly higher in
mice injected with MLN4924 three hours after training compared
to vehicle-injected mice (Fig. 5h, i). Six hours following training
DNMT3A1 protein levels were no longer different between
treatment groups and returned to baseline levels (Fig. 5j, k). the induction of LTP and confirmed the change in promoter
methylation. Less amplicons were generated with primers
targeting the Bdnf IV promoter that cover multiple cytosine
residues (Fig. S7H) known to regulate mRNA expression (Fig. S7E). More amplicons
were detected
in
MLN4924-treated
slices
following the induction of LTP (Fig. S7E), indicating increased
promoter methylation. Among the different Bdnf promoters that
were
investigated,
activity-dependent
DNA
methylation
is
particularly prominent for promoter IV, whereas promoter I
methylation was not altered following either LTP induction or
NEDD8 inhibition with MLN4924 (Fig. S7F). the induction of LTP and confirmed the change in promoter
methylation. Less amplicons were generated with primers
targeting the Bdnf IV promoter that cover multiple cytosine
residues (Fig. S7H) known to regulate mRNA expression (Fig. S7E). More amplicons
were detected
in
MLN4924-treated
slices
following the induction of LTP (Fig. S7E), indicating increased
promoter methylation. Among the different Bdnf promoters that
were
investigated,
activity-dependent
DNA
methylation
is
particularly prominent for promoter IV, whereas promoter I
methylation was not altered following either LTP induction or
NEDD8 inhibition with MLN4924 (Fig. S7F). DNMT3A1 is degraded in the hippocampus as a result of learning
In the final set of experiments, we investigated whether DNMT3A1
degradation occurs in vivo as a result of CA1-dependent learning
and
whether
this
degradation
and
memory
formation
is
neddylation-sensitive. Formation of a memory for the spatial
location of objects in an open field (Fig. 5a) requires synaptic
activity of CA1 neurons [45, 46] and is responsive to changes in
the expression of BDNF [47, 48]. We observed that DNMT3A1
protein levels were reduced in mice for three hours following
training (Fig. 5b, c). DNMT3A1 protein levels returned to control
values within 6 h, which may reflect less intense synaptic activity
as compared to tetanization of slices by high-frequency stimula-
tion (Fig. 5d, e). Bilateral intrahippocampal infusion of MLN4924 DISCUSSION
ll Compelling evidence exists for the necessity of active DNA
methylation as well as demethylation during memory consolida-
tion in the hippocampus [1, 2, 11–13]. However, the underlying
signaling machinery is not understood and it is essentially unclear
how synaptic signals conveyed to the nucleus impact DNA
methylation and demethylation. Here, we show that activation of
synaptic GluN2A-containing NMDARs drives the neddylation-
dependent proteasomal degradation of DNMT3A1, the principal
de novo DNA-methyltransferase in the adult brain. The finding that signals deriving from synaptic GluN2A-
containing NMDARs evoke degradation of DNMT3A1 raises several Neuropsychopharmacology (2020) 45:2120 – 2130 Synaptic control of DNA methylation involves activity-dependent. . . G Bayraktar et al. 2128 A
B
D
G
H
J
anti-DNMT3AN
anti-HistoneH3
saline
kDa
MLN4924
15
130
MLN4924 or Saline
training
test
3h
anti-DNMT3AN
anti-HistoneH3
saline
kDa
15
130
MLN4924
MLN4924 or Saline
training
test
6h
anti-DNMT3AN
anti-HistoneH3
control
kDa
trained
15
130
training
dissection
no training
dissection
3h
3h
F
Training
6h
20 min session
20 min session
Novel Location
training
test
6h
intrahippocampal injection
of MLN4924 or Saline
C
E
I
K
anti-HistoneH3
control
kDa
trained
15
130
training
6h
dissection
no training
6h
dissection
anti-DNMT3AN
25
50
75
100
125
150
175
200
Saline
MLN4924
25
50
75
100
125
150
175
200
Saline
MLN4924
*
Control
Trained
**
25
50
75
100
125
150
175
200
DNMT3A1 IR
(normalized to Histone)
9
8
Control
Trained
n.s. 25
50
75
100
125
150
175
200
DNMT3A1 IR
(normalized to Histone)
10
7
7
8
8
7
n.s. DNMT3A1 IR
(normalized to Histone)
DNMT3A1 IR
(normalized to Histone)
CA3
DG
▼
CA1
-40
-20
0
20
40
***
Saline
MLN4924
Naive
Discrimination index (%)
7
8
8
Fig. 5
Inhibition of neddylation in CA1 impairs object location memory and the learning-induced degradation of DNMT3A1. a Schematic
representation of the experimental protocol for object location memory. b, c DNMT3A1 protein levels are reduced 3 h after training. Unpaired
Student’s t-test *p < 0.05. d, e DNMT3A1 protein levels are not changed in trained mice 6 h after training. Histone was used as a loading
control for normalization. Unpaired Student’s t-test n.s. = not significant. f Injection timeline and representative image of injection site in CA1. g Intra-hippocampal infusion of MLN4924 reduces the discrimination index of animals tested in the object location memory test. Unpaired
Student’s t-test with Welch correction ***p < 0.001. DISCUSSION
ll h, i Learning induced reduction of DNMT3A1 protein levels in trained, but not MLN4924
injected mice 3 h after training. Unpaired two-tailed Student’s t-test *p < 0.01. j, k DNMT3A1 protein levels were not altered in trained
MLN4924 injected or control mice 6 h after training. Histone was used as a loading control for normalization. Data are represented as mean ±
S.E.M. Unpaired Student’s t-test *p < 0.05. Sample numbers for each experimental group indicate mice used per group. 8 C
no
Control
Trained
**
25
50
75
100
125
150
175
200
DNMT3A1 IR
(normalized to Histone)
9
8 A
Training
6h
20 min session
20 min session
Novel Location D
anti-HistoneH3
control
kDa
trained
15
130
training
6h
dissection
no training
6h
dissection
anti-DNMT3AN E
Control
Trained
n.s. 25
50
75
100
125
150
175
200
DNMT3A1 IR
(normalized to Histone)
10
7 B
anti-DNMT3AN
anti-HistoneH3
control
kDa
trained
15
130
training
dissection
no training
dissection
3h
3h C C E B D A H
anti-DNMT3AN
anti-HistoneH3
saline
kDa
MLN4924
15
130
MLN4924 or Saline
training
test
3h
I
25
50
75
100
125
150
175
200
Saline
MLN4924
*
7
8
DNMT3A1 IR
(normalized to Histone) G
F
training
test
6h
intrahippocampal injection
of MLN4924 or Saline
CA3
DG
▼
CA1
-40
-20
0
20
40
***
Saline
MLN4924
Naive
Discrimination index (%)
7
8
8 K
25
50
75
100
125
150
175
200
Saline
MLN4924
8
7
n.s. DNMT3A1 IR
(normalized to Histone) J
anti-DNMT3AN
anti-HistoneH3
saline
kDa
15
130
MLN4924
MLN4924 or Saline
training
test
6h K J H F G Fig. 5
Inhibition of neddylation in CA1 impairs object location memory and the learning-induced degradation of DNMT3A1. a Schematic
representation of the experimental protocol for object location memory. b, c DNMT3A1 protein levels are reduced 3 h after training. Unpaired
Student’s t-test *p < 0.05. d, e DNMT3A1 protein levels are not changed in trained mice 6 h after training. Histone was used as a loading
control for normalization. Unpaired Student’s t-test n.s. = not significant. f Injection timeline and representative image of injection site in CA1. g Intra-hippocampal infusion of MLN4924 reduces the discrimination index of animals tested in the object location memory test. Unpaired
Student’s t-test with Welch correction ***p < 0.001. DISCUSSION
ll h, i Learning induced reduction of DNMT3A1 protein levels in trained, but not MLN4924
injected mice 3 h after training. Unpaired two-tailed Student’s t-test *p < 0.01. j, k DNMT3A1 protein levels were not altered in trained
MLN4924 injected or control mice 6 h after training. Histone was used as a loading control for normalization. Data are represented as mean ±
S.E.M. Unpaired Student’s t-test *p < 0.05. Sample numbers for each experimental group indicate mice used per group. critical for novel object location memory [45, 46] and increased
BDNF expression in the hippocampal CA1 region supports object
location learning [47, 48]. We have, therefore, chosen Bdnf as a
paradigmatic example for our studies, which is one of the target
genes that undergoes promoter-specific DNA demethylation in
the CA1 region of the hippocampus during memory consolidation
[14] and impaired spatial learning and memory, as well as
attenuated CA1-LTP, have been reported following a forebrain
specific Dnmt1 and -3 gene knockout in principal neurons [16, 17]. Aberrant DNA methylation has been implicated in a plethora of
studies on neuropsychiatric diseases including schizophrenia,
bipolar, and major depressive disorders [1, 7, 8]. One of the
hallmarks of schizophrenia is a downregulation of BDNF expres-
sion that is associated with the enrichment of 5-methylcytosine at
gene regulatory domains within the Bdnf promoter [50]. Moreover,
elevated hippocampal DNMT3A expression has been reported in
the postmortem brain of schizophrenia patients [51]. questions about the underlying mechanism of long-distance
signaling and the rationale behind it. Since GluN2A-containing
NMDARs are in contrast to those containing GluN2B preferentially
found at synaptic sites [49], it is possible if not likely that steep and
fast synaptic Ca2+-influx through these receptors is necessary to
elicit nuclear Ca2+-responses that in turn enhance neddylation of
Cullins in a CaMKIV-dependent manner. Neddylation as such has
not been investigated in any detail in neurons yet and not much
information is currently available on how NAE activity itself is
regulated. The present study, therefore, provides first evidence
that an NMDAR-derived synaptic calcium signal is coupled to
neddylation of Cullins in the nucleus. Two previous reports have
shown that blocking neddylation for extended periods of time (in
contrast to the administration regime in the present study) leads
to reductions in spine size and impairment of synapse maturation
in neurons [34, 35]. DISCUSSION
ll In addition, neddylation alters synapse
function and morphology by directly modifying one of the major
synaptic scaffolding proteins PSD95 [35]. We found that NEDD8 is
most abundant in neuronal nuclei and it is tempting to speculate
that activity-dependent neddylation might reduce the protein
levels not only of DNMT3A1 but also of other nuclear epigenetic
modifiers, which contribute to object location memory. Along
these lines the contribution of neddylation to object location
memory seems to be substantial, considering the near-complete
removal of the discrimination upon the inhibition of neddylation. This is, however, not reflected in the extent of reduction in the
levels of DNMT3A1 induced by the behavioral training. Moreover,
neddylation, like other post-translational modifications, is rever-
sible, which adds potentially another level of regulation. In
addition, different efficiencies of proteasomal degradation in
neuronal sub-compartments, the necessity for the integration of
signaling pathways in the nucleus as well as complex formation
and potential nuclear export of ubiquitinated DNMT3A1 may
account for the relatively slow decline. questions about the underlying mechanism of long-distance
signaling and the rationale behind it. Since GluN2A-containing
NMDARs are in contrast to those containing GluN2B preferentially
found at synaptic sites [49], it is possible if not likely that steep and
fast synaptic Ca2+-influx through these receptors is necessary to
elicit nuclear Ca2+-responses that in turn enhance neddylation of
Cullins in a CaMKIV-dependent manner. Neddylation as such has
not been investigated in any detail in neurons yet and not much
information is currently available on how NAE activity itself is
regulated. The present study, therefore, provides first evidence
that an NMDAR-derived synaptic calcium signal is coupled to
neddylation of Cullins in the nucleus. Two previous reports have
shown that blocking neddylation for extended periods of time (in
contrast to the administration regime in the present study) leads
to reductions in spine size and impairment of synapse maturation
in neurons [34, 35]. In addition, neddylation alters synapse
function and morphology by directly modifying one of the major
synaptic scaffolding proteins PSD95 [35]. We found that NEDD8 is
most abundant in neuronal nuclei and it is tempting to speculate
that activity-dependent neddylation might reduce the protein
levels not only of DNMT3A1 but also of other nuclear epigenetic
modifiers, which contribute to object location memory. Along
these lines the contribution of neddylation to object location
memory seems to be substantial, considering the near-complete
removal of the discrimination upon the inhibition of neddylation. REFERENCES 29. Fenteany G, Standaert RF, Lane WS, Choi S, Corey EJ, Schreiber SL. Inhibition of
proteasome activities and subunit-specific amino-terminal threonine modifica-
tion by lactacystin. Science. 1995;268:726–31. 1. Bayraktar G, Kreutz MR. Neuronal DNA methyltransferases: epigenetic mediators
between synaptic activity and gene expression? Neuroscientist. 2018;24:171–85. 1. Bayraktar G, Kreutz MR. Neuronal DNA methyltransferases: epigenetic mediators
between synaptic activity and gene expression? Neuroscientist. 2018;24:171–85. 2. Bayraktar G, Kreutz MR. The role of activity-dependent DNA demethylation in the
adult brain and in neurological disorders. Front Mol Neurosci. 2018;11:169. 30. Lee DH, Goldberg AL. Proteasome inhibitors: valuable new tools for cell biolo-
gists. Trends Cell Biol. 1998;8:397–403. 2. Bayraktar G, Kreutz MR. The role of activity-dependent DNA demethylation in the
adult brain and in neurological disorders. Front Mol Neurosci. 2018;11:169. 3. Campbell RR, Wood MA. How the epigenome integrates information and
reshapes the synapse. Nat Rev Neurosci. 2019;20:133–47. 31. Meng L, Mohan R, Kwok BH, Elofsson M, Sin N, Crews CM. Epoxomicin, a potent
and selective proteasome inhibitor, exhibits in vivo antiinflammatory activity. PNAS. 1999;96:10403–8. 3. Campbell RR, Wood MA. How the epigenome integrates information and
reshapes the synapse. Nat Rev Neurosci. 2019;20:133–47. 4. Day JJ, Sweatt JD. DNA methylation and memory formation. Nat Neurosci. 2010;13:1319–23. 4. Day JJ, Sweatt JD. DNA methylation and memory formation. Nat Neurosci. 2010;13:1319–23. 32. Sarikas A, Hartmann T, Pan ZQ. The cullin protein family. Genome Biol. 2011;
12:220. 5. Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA, et al. Neuronal activity
modifies the DNA methylation landscape in the adult brain. Nat Neurosci. 2011;14:1345–51. 5. Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA, et al. Neuronal activity
modifies the DNA methylation landscape in the adult brain. Nat Neurosci. 2011;14:1345–51. 33. Petroski MD, Deshaies RJ. Function and regulation of cullin-RING ubiquitin
ligases. Nat Rev Mol Cell Biol. 2005;6:9–20. 6. Miller CA, Sweatt JD. Covalent modification of DNA regulates memory formation. Neuron. 2007;53:857–69. 6. Miller CA, Sweatt JD. Covalent modification of DNA regulates memory formation. Neuron. 2007;53:857–69. 34. Scudder SL, Patrick GN. Synaptic structure and function are altered by the ned-
dylation inhibitor MLN4924. Mol Cell Neurosci. 2015;65:52–7. 35. Vogl AM, Brockmann MM, Giusti SA, Maccarrone G, Vercelli CA, Bauder CA, et al. Neddylation inhibition impairs spine development, destabilizes synapses and
deteriorates cognition. Nat Neurosci. 2015;18:239–51. 7. Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, Bouchard L, et al. ACKNOWLEDGEMENTS We would like to thank Monika Marunde, Corinna Borutzki, and Stefanie Hochmuth
for excellent technical assistance. We would like to thank Masayoshi Mishina from the
University of Tokyo (Graduate School of Medicine) for the generous gift of GluRε1
(GluN2A) KO mice. We would like to thank Dr. Julien Bauer and Marta Andrada
Almeida from Cambridge Genomics Services, at the Department of Pathology at the
University of Cambridge for the bisulfite sequencing analysis. We would like to thank
Daniel Giffney for proofreading of the manuscript. 20. Karpova A, Mikhaylova M, Thomas U, Knopfel T, Behnisch T. Involvement of
protein synthesis and degradation in long-term potentiation of Schaffer collateral
CA1 synapses. J Neurosci. 2006;26:4949–55. 21. Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for
bisulfite-seq applications. Bioinformatics. 2011;27:1571–2. 22. Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, et al. methylKit: a comprehensive R package for the analysis of genome-wide DNA
methylation profiles. Genome Biol. 2012;13:R87. AUTHOR CONTRIBUTIONS 23. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and
powerful approach to multiple testing. J R Stat Soc Ser B (Methodol). 1995;57:
289–300. GB designed, performed experiments, analyzed data, and wrote the paper. PY, ADC,
and AK performed experiments and analyzed data. GMG, SAR, and OS designed,
performed, and analyzed data from behavioral experiments. ST and IS provided and
characterized the DNMT3AN and DNMT3A-mid antibodies. FY designed and
supervised DNA methylation analysis experiments. MRK designed and supervised
the study, analyzed data, and wrote the paper. 24. Joseph A, Turrigiano GG. All for one but not one for all: excitatory synaptic scaling
and intrinsic excitability are coregulated by CaMKIV, whereas inhibitory synaptic
scaling is under independent control. J Neurosci. 2017;37:6778–85. 25. Wayman GA, Tokumitsu H, Davare MA, Soderling TR. Analysis of CaM-kinase
signaling in cells. Cell Calcium. 2011;50:1–8. 26. Sakai Y, Suetake I, Shinozaki F, Yamashina S, Tajima S. Co-expression of de novo
DNA methyltransferases Dnmt3a2 and Dnmt3L in gonocytes of mouse embryos. Gene Expr Patterns. 2004;5:231–7. FUNDING AND DISCLOSURE 13. Rudenko A, Dawlaty MM, Seo J, Cheng AW, Meng J, Le T, et al. Tet1 is critical for
neuronal activity-regulated gene expression and memory extinction. Neuron. 2013;79:1109–22. The authors have no conflict of interest to declare. Supported
by grants from the Deutsche Forschungsgemeinschaft (DFG)
(Kr 1879/9-1/FOR 2419, Kr1879/5-1/6-1/10-1; CRC 779 TPB8; Research
Training Group 2413 SynAGE), BMBF ‘Energi’ FKZ: 01GQ1421B, The
EU Joint Programme—Neurodegenerative Disease Research (JPND)
project STAD (01ED1613) and Leibniz Foundation SAW to MRK. CRC
779 TPB8 to AK. Deutsche Forschungsgemeinschaft SFB 779 TPB5 to
OS. Grants-in-Aid for Scientific Research B from the Japan Society for
the Promotion of Science to ST; Deutsche Forschungsgemeinschaft
EXC 257/2 to FY. GMG was supported by a CAPES-Alexander von
Humboldt Research Fellowship (1756/14-1). Open access funding
provided by Projekt DEAL. 14. Lubin FD, Roth TL, Sweatt JD. Epigenetic regulation of BDNF gene transcription in
the consolidation of fear memory. J Neurosci. 2008;28:10576–86. 15. Feng J, Chang H, Li E, Fan G. Dynamic expression of de novo DNA methyl-
transferases Dnmt3a and Dnmt3b in the central nervous system. J Neurosci Res. 2005;79:734–46. 16. Feng J, Zhou Y, Campbell SL, Le T, Li E, Sweatt JD, et al. Dnmt1 and Dnmt3a
maintain DNA methylation and regulate synaptic function in adult forebrain
neurons. Nat Neurosci. 2010;13:423–30. 17. Morris MJ, Adachi M, Na ES, Monteggia LM. Selective role for DNMT3a in learning
and memory. Neurobiol Learn Mem. 2014;115:30–7. 18. Dong C, Bach SV, Haynes KA, Hegde AN. Proteasome modulates positive and
negative translational regulators in long-term synaptic plasticity. J Neurosci. 2014;34:3171–82. 19. Jarome TJ, Helmstetter FJ. The ubiquitin-proteasome system as a critical regulator
of synaptic plasticity and long-term memory formation. Neurobiol Learn Mem. 2013;105:107–16. ADDITIONAL INFORMATION Supplementary Information accompanies this paper at (https://doi.org/10.1038/
s41386-020-0780-2). 27. Dieterich DC, Karpova A, Mikhaylova M, Zdobnova I, Konig I, Landwehr M, et al. Caldendrin-Jacob: a protein liaison that couples NMDA receptor signalling to the
nucleus. PLoS Biol. 2008;6:e34. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims
in published maps and institutional affiliations. 28. Auberson YP, Allgeier H, Bischoff S, Lingenhoehl K, Moretti R, Schmutz M. 5-
Phosphonomethylquinoxalinediones as competitive NMDA receptor antagonists
with a preference for the human 1A/2A, rather than 1A/2B receptor composition. Bioorg Med Chem Lett. 2002;12:1099–102. DISCUSSION
ll This is, however, not reflected in the extent of reduction in the
levels of DNMT3A1 induced by the behavioral training. Moreover,
neddylation, like other post-translational modifications, is rever-
sible, which adds potentially another level of regulation. In
addition, different efficiencies of proteasomal degradation in
neuronal sub-compartments, the necessity for the integration of
signaling pathways in the nucleus as well as complex formation
and potential nuclear export of ubiquitinated DNMT3A1 may
account for the relatively slow decline. p
p
p
Collectively our data point to a mechanism that allows for the
synaptic control of DNMT3A1 levels and thereby creates a time
window for reduced de novo DNA methylation at a subset of
target genes. DNMT3A1-mediated methylation has been largely
associated with the silencing of promoters, which would in turn
attenuate activity-dependent gene expression. A shorter splice
isoform, DNMT3A2, was shown to associate with transcription of
plasticity-relevant genes presumably via methylation of CpG
islands in their promoter and coding regions [52, 53]. Dnmt3a2
is an immediate early gene that is identical to Dnmt3a1 except
that it lacks the sequence encoding the N-terminal 219 amino
acids of the enzyme, which encompasses the epitope of the
antibody that was used in the current study. Intriguingly, we
found increased expression of Dnmt3a2 mRNA (Fig. S3I) and
downregulation of DNMT3A1 is induced by the same stimulus, i.e. activation of synaptic GluN2A-containing NMDARs. It is currently
unknown whether Dnmt3a2 mRNA will be immediately translated,
as expected for an immediate early gene. In this case, it may not
replace DNMT3A1 but independently facilitate activity-dependent
gene expression. The proposed long-distance signaling pathway can provide a
potential link between different observations. Converging evi-
dence suggests that NMDAR function in the dorsal CA1 area is Neuropsychopharmacology (2020) 45:2120 – 2130 Synaptic control of DNA methylation involves activity-dependent. . . G Bayraktar et al. 2129 G Bayraktar et al. 2130 41. Aid T, Kazantseva A, Piirsoo M, Palm K, Timmusk T. Mouse and rat BDNF gene
structure and expression revisited. J Neurosci Res. 2007;85:525–35. 50. Zheleznyakova GY, Cao H, Schioth HB. BDNF DNA methylation changes as a
biomarker of psychiatric disorders: literature review and open access database
analysis. Behav Brain Funct. 2016;12:17. 50. Zheleznyakova GY, Cao H, Schioth HB. BDNF DNA methylation changes as a
biomarker of psychiatric disorders: literature review and open access database
analysis. Behav Brain Funct. 2016;12:17. 42. Zheng F, Zhou X, Luo Y, Xiao H, Wayman G, Wang H. Regulation of brain-derived
neurotrophic factor exon IV transcription through calcium responsive elements in
cortical neurons. PloS One. 2011;6:e28441. 51. Zhubi A, Veldic M, Puri NV, Kadriu B, Caruncho H, Loza I, et al. An upregulation of
DNA-methyltransferase 1 and 3a expressed in telencephalic GABAergic neurons
of schizophrenia patients is also detected in peripheral blood lymphocytes. Schizophr Res. 2009;111:115–22. 43. Kundakovic M, Gudsnuk K, Herbstman JB, Tang D, Perera FP, Champagne FA. DNA methylation of BDNF as a biomarker of early-life adversity. Proc. Natl Acad. Sci. USA. 2015;112:6807–13. 52. Oliveira AM, Hemstedt TJ, Bading H. Rescue of aging-associated decline in
Dnmt3a2 expression restores cognitive abilities. Nat Neurosci. 2012;15:1111–3. 44. Maynard KR, Hill JL, Calcaterra NE, Palko ME, Kardian A, Paredes D, et al. Func-
tional role of BDNF production from unique promoters in aggression and ser-
otonin signaling. Neuropsychopharmacology. 2016;41:1943–55. 53. Oliveira AM, Hemstedt TJ, Freitag HE, Bading H. Dnmt3a2: a hub for enhancing
cognitive functions. Mol Psychiatry. 2016;21:1130–6. 45. Assini FL, Duzzioni M, Takahashi RN. Object location memory in mice: pharma-
cological validation and further evidence of hippocampal CA1 participation. Behav Brain Res. 2009;204:206–11. 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 license, and indicate if changes were made. The images or other third party
material in this article are included in the article’s Creative Commons license, unless
indicated otherwise in a credit line to the material. If material is not included in the
article’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. Neuropsychopharmacology (2020) 45:2120 – 2130 REFERENCES Epigenomic
profiling reveals DNA-methylation changes associated with major psychosis. Am
J Hum Genet. 2008;82:696–711. 36. Soucy TA, Smith PG, Milhollen MA, Berger AJ, Gavin JM, Adhikari S, et al. An
inhibitor of NEDD8-activating enzyme as a new approach to treat cancer. Nature. 2009;458:732–6. 8. Murgatroyd C, Patchev AV, Wu Y, Micale V, Bockmuhl Y, Fischer D, et al. Dynamic
DNA methylation programs persistent adverse effects of early-life stress. Nat
Neurosci. 2009;12:1559–66. 9. Paoletti P, Bellone C, Zhou Q. NMDA receptor subunit diversity: impact on
receptor properties, synaptic plasticity and disease. Nat Rev Neurosci. 2013;14:
383–400. 37. Brockmann MM, Dongi M, Einsfelder U, Korber N, Refojo D, Stein V. Neddylation
regulates excitatory synaptic transmission and plasticity. Sci Rep. 2019;9:17935. 38. Sakimura K, Kutsuwada T, Ito I, Manabe T, Takayama C, Kushiya E, et al. Reduced
hippocampal LTP and spatial learning in mice lacking NMDA receptor epsilon
1 subunit. Nature. 1995;373:151–5. 10. Zhou Q, Sheng M. NMDA receptors in nervous system diseases. Neuropharma-
cology. 2013;74:69–75. 39. Kiyama Y, Manabe T, Sakimura K, Kawakami F, Mori H, Mishina M. Increased
thresholds for long-term potentiation and contextual learning in mice lacking the
NMDA-type glutamate receptor epsilon1 subunit. J Neurosci. 1998;18:6704–12. 11. Kaas GA, Zhong C, Eason DE, Ross DL, Vachhani RV, Ming GL, et al. TET1 controls
CNS 5-methylcytosine hydroxylation, active DNA demethylation, gene tran-
scription, and memory formation. Neuron. 2013;79:1086–93. 12. Oliveira AM. DNA methylation: a permissive mark in memory formation and
maintenance. Learn Mem. 2016;23:587–93. 40. Karpova NN. Role of BDNF epigenetics in activity-dependent neuronal plasticity. Neuropharmacology. 2014;76(Pt C):709–18. Neuropsychopharmacology (2020) 45:2120 – 2130 Synaptic control of DNA methylation involves activity-dependent. . . G Bayraktar et al. y
G Bayraktar et al. G Bayraktar et al. To view a copy of this license, visit http://creativecommons. org/licenses/by/4.0/. 46. Haettig J, Sun Y, Wood MA, Xu X. Cell-type specific inactivation of hippocampal
CA1 disrupts location-dependent object recognition in the mouse. Learn Mem. 2013;20:139–46. 47. Intlekofer KA, Berchtold NC, Malvaez M, Carlos AJ, McQuown SC, Cunningham MJ,
et al. Exercise and sodium butyrate transform a subthreshold learning event into
long-term memory via a brain-derived neurotrophic factor-dependent mechan-
ism. Neuropsychopharmacology. 2013;38:2027–34. 48. Wang M, Li D, Yun D, Zhuang Y, Repunte-Canonigo V, Sanna PP, et al. Translation
of BDNF-gene transcripts with short 3’ UTR in hippocampal CA1 neurons
improves memory formation and enhances synaptic plasticity-relevant signaling
pathways. Neurobiol Learn Mem. 2017;138:121–34. pathways. Neurobiol Learn Mem. 2017;138:121–34. 49. Wyllie DJ, Livesey MR, Hardingham GE. Influence of GluN2 subunit identity on
NMDA receptor function. Neuropharmacology. 2013;74:4–17. © The Author(s) 2020 Neuropsychopharmacology (2020) 45:2120 – 2130 Neuropsychopharmacology (2020) 45:2120 – 2130
|
https://openalex.org/W4242633643
|
https://zenodo.org/records/3396603/files/16549__1_229146_LE_335629.pdf
|
English
| null |
SUMMARY
|
MAB
| 1,954
|
cc-by
| 994
|
stop shopping is een rustverstorend element. De bestaanszekerheid
van een groot aantal middenstanders wordt aangetast. Sommigen
zullen in staat zijn zich aan de ontwikkeling aan te passen. Anderen
zullen ten onder gaan of een minder rendabele bedrijfsvoering als
gevolg zien.
I h t
t h
lijk t b h l
d l
t
d
h t ff stop shopping is een rustverstorend element. De bestaanszekerheid
van een groot aantal middenstanders wordt aangetast. Sommigen
zullen in staat zijn zich aan de ontwikkeling aan te passen. Anderen
zullen ten onder gaan of een minder rendabele bedrijfsvoering als
gevolg zien. I h t
t h
lijk t b h l
d l
t
d
h t ff g
g
Is het maatschappelijk te behalen voordeel groter dan het offer,
dat gebracht wordt? Ongetwijfeld zal deze vraag in de komende
maanden voorwerp van onderzoek zijn. Wij ill
hi
i t
it l
l d
d ht p
j
Wij willen hierop niet vooruit lopen, maar wel de aandacht ves
tigen op de grote economische en sociale winst, die samenhangt met
de grotere gemiddelde bedrijfsgrootte in de detailhandel ........... E
t
b d ijf
t t l
b
i
lijk g
g
j g
Een grotere bedrijfsomvang opent tal van besparingsmogelijk-
heden: meer gelegenheid tot kwantitatieve en kwalitatieve arbeids
verdeling; de mogelijkheid tot differentiatie van de leiding; meer
aandacht voor een doeltreffende bedrijfsadministratie en daarmede
samenhangende een meer verantwoord bedrijfseconomisch beheer.” Het komt ons voor, dat inderdaad de betekenis van deze studiereis en
van dit rapport voor de gehele middenstandspolitiek in ons land van groot
gewicht is. SUMMARY In this article some results are discussed at which a team which visited
the United States under the direction of Drs S. C. Bakkenist, has arrived. The motive that drives the entrepreneur there appears to be not the
maximizing of the profit, but the maximizing of the turnover. This also
explains the attitude of the trade as regards its customers. For the who
lesale trade the general rule is: „think retail”. Th t
h
i d t th
l i
th t th
t i
t t diff g
The team has arrived at the conclusion that the most important diffe
rence as regards the Netherlands groceries is not the self-service but the
one-spot-shopping. This means the attracting of articles from other trades
(meat and vegetables) which are usually sold elsewhere with higher dis
tributive costs. Thus the one-spot-shopping leads to a saving in the dis
tributive costs on the one hand and to an increase of the turnover and
hence of the size of the enterprises on the other hand. With th h l
f l
ith i
b bilit
th f
di t i p
With the help of logarithmic probability paper the frequency-distri
bution of American groceries is compared to Dutch ones. It turns out that
there is a structural difference as regards the enterprises with a great
turnover but not as regards those with a small turnover. Thi i th
h th
i l i ifi
f th
t t il
t g
This is the reason why the social significance of the great retail enter
prises is much more important in the U.S.A. than in the Netherlands. The selling of meat-products and vegetables in the grocery-store has
influenced the place which the specialized shop takes in the U.S.A. It h
b
li itl
t k d i th
t th t th i tit ti
l i p
p
p
It has been explicitly staked in the report that the institutional in
vestors are more interested in foodstuff-enterprises in the U.S.A. than
in the Netherlands. The fact that these enterprises are less subject to
changes in the business cycle constitutes a positive value for investors
in the U.S.A. m a b biz. 206 RÉSUMÉ RÉSUMÉ Cet article passe en revue quelques résultats auxquels est parvenue
la mission d’études qui a visité les Etats-Unis, sous la direction du Drs
S. C. Bakkenist. Le mobile qui pousse les entrepreneurs de ce pays ne
semble pas être l’obtention du bénéfice maximum, mais la réalisation du
plus gros chiffre d’affaires possible. Ceci explique l’attitude des commer
çants à l’égard des clients. La politique du commerce en gros se résume
dans le slogan: „Think retail”. L Mi i
t
i é à l
l i
l diffé
l
l
i g
La Mission est arrivée à la conclusion que la différence la plus im
portante avec les entreprises néerlandaises de comestibles n’est pas dans
l’auto-service, mais plutôt dans ce que l’on appelle one-spot-shopping. Cela veut dire que ces entreprises englobent dans leur vente des articles
variés (viandes, légumes), lesquels sont vendus ailleurs avec des frais
de vente plus élevés. Ainsi ce système conduit à réduire les frais de vente
d’une part, de l’autre à un accroissement du chiffre d’affaires et partant
à une extension des entreprises de comestibles. L
b d f é
d
b ti
d
tibl
é i i
t p
La courbe de fréquence des boutiques de comestibles américaines et
néerlandaises est comparée à l’aide d’un papier logarithmique de proba
bilité et fait ressortir une différence structurelle en ce qui concerne les
entreprises faisant un gros chiffre d’affaires; cette différence n’existe pas
pour les entreprises ayant un petit chiffre d’affaires. U
é
d
t ét t d
h
t
l’i
t
i l d p
p
y
p
Une conséquence de cet état de choses est que l’importance sociale des
grosses entreprises de détail est plus grande aux Etats-Unis qu’aux Pays-
Bas. Les ventes de viande, de charcuterie et de légumes a influé sur la
place tenue par la boutique spécialisée aux Etats-Unis. Le rapport dit
explicitement que les syndicats d’investissements dans ces Etats témoig
nent plus d’intérêt pour l’industrie et le commerce alimentaires qu’aux
Pays-Bas, la faible sensibilité conjoncturelle étant manifestement appré
ciée de manière positive par les fournisseurs de capitaux américains. m a b blz. 207 m a b blz. 207 m a b blz. 207
|
https://openalex.org/W3107625152
|
https://bmcinfectdis.biomedcentral.com/track/pdf/10.1186/s12879-020-05600-8
|
English
| null |
Describing nearly two decades of Chagas disease in Germany and the lessons learned: a retrospective study on screening, detection, diagnosis, and treatment of Trypanosoma cruzi infection from 2000 – 2018
|
BMC infectious diseases
| 2,020
|
cc-by
| 9,294
|
Describing nearly two decades of Chagas
disease in Germany and the lessons
learned: a retrospective study on screening,
detection, diagnosis, and treatment of
Trypanosoma cruzi infection from 2000 –
2018 Jessica Michelle Guggenbühl Noller1,2†, Guenter Froeschl1,2*†
, Philip Eisermann3, Johannes Jochum4,
Stefanie Theuring5, Ingrid Reiter-Owona6, Alfred Lennart Bissinger7, Michael Hoelscher1,8, Abhishek Bakuli1,
Franz-Josef Falkner von Sonnenburg1ˆ, Camilla Rothe1, Gisela Bretzel1, Pedro Albajar-Viñas9, Lise Grout9 and
Michael Pritsch1 Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919
https://doi.org/10.1186/s12879-020-05600-8 Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919
https://doi.org/10.1186/s12879-020-05600-8 Open Access * Correspondence: froeschl@lrz.uni-muenchen.de †Jessica Michelle Guggenbühl Noller and Guenter Froeschl contributed
equally to this work. y
Full list of author information is available at the end of the article Abstract Background: The highly complex and largely neglected Chagas disease (CD) has become a global health problem
due to population movements between Latin America and non-endemic countries, as well as non-vectorial
transmission routes. Data on CD testing and treatment from routine patient care in Germany of almost two
decades was collected and analysed. Methods: German laboratories offering diagnostics for chronic Trypanosoma cruzi (T. cruzi) infection in routine
patient care were identified. All retrievable data on tests performed during the years of 2000–2018 were analysed. Additional clinical information regarding patients diagnosed with CD was collected through questionnaires. (Continued on next page) Background Chagas disease (CD) —a highly complex parasitic disease
caused by Trypanosoma cruzi (T. cruzi) infection— can
lead to chronic morbidity, complications, and premature
death
with
all
associated
socio-economic
effects. Estimates by WHO state that there are between 6 and 7
million infected individuals world-wide, mostly in Latin
American (LA) countries [1]. The initial acute phase of
CD is followed by chronic infection. After a variable
period of latency, about 30–40% of people develop clin-
ical alterations that can be both symptomatic as well as
asymptomatic. Vectorial transmission accounts for most
infections in LA. However, population movements be-
tween endemic and non-endemic areas as well as non-
vectorial transmission routes expanded the geographical
distribution of CD, with some 400,000 infected persons
living all over the world [2]. A total of n = 127,615 immigrants from endemic coun-
tries were registered in Germany in 2018 [11], not taking
into account undocumented migrants or migrants with
European citizenship. Many experience difficulties to ap-
proach the German healthcare system due to legal, eco-
nomic, and linguistic problems among others [12]. The
first German epidemiologic study on CD was published
in 1997, in which n = 100 LA migrants were screened
for CD and n = 2 were diagnosed with CD [13]. Since
then, there has been a lack of published epidemiological
data regarding CD in Germany. In a study where the lit-
erature and official data of six different European coun-
tries, was analysed, the results showed that by 2009, only
4290 of the 68,000–122,000 CD cases that were expected
in Europe were diagnosed and reported. In Germany,
the observed rate was only 0.002%, which according to
the expected prevalence of CD indicated that 99% of the
cases in the immigrant population were undiagnosed,
based on the number of LA migrants [9]. Only one add-
itional study performed —in Munich, Germany— aimed
to find the prevalence of CD in a specific community of
LA migrants between 2013 and 2014, within the city of
Munich. This
study
showed
that
four
of
the
43 The initial period of reported CD infections in Europe
started in 1981 with the first published report: A prob-
able case of congenital transmission in Romania was de-
scribed, that likely took place in 1975 [3]. Then a report
in 1990 described the first known T. cruzi infection in
Switzerland, dated in 1979 [4]. A growing number of
publications on T. © 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 12 Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919 (Continued from previous page) (Continued from previous page) Results: Five German laboratories with diagnostics for T. cruzi infection in routine patient care were identified. Centres in Hamburg and Munich offered two independent serological tests to confirm the CD diagnosis, as
recommended by WHO during the entire time period 2000–2018. Overall, a total of n = 10,728 independent tests
involving n = 5991 individuals were identified with a progressive increase in testing rates over time, only n = 130
(16.0%) of the tested individuals with known nationality came from CD endemic countries. Of all test units
conducted at the included institutes, a total of n = 347/10,728 (3.2%) tests on CD were positive, of which n = 200/
347 (57.6%) were ELISA, n = 133/347 (38.3%) IFT, n = 10/347 (2.9%) PCR, and n = 4/347 (1.2%) RDT. Of the n = 5991
individuals only n = 81 (1.4%) with chronic infection were identified, n = 52 females and n = 28 males. Additional
clinical information could only be collected from n = 47. Conclusion: The results of this study give insight into the deployment of screening, detection, diagnosis, and
treatment of T. cruzi over the last two decades in Germany and existing deficits therein; the creation of guidelines
for Germany could be a step forward to improve the existing gaps. Keywords: Trypanosoma cruzi, Chagas, Germany, Screening, Diagnosis, Treatment In a study performed in 2015, Requena-Mendez and
colleagues estimated an overall prevalence of 4.2%
among the adult LA migrant population in Europe [8]
and that some 94–96% of those infected likely have not
been diagnosed [9]. This lack of reliable epidemiological
data impedes adequate screening, detection, diagnosis,
and eventually treatment. Furthermore, knowledge on
CD is very limited among physicians, although adequate
diagnosis and treatment can potentially cure patients, as
well as prevent chronic morbidity, complications, sudden
cardiac death, and non-vectorial transmission [1]. Thus,
screening of LA migrants for CD in Europe can be con-
sidered cost-effective [10]. Data collection and analysis Laboratories were asked to provide all available data on
CD diagnostics for the years 2000–2018. Data on type,
laboratory number, year, and result of each individual
test performed as well as the demographic data (age, sex,
nationality) of the tested individual were collected in a
pseudonymised way, by extracting available databases. The diagnosis of CD was considered to be established if
(i) two different serological tests were positive, or (ii) a
CD-specific PCR was positive, or (iii) a patient had pre-
viously been diagnosed elsewhere (e.g. abroad). In some
cases, the second serological test for confirmation was
conducted outside the reporting laboratories by forward-
ing samples to an external facility. For all identified CD
cases, the responsible physicians were asked to fill in a
questionnaire, containing more detailed questions about
medical data (see S1 File). In order to diagnose CD it is currently recommended
to perform two different serological tests [16]. Enzyme-
linked immunosorbent assays (ELISA), immunofluores-
cence tests (IFT), as well as rapid diagnostic tests (RDT)
–among others– are currently commercially available in
Germany. Polymerase chain reaction (PCR) can also be
used to monitor patients in certain situations, making it
an effective alternative [17]. Additionally, benznidazole
(BNZ) and nifurtimox are used for etiologic treatment
and despite being included in the Model List of Essential
Medicines [18], are neither licensed nor available on the
market in Germany and obtainable only through WHO
donations [12]. Data quality was analysed throughout the collection
phase and pseudonymised data were entered in a pass-
word secured Excel database. Duplicates were identified
by using the laboratory ID, gender, and date of birth of
the patients. Once all the data were collected and data
quality was assured, the data were irreversibly anonymised
and analysed. Descriptive statistical analyses were per-
formed using the statistical computing software CRAN R
3.6.0 [20] and the corresponding libraries ggplot2 for
graphics, reshape2 for tabulations, and FSA for the tables
with summary statistics. Continuous data means and
standard deviations were calculated. Logistic regression
was performed to obtain the Odds Ratio (OR) and 95%
confidence interval (95% CI) estimates to evaluate risk fac-
tors {(Sex- (Male, Female, Missing), Age (continuous), Na-
tionality (Brazilian/Bolivian, Others, Missing)} for having
positive test results vs. Background cruzi infections in Europe [5] during
the second period were sparked by increasing migration
from LA to Europe, specifically to Spain between 1996
and 2001 [6]. The third period began in 2007 when the
WHO and PAHO convoked a meeting and the presence
of CD in non-endemic countries was officially recog-
nized. In the following year, a meeting in Spain was used
to assess the status of CD in Europe and develop strat-
egies for screening and detection, as well as diagnosis. A
statement during the 6th European Congress on Trop-
ical Medicine and International Health in Verona 2009
considered the evidence sufficient in order to officially
recognize CD as a public health concern in Europe [7]. Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919 Page 3 of 12 Page 3 of 12 participants (9.3%) tested positive for CD. Nonetheless,
there is limited supplementary information regarding the
epidemiological prevalence of CD in Germany, including
the geographical distribution and the specification of dif-
ferent cases —for example, infections through congenital
transmission. Additionally, German guidelines and pol-
icies concerning CD are missing [12]: Presently, there
are no screening measures for non-vectorial transmis-
sion; such as screening of blood products or pregnant
women originating from endemic countries [9, 12, 14]. In order to break these identified barriers for access to
adequate diagnosis and treatment, a multidimensional
approach is needed, far beyond a biomedical one [15]. asked about laboratories offering quality-assured CD
diagnostics for routine patient care in Germany; and (ii)
an extensive search for German laboratories offering CD
diagnostics in patient care was carried out in PubMed
and EBSCO (see also Fig. 1). After establishing contact
with the respective laboratories, information on existing
CD diagnostics as well as consent to participate in this
study were sought out. Data collection and analysis negative test results within the data
observed for Munich (the subgroup from Munich was
chosen due to availability of data for the variables to be in-
cluded in the regression analysis); p < 0.05 was considered
statistically significant. Due to the high proportion of
missing data for the risk factor categories (like nationality
and sex), and very small count of positives we used Fischer
Exact tests to obtain updated OR and 95% CI leaving out
the missing data category. Due to the aforementioned lack of information, educa-
tion, awareness, and severe structural barriers, up to 99%
of CD cases might not be diagnosed in Germany and
only a fraction of those diagnosed might receive ad-
equate care [9]. The objective herein is to describe retro-
spectively available data on testing and treatment of CD
in Germany during nearly two decades. This will hope-
fully fuel discussion on this highly neglected tropical dis-
ease and lay a foundation for the development of
German guidelines as well as improving policies con-
cerning all aspects of CD. German laboratories with CD diagnostics for patient care
during 2000–2018 A total of n = 10,728 individual tests (ELISA, IFT, (q)
PCR, and RDT) on n = 5991 patients could be included
as depicted in Table 1 as well as Fig. 1. The annual fre-
quency of tests and patients increased over time (Fig. 2). Data on a total of n = 2479 negatively tested individuals
in Hamburg during 2000–2009 could only be retrieved
in aggregated form without demographic details. Thus,
these were not included in Table 1 and subsequent
analyses. g
A total of five German laboratories were identified as
having offered serological and/or molecular CD tests for
routine patient care during 2000–2018 (Table 1). All
identified laboratories agreed to participate in this study
(see Fig. 1). All belong to medical centres specialised in
tropical medicine and tests offered were quality con-
trolled according to the respective German regulations
and existing laboratory standards for routine patient
care. Only two centres —one in Hamburg, the other in
Munich— offered the internationally-required two inde-
pendent serological assays for CD diagnosis, throughout
the years of 2000–2018 as required by international
standards [16]. The range of diagnostics available in
Germany changed over the years 2000–2018 (Table 1). A more detailed description on test types as well as pro-
cedures used can be found in Supplement S2. Study design The study protocol was approved by the Institutional
Review Board at the Ludwig-Maximilians-Universität in
Munich, Germany (opinion date 21 December 2018,
number 18–889) and adhered to the most recent version
of the Declaration of Helsinki. It is a retrospective de-
scriptive analysis of retrievable data on CD testing and
cases during routine patient care in Germany and the
years of 2000–2018. Firstly, all laboratories offering
quality-assured serological and/or molecular T. cruzi
diagnostics for routine patient care in Germany were
identified by considering two sources of information: (i)
all centres specialised in tropical medicine listed by the
German Society for Tropical Medicine and Global
Health (DTG) on their webpage [19] were contacted and Double nationality was handled by acknowledging only
the endemic country, as all cases consisted of German
nationality plus one of a CD endemic country. Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919 Page 4 of 12 Fig. 1 Methodological flow diagram Number of diagnostic tests on CD Data on all tested individuals In Table 2, demographic data on all tested individuals is
presented as available. Mean age was 39.1 (SD 16.7)
years at the time of testing and roughly the same pro-
portion of females and males were tested, with females
being slightly younger at the time of testing. A total of
n = 1695 (73.3%) tested females were of childbearing age
(range 15–49 years). Information on nationality was only Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919 Page 5 of 12 Table 1 German centres with CD diagnostics for routine patient care during 2000–2018
Center
City
Type of
test
Test availability
(years)
Number of
retrieved tests
Data availability
(years)
Institute of Tropical Medicine and International Health, Charité
– Universitätsmedizin in Berlin
Berlin
in-house IFT
2000–2010
204
2002–2018
in-house
ELISA
2000–2018
830
Institute of Medical Microbiology, Immunology and
Parasitology, University Hospital Bonn
Bonn
in-house IFT
2000–2010
201
2004–2018
commercial
ELISA
2011–2018
190
commercial
RDT
2000–2010
116
Bernhard Nocht Institute for Tropical Medicine
Hamburg
in-house IFT
2000–2018
2641
2000–2018a
in-house
ELISA
2000–2018
2654
PCRb
2000–2018
200
Division of Infectious Diseases and Tropical Medicine,
University Hospital, LMU Munich
Munich
in-house IFT
2000–2018
1670
2000–2018
in-house
ELISA
2000–2018
1668
PCRb
2013–2018
35
Institute of Tropical Medicine, Medical Department, University
Hospital Tübingen
Tuebingen in-house IFT
2009–2018
319
2009–2018
Total
10,728
CD Chagas disease, ELISA Enzyme-linked immuno-sorbent assay, IFT Immunofluorescence test, PCR Polymerase chain reaction, RDT Rapid diagnostic test
aIndividual positive tests 2000–2018 and negative tests 2010–2018 could be retrieved
bHamburg offered a conventional PCR that was followed up by sequencing of the PCR product if positive, whereas Munich performed a conventional PCR that
was followed up with an independent commercially available qPCR if positive (for details please see Supplement S2) CD Chagas disease, ELISA Enzyme-linked immuno-sorbent assay, IFT Immunofluorescence test, PCR Polymerase chain reaction, RDT Rapid diagnostic test
aIndividual positive tests 2000–2018 and negative tests 2010–2018 could be retrieved
bHamburg offered a conventional PCR that was followed up by sequencing of the PCR product if positive, whereas Munich performed a conventional PCR that
was followed up with an independent commercially available qPCR if positive (for details please see Supplement S2) bHamburg offered a conventional PCR that was followed up by sequencing of the PCR product if positive, whereas Munich performed a conventional PCR that
was followed up with an independent commercially available qPCR if positive (for details please see Supplement S2) Fig. bHamburg offered a conventional PCR that was followed up by sequencing of the PCR product if positive, whereas Munich performed a conventional PCR that
was followed up with an independent commercially available qPCR if positive (for details please see Supplement S2) Data on all tested individuals 2 Retrieved tests for T. cruzi infection per centre in the years 2000-2018 in Germany. Berlin performed in-house ELISA (2000-2018) and in-
house IFT (2000-2010). Bonn performed commercial ELISA (2011-2018), in-house IFT (2000-2010), and commercially available RDT (2000-2010);
Hamburg performed in-house ELISA, in-house IFT, and PCR (2000-2018); Munich performed in-house ELISA (2000-2018), in-house IFT (2000-2018),
and PCR (2013-2018); Tübingen in-house IFT (2009-2018); a*Data could be retrieved for the years 2002-2018; b*Data could be retrieved for the
years 2004-2018; c*Only individual positive tests from 2000-2009 could be retrieved Fig. 2 Retrieved tests for T. cruzi infection per centre in the years 2000-2018 in Germany. Berlin performed in-house ELISA (2000-2018) and in-
house IFT (2000-2010). Bonn performed commercial ELISA (2011-2018), in-house IFT (2000-2010), and commercially available RDT (2000-2010);
Hamburg performed in-house ELISA, in-house IFT, and PCR (2000-2018); Munich performed in-house ELISA (2000-2018), in-house IFT (2000-2018),
and PCR (2013-2018); Tübingen in-house IFT (2009-2018); a*Data could be retrieved for the years 2002-2018; b*Data could be retrieved for the
years 2004-2018; c*Only individual positive tests from 2000-2009 could be retrieved Fig. 2 Retrieved tests for T. cruzi infection per centre in the years 2000-2018 in Germany. Berlin performed in-house ELISA (2000-2018) and in-
house IFT (2000-2010). Bonn performed commercial ELISA (2011-2018), in-house IFT (2000-2010), and commercially available RDT (2000-2010);
Hamburg performed in-house ELISA, in-house IFT, and PCR (2000-2018); Munich performed in-house ELISA (2000-2018), in-house IFT (2000-2018),
and PCR (2013-2018); Tübingen in-house IFT (2009-2018); a*Data could be retrieved for the years 2002-2018; b*Data could be retrieved for the
years 2004-2018; c*Only individual positive tests from 2000-2009 could be retrieved Guggenbühl Noller et al. Data on all tested individuals BMC Infectious Diseases (2020) 20:919 Page 6 of 12 Table 2 Demographic data of individuals tested for Trypanosoma cruzi infection in Germany and the years 2000–2018
Sex
Female
n = 2389/5991
39.9%
Male
n = 2365/5991
39.5%
Unknown
n = 1237/5991
20.6%
All
n = 5991
100.0%
Age at time of testing
Data on age available on 2312/
2389 (96.8%)
n = 2312
Data on age available on 2322/
2365 (98.2%)
n = 2322
Data on age available
on
277/1237 (22.4%)
n = 277
Data on age available on 4911/
5991 (82.0%)
n = 4911
Mean (SD)
37.4 years (SD = 16.0)
41.2 years (SD = 16.6)
35.4 years (SD = 21.3)
39.1 years (SD = 16.7)
≤14
78 (3.4%)
87 (3.7%)
67 (24.2%)
232 (4·7%)
15–49
1695 (73.3%)
1474 (63.5%)
146 (52.7%)
3315 (67.5%)
≥50
539 (23.3%)
761 (32.8%)
64 (23.1%)
1364 (27.8%)
Nationality
Data on nationality available on
417/2389 (17.5%) n = 417
Data on nationality available on
378/2365 (16.0%) n = 378
Data on nationality
available on
19/1237 (1.5%) n = 19
Data on nationality available on
814/5991 (13.6%) n = 814
Argentina
7 (1.7%)
0
0
7 (0.9%)
Bolivia
18 (4.3%)
13 (3.4%)
0
31 (3.8%)
Brazil
24 (5.8%)
9 (2.4%)
3 (15.8%)
36 (4.4%)
Colombia
11 (2.6%)
2 (0.5%)
0
13 (1.6%)
Costa Rica
1 (0.2%)
0
0
1 (0.1%)
Ecuador
4 (1.0%)
4 (1.1%)
0
8 (1.0%)
El Salvador
1 (0.2%)
0
0
1 (0.1%)
Guatemala
1 (0.2%)
0
0
1 (0.1%)
Mexico
5 (1.2%)
0
0
5 (0.6%)
Nicaragua
1 (0.2%)
0
0
1 (0.1%)
Panama
0
1 (0.3%)
0
1 (0.1%)
Paraguay
5 (1.2%)
2 (0.5%)
0
7 (0.9%)
Peru
6 (1.4%)
6 (1.6%)
0
12 (1.5%)
Venezuela
4 (1.0%)
1 (0.3%)
1 (5.3%)
6 (0.7%)
Germany
297 (71.2%)
318 (84.1%)
12 (63.2%)
627 (77.0%)
Other non-endemic
countries
32 (7.7%)
22 (5.8%)
3 (15.8%)
57 (7.0%)
SD Standard deviation SD Standard deviation For all n = 81 CD patients identified, treating physi-
cians were asked to provide additional information via
questionnaires. A total of n = 47 (58.0%) were returned. Based on the returned questionnaire data, n = 15/43
(34.9%) CD cases were diagnosed for the first time. Of
all n = 29 CD patients for whom information on treat-
ment was provided, a total of n = 16 (55.2%) were identi-
fied not to have received etiologic treatment. Data on all tested individuals For n = 7
patients without etiologic treatment (46.7%), physicians
stated justifications that were in accordance with current
recommendations and included advanced age, refusal by
patient, and severe organ dysfunction. In n = 8 patients
without etiologic treatment (53.3%), physicians stated
justifications that were not in accordance with current
recommendations and included “no symptoms by the
patient,” “no sign of active CD,” “no proof of chronic
CD,” “negative PCR result,” and “chronic case of CD.” A
total of n = 35/80 (43.8%) patients were females of available in 13.6% of all tested individuals. Of these, n =
130 individuals (16.0%) were from 14 endemic countries,
with Brazil (n = 36), Bolivia (n = 31), Colombia (n = 13),
Peru (n = 12), Ecuador (n = 8), Argentina (n = 7), and
Venezuela (n = 6) being the most frequent nationalities
mentioned. Data on patients diagnosed with CD Of all test units conducted at the included institutes, a
total of n = 347/10,728 (3.2%) tests on CD were positive,
of which there were n = 200/347 (57.6%) ELISA, n =
133/347 (38.3%) IFT, n = 10/347 (2.9%) PCR, and n = 4/
347 (1.2%) RDT. From an individual patient perspective,
of all n = 5991 included individuals, a total of n = 81
(1.4%) CD patients could be identified (Table 3). Of the
n = 81 identified CD patients all had positive serology, in
addition in 10 patients there was an additional positive
PCR result. Guggenbühl Noller et al. Data on patients diagnosed with CD BMC Infectious Diseases (2020) 20:919 Page 8 of 12 Table 3 Characteristics of patients diagnosed with CD, Germany, 2000–2018 (Continued)
Sexa
Female
n = 52/81
(64.2%)
Male
n = 28/81
(34.6%)
All
n = 81
(100.0%)
Stopped treatment
3 (37.5%)
1 (100%)
4 (44.4%)
Side effects
Available on n = 3/10
treatments
(30.0%)
Available on n = 1/3
treatments
(33.3%)
Available on n = 4/13 treatments
(30.8%)
Yes
3 (100%)
1 (100%)
4 (100%)
No
0
0
0
Reason for no treatment
Available on n = 11/12 (91.7%)
Available on n = 4/4
(100%)
Available on n = 15/16 (93.8%)
Recommendations-based reason
5 (45.5%)
2 (50.0%)
7 (46.7%)
Non-recommendations-based
reason
6 (54.5%)
2 (50.0%)
8 (53.3%)
Follow-up
Available on n = 13/52 (25.0%)
Available on n = 4/28 (14.3%)
Available on n = 17/81 (21.0%)
> 12 months
7 (53.8%)
3 (75.0%)
10 (58.8%)
≤12 months
4 (30.8%)
1 (25.0%)
5 (29.4%)
No follow-up
2 (15.4%)
0
2 (11.8%)
ain one CD case none of the data was available; CD Chagas disease, NA Not available, SD Standard deviation Table 3 Characteristics of patients diagnosed with CD, Germany, 2000–2018 (Continued) lable; CD Chagas disease, NA Not available, SD Standard deviation childbearing age and the most prevalent nationality
among those with respective information available was
Bolivian n = 20/35 (57.1%). was pioneering work in the country. Nevertheless, it has
to be stated that 20 years later there is still a precarious
lack of standardized policies in this regard. Previous
studies named the absence of clear recommendations as
well as standardisation in respect of screening, detection,
diagnosis, and treatment as an important risk factor for
inadequate care of individuals at risk [21, 22]. For the subgroup of the data collected in Munich
(n = 1596) a logistic regression was conducted for the vari-
ables sex, age and nationality, as these data were readily
available at the Munich site. The analysis revealed that
males were significantly less frequently positive than fe-
males (OR (95%CI) = 0.17 (0.03–0.60) (Logistic regres-
sion), −0.17 (0.02–0.74) (Fisher Exact)). Similarly, people
with Brazilian/Bolivian nationality were significantly
more often having a positive test result than other
nationalities
(OR
(95%CI) = 273.48
(51.68–5059.88)
(Logistic regression), 264.91(37.35–10,678.77) (Fisher
Exact). Finally, for every unit increase in age the
probability of being positive to the test significantly
increased by 1.03 (1.01–1.06). Data on patients diagnosed with CD The data presented here is likely patchy; some smaller
and/or private laboratories performing commercially
available CD diagnostics during patient care might have
been missed in this study. Furthermore, the identifica-
tion of individual patients could not be performed with
absolute reliability due to the pseudonymised nature of
retrieved data. Although data was cleaned and controlled
for quality, likely not all duplicate cases could be de-
tected. For diverse reasons (including water damages on
as well as disposal of paper-based patient records or
technical problems with aged laboratory information
systems leading to data loss) not all data could be re-
trieved. This proves the difficulty of digitalization and
data availability/storage. In Germany, a total of n = 127,
615 migrants from endemic countries have been regis-
tered in 2018 [11]. However, when reflecting on preva-
lence and testing frequencies, a presumably significant
number of undocumented migrants as well as migrants
with European citizenship that originated from endemic
countries have to be taken into account. According to
the available data in this study, a total of n = 5991 tested
patients could be identified in Germany during the time
period 2000–2018, whereas only n = 130 (16.0%) of
tested individuals with known nationality were from en-
demic countries; thus, all numbers presented have to be
interpreted carefully. Data on patients diagnosed with CD BMC Infectious Diseases (2020) 20:919 Page 7 of 12 s diagnosed with CD, Germany, 2000–2018
Female
n = 52/81
(64.2%)
Male
n = 28/81
(34.6%)
All
n = 81
(100.0%)
43.3 years (SD = 3.8)
46.1 years (SD = 6.9)
44.0 years (SD = 3.4)
0
1 (3.6%)
1 (1.2%)
35 (67.3%)
16 (57.1%)
51 (63.0%)
17 (32.7%)
11 (39.3%)
28 (34.6%)
0
0
1 (1.2%)
Available on n = 26/52 (50.0%)
Available on n = 9/28 (32.1%)
Available on n = 35/81 (43.2%)
13 (50.0%)
7 (77.8%)
20 (57.1%)
0
2 (22.2%)
2 (5.7%)
5 (19.2%)
0
5 (14.3%)
2 (7.7%)
0
2 (5.7%)
3 (11.5%)
0
3 (8.6%)
2 (7.7%)
0
2 (5.7%)
1 (3.8%)
0
1 (2.9%)
Available on n = 33/52 (63.5%)
Available on n = 12/28 (42.9%)
Available on n = 45/81 (55.6%)
17 (51.5%)
7 (58.3%)
24 (53.3%)
7 (21.2%)
2 (16.7%)
9 (20.0%)
9 (27.3%)
3 (25.0%)
12 (26.7%)
Available on n = 23/52 (44.2%)
Available on n = 9/28 (32.1%)
Available on n = 32/81 (39.5%)
0
2 (22.2%)
2 (6.3%)
9 (39.1%)
2 (22.2%)
11 (34.4%)
3 (13.0%)
0
3 (9.4%)
1 (4.3%)
2 (22.2%)
3 (9.4%)
10 (43.5%)
3 (33.3%)
13 (40.6%)
Available on n = 30/52 (57.7%)
Available on n = 13/28 (46.4%)
Available on n = 43/81 (53.1%)
10 (33.3%)
5 (38.5%)
15 (34.9%)
20 (66.7%)
8 (61.5%)
28 (65.1%)
Available on n = 18/52 (34.6%)
Available on n = 5/28 (17.9%)
Available on n = 23/81 (28.4%)
16 (88.9%)
3 (60.0%)
19 (82.6%)
0
1 (20.0%)
1 (4.3%)
2 (11.1%)
1 (20.0%)
3 (13.0%)
Available on n = 18/52 (34.6%)
Available on n = 9/28 (32.1%)
Available on n = 27/81 (33.3%)
16 (88.9%)
6 (66.7%)
22 (81.5%)
2 (11.1%)
2 (22.2%)
4 (14.8%)
0
1 (11.1%)
1 (3.7%)
Available on n = 22/52
(42.3%)
Available on n = 7/28
(25.0%)
Available on n = 29/81
(35.8%)
8 (36.4%)
3 (42.9%)
11 (37.9%)
2 (9.1%)
0
2 (6.9%)
12 (54.5%)
4 (57.1%)
16 (55.2%)
Available on n = 8/10 (80.0%)
Available on n = 1/3
treatments
(33.3%)
Available on n = 9/13 treatments
(69.2%)
5 (62.5%)
0
5 (55.6%) Table 3 Characteristics of patients diagnosed with CD, Germany, 2000–2018
Sexa
Female
n = 52/81
(64.2%)
Male
n = 28/81
(34.6%)
All
n = 81
(100.0%)
Age in years at the time of testing
Mean (SD)
43.3 years (SD = 3.8)
46.1 years (SD = 6.9)
44.0 years (SD = 3.4)
≤14
0
1 (3.6%)
1 (1.2%)
15–49
35 (67.3%)
16 (57.1%)
51 (63.0%)
≥50
17 (32.7%)
11 (39.3%)
28 (34.6%)
NA
0
0
1 (1.2%)
Nationality
Available on n = 26/52 (50.0%)
Available on n = 9/28 (32.1%)
Available on n = 35/81 (43.2%)
Bolivia
13 (50.0%)
7 (77.8%)
20 (57.1%)
Germany
0
2 (22.2%)
2 (5.7%)
Brazil
5 (19.2%)
0
5 (14.3%)
Paraguay
2 (7.7%)
0
2 (5.7%)
Argentina
3 (11.5%)
0
3 (8.6%)
Peru
2 (7.7%)
0
2 (5.7%)
South America
1 (3.8%)
0
1 (2.9%)
Reason for testing
Available on n = 33/52 (63.5%)
Available on n = 12/28 (42.9%)
Available on n = 45/81 (55.6%)
Known CD
17 (51.5%)
7 (58.3%)
24 (53.3%)
Endemic national
7 (21.2%)
2 (16.7%)
9 (20.0%)
Other
9 (27.3%)
3 (25.0%)
12 (26.7%)
Symptoms
Available on n = 23/52 (44.2%)
Available on n = 9/28 (32.1%)
Available on n = 32/81 (39.5%)
Fatigue
0
2 (22.2%)
2 (6.3%)
Gastrointestinal
9 (39.1%)
2 (22.2%)
11 (34.4%)
Cardiac
3 (13.0%)
0
3 (9.4%)
Other
1 (4.3%)
2 (22.2%)
3 (9.4%)
No symptoms
10 (43.5%)
3 (33.3%)
13 (40.6%)
Initial diagnosis of CD
Available on n = 30/52 (57.7%)
Available on n = 13/28 (46.4%)
Available on n = 43/81 (53.1%)
Yes
10 (33.3%)
5 (38.5%)
15 (34.9%)
No
20 (66.7%)
8 (61.5%)
28 (65.1%)
Echocardiography
Available on n = 18/52 (34.6%)
Available on n = 5/28 (17.9%)
Available on n = 23/81 (28.4%)
Normal
16 (88.9%)
3 (60.0%)
19 (82.6%)
Abnormal
0
1 (20.0%)
1 (4.3%)
Not performed
2 (11.1%)
1 (20.0%)
3 (13.0%)
Electrocardiography
Available on n = 18/52 (34.6%)
Available on n = 9/28 (32.1%)
Available on n = 27/81 (33.3%)
Normal
16 (88.9%)
6 (66.7%)
22 (81.5%)
Abnormal
2 (11.1%)
2 (22.2%)
4 (14.8%)
Not performed
0
1 (11.1%)
1 (3.7%)
Etiologic treatment
Available on n = 22/52
(42.3%)
Available on n = 7/28
(25.0%)
Available on n = 29/81
(35.8%)
Benznidazole
8 (36.4%)
3 (42.9%)
11 (37.9%)
Nifurtimox
2 (9.1%)
0
2 (6.9%)
No treatment
12 (54.5%)
4 (57.1%)
16 (55.2%) Table 3 Characteristics of patients diagnosed with CD, Germany, 2000–2018 0 Guggenbühl Noller et al. Discussion It is therefore difficult to
compare
our
results
to
previous
European
studies
[28–31]. Of all n = 130 individuals tested that are known
to be LA migrants, a total of n = 35 (26.9%) tested posi-
tive for T. cruzi infection. Other studies performed in
Europe, focused exclusively on the LA population and
on different subgroups. For instance, in a study per-
formed in Switzerland a prevalence of 12.8% CD was
found, however the screening only focused on Latin
American adults [32]. Additional data from the risk factor analysis for the
Munich data demonstrated that men were less likely to
be positive for Chagas when compared to women. Also,
the risk for being positive increases with increased age
and nationality being in the Chagas hotspots such as
Brazil and Bolivia compared to other places. Many CD
studies suggest different results regarding the association
between CD and sex. Nevertheless, it has been shown,
that women are not necessarily more prone to be in-
fected with CD, but that they are screened more often
and hence CD infections could potentially be found
more often in women than in men. This mainly occurs
because of the different screening programs that have
been implemented for women at a fertile age or for
pregnant women, both in LA countries and in European
countries like Switzerland, Spain, and Italy [33]. In
regards to the association of age with CD, other studies
have suggested that CD vectorial transmission in en-
demic countries has decreased over the past 20 years. In-
dividuals that are now tested positive in European
countries were probably infected a long time ago before
migrating and are now becoming symptomatic, or have
been previously diagnosed in their home countries [31]. The association with nationality and CD, has been dem-
onstrated in many studies. For instance, based on sero-
positivity studies conducted on LA migrants in Europe,
Bolivians had the highest prevalence of CD (18.2%) when
compared with other endemic countries like El Salvador,
or Argentina [34]. This is also dependent on the current
rates of infection in the endemic countries, for which
Bolivia has been shown to be higher [1]. The cumulative quantity of tests performed that could
be retrieved for this study showed an increase over time,
especially during the last 5 years. Discussion This study represents the first comprehensive descrip-
tion of screening, detection, diagnosis, and treatment of
CD in Germany. Of the five centres identified to
perform CD testing for routine patient care, only the
centres in Hamburg and in Munich offered two inde-
pendent serological assays during the complete time
period 2000–2018 as required by WHO for diagnosis. The centre in Bonn offered two independent tests dur-
ing the interval of 2000–2010 and thus most German
centres were only able to perform screening measures, if
current recommendations are considered [16]. Taking
into consideration that T. cruzi infections were relatively
new to Germany in the beginning of the 2000’s as de-
tailed in the introduction section, laboratory diagnosis Page 9 of 12 Page 9 of 12 Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919 Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919 Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919 Due to missing information, it is difficult to draw
conclusions on the distribution of CD testing performed
between German expatriates/travellers, people originat-
ing from LA countries with German nationality, or LA
migrants. A previous study has calculated an overall
prevalence of 4.2% among LA migrants in Europe [8]. When taking into account the number of registered mi-
grants, undocumented migrants as well as LA migrants
with European citizenship in Germany, and signs that
potentially most tests in this study have been performed
on German expatriates/travellers, access to screening,
detection, diagnosis, and eventually medical care appears
to be alarmingly low for people at highest risk for CD. This has also been mentioned as a problem in studies
performed in other European countries. The definition
of “migrant,” which is not universally defined, and the
lack of information about participants’ country of birth
negatively influences the collection of data regarding CD
in European countries. In order to assess the actual
prevalence of CD, the number of undocumented mi-
grants and the number of LA migrants with European
citizenship has to be included. Most European countries
lack databases that facilitate the viewing of such infor-
mation [23]. although it would correspond to a CD prevalence of
1.4% among all individuals tested, it includes already
previously diagnosed CD patients (n = 28/43, 65.1%; de-
nominator is patients for whom data on initial diagnosis
was given) actively seeking follow-up as well as many
German expatriates/travellers. Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919 Discussion A distinct increase in
tests performed in the years 2014–2018 might possibly
be explained by migratory patterns of LA migrants to
Germany: an increase of immigration could also be ob-
served during this time period, specifically for females
[24]. This could partly be caused by the economic crisis
in Spain 2010–2015. Spain is the European country with
the largest proportion of LA migrants and the largest
number of reported CD cases [9]. With this, it plays a
major role in the LA migrant flow and experienced in-
creased emigration during the years of the crisis [25]. According to the national statistical institute in Spain,
there was an increased number of LA migrants moving
to Germany with a peak in 2013 and a total of n = 25,
397 LA emigrants from Spain respectively [26]. How-
ever, this dynamic might partly be caused by the fact
that older data were more difficult to be retrieved at
some of the centres in this study leading to potential loss
of data. Additionally, increased activities to raise aware-
ness and to actively detect CD in Germany could also
have contributed to the increase [12]. Similar trends can
be observed, when comparing mean ages of the LA mi-
grant population in Germany with the mean ages of the
individuals included in this study. In our study, mean
age was 39.1 years (SD = 16.7) compared to the mean
age of the German population being 45.9 in 2019 [27]. Pregnancy was not mentioned as a reason for testing,
even though n = 35/80 (43.8%) of detected patients were
females of childbearing age. Of the n = 29 patients, infor-
mation was available concerning etiologic treatment: only
n = 13 (44.8%) of these received either benznidazole or
nifurtimox. Reasons for not etiologically treating patients
mentioned by the responsible physicians were frequently
not in line with contemporary recommendations. Previous A total of n = 81 CD patients was identified in this
study. Again, this number has to be interpreted carefully; Page 10 of 12 Page 10 of 12 Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919 current practices in terms of screening, diagnosis, and
treatment of CD in Germany taking into account that
the time period that was included was only the begin-
ning in the development of knowledge of CD in this
country. Discussion Screening should also be implemented in blood donors,
for example in France a systematic screening of all blood
donors that were born or lived in CD endemic countries
was implemented [39]; policies that include this kind of
screening could be cost-effective [10]. Due to the previ-
ously mentioned reasons, existing efforts to create Ger-
man guidelines on screening, detection, diagnosis, and
treatment of T. cruzi infection should be materialized,
with the ultimate goal to improve access and quality of
care regarding this highly neglected disease. studies estimated that globally only 1% of people affected
with CD receive etiological treatment [35]. Even in a
country like Germany with substantial resources in the
health care sector, these estimations don’t seem to be con-
tradicted. BNZ and nifurtimox are neither registered nor
available in Germany, hence they have to be obtained else-
where (e.g. WHO) and used unlicensed. This certainly
could contribute to low deployment rates. In
Germany,
blood
donors
currently
are
being
screened for CD by asking whether they are suffering
from a parasitic infection (and sometimes specifically for
CD) and some might be excluded when originating from
for malaria endemic areas [12, 36]. At the same time, it
should be considered that 94–96% of T. cruzi infected
individuals from endemic countries are unaware of their
infection status [9, 37]. In comparison, countries like
Spain or USA have implemented serological screening
measures in the transfusional/transplantational sector by
law [1]. There is no routine screening performed on
pregnant women from endemic countries [9, 37]. It was
already stated by WHO in 2009 that women of fertile
age should be a target group for CD screening in order
to prevent vertical transmission of T. cruzi infections [7]. All in all, prevention of non-vectorial transmission of T. cruzi infection seems ineffective in Germany. These are
important points to consider for future policy changes. Several previous studies looked at personal and struc-
tural barriers to access of healthcare in Germany and in
Europe, also with regard to CD [12, 38]. As an example,
migrants from CD endemic countries without a valid resi-
dence permit and without health insurance are known to
have the highest CD prevalence rates while their access to
healthcare in Germany is outmost limited [12]. Supplementary information Supplementary information
The online version contains supplementary material available at https://doi. org/10.1186/s12879-020-05600-8. pp
y
The online version contains supplementary material available at https://doi. org/10.1186/s12879-020-05600-8. pp
y
The online version contains supplementary material available at https://doi. org/10.1186/s12879-020-05600-8. pp
y
The online version contains suppleme
org/10.1186/s12879-020-05600-8. Additional file 1: S1 File. English translation of the questionnaire for
physicians treating patients with Chagas disease. Additional file 1: S1 File. English translation of the questionnaire for
physicians treating patients with Chagas disease. Additional file 2: S2 Table. Detailed description of tests and
procedures in each institution. Discussion It is clear that the way forward should include
an increase in training for certain groups of physicians
(e.g. general practitioners, gynaecologists, paediatricians,
and cardiologists) and Latin American communities, as
well as the involvement of CD patient groups. Informa-
tion campaigns should be developed, in order to directly
approach members of the Latin American communities
—for example in cultural events and via NGO’s that are
working with migrants and/or churches. In addition,
easy and reliable access to healthcare especially needs to
be facilitated for undocumented migrants in order to
render control measures effective. Additionally, system-
atic screening of pregnant women who come from CD
endemic countries should be implemented, following the
response in countries like Spain, Italy, and Switzerland. Screening should also be implemented in blood donors,
for example in France a systematic screening of all blood
donors that were born or lived in CD endemic countries
was implemented [39]; policies that include this kind of
screening could be cost-effective [10]. Due to the previ-
ously mentioned reasons, existing efforts to create Ger-
man guidelines on screening, detection, diagnosis, and
treatment of T. cruzi infection should be materialized,
with the ultimate goal to improve access and quality of
care regarding this highly neglected disease. current practices in terms of screening, diagnosis, and
treatment of CD in Germany taking into account that
the time period that was included was only the begin-
ning in the development of knowledge of CD in this
country. It is clear that the way forward should include
an increase in training for certain groups of physicians
(e.g. general practitioners, gynaecologists, paediatricians,
and cardiologists) and Latin American communities, as
well as the involvement of CD patient groups. Informa-
tion campaigns should be developed, in order to directly
approach members of the Latin American communities
—for example in cultural events and via NGO’s that are
working with migrants and/or churches. In addition,
easy and reliable access to healthcare especially needs to
be facilitated for undocumented migrants in order to
render control measures effective. Additionally, system-
atic screening of pregnant women who come from CD
endemic countries should be implemented, following the
response in countries like Spain, Italy, and Switzerland. Conclusions Data on Chagas disease is patchy in Germany, and sys-
tematic screening of risk groups or notification mecha-
nisms are lacking. Over the course of the studied time
period, the different included centers disposed of diver-
ging diagnostic means, rendering comparison of the col-
lected data difficult. Coherent national guidelines are
urgently missing for screening, diagnosis and treatment
of this potentially fatal parasitic infection. Several limitations of retrospective observation have
already been mentioned —notably the absence of clear
criteria for testing, differences in diagnostic algorithms
across the different institutes, the large amount of miss-
ing information, and the non-respect of the full diagno-
sis algorithm. Despite the aforementioned limitations,
this study highlights that even though Germany per-
formed a pioneering implementation of screening, detec-
tion, diagnosis, and treatment of T. cruzi infections in
regard to the knowledge that was available during the
first period of the nearly two decades included in this
study, currently there seems to be only a small percent-
age of individuals at risk of T. cruzi infection receiving
adequate care. Previous studies show that a lack of
guidelines is an important risk factor for inadequate care
[21, 22] and regard the implementation of a screening
programme for T. cruzi infection among Latin American
adults living in Europe a cost-effective strategy [10]. A
prospective survey will be needed in the future to have a
better estimation of the prevalence of CD in Germany. This study was rather aiming at exploring past and Supplementary information
h
l
l Funding 10. Requena-Méndez A, Bussion S, Aldasoro E, Jackson Y, Angheben A, Moore
D, et al. Cost-effectiveness of Chagas disease screening in Latin American
migrants at primary health-care centres in Europe: a Markov model analysis. Lancet Glob Health. 2017;5:e439–47. https://doi.org/10.1016/S2214-
109X(17)30073-6. 10. Requena-Méndez A, Bussion S, Aldasoro E, Jackson Y, Angheben A, Moore
D, et al. Cost-effectiveness of Chagas disease screening in Latin American
migrants at primary health-care centres in Europe: a Markov model analysis. Lancet Glob Health. 2017;5:e439–47. https://doi.org/10.1016/S2214-
109X(17)30073-6. This study did not receive external funding. Open Access funding enabled
and organized by Projekt DEAL. Abbreviations Abbreviations
BNZ: Benznidazole; DTG: German Society for Tropical Medicine and Global
Health; ELISA: Enzyme Linked Immunosorbent Assay;
IFT: Immunofluorescence Tests; PCR: Polymerase Chain Reaction; RDT: Rapid
Diagnostic Testing Page 11 of 12 Page 11 of 12 Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919 Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919 Availability of data and materials The datasets generated and/or analysed during the current study are not
publicly available due to data ownership by the different involved
institutions, but are available from the corresponding author on reasonable
request. 11. DESTATIS Statistisches Bundesamt. Bevölkerung und Erwerbstätigkeit; c2018. Available from: https://www.destatis.de/DE/Service/Bibliothek/_
publikationen-fachserienliste-1.html [cited 2019 Aug]. institutions, but are available from the corresponding author on reasonable
request. 12. Navarro M, Berens-Riha N, Hohnerlein S, Seiringer P, von Saldern C, Garcia S,
et al. Cross-sectional, descriptive study of Chagas disease among citizens of
Bolivian origin living in Munich, Germany. BMJ Open. 2017;7:e013960. https://doi.org/10.1136/bmjopen-2016-013960. Received: 28 July 2020 Accepted: 9 November 2020 Received: 28 July 2020 Accepted: 9 November 2020 Received: 28 July 2020 Accepted: 9 November 2020 22. Manne JM, Snively CS, Ramsey JM, Salgado MO, Bärnighausen T, Reich
MR. Barriers to treatment access for Chagas disease in Mexico. PLoS
Negl Trop Dis. 2013 Oct;7:e2488. https://doi.org/10.1371/journal.pntd. 0002488. Acknowledgements
ff
f 5. Albajar-Viñas P, Jannin J. The hidden Chagas disease burden in Europe. Euro
Surveill. 2011;22:16. https://doi.org/10.2807/ese.16.38.19975-en. 5. Albajar-Viñas P, Jannin J. The hidden Chagas disease burden in Europe. Euro
Surveill. 2011;22:16. https://doi.org/10.2807/ese.16.38.19975-en. We thank the staff of all participating centres for providing us with data as
well as helpful advice. We would also like to thank all physicians who filled
out questionnaires on CD patients. 6. International Organization for Migration. Migration from Latin America to
Europe: Trends and Policy challenges; c2004. Available from: https://
publications.iom.int/system/files/pdf/mrs_16.pdf [cited 2020 Feb]. 6. International Organization for Migration. Migration from Latin America to
Europe: Trends and Policy challenges; c2004. Available from: https://
publications.iom.int/system/files/pdf/mrs_16.pdf [cited 2020 Feb]. p
g
The authors declare that they have no competing interests. 15. WHO. Control of Chagas disease: second report of the WHO Expert
Committee. Geneva: WHO; 2002. p. 109. Control of Chagas disease. 15. WHO. Control of Chagas disease: second report of the WHO Expert
Committee. Geneva: WHO; 2002. p. 109. Control of Chagas disease. Authors’ contributions 7. WHO. Report of WHO Informal Consultation (jointly organized by WHO
headquarters and the WHO regional office for Europe). 2009. 7. WHO. Report of WHO Informal Consultation (jointly organized by WHO
headquarters and the WHO regional office for Europe). 2009. GF, JMGN and MP designed the study. Data collection was performed or
facilitated by FFVS, GF, IRO, JJ, JMGN, MP, PE, ALB, MH, CR, GB and ST. AB,
JMGN, LG, and MP analysed the data. PAV provided helpful advice. GF, JMGN
and MP drafted the manuscript. All authors contributed to, critically
reviewed, and accepted the final manuscript version. The author(s) read and
approved the final manuscript. GF, JMGN and MP designed the study. Data collection was performed or
facilitated by FFVS, GF, IRO, JJ, JMGN, MP, PE, ALB, MH, CR, GB and ST. AB,
JMGN, LG, and MP analysed the data. PAV provided helpful advice. GF, JMGN
and MP drafted the manuscript. All authors contributed to, critically 8. Requena-Méndez A, Aldasoro E, de Lazzari E, Sicuri E, Brown M, Moore DAJ,
et al. Prevalence of Chagas disease in Latin-American migrants living in
Europe: a systematic review and meta-analysis. PLoS Negl Trop Dis. 2015;9:
e0003540. https://doi.org/10.1371/journal.pntd.0003540. 8. Requena-Méndez A, Aldasoro E, de Lazzari E, Sicuri E, Brown M, Moore DAJ,
et al. Prevalence of Chagas disease in Latin-American migrants living in
Europe: a systematic review and meta-analysis. PLoS Negl Trop Dis. 2015;9:
e0003540. https://doi.org/10.1371/journal.pntd.0003540. reviewed, and accepted the final manuscript version. The author(s) read and
approved the final manuscript. 9. Basile L, Jansá JM, Carlier Y, Salamanca DD, Angheben A, Bartoloni A, et al. Chagas disease in European countries: the challenge of a surveillance
system. Eurosurveillance. 2011;16. https://doi.org/10.2807/ese.16.37.19968-en. 9. Basile L, Jansá JM, Carlier Y, Salamanca DD, Angheben A, Bartoloni A, et al. Chagas disease in European countries: the challenge of a surveillance
system. Eurosurveillance. 2011;16. https://doi.org/10.2807/ese.16.37.19968-en. Competing interests
The authors declare that they have no competing interests. Competing interests
The authors declare that they have no competing interests. Author details
1 16. Organización Panamericana de la Salud. Guidelines for the Diagnosis and
Treatment of Chagas Disease; c2018. Available from: http://iris.paho.org/
xmlui/bitstream/handle/123456789/49653/9789275320433_spa. pdf?sequence=9&isAllowed=y [cited 2020 Nov 2]. 1Division of Infectious Diseases and Tropical Medicine, University Hospital,
LMU Munich, Munich, Germany. 2Center for International Health, University
Hospital, LMU Munich, Munich, Germany. 3National Reference Centre for
Tropical Pathogens, Bernhard Nocht Institute for Tropical Medicine,
Hamburg, Germany. 4Department of Tropical Medicine, Bernhard Nocht
Institute for Tropical Medicine & I. Department of Medicine, University
Medical Centre Hamburg-Eppendorf, Hamburg, Germany. 5Institute of
Tropical Medicine and International Health, Charité –Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität
Berlin, and Berlin Institute of Health, Berlin, Germany. 6Institute of Medical
Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn,
Germany. 7Institute of Tropical Medicine, Medical Department, University
Hospital Tübingen, Tübingen, Germany. 8German Center for Infection
Research (DZIF), Partner Site Munich, Munich, Germany. 9Department of
Control of Neglected Tropical Diseases, World Health Organization, Geneva,
Switzerland. 17. Seiringer P, Pritsch M, Flores-Chavez M, Marchisio E, Helfrich K, Mengele C,
et al. Comparison of four PCR methods for efficient detection of
Trypanosoma cruzi in routine diagnostics. Diagn Microbiol Infect Dis. 2017;
88:225–32. https://doi.org/10.1016/j.diagmicrobio.2017.04.003. 18. WHO. WHO Model List of Essential Medicines; c2017. Available from: https://
www.who.int/selection_medicines/list/en/ [cited 2019 Dec]. 19. Tropenmedizinische Institutionen. Deutsche Gesellschaft für Tropenmedizin
und Globale Gesundheit e.V; c2019. Available from: https://www.dtg.org/
liste-tropenmedizinischer-institutionen.html [cited 2019 Aug]. 20. The R Foundation. The R Project for Statistical Computing; c2020. Available
from: https://www.r-project.org/ [cited 2019 Aug]. 21. Pane S, Giancola ML, Piselli P, Corpolongo A, Repetto E, Bellagamba R, et al. Serological evaluation for Chagas disease in migrants from Latin American
countries resident in Rome, Italy. BMC Infect Dis. 2018;18:212. https://doi. org/10.1186/s12879-018-3118-5. Ethics approval and consent to participate The study protocol was approved by the Institutional Review Board at the
Ludwig-Maximilians-Universität in Munich, Germany (opinion date 21 De-
cember 2018, number 18–889) and adhered to the most recent version of
the Declaration of Helsinki. Adminstrative permissions to access raw data
were not required. Data were irreversibly anonymised prior to analysis. 13. Frank M, Hegenscheid B, Janitschke K, Weinke T. Prevalence and
epidemiological significance of Trypanosoma cruzi infection among latin
american immigrants in Berlin, Germany. Infection. 1997;25:355–8. https://
doi.org/10.1007/BF01740817. 13. Frank M, Hegenscheid B, Janitschke K, Weinke T. Prevalence and
epidemiological significance of Trypanosoma cruzi infection among latin
american immigrants in Berlin, Germany. Infection. 1997;25:355–8. https://
doi.org/10.1007/BF01740817. 14. Bundesärztekammer. Richtlinie zur Gewinnung von Blut und
Blutbestandteilen und zur Anwendung von Blutprodukten (Richtlinie
Hämotherapie); c2017. Available from: https://www.bundesaerztekammer. de/fileadmin/user_upload/downloads/pdf-Ordner/MuE/Richtlinie_
Haemotherapie_E_A_2019.pdf [cited 2019 Dec]. 14. Bundesärztekammer. Richtlinie zur Gewinnung von Blut und
Blutbestandteilen und zur Anwendung von Blutprodukten (Richtlinie
Hämotherapie); c2017. Available from: https://www.bundesaerztekammer. de/fileadmin/user_upload/downloads/pdf-Ordner/MuE/Richtlinie_
Haemotherapie_E_A_2019.pdf [cited 2019 Dec]. Consent for publication
Not applicable. Consent for publication
Not applicable. Consent for publication
Not applicable. References 1. WHO. Integrating neglected tropical diseases into global health and
development: fourth WHO report on neglected tropical diseases 2017;
c2017. Available from: https://apps.who.int/iris/bitstream/handle/10665/255
011/9789241565448-eng.pdf [cited 2019 Dec]. 1. WHO. Integrating neglected tropical diseases into global health and
development: fourth WHO report on neglected tropical diseases 2017;
c2017. Available from: https://apps.who.int/iris/bitstream/handle/10665/255
011/9789241565448-eng.pdf [cited 2019 Dec]. 23. Rechel B, Mladovsky P, Ingleby D, Mackenbach JP, McKee M. Migration and
health in an increasingly diverse Europe. Lancet. 2013;381:1235–45. https://
doi.org/10.1016/S0140-6736(12)62086-8. 2. Schmunis GA, Yadon ZE. Chagas disease: a Latin American health problem
becoming a world health problem. Acta Trop. 2010;115:14–21. https://doi. org/10.1016/j.actatropica.2009.11.003. 24. Statistisches Bundesamt. Genesis-Online Datenbank: DESTATIS; c2019. Available from: https://www-genesis.destatis.de/genesis/online/data/12521-
0002.xls;sid=CDD6C070762FBA8CE3880856C4589214.GO_1_3?operation=
ergebnistabelleDownload&levelindex=2&levelid=1566517502587&option=
xls&doDownload=xls&contenttype=xls [cited 2019 Jul]. 3. Pehrson P-O, Wahlgren M, Bengtsson E. Asymptomatic congenital Chagas’
disease in a 5-year-old child. Scand J Infect Dis. 1981;13:307–8. https://doi. org/10.3109/inf.1981.13.issue-4.14. 25. Bayona-i-Carrasco J, Pujadas Rúbies I, Avila TR, et al. Europa como nuevo
destino de las migraciones latinoamericanas y caribeñas. Biblio3W. 2018;
23(1,242):742–98 Spanish. 4. Liechti M, Baur HR, Gurtner HP, Straub PW. Cardiac complications of
American trypanosomiasis (Chagas disease). Various case reports and
general observations. Schweiz Med Wochenschr. 1990;120:1493–6. Page 12 of 12 Guggenbühl Noller et al. BMC Infectious Diseases (2020) 20:919 26. Instituto Nacional de Estadistica. INEbase; c2019. Available from: https://
www.ine.es/ [cited 2019 Aug]. 27. Worldometer. Germany Population; c2019. Available from: https://www. worldometers.info/world-population/germany-population/ [cited 2019 Dec] 28. Roca C, Pinazo MJ, López-Chejade P, Bayó J, Posada E, López-Solana J, et al. Chagas disease among the Latin American adult population attending in a
primary care center in Barcelona, Spain. PLoS Negl Trop Dis. 2011;5:e1135. https://doi.org/10.1371/journal.pntd.0001135. 29. Angheben A, Anselmi M, Gobbi F, Marocco S, Monteiro G, Buonfrate D,
et al. Chagas disease in Italy: breaking an epidemiological silence. Euro
Surveill. 2011;16 PubMed PMID: 21944554. 30. Prevalence and epidemiological significance ofTrypanosoma cruzi infection
among latin american immigrants in Berlin, Germany https://doi.org/10. 1371/journal.pntd.0000592. 30. Prevalence and epidemiological significance ofTrypanosoma cruzi infection
among latin american immigrants in Berlin, Germany https://doi.org/10. 1371/journal.pntd.0000592. 31. Da Costa-Demaurex C, Crdenas MT, Aparicio H, Bodenmann P, Genton B,
DAcremont V. Screening strategy for Chagas disease in a non-endemic
country (Switzerland): a prospective evaluation. Swiss Med Wkly. 2019. https://doi.org/10.4414/smw.2019.20050. 32. Jackson Y, Gétaz L, Wolff H, Holst M, Mauris A, Tardin A, et al. Prevalence,
Clinical Staging and Risk for Blood-Borne Transmission of Chagas Disease
among Latin American Migrants in Geneva, Switzerland. PLoS Negl Trop Dis. 2010;4:e592. References https://doi.org/10.1371/journal.pntd.0000592 Boelaert M, editor. 33. Rassi A, Rassi A, Marin-Neto JA. Chagas disease. Lancet. 2010;375:1388–402. https://doi.org/10.1016/S0140-6736(10)60061-X. 34. Monge-Maillo B, López-Vélez R. Challenges in the management of Chagas
disease in Latin-American migrants in Europe. Clin Microbiol Infect. 2017;23:
290–5. https://doi.org/10.1016/j.cmi.2017.04.013. 35. Ribeiro I, Sevcsik A-M, Alves F, Diap G, Don R, Harhay MO, et al. New,
Improved Treatments for Chagas Disease: From the R&D Pipeline to the
Patients. PLoS Negl Trop Dis. 2009;3:e484. https://doi.org/10.1371/journal. pntd.0000484 Gürtler RE, editor. 36. Deutsches Rotes Kreuz. Blutspendedienst; c2019. Available from: https://
www.blutspende-leben.de/blutspende/weg-der-blutspende [cited 2019
December]. 36. Deutsches Rotes Kreuz. Blutspendedienst; c2019. Available from: https://
www.blutspende-leben.de/blutspende/weg-der-blutspende [cited 2019
December]. 37. Stimpert KK, Montgomery SP. Physician awareness of Chagas disease, USA. Emerg Infect Dis. 2010;16:871–2. https://doi.org/10.3201/eid1605.091440. 37. Stimpert KK, Montgomery SP. Physician awareness of Chagas disease, USA. Emerg Infect Dis. 2010;16:871–2. https://doi.org/10.3201/eid1605.091440. 38. Ventura-Garcia L, Roura M, Pell C, Posada E, Gascón J, Aldasoro E, et al. Socio-Cultural Aspects of Chagas Disease: A Systematic Review of
Qualitative Research. PLoS Negl Trop Dis. 2013;7:e2410. https://doi.org/10. 1371/journal.pntd.0002410 Correa-Oliveira R, editor. 39. Ortí-Lucas RM, Parada-Barba MC, de la Rubia-Ortí JE, Carrillo-Ruiz A, Beso-
Delgado M, Boone ALD. Impact of Chagas disease in Bolivian immigrants
living in Europe and the risk of stigmatization. J Parasitol Res. 2014;2014:1–7
https://doi.org/10.1155/2014/514794. 39. Ortí-Lucas RM, Parada-Barba MC, de la Rubia-Ortí JE, Carrillo-Ruiz A, Beso-
Delgado M, Boone ALD. Impact of Chagas disease in Bolivian immigrants
living in Europe and the risk of stigmatization. J Parasitol Res. 2014;2014:1–7. https://doi.org/10.1155/2014/514794. 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.
|
https://openalex.org/W4285107582
|
https://synopsis.kubg.edu.ua/index.php/synopsis/article/download/516/422
|
Russian
| null |
Emotion concepts for representing the vicissitudes of fate in Markus Zusak’s “Bridge of Clay”
|
Sinopsis: tekst, kontekst, medìa
| 2,022
|
cc-by
| 7,392
|
EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY The problem of studying emotionally expressive information contained in a text is of considera-
ble interest since it interprets reality, expressing value or emotionally significant attitudes toward this
reality. The analysis of the emotivity and expressiveness of a literary text focuses primarily on its re-
search from the cognitive (separation of emotiogenic knowledge) and semantic (determining the fea-
tures of its use to indicate the author’s purposes) perspectives. A literary text is considered as a dual
dimension: on the one hand, it is related to emotions, and on the other hand, it is specified by them. The aim of the article is to identify and examine the emotional concepts represented in Markus Zu-
sak’s Bridge of Clay for portraying the vicissitudes of fate. The breath-taking story revolves around the
Dunbar family of ‘ramshackle tragedy’ and brims with pathos. To analyse the emotion concepts, the
following methods have been employed: the methods of interpretation and systematisation; contex-
tual, stylistic, and distributive analysis as also a method of emotional valence, and the hypothetico-
deductive method. The results of the study show that emotion concepts in Zusak’s Bridge of Clay are realised at the
following levels: phonetics, morphology, and semantics, which shows the universality of functioning
emotion concepts in fictional discourse. The emotion concept appears as a single entity that consists
of attributes of emotivity, which are anthropocentric and character-creating. The lexical units, chosen
by Zusak, convey the author’s intentions, explicitly or implicitly indicating the emotional nature of the
text. Since characters belong to the category of essential universals of a literary text, the emotional
meanings included in its structure have a special informative significance. The character’s emotions
are represented as the special psychological reality, and the set of emotions in the text appears as a
kind of dynamic plurality that changes as the story develops. y
p
y
g
y
p
Keywords: literary text; reality; mental world; expressiveness; narrative. creation, and the relevant linguistic culture (Wildgen,
2004). Emotions are considered an essential part of hu-
man life and a complex form of reflection of reality. Humans have a great variety of ways of expressing
their “states of mindˮ (Sias & Bar-On, 2016, p. 48). Emotional processes in various aspects and for dif-
ferent purposes are under consideration by many
branches of knowledge (Nelson, 2007). ISSN 2311-259X ISSN 2311-259X Synopsis: text, context, media
pp. 14–20, 28(1), 2022 Синопсис: текст, контекст, медіа
2022, 28(1), с. 14–20 https://doi.org/10.28925/2311-259x.2022.1.3
UDC 82-3:159.942 https://doi.org/10.28925/2311-259x.2022.1.3
UDC 82-3:159.942 https://doi.org/10.28925/2311-259x.2022.1.3
UDC 82-3:159.942 Andrii Bezrukov
Ukrainian State University of Science and Technologies
2 Lazarian St., Dnipro, 49010, Ukraine
https://orcid.org/0000-0001-5084-6969
dronnyy@gmail.com Oksana Bohovyk
Ukrainian State University of Science and Technologies
2 Lazarian St., Dnipro, 49010, Ukraine
https://orcid.org/0000-0003-4315-2154
oksana.a.bogovik@gmail.com © A. Bezrukov, O. Bohovyk, 2022 EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY Language is a key to the study of human emotions
because it nominates, expresses, describes, imitates,
stimulates, classifies, and structures them. A lan-
guage is what creates the emotional worldview of the
representatives of a particular linguistic culture. and feelings expressed in language. Galasinski (2004)
claims that the textual function of language “makes it
intelligible to the addressee precisely as a text that
makes sense within itself and within the context of
its appearanceˮ (p. 22). A writer uses the author’s
word to convey the language of a character and nar-
rator as “simulation involves an ineliminable ego-
centred elementˮ (Meskin, 2003, p. 18). The author’s
word is already created by means of language which
relates to its evaluation and attitude to the world. Language is a key to the study of human emotions
because it nominates, expresses, describes, imitates,
stimulates, classifies, and structures them. A lan-
guage is what creates the emotional worldview of the
representatives of a particular linguistic culture. morphology, and semantics. Emotion concepts that
are usually characterised as oppositional emotions
have a dual nature as in different contexts they can
attain positive or negative connotations or even
evoke mixed emotions. We consider it expedient to analyse the emotion
concepts contained in the novel using the following
classification of the emotiogenic means: graphical
and visual, punctuation, and semantic-stylistic ones
(Bezrukov & Bohovyk, 2021, p. 10) with the inclu-
sion of the phonetic level which deserves special
attention for in-depth analysis and systematic de-
scription of emotional reactions of the readers to the
created images and events in the novel. The purpose of the study is to identify and exam-
ine the ways of representing the emotion concepts
used by Markus Zusak to portray the vicissitudes of
fate in his novel Bridge of Clay as this breath-taking
story of the family of ‘ramshackle tragedy’ brims
with energy and pathos. The study of functioning emotion concepts in fic-
tional discourse allows for the understanding of the
author’s intentions through the analysis of the means
of expression of concepts at all levels of language. Expressive vocabulary is inherent in units of all levels
of the language structure; it draws attention to the
nuances of thought, emotional assessments of what
is said. Adolphs (2017) underlines that the problem
of emotion concepts is intrinsically tied to the nature
of emotions (p. 29). In research from Winkielman et
al. EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY (2018), crucial among such concepts are those
that refer to affect, valence and emotion. The methodology is presented by the methods of
interpretation and systematisation with the ele-
ments of semantic and linguistic analysis as well as
the hypothetico-deductive method. The object of
study has dictated the need also to use the following
textual research methods: contextual analysis is to
identify emotional topics and the emotional struc-
ture of a text; stylistic analysis is to study functional
and stylistic features of textual emotionality; distri-
butional analysis and the method of emotional va-
lence are to express emotiogenic language means
and their combinations in a text and describe the
extent to which an emotion is positive or negative. Of great interest in this aspect is a new novel
Bridge of Clay (2018) by Markus Zusak (born 1975),
an Australian writer with Austrian and German roots
and international bestselling author of six novels. They have won the attention of critics as well as the
affection of readers all over the world. Zusak has
received the Margaret A. Edwards Award from the
American Library Association, and his works have
been translated into more than 40 languages. Bridge
of Clay can be regarded as Zusak’s magnum opus
(Sebag-Montefiore, 2019). Phonetic Realisation of Emotion Concepts. At
the phonetic level, emotion concepts are realised
through a variety of means. The following list in-
cludes the excerpts with detailed analysis and em-
phasising emotionally significant elements. Bridge of Clay is a kind of psychological writing
which clearly emphasises the characters’ dialectic of
the soul. Therefore, the study of using literary devic-
es, the principles of meaning-making also opens the
way for a fuller understanding of the creative per-
sonality of writers, their style, and the patterns of
human understanding in the literary dimension. The
fictional narrative has its impact primarily through
emotions (Oatley, 2013, p. 39). “When he [cat] changed positions, fur flew off
him in droves, but he slept on, undiminished, and
purring”1 (Zusak, 2019, p. 33). Zusak uses onomato-
poeia (purring) imitating the sounds of the animal to
create the emotion concept of calmness with a posi-
tive meaning. “It’s me and the typewriter — me and the old TW,
as our long-lost father said our long-lost grandmother
used to say” (BC, p. 3). EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY The studies
of emotions are influenced by perspectives from
sociology, philosophy, ethnology, psychology, neuro-
science, anthropology, computer science, etc. They
primarily focus on what makes humans react to cer-
tain stimuli and how those reactions affect us. How-
ever, there has recently been a surge of interest in
the emotional content of language and ways and
forms of expression of emotions in a text by linguis-
tics as the emotional function of language is among
the key ones (Maia & Santos, 2018), and a text con-
tains not only cognitive or aesthetic but also emo-
tional information, as Dijkstra et al. (1995) stress. The ways and means of expressing emotions may
differ depending on the type of text, the time of its The expression of emotions may be clearly seen
in texts of different genres. Since fictional discourse
is an objective recording of literary communication
and the interaction of an author and reader with
linguistic socio-interactional and cultural canons
(Predelli, 2020; Groves & Smith, 2019; Stamou, 2018;
Phillips, 2000), understanding the means of influ-
ence, that appear in literary texts as a projection into
the emotional perception of what is read, is a relevant
issue of modern humanities (Bezrukov & Bohovyk,
2021, p. 2). Fiction is a depository of emotions: it de-
scribes emotional situations, verbal emotional beha-
viour, means, and ways of communicating emotions;
it depicts the emotional individual experience, forms
of its emotional reflection and emotional responses
(Kim, 2010). Emotions are central to the experience
of literary narrative fiction (Mar et al., 2011). The texts of literary works do not contain mere
language but above all represent the author’s thoughts © A. Bezrukov, O. Bohovyk, 2022 14 ISSN 2311-259X Synopsis: text, context, media
pp. 14–20, 28(1), 2022 Синопсис: текст, контекст, медіа
2022, 28(1), с. 14–20 and feelings expressed in language. Galasinski (2004)
claims that the textual function of language “makes it
intelligible to the addressee precisely as a text that
makes sense within itself and within the context of
its appearanceˮ (p. 22). A writer uses the author’s
word to convey the language of a character and nar-
rator as “simulation involves an ineliminable ego-
centred elementˮ (Meskin, 2003, p. 18). The author’s
word is already created by means of language which
relates to its evaluation and attitude to the world. 1 Zusak, M. (2019). Bridge of Clay. Black Swan; hereafter abbreviated
as BC. EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY Writing about the late grand-
mother and the father who left his sons, the author
uses alliteration to make the readers feel the sadness
of one of the brothers on whose behalf the story is
being told. The personified expression of the author’s posi-
tion is the choice of characters. Zusak’s characters
are not idealised but instead are real: dreamy, chal-
lenging, childishly reckless, trusting, and deep in
thought. The writer is interested not in the social
environment but in the individual microcosm which
he portrays through the vicissitudes of fate. “There was an old typewriter buried in the old
backyard of an old-backyard-of-a-town, but I’d had
to get my measurements right, or I might dig up a
dead dog or a snake instead (which I did, on both
counts)” (BC, p. 4). Through assonance, Zusak shows
the emotion concept of interest creating a gradation
effect that provokes the readers to learn a hidden According to Bamberg (1997), the relationship
between language and emotions can be viewed from
two angles: the interpretation of language as being done
(performed) ‘emotively’, and language as a ‘reflec-
tion’ of the objects in the world, among them the emo-
tions (p. 309). Zusak’s emotion concepts are imple-
mented at different levels of language — phonetics, 15 ISSN 2311-259X Synopsis: text, context, media
pp. 14–20, 28(1), 2022 Синопсис: текст, контекст, медіа
2022, 28(1), с. 14–20 secret that is gradually revealed in the novel by rep-
resenting the vicissitudes of fate. emotion concept of anger which is reinforced by the
offensive word stupid. Negative feelings are also
caused by the sound combination [scr]: “God, I can
still hear it. I try so much to keep my distance from
that moment. Thousands of miles if I can. But even
now, that depth of scream” (BC, p. 334). Zusak de-
scribes the reaction of one of the brothers, Rory, who
learns of his mother’s deadly disease. Grief and des-
pair are contained in the last sentence wherein
scream is reinforced by the noun depth. Among the
sound combinations that convey unpleasant associa-
tions, we also single out [sl] and [kr]: “They buried
me fast and furiously” (BC, p. 380), “He nearly cried
when he brought the cat close, the stripes against his
chest” (BC, p. 383). The mentioned combinations are
contained in the negative units furiously, cried, and
indicate the emotion concepts of anger and fear. “Her mouth. EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY Her bones, her breast, and finally,
her breath” (BC, p. 19). The writer describes the
feelings of the protagonist Clay to his girlfriend using
euphony. The chosen lexical units contribute to creat-
ing a symmetrical sound system. Zusak skilfully
combines alliteration with sentence fragment as “an
indicator of highlighting, expanding, and clarifying
important information” (Bezrukov & Bohovyk, 2021,
p. 9). The excerpt contains the emotion concept of
love and is perceived as a confession of the character
in love. Prose usually does not rhyme as poetical works
do but Zusak violates this rule to sophisticate his
novel. The following lines describe the emotions that
Penelope feels when she finds herself in a new city
and starts a new life: “Then fear of its newness, and
heat. And then, of course, the guilt: A hundred years
he’d never live. So selfish, so callous to leave” (BC,
p. 102). We believe that in this way the writer adds a
poetic component to the image, thoughts, aspira-
tions, and hopes of the woman which in turn allows
for seeing the inner world of Penny Dunbar, the
mother of boys who appears in front of the readers’
eyes when she has fled Poland: “But now the woman
who was nearly twenty-one but appeared sixteen
gripped him firmly in the face” (BC, p. 66). Phonetic meaning has a connotative character i.e. sounds can evoke certain emotions as well as intona-
tions: “I said my maiden ‘Je-sus Christ!’” (BC, p. 395). It is characteristic of the expression of anxiety, uncer-
tainty, or annoyance in portraying the vicissitudes of
fate. Interjections add an emotional-expressive ele-
ment to the text. It is worth noting that the author
uses a hyphen to emphasise pronunciation. Graphical and Visual Means of Emotional In-
tensity. Graphical means include italic, oblique, or
regular types, light, semi-bold, bold, black font-
weights, underlined, and capitalised letters which
play an important role in literary texts (Bezrukov &
Bohovyk, 2021, p. 4). In no way diminishing the role
of these means, we consider it appropriate to start
with what in some way combines the graphical im-
age and phonetic features, i.e. graphical fixation of
phonetic peculiarities of pronunciation, graphons,
found in Zusak’s novel: “Unforchantly, Spook, you
pale, poor bastard, Crapps has got something we can
use; he’s useful” (BC, pp. 38–39). The writer uses the
word unforchantly to emphasise the undereducation
of the character. EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY In this case, Zusak attracts reader’s
attention additionally using italics to depict the emo-
tion concepts of frustration and anger intensified by
pale, poor bastard. The writer follows the same prin-
ciple in the following: “‘Stubborn,’ he said, ‘but friend-
ly’” (BC, p. 383). Rhythm is a way to implement the emotion con-
cept of interest that we come across in Zusak’s Bridge
of Clay: “One of them talked. One of them trained. One of them hung on for dear life” (BC, p. 19). Paral-
lelism in the alternation of speech and sounds, as
well as a periodic division of sounds on the basis of
their duration, leads to the structuring of the text. The interaction of syntactic structures through paral-
lelism and assonance and the shift from short sen-
tences to longer ones produce an effect of tension
and exacerbation of the situation: “Out here some-
where was where waters led. Out here somewhere
was where murderers fled” (BC, p. 145). Considering the system of emotional elements at
the phonetic level, it should be noted that some in-
formation can be expressed by repeating sounds to
create additional rhythm: “To top it all off, she lay
awake that night, throbbing hotly amongst her sun-
burn, and the pitter-patter of insect feet” (BC, p. 112). The expressiveness of emotional units is sometimes
based on a certain distortion of phonetic sound
which, however, does not cause misunderstanding
and does not lead to the effect of cacophony: “Henry,
half-grin, half-grim” (BC, p. 278); “She had no busi-
ness with the rest of this riffraff” (BC, p. 46). Most of
these combinations contain the positive emotion
concept of fun. The author also uses graphons to show the im-
perfect pronunciation of immigrants who do not
speak the language well enough. Thus, Penelope, an
emigrant from Poland, who has lived abroad for
some time and works as a teacher, mispronounces
English words which make her eldest son be ironic:
“She never did manage to teach us her original lan-
guage — it was hard enough practicing piano — but
we loved that ambulance could be umboolunce, and
that she told us to shurr up rather than shut up. And
juice was often chooce. Or ‘Quiet! I can’t even hear
myself fink!’” (BC, p. 113). Certain sounds can evoke a corresponding range
of associations as they have a certain meaning. EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY Thus,
phonemes are mainly sensory-emotional infor-
mation. For example, the sound combination [gr]
conveys unpleasant associations: “Stop that stupid
grin” (BC, p. 193).The excerpt contains the negative Punctuation has a special place among graphical
means because it allows not only for dividing sentenc-
es into syntactic parts, dividing the text into sen-
tences, and determining their general characteristics 16 ISSN 2311-259X Synopsis: text, context, media
pp. 14–20, 28(1), 2022 Синопсис: текст, контекст, медіа
2022, 28(1), с. 14–20 but also indicates the elements that are important
for depicting the emotion concepts. the titles of each part are duplicated at the top left of
the pages, and the titles of the chapters are duplicat-
ed at the top right. This style is also referred to as
individual author’s style but it should be noted that
this arrangement makes it somewhat difficult to
work with the book. The writer uses ellipsis to indicate expectant
pauses: “‘THREE... TWO... ONE... Now.’ The stopwatch
clicked, and Clay was on his way” (BC, p. 49). It con-
tains the emotion concept of anxiety. In the following
example, using this punctuation mark, the writer
shows uncertainty: “Don’t do it, Clay, don’t go, don’t
leave me... but go” (BC, p. 121). To draw the readers’
attention to a pause, to make them think and antici-
pate the author’s intention in representing the vicis-
situdes of fate, Zusak sometimes uses dashes to indi-
cate the indecision of his character who continues
expressing his/her opinion: “I’ll need help to build it,
and I’m asking if any of you might —” (BC, p. 85). The use of the mentioned graphical elements is
perceived as filmed prose against which events run
and dialogues sound. On an emotional level, this use
of typography provokes the emotion concept of sur-
prise, and the plot itself leads to the experience of
polar opposite emotions: love — hatred; joy, pleas-
ure — grief, sorrow, sadness; happiness — unhappi-
ness; calmness — anxiety, concern. Using any punctuation mark thrice always at-
tracts the readers’ attention: “Last week I got my first
mount. Can you believe it???” (BC, p. 237), and then
“I just talked to him and got him to the line on hands-
and-heels, and he came in third. Third!!!ˮ (BC, p. 237). The emotion concepts of surprise, unhappiness, and
anger are included in the examples. EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY Sometimes the
author uses an excessive number of punctuation
marks to emphasise the emotion concepts of sorrow
and unhappiness: “I don’t have much to say except
that Achilles misses you. I got Henry to help me check
his hooves — THAT’S what I call USELESS!!!!!! (And I
miss you, too.)” (BC, p. 236). Such a short but emo-
tional letter was written to Clay by his youngest
brother Tommy. This way the little one expresses his
longing and sadness for his older brother. The writer’s style is characterised by font selec-
tion as “by distinguishing some units, parts of a sen-
tence, and sometimes whole sentences, the author
puts
additional
meanings
into
the
context”
(Bezrukov & Bohovyk, 2021, p. 4): “He knew right
then that this was the world, and all it was was a vi-
sion” (BC, p. 45). Zusak graphically highlights the
entire sentence to show the positive emotion con-
cept of love. To emphasise that the past remains the
past, the author uses the contact repetition of the
verb was. One of the important novel’s symbols is the book
about Michelangelo THE QUARRYMAN (BC, p. 44). The author writes its title in capital letters, places it
in the middle of the page, leaves spaces above and
below it to make the readers pay special attention
to the title and predict how the mentioned subject is
embodied. Morphological Units for Creating Positive and
Negative Emotion Concepts. Morphological units
serve for creating the various emotion concepts by the
writer and the perception of these concepts by the
readers. This makes us pay attention to using suffixes
for word-building. Thus, a careful analysis of Zusak’s
Bridge of Clay allows us to distinguish between suf-
fixes that contain negative and positive markings. Certain details that can be called individual au-
thor’s style include: • The graphic drawing of the bridge is located
under the title “Final Bridge Plan: First Sketchˮ (BC,
p. 196). Zusak uses italics to capture the readers’
attention and show the emotion concept of interest. A graphic image wherein the capital letters are sepa-
rated by vertical bars resembles piano keys: “She
opened the lid and saw the words, on the keys, and
they were lettered there simply, yet beautifully:
P|E|N|E|L|O|P|E
L|E|S|C|I|U|S|Z|K|O
P|L|E|A|S|E
M|A|R|R|Y M|E” (BC, p. 225), and “She’d played the
keys of Y|E|S|” (BC, p. EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY Adjectives are verbal-
ised by adjectives: “She laughed, and her fingers
touched the pocket; her other hand went for his
ribs – and it’s always something awful and anxious,
when a face ignites, then changes; he’d taken her and
shoved her away” (BC, p. 482); “She was beautiful
even when sad” (BC, p. 496). The novel also contains
adverbial means to denote emotional states: “‘If you
say aggressive,’ said our dad, and he’d pointed, calmly,
at Rory, ‘I’m going to — See that kid?’” (BC, p. 519). Verbal means of direct nomination can be represent-
ed by the following examples: “I’m especially so be-
cause I love this kitchen now, and all its great and
terrible history” (BC, pp. 9–10); “No, the animals
didn’t remotely pose a threat; it was the two eldest of
us he feared most” (BC, p. 26); “He knew that de-
spite being happy to say it, her eyes were close to
tears then, and he held her that extra piece tighter —
and Carey used the momentum, to slip down, to put
her head upon his chest” (BC, p. 119); “Her fears,
through the months, were calmed” (BC, p. 222). The above examples show that emotionality can
be contained in the lexical meanings of the words or
due to the use of appropriate suffixes. Grammatical descriptors reinforce the utterance
and bring emotional information to the front. Inver-
sion is one of the expressive means to indicate the
emotional state: “To our parents, in particular, he
was the special one, I’m sure of it, for he rarely
fought, hardly cried, and loved everything they spoke
of and told him” (BC, p. 263) — the emotion concept
of love; “In the beginning there was one murderer,
one mule and one boy…” (BC, p. 3) — the emotion
concept of interest; “But make no mistake — he was
a wasteland in a suit; he was bent-postured, he was
broken” (BC, p. 13) — the emotion concept of sor-
row. Another emotiogenic means includes the em-
phatic use of the verb do: “Only when he started to
run did he feel a pair of tears, bitten and burning,
swell inside his eyes. Only then did his fists tighten;
he was ready for it now, this idiots’ brigade, this ter-
rifically teenaged world” (BC, p. EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY 226).We have not found this
way of portraying the marriage proposal in fiction,
and therefore define it as Zusak’s style. Conflicts of
surprise, interest, joy, pleasure, happiness are contained
in the example. For sure, the emotion concept can be
changed to the opposite one if the answer is |N|O|. The negative suffixes include the following: -ish —
“In the beginning it was me who trained him, then
Rory, and if I did it with an old-school brand of fool-
ish integrity, Rory bludgeoned but never broke him”
(BC, p. 22), wherein the emotion concept of con-
tempt is contained; -ard — “Hit him hard, Starkers,
y’ ugly bastard!” (BC, p. 46) — the emotion concept
of fear; -ster — “She was getting flustered and it
wasn’t English forming in her mouth; each sentence
was exactly that – its own small punishment” (BC,
p. 46) — the emotion concept of anxiety; -іe — “And
next (and this was an extension of the first), he didn’t
confess that somewhere in his murkiest depths, he
wasn’t so much afraid of being left again as condemn-
ing someone else to second best” (BC, p. 216) — the
emotion concept of fear. • For the titles of the novel’s parts, the author us-
es lowercase letters and the font typical of the old
Remington, underlines words that he considers more
semantically significant, uses capital letters, and
connects words with a mathematical character +:
“part two cities + WATERS” (BC, p. 63). Using such suffixes as -y and -let has the opposite
effect creating positive connotations: -y — “It’s funny,
I guess, how confessions come out: We admit to al-
most everything, and the almost is all that counts”
(BC, p. 216) — the emotion concept of joy; -let —
“He clenched her flannelette arm” (BC, p. 377) — the
emotion concept of tenderness. • For the chapters’ titles, the writer uses lower-
case letters, a typical typographic font, and under-
lines words: “the mistake maker” (BC, p. 65). Notably,
there is no table of contents in Zusak’s Bridge of Clay: 17 ISSN 2311-259X Synopsis: text, context, media
pp. 14–20, 28(1), 2022 Синопсис: текст, контекст, медіа
2022, 28(1), с. 14–20 pleasure — oh, grabbing his arm” (BC, p. 58); “De-
spite the boyish outlook, you could swim in the sor-
rows of his face” (BC, p. 431). EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY 49) — the emotion
concept of hatred; “In that regard, Penelope did find
others from her own part of the world, and even her
own city” (BC, p. 103) — the emotion concept of
confidence; “Only when children came running up
the beach, in varied states of distress, did she realize
they’d all been stung” (BC, p. 111) — the emotion
concept of realisation; “What I do know is that her
directions were spot-on” (BC, p. 5) — the emotion
concept of confidence. The semantic purpose of the emotion concepts is
not so much in the nomination of the denotation but
in the expression of the emotional attitude of the nar-
rator to it, to the subject of speech, to the communica-
tive situation. This distinguishes emotional vocabu-
lary from nominative at all language levels. The se-
mantic purpose of such lexical units is subject-logical,
i.e. simple, uncomplicated connotation, nomination. At the morphological level, the constructions with
what, such, how, so indicate emotionality: “What a
fucking poofter!” (BC, p. 238) — the emotion concept
of hatred; “There was resolve there as well, and sure,
throwing him out would have been such a pleasure —
oh, grabbing his arm” (BC, p. 58) — the emotion
concepts of pleasure and anger; “How typical, then,
and perfect” (BC, p. 123) — the emotion concept of
calmness; “Even more so a second time” (BC, p. 123) —
the emotion concept of confidence. Exclamatory one-
word sentences and interrogative one-word sentenc-
es due to their form indicate the emotional connota-
tion of addressers: “Poetry!” (BC, p. 172) — the emo-
tion concept of pleasure; “Sorry?” (BC, p. 176) — the
emotion concepts of annoyance and incomprehen-
sion; “See?!” (BC, p. 278) — the emotion concept of
disbelief. Readers’ Emotional Responses through Stylis-
tic Devices. Zusak uses a number of semantic and
stylistic means to create an emotionally rich text. Stylistic devices serve as the means of expression of
fiction and are read in the text due to a deliberate
deviation from the neutral syntactic norm. Zusak’s Bridge of Clay is distinguished by its nar-
rative style: first, attracting the readers in a leisurely
and thoughtful manner, and then, like a whirlpool, it
quickly and powerfully draws the readers into the
course of events. EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY The author uses
the Polish language to indicate the origin of the char-
acter but chooses a strategy of introducing exotic
language units accompanied by a literal translation. • Repetition is often used by the character in a
state of emotional tension, stress. It is expressed in
the repetition of certain words: “Almost on cue, an
old guy started shouting, asking if it was her bloody
card holding up bloody traffic at the bloody bank
machine, and she ran back up to retrieve it” (BC,
p. 5). The repetition of the obscene bloody indicates
the emotion of anger and irritancy. Contact repeti-
tion of lexical units used to express gratitude empha-
sising mixed feelings of excitement and awkward-
ness: “Thank you, thank you, young man. For my
William” (BC, p. 23). • Repetition is often used by the character in a
state of emotional tension, stress. It is expressed in
the repetition of certain words: “Almost on cue, an
old guy started shouting, asking if it was her bloody
card holding up bloody traffic at the bloody bank
machine, and she ran back up to retrieve it” (BC,
p. 5). The repetition of the obscene bloody indicates
the emotion of anger and irritancy. Contact repeti-
tion of lexical units used to express gratitude empha-
sising mixed feelings of excitement and awkward-
ness: “Thank you, thank you, young man. For my
William” (BC, p. 23). Conclusion. Emotionality is a universal category
of fiction characterised by the constant content and
constant linguistic, communicative, and stylistic ex-
pression to reflect the emotional status and the axi-
ology of a character, and represents the author’s
style. This category includes cognitive, pragmatic,
and semantic components of emotions, and each has
its own manifested status, its own way of expression,
and content in a literary text, which allows for estab-
lishing a hierarchy of selected emotional units. • Paralleled constructions indicate the sequence of
actions wherein short segments emphasise the char-
acter’s calmness: “I parked the car, I shut the door,
and crossed the crispy lawn” (BC, p. 6). py
(
p
)
• Personification allows the writer to create life
and motion within inanimate objects by assigning
them recognisable human behaviours and emotions:
“There was tea and Scotch Fingers, and sun clapped
hard at the window.” (BC, p. 6). The sun which is
usually portrayed in a positive light here evokes the
emotion of anxiety. EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY In the following excerpt, personi-
fication evokes the emotion of fear and anxiety: “Its
[shade] darkness ate him up” (BC, p. 31). The celes-
tial body in the novel is a threat: it is burning, scorch-
ing, aggressive. So, the author uses personification in
combination with simile and each time makes the
readers feel the threat posed by the burning star:
“The sun was some sort of barbarian, a Viking in the
sky” (BC, p. 65). The emotion concepts in Zusak’s Bridge of Clay
are realised on phonetic, morphological, lexical, and
syntactic levels. Each level is rich in its examples of
the description of emotion concepts and their im-
plementation in text and speech. However, the study
of emotion concepts is not limited to the study of the
role of multilevel linguistic means in the expression
of emotions. Emotion concepts can change their
places in the structure of the language unit’s mean-
ing appearing to be a component of denotation and
connotation, or depend on the context but not as
a permanent component of the particular linguistic
unit’s structure. The analysis of emotion concepts in the novel
does not allow for preferring those that have only
a positive or negative meaning in portraying the
vicissitudes of characters’ lives because there are
many emotion concepts thus emphasising the range
of emotional states in the novel. • Simile, if it is effective, eliminates the need for
excessive explanation or description on the part of
the writer: “Those black keys [of the old Remington],
like monsters’ teeth, but friendly” (BC, p. 7). The
author mixes simile, personification, and an oxymo-
ron to evoke an emotion of interest. The mental world is formed under the influence
of many factors one of which is fiction. Linguistic and
conceptual worldviews reflected in the emotionality
of the text, demonstrate the integrity of the mental
nature of the representation of its emotional compo-
nents. Expressiveness is an integral part of the emo-
tional realisation on all language levels but each of them
has its own peculiarities. A more detailed study of
these entities may be the subject of further research. • Anadiplosis which consists in the contact repeti-
tion of a lexical unit indicates the author’s desire to
capture the readers’ attention to the information:
“I’m sure it’s because I was glad. Glad. EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY 14–20, 28(1), 2022 Синопсис: текст, контекст, медіа
2022, 28(1), с. 14–20 • Gradation in paralleled constructions serves to
clarify the information: “Around it, a wilderness of
low scrub and gum trees stood close by, and it was
true, it was so damn true: the people sloped and
slouched” (BC, p. 3). The use of the obscene damn
indicates the emotion of anger and irritancy. • Annomination is built on a sharp shift in seman-
tics in words close in sound, and creates a comic ef-
fect: “Somewhere in the top five, also, was unfortu-
nately. We liked it better as unforchantly” (BC, p. 113). • Colloquialisms, dialectisms, jargon, and vulgar-
isms are used with certain pragmatic purposes and
create clarity of live speech: “Ugly bastard he didn’t
mind one bit, but he couldn’t abide Starkers” (BC,
p. 46). Such words are clearly opposed to the literary
standard, and are, in a manner of speaking, more
expressive than usual lexical units, the names of
subjects or objects that evoke an emotional response
in the readers. The expressiveness of such words is
based on imagery, wit, surprise, sometimes on the
funny twist of vocabulary’s meaning. g
y
• Epithets express the author’s perception and
always have an emotional tone, which has a wide
range, depending on the author’s intentions: “A fami-
ly of ramshackle tragedy” (BC, p. 9). Zusak uses the
emotion concept of grief and sadness. The author
describes the boys’ father as “A man in a burning
suit” (BC, p. 14) which indicates the character’s anxi-
ety and unspeakable pain, his bitter experience of
losing his beloved wife. This disaster burns a man
internally and externally. • Exotic language units are used to create an exot-
ic atmosphere or immerse the readers in a foreign
culture: “‘Juz wystarczy,’ he said, ‘dziewczyna
błędo w...,’ which she translated, for us, as this: ‘That’s
enough, mistake maker.’” (BC, p. 70). The author uses
the Polish language to indicate the origin of the char-
acter but chooses a strategy of introducing exotic
language units accompanied by a literal translation. • Exotic language units are used to create an exot-
ic atmosphere or immerse the readers in a foreign
culture: “‘Juz wystarczy,’ he said, ‘dziewczyna
błędo w...,’ which she translated, for us, as this: ‘That’s
enough, mistake maker.’” (BC, p. 70). EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY To reflect the characters’ speech, thoughts, and
emotions, the writer uses a variety of stylistic devic-
es, such as: • Sentence fragments add emotionality to the
statement’s content and become one of the expres-
sive means of emotionality: “I’d driven out the day
after my wedding day. Out from the city. Right
through the night. Out through the reams of empty
space, and then some” (BC, p. 4). The sentence divid-
ed into separate segments creates a rhythm and
shows the fragmentation of the character’s thoughts. Sentence fragments are aimed at semantically deep-
ening the content of the basic structure and expres-
sive selection of the information that the author con-
siders the most important. Here Zusak uses the emo-
tion concept of calmness. • Sentence fragments add emotionality to the
statement’s content and become one of the expres-
sive means of emotionality: “I’d driven out the day
after my wedding day. Out from the city. Right
through the night. Out through the reams of empty
space, and then some” (BC, p. 4). The sentence divid-
ed into separate segments creates a rhythm and
shows the fragmentation of the character’s thoughts. Sentence fragments are aimed at semantically deep-
ening the content of the basic structure and expres-
sive selection of the information that the author con-
siders the most important. Here Zusak uses the emo-
tion concept of calmness. Speaking of lexical means of expressing emotions, it
should be noted that in emotional contexts, the mean-
ing of such verbal means directly shows the emo-
tional state of the character. They do not arise simply
because people have emotions towards what, in fact,
are fictional characters (Yanal, 1999). We have iden-
tified and analysed four groups of emotion concepts
in Zusak’s Bridge of Clay: nouns, adjectives, adverbs,
and verbs of direct lexical-semantic nomination. The nominals are represented by nouns that di-
rectly nominate emotions: “I was torn between love
and hatred for them, but now I just see it was train-
ing” (BC, p. 290); “There was resolve there as well,
and sure, throwing him out would have been such a • Polysyndeton gives the equal power rhythm and
adds ‘gravity’ to joined clauses: “There was a boy and
a son and a brother” (BC, p. 3). 18 ISSN 2311-259X Synopsis: text, context, media
pp. 14–20, 28(1), 2022 Synopsis: text, context, media
pp. Андрій Безруков др
ру
Украї нськии державнии університет науки і технологіи , Украї на Оксана Боговик
Украї нськии державнии університет науки і технологіи , Украї на References Meskin, A. (2003). Emotions, fiction, and cognitive architecture. The British Journal of Aesthetics, 43(1), 18–34. https://
doi.org/10.1093/bjaesthetics/43.1.18 Adolphs, R. (2016). How should neuroscience study emotions? By
distinguishing emotion states, concepts, and experiences. So-
cial Cognitive and Affective Neuroscience, 12(1), 24–31. https://doi.org/10.1093/scan/nsw153 Nelson, B. (2007). The emotion code. Wellness Unmasked Publishi Oatley, K. (2013). Emotions and the story worlds of fiction. In
M. C. Green, J. J. Strange, & T. C. Brock (Eds.). Narrative impact:
Social and cognitive foundations (pp. 39–70). Psychology Press. ocial and cognitive foundations (pp. 39–70). Psychology Press. Bamberg, M. (1997). Language, concepts and emotions: The role of
language in the construction of emotions. Language Sciences, 19(4),
309–340. https://doi.org/10.1016/s0388-0001(97)00004-1 Phillips, J. (2000). Two theories of fictional discourse. American
Philosophical Quarterly, 37(2), 107–119. Predelli, S. (2020). Fictional discourse: A radical fictionalist seman-
tics. Oxford
University
Press. https://doi.org/10.1093/
oso/9780198854128.001.0001 Bezrukov, A., & Bohovyk, O. (2021). Creating communicative space
and textual reality via emotiogenic means in fictional discourse. Rupkatha Journal on Interdisciplinary Studies in Humanities,
13(1), 1–14. https://doi.org/10.21659/rupkatha.v13n1.21 Sebag-Montefiore, C. (2019, October 21). Markus Zusak on how
Bridge of Clay left him “beaten up and bruised.” The Guardian. https://www.theguardian.com/books/2018/dec/17/markus-
zusak-on-how-bridge-of-clay-left-him-beaten-up-and-bruised Dijkstra, K., Zwaan, R. A., Graesser, A. C., & Magliano, J. P. (1995). Character and reader emotions in literary texts. Poetics, 23(1–2),
139–157. https://doi.org/10.1016/0304-422x(94)00009-u usak-on-how-bridge-of-clay-left-him-beaten-up-and-bruised Sias, J., & Bar-On, D. (2016). Emotions and their expressions. In C. Abell
& J. Smith (Eds.), The Expression of emotion: Philosophical, psycho-
logical and legal perspectives (pp. 46–72). Cambridge University
Press. https://doi.org/10.1017/CBO9781316275672.003 p //
g/
/
(
)
Galasinski, D. (2004). Men and the language of emotions. Palgrave
Macmillan. https://doi.org/10.1057/9780230510128 Groves, A. J., & Smith, W. T. (2019). Untangling emotions. Crossway. Kim, S. (2010). The rationality of emotion toward fiction. Midwest
Studies in Philosophy, 34(1), 106–119. https://doi.org/
10.1111/j.1475-4975.2010.00203.x Stamou, A. G. (2018). Sociolinguistics of fiction. Discourse, Context
& Media, 23, 1–5. https://doi.org/10.1016/j.dcm.2018.03.003 Wildgen, W. (2004). The evolution of human language: Scenarios,
principles, and cultural dynamics. John Benjamins Publishing
Company. https://doi.org/10.1075/aicr.57 Maia, B., & Santos, D. (2018). Language, emotion, and the emotions:
The multidisciplinary and linguistic background. Language and
Linguistics Compass, 12(6), e12280. https://doi.org/10.1111/
lnc3.12280 Winkielman, P., Coulson, S., & Niedenthal, P. (2018). Dynamic
grounding of emotion concepts. Philosophical Transactions of
the Royal Society B: Biological Sciences, 373(1752), 20170127. https://doi.org/10.1098/rstb.2017.0127 Mar, R. A., Oatley, K., Djikic, M., & Mullin, J. (2011). Emotion and
narrative fiction: Interactive influences before, during, and after
reading. EMOTION CONCEPTS FOR REPRESENTING THE VICISSITUDES OF FATE
IN MARKUS ZUSAK’S BRIDGE OF CLAY Glad is a stu-
pid-seeming word, but I’m writing and telling you all
of this purely and simply because that’s exactly how
we are” (BC, p. 9). In this context, anadiplosis is used
to create the emotion of exaltation and happiness. 19 ISSN 2311-259X Synopsis: text, context, media
pp. 14–20, 28(1), 2022 Synopsis: text, context, media
pp. 14–20, 28(1), 2022 Synopsis: text, context, media
pp. 14–20, 28(1), 2022 Синопсис: текст, контекст, медіа
2022, 28(1), с. 14–20 Синопсис: текст, контекст, медіа
2022, 28(1), с. 14–20 References Cognition & Emotion, 25(5), 818–833. https://doi. org/10.1080/02699931.2010.515151 Yanal, R. J. (1999). Paradoxes of emotion and fiction. Penn State
University Press. Z
k M (2019) B id
f Cl
Bl
k S Yanal, R. J. (1999). Paradoxes of emotion and fiction. Penn State
University Press. Zusak, M. (2019). Bridge of Clay. Black Swan. КОНЦЕПТИ ЕМОЦІЙ ДЛЯ ЗОБРАЖЕННЯ ПЕРИПЕТІЙ ДОЛІ
У РОМАНІ МАРКУСА ЗУСАКА «BRIDGE OF CLAY» Проблема дослідження емоціи но-експресивної інформації , яку порушує стаття, стано-
вить значнии інтерес, оскільки вона інтерпретує фрагменти діи сності, висловлюючи став-
лення до них — ціннісне або емоціи но значуще. Аналіз емотивності художнього тексту зо-
середжується насамперед на и ого студіюванні в когнітивному (виокремлення емоціогенних
знань) і семантичному (визначення особливостеи ї х застосування для позначення автор-
ських інтенціи ) вимірах. Художніи текст розглядається в дуальному взаємозв’язку: з одного
боку, він пов’язании з емоціями, а з іншого — визначається ними. Мета статті — ідентифі-
кувати концепти емоціи , експліковані в романі Маркуса Зусака «Bridge of Clay» для зобра-
ження перипетіи долі. Ця сповнена пафосом захоплива історія розгортається на тлі трагічної
історії родини Данбар. Для аналізу концептів емоціи роману застосовано методи інтерпре-
тації і систематизації , контекстуальнии , функціонально-стилістичнии і дистрибутивнии
аналіз, а також метод емотивної валентності і гіпотетично-дедуктивнии метод. У результаті дослідження з’ясовано, що концепти емоціи у мові роману «Bridge of Clay»
реалізуються на всіх рівнях: фонетичному, морфологічному, лексичному та синтаксичному,
що свідчить про універсальність функціонування концептів емоціи у художньому дискурсі. Концепти емоціи постають певною єдністю; за ї х змістове наповнення відповідають інди-
катори емотивності, які визначені антропоцентрично і виконують характеротвірну функцію. Лексичні одиниці, які вибрав Зусак, передають інтенції автора, експліцитно чи імпліцитно
вказують на емоціи нии характер тексту. Оскільки персонажі твору належать до розряду
основних універсаліи художнього тексту, емотивні смисли, що містяться в и ого структурі,
мають особливу інформативну значущість. Емоції персонажів «Bridge of Clay» репрезенту-
ються як особлива психологічна реальність, а сукупність емоціи у тексті постає своєрідною
динамічною множинністю, яка змінюється з розвитком сюжету. Ключові слова: художніи текст; діи сність; ментальнии світ; експресивність; наратив. Стаття надійшла до редколегії 11.01.2022 20
|
https://openalex.org/W4220915755
|
https://zenodo.org/records/6354262/files/silvesan.pdf
|
Romanian, Moldavan
| null |
Baptist Theological Seminary - An Example of Integrity and Assertion of Freedoms of Conscience
|
Zenodo (CERN European Organization for Nuclear Research)
| 2,022
|
cc-by
| 5,476
|
Source:
Jurnalul Libertății de Conștiință
Journal for Freedom of Conscience
Location:
Romania
Author(s):
Marius Silveșan
Title:
SEMINARUL TEOLOGIC BAPTIST — UN EXEMPLU DE INTEGRITATE ȘI AFIRMARE A
LIBERTĂȚII DE CONȘTIINȚĂ
Baptist Theological Seminary - An Example of Integrity and Assertion of Freedoms of
Conscience
Issue:
2/2020
Citation
style:
Marius Silveșan. "SEMINARUL TEOLOGIC BAPTIST — UN EXEMPLU DE INTEGRITATE
ȘI AFIRMARE A LIBERTĂȚII DE CONȘTIINȚĂ". Jurnalul Libertății de Conștiință 2:697-708.
https://www.ceeol.com/search/article-detail?id=1009116
The Central and Eastern European Online Library
The joined archive of hundreds of Central-, East- and South-East-European publishers,
research institutes, and various content providers
You have downloaded a document from You have downloaded a document from The Central and Eastern European Online Library The joined archive of hundreds of Central-, East- and South-East-European publishers,
research institutes, and various content providers CEEOL copyright 2022 CEEOL copyright 2022 SEMINARUL TEOLOGIC BAPTIST UN
EXEMPLU DE INTEGRITATE ȘI AFIRMARE A
LIBERTĂȚII DE CONȘTIINȚĂ Prof. dr. Marius SILVEȘAN
C. N. M. George Enescu București
C. T. „Gheorghe Asachi” București
marius.silvesan@yahoo.com Prof. dr. Marius SILVEȘAN
C. N. M. George Enescu București
C. T. „Gheorghe Asachi” București
marius.silvesan@yahoo.com Abstract: Baptist Theological Seminary - An Example of Integrity and
Assertion of Freedoms of Conscience Abstract: Baptist Theological Seminary - An Example of Integrity and
Assertion of Freedoms of Conscience Trough this study we want to present some data from the history of the
Baptist Teological Seminary in Romania on the account of integrity and
religious freedom. Founded in 1921, it continued its existence under this
name until 1990 when it was transformed into a Teological Institute with
a university fence. Tis was achieved after the December 1989 Revolution,
which brought much-needed religious freedom. At the same time, the
Baptist Teological Seminary and then the Baptist Teological Institute
together with the Faculty of Baptist Teology have offered and continue to
offer trust, support to those in need, to promote integrity and to campaign
for respect for the fundamental rights and freedoms of man and citizen
among which and religious freedom. Keywords: Baptist Teological Seminary of Bucharest, Baptist Teological
Institute of Bucharest, Baptist School for Girls, Earl Hester Truța, Constantin
Adorian, Ioan R. Socaciu, Alexa Popovici, Vasile Talpoș, Daniel Mariș,
theological education, integrity, religious freedom, Romania Prin intermediul acestui studiu, dorim să prezentăm câteva date din is-
toria Seminarului Teologic Baptist din România în contul integrității și
al libertății religioase. Înființat în 1921, acesta și-a continuat existența
sub acest nume până în anul 1990, când a fost transformat în Institut
Teologic de gard universitar. Acest lucru s-a putut realiza după Revoluția
din decembrie 1989 care aduce mult dorita libertate religioasă. Totodată, 697 CEEOL copyright 2022 CEEOL copyright 2022 CEEOL copyright 2022 JURNALUL LIBERTĂȚII DE CONȘTIINȚĂ VOL. 8, NR. 2, 2020 698 Seminarul Teologic Baptist și apoi Institutul Teologic Baptist alături de
Facultatea de Teologie Baptistă au oferit și continuă să ofere încredere,
susținere celor care au nevoie de așa ceva, să promoveze integritatea și să
militeze pentru respectarea drepturilor și libertăților fundamentale ale
omului și cetățeanului printre care și libertatea religioasă. Istoria Seminarului Teologic Baptist este legată de afirmarea inte-
grității și a libertății de conștiință. În fapt, după cum afirmă și profesorul
Eugen Matei, „libertatea conștiinței, piatră de temelie a principiului li-
bertății religioase, face parte din însăși fibra baptismului, așa cum a fost
exprimat în timpuri moderne (1905) de E. Y. Mullins prin ceea ce el a
numit „principul competenței sufletului” sau chiar dintru începuturi de
Tomas Helwys (c.1575- c.1617) pe când încerca să-l convingă pe regele
James I al Angliei că Măria sa nu are nicio autoritate asupra conștiinței
supușilor. Fapt pentru care i-au și putrezit oasele pe undeva prin închi-
soare. 1 Eugen Matei, „J. H. Rushbrooke și libertatea religioasă a baptiștilor români” disponibil
online
la
adresa
https://chibzuieli.wordpress.com/2013/09/01/j-h-rushbrooke-si-
libertatea-religioasa-a-baptistilor-romani/, (31.07.2020). 2 Teodor-Ioan Colda, „Baptiștii din România, victime ale discursului naționalist după
Marea Unire de la 1918 și susținătorii discursului naționalist un secol mai târziu” în Jurnalul
Libertății de Conștiință, Vol. 6, Nr. 1/2018, p. 479. 4 Parte din informațiile publicate în cadrul acestui articol se regăsesc în Marius Silveșan,
Bisericile Creștine Baptiste din România: între persecuție, acomodare și rezistență (1948-1965),
Editura Cetatea de Scaun, Târgoviște, 2012; ... Teodor-Ioan Colda, „Proselytism and other isms in the Contextof Social Security in
resent Day Romania” în Jurnalul Libertății de Conștiință – supliment – 2016, p. 22. Marea Unire de la 1918 și susținătorii discursului naționalist un secol mai târziu” în Jurnalul
Libertății de Conștiință, Vol. 6, Nr. 1/2018, p. 479.
3 Teodor-Ioan Colda, „Proselytism and other isms in the Contextof Social Security in
Present Day Romania” în Jurnalul Libertății de Conștiință – supliment – 2016, p. 22.
4 Parte din informațiile publicate în cadrul acestui articol se regăsesc în Marius Silveșan,
Bisericile Creștine Baptiste din România: între persecuție, acomodare și rezistență (1948-1965),
Editura Cetatea de Scaun, Târgoviște, 2012; ... 1 Eugen Matei, „J. H. Rushbrooke și libertatea religioasă a baptiștilor români” disponibil
online
la
adresa
https://chibzuieli.wordpress.com/2013/09/01/j-h-rushbrooke-si-
libertatea-religioasa-a-baptistilor-romani/, (31.07.2020).
2 Teodor-Ioan Colda, „Baptiștii din România, victime ale discursului naționalist după
Marea Unire de la 1918 și susținătorii discursului naționalist un secol mai târziu” în Jurnalul
Libertății de Conștiință, Vol. 6, Nr. 1/2018, p. 479.
3 Teodor-Ioan Colda, „Proselytism and other isms in the Contextof Social Security in
Present Day Romania” în Jurnalul Libertății de Conștiință – supliment – 2016, p. 22.
4 Parte din informațiile publicate în cadrul acestui articol se regăsesc în Marius Silveșan,
Bisericile Creștine Baptiste din România: între persecuție, acomodare și rezistență (1948-1965),
Editura Cetatea de Scaun, Târgoviște, 2012; ... Abstract: Baptist Theological Seminary - An Example of Integrity and
Assertion of Freedoms of Conscience De atunci, cam oriunde s-au extins baptiștii, au trecut printr-o fază
de persecuție religioasă, tipic promovată de biserica oficială, care era una
cu statul. Așa au stat lucrurile și în Romania”.1 Astfel dar, baptiștii români au fost printre cei mai înaintați și intere-
sați în promovarea conceptului libertății religioase pentru că acesta se afla
în însăși fibra baptismului, chiar dacă „libertatea de gândire, de exprima-
re, de asociere sunt specifice gândirii și vieții moderne sau a modernității. Lumea premodernă nu era familiară cu ideea de democrație, libertăți sau
drepturi cetățenești.”2 Vorbind despre libertatea religioasă, Teodor-Ioan
Colda subliniază faptul că „istoric, baptiștii cred că acesta este un drept
divin. Nu este acordat de autoritățile seculare, nu este acordat de o con-
stituție, nu este acordat de Biserică, ci este acordat de Dumnezeu În-
suși.”3 Acesta este cadrul general în care dorim să realizăm o incursiune
succintă în istoria Seminarului Teologic Baptist din București4, cea mai CEEOL copyright 2022 CEEOL copyright 2022 699
Seminarul Teologic Baptist – un exemplu de integritate 699 veche instituție de învățământ teologic baptist din România. Înființat în
toamna anului 1921 la Buteni, județul Arad, acesta s-a mutat curând la
Arad datorită persecuțiilor și presiunilor la care profesorii și seminariștii
au fost supuși de către autorități. De la Arad, la sugestia lui Constantin
Adorian, probabil „cel mai mare baptist român”5, după cum îl prezintă
Teodor-Ioan Colda, Seminarul și-a schimbat din nou locația, destinația
finală fiind capitala țării.6 Atunci când vorbim de educația teologică baptistă în România ne
referim la misiune, la o viziune misionară. Aceasta a venit din partea Bor-
dului de Misiune al Convenției Baptiste de Sud care a văzut nevoia de a
pregăti lucrători în Europa Centrală și de Sud Est. Aceste probleme au
apărut în contextul schimbărilor și oportunităților provocate de Primul
Război Mondial. Un aport important în ceea ce privește ducerea la înde-
plinire a acestui obiectiv i-a aparținut lui Everett Gill. Cu suport logistic din partea baptiștilor americani (Foreign Mission
Board – FMB- of Te Southern Baptist Convension), în toamna anului
1921, respectiv în luna septembrie, a fost deschis Seminarul Teologic
Baptist, prima instituție de învățământ teologic baptist din România. Deschiderea a avut loc la Buteni, apoi, ca urmare a persecuțiilor, Seminarul
s-a mutat la Arad şi în final la București, instituție ce există şi astăzi sub
numele de Institutul Teologic Baptist din București (ITBB). .... 4 Marius Silveșan „Istoria unei instituții evanghelice: Seminarul Teologic Baptist din
România” în volumul Tradiție, istorie, armată. Lucrările Sesiunii Internaționale de Comunicări
Științifice „Tradiție, Istorie, Armată”, Ediția a II-a, Constanța, 4-5 iunie 2015, coordonat de
Olimpiu Manuel Glodarenco, Editura Muzeului Militar Național „Regele Ferdinand I”,
Editura SITECH, Craiova, pp. 323-335. 5 Teodor-Ioan Colda, „Contribuția pastorului Constantin Adorian în obținerea libertății
religioase pentru baptiștii din România după Marea Unire de la 1918” în Libertatea religioasă
mereu în actualitate, volum coordonat de Dr. Nelu Burcea, Dr. Ioan-Gheorghe Rotaru, Lect.
univ. dr. Ieremia Rusu, Editura Uniersitară, București, 2012, p. 189. 6 Despre relația lui Constantin Adorian cu Seminarul Baptist vezi volumul: Daniel Marius
Mariș, Teodor - Ioan Colda, Constantin Adorian: un lider baptist vizionar, Editura Carmel
Print, Arad, 2015, pp. 53-64. 10 Alexa Popovici, Istoria Baptiştilor din România, 1856–1989, p. 126. Cursurile au început
cu nouă tineri: Dumitru Baban, Ioan Cristea, Nicolae Iancu, Ilie Mârza, Loghin Motrescu,
Gheorghe Olteanu, Teodor Pușcaș, A. Roșca și Florian Tenț, Ibidem. 9 Pentru mai multe detalii despre Ioan Rose Socaciu a se vedea numărul 5 (2)/ 2020 al
Revistei Arhiva Baptistă, editată de Centrul de Istorie, Genealogie și Statistică Baptistă din
Arad, având ca titlu generic: Ioan R. Socaciu cel mai longeviv conducător baptist. Alexa Popovici, Istoria Baptiştilor din România, 1856–1989, 3 vol., ed. rev., Editura Făclia,
Oradea, 2007, p. 325. 11 Bordul de Misiune American al Convenției Baptiste de Sud din Statele Unite al
Americii. 7 Home and Foreign Fields, Nr. 5, mai 1922, p. 8. 7 Home and Foreign Fields, Nr. 5, mai 1922, p. 8. 7 Home and Foreign Fields, Nr. 5, mai 1922, p. 8.
8 Alexa Popovici, Istoria Baptiştilor din România, 1856–1989, 3 vol., ed. rev., Editura Făclia,
Oradea, 2007, p. 325.
9 Pentru mai multe detalii despre Ioan Rose Socaciu a se vedea numărul 5 (2)/ 2020 al
Revistei Arhiva Baptistă, editată de Centrul de Istorie, Genealogie și Statistică Baptistă din
Arad, având ca titlu generic: Ioan R. Socaciu cel mai longeviv conducător baptist.
10 Alexa Popovici, Istoria Baptiştilor din România, 1856–1989, p. 126. Cursurile au început
cu nouă tineri: Dumitru Baban, Ioan Cristea, Nicolae Iancu, Ilie Mârza, Loghin Motrescu,
Gheorghe Olteanu, Teodor Pușcaș, A. Roșca și Florian Tenț, Ibidem.
11 Bordul de Misiune American al Convenției Baptiste de Sud din Statele Unite ale
Americii. Abstract: Baptist Theological Seminary - An Example of Integrity and
Assertion of Freedoms of Conscience În cadrul unui
articol din anul 1920 apărut în Revista Home and Foreign Fields, Jurnalul de
misiune al Convenției Baptiste de Sud se menționa faptul că în România
sunt mulți tineri dornici care așteaptă să beneficieze de avantajul de a se
pregăti din punct de vedere teologic. Articolul menționa în continuare un
îndemn, astfel că „dacă mergem să cucerim Europa pentru Cristos, trebuie
să-i ajutăm pe acești tineri să-și ascută secerile și grăbiții către holdele care CEEOL copyright 2022 CEEOL copyright 2022 JURNALUL LIBERTĂȚII DE CONȘTIINȚĂ VOL. 8, NR. 2, 2020 700 sunt deja coapte până la cădere”.7 Această manieră de prezentare a câmpului
de misiune este una extraordinară și ne conduce către imaginea unui lan de
grâu care este copt, gata de recoltă și mai are puțin și cade jos de greutatea
spicelor de grâu dacă nu este recoltat. Este remarcabilă această viziune și
modul de implementare al acesteia. Seminarul Teologic Baptist a fost înființat în anul 1921 ca urmare
a deciziei aprobată în cadrul Congresului Uniunii Bisericilor Baptiste din
România ce a avut loc la Buteni lângă Arad în 19208. La 1 septembrie
1921 au început cursurile Seminarului sub directoratul lui Ioan R. Soca-
ciu9, care făcea parte și din corpul profesoral alături de Ioan Popa și Vasile
Berbecar10. În anul 1924 a absolvit Seminarul Teologic Baptist din Bucu-
rești și prima promoție de elevi, iar în anul 1925 Seminarul este recu,-
noscut ca instituție de învățământ prin Legea Învățământului Particular
promulgată în anul 1925, iar ulterior, ca urmare a aprobării Statutului
Comunității Bisericești Baptiste de către Ministerul Cultelor în luna ia-
nuarie 1928. Seminarul a funcționat din anul 1921 până în anul 1931, când
Ioan R. Socaciu, directorul Seminarului, a rupt relațiile cu Ervett Gill,
reprezentant în România al Te Foreign Mission Board of Te Southern
Baptist Convention11. În acest context Seminarul Teologic s-a mutat la
Arad, însă fără susținere financiară din partea comunității locale și a Uni-
unii care se aflau în criză financiară. Datorită acestui fapt cursurile au
fost întrerupte după o lună de zile. Seminarul s-a redeschis abia la 15
septembrie 1933, după ce la Congresul Cultului din anul 1932 ce s-a
ținut la Timișoara Uniunea s-a rupt, formându-se astfel două Uniuni, iar
Uniunea nouă a reluat relațiile „de frățietate cu reprezentanții Bordului CEEOL copyright 2022 CEEOL copyright 2022 Seminarul Teologic Baptist – un exemplu de integritate 701 de misiune american”.12 Lucașa L. Abstract: Baptist Theological Seminary - An Example of Integrity and
Assertion of Freedoms of Conscience Sezonov a fost numit director activ, iar
profesorul dr. Everett Gill, reprezentantul Bordului American de Misiu-
ne, a fost considerat director onorific13. În contextul trecerii la un regim autoritar, cel al dictaturii antones-
ciene, Seminarul a fost desființat în martie 1942, prin Jurnalul Consi-
liului de Miniștri, nr. 723/1942, fiind redeschis în 1 noiembrie 1946. A
urmat o perioadă în care învățământul teologic baptist s-a desfășurat în
bune condiții, până la instaurarea regimului comunist. Revenind la perioada interbelică dorim să menționăm faptul că
în a doua parte a anilor '20 alături de pregătirea pe care Seminarul o făcea
pentru băieți se inițiază una și pentru fete. 12 Alexa Popovici, Istoria baptiștilor din România 1856-1989, p. 332.
13 Ibidem.
14 Pentru mai multe detalii despre Școala de fete a se vedea Revista Arhiva Baptistă Nr 1
(4) – 2020 ce a avut ca temă „Femeia creștină baptistă din România interbelică”.
15 Marius Silveșan, Bisericile Creștine Baptiste din România : între persecuție, acomodare și
rezistență : 1948-1965, Editura Cetatea de Scaun, Târgoviște, 2002, pp. 200-206.
16 Alexa Popovici, Istoria baptiștilor din România 1856-1989, p. 331. 12 Alexa Popovici, Istoria baptiștilor din România 1856-1989, p. 332. 4 Pentru mai multe detalii despre Școala de fete a se vedea Revista Arhiva Baptistă Nr 1
4) – 2020 ce a avut ca temă „Femeia creștină baptistă din România interbelică”. 16 Alexa Popovici, Istoria baptiștilor din România 1856-1989, p. 331. 5 Marius Silveșan, Bisericile Creștine Baptiste din România : între persecuție, acomodare și
ezistență : 1948-1965, Editura Cetatea de Scaun, Târgoviște, 2002, pp. 200-206. Școala de fete Una din modalitățile prin care s-a făcut misiune de către bisericile bap-
tiste din România în perioada interbelică a fost prin intermediul edu-
cației. Astfel, în anii ‘20, la inițiativa International Mission Board of the
Southern Baptist Convention s-a deschis pe lângă Seminarul Teologic
Baptist din București, Școala de Fete sau Seminarul Baptist de Fete14 cum
a mai fost denumit în perioada respectivă15. Inițial a fost o viziune, apoi
această viziune a avut nevoie și de un spațiu, de o clădire în care să-și des-
fășoare activitatea. Astfel, după construirea clădirii din spate a fost ridicat
un corp de clădire aflat în fața primului destinat pentru o „Școală de Fete. [Acesta] s-a construit în perioada 1925-1926 pe cheltuiala unei credin-
cioase baptiste din America, Mrs. W. C. James.”16 Informația menționată
de Alexa Popovici trebuie corectată în sensul că finalizarea construcției
nu s-a realizat în 1926, ci abia în 1929. În documentele americane școala
de fete este menționată cu numele James Memorial Training School, iar
construcția s-a realizat cu contribuția deosebită din punct de vedere fi-
nanciar a Convenției Baptiste de Sud. De menționat și faptul că clădirea CEEOL copyright 2022 CEEOL copyright 2022 JURNALUL LIBERTĂȚII DE CONȘTIINȚĂ VOL. 8, NR. 2, 2020 702 a fost ridicată în onoarea17 Mrs. W. C. James care a fost președinte al
Woman’s Missionary Union [WMU – Uniunea Misionară a Femeilor]
din cadrul Convenției Baptiste de Sud [SBC], în perioada 1916-192518. Construcția urma să fie casa a 50 de femei tinere care urmau să fie pregă-
tite din punct de vedere religios pentru a lucra cu femeile și copiii19. Pregătirea femeilor baptiste a fost parte a viziunii Convenției Bap-
tiste de Sud din America (Sowthern Baptist Convention SBC) prin
intermediul International Mission Board (IBM), Bpordul de Misiune
Externă. Prima directoare a Școlii de fete a fost Miss Earl Hester20, care
vine în București în anul 1929 cu acordul IMB. Pentru a prelua poziția
de directoare a Școlii de fete din București aceasta a fost numită ca misi-
onară în România la 16 iulie 192921. În anul școlar 1929-1930, s-a înființat o școală separată pentru
fete, cu durata studiilor de doi ani. 22 Teodor-Ioan Colda, „Credincioșii baptiști și Holocautul din România, sau cum li s-a
negat pocăiților și evreilor demnitatea umană în România anilor 1940-1944” în Jurnalul
Libertății de Conștiință, Vol. 7, Nr. 2/2019, p. 68. 18 Mihai Ciucă, „James Memorial Training School” în loc. cit., p. 26; Mark Edworthy, Te
wall that remains, International Mission Board of the Southern Baptist Convention, Ricmond,
Virginia, 2012, p. 17. 17 Mihai Ciucă spune că numele școlii a fost „dat în memoria credincioasei baptiste
americane, W. C. James” cf. Mihai Ciucă, „James Memorial Training School” în Revista Arhiva
Baptistă, Anul I, Nr. 1/2019, p. 26. 21 Home and Foreign Fields, Te Missionary Journal of the Southern Baptist Convention,
Nr. 10, October 1929, p. 30; Daniel Stoica, „Earl Hester Truța” în Revista Arhiva Baptistă,
Anul II, Nr. 1, aprilie 2020. 19 Mark Edworthy, Te wall that remains, p. 17. 20 Earl Hester (1902-1993) 25 Pastorul Hușan, fost președinte al Cultului baptist în anii ’80, consideră că pe parcursul
perioadei comuniste a existat o discriminare din partea statului cu privire la școlile teologice.
În timp ce ortodocșilor li se permitea înscrierea unui număr mai mare de cursanți și o
școală de nivel universitar, baptiștii erau supuși constrângerilor de tot felul. Vezi interviul
cu pastorul Mihai Hușan în Denisa Bodeanu, Neoprotestanții din Transilvania în timpul
regimului comunist. Studiu de caz: baptiștii din județul Cluj: mărturii și documente, Editura
Argonaut, Cluj-Napoca, 2007, pp. 179-197. 23 Dintre normele legale referitoare la învățământul teologic în vigoare pe parcursul
anilor ’80 menționăm: 1. Constituția R.S.R. din anul 1965, 2. Decretul nr. 177/1948
pentru regimul general al cultelor religioase care stipula în articolele 44-54 dreptul cultelor
religioase de a organiza învățământ eclesial sub controlul statului, 3. Decretul nr. 334/1970
privind organizarea și funcționarea Departamentului Cultelor, 4. Statutul de organizare
și funcționare al Cultului Creștin Baptist, 5. Decretul nr.141/1975 privind retribuirea
personalului din unitățile de cult, 6. Legea nr. 57/1974 privind retribuirea după cantitatea
și calitatea muncii, Cf. ASSC Învățământul teologic. Anexa 2: Norme legale referitoare la
învățământul teologic”, 26 noiembrie 1976. 24 S-a avut în vedere şi limitarea acţiunilor cultelor vizând educaţia religioasă a copiilor
şi tineretului. 26 Marius Silveșan, „Incursiune în istoria Bisericilor Creștine Baptiste din România anilor
‚80” în : „Studii de Istorie Eclesiastică”, vol. II, coord: Marius Oanță, Ed. Sitech, Craiova
2020, pp.259-286. 23 Dintre normele legale referitoare la învățământul teologic în vigoare pe parcursul
anilor ’80 menționăm: 1. Constituția R.S.R. din anul 1965, 2. Decretul nr. 177/1948
pentru regimul general al cultelor religioase care stipula în articolele 44-54 dreptul cultelor
religioase de a organiza învățământ eclesial sub controlul statului, 3. Decretul nr. 334/1970
privind organizarea și funcționarea Departamentului Cultelor, 4. Statutul de organizare
și funcționare al Cultului Creștin Baptist, 5. Decretul nr.141/1975 privind retribuirea
personalului din unitățile de cult, 6. Legea nr. 57/1974 privind retribuirea după cantitatea
și calitatea muncii, Cf. ASSC Învățământul teologic. Anexa 2: Norme legale referitoare la
învățământul teologic”, 26 noiembrie 1976.
24 S-a avut în vedere şi limitarea acţiunilor cultelor vizând educaţia religioasă a copiilor
şi tineretului.
25 Pastorul Hușan, fost președinte al Cultului baptist în anii ’80, consideră că pe parcursul
perioadei comuniste a existat o discriminare din partea statului cu privire la școlile teologice.
În timp ce ortodocșilor li se permitea înscrierea unui număr mai mare de cursanți și o
școală de nivel universitar, baptiștii erau supuși constrângerilor de tot felul. Vezi interviul
cu pastorul Mihai Hușan în Denisa Bodeanu, Neoprotestanții din Transilvania în timpul
regimului comunist. Studiu de caz: baptiștii din județul Cluj: mărturii și documente, Editura
Argonaut, Cluj-Napoca, 2007, pp. 179-197.
26 Marius Silveșan, „Incursiune în istoria Bisericilor Creștine Baptiste din România anilor
‚80” în : „Studii de Istorie Eclesiastică”, vol. II, coord: Marius Oanță, Ed. Sitech, Craiova
2020, pp.259-286. Școala de fete Această școală a funcționat până în
anul școlar 1940-1941, când prin legile antonesciene activitatea confesi-
unii baptiste a fost restrânsă până la desființare, chiar dacă, în opinia lui
Teodor-Ioan Colda, „[mareșalul Ion] Antonescu avea sentimente ames-
tecate față de sectanți și față de imaginea pe care și-a creat-o biserica
ortodoxă în societatea interbelică.”22 Fetele pregătite în această școală
aveau misiunea de a lucra cu femeile din bisericile baptiste și cu copiii din
Școala Duminicală. Ș
Într-o anumită măsură tradiția este reluată după anul 1990 prin
înființarea Facultății de Teologie Baptistă în cadrul Universității din
București. Astfel că la Facultatea de Teologie Baptistă (FTB) pot studia
și fete. Mai mult decât atât acestea au acces și la studii postuniversitare
teologice în baza programului de master oferit de aceeași instituție de CEEOL copyright 2022 CEEOL copyright 2022 Seminarul Teologic Baptist – un exemplu de integritate 703 învățământ teologic care îl are ca decan pe domnul profesor universitar
Otniel Ioan Bunaciu. Educația, element vital în regimurile comuniste a
fost strict controlată, aspect legiferat atât în constituții, cât și în celelalte
legi23. Biserica a fost despărțită de școală, iar educația religioasă a fost
restrânsă și controlată24. În anul 1957 Partidul Comunist Român a tipărit, prin oficialele
sale, operele lui Lenin, în volumul 15 al acestor opere, sunt redate cuvin-
tele lui Lenin: „Marxismul consideră totdeauna toate religiile şi bisericile
contemporane, toate organizațiile, ca pe niște organe ale reacţiunii bur-
gheze, care slujesc la apărarea exploatării şi la narcotizarea clasei munci-
toare”. Aceste cuvinte au devenit temeiul luptelor comuniste împotriva
religiilor din România, implicit împotriva Cultului Baptist. Activitatea Seminarului Teologic Baptist25 din București era de
asemenea controlată atât ca număr de elevi, cât și ca profesori și mate-
rii. Departamentul Cultelor a impus Cultului Baptist începând cu anul
1961 o schemă fixă de posturi care a afectat și Seminarul baptist26. Astfel,
numărul de elevi era calculat pe baza unui algoritm în funcție de numă-
rul de posturi vacante pe care-l dădea Cultul Baptist Departamentului
Cultelor. Media era în jur de 20 de elevi pentru o perioadă de 4 ani, iar
următoarea aprobare venea după ce termina seria respectivă. Aceste as-
pecte sunt prezentate și de către pastorul Ioan Bunaciu astfel: ,,În anul CEEOL copyright 2022 CEEOL copyright 2022 JURNALUL LIBERTĂȚII DE CONȘTIINȚĂ VOL. 8, NR. 2, 2020 704 1961 toamna ni s-a aprobat 7 seminariști la seminar. Școala de fete După ce au termi-
nat aceștia, ni s-a dat 6 seminariști, iar în anul 1969 seminarul n-a func-
ționat. În toamna anului 1970 ne-a aprobat 12 seminariști. În anul 1974
ne-a aprobat 20 de seminariști, iar după 2 ani, în 1976, ne-a mai aprobat
20, așa că aveam în acea perioadă 40 de seminariști. După ce a terminat
seria primită în 1976, adică în toamna anului 1980, ni s-a aprobat 10 se-
minariști pentru anul I de seminar. După 1984 ni se aprobă câte 4 semi-
nariști în fiecare an dar noi luam 5, al 5-lea reușit era în limba maghiară și
Departamentul Cultelor înghițea hapul și ni-l lăsa. Așa că revoluția ne-a
prins cu 17 studenți seminariști.”27 Activitatea Seminarului a fost redusă pe toată perioada comunis-
tă, anul 1989 reprezentând reinstaurarea libertăţii religioase. În acest
context în anul 1990 Seminarul a fost transformat în Institut Teologic
de Grad Universitar un rol important în acest demers l-a avut profeso-
rul universitar Vasile Talpoș, directorul Seminarului Teologic Baptist
din București (1988-1990) și apoi primul rector al Institutului Teologic
Baptist de Grad Universitar, transformat ulterior în Institutul Teologic
Baptist din București. Contribuția profesorului Vasile Talpoș a fost una
însemnată, putând fi contabilizată și datorită perioadei îndelungate cât
s-a aflat la conducerea instituției, respectiv 1990-2011. Începând din 29 noiembrie 2011, conf.univ.dr. Daniel Mariș a fost
ales în funcția de rector al Institutului Teologic Baptist din București28. În paralel cu activitatea profesorală la Institutul Teologic Baptist din Bu-
cești, Daniel Mariș este și profesor la Facultatea de Teologie Baptistă din
Universitatea București29. 29 Marius Silveșan „Istoria unei instituții evanghelice: Seminarul Teologic Baptist din
România” în volumul Tradiție, istorie, armată. Lucrările Sesiunii Internaționale de Comunicări
Științifice „Tradiție, Istorie, Armată”, Ediția a II-a, Constanța, 4-5 iunie 2015, coordonat de
Olimpiu Manuel Glodarenco, Editura Muzeului Militar Național „Regele Ferdinand I”,
Editura SITECH, Craiova, pp. 323-335. 28 http://www.itb.ro/?q=noutati/confdr-daniel-maris-noul-rector-itb (accesat 19.09.2012). 27 Ioan Bunaciu, Bisericile Creștine Baptiste din România între anii 1994-1990, Editur
Universității din București, București, 2002, p. 215. 27 Ioan Bunaciu, Bisericile Creștine Baptiste din România între anii 1994-1990, Editura
Universității din București, București, 2002, p. 215.
28 http://www.itb.ro/?q=noutati/confdr-daniel-maris-noul-rector-itb (accesat 19.09.2012).
29 Marius Silveșan „Istoria unei instituții evanghelice: Seminarul Teologic Baptist din
România” în volumul Tradiție, istorie, armată. Lucrările Sesiunii Internaționale de Comunicări
Științifice „Tradiție, Istorie, Armată”, Ediția a II-a, Constanța, 4-5 iunie 2015, coordonat de
Olimpiu Manuel Glodarenco, Editura Muzeului Militar Național „Regele Ferdinand I”,
Editura SITECH, Craiova, pp. 323-335. Bibliografie • „Daniel Mariș noul rector al ITBB”, http://www.itb.ro/?q=noutati/
confdr-daniel-maris-noul-rector-itb (accesat 19.09.2012). • „Daniel Mariș noul rector al ITBB”, http://www.itb.ro/?q=noutati/
confdr-daniel-maris-noul-rector-itb (accesat 19.09.2012). • Arhiva Secretariatului de Stat pentru Culte (ASSC), „Învățământul
teologic. Anexa 2: Norme legale referitoare la învățământul teologic”, 26
noiembrie 1976. • Arhiva Secretariatului de Stat pentru Culte (ASSC), „Învățământul
teologic. Anexa 2: Norme legale referitoare la învățământul teologic”, 26
noiembrie 1976. • Bodeanu Denisa, Neoprotestanții din Transilvania în timpul regimului
comunist. Studiu de caz: baptiștii din județul Cluj: mărturii și documente,
Editura Argonaut, Cluj-Napoca, 2007. • Bodeanu Denisa, Neoprotestanții din Transilvania în timpul regimului
comunist. Studiu de caz: baptiștii din județul Cluj: mărturii și documente,
Editura Argonaut, Cluj-Napoca, 2007. • Bunaciu Ioan, Bisericile Creștine Baptiste din România între anii 1994-
1990, Editura Universității din București, București, 2002. • Bunaciu Ioan, Bisericile Creștine Baptiste din România între anii 1994-
1990, Editura Universității din București, București, 2002. • Ciucă Mihai, „James Memorial Training School” în loc. cit., p. 26; • Ciucă Mihai, „James Memorial Training School” în loc. cit., p. 26; • Ciucă Mihai, „James Memorial Training School” în Revista Arhiva
Baptistă, Anul I, Nr. 1/2019. • Ciucă Mihai, „James Memorial Training School” în Revista Arhiva
Baptistă, Anul I, Nr. 1/2019. • Colda Teodor-Ioan, „Baptiștii din România, victime ale discursului
naționalist după Marea Unire de la 1918 și susținătorii discursului
naționalist un secol mai târziu” în Jurnalul Libertății de Conștiință, Vol. 6, Nr. 1/2018. • Colda Teodor-Ioan, „Baptiștii din România, victime ale discursului
naționalist după Marea Unire de la 1918 și susținătorii discursului
naționalist un secol mai târziu” în Jurnalul Libertății de Conștiință, Vol. 6, Nr. 1/2018. • Colda Teodor-Ioan, „Proselytism and other isms in the Contextof Social
Security in Present Day Romania” în Jurnalul Libertății de Conștiință –
supliment – 2016. • Colda Teodor-Ioan, „Proselytism and other isms in the Contextof Social
Security in Present Day Romania” în Jurnalul Libertății de Conștiință –
supliment – 2016. • Colda Teodor-Ioan, „Contribuția pastorului Constantin Adorian în
obținerea libertății religioase pentru baptiștii din România după Marea
Unire de la 1918” în Libertatea religioasă mereu în actualitate, volum
coordonat de Dr. Nelu Burcea, Dr. Ioan-Gheorghe Rotaru, Lect. univ. dr. Ieremia Rusu, Editura Uniersitară, București, 2012, p. 189. • Colda Teodor-Ioan, „Contribuția pastorului Constantin Adorian în
obținerea libertății religioase pentru baptiștii din România după Marea
Unire de la 1918” în Libertatea religioasă mereu în actualitate, volum
coordonat de Dr. Nelu Burcea, Dr. Concluzii Această scurtă incursiune are rolul de a releva faptul că dincolo de vicisi-
tudinile perioadelor interbelică și comunistă, Seminarul Teologic Baptist
din București a fost un far în lumea teologică din România care și-a
propus să promoveze integritatea alături de celelalte valori ale moralei CEEOL copyright 2022 CEEOL copyright 2022 Seminarul Teologic Baptist – un exemplu de integritate 705 creștine și să solicite de fiecare dată când a fost cazul dreptul la propria
existență în baza dreptului la libertate religioasă care se regăsea în docu-
mentele oficiale și în legea fundamentală a țării, Constituția. Bibliografie Ioan-Gheorghe Rotaru, Lect. univ. dr. Ieremia Rusu, Editura Uniersitară, București, 2012, p. 189. • Colda Teodor-Ioan, „Credincioșii baptiști și Holocautul din România,
sau cum li s-a negat pocăiților și evreilor demnitatea umană în România
anilor 1940-1944” în Jurnalul Libertății de Conștiință, Vol. 7, Nr. 2/2019. • Colda Teodor-Ioan, „Credincioșii baptiști și Holocautul din România,
sau cum li s-a negat pocăiților și evreilor demnitatea umană în România
anilor 1940-1944” în Jurnalul Libertății de Conștiință, Vol. 7, Nr. 2/2019. • Edworthy Mark, Te wall that remains, International Mission Board of
the Southern Baptist Convention, Ricmond, Virginia, 2012. • Edworthy Mark, Te wall that remains, International Mission Board of
the Southern Baptist Convention, Ricmond, Virginia, 2012. •
Home and Foreign Fields, Nr. 5, mai 1922. •
Home and Foreign Fields, Nr. 5, mai 1922. •
Home and Foreign Fields, Te Missionary Journal of the Southern
Baptist Convention, Nr. 10, October 1929, p. 30; •
Home and Foreign Fields, Te Missionary Journal of the Southern
Baptist Convention, Nr. 10, October 1929, p. 30; CEEOL copyright 2022 CEEOL copyright 2022 JURNALUL LIBERTĂȚII DE CONȘTIINȚĂ VOL. 8, NR. 2, 2020
706 • Mariș Marius Daniel, Colda Teodor - Ioan, Constantin Adorian: un lider
baptist vizionar, Editura Carmel Print, Arad, 2015. • Mariș Marius Daniel, Colda Teodor - Ioan, Constantin Adorian: un lider
baptist vizionar, Editura Carmel Print, Arad, 2015. • Matei Eugen, „J. H. Rushbrooke și libertatea religioasă a baptiștilor
români”, disponibil online la adresa https://chibzuieli.wordpress. com/2013/09/01/j-h-rushbrooke-si-libertatea-religioasa-a-
baptistilor-romani/, (31.07.2020) • Matei Eugen, „J. H. Rushbrooke și libertatea religioasă a baptiștilor
români”, disponibil online la adresa https://chibzuieli.wordpress. com/2013/09/01/j-h-rushbrooke-si-libertatea-religioasa-a-
baptistilor-romani/, (31.07.2020) • Popovici Alexa, Istoria baptiștilor din România, 1856–1989, 3 vol., ed. rev., Editura Făclia, Oradea, 2007. • Popovici Alexa, Istoria baptiștilor din România, 1856–1989, 3 vol., ed. rev., Editura Făclia, Oradea, 2007. • Revista Arhiva Baptistă Nr 1 (4) – 2020 ce a avut ca temă „Femeia
creștină baptistă din România interbelică”. • Revista Arhiva Baptistă Nr 1 (4) – 2020 ce a avut ca temă „Femeia
creștină baptistă din România interbelică”. • Revistei Arhiva Baptistă Nr. 2 (5)/ 2020, editată de Centrul de Istorie,
Genealogie și Statistică Baptistă din Arad, având ca titlu generic: Ioan
R. Socaciu cel mai longeviv conducător baptist. • Revistei Arhiva Baptistă Nr. 2 (5)/ 2020, editată de Centrul de Istorie,
Genealogie și Statistică Baptistă din Arad, având ca titlu generic: Ioan
R. Socaciu cel mai longeviv conducător baptist. Bibliografie • Silveșan Marius „Istoria unei instituții evanghelice: Seminarul Teologic
Baptist din România” în volumul Tradiție, istorie, armată. Lucrările
Sesiunii Internaționale de Comunicări Științifice „Tradiție, Istorie, Armată”,
Ediția a II-a, Constanța, 4-5 iunie 2015, coordonat de Olimpiu Manuel
Glodarenco, Editura Muzeului Militar Național „Regele Ferdinand I”,
Editura SITECH, Craiova, pp. 323-335. • Silveșan Marius „Istoria unei instituții evanghelice: Seminarul Teologic
Baptist din România” în volumul Tradiție, istorie, armată. Lucrările
Sesiunii Internaționale de Comunicări Științifice „Tradiție, Istorie, Armată”,
Ediția a II-a, Constanța, 4-5 iunie 2015, coordonat de Olimpiu Manuel
Glodarenco, Editura Muzeului Militar Național „Regele Ferdinand I”,
Editura SITECH, Craiova, pp. 323-335. • Silveșan Marius „Istoria unei instituții evanghelice: Seminarul Teologic
Baptist din România” în volumul Tradiție, istorie, armată. Lucrările
Sesiunii Internaționale de Comunicări Științifice „Tradiție, Istorie, Armată”,
Ediția a II-a, Constanța, 4-5 iunie 2015, coordonat de Olimpiu Manuel
Glodarenco, Editura Muzeului Militar Național „Regele Ferdinand I”,
Editura SITECH, Craiova, pp. 323-335. • Silveșan Marius „Istoria unei instituții evanghelice: Seminarul Teologic
Baptist din România” în volumul Tradiție, istorie, armată. Lucrările
Sesiunii Internaționale de Comunicări Științifice „Tradiție, Istorie, Armată”,
Ediția a II-a, Constanța, 4-5 iunie 2015, coordonat de Olimpiu Manuel
Glodarenco, Editura Muzeului Militar Național „Regele Ferdinand I”,
Editura SITECH, Craiova, pp. 323-335. • Silveșan Marius, „Incursiune în istoria Bisericilor Creștine Baptiste din
România anilor ‘80” în : „Studii de Istorie Eclesiastică”, vol. II, coord:
Marius Oanță, , Ed. Sitech, Craiova 2020, pp.259-286. • Silveșan Marius, „Incursiune în istoria Bisericilor Creștine Baptiste din
România anilor ‘80” în : „Studii de Istorie Eclesiastică”, vol. II, coord:
Marius Oanță, , Ed. Sitech, Craiova 2020, pp.259-286. • Silveșan Marius, Bisericile Creștine Baptiste din România: între persecuție,
acomodare și rezistență (1948-1965), Editura Cetatea de Scaun,
Târgoviște, 2012; • Silveșan Marius, Bisericile Creștine Baptiste din România: între persecuție,
acomodare și rezistență (1948-1965), Editura Cetatea de Scaun,
Târgoviște, 2012; • Stoica Daniel, „Earl Hester Truța” în Revista Arhiva Baptistă, Anul II,
Nr. 1, aprilie 2020. • Stoica Daniel, „Earl Hester Truța” în Revista Arhiva Baptistă, Anul II,
Nr. 1, aprilie 2020. CEEOL copyright 2022 CEEOL copyright 2022 CEEOL copyright 2022 707
Seminarul Teologic Baptist – un exemplu de integritate 707 707
Seminarul Teologic Baptist – un exemplu de integritate
Directorii Seminarului Teologic Baptist Directorii Seminarului Teologic Baptist Directorii Seminarului Teologic Baptist CEEOL copyright 2022 CEEOL copyright 2022 JURNALUL LIBERTĂȚII DE CONȘTIINȚĂ VOL. 8, NR. 2, 2020
708 Rectorii Institutului Teologic Baptist din București CEEOL copyright 2022 Rectorii Institutului Teologic Baptist din București Rectorii Institutului Teologic Baptist din București
|
https://openalex.org/W4390090334
|
https://geoscience.cz/ojs/index.php/GSE/article/download/425/308
|
English
| null |
Sediment Transport Modeling at the Oued Fodda Watershed Level Using HEC-RAS 1D Software
|
GeoScience Engineering
| 2,023
|
cc-by
| 6,055
|
ABSTRACT The objective of the current work is to determine the amount of sediments transported upstream and at the level
of Oued Fodda dam. The latter is considered one of the first large dams built in Algeria. It’s exposed to a serious
siltation problem that reduces its capacity every year. The simulation was executed using the HEC-RAS software,
for the period varied from January 01, 2016 to April 30, 2016. The modeled section consisted of about 9999 m
length, subdivided into 141 river stations distant from each other by 70 m. The observation of the studied river
section bed- profile was selected as a criterion for comparing the results of the model with the real values observed. A roughness coefficient of 0.031 was used. A quantitative estimate with a determination coefficient, R2, of 0.92
was used to support the validity. The mass and concentration of sediments increased significantly in the cross-
sections located at the dam upstream. A total cumulative mass was estimated at approximately 712699 tons, just
upstream of the dyke, and a maximum concentration of 22.35 g/l was observed, particularly for three main sections
selected upstream of the Fodda wadi. However, at the reservoir level, the concentration variability is observed
during flood periods, i.e., only for the most important flows. Keywords: GIS; HEC-RAS; Oued Fodda dam; Sediment transport; Siltation. Keywords: GIS; HEC-RAS; Oued Fodda dam; Sediment transport; Siltation SEDIMENT TRANSPORT MODELING AT THE OUED FODDA
WATERSHED LEVEL USING HEC-RAS 1D SOFTWARE Souhila BENKACI , Boualem REMINI Blida 1 University, Faculty of Technology, Department of Water Science and Environment, 9000 Blida, Algeria
E-mail: ssbenkaci73@gmail.com, reminib@yahoo.fr 1
INTRODUCTION Due to its importance, the transport of solid materials is a major problem in the Maghreb countries [1]. In Algerian
rivers, this problem has always arisen in an acute way. Due to the lack of data, its assessment remains complex. The enormous quantities of sediments transported are at the origin of the progressive reduction of the reservoirs
storage capacity. In fact, around 65 million cubic meters of silt is deposited annually in Algerian dams [2]. The
various bathymetric surveys effected during the period (1986–2008) by the National Agency for Dams and
Transfers (ANBT) on all 59 dams in exploitation revealed that the volume lost through silting was 898 mm³, i.e. 13.4% of the total reservoirs volume [3–4]. Numerous methods for estimating solid transport exist in the literature, including models that explore physical
laws such the St. Venant equation for the liquid phase, and the transport equations for the solid phase [5]. Although
they faithfully represent transport phenomena, these models require the introduction of a large number of
parameters. Mathematical models have been developed using three approaches: empirical models, which relate
the flow of sediment to the outfall, the various climatic and biophysical explanatory variables [5]. Its major
disadvantage is the difficulty of its calibration for large basins [6]. Regressive models (flow-TSS) deduced from
the ratio, between the observed flow, the values of the suspended solids concentration (Lefkir, 2009), and the
conceptual models, which consider erosion dynamics. These models have the advantage of estimating flows for
different time steps, but they require a relatively long calibration period, and peaks in TSS concentration which
are generally underestimated [7]. Researches has intensified and expanded to establish new methods: 1D models, numerous 2D models and finally
3D models, which have been developed to simulate sediment transport processes [8]. In view of this, our work is Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz GeoScience Engineering
geoscience.cz 161 a part of a one-dimensional solid material transport modeling using the HEC-RAS software. This code was created
by the U.S. Army Corps of Engineers and has been employed by several engineering firms and governmental
organizations [9]. It calculates the sediment transport capacity associated with each cross-section as a control
volume for all grain sizes [10]. The Wadi Fodda sub-watershed was selected for this study. 1
INTRODUCTION This basin is exposed
to a major problem of soil degradation, which accelerates the silting phenomenon at the level of the Wadi Fodda
dam. The latter is considered one of the first large dams built in Algeria. It’s intended for the irrigation of the
Middle Cheliff perimeter [11]. Its storage capacity has decreased considerably over the last 18 years. The siltation
rate has been estimated at about 54.29% and the bathymetric condition of the reservoir has become very worrying
[12]. 2
STUDY AREA The Upper and Middle Cheliff watershed is located in the west of the Fodda Wadi basin, which is covering a
surface area of 1153.5 km2. The larger Cheliff watershed, which is in the northwestern Algeria, is mostly occupied
by the latter and located in its northeastern portion (Fig. 1). Figure 1. Oued Fodda watershed Figure 1. Oued Fodda watershed The Oued Fodda sub-basin has a considerable relief, an elongated shape (Fig. 2), and a highest point can reach
1950,7 m [13]. With 282 temporary wadis and 81 permanent wadis totaling roughly 1053.45 km and 897.16 km,
respectively, it features a complex hydrographic network. It is mostly drained over a 92.14 km length by the Oued
Rouina [11]. Our study area is exposed to a serious problem of soil degradation. Gully erosion has been identified
towards the upstream of the basin [14] (Fig. 3). This is at the origin of an important production of sediment, which
accelerates the silting process at the level of the Wadi Fodda dam reservoir (Figs. 4 and 5). It collects an annual
volume of silt of 3.2 million m3 [15]. An annual loss of its storage capacity has been estimated to be about
4,248 km3, i.e. a silting rate of 45.43% in 2015 [13]. The Oued Fodda sub-basin has a considerable relief, an elongated shape (Fig. 2), and a highest point can reach
1950,7 m [13]. With 282 temporary wadis and 81 permanent wadis totaling roughly 1053.45 km and 897.16 km,
respectively, it features a complex hydrographic network. It is mostly drained over a 92.14 km length by the Oued
Rouina [11]. Our study area is exposed to a serious problem of soil degradation. Gully erosion has been identified
towards the upstream of the basin [14] (Fig. 3). This is at the origin of an important production of sediment, which
accelerates the silting process at the level of the Wadi Fodda dam reservoir (Figs. 4 and 5). It collects an annual
volume of silt of 3.2 million m3 [15]. An annual loss of its storage capacity has been estimated to be about
4,248 km3, i.e. a silting rate of 45.43% in 2015 [13]. Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz GeoScience Engineering
geoscience.cz 162 Figure 2. Hypsometric Oued Fodda watershed map Figure 2. Hypsometric Oued Fodda watershed map Figure 5. Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz The physiographic characteristics of the Oued Fodda sub-watershed were calculated based on ArcGisTM software
[16] and summarized in Table 1 below: Table 1. Physiographic characteristics of the Oued Fodda sub-basin
Characteristics
Value
Observation
Area (km2)
1153.5
-
Compactness index Kc
1.74
the basin is elongated favoring slow flow of runoff
Max. Altitude (m)
1950.7
Highest point of the basin
Average Altitude (m)
709.40
-
Median Altitude (m)
750
Represents 50% of the total surface area of the basin
Minimal Altitude (m)
142
Watershed outfall
Equivalent rectangle length (km)
93.144
-
Equivalent rectangle width (km)
12.384
-
Mean slope index Imoy (%)
1.72
-
Global slope Index Ig
0.1
Strong relief
Drainage density Ds (m)
328.16
- Table 1. Physiographic characteristics of the Oued Fodda sub-basin 2
STUDY AREA Vase deposit upstream of the Oued Fodda dam (Photo: Benkaci, August 2017)
Figure 3. Gully formation at the Oued
Fodda watershed
Figure 4. Oued Fodda dam reservoir view with an
initial capacity of 228 Mm3 (Photo: Remini, 2008) Figure 4. Oued Fodda dam reservoir view with an
initial capacity of 228 Mm3 (Photo: Remini, 2008) Figure 3. Gully formation at the Oued
Fodda watershed Figure 4. Oued Fodda dam reservoir view with an
initial capacity of 228 Mm3 (Photo: Remini, 2008) Figure 3. Gully formation at the Oued
Fodda watershed Figure 3. Gully formation at the Oued
Fodda watershed Figure 5. Vase deposit upstream of the Oued Fodda dam (Photo: Benkaci, August 2017) Figure 5. Vase deposit upstream of the Oued Fodda dam (Photo: Benkaci, August 2017) Figure 5. Vase deposit upstream of the Oued Fodda dam (Photo: Benkaci, August 2017) 163 The physiographic characteristics of the Oued Fodda sub-watershed were calculated based on ArcGisTM software
[16] and summarized in Table 1 below: The physiographic characteristics of the Oued Fodda sub-watershed were calculated based on ArcGisTM software
[16] and summarized in Table 1 below: 3.1 Model input parameters The calculation of sediment transport upstream and at the Fodda Wadi Dam requires three input data files, as
shown in Fig. 7. The calculation of sediment transport upstream and at the Fodda Wadi Dam requires three input data files, as
shown in Fig. 7. Figure 7. Methodological diagram of the input parameters in the HEC-RAS model
Model input parameters
Geometric Data
-
Image Shuttle Radar Topography
Mission (SRTM)
Triangulated irregular network (TIN)
Flow Data
Daily liquid flow rates
Mean slope
Sediment Data
Initial conditions and transport parameters
Bed gradation
Sediment boundary conditions Image Shuttle Radar Topography
Mission (SRTM)
Triangulated irregular network (TIN) Geometric Data Flow Data Sediment Data Figure 7. Methodological diagram of the input parameters in the HEC-RAS model The Manning’s coefficient is the most important parameter to be adjusted in the calibration of the HEC-RAS
model. The use of a single Manning’s coefficient may not be sufficient and adequate to represent the true roughness
of a river under different flow conditions [18]. Due to assumptions in the data or the model limitations, no model
will give findings that are exactly in line with the real results. But it is necessary to achieve a reasonable correlation
between observed values and model outcomes [10]. For our model, the adjustment of the Manning coefficient is performed following the hydraulic simulation of the
unstable flow over a period from January 01, 2016 until April 30, 2016. The water surface elevations (WSEl)
associated with the measured flow rates and the output flow rates estimated by the HEC RAS software are
compared as part of the calibration procedure. The values of the observed (measured) liquid flows are based on
the daily liquid flows obtained at the level of the Oued Fodda dam direction during the considered period. Several
roughness values were tested: 0.030, 0.031, 0.032, 0.033, 0.034 and 0.035. The Manning value retained (for which
the error is minimal) is equal to 0.031 [13]. 3
MATERIALS AND METHODS At the Wadi Fodda dam reservoir, the HEC-RAS program was primarily used to model the transport of sediment. It enables for all grain sizes and a control volume calculation of the transport capacity associated with each cross-
section (Fig.6). The Exner equation, also known as the mass conservation and the sediment continuity equation,
provides the foundation for its basic idea [10]: (1 −𝜆𝑝)𝐵
𝜕𝜂
𝜕𝑡= −
𝜕𝑄𝑠
𝜕𝑥 (1) (1) where: porosity of active layer, Figure 6. Control volume used in HEC-RAS sediment calculations [17] Figure 6. Control volume used in HEC-RAS sediment calculations [17] GeoScience Engineering
Vol. 69 (2023), No. 2
geoscience.cz
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz 164 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz 3.1.1 Geometric Data The geometry of the studied section was initially created in ArcGisTM using a form of digital geographic vector
data “TIN” (Fig. 8) extracted from the SRTM Worldwide Elevation Data (3 arc second Resolution 90 m) of the
Oued Fodda watershed (Fig. 9). These data are then exported using the HEC-GeoRas software and visualized
through the “Geometric Data” window (Fig. 10) with the HEC-RAS software [13]. The modeled section was
approximately 9999 m in length ، subdivided into 141 river stations of approximately 70 m per part. Section 69 is
located downstream (immediately upstream of the Wadi Fodda dam) at a distance of about 50 m (Fig. 11). On the
other hand, section 9945 is located upstream. It is therefore, considered as the first section of the upstream Oued
Fodda. Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz GeoScience Engineering
geoscience.cz 165 Figure 8. Triangulated irregular network (Tin) of the Oued Fodda watershed Figure 8. Triangulated irregular network (Tin) of the Oued Fodda watershed Figure 9. Shuttle Radar Topography Mission image, SRTM Worldwide Elevation Data (3 arc second
Resolution) of the Oued Fodda watershed Figure 9. Shuttle Radar Topography Mission image, SRTM Worldwide Elevation Data (3 arc second
Resolution) of the Oued Fodda watershed Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz 166 Figure 10. Geometrical data window visualized through a Google Earth image Figure 10. Geometrical data window visualized through a Google Earth image Figure 11. Characteristics of the upstream cross-section (69) of the Oued Fodda Dam dike Figure 11. Characteristics of the upstream cross-section (69) of the Oued Fodda Dam dike GeoScience Engineering
Vol. 69 (2023), N
geoscience.cz
pp. 160–178, ISSN 1802-5
DOI 10.35180/gse-2023-0 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz 167 3.1.3 Sediments data ta file is based on three main input quantities. These are illustrated in Fig. 14. The sediment data file is based on three main input quantities. These are illustrated in Fig. 14. The sediment data file is based on three main input quantities. These are illustrated in Fig. 14. Figure 14. Methodological diagram of the sediment data file
Sediment Data
Initial conditions and
Transport parameters
Transport
Functions
Bed evolution
Functions
Sedimentary
Sedimentation rate
Bed
Gradation
Granulometric
Analysis
Sediment boundary
conditions
Rating curve
Solid Flow Initial conditions and
Transport parameters Bed
Gradation Sediment boundary
conditions Bed evolution
Functions
Sedimentary Figure 14. Methodological diagram of the sediment data file 3.1.2 Flow data and boundary condition The simulation of sediment transport begins with the creation of a quasi-unstable flow file. Two boundary
conditions are considered (Fig. 12). •
The first is selected at the first cross section of the Fodda wadi (section 9945). For this condition, the data
of the daily liquid flows observed at the dam upstream have been introduced with a time step of 12 days
considering the duration of the simulation, which runs from January 1, 2016 to April 30, 2016. •
The first is selected at the first cross section of the Fodda wadi (section 9945). For this condition, the data
of the daily liquid flows observed at the dam upstream have been introduced with a time step of 12 days
considering the duration of the simulation, which runs from January 1, 2016 to April 30, 2016. •
The second boundary condition is located at the downstream (wadi Fodda dam dike). It simply
corresponds to the value of the average slope (0.0242) at the level of the cross-section considered (section
69). •
The second boundary condition is located at the downstream (wadi Fodda dam dike). It simply
corresponds to the value of the average slope (0.0242) at the level of the cross-section considered (section
69). Figure 12. HEC-RAS window of the quasi-unstable flow boundary conditions Figure 12. HEC-RAS window of the quasi-unstable flow boundary conditions The obtained flow hydrograph (Fig. 13) illustrates the occurrence of two major floods in March 2016. The first is
observed on March 12, corresponding to a flow rate of about 27 m3/s, and the second is observed on March 20
with an estimated flow rate of 20.66 m3/s. GeoScience Engineering
Vol. 69 (2023), No. 2
geoscience.cz
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097
Figure 13. Flow hydrograph Figure 13. Flow hydrograph Figure 13. Flow hydrograph Figure 13. Flow hydrograph Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz 168 3.1.3.2 Initial conditions and transport parameters Several combinations have been affected based on the eight transport functions, the five sedimentation rate
equations and the two sedimentary bed evolution models "Active layer and Exner 5". The input parameters are
defined and justified as follows: 3.1.3.1 Bed gradation The "bed gradation" data file is based on the results of the Granulometric analysis (Table 2). Samples were
collected from several segments along Wadi Fodda, just at the dam upstream. The granulometric analysis sample
was effected at the National Laboratory of Habitat and Construction (LNHC) of Oued Samar (Algiers). The curve
is represented in Fig. 15. Figure 15. Grading curve of the sample taken along the upstream section
of the Oued Fodda dam Figure 15. Grading curve of the sample taken along the upstream section
of the Oued Fodda dam Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz 169 Table 2. Granulometric analysis results Upstream Oued Fodda Sample
Grains (mm)
Coarse sand
Gravel
Fine sand
Percentages (%)
73.98 %
22.63 %
3.39 % By default, HEC-RAS uses 20-grain classes. The fraction of each class is specified as a percentage, or converted
to millimeters. (Fig. 16) illustrates the gradation curve at the upstream bed section of the Oued Fodda dam. fault, HEC-RAS uses 20-grain classes. The fraction of each class is specified as a percentage, or converte
limeters. (Fig. 16) illustrates the gradation curve at the upstream bed section of the Oued Fodda dam. By default, HEC-RAS uses 20-grain classes. The fraction of each class is specified as a percentage, or converted
to millimeters. (Fig. 16) illustrates the gradation curve at the upstream bed section of the Oued Fodda dam. Figure 16. Bed gradation of the upstream Oued Fodda section Figure 16. Bed gradation of the upstream Oued Fodda section • Sedimentary bed evolution functions • Sedimentary bed evolution functions The HEC RAS software proposes two functions: the Exner model: which considers an active three- bed layer and
the "Active Layer" model, which is an approximate simplification of two active bed layers. Both models are based
on the principle that the bed level increases proportional to the amount of mobilized particles (Fig. 17). Figure 17. Sedimentary bed evolution Models [20] Figure 17. Sedimentary bed evolution Models [20] The simulation did not work for the Active Layer model. However, Thomas' method (Exner 5) has been validated
for all transport functions. • Sedimentation rate Of the five methods generated by the HEC-RAS software, the Van Rijn method was selected. It is based on three
formulas expressed as a function of grain size: 𝜔=
(𝑠−1)𝑔.𝑑
18.𝜈
; 𝑆𝑖 0.001 < 𝑑≤0.1 𝑚𝑚
(3)
𝜔=
10.𝜈
𝑑[(
1+0.01 (𝑠−1)0.5
𝜈2
) −1] 𝑆𝑖 0.1 < 𝑑< 1 𝑚𝑚
(4)
𝜔= 1.1[(𝑠−1)𝑔. 𝑑]0.5 𝑆𝑖 𝑑≥1 𝑚𝑚
(5) 𝜔=
(𝑠−1)𝑔.𝑑
18.𝜈
; 𝑆𝑖 0.001 < 𝑑≤0.1 𝑚𝑚
(3)
𝜔=
10.𝜈
𝑑[(
1+0.01 (𝑠−1)0.5
𝜈2
) −1] 𝑆𝑖 0.1 < 𝑑< 1 𝑚𝑚
(4)
𝜔= 1.1[(𝑠−1)𝑔. 𝑑]0.5 𝑆𝑖 𝑑≥1 𝑚𝑚
(5) (5) where: where: where:
𝜔
particle velocity (m/s),
𝜈
kinematic viscosity (kg/m.s),
s
specific gravity of the particles,
d
particle diameter (m). The Van Rijn used a form factor of 0.7 to calculate the sedimentation rate of the particles, which is also the same
factor for the natural sand. Therefore, this method was used for our model (21–10). • Transport Functions Engelund Hansen's empirical formula for calculating the total load of sandy rivers, for a limited diameter range of
0.15mm < d < 5mm, is the suitable function for the evaluation of sediment transport upstream of the Wadi Fodda
Dam. It is given in the following dimensionless form [19]: 𝑞𝑠
̅
√(
𝛾𝑠
(𝛾𝑤−1))𝑔.𝑑3 = 0.08 (
𝐾2.𝑦
1
3
𝑔) 𝜏∗5
2
(2) 𝑞𝑠
̅
√(
𝛾𝑠
(𝛾𝑤−1))𝑔.𝑑3 = 0.08 (
𝐾2.𝑦
1
3
𝑔) 𝜏∗5
2 (2) where: K
overall Stickler’s coefficient including the roughness of the banks and the grains that constitute
the background, K
overall Stickler’s coefficient including the roughness of the banks and the grains that cons K
overall Stickler’s coefficient including the roughness of the banks and the grains that constitute
the background,
Y
flow height. the background, g
Y
flow height. g
Y
flow height. GeoScience Engineering
Vol. 69 (2023), No. 2
geoscience.cz
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz 170 This choice is validated based on the results of the granulometric analysis of our sample (Fig. 13). This choice is validated based on the results of the granulometric analysis of our sample (Fig. 13) It shows that the upstream bed section of oued Fodda consist about 77.37% of sand with a grain size of between
0.177–0.707 mm in diameter and about 22.63% by gravel with a size ranging from 2 mm to 16 mm. So more than
90% of our sample are within Enguland Hansen’s granulometric validity range. GeoScience Engineering
geoscience.cz 3.1.3.3 Sediment boundary conditions Sediment specific load curve
y = 4,0995x1,2546
R² = 0,2553
0,10
1,00
10,00
100,00
1000,00
10000,00
0,10
1,00
10,00
100,00
1000,00
Solide Flows Qs (m3/s)
Liquid Flows Ql (m3/s) Figure 19. Liquid-Solid Flow Correlation
y = 4,0995x1,2546
R² = 0,2553
0,10
1,00
10,00
100,00
1000,00
10000,00
0,10
1,00
10,00
100,00
1000,00
Solide Flows Qs (m3/s)
Liquid Flows Ql (m3/s) Figure 19. Liquid-Solid Flow Correlation Figure 20. Sediment specific load curve Figure 20. Sediment specific load curve 3.1.3.3 Sediment boundary conditions A “rating curve“ serves as the boundary condition for the upstream river station (9945). This determines a sediment
load based on the water flow. It represents the sediment load, from the upstream station, during the simulation. Therefore, the model uses this condition and calculates the change in bed shape, based on the sediment properties,
the selected transport function, and other hydraulic parameters. In our study, the evaluation of sediment transported
to the Oued Fodda dam, depends mainly on the solid flow series input data. The available observation file was Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz 171 provided from the Pontéba défluent hydrometric station obtained at the level of the national water resources agency
(ANRH). It is a series of solid transport data over a 29-year hydrological period (1983–2011). This station is
located on the downstream section of the Wadi Fodda dam. However, no hydrometric station is available at the
upstream section (Fig. 18) [13]. Figure 18. Situation of the Pontéba- défluent hydrometric station Figure 18. Situation of the Pontéba- défluent hydrometric station To determine the sediment transport data at the upstream sections dam, we proceed as follows: To determine the sediment transport data at the upstream sections dam, we proceed as follows: To determine the sediment transport data at the upstream sections dam, we proceed as follows: • we performed a liquid-solid flow correlation based on data from the Pontéba-Défluent downstream
station. The founded results are illustrated in Fig.19. • we used the established relation for the calculation of the upstream solid flows, based on the daily liquid
flows file obtained within the Fodda Wadi Dam Directorate. The relationship was found to have the
following form: 𝑄𝑠= 4.0995 𝑄𝑙
1.2546
(6) 𝑄𝑠= 4.0995 𝑄𝑙
1.2546 𝑄𝑠= 4.0995 𝑄𝑙
1.2546 (6) The sediment calibration curve, chosen as a boundary condition, was produced by taking into account the data
computed using equation 6 above. The resulting curve (Fig. 20) shows the proportional increase in sediment load
as a function of liquid flow [13]. Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz GeoScience Engineering
geoscience.cz 172 Figure 19. Liquid-Solid Flow Correlation
Figure 20. 4
RESULTS Several parameters are displayed following the final sediment transport simulation, at the upstream and at the level
of wadi Fodda dam. The main ones are: 3.2 Model calibration and validation The simulation was executed for the period from January 01, 2016 to April 30, 2016. An output file of all the
hydraulic parameters is obtained for the full simulation period. For sediment transport, the results are also
displayed in a “Sediment Output” file. These were quite vulnerable to the new bed gradation. In order to compare
the model findings with the actual observed values, bed profile observation (change in minimum elevation) was
used as the comparison criterion. (Fig.21). The validation was selected particularly for the flood of March 12, 2016
with a liquid flow rate of 27 m3/s. A lack of real data, since the solid flows used were obtained following the results of a correlation, which is due to
the fact that there is no hydrometric station at the upstream. Moreover, the calibration of the modelled and observed
profiles, showed the existence of an overestimation upstream (at the beginning of the simulation) and an
underestimation downstream (near the dike). A quantitative estimate with a determination coefficient R2 of 0.92,
supported the model validation. This suggests a respectable level of agreement between model predictions and
actual data. Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz GeoScience Engineering
geoscience.cz 173 Figure 21. Comparison of the observed and modelled bed profile by HEC-RAS
200
250
300
350
400
450
0
2000
4000
6000
8000
10000
Invert elevation (m)
Distance (m)
Hec-RAS bed profile
observed bed profile Figure 21. Comparison of the observed and modelled bed profile by HEC-RAS 4.1 Sediment mass cumulative variability The cumulative mass of the studied, sediment bed section (in tons), can be calculated in time and space for each
of the cross-sections. A gradual increase was observed throughout the simulation time (Fig. 22). The maximum
sediment mass (accumulated) is that formed by very coarse sand (VCS). It reaches a value of approximately
653581.375 tons. However, very fine sand (VFS) is the material with the lowest mass. It is estimated at 22537,283
tons. Figure 22. Sediment mass accumulation as a function of time at section 69 (downstream) Figure 22. Sediment mass accumulation as a function of time at section 69 (downstream) Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz GeoScience Engineering
geoscience.cz 174 The spatial accumulated mass sediment profile can also be plotted for each day of the simulation period. As an
example of that, the March 12, 2016 flood, as shown in Fig. 23. Figure 23. Spatial sediment accumulation profile for the March 12, 2016 flood Figure 23. Spatial sediment accumulation profile for the March 12, 2016 flood An increase in the (cumulative) sedimentary mass is observed from upstream (station 9945) to the downstream
(5000–6500 m) from which the mass gradually stabilizes to reach a value of 712699.25 tons immediately upstream
of the dike. Low flows or low velocities are responsible for the Fodda Wadi Dam reservoir's low fluctuation. Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 4.2 Sediments concentration variability The total sediment concentration (in mg/litre) gradually increases in space and time. This variation can be affected
by several parameters including flow rate, slope and bed roughness. A significant increase is observed particularly
in the upstream cross-sections of the Fodda wadi dam. As an example of the sections: 9883, 8971 and 6824 are
illustrated in Fig. 24. The maximum value reached for the three sections is estimated around 22.35 g/l. However,
within the dam reservoir, the variation in concentration is only observed during high-water periods (month of
March), i.e., only for the most important flows (stations 4861, 2896, 1182, 133 in Fig. 25). Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz 175 Figure 24. Temporal concentration variability at the upstream sections of the Fodda Wadi Dam Figure 24. Temporal concentration variability at the upstream sections of the Fodda Wadi Dam Figure 25. Temporal concentration variability at the Wadi Fodda Dam Figure 25. Temporal concentration variability at the Wadi Fodda Dam Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz GeoScience Engineering
geoscience.cz GeoScience Engineering
geoscience.cz 176 The spatial variation profile of the sediment concentration can be displayed for duration of simulation. A very
significant variation is observed at the upstream cross-sections of the Fodda wadi and also at the sections from the
downstream. An example is illustrated (Fig. 26) considering the two floods: 23 January and 2 February 2016. The
maximum value of the sediment concentration was estimated around 6736.267 mg/l for the January 23rd flood and
12278.532 mg/l for the February 2nd flood. The spatial variation profile of the sediment concentration can be displayed for duration of simulation. A very
significant variation is observed at the upstream cross-sections of the Fodda wadi and also at the sections from the
downstream. An example is illustrated (Fig. 26) considering the two floods: 23 January and 2 February 2016. The
maximum value of the sediment concentration was estimated around 6736.267 mg/l for the January 23rd flood and
12278.532 mg/l for the February 2nd flood. Figure 26. Spatial sediment concentration variability (Example of: 23 January and 02 February 2016 floods) Figure 26. Spatial sediment concentration variability (Example of: 23 January and 02 February 2016 floods) ACKNOWLEDGEMENT I would like to address a great thanks to the Algiers direction of dams and transfers (ANBT), to the chief of
exploitation and all the staff of the Oued Fodda dam, who facilitated my access to the Oued Fodda dam and who
put at my disposal all the necessary technical and operating data, and who accompanied me particularly, for the
recovery of the samples of silt at the level of the dam and at the level of the wadis located upstream. 5
CONCLUSION HEC RAS software was used to model solid transport at the Fodda Wadi dam reservoir. Once all of the parameters
were set to within their useful ranges, the model worked as expected. The observation of the bed profile was chosen
as a standard for contrasting the output of the model with the actual values that were observed. Also the R2, which
is equal to 0,92, is the coefficient of determination that supported the validation. This demonstrates strong
concordance between model predictions and actual data. We can therefore accept our model as suitable for
simulating sedimentary transport in one dimension. The bathymetric levees at Algerian reservoirs are rarely
performed. The employed method is especially useful for watersheds missing bathymetric data or without
hydrometric stations upstream of dams. [1] MEDDI, M. Contribution à l’étude du transport solide en Algérie du Nord [Contribution to the study of solid
transport in northern Algeria]. Larhyss Journal. 2015, no. 24, pp. 315–336. ISSN 1112-3680. Available at:
https://larhyss.net/ojs/index.php/larhyss/article/view/346 REFERENCES [1] MEDDI, M. Contribution à l’étude du transport solide en Algérie du Nord [Contribution to the study of solid
transport in northern Algeria]. Larhyss Journal. 2015, no. 24, pp. 315–336. ISSN 1112-3680. Available at:
https://larhyss.net/ojs/index.php/larhyss/article/view/346 p
y
j
p p
y
[2] REMINI, B. and D. BENSAFIA. (2016). Envasement des barrages dans les régions arides [Siltation of dams
in arid regions: Algerian examples]. Larhyss Journal. 2016. no. 27, pp. 63–90. ISSN 1112-3680. Available
at: https://larhyss.net/ojs/index.php/larhyss/article/view/450 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz 177 [3] TOUAHIR, S., A. ASRI, B. REMINI & S. HAMOUDI. Prédiction de l’érosion hydrique dans le bassin
versant de l’oued Zeddine et de l’envasement du barrage Ouled Mellouk (Nord-Ouest algérien) [Prediction
of water erosion in wadi Zeddine watershed and the silting of the Ouled Mellouk Dam (North-West of
Algeria)]. Géomorphologie: Relief, Processus, Environnement. 2018, vol. 24(2), pp. 167–182. ISSN 1957-
777X. DOI: 10.4000/geomorphologie.12083 g
p
g
[4] MINISTRY OF WATER RESOURCES REALIZATION. Siltation of dams. MEDA program
European Union – Directorate of hydraulic studies and development. 2010, vol. 3. [5] LEFKIR, A. Modélisation du transport solide par les modèles neuroflous [Modeling of solid transport by
neuroflous models]. Alger, 2009. Doctoral thesis. Ecole Nationale Polytechnique, Département
d'Hydraulique. y
q
[6] RASSI, W. Le transport solide: estimation et mesure [Solid Transport: Estimation and Measu
Limoges: Office international de l’eau, 2004. [7] PICOUET, C., B. HINGRAY & J.C. OLIVRY. Empirical and conceptual modelling of the suspended
sediment dynamics in a large tropical African river: the Upper Niger River basin. Journal of Hydrology. 2001, vol. 250(1–4), pp. 19–39. ISSN 0022-1694. DOI: 10.1016/S0022-1694(01)00407-3 [8] GHARBI, M. Étude des inondations et du transport de sédiments associé – application au bassin versant de
la Medjerda [Study of floods and associated sediment transport – application to the Medjerda watershed]. Toulouse, 2016. Doctoral thesis. Université de Toulouse, Institut National Polytechnique de Toulouse. Available at: https://oatao.univ-toulouse.fr/17382/ p
[9] ÉCOLE DE TECHNOLOGIE SUPÉRIEURE. HEC-RAS River Analysis System Guide de laboratoire:
Exemple pour la rivière du Loup [Example laboratory guide for the Rivière du Loup]. Version 3.1.3, CTN-
762 Ressources hydriques. Quebec: University of Quebec, École de technologie supérieure, Département de
Génie de la construction. [10] BEEBO, Q.N. & R.A. BILAL. Simulating bathymetric changes in reservoirs due to sedimentation. Application to Sakuma dam, Japan. Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 REFERENCES Lund, Sweden: Lund University, Department of Building and
Environmental Technology, Division of Water Resources Engineering, 2012. Available at:
https://lup.lub.lu.se/luur/download?func=downloadFile&recordOId=3051998&fileOId=3052010 [11] AGENCE DU BASSIN HYDROGRAPHIQUE CHELIFF-ZAHREZ. Cadastre hydraulique du bassin
hydrographie du Cheliff – Aval du barrage de Boughzoul [Hydraulic cadastre of the Cheliff hydrographic
basin – Downstream of the Boughzoul dam. Chlef: ABH CZ, 2004. [12] Rapport technique du barrage oued Fodda, Wilaya De Chlef. 2004. echnique du barrage oued Fodda, Wilaya De Chlef. 2 q
[13] BENKACI, S. Impact du transport solide sur l’évolution des dépôts boueux dans les barrages [Impact of
solid transport on the evolution of muddy deposits in dams]. Blida, 2020. Doctoral thesis. Université Saad
Dahlab de Blida, Faculté de Technologie, Département de Science de l’Eau et Environnement. [14] BENKACI, S., D. ABIR, A. OUMELLAL & B. REMINI. Modélisation de l’érosion du bassin haut et moyen
Cheliff par l’application Model builder sur ArcGis [Modeling of the erosion of the upper and middle Cheliff
basin by the Model builder application on ArcGis]. Journal of Materials and Engineering Structures. 2018,
vol.5(1), pp. 81–93. ISSN 2170-127X. Available at:
https://revue.ummto.dz/index.php/JMES/article/view/1676 [15] REMINI, B. & W. HALLOUCHE. Evolution de l’envasement du barrage d’Oued El Fodda (Algérie)
[Evolution of the silting up of the Oued El Fodda dam (Algeria)]. Wasser Energie Luft / Eau énergie air /
Acqua energia aria. 2007, vol. 99(1), pp. 75–78. ISSN 0377-905X. Available at: https://www.e-
periodica.ch/cntmng?pid=wel-004%3A2007%3A99%3A%3A414 p
g p
[16] ESRI. ArcGis 10.2.1 for desktop [software]. January 29, 2019. Available at: https://support.esri.com/en-
us/patches-updates/2019/arcgis-10-2-1-for-desktop-engine-server-utilities-and-t-7680 [17] BRUNNER, G.W. HEC-RAS River Analysis System User’s Manual. Version 4.1, CPD-68. Davis, CA: US
Army
Corps
of
Engineers,
Hydrological
Engineering
Center
(HEC),
2010. Available
at:
https://www.hec.usace.army.mil/software/hec-ras/documentation/HEC-RAS_4.1_Users_Manual.pdf p
y
p
[18] ENVIRONMENTAL CONSULTING & TECHNOLOGY. Appendix I: HEC-RAS Modeling of Rainbow
River. MFL Technical Support – Freshwater Stream. Final Report. Tampa, FL: Environmental Consulting
& Technology, Inc., 2017. Available at: https://www.swfwmd.state.fl.us/sites/default/files/documents-and-
t /
di /A
di
I df [19] BRUNNER, G.W. HEC-RAS, River Analysis System Hydraulic Reference Manual. Version 4.1, CPD-69. Davis, CA: US Army Corps of Engineers, Hydrologic Engineering Center (HEC), 2010. Available at:
https://www.hec.usace.army.mil/software/hec-ras/documentation/HEC-RAS_4.1_Reference_Manual.pdf p
y
_
_
_
p
[20] BRUNNER, G.W. HEC-RAS, River Analysis System Hydraulic Reference Manual. Version 5.0, CPD-69. Davis, CA: US Army Corps of Engineers, Hydrologic Engineering Center (HEC), 2016. Available at: Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 Vol. 69 (2023), No. 2
pp. 160–178, ISSN 1802-5420
DOI 10.35180/gse-2023-0097 GeoScience Engineering
geoscience.cz https://www.hec.usace.army.mil/software/hec-ras/documentation/HEC-
RAS%205.0%20Reference%20Manual.pdf
[21] JIMENEZ, J.A. & O.S. MADSEN. A Simple Formula to Estimate Settling Velocity of Natural Sediments.
Journal of Waterway, Port, Coastal, and Ocean Engineering. 2003, vol. 129(2), pp. 70–78. ISSN 0733-950X.
DOI: 10.1061/(ASCE)0733-950X(2003)129:2(70) 178
https://www.hec.usace.army.mil/software/hec-ras/documentation/HEC-
RAS%205.0%20Reference%20Manual.pdf
[21] JIMENEZ, J.A. & O.S. MADSEN. A Simple Formula to Estimate Settling Velocity of Natural Sediments.
Journal of Waterway, Port, Coastal, and Ocean Engineering. 2003, vol. 129(2), pp. 70–78. ISSN 0733-950X.
DOI: 10.1061/(ASCE)0733-950X(2003)129:2(70) 178 GeoScience Engineering
geoscience.cz GeoScience Engineering
geoscience.cz
|
https://openalex.org/W2800287677
|
https://link.springer.com/content/pdf/10.1007%2Fs00431-018-3135-9.pdf
|
English
| null |
Dutch guideline for clinical foetal-neonatal and paediatric post-mortem radiology, including a review of literature
|
European journal of pediatrics
| 2,018
|
cc-by
| 9,153
|
Dutch guideline for clinical foetal-neonatal and paediatric post-mortem
radiology, including a review of literature L. J. P. Sonnemans1 & M. E. M. Vester2,3,4 & E. E. M. Kolsteren5 & J. J. H. M. Erwich6 & P. G. J. Nikkels7 & P. A. M. Kint8 &
R. R. van Rijn2,3,4 & W. M. Klein1,9 & On behalf of the Dutch post-mortem imaging guideline group Received: 22 November 2017 /Revised: 5 February 2018 /Accepted: 26 March 2018 /Published online: 19 April 2018
# The Author(s) 2018 Abstract Clinical post-mortem radiology is a relatively new field of expertise and not common practice in most hospitals yet. With the
declining numbers of autopsies and increasing demand for quality control of clinical care, post-mortem radiology can offer a
solution, or at least be complementary. A working group consisting of radiologists, pathologists and other clinical medical
specialists reviewed and evaluated the literature on the diagnostic value of post-mortem conventional radiography (CR), ultra-
sonography, computed tomography (PMCT), magnetic resonance imaging (PMMRI), and minimally invasive autopsy (MIA). Evidence tables were built and subsequently a Dutch national evidence-based guideline for post-mortem radiology was devel-
oped. We present this evaluation of the radiological modalities in a clinical post-mortem setting, including MIA, as well as the
recently published Dutch guidelines for post-mortem radiology in foetuses, neonates, and children. In general, for post-mortem
radiology modalities, PMMRI is the modality of choice in foetuses, neonates, and infants, whereas PMCT is advised in older
children. There is a limited role for post-mortem CR and ultrasonography. In most cases, conventional autopsy will remain the
diagnostic method of choice. g
Conclusion: Based on a literature review and clinical expertise, an evidence-based guideline was developed for post-mortem
radiology of foetal, neonatal, and paediatric patients. L. J. P. Sonnemans and M. E. M. Vester shared first authorship and
contributed equally to this work. 1
Department of Radiology, Radboud University Medical Center,
Nijmegen, The Netherlands
2
Department of Radiology, Academic Medical Center,
Amsterdam, The Netherlands
3
Department of Forensic Medicine, Netherlands Forensic Institute,
The Hague, The Netherlands
4
Amsterdam Centre for Forensic Science and Medicine,
Amsterdam, The Netherlands
5
Knowledge Institute of Medical Specialists, Utrecht, The Netherlands
6
Department of Obstetrics and Gynaecology, University Medical
Center Groningen, University of Groningen,
Groningen, The Netherlands
7
Department of Pathology, University Medical Center Utrecht,
Utrecht, The Netherlands
8
Department of Radiology, Amphia Hospital, Breda, The Netherlands
9
Department of Radiology, Maastricht University Medical Center,
Maastricht, The Netherlands 1
Department of Radiology, Radboud University Medical Center,
Nijmegen, The Netherlands * M. E. M. Vester
m.e.vester@amc.uva.nl L. J. P. Sonnemans
lianne.sonnemans@radboudumc.nl
E. E. M. Kolsteren
e.kolsteren@kennisinstituut.nl
J. J. H. M. Erwich
j.j.h.m.erwich@umcg.nl
P. G. J. Nikkels
P.G.J.Nikkels@umcutrecht.nl
P. A. M. Kint
pkint@amphia.nl
R. R. van Rijn
r.r.vanrijn@amc.uva.nl
W. M. REVIEW
Dutch guideline for clinical foetal-neonatal and paediatric post-mortem
radiology, including a review of literature
L. J. P. Sonnemans1 & M. E. M. Vester2,3,4 & E. E. M. Kolsteren5 & J. J. H. M. Erwich6 & P. G. J. Nikkels7 & P. A. M. Kint8 &
R. R. van Rijn2,3,4 & W. M. Klein1,9 & On behalf of the Dutch post-mortem imaging guideline group REVIEW REVIEW European Journal of Pediatrics (2018) 177:791–803
https://doi.org/10.1007/s00431-018-3135-9 European Journal of Pediatrics (2018) 177:791–803
https://doi.org/10.1007/s00431-018-3135-9 Materials and methods The guideline was developed under the guidance of the
Dutch knowledge institute of medical specialists. An im-
portant objective of the Dutch knowledge institute is to
preserve and pool knowledge and expertise about the de-
sign and execution of quality assurance projects in the
realm of specialist medical care. Medline and Embase were
searched for studies comparing clinical post-mortem radi-
ology to autopsy in foetal, neonatal, and paediatric patients
from January 2000 up to January 2016, when the guideline
committee started her work (Appendix 1, a further detailed
search strategy is available upon request). Language selec-
tion was restricted to studies published in Dutch and
English. The study selection and analysis was performed
separately for the group of foetal and neonatal cases (de-
ceased within 28 days post-partum) and for the group of
paediatric cases (aged 1 month to 18 years). Studies were
initially screened on title and abstract (JE, RR), and here-
after analysed on full text (EK, JE, RR). Case reports and
forensic articles were excluded. Outcomes in sensitivity
and specificity were mandatory. Reference lists of included
studies were screened for additional relevant studies. What is Known: • Post-mortem investigations serve as a quality check for the provided health care and are important for reliable epidemiological registration. • Post-mortem radiology, sometimes combined with minimally invasive techniques, is considered as an adjunct or alternative to autopsy. What is New: • We present the Dutch guidelines for post-mortem radiology in foetuses, neonates and children. • Autopsy remains the reference standard however minimal invasive autopsy with a skeletal survey post-mortem com • We present the Dutch guidelines for post-mortem radiology in foetuses, neonates and children. • Autopsy remains the reference standard, however minimal invasive autopsy with a skeletal survey, post-mortem computed tomography, or post-mortem
magnetic resonance imaging can be complementary thereof. Keywords Post-mortem . Paediatric . Neonatal . Foetal . Radiology . Autopsy Keywords Post-mortem . Paediatric . Neonatal . Foetal . Radiology . Autopsy the basis for the evidence-based Dutch guideline for clinical
foetal, neonatal, and paediatric post-mortem radiology [17]. Abbreviations
CR
Conventional radiography
GRADE
Grading Recommendations Assessment,
Development and Evaluation
MaRIAS
Magnetic Resonance Imaging Autopsy Study
MIA
Minimally invasive autopsy
PMCT
Post-mortem computed tomography
PMMRI
Post-mortem magnetic resonance imaging Abbreviations
CR
Conventional radiography
GRADE
Grading Recommendations Assessment,
Development and Evaluation
MaRIAS
Magnetic Resonance Imaging Autopsy Study
MIA
Minimally invasive autopsy
PMCT
Post-mortem computed tomography
PMMRI
Post-mortem magnetic resonance imaging Abstract Klein
willemijn.klein@radboudumc.nl 2
Department of Radiology, Academic Medical Center,
Amsterdam, The Netherlands 2
Department of Radiology, Academic Medical Center,
Amsterdam, The Netherlands 3
Department of Forensic Medicine, Netherlands Forensic Institute,
The Hague, The Netherlands 3
Department of Forensic Medicine, Netherlands Forensic Institute,
The Hague, The Netherlands 4
Amsterdam Centre for Forensic Science and Medicine,
Amsterdam, The Netherlands 6
Department of Obstetrics and Gynaecology, University Medical
Center Groningen, University of Groningen,
Groningen, The Netherlands 7
Department of Pathology, University Medical Center Utrecht,
Utrecht, The Netherlands 9
Department of Radiology, Maastricht University Medical Center,
Maastricht, The Netherlands Eur J Pediatr (2018) 177:791–803 792 Introduction Paediatric post-mortem radiology, in addition to autopsy, is
becoming widely accepted as an important component of
cause of death determination [1–5]. The trend in declining
clinical autopsy rates in adults [6–9] is also evident in the
foetal and paediatric population, though higher autopsy rates
of approximately 50% remain [3, 10–13]. This decline is in
spite of evidence that clinical error rates persist: approximately
25% discrepancy between clinical ante-mortem diagnosis and
autopsy cause of death diagnosis [3, 11, 14, 15]. If an alternative, less- or non-invasive diagnostic method
could adequately determine the cause of death, current objec-
tions to conventional autopsy (e.g. its invasiveness) could be
met. Consequently, this might increase quality control and
subsequently improve clinical care. Post-mortem radiology
might be such an alternative diagnostic method. It can be
helpful for diagnosing anatomic abnormalities, identification
of syndromes, or to narrow down the differential diagnosis of
genetic disorders. Consequently, it can also be useful for
identifying potential siblings at risk, counselling for future
pregnancies, and helping the parents in their process of grief
[7, 16]. Methodological quality assessment of included studies was
performed (EK) according to the AMSTAR checklist,
PRISMA checklist, or QUADAS II, depending on the type
of article [18–20]. The joint evidence of included articles was
scored (EK) according to the Grading Recommendations
Assessment, Development and Evaluation (GRADE) tool
[21]. GRADE divides the quality (or certainty) of evidence
and conclusions into four categories: high, medium, low or
very low. A high GRADE level of evidence means that the
conclusion is unlikely to change with future research, whereas
in a very low GRADE level of evidence the conclusion is very
precarious. In addition to the level of evidence in literature,
expertise from the Dutch post-mortem imaging guideline
group members was taken into account, along with prefer-
ences of bereaved relatives, costs, availability of devices, Post-mortem radiology is evolving into a subspecialty,
reflected by the large increase of publications and the broad
spectrum of used techniques [1]. Nevertheless, a guideline on
the indications and contraindications for the use of post-
mortem conventional radiography (CR), ultrasonography,
computed tomography (PMCT), magnetic resonance imaging
(PMMRI), and minimally invasive autopsy (MIA), was not
yet available. This article provides the literature review that is 793 Eur J Pediatr (2018) 177:791–803 Fig. 2 Paediatric study selection. * Several papers had multiple reasons
for full text exclusion. Study identification The literature search resulted in 268 eligible articles for foe-
tuses and neonates and 415 articles for paediatric studies. After title, abstract, and full-text selection 14 foetal-neonatal
articles and 9 paediatric studies remained (Figs. 1 and 2). Studies on CR, PMCT, PMMRI, and MIA were included,
other post-mortem imaging methods (e.g. post-mortem ultra-
sound) did not meet the inclusion criteria. Fig. 2 Paediatric study selection. * Several papers had multiple reasons
for full text exclusion. Maximum one reason per article was scored,
according to the order presented Introduction Maximum one reason per article was scored,
according to the order presented and organisational issues when formulating the guideline
recommendations. and organisational issues when formulating the guideline
recommendations. Foetal-neonatal Both in foetal and neonatal patients, as well as in paediatric
patients, the GRADE evidence for post-mortem CR, PMCT,
and MIA was graded as low because few studies, with few
patients included, have been performed. More studies were pub-
lished on PMMRI, yet the evidence for PMMRI was also graded
as low in both groups, because almost all results were based on
the Magnetic Resonance Imaging Autopsy Study (MaRIAS). This study was performed in a specialised setting with well-
trained specialists and a relatively low number of patients. A clinical, foetal post-mortem skeletal survey consists
mainly of a whole-body radiograph; a ‘babygram’
(Fig. 3). A study of 377 foetal post-mortem skeletal surveys
showed a 100% sensitivity and 97% specificity for Fig. 3 Example of a diagnostic babygram. This pregnancy was
terminated at 22 weeks of gestation because of micromelia on prenatal
2nd trimester ultrasound, suspected to be a skeletal dysplasia. The
babygram showed skeletal abnormalities with shortened ribs,
metaphyseal flaring (1) and shortened and bowed long bones (2). Histology revealed abnormalities in the liver, kidneys, lungs, bone and
cartilage compatible with ciliopathy with major skeletal involvement. Jeune syndrome is the most likely diagnosis Post-mortem conventional radiography (CR) One article was included from the literature review on post-
mortem CR in foetal and neonatal patients. No articles on
post-mortem CR of paediatric patients met the inclusion
criteria. Fig. 1 Foetal-neonatal study selection. * Several papers had multiple
reasons for full text exclusion. Maximum one reason per article was
scored, according to the order presented Fig. 3 Example of a diagnostic babygram. This pregnancy was
terminated at 22 weeks of gestation because of micromelia on prenatal
2nd trimester ultrasound, suspected to be a skeletal dysplasia. The
babygram showed skeletal abnormalities with shortened ribs,
metaphyseal flaring (1) and shortened and bowed long bones (2). Histology revealed abnormalities in the liver, kidneys, lungs, bone and
cartilage compatible with ciliopathy with major skeletal involvement. Jeune syndrome is the most likely diagnosis Fig. 1 Foetal-neonatal study selection. * Several papers had multiple
reasons for full text exclusion. Maximum one reason per article was
scored, according to the order presented Eur J Pediatr (2018) 177:791–803 794 Table 1
Table of evidence of diagnostic performance of PMCT in foetuses, neonates and paediatric patients
Author (ref)
Year
Study design
Anatomical system
Outcome parameter
Foetuses < 24 weeks
of gestation
Foetuses > 24 weeks
of gestation
Neonates and children
Sensitivity
(95%CI)
Specificity
(95%CI)
Sensitivity
(95%CI)
Specificity
(95%CI)
Sensitivity
(95%CI)
Specificity
(95%CI)
Arthurs [23]
2016
Prospective
(MaRIAS)
General
Main diagnosis or cause of death
28 (13–51)
100 (44–100)
50 (22–79)
100 (61–100)
50 (29–71)
100 (74–100)
Any lesion (cardiac, thoracic,
neurologic, abdominal or skeletal)
67 (35–88)
91 (81–96)
62 (36–82)
93 (80–97)
58 (42–72)
95 (89–98)
Cardiac
Cardiac lesions
NA
100 (61–100)
100 (21–100)
100 (65–100)
50 (22–79)
100 (83–100)
Non-cardiac thoracic
Non-cardiac thoracic lesions
0 (0–79)
100 (51–100)
100 (34–100)
80 (38–96)
60 (36–80)
85 (58–96)
Neurologic
Neurologic lesions
100 (44–100)
67 (44–84)
50 (22–79)
100 (57–100)
58 (32–81)
100 (82–100)
Abdominal
Abdominal lesions
0 (0–79)
100 (65–100)
100 (21–100)
67 (30–90)
50 (10–91)
93 (77–98)
Musculo-skeletal
Skeletal lesions
75 (30–95)
100 (89–100)
0 (0–79)
100 (82–100)
100 (21–100)
96 (82–99)
Arthurs [24]
2015
Prospective
Non-cardiac thoracic
Abnormal lung areas
100 (52–100)a
63% (31–86)a detection of skeletal abnormalities compared to diagnosis
based on autopsy, genetics, and prenatal investigations
[22]. However, the number of diagnostic abnormalities in
this population was limited. Post-mortem computed tomography (PMCT) One study was included on the sensitivity and specificity of
PMCT for both foetal-neonatal and paediatric patients, and an
additional article on paediatric patients (Table 1). Foetal-neonatal PMCT and PMMRI were both compared to autopsy, and to
each other in 53 foetuses, finding 40% of the PMCT’s non-
diagnostic in foetuses below 24 weeks of gestation (n = 35)
compared to 11% of PMMRI’s, with twice as many correct
diagnoses on PMMRI compared to PMCT (10 vs. 5, p <
0.005) [23]. In foetuses above 24 weeks of gestation (n =
18), 22% of PMCT’s were non-diagnostic, compared to 0%
of PMMRI’s (p < 0.005). In cases where radiology was diag-
nostic, both PMCTand PMMRI showed a 50% sensitivity and
100% specificity for main diagnosis or cause of death. Also,
no significant differences were observed for identification of
pathological lesions in individual organ systems, irrespective
of contribution to death. Post-mortem conventional radiography (CR) The authors concluded that
there is no indication for a foetal post-mortem skeletal sur-
vey in cases without previous suspicion of skeletal abnor-
malities on prenatal ultrasound or during post-mortem ex-
ternal inspection. If a foetal ‘babygram’ is obtained, it
should preferably be done using a high resolution ‘cabinet
radiography’ system. If this is not available, the use of a
mammography system is advised. Paediatric Sensitivity of PMCT for cause of death determination depends
on the type of pathology and age of the child [23, 24]. The
same study as for foetuses and neonates, included 29 children
with an average age of 6.9 months (range 1 day–16 years)
[23]. In this small group, both PMCT and PMMRI showed a
50% sensitivity and 100% specificity for the main diagnosis or
cause of death. The overall concordance was slightly lower for
PMCT than PMMR (59.4% vs. 62.8%). In another study with
12 children under the age of 1 year, PMCT’s of the lungs were
non-diagnostic in 75% prior to post-mortem ventilation, com-
pared to 0% of PMCT’s with ventilation [24]. A 100% sensi-
tivity and 63% specificity were found for the detection of
abnormal lung areas with ventilated PMCT. Therefore, venti-
lated PMCT could be used to improve identification of abnor-
mal areas of the lungs. Eur J Pediatr (2018) 177:791–803 795 Foetal-neonatal MaRIAS reported a 100% sensitivity and 98% specificity for
major and minor structural heart defects in neonates and chil-
dren with 1.5 T PMMRI [25]. A substantial lower sensitivity
of 62% was observed for any cardiac pathology, both struc-
tural and non-structural. Identification of non-cardiac, thoracic
abnormalities was difficult, especially in case of pneumonia
[27]. Sensitivities of 100% and specificities of 98–100% were
reported for the detection of brain malformations and minor
and major intracranial haemorrhages [28]. In contrast to foe-
tuses, PMMRI showed a high sensitivity (93%) for ischaemic
brain injury in neonates and children. Just as in foetuses,
PMMRI showed a moderate sensitivity (71%) and high spec-
ificity (87%) for abdominal abnormalities [29]. The sensitivity
for skeletal abnormalities was poor (31%) [30]. Before the MaRIAS study, a systematic review, investigating
the diagnostic accuracy of PMMRI, included five studies on
foetuses [33]. In four of those five studies, a complete autopsy
was used as the reference standard. The included studies were
of moderate quality as the groups were small and the popula-
tion heterogeneity large. There was a pooled sensitivity of
69% (95%CI 56–80) and a pooled specificity of 95%
(95%CI 88–98) for detection of clinically significant
abnormalities. The MaRIAS study reported high sensitivities (82–100%)
and high specificities (93–97%) for both major and minor
cardiac pathology, as well as for structural and non-structural
heart disease in foetuses below and above 24 weeks of gesta-
tion [25]. Votino et al. (2012) compared high-field PMMRI
(9.4 T) to lower-field PMMRI (1.5 T and 3.0 T) and stereo-
microscopic autopsy (MIA) [26]. In contrast to lower-field
PMMRI, the heart situs, four-chamber view and outflow tracts
could be visualised in all foetuses with 9.4 T, irrespective of
gestational age. High-field PMMRI identified seven out of
eight cases with major congenital heart disease. In foetuses
below and above 24 weeks of gestation, MaRIAS reported
low sensitivities of 30 and 38% and high specificities of 96
and 88% respectively for the detection of non-cardiac, thorac-
ic abnormalities with 1.5 T [27]. Based on these results and the
reasonable negative predictive values of approximately 85%,
PMMRI appeared to be more useful in the exclusion of tho-
racic abnormalities, rather than in its identification. Detection
of pulmonary tract infection and diffuse alveolar haemorrhage
was difficult, whereas PMMRI was most sensitive for detec-
tion of anatomical abnormalities, including pleural effusions
and lung hypoplasia. Minimal invasive autopsy (MIA) One article included from the literature search reported on
MIA in both foetal-neonatal and paediatric patients
(MaRIAS) [31]. This study compared the diagnostic accuracy
of MIA to conventional autopsy. MIA consisted of PMMRI,
combined with other post-mortem radiology, genetic and met-
abolic tests (ante-mortem and post-mortem blood sampling), a
review of the clinical history, external examination, and ex-
amination of placental tissue, if available. No foetal-neonatal
or paediatric studies combining PMMRI or PMCT with tissue
biopsies or angiography met the inclusion criteria. Post-mortem magnetic resonance imaging (PMMRI) provided clinically important information in 23 out of 43 foe-
tuses in whom neuropathological examination was non-
diagnostic due to maceration. Seven articles were included on the diagnostic performance of
PMMRI in foetuses and neonates, along with five articles on
paediatric patients (Table 2). The majority of these studies
reported on the Magnetic Resonance Imaging Autopsy
Study (MaRIAS) (sub)population [23, 25, 27–30]. MaRIAS
is a large, 3.5 year, double-blind prospective study in 277
foetuses (185 foetuses of 24 weeks gestation or less and 92
foetuses of 24 weeks gestation or more) and 123 children (42
neonates, 53 infants up to 1 year of age, and 28 children above
1 year of age), which compared the diagnostic accuracy of
1.5 T PMMRI to conventional autopsy [31, 32]. PMMRI showed moderate sensitivities of 77 and 65% for
abdominal abnormalities in foetuses below and above
24 weeks gestation, respectively [29]. Diagnostic accuracy
was variable per organ system, with the highest sensitivity
for renal abnormalities (18/21 = 86%) and the lowest for in-
testinal abnormalities (2/7 = 29%). In addition, MaRIAS re-
ported moderate and very low sensitivities for detection of
musculoskeletal abnormalities in foetuses below and over
24 weeks of gestation, respectively 69 and 17% [30]. Foetal-neonatal Both a high sensitivity (100%, 95%CI 97–100) and high spec-
ificity (98%, 95%CI 88–100) were reported for the detection
of major pathological abnormalities or cause of death in foe-
tuses below 24 weeks of gestation [31]. In foetuses above
24 weeks of gestation, sensitivity and specificity were also
high (respectively 96%, 95%CI 86–99, and 95%, 95%CI
84–99). Moreover, MIA had a higher sensitivity and specific-
ity compared to PMMRI alone. In both groups of foetuses, the Based on MaRIAS, very high sensitivities (80–100%) and
specificities (87–100%) were found for the detection of brain
malformations (Fig. 4) and minor and major intracranial
bleedings [28]. A lower sensitivity of 30% was found for the
detection of hypoxic-ischaemic brain injury in foetuses above
24 weeks of gestation. Foetal-neonatal Furthermore, cerebral PMMRI 796 Eur J Pediatr (2018) 177:791–803 Table 2
Table of evidence of diagnostic performance of PMMRI in foetuses, neonates and paediatric patients
Author (ref) Year Study design
Anatomical system
Outcome parameter
Foetuses < 24 weeks
of gestation
Foetuses > 24 weeks
of gestation
Neonates and children
Sensitivity
(95%CI)
Specificity
(95%CI)
Sensitivity
(95%CI)
Specificity
(95%CI)
Sensitivity
(95%CI)
Specificity
(95%CI)
Arthurs [23] 2016 Prospective (MaRIAS) General
Main diagnosis or cause of death
40 (23–59)
100 (61–100)
50 (24–76)
100 (68–100)
50 (29–71)
100 (74–100)
Any lesion (cardiac, thoracic, neurologic,
abdominal or skeletal)
58 (39–76)
88 (81–93)
79 (57–92)
92 (83–96)
70 (55–82)
84 (76–90)
Cardio-vascular
Cardiac lesions
100 (44–100) 86 (69–94)
100 (44–100) 100 (80–100)
63 (31–86)
95 (77–99)
Non-cardiac thoracic Non-cardiac thoracic lesions
20 (4–62)
96 (78–99)
67 (21–94)
87 (62–96)
47 (26–69)
50 (25–75)
Neurological
Neurologic lesions
83 (44–97)
52 (32–72)
75 (41–93)
70 (40–89)
100 (76–100)
77 (53–90)
Abdominal
Abdominal lesions
40 (12–77)
100 (86–100) 100 (51–100)
93 (69–99)
100 (34–100)
82 (63–92)
Musculo-skeletal
Skeletal lesions
60 (23–88)
100 (88–100)
0 (0–79)
100 (82–100) 100 (21–100)
96 (82–99)
Taylor [25]
2014 Prospective (MaRIAS) Cardio-vascular
Structural and non-structural heart diseases 82 (59–94)
96 (91–98)
83 (44–97)
94 (87–97)
62 (41–79)
98 (93–100)
Structural heart defects (major and minor)
83 (61–94)
97 (92–99)
100 (57–100)
93 (85–98)
100 (77–100)
98 (94–100)
Major structural heart defects
87 (62–96)
99 (95–100)
100 (51–100)
99 (94–100) 100 (68–100) 100 (97–100)
Votino [26]
2012 Prospective (High-field
MRI, 9.4 T)
Cardio-vascular
Abnormalities of the four-chamber view
67 (30–92)
80 (52–95)
Outflow-tract-abnormalities
75 (20–96)
100 (83–100)
Abnormalities of the aortic arch
100a
100a
Abnormalities of the systemic veins
100a
100a
Arthurs [27] 2014 Prospective (MaRIAS) Non-cardiac thoracic Non-cardiac thoracic abnormalities
30 (17–47)
96 (91–98)
38 (19–61)
88 (79–94)
45 (33–58)
61 (48–72)
Arthurs [28] 2015 Prospective (MaRIAS) Neurological
Ischaemic brain injury
NA
100 (97–100)
30 (11–60)
90 (81–95)
93 (70–99)
95 (89–98)
Major intracranial bleed
100 (21–100) 99 (95–97)
100 (21–100) 100 (96–100) 100 (82–100)
99 (95–100)
Minor intracranial bleed
100 (21–100) 87 (80–91)
80 (38–96)
99 (93–100) 100 (44–100)
98 (94–100)
Brain malformations
86 (69–94)
90 (83–94)
90 (60–98)
96 (87–99)
100 (57–100) 100 (97–100)
Overall brain pathology
87 (71–95)
69 (60–77)
71 (53–84)
77 (64–86)
98 (90–100)
81 (70–89)
Arthurs [29] 2015 Prospective (MaRIAS) Abdominal
Abdominal abnormalities
77 (61–88)
95 (90–98)
65 (41–83)
89 (80–95)
71 (47–87)
87 (79–92)
Arthurs [30] 2014 Prospective (MaRIAS) Musculo-skeletal
Skeletal abnormalities
69 (50–84)
100 (97–100)
17 (3–56)
98 (92–99)
31 (13–58)
96 (91–99) 797 Eur J Pediatr (2018) 177:791–803 ventricle (3) was found on PMMRI along with the additional findings
of a left choroid plexus cyst (4) and polymicrogyria (5). Foetal-neonatal Furthermore,
autopsy diagnosed a choroid plexus papilloma in the left lateral ventricle,
but the additional finding of polymicrogyria (5) on PMMRI revealed
Aicardi syndrome as the most likely diagnosis. a Axial. b Sagittal Fig. 4 a, b Example of abnormalities of the central nervous system
diagnosed at PMMRI in a female foetus. This pregnancy was
terminated at 23 weeks of gestation because of corpus callosum
agenesis (1), an interhemispheric cyst (2) and fossa posterior anomalies
on prenatal 2nd trimester ultrasound, which were confirmed by PMMRI
and/or conventional autopsy. A non-cystic dilatation of the fourth ventricle (3) was found on PMMRI along with the additional findings
of a left choroid plexus cyst (4) and polymicrogyria (5). Furthermore,
autopsy diagnosed a choroid plexus papilloma in the left lateral ventricle,
but the additional finding of polymicrogyria (5) on PMMRI revealed
Aicardi syndrome as the most likely diagnosis. a Axial. b Sagittal Fig. 4 a, b Example of abnormalities of the central nervous system
diagnosed at PMMRI in a female foetus. This pregnancy was
terminated at 23 weeks of gestation because of corpus callosum
agenesis (1), an interhemispheric cyst (2) and fossa posterior anomalies
on prenatal 2nd trimester ultrasound, which were confirmed by PMMRI
and/or conventional autopsy. A non-cystic dilatation of the fourth Paediatric sensitivity and specificity for detection of non-infectious pa-
thologies were above 95%. Sensitivity for infectious patholo-
gies was with 80% (95%CI 38–96) lower in foetuses above
24 weeks of gestation than in foetuses below 24 weeks of
gestation (100%, 95%CI 92–100). A 69% sensitivity (95%CI 58–78) and 93% specificity
(95%CI 81–98) were found for major pathological abnor-
malities or cause of death in children [31]. Sensitivities of Fig. 5 Flowchart for post-mortem radiology in foetal and neonatal
deaths*. * adapted from the Dutch guideline for clinical foetal, neonatal,
and paediatric post-mortem radiology [17]. GA: gestational age. US:
ultrasonography. The ‘routine 2nd trimester ultrasound’ is a standard pre-
natal US in all growing foetuses. The ‘US for foetal death determination’
is a second, separate antenatal US by the gynaecologist in order to
confirm death. PMMRI: post-mortem magnetic resonance imaging. CNS: central nervous system. NODOK:: The Dutch ‘Nader Onderzoek
naar de DoodsOorzaak van Kinderen’ (i.e. ‘further examination of cause
of death in children’) procedure is a stepwise approach to investigate the
cause of death in children with an assumed natural unexpected and un-
explained death [34] Fig. 5 Flowchart for post-mortem radiology in foetal and neonatal
deaths*. * adapted from the Dutch guideline for clinical foetal, neonatal,
and paediatric post-mortem radiology [17]. GA: gestational age. US:
ultrasonography. The ‘routine 2nd trimester ultrasound’ is a standard pre-
natal US in all growing foetuses. The ‘US for foetal death determination’
is a second, separate antenatal US by the gynaecologist in order to confirm death. PMMRI: post-mortem magnetic resonance imaging. CNS: central nervous system. NODOK:: The Dutch ‘Nader Onderzoek
naar de DoodsOorzaak van Kinderen’ (i.e. ‘further examination of cause
of death in children’) procedure is a stepwise approach to investigate the
cause of death in children with an assumed natural unexpected and un-
explained death [34] 798 Eur J Pediatr (2018) 177:791–803 Fig. 6 Flowchart for post-mortem radiology in paediatric deaths*. *
adapted from the Dutch guideline for clinical foetal, neonatal, and paedi-
atric post-mortem radiology [17]. PMMRI: post-mortem magnetic reso-
nance imaging. PMCT: post-mortem computed tomography. NODOK:
The Dutch ‘Nader Onderzoek naar de DoodsOorzaak van Kinderen’ (i.e. ‘further examination of cause of death in children’) procedure is a step-
wise approach to investigate the cause of death in children with an as-
sumed natural unexpected and unexplained death [34] Fig. 6 Flowchart for post-mortem radiology in paediatric deaths*. Paediatric *
adapted from the Dutch guideline for clinical foetal, neonatal, and paedi-
atric post-mortem radiology [17]. PMMRI: post-mortem magnetic reso-
nance imaging. PMCT: post-mortem computed tomography. NODOK: The Dutch ‘Nader Onderzoek naar de DoodsOorzaak van Kinderen’ (i.e. ‘further examination of cause of death in children’) procedure is a step-
wise approach to investigate the cause of death in children with an as-
sumed natural unexpected and unexplained death [34] Discussion respectively 94% (95%CI 84–98) and 27% (95%CI 14–44)
were reported for the detection of non-infectious and in-
fectious pathologies, with specificities of respectively 96%
(95%CI 89–99) and 100% (95%CI 96–100). Pneumonia
and myocarditis were the main undetected abnormalities. This study showed an increase in the diagnostic accuracy
of post-mortem radiology when PMMRI was extended
with additional (minimal-invasive, genetic and metabolic)
tests or examination of placental tissue. Like in the foetal
patient group, MIA showed better results than PMMRI
alone. Autopsy is traditionally considered as the gold standard for
post-mortem diagnoses and quality assessment of provided
health care. However, the declining autopsy rates of the last
decennia result in decreasing expertise, especially in foetal-
neonatal and paediatric cases where mortality rates are low. Although autopsy remains the preferred diagnostic method in
foetal, neonatal, and paediatric death, post-mortem radiology,
after consent, can be used in adjunct to autopsy or as an alter-
native in cases without consent for conventional autopsy. In
general, PMMRI is advised in foetuses, neonates, and young
children, as PMMRI has a higher soft-tissue contrast com-
pared to PMCT. The small body size enables high-resolution
whole-body imaging in a reasonable amount of time. The
limited value of PMCT in young children is illustrated in a
study of 54 children (median age 1.0 years old, range 2 days–
17.9 years) who died of an assumed natural cause, where
PMCT could establish the cause of death in mere 12.9%
[34]. In older children, just as in adults, PMCT is the preferred
modality because of the lack of evidence of superiority of
PMMRI over PMCT, its high availability, lower costs, and
reduced scan time compared to PMMRI. With the limited Fig. 8 a, b Example of the
difference in resolution between
1.5 (a) and 7 (b) Tesla PMMRI in
a foetus of 18 weeks and 2 days of
gestation. The 7 T image shows
development of polymicrogyria
(arrow) of the left temporal cor-
tex, which is not detectable at the
1.5 T images Dutch post-mortem imaging guideline The Dutch guideline working group developed an evidence
and practice-based flowchart for post-mortem radiology in
non-forensic foetal and neonatal deaths (Fig. 5), and pae-
diatric deaths (Fig. 6). It must be emphasised that, based on
the literature, due to the low GRADE level of evidence,
post-mortem radiology without clinical autopsy should be
considered as insufficient for best-practice post-mortem
diagnosis. PMCTand PMMRI showed a volvulus of the ileum around its mesentery
(whirl sign) (arrow). Ischemic haemorrhagic volvulus of the ileum was
confirmed by autopsy (b) as the cause of death Fig. 7 a, b Example of a PMCT (a) of a 4-year-old child with an unex-
pected and unexplained but assumed natural cause of death. Cardiopulmonary resuscitation was performed but not successful. PMCTand PMMRI showed a volvulus of the ileum around its mesentery
(whirl sign) (arrow). Ischemic haemorrhagic volvulus of the ileum was
confirmed by autopsy (b) as the cause of death Fig. 7 a, b Example of a PMCT (a) of a 4-year-old child with an unex-
pected and unexplained but assumed natural cause of death. Cardiopulmonary resuscitation was performed but not successful. Fig. 9 a, b Examples of normal
post-mortem findings. (a)
Opacification dorsal in the lung
lobes due to septal oedema and
pleural fluid (arrow). (b)
Distension of bowel lumen due to
post-mortem gas formation, and
portal venous (1) and ventricular
gas (2) Eur J Pediatr (2018) 177:791–803 799 amount of studies in children, it is not possible to be more
specific about the age range where PMCT and PMMRI have
equal diagnostic performances. The Dutch guideline for pae-
diatric post-mortem radiology describes PMCT as a possible
adjunct to PMMRI and autopsy, in children of 2 to 5 years of
age (Fig. 7). Furthermore, either PMCT or PMMRI is advised
in children of 5 years or older, depending on the type of pa-
thology expected. Given the limited amount of evidence, we
would like to underline that, especially in infants and children,
post-mortem imaging should be seen as an adjunct to the
autopsy and not as a replacement. The cut-off age levels were
the results of combined expert opinion, this as there is insuf-
ficient evidence to define a set cut-off age level. survey or conventional radiographs in natural causes of death. In a study in 542 perinatal deaths (from 16 weeks gestation to
1 week after birth), the diagnostic value was very limited: 30%
had abnormal radiographs, of which only 0.9% were of diag-
nostic importance for establishing the cause of death [40]. Although ultrasound did not meet the inclusion criteria for
the guideline it is a technique that could be considered in
selected cases where parents do not approve the use of
PMCT or PMMRI [41–43]. Due to open sutures and absence
of inhaled air, the brain and lungs can be examined by ultra-
sonography in cases of foetal demise [44]. In 88 foetuses of
11–40 weeks of gestation sensitivities of 91, 88, and 87% and
specificities of respectively 90, 92, and 95% were reported
with ultrasound for respectively brain, thoracic and abdominal
anomalies [45]. No eligible paediatric studies on post-mortem CR were
included. Nevertheless, in deceased children up to 4 years of
age, a skeletal survey (consisting of 20–30 images) is advised
to detect fractures, potentially caused by non-accidental injury
[35–39]. In deceased children of 5 years or older, with possi-
ble child abuse, conventional radiographs of the areas of in-
terest are advised on a low-threshold basis. This is despite a
lack of evidence for the supplementary value of a skeletal To meet the demand for less invasive alternatives to autop-
sy [46, 47], as well as a high diagnostic performance, it is
likely that a combination of imaging and minimal invasive
tissue acquisition will be increasingly used in future. Eur J Pediatr (2018) 177:791–803 Other
minimal invasive techniques such as genetic and metabolic
testing as well as virology and microbiology sampling can . 9 a, b Examples of normal
st-mortem findings. (a)
acification dorsal in the lung
es due to septal oedema and
ural fluid (arrow). (b)
stension of bowel lumen due to
st-mortem gas formation, and
rtal venous (1) and ventricular
(2) 800 Eur J Pediatr (2018) 177:791–803 J.J.E. screened studies on title, abstract, and full text for the Dutch
guideline development, and developed the Dutch guideline for clinical
postmortem radiology. be added on indication. The more post-mortem radiology is
expanded with minimally invasive investigations, the higher
the diagnostic yield will be; the border area of a minimal
invasive radiological test and a restricted autopsy demands
for close collaboration between these two specialities. Furthermore, the diagnostic performance of post-mortem ra-
diology will increase by improvements of diagnostic tech-
niques such a high-field PMMRI (Fig. 8), post-mortem angi-
ography, and post-mortem ventilation [24, 48, 49]. Non- or
minimally invasive autopsy evokes much less objections from
parents compared to conventional autopsy, resulting in overall
increasing post-mortem investigation rates [46, 47]. Hence,
post-mortem radiology can increase post-mortem investiga-
tion rates, and subsequently improve family counselling and
quality control of clinical diagnosis. p
gy
P.K. developed the Dutch guideline for clinical postmortem radiology. P.K. developed the Dutch guideline for clinical postmortem radiology. P.N. developed the Dutch guideline for clinical postmortem radiology. P.N. developed the Dutch guideline for clinical postmortem radiology. R.R. screened studies on title, abstract, and full text for the Dutch
guideline development, and developed the Dutch guideline for clinical
postmortem radiology. W.K. chaired the Dutch post-mortem imaging guideline group and
developed the Dutch guideline for clinical postmortem radiology. All authors contributed to the interpretation of the data and revision of
the manuscript for important intellectual content. Funding The development of the Dutch postmortem imaging guideline
was funded by the Quality Foundation of the Dutch Medical Specialists
(SKMS). Guideline working group This guideline was developed and sponsored by the
Radiological Society of the Netherlands (NVvR), using gov-
ernmental funding from the Stichting Kwaliteitsgelden
Medisch Specialisten in the Netherlands (SKMS, Quality
foundation of the Dutch Federation of Medical Specialists). The early preparative phase started July 2015 and the guide-
line will officially be authorized by the Radiological Society
of the Netherlands at the end of 2017. The working group had
nine in-person meetings (between September 2015 and
September 2017) and otherwise communicated by phone
and email. Decisions were made by consensus. At the start
of guideline development, all working group members com-
pleted conflict of interest forms. Acknowledgements M.M.J. Ploegmakers (Knowledge Institute of
Medical Specialists, Utrecht, The Netherlands), M. Wessels
(Knowledge Institute of Medical Specialists, Utrecht, The Netherlands),
I.M.B. Russel (Department of Paediatrics, University Medical Center
Utrecht, the Netherlands), M. ten Horn (Patientfederation, Utrecht, the
Netherlands), R. Kranenburg (Patientfederation, Utrecht, the
Netherlands), D. van Meersbergen (The Royal Dutch Medical
Association (KNMG), the Netherlands). Compliance with ethical standards As post-mortem radiology is a relatively new subspecialty,
images should be evaluated by an experienced radiologist. This should preferably be a paediatric radiologist who is fa-
miliar with normal post-mortem changes, which to the un-
trained eye can mimic pathologic abnormalities (Fig. 9) [50,
51]. Therefore, it is advised for non-specialised centres to ask
assistance from experienced radiologists. Conflict of interest
The authors declare that they have no conflict of
interest. Appendix 1. Materials and methods To conclude, post-mortem radiology without clinical au-
topsy is yet considered as insufficient to establish the cause
of death, due to the low GRADE level of evidence. Autopsy is
therefore still regarded as the reference standard [23]. Post-
mortem radiology, especially as part of a MIA procedure, is
considered a useful adjunct or valuable alternative in cases
where autopsy is not performed. In general, neonatologists
or paediatricians will be the referring physicians and as such
they will be the ones obtaining parental informed consent. Therefore, it is imperative that they are aware of the advan-
tages and limitations of post-mortem imaging. A multidisci-
plinary approach including clinicians, radiologists, and pa-
thologists seems most beneficial. At present, PMMRI is the
imaging modality of choice in foetuses, neonates, and young
children, whereas PMCT is preferred in in older children. Text adjusted from Acta Orthopedica (Besselaar et al [52];
PubMed PMID: 28266239). Text adjusted from Acta Orthopedica (Besselaar et al [52];
PubMed PMID: 28266239). Methodology bodyofevidenceacrossallrelevant outcomes,valuesandprefer-
ences, and resource use. The strength of a recommendation re-
flects the extent to which the guideline panel was confident that
desirableeffectsoftheinterventionoutweighundesirableeffects,
or vice versa, across the range of patients for whom the recom-
mendation is intended. The strength of a recommendation is de-
terminedbyweightingallrelevantargumentstogether,theweight
ofthebodyofevidence from thesystematicliterature analysis,as
well as the weight of all complementary arguments. Guideline
panels must use judgment in integrating these factors to make a
strong or weak recommendation. Thus, a low quality of the body
of evidence from the systematic literature analysis does not ex-
clude a strong recommendation, and weak recommendations
may follow from high quality evidence [56]. The guideline was developed in agreement with the criteria set
by the advisory committee on guideline development of the
Federation of Medical Specialists in the Netherlands (Medisch
Specialistische Richtlijnen 2.0; OMS [53], which are based on
theAGREEII instrument (Brouwers [54]; www.agreetrust.org). Theguidelinewasdevelopedusinganevidence-basedapproach
endorsing GRADE methodology, and meeting all criteria of
AGREE-II. Grading of Recommendations Assessment,
Development and Evaluation (GRADE) is a systematic ap-
proach for synthesizing evidence and grading of recommenda-
tions offering transparency at each stage of the guideline devel-
opment [55, 56]. The guideline development process involves a number of
phases, a preparative phase, development phase, commentary
phase, and authorization phase. After authorization, the guide-
line has to be disseminated and implemented, and uptake and
use have to be evaluated. Finally, the guideline has to be kept
up-to-date. Each phase involves a number of practical steps
(see Schünemann [57]). After reaching consensus in the working group, the concept
guideline was subjected to peer review by all relevant
stakeholders. Amendments were made and agreed upon by
the working group, and the final text was presented to the
Dutch societies of medical specialists and other organiza-
tions that participated in the working group for approval
and formal authorization. The guideline will be published
and be freely accessible in the Dutch guideline database
(Richtlijnendatabase, www.richtlijnendatabase.nl). The Dutch
guideline database has a modular structure, with each clinical
question as a separate entry, thus allowing for modular updates. A methodologist together with the chairman of the working
group drafted a concept list of key issues which was exten-
sively discussed in the working group. The selected (high
priority) issues were translated into carefully formulated clin-
ical questions, defining patient/problem, intervention, and pri-
oritizing the outcomes relevant for decision-making. Target group and aims This guideline was developed for Dutch radiologists con-
cerned with postmortem radiology, and other medical special-
ists involved in postmortem diagnostics. The main purpose of
the guideline is to provide best possible care to fetuses or
neonates, children and their relatives in a postmortem radiol-
ogy setting, by informing optimal treatment decisions, and
reduce unwarranted variation in the delivery of postmortem
diagnostic care. Authors’ contributions L.S. reported on the literature review and Dutch
guideline for postmortem radiology/wrote the submitted manuscript, and
provided tables and figures for the manuscript. M.V. reported on the literature review and Dutch guideline for post-
mortem radiology/wrote the submitted manuscript, and provided tables
and figures for the manuscript. E.K. analysed appropriate articles on full text, performed methodolog-
ical quality assessment of included studies, and assessed the joint evi-
dence of included articles according to the GRADE tool. Eur J Pediatr (2018) 177:791–803 801 Methodology Particular attention was paid to relevant outcomes for relatives
of fetuses or children undergoing postmortem radiology and
defining minimal clinically important differences. Therefore,
a focus group was organized in cooperation with the
Federation of Patient Organizations in the Netherlands. Dutch post-mortem imaging guideline group Apart from the
named authors, the following persons are the collaborators in the
Dutch post-mortem imaging guideline group: W.L.J.M. Duijst
(GGD IJsselland Zwolle, the Netherlands, and Maastricht
University, the Netherlands), P.A.M. Hofman (Department of
Radiology, Maastricht University Medical Center, the
Netherlands), J.J.F. Kroll (Department of Radiology, Maastricht
University Medical Center, the Netherlands), N.S. Renken
(Department of Radiology, Reinier de Graaf Gasthuis, Delft, the
Netherlands), Y.O. Rosier (NVMBR Utrecht, the Netherlands),
C.I.E. Scheeren (Department of Intensive Care, Zuyderland
Heerlen, the Netherlands), S.J. Stomp (GGD, Amsterdam, the
Netherlands), P. van der Valk (Department of Pathology, Free
University Medical Center, Amsterdam, the Netherlands). Theliteraturewassystematicallysearchedusingthedatabases
MEDLINE (Ovid) and Embase (a detailed search strategy is
available upon request). Selection of the relevant literature was
based on predefined inclusion and exclusion criteria and was
carried out by members of the working group (JE, RR) in collab-
oration with the methodologist (EK). For each of the clinical
questions, the evidence was summarized by the guideline meth-
odologist using the GRADE approach: a systematic review was
performed for each of the relevant outcomes and the quality of
evidencewasassessedinoneoffourgrades(high,moderate,low,
very low) by analyzing limitations in study design or execution
(risk of bias), inconsistency of results, indirectness of evidence,
imprecision, and publication bias. The evidence synthesis was
complemented by a working group member (JE or RR) consid-
ering any additional arguments relevant to the clinical question,
including relatives values and preferences, and resource use
(costs, organization of care issues). Evidence synthesis, comple-
mentary arguments, and concept recommendations were exten-
sivelydiscussedintheworkinggroupandfinalrecommendations
were formulated. Final recommendations are based on the bal-
ance of desirable and undesirable outcomes, the quality of the 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 appro-
priate credit to the original author(s) and the source, provide a link to the
Creative Commons license, and indicate if changes were made. 1.
Baglivo M, Winklhofer S, Hatch GM, Ampanozi G, Thali MJ,
Ruder TD (2013) The rise of forensic and post-mortem References Burton JL, Underwood J (2007) Clinical, educational, and epide-
miological value of autopsy. Lancet 369(9571):1471–1480. https://
doi.org/10.1016/s0140-6736(07)60376-6 8. Hutchinson JC, Arthurs OJ, Ashworth MT, Ramsey AT, Mifsud W,
Lombardi CM, Sebire NJ (2016) Clinical utility of postmortem
microcomputed tomography of the fetal heart: diagnostic imaging
vs macroscopic dissection. Ultrasound Obstet Gynecol 47(1):58–
64. https://doi.org/10.1002/uog.15764 24. Arthurs OJ, Guy A, Kiho L, Sebire NJ (2015) Ventilated postmor-
tem computed tomography in children: feasibility and initial expe-
rience. Int J Legal Med 129(5):1113–1120. https://doi.org/10.1007/
s00414-015-1189-z 9. Sieswerda-Hoogendoorn T, Soerdjbalie-Maikoe V, Maes A, van
Rijn RR (2013) The value of post-mortem CT in neonaticide in
case of severe decomposition: description of 12 cases. Forensic
Sci Int 233(1–3):298–303. https://doi.org/10.1016/j.forsciint.2013. 09.023 25. Taylor AM, Sebire NJ, Ashworth MT, Schievano S, Scott RJ, Wade
A, Chitty LS, Robertson N, Thayyil S (2014) Postmortem cardio-
vascular magnetic resonance imaging in fetuses and children: a
masked comparison study with conventional autopsy. Circulation
129(19):1937–1944. https://doi.org/10.1161/circulationaha.113. 005641 10. Adappa R, Paranjothy S, Roberts Z, Cartlidge PH (2007) Perinatal
and infant autopsy. Arch Dis Child Fetal Neonatal Ed 92(1):F49–
F50. https://doi.org/10.1136/adc.2005.091447 26. Votino C, Jani J, Verhoye M, Bessieres B, Fierens Y, Segers V,
Vorsselmans A, Kang X, Cos T, Foulon W, De Mey J, Cannie M
(2012) Postmortem examination of human fetal hearts at or below
20 weeks’ gestation: a comparison of high-field MRI at 9.4 T with
lower-field MRI magnets and stereomicroscopic autopsy. Ultrasound Obstet Gynecol 40(4):437–444. https://doi.org/10. 1002/uog.11191 11. Brodlie M, Laing IA, Keeling JW, McKenzie KJ (2002) Ten years
of neonatal autopsies in tertiary referral centre: retrospective study. BMJ 324(7340):761–763. https://doi.org/10.1136/bmj.324.7340. 761 12. Hickey L, Murphy A, Devaney D, Gillan J, Clarke T (2012) The
value of neonatal autopsy. Neonatology 101(1):68–73. https://doi. org/10.1159/000329094 27. Arthurs OJ, Thayyil S, Olsen OE, Addison S, Wade A, Jones R,
Norman W, Scott RJ, Robertson NJ, Taylor AM, Chitty LS, Sebire
NJ, Owens CM (2014) Diagnostic accuracy of post-mortem MRI
for thoracic abnormalities in fetuses and children. Eur Radiol
24(11):2876–2884. https://doi.org/10.1007/s00330-014-3313-8 13. Khong TY (1996) A review of perinatal autopsy rates worldwide,
1960s to 1990s. Paediatr Perinat Epidemiol 10(1):97–105; discus-
sion 106–109. https://doi.org/10.1111/j.1365-3016.1996.tb00030.x 14. Custer JW, Winters BD, Goode V, Robinson KA, Yang T,
Pronovost PJ, Newman-Toker DE (2015) Diagnostic errors in the
pediatric and neonatal ICU: a systematic review. Pediatr Crit Care
Med 16(1):29–36. https://doi.org/10.1097/pcc.0000000000000274 28. References 1. Baglivo M, Winklhofer S, Hatch GM, Ampanozi G, Thali MJ,
Ruder TD (2013) The rise of forensic and post-mortem 802 Eur J Pediatr (2018) 177:791–803 radiology—analysis of the literature between the year 2000 and
2011. J Forensic Radiol Imaging 1(1):3–9. https://doi.org/10. 1016/j.jofri.2012.10.003 19. Shea BJ, Grimshaw JM, Wells GA, Boers M, Andersson N, Hamel
C, Porter AC, Tugwell P, Moher D, Bouter LM (2007)
Development of AMSTAR: a measurement tool to assess the meth-
odological quality of systematic reviews. BMC Med Res Methodol
7(1):10. https://doi.org/10.1186/1471-2288-7-10 2. Flach PM, Thali MJ, Germerott T (2014) Times have changed! Forensic radiology–a new challenge for radiology and forensic pa-
thology. AJR Am J Roentgenol 202(4):W325–W334. https://doi. org/10.2214/ajr.12.10283 20. Whiting PF, Rutjes AW, Westwood ME, Mallett S, Deeks JJ,
Reitsma JB, Leeflang MM, Sterne JA, Bossuyt PM (2011)
QUADAS-2: a revised tool for the quality assessment of diagnostic
accuracy studies. Ann Intern Med 155(8):529–536. https://doi.org/
10.7326/0003-4819-155-8-201110180-00009 3. Gordijn SJ, Erwich JJ, Khong TY (2002) Value of the perinatal
autopsy: critique. Pediatr Dev Pathol 5(5):480–488. https://doi. org/10.1007/s10024-002-0008-y 4. Lawn JE, Cousens S, Zupan J, Team LNSS (2005) 4 million neo-
natal deaths: when? Where? Why? Lancet 365(9462):891–900. https://doi.org/10.1016/S0140-6736(05)71048-5 21. Atkins D, Eccles M, Flottorp S, Guyatt GH, Henry D, Hill S,
Liberati A, O'Connell D, Oxman AD, Phillips B (2004) Systems
for grading the quality of evidence and the strength of recommen-
dations I: critical appraisal of existing approaches the GRADE
working group. BMC Health Serv Res 4(1):38. https://doi.org/10. 1186/1472-6963-4-38 5. Nijkamp JW, Sebire NJ, Bouman K, Korteweg FJ, Erwich JJHM,
Gordijn SJ (2017) Perinatal death investigations: what is current
practice? Semin Fetal Neonatal Med 22(3):167–175. https://doi. org/10.1016/j.siny.2017.02.005 22. Kamphuis-van Ulzen K, Koopmanschap DHJLM, Marcelis CLM,
van Vugt JMG, Klein WM (2016) When is a post-mortem skeletal
survey of the fetus indicated, and when not? J Matern Fetal
Neonatal Med 29(6):991–997. https://doi.org/10.3109/14767058. 2015.1029913 6. Blokker BM, Wagensveld IM, Weustink AC, Oosterhuis JW,
Hunink MG (2016) Non-invasive or minimally invasive autopsy
compared to conventional autopsy of suspected natural deaths in
adults: a systematic review. Eur Radiol 26(4):1159–1179. https://
doi.org/10.1007/s00330-015-3908-8 23. Arthurs OJ, Guy A, Thayyil S, Wade A, Jones R, Norman W, Scott
R, Robertson NJ, Jacques TS, Chong WK, Gunny R, Saunders D,
Olsen OE, Owens CM, Offiah AC, Chitty LS, Taylor AM, Sebire
NJ (2016) Comparison of diagnostic performance for perinatal and
paediatric post-mortem imaging: CT versus MRI. Eur Radiol 26(7):
2327–2336. https://doi.org/10.1007/s00330-015-4057-9 7. References Kleinman PK, Morris NB, Makris J, Moles RL, Kleinman PL
(2013) Yield of radiographic skeletal surveys for detection of hand,
foot, and spine fractures in suspected child abuse. AJR Am J
Roentgenol 200(3):641–644. https://doi.org/10.2214/ajr.12.8878 52. Besselaar AT, Sakkers RJB, Schuppers HA, Witbreuk MMEH,
Zeegers EVCM, Visser JD, Boekestijn RA, Margés SD, Van der
Steen MCM, Burger KNJ (2017) Guideline on the diagnosis and
treatment of primary idiopathic clubfoot. Acta Orthop 88(3):305–
309. https://doi.org/10.1080/17453674.2017.1294416 38. van Rijn RR, Sieswerda-Hoogendoorn T (2012) Educational paper:
imaging child abuse: the bare bones. Eur J Pediatr 171(2):215–224. https://doi.org/10.1007/s00431-011-1499-1 39. Wootton-Gorges SL, Soares BP, Alazraki AL, Anupindi SA, Blount
JP, Booth TN, Dempsey ME, Falcone RA Jr, Hayes LL, Kulkarni
AV, Partap S, Rigsby CK, Ryan ME, Safdar NM, Trout AT,
Widmann RF, Karmazyn BK, Palasis S (2017) ACR appropriate-
ness criteria(R) suspected physical abuse-child. J Am Coll Radiol
14(5s):S338–s349. https://doi.org/10.1016/j.jacr.2017.01.036 53. OMS, Orde van Medisch Specialisten (2011). Eindrapport Medisch
Specialistische Richtlijnen 2.0. Available from: www. kwaliteitskoepel.nl/kwaliteitsbibliotheek/leidraden/eindrapport-
medisch-specialistische-richtlijnen-2-0.html. 54. Brouwers M, Kho ME, Browman GP, Cluzeau F, Feder G, Fervers
B, Hanna S, Makarski J, on behalf of the AGREE Next Steps
Consortium (2010) AGREE II: Advancing guideline development,
reporting and evaluation in healthcare. Can Med Assoc J 182:
E839–E842. https://doi.org/10.1503/cmaj.090449 40. Olsen ØE, Espeland A, Maartmann-Moe H, Lachman R,
Rosendahl K (2003) Diagnostic value of radiography in cases of
perinatal death: a population based study. Arch Dis Child Fetal
Neonatal Ed 88(6):F521–F524. https://doi.org/10.1136/fn.88.6. F521 p
g
j
55. Guyatt G, Oxman AD, Akl EA, Kunz R, Vist G, Brozek J, Norris S,
Falck-Ytter Y, Glasziou P, de Beer H et al (2011) GRADE guide-
lines: 1. Introduction-GRADE evidence profiles and summary of
findings tables. J Clin Epidemiol 64:383–394. https://doi.org/10. 1016/j.jclinepi.2010.04.026 41. Charlier P, Chaillot PF, Watier L, Menetrier M, Carlier R, Cavard S,
Herve C, de la Grandmaison GL, Huynh-Charlier I (2013) Is post-
mortem ultrasonography a useful tool for forensic purposes? Med Sci
Law 53(4):227–234. https://doi.org/10.1177/0025802413479946 42. Prodhomme O, Baud C, Saguintaah M, Béchard-Sevette N, Bolivar
J, David S, Taleb-Arrada I, Couture A (2015) Comparison of post-
mortem ultrasound and X-ray with autopsy in fetal death: retrospec-
tive study of 169 cases. J Forensic Radiol Imaging 3(2):120–130. https://doi.org/10.1016/j.jofri.2015.04.002 56. Schünemann H, Brożek J, Guyatt G, Oxman A, editors. (2013)
GRADE handbook for grading quality of evidence and strength
of recommendations. Updated October 2013. The GRADE
Working Group. Available from www.guidelinedevelopment.org/
handbook. 57. References Arthurs OJ, Thayyil S, Pauliah SS, Jacques TS, Chong WK, Gunny
R, Saunders D, Addison S, Lally P, Cady E, Jones R, Norman W,
Scott R, Robertson NJ, Wade A, Chitty L, Taylor AM, Sebire NJ
(2015) Diagnostic accuracy and limitations of post-mortem MRI for
neurological abnormalities in fetuses and children. Clin Radiol
70(8):872–880. https://doi.org/10.1016/j.crad.2015.04.008 15. Shojania KG, Burton EC, McDonald KM, Goldman L (2003)
Changes in rates of autopsy-detected diagnostic errors over time:
a systematic review. JAMA 289(21):2849–2856. https://doi.org/10. 1001/jama.289.21.2849 29. Arthurs OJ, Thayyil S, Owens CM, Olsen OE, Wade A, Addison S,
Jones R, Norman W, Scott RJ, Robertson NJ, Taylor AM, Chitty
LS, Sebire NJ (2015) Diagnostic accuracy of post mortem MRI for
abdominal abnormalities in foetuses and children. Eur J Radiol
84(3):474–481. https://doi.org/10.1016/j.ejrad.2014.11.030 16. Rankin J, Wright C, Lind T (2002) Cross sectional survey of par-
ents’ experience and views of the postmortem examination. BMJ
324(7341):816–818. https://doi.org/10.1136/bmj.324.7341.816 17. Knowledge Institute of Medical Specialists (2017) Klinische post-
mortem radiologie. https://richtlijnendatabase.nl/. Accessed 2017 30. Arthurs OJ, Thayyil S, Addison S, Wade A, Jones R, Norman W,
Scott R, Robertson NJ, Chitty LS, Taylor AM, Sebire NJ, Offiah
AC (2014) Diagnostic accuracy of postmortem MRI for musculo-
skeletal abnormalities in fetuses and children. Prenat Diagn 34(13):
1254–1261. https://doi.org/10.1002/pd.4460 18. Moher D, Liberati A, Tetzlaff J, Altman DG, Group P (2009)
Preferred reporting items for systematic reviews and meta-analyses:
the PRISMA statement. Ann Intern Med 151(4):264–269. https://
doi.org/10.7326/0003-4819-151-4-200908180-00135 Eur J Pediatr (2018) 177:791–803 803 31. Thayyil S, Sebire NJ, Chitty LS, Wade A, Chong W, Olsen O,
Gunny RS, Offiah AC, Owens CM, Saunders DE, Scott RJ, Jones
R, Norman W, Addison S, Bainbridge A, Cady EB, Vita ED,
Robertson NJ, Taylor AM (2013) Post-mortem MRI versus con-
ventional autopsy in fetuses and children: a prospective validation
study. Lancet 382(9888):223–233. https://doi.org/10.1016/s0140-
6736(13)60134-8 45. Votino C, Bessieres B, Segers V, Kadhim H, Razavi F, Condorelli
M, Votino R, D'Ambrosio V, Cos T (2014) Minimally invasive fetal
autopsy using three-dimensional ultrasound: a feasibility study. Ultrasound Obstet Gynecol. https://doi.org/10.1002/uog.14642 46. Cannie M, Votino C, Moerman P, Vanheste R, Segers V, Van Berkel
K, Hanssens M, Kang X, Cos T, Kir M, Balepa L, Divano L, Foulon
W, De Mey J, Jani J (2012) Acceptance, reliability and confidence
of diagnosis of fetal and neonatal virtuopsy compared with conven-
tional autopsy: a prospective study. Ultrasound Obstet Gynecol
39(6):659–665. https://doi.org/10.1002/uog.10079 32. References Thayyil S, Sebire NJ, Chitty LS, Wade A, Olsen O, Gunny RS,
Offiah A, Saunders DE, Owens CM, Chong WK, Robertson NJ,
Taylor AM (2011) Post mortem magnetic resonance imaging in the
fetus, infant and child: a comparative study with conventional au-
topsy (MaRIAS protocol). BMC Pediatr 11:120. https://doi.org/10. 1186/1471-2431-11-120 47. Kang X, Cos T, Guizani M, Cannie MM, Segers V, Jani JC (2014)
Parental acceptance of minimally invasive fetal and neonatal autop-
sy compared with conventional autopsy. Prenat Diagn 34(11):
1106–1110. https://doi.org/10.1002/pd.4435 33. Thayyil S, Chandrasekaran M, Chitty LS, Wade A, Skordis-Worrall
J, Bennett-Britton I, Cohen M, Withby E, Sebire NJ, Robertson NJ,
Taylor AM (2010) Diagnostic accuracy of post-mortem magnetic
resonance imaging in fetuses, children and adults: a systematic
review. Eur J Radiol 75(1):e142–e148. https://doi.org/10.1016/j. ejrad.2009.10.007 48. Barber JL, Sebire NJ, Chitty LS, Taylor AM, Arthurs OJ (2015)
Lung aeration on post-mortem magnetic resonance imaging is a
useful marker of live birth versus stillbirth. Int J Legal Med
129(3):531–536. https://doi.org/10.1007/s00414-014-1125-7 49. Thayyil S, Cleary JO, Sebire NJ, Scott RJ, Chong K, Gunny R,
Owens CM, Olsen OE, Offiah AC, Parks HG, Chitty LS, Price
AN, Yousry TA, Robertson NJ, Lythgoe MF, Taylor AM (2009)
Post-mortem examination of human fetuses: a comparison of
whole-body high-field MRI at 9.4 T with conventional MRI and
invasive autopsy. Lancet 374(9688):467–475. https://doi.org/10. 1016/s0140-6736(09)60913-2 34. van Rijn RR, Beek EJ, van de Putte EM, Teeuw AH, Nikkels PG,
Duijst WL, Nievelstein R-JA, Group DN (2017) The value of post-
mortem computed tomography in paediatric natural cause of death:
a Dutch observational study. Pediatr Radiol 47(11):1514–1522 35. Belfer RA, Klein BL, Orr L (2001) Use of the skeletal survey in the
evaluation of child maltreatment. Am J Emerg Med 19(2):122–124. https://doi.org/10.1053/ajem.2001.21345 50. Klein WM, Bosboom DG, Koopmanschap DH, Nievelstein RA,
Nikkels PG, van Rijn RR (2015) Normal pediatric postmortem
CT appearances. Pediatr Radiol 45(4):517–526. https://doi.org/10. 1007/s00247-014-3258-8 36. Dubbins P, Price J, Johnson K, Maguire SA, Wall M, Jaspan T,
Hobbs C, Stoodley N, Chapman S, Kemp AM (2008) Standards
for radiological investigations of suspected non-accidental injury. Royal College of Paediatrics and Child Health, London 51. Offiah CE, Dean J (2016) Post-mortem CT and MRI: appropriate
post-mortem imaging appearances and changes related to cardio-
pulmonary resuscitation. Br J Radiol 89(1058):20150851. https://
doi.org/10.1259/bjr.20150851 37. References Schünemann HJ, Wiercioch W, Etxeandia I, Falavigna M, Santesso
N, Mustafa R, Ventresca M, Brignardello-Petersen R, Laisaar KT,
Kowalski S, Baldeh T, Zhang Y, Raid U, Neumann I, Norris SL,
Thornton J, Harbour R, Treweek S, Guyatt G, Alonso-Coello P,
Reinap M, Brozek J, Oxman A, Akl EA (2014) Guidelines 2.0:
systematic development of a comprehensive checklist for a success-
ful guideline enterprise. CMAJ 186(3):E123–E142. https://doi.org/
10.1503/cmaj.131237 43. Uchigasaki S, Oesterhelweg L, Gehl A, Sperhake JP, Puschel K,
Oshida S, Nemoto N (2004) Application of compact ultrasound
imaging device to postmortem diagnosis. Forensic Sci Int 140(1):
33–41. https://doi.org/10.1016/j.forsciint.2003.11.029 p
g
j
44. Prodhomme O, Baud C, Saguintaah M, Béchard-Sevette N, Bolivar
J, David S, Taleb-Arrada I, Couture A (2015) Principles of fetal
postmortem ultrasound: a personal review. J Forensic Radiol
Imaging 3(1):12–15. https://doi.org/10.1016/j.jofri.2015.01.008
|
https://openalex.org/W4385610085
|
https://www.researchsquare.com/article/rs-2799972/latest.pdf
|
English
| null |
Determinants of Pregnancy Outcomes After Assisted Reproductive Therapy: A Sample From the West Bank, Palestine
|
Curēus
| 2,023
|
cc-by
| 4,069
|
Determinants of Pregnancy Outcomes after
Assisted Reproductive Therapy: A Sample from the
West Bank, Palestine Hasan Arafat
(
hasan.arafat14@gmail.com
)
Augusta Victoria Hospital
https://orcid.org/0000-0002-6484-5606 Diaeddin Qamhia
Specialty Arab Hospital
Husam Maqboul
Al-Watani Hospital
Abdulsalam Al-Khayyat
An-Najah National University Diaeddin Qamhia
Specialty Arab Hospital
Husam Maqboul
Al-Watani Hospital
Abdulsalam Al-Khayyat
An-Najah National University Research Article License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full License Page 1/11 Page 1/11 Abstract Objective: Infertility is a public health issue with a huge impact on the well-being of affected couples. Despite the traditional valuing of fertility within the Palestinian society, no studies were conducted to
detect the determinants of pregnancy outcome in Palestine. This paper aims at detecting the
characteristics and pregnancy outcome after assisted reproductive technology (ART) of a sample of the
Palestinian society. Materials & Methods: A retrospective observational study was carried out at Razan Medical Center for
Infertility. Subjects were assigned 2 categories based on the type of infertility, 7 different categories
according to the cause of infertility, and 3 categories for the modality of treatment. Age at marriage, age
at presentation, duration of infertility, in addition to regularity of menstruation were also studied. Biochemical pregnancy was considered the endpoint for the purpose of analysis. Results: We reviewed the files of 459 subjects diagnosed with infertility. Of the studied subjects, 79.74%
had primary infertility, while 20.26% had secondary. According to diagnosis, 28.85% were found to be
infertile due to anovulation, 2.86% due to endometriosis, 16.74% attributed to male factor, 3.3% had tubal
damage, while 34.80% had no explainable cause. 13.43% of cases were multifactorial. Four biochemical
markers were assessed in our study, thyroid-stimulating hormone (TSH) (x̄=2.32±2.46), leutinizing
hormone (LH) (x̄=6.71±4.90), follicle-stimulating hormone (FSH) (x̄=6.59±6.11), and human prolactin
(hPRL) (x̄=41.88±6.50). The menstrual cycle was regular in 70.58% of subjects, in contrast to 29.41%
with irregular cycles. Female mean age at presentation 22.76±5.58, while their mean age of marriage was
22.76±4. Mean duration of infertility was 3.97±6.87. Patients were treated via 3 modalities, ovarian
stimulation (2.2%), intrauterine insemination (IUI) (29.58%), and intracytoplasmic sperm injection (ICSI)
(68.21%), with a rate of success of 51.85%. Of the studied factors, only diagnosis, FSH, and modality of
treatment had a significant impact on the outcome, with p-values of 0.040, 0.003, and <.0.001,
respectively. Conclusions: there is a strong relationship between diagnosis prior to intervention, level of FSH and
treatment modality on successful outcome of ART. ICSI was found to be superior to other modalities of
treatment. We recommend starting with ICSI to save patient time & effort. Study design and settings This is a retrospective cohort study. Data was collected from the electronic records of the patients who
presented to Razan Center for management and evaluation of infertility between 2015-2018. The study
included patients from Razan branches in three major cities in the West Bank of the Palestinian
Territories: Nablus, Ramallah and Bethlehem, which serve the whole Palestinian population in the West
Bank. Background Infertility is defined as failure to achieve clinical pregnancy after 12 months or more of regular,
unprotected sexual intercourse according to the World Health Organization (WHO) [1]. For many couples,
the lack of ability to have children will have a huge impact on social, physical and sexual activities in their
lives [2]. Infertility is a public health issue for couples in the reproductive age, affecting about 72.4 million
women aged 20-44 with an estimation of prevalence of 9% [3]. Infertility can be classified into primary
and secondary; primary infertility refers to couples who have never achieved pregnancy, whereas
secondary infertility refers to couples who have conceived at least once before, but now are unable to [4]. Infertility is defined as failure to achieve clinical pregnancy after 12 months or more of regular, Page 2/11 Page 2/11 As a result of the huge impact of infertility on individual and social well-being, many epidemiological
studies reviewed and analyzed the factors that have been attributed to infertility to provide guidance for
the prevention of infertility. Conventionally, these parameters include the age at which to start a family,
body mass index, duration of infertility, obstetric history, psychological stress, menstrual regularity,
environmental factors, and occupational exposures [5]. All of the steps must occur correctly during ovulation, fertilization, and implantation in order to achieve
pregnancy. Several factors can cause disturbance at any step, whether due to female or male reasons. Female reasons leading to infertility included: hormonal disorders [6], polycystic ovarian syndrome [7],
premature ovarian failure [8], endometriosis [9], fallopian tube obstruction [10], congenital uterine
anomalies [11], or due to complication of medical diseases (diabetes and hypothyroidism) [12,13]. Male
infertility is usually due to sperm abnormalities or hormonal imbalance [2,14]. Middle Eastern cultures, in which the Palestinian culture is part of, put a great emphasis on having larger
families, preferably early in their life. [15]. Palestinian women fertility rate is considered one of the highest
in the world, with an average of 4.38 births per woman [16]. Unfortunately, no studies were conducted to
detect the determinants of pregnancy outcome in Palestinian women. This paper aims at detecting the
characteristics and pregnancy outcome after assisted reproductive technology (ART) at Razan Medical
Center for Infertility. Inclusion and exclusion criteria All cases that met WHO definition of infertility, defined as the inability to conceive despite regular,
unprotected sexual intercourse for 12 consecutive months were included. Cases that presented for follow-
up of normal pregnancy, gender selection, frozen embryo transfer as well as records with missing data
were excluded. In addition, cases that did not meet the WHO definition of infertility in terms of duration
and inability to have regular sexual intercourse were also excluded. Sample and data collection Sample and data collection Page 3/11 Page 3/11 A total of 459 files were reviewed according to the above-mentioned inclusion & exclusion criteria. Patients were assigned into the following 6 different categories, based on their cause of infertility: male
factor, anovulation (including those with polycystic ovarian syndrome (PCOS), ovarian insufficiency,
whether premature or age rated, and hypogonadotropic hypogonadism), endometriosis, assigned a
separate category due to the ambiguity of the exact mechanism by which it causes infertility, tubal
damage, multifactorial, patients with more than one cause of infertility in which a single cause of
infertility couldn’t be identified. The unexplained category was reserved for patients with no apparent
cause of infertility despite having a regular menstrual cycle; male seminal analysis was found to be
normal; normal sexual activity (at least twice a week); and uterine cavity and tubes were found to be
normal on hysterosalpingogram. Biochemical markers of infertility included follicle stimulating hormone (FSH), leutenizing hormone (LH),
thyroid stimulating hormone (TSH) and human prolactin (hPRL). Other sociodemographic factors were
extracted including age at presentation & duration of marriage. Gravidity and parity were recorded using
the gravida/para/abortus system (GPA). Patient menstrual status was recorded as regular or irregular
based on the patient own answer. At Razan Center for Infertility, three modalities were used for treatment:
ovarian stimulation, intrauterine insemination (IUI), and intracytoplasmic sperm injection (ICSI). Data Analysis The primary endpoint of the study was biochemical pregnancy, defined as a positive serum β-human
gonadotropin (β-hCG) test. The predictors investigated for association with a positive biochemical
pregnancy were diagnosis, level of TSH, day two LH, day two FSH, hPRL, age at marriage, age at
presentation, duration of infertility, regularity of the menstrual cycle, and modality of treatment. Endpoint
and predictors were described as means and standard deviations (SD) for quantitative variables and as
absolute values and percentages for categorical variables. Differences in predictor variables according to
the presence or absence of biochemical pregnancy were described using chi-squared test and t-test, as
appropriate. Statistical significance was defined as a two-sided p-value <0.05. All data were analyzed
using the STATA Data Analysis and Statistical Software, version 14. Results The total number of infertile females who met the inclusion criteria was 459. The mean age of the
sample was 26.81 (SD ± 5.84, range 17 to 45 years). The duration of infertility was less than 5 years in
390 females (80.2%), and was 5 years or more in 96 females (19.75%). Three hundred and sixty-six
(79.7%) females had primary infertility with the rest of the sample (20.2%) having secondary infertility. Details of the demographic data of the females are listed in Table 1. Page 4/11 Table 1. Sample Characteristics (N=459)
Mean Age ± SD in years
26.81 ± 5.84
Mean Duration of infertility ± SD in years
3.97 ± 6.87
Primary infertility, N (%)
366 (79.7)
Secondary infertility, N (%)
93(20.2) 131 cases (28.85%) were diagnosed as infertile due to anovulation, disregarding whether anovulating
was due to PCOS, hypogonadotropic hypogonadism, or premature ovarian failure.76 cases (16.74%) were
attributed to male factors, 15 cases (3.3%) were due to tubal damage, 13 cases (2.86%) were due to
endometriosis, 158 cases (34.8%) were due to an unexplained cause, defined as patients with no
apparent cause of infertility despite having a regular menstrual cycle, and 61 cases (13.43%) being
multifactorial (infertility attributed to more than one of the above mentioned causes). 131 cases (28.85%) were diagnosed as infertile due to anovulation, disregarding whether anovulating
was due to PCOS, hypogonadotropic hypogonadism, or premature ovarian failure.76 cases (16.74%) were
attributed to male factors, 15 cases (3.3%) were due to tubal damage, 13 cases (2.86%) were due to
endometriosis, 158 cases (34.8%) were due to an unexplained cause, defined as patients with no
apparent cause of infertility despite having a regular menstrual cycle, and 61 cases (13.43%) being
multifactorial (infertility attributed to more than one of the above mentioned causes). 366 (79.74%) were attributed to primary infertility, defined as the inability to conceive despite 12 months
of regular, unprotected vaginal intercourse, 324 (70.58%) had regular menses. Ten cases (2.2%) were
treated with ovarian stimulation with hormonal treatment constituted. 134 (29.58%) of cases were treated
with IUI made, while the majority of the cases (68.21%) were treated with ICSI. Table 2 shows the
categorical variables and outcome with p-values. Table 3 lists the mean and SD for biochemical markers
of infertility, age at marriage and at presentation and duration of infertility for the total sample, pregnancy
and no pregnancy outcomes Page 5/11 Page 5/11 Page 5/11 Table2. Results Type of infertility, diagnose, menstrual status and modality of treatment for the total
sample, pregnancy and non-pregnancy outcomes with p-values (N=459)
Total
N (%)
Pregnant
N (%)
Non-
pregnant
N (%)
p-value
Type of Infertility
Primary
366
(79.74)
189
(51.64)
177 (48.36)
0.268
Secondary
93 (20.26)
54 (58.06)
39 (41.94)
Diagnosis
Anovulation
131
(28.85)
65 (49.62)
66 (50.38)
0.040
Endometriosis
13 (2.86)
10 (76.92)
3 (22.08)
Male Factor
76 (16.74)
46 (60.53)
30 (39.47)
Tubal Damage
15 (3.30)
11 (73.33)
4 (26.67)
Unexplained
158
(34.80)
73 (46.20)
85 (53.80)
Multifactorial
61 (13.43)
36 (59.02)
25 (40.98)
Menstrual Status
Regular
324
(70.58)
168
(51.85)
156 (48.15)
0.469
Irregular
135
(29.41)
75 (55.56)
60 (44.44)
Modality of
Treatment
Ovarian
Stimulation
10 (2.20)
4 (40.00)
6 (60.00)
<0.001
IUI
134
(29.58)
33 (24.63)
101 (75.37)
ICSI
309
(68.21)
201
(65.05)
108 (34.95) Table 3. Mean and SD for biochemical markers of infertility, age at marriage and at
presentation and duration of infertility for the total sample, pregnancy and no pregnancy
outcomes
Total Sample
Mean (±SD)
Pregnant
Mean (±SD)
Non-Pregnant
Mean (±SD)
p-value
TSH
0.592
2.32 ± 2.46
2.25 ± 2.38
2.38 ± 2.54
LH
0.995
6.71 ± 4.90
6.71 ± 4.91
6.71 ± 4.89
FSH
0.003
6.59 ± 6.11
6.06 ± 5.72
7.12 ± 6.50
hPRL
36.94 ± 5.78
46.82 ± 7.21
0.282
41.88 ± 6.50
Age at Marriage
0.308
22.76 ±5.58
22.49 ± 4.82
23.03 ± 6.34
Age at Presentation
0.805
26.81 ± 5.84
26.75 ± 5.30
26.88 ± 5.30
Duration of Infertility
0.99
3.97 ± 6.87
3.97 ± 0.29
3.98 ± 0.60 Discussion Page 6/11 In our study, we aimed at evaluating the effect of hormones, demographic determinants as well as
treatment modality on biochemical pregnancy among a female sample from Palestine. Despite being a
developing country, Palestine pattern of fertility is considered distinct compared to that of other,
surrounding developing nations in that the high fertility rate coexists with a high level of educations and
low level of infant mortality. Moreover, due to the special political situation in Palestine, fertility is not
considered a mere biological reality, but a political one; Palestinian women desire to have more children
as a means of resisting the continuous displacement and human loss due to ongoing conflict [16]. In our study, we found a statistically significant relationship (p-value of 0.003) between pre-in
vitro fertilization (IVF) FSH level and biochemical pregnancy, which was in agreement with several studies
in which FSH level was found to be a significant negative predictive factor of clinical pregnancy [17,18]. LH level was not statistically insignificant (p-value of 0.995) with regard to biochemical pregnancy test. This finding was opposed to some studies showing the mean serum concentration of LH was
significantly low in couples who conceive in comparison to couples who did not [19,20]. The other studied
hormones, namely TSH, and hPRL (p = 0.592, 0.282, respectively), did not have a statistically significant
relationship with the outcome and the success of the pregnancy trial, which was in agreement with
previous studies that showed no significant difference between the two groups in the serum
concentration of TSH and hPRL [19]. In addition, we found a very strong relationship between the
modality of treatment and biochemical pregnancy. As we predicted, the pre-treatment diagnosis had a
statistically significant relationship (p = 0.04) with the outcome, but in the clinical practice, it is rare for
child-bearing age women to have an isolated reproductive disorder, as most of them suffer from multiple
conditions [21], this means that multiple, coexisting reproductive disorders should be taken into account
when studying pregnancy outcome, our finding coincides with another study that summarizes all
reproductive disorders that could affect the pregnancy outcome in women-childbearing age [22]. Our
results revealed that whether the patient hadn’t had a previous pregnancy (primary infertility), or failed to
conceive after one or more successful pregnancies (secondary infertility) had no statistical significance
on the outcome (p = 0.268). Discussion Whether the patient had a regular menstrual cycle or not did not impact the
outcome of treatment (p = 0.469). Chronological parameters of the patient did not impact the outcome of
treatment as well, the mean age at marriage was relatively the same when comparing that of women with
successful outcome compared to those with a failure result (23.03 years of age vs. 22.49 years), the
relationship, as expected, was not statistically significant (p = 0.308). The age of presentation did not
have any significant effect on outcome (p = 0.805), as expected by the close means of the age of
successful vs unsuccessful cases (26.75 vs. 26.88). The duration of infertility, measured as the number
of years between getting married and presenting to the infertility center. Those who presented before
fulfilling one year of infertility were told to come back after fulfilling the required duration, as there were
no difference between successful and unsuccessful cases regarding the duration of infertility (both
groups had a mean of 3.98), the relationship was statistically insignificant (p =0.99). These findings
might be attributed to the fact that most of the women studied belonged to the same categorical age, and
further studies, including more women of a wider spectrum of age categories, should be conducted. Regarding the modality of treatment, a very strong relationship was found between the type of modality Page 7/11 Page 7/11 and the success of the cycle, as the rate of success for intracytoplasmic sperm injection (ICSI) was
significantly higher compared to intrauterine injection and ovarian stimulation (68.21% vs 29.58% vs
2.20%), with p-value of 0.001. and the success of the cycle, as the rate of success for intracytoplasmic sperm injection (ICSI) was
significantly higher compared to intrauterine injection and ovarian stimulation (68.21% vs 29.58% vs
2.20%), with p-value of 0.001. This clinical audit is considered the first of its type at Razan Medical Center for infertility, as it will help
modify and enhance the clinical practice and patient care. In addition, the large sample size helped define
the actual relationships between different determinants. Being a retrospective cohort study, its results are
considered relatively strong and reliable. Our study was limited by the high number of incomplete files,
manifested by the fact that of the total of 459 infertile females enrolled in the study, only 291 completed
their investigations, giving a rate of (63.5%). Discussion The insufficient data were in the biochemical markers of
infertility included follicle stimulating hormone, and leutenizing hormone. In addition to patient non-
adherence and lack of follow-up for some patients, preventing us from knowing the outcome of the
treatment. Conclusion & Recommendations In conclusion, we found a strong relationship between FSH and diagnosis with the success of treatment. Our most important finding was the extremely significant relationship between ICSI and positive outcome,
as it was superior to both IUI and ovarian stimulation when it comes to achieving a positive end-result. We recommend starting with ICSI with patients adequate for this modality of treatment to save patient
time and effort in achieving their desired results. However, this remained an obstacle given how expensive
ICSI is compared to IUI. Furthermore, we recommend testing FSH hormone as routine for patient who
present to IVF center. Abbreviations Page 8/11 Page 8/11 Abbreviation
Stands for
WHO
World Health Organization
ART
Assisted reproductive technology
PCOS
Polycystic ovary syndrome
FSH
Follicle-stimulating hormone
LH
Leutinizing hormone
TSH
Thyroid-stimulating hormone
hPRL
Human prolactin
GPA
Gravida/porta/abortus
IUI
Intrauterine insemination
ICSI
Intracytoplasmic sperm injection
hCG
Human chorionic gonadotropin
SD
Standard deviation
IVF
In vitro fertilization References 1. Zegers-Hochschild F, Adamson GD, de Mouzon J, et al.: International Committee for Monitoring
Assisted Reproductive Technology (ICMART) and the World Health Organization (WHO) revised glossary
of ART terminology, 2009. Fertility and sterility. 2009, 92:1520-1524. 10.1016/j.fertnstert.2009.09.009 1. Zegers-Hochschild F, Adamson GD, de Mouzon J, et al.: International Committee for Monitoring
Assisted Reproductive Technology (ICMART) and the World Health Organization (WHO) revised glossary
of ART terminology, 2009. Fertility and sterility. 2009, 92:1520-1524. 10.1016/j.fertnstert.2009.09.009 2. Smith JF, Walsh TJ, Shindel AW, et al.: Sexual, marital, and social impact of a man's perceived infertility
diagnosis. The journal of sexual medicine. 2009, 6:2505-2515. 10.1111/j.1743-6109.2009.01383.x 2. Smith JF, Walsh TJ, Shindel AW, et al.: Sexual, marital, and social impact of a man's perceived infertility
diagnosis. The journal of sexual medicine. 2009, 6:2505-2515. 10.1111/j.1743-6109.2009.01383.x 2. Smith JF, Walsh TJ, Shindel AW, et al.: Sexual, marital, and social impact of a man's perceived infertility
diagnosis. The journal of sexual medicine. 2009, 6:2505-2515. 10.1111/j.1743-6109.2009.01383.x 3. Boivin J, Bunting L, Collins JA, Nygren KG: International estimates of infertility prevalence and
treatment-seeking: potential need and demand for infertility medical care. Human reproduction (Oxford,
England). 2007, 22:1506-1512. 10.1093/humrep/dem046 3. Boivin J, Bunting L, Collins JA, Nygren KG: International estimates of infertility prevalence and
treatment-seeking: potential need and demand for infertility medical care. Human reproduction (Oxford,
England). 2007, 22:1506-1512. 10.1093/humrep/dem046 4. Tabong PT-N, Adongo PB: Infertility and childlessness: a qualitative study of the experiences of infertile
couples in Northern Ghana. BMC Pregnancy and Childbirth. 2013, 13:72. 10.1186/1471-2393-13-72 4. Tabong PT-N, Adongo PB: Infertility and childlessness: a qualitative study of the experiences of infertile
couples in Northern Ghana. BMC Pregnancy and Childbirth. 2013, 13:72. 10.1186/1471-2393-13-72 5. Sharma R, Biedenharn KR, Fedor JM, Agarwal A: Lifestyle factors and reproductive health: taking
control of your fertility. Reprod Biol Endocrinol. 2013, 11:66-66. 10.1186/1477-7827-11-66 5. Sharma R, Biedenharn KR, Fedor JM, Agarwal A: Lifestyle factors and reproductive health: taking
control of your fertility. Reprod Biol Endocrinol. 2013, 11:66-66. 10.1186/1477-7827-11-66 6. Kazerooni T, Dehghan-Kooshkghazi M: Effects of metformin therapy on hyperandrogenism in women
with polycystic ovarian syndrome. Gynecological endocrinology : the official journal of the International
Society of Gynecological Endocrinology. 2003, 17:51-56. 7. Lash MM, Yaghamee A, Strohsnitter W, Lalwani S: Association between secondary infertility and
fallopian tube obstruction on hysterosalpingography. The Journal of reproductive medicine. 2008,
53:677-680. 8. Declarations Ethical approval: this manuscript was reviewed and accepted by An-Najah National University
International Review Board (IRB) committee Ethical approval: this manuscript was reviewed and accepted by An-Najah National University
International Review Board (IRB) committee Consent for publication: not applicable Availability of data and material: Data essential for the conclusion are included in this manuscript. Additional data can be obtained from the corresponding author on a reasonable request. mpeting interests: the authors declare that they have no competing interests. Competing interests: the authors declare that they have no competing interests. Competing interests: the authors declare that they have no competing interests. Funding: the authors received no financial support for the research, authorship, and publication of this
article. Funding: the authors received no financial support for the research, authorship, and publication of this
article. Authors’ contribution: HA, DQ, and HM conceived the study. AK performed analysis. HA, DQ, and HM
wrote the original draft of the manuscript. HA and AK revised the manuscript. HA wrote the final
manuscript. All authors contributed to the writing and reviewed and approved the manuscript. Acknowledgement: We would like to acknowledge Dr. Salem Abu-Khaizaran, founder and manager of
Razan Medical Center for Infertility who helped during the data collection period and provided us with the
necessary access. Page 9/11 Page 9/11 Page 9/11 References Shen S-Y, Huang S-Y, Hsieh C-H, Hsu M-I, Cheng C-Y, Hsu C-S: Clinical and biochemical characteristics
of women with menstrual disturbance. Taiwanese Journal of Obstetrics and Gynecology. 2014, 53:178-
182. https://doi.org/10.1016/j.tjog.2014.04.009 9. Wang PH, Su WH, Sheu BC, Liu WM: Adenomyosis and its variance: adenomyoma and female fertility. Taiwanese journal of obstetrics & gynecology. 2009, 48:232-238. 10.1016/s1028-4559(09)60295-3 10. Lavy G, Diamond MP, DeCherney AH: Ectopic pregnancy: its relationship to tubal reconstructive
surgery. Fertility and sterility. 1987, 47:543-556. 10.1016/s0015-0282(16)59100-6 11. Barbanti S, Chiamulera N, Botelho B: Vaginal septoplasty in septate uterus with double cervix. Case
Rep Obstet Gynecol. 2014, 2014:367360-367360. 10.1155/2014/367360 12. Codner E, Merino PM, Tena-Sempere M: Female reproduction and type 1 diabetes: from mechanisms
to clinical findings. Human reproduction update. 2012, 18:568-585. 10.1093/humupd/dms024 Page 10/11 13. Päkkilä F, Männistö T, Hartikainen A-L, Suvanto E: Maternal Thyroid Function During Pregnancy and
the Child's Linguistic and Sensory Development in the Northern Finland Birth Cohort 1986. Front
Endocrinol (Lausanne). 2018, 9:127-127. 10.3389/fendo.2018.00127 14. Ugwuja EI, Ugwu NC, Ejikeme BN: Prevalence of low sperm count and abnormal semen parameters in
male partners of women consulting at infertility clinic in Abakaliki, Nigeria. African journal of reproductive
health. 2008, 12:67-73. 14. Ugwuja EI, Ugwu NC, Ejikeme BN: Prevalence of low sperm count and abnormal semen parameters in
male partners of women consulting at infertility clinic in Abakaliki, Nigeria. African journal of reproductive
health. 2008, 12:67-73. 15. Klaus D, Suckow J, Nauck B: The Value of Children in Palestine and Turkey: Differences and the
Consequences for Fertility. Current Sociology. 2007, 55:527-544. 10.1177/0011392107077637 16. Pell S: Reproductive decisions in the lives of West Bank Palestinian women: Dimensions and
contradictions. Global Public Health. 2017, 12:135-155. 10.1080/17441692.2016.1151541 17. Frazier LM, Grainger DA, Schieve LA, Toner JP: Follicle-stimulating hormone and estradiol levels
independently predict the success of assisted reproductive technology treatment. Fertility and sterility. 2004, 82:834-840. 10.1016/j.fertnstert.2004.02.144 18. Chen YP, Wu WH, Wu HM, Chen CK, Wang HS, Huang HY: Effects of anti-Mullerian hormone and
follicle stimulating hormone levels on in vitro fertilization pregnancy rate. Taiwanese journal of obstetrics
& gynecology. 2014, 53:313-316. 10.1016/j.tjog.2013.06.012 19. Ashrafi M, Jahanian Sadatmahalleh S, Akhoond MR, Ghaffari F, Zolfaghari Z: ICSI Outcome in Infertile
Couples with Different Causes of Infertility: A Cross-Sectional Study. International journal of fertility &
sterility. 2013, 7:88-95. 20. Shanmugham D, Vidhyalakshmi RK, M. References SH: The effect of baseline serum luteinizing hormone levels
on follicular development, ovulation, conception and pregnancy outcome in infertile patients with
polycystic ovarian syndrome. 2017. 2017, 7:5. 10.18203/2320-1770.ijrcog20175869 21. Holoch KJ, Savaris RF, Forstein DA, et al.: Coexistence of Polycystic Ovary Syndrome and
Endometriosis in Women with Infertility. Journal of Endometriosis and Pelvic Pain Disorders. 2014, 6:79-
83. 10.5301/je.5000181 22. Vannuccini S, Clifton VL, Fraser IS, et al.: Infertility and reproductive disorders: impact of hormonal
and inflammatory mechanisms on pregnancy outcome. Human reproduction update. 2016, 22:104-115. 10.1093/humupd/dmv044 22. Vannuccini S, Clifton VL, Fraser IS, et al.: Infertility and reproductive disorders: impact of hormonal
and inflammatory mechanisms on pregnancy outcome. Human reproduction update. 2016, 22:104-115. 10.1093/humupd/dmv044 22. Vannuccini S, Clifton VL, Fraser IS, et al.: Infertility and reproductive disorders: impact of hormonal
and inflammatory mechanisms on pregnancy outcome. Human reproduction update. 2016, 22:104-115. 10.1093/humupd/dmv044 Page 11/11
|
https://openalex.org/W2605067649
|
http://thesai.org/Downloads/Volume8No3/Paper_57-Dynamic_Gesture_Classification_for_Vietnamese_Sign.pdf
|
English
| null |
Dynamic Gesture Classification for Vietnamese Sign Language Recognition
|
International journal of advanced computer science and applications/International journal of advanced computer science & applications
| 2,017
|
cc-by
| 4,621
|
(IJACSA) International Journal of Advanced Computer Science and Applications,
Vol. 8, No. 3, 2017 (IJACSA) International Journal of Advanced Computer Science and Applications,
Vol. 8, No. 3, 2017 I.
INTRODUCTION In recent decades, computer vision algorithms have been
employed in many systems such as surveillance, human-
computer interaction, robotic, smart home, and communica-
tion [1]. Among various vision-related problems, hand gesture
recognition is the one which is widely being studied, in which a
suitable approach can give supports for hard-of-hearing people
in communication, as well as help to perform interacting
between human and computer without touching. According
to gesture types, researchers separated such problems into
two sub-problems. Methods working on static gestures usually
describes local and/or global features of hand shape and
posture, while the hand motion is mostly estimated to represent
dynamic gestures. Some researchers proposed approaches for
dynamic gestures based on static ones. This work focuses on the problem of recognizing dynamic
hand gestures, which is considered to be more difficult than
the similar objective on static ones. The input of this system
is a sequence of depth images captured by a depth camera
(Microsoft Kinect in our experiments) via an infrared (IR)
sensor. II.
RELATED WORK Abstract—This paper presents an approach of feature ex-
traction and classification for recognizing continuous dynamic
gestures corresponding to Vietnamese Sign Language (VSL). Input data are captured by the depth sensor of a Microsoft
Kinect, which is almost not affected by the light of environment. In detail, each gesture is represented by a volume corresponding
to a sequence of depth images. The feature extraction stage is
performed by dividing such volume into a 3D grid of same-size
blocks in which each one is then converted into a scalar value. This step is followed by the process of classification. The well-
known method Support Vector Machine (SVM) is employed in
this work, and the Hidden Markov Model (HMM) technique is
also applied in order to provide a comparison on recognition
accuracy. Besides, a dataset of 3000 samples corresponding to
30 dynamic gestures in VSL was created by 5 volunteers. The
experiments on this dataset to validate the approach and that
shows the promising results with average accuracy up to 95%. In recent studies, the stage of data acquisition was usually
performed with the support of sensors mounted on gloves or
vision-based systems. Therefore they could be separated into
two categories with different pros and cons. Dynamic Gesture Classification for Vietnamese Sign
Language Recognition Duc-Hoang Vo, Huu-Hung Huynh
University of Science and Technology
The University of Danang, Vietnam Jean Meunier
DIRO, University of Montreal
Montreal, Canada Phuoc-Mien Doan
Tra Vinh University
Tra Vinh, Vietnam A. Sensor-based approach In recent studies, many approaches focusing on the problem
of recognizing hand gestures have been proposed. For example,
the work [2] introduced a method for classifying 6 hand
gestures of Korean signal language. The study [3] also built
a game controller and performed hand symbol recognition
based on the collection of a 3D acceleration sensor and
electromechanical biological sensors. In [4], researchers devel-
oped a system of classifying symbols in Greek sign language
using the energy obtained from bodies with biosensors (EMG)
and the assembled data from an acceleration sensor mounted
on the arm. For VSL, the researchers in [5] used gloves
which are combined with sensors to identify 23 character
gestures in the Vietnamese alphabet. These methods focused
on the medical field as well as controlling, they thus still
have a limited capability to identify the actual sign language
gestures. Besides, it is inconvenient for users to carry the
data acquisition devices on the body. Several other studies
use gloves to capture the change of shapes and movements
of the hand. In [6], [7], a glove which was equipped with
sensors on all fingers and palm was used to detect movement
and bending of the fingers. Besides, such glove also helps to
retrieve the location, speed and direction of the hand under a
predefined reference system. Some other studies used colored
gloves combined with a computer vision system instead of
using sensors [8]–[11], in which the fingers are marked by
different colors. The use of gloves can support such features
simplify the preprocessing step, but brings inconvenience to
users when they have to wear gloves during performing sign
language. Keywords—Dynamic gesture; feature extraction; depth infor-
mation; Vietnamese Sign Language B. Preprocessing As mentioned, a dynamic hand gesture is performed con-
tinuously over time, thus the location and movement of the
hands and head should be focused. Besides, the beginning and
ending time of each gesture is also an important factor. In this
study, the position of the hands and the head of performers
are focused. The time for executing every gesture is different
so that a long-time gesture corresponds to a large number of
consecutive images, vice versa. In the preprocessing step, the
object of interest, i.e. the performer, in each input image is
determined by applying a thresholding technique. In detail,
all pixels in the depth image are classified into two groups
specifying the object and background (see Fig. 1). In fact, the
performer can stand near or far from the camera at an arbitrary
distance, as long as in the active area of Kinect. If a predefined
threshold is employed to binarize a depth map, the obtained
result is not really good since the intensity of object pixels
depends on the distance between the object and the Kinect. Therefore, the well-known Otsu thresholding technique [24] is
employed to separate the object from background. In order to overcome mentioned limitations, recent re-
searchers performed data acquisition using a depth camera. The
study [17] built a system supporting hand gesture recognition,
in which the data was collected by a Kinect sensor. An
obvious drawback of this study is that characteristics, which
describe the hand posture, might be significantly affected be
the finger detection result. Therefore the system in [17] has to
be improved much for applying on alphabetic gestures. This
disadvantage also occurred in [18] where the hand gesture
was represented based on detected fingers. Another gesture
recognition method working on depth images was presented
in [19]. The researchers proposed approaches for both static
and dynamic gestures. In experiment, the reported error rate
was 5%. However, their main disadvantage is that the fea-
tures, which were based on hand shape, were limited on the
orientation, the template matching thus could perform the
classification with low accuracy. After obtaining binary masks corresponding to all depth
frame in a sequence, the smallest bounding box that covers
all appeared objects in the sequence is estimated. B. Vision-based approach The work [12] published a database which consists of hand
images performing 26 different gestures, in which each one
includes 86 images captured from different directions in the
3D space. In total, a collection of 107328 sample images
was obtained. In [13], the authors built 249 samples of 49
word symbols in American Sign Language (ASL). In order to
detect and distinguish hand movements, they used 2 different
colored-gloves to perform gestures. The testing stage was
done in the laboratory environment with a dark background The remaining content of this article is organized as
follows: some related studies as well as existing limitations
are described in Section II; the details of this approach is
then presented step by step in Section III; Section IV shows
experiments and obtained results; and the conclusion is finally
given in Section V. www.ijacsa.thesai.org 415 | P a g e 415 | P a g e (IJACSA) International Journal of Advanced Computer Science and Applications,
Vol. 8, No. 3, 2017 (IJACSA) International Journal of Advanced Computer Science and Applications,
Vol. 8, No. 3, 2017 Fig. 1. Bounding box of the object in a depth frame. to enhance the ability of segmenting and distinguishing the
two hands. The study [14] also built another database of ASL
consisting of 2576 videos corresponding to 14 gestures. The
data were recorded by a RGB camera, but the performers
must wear long-sleeved shirts in which the color is similar
to the background. In [15] presented a database of 19 gestures
with 4121022 colored image samples. Although the achieved
identification accuracy was about 94%, this work strongly
depended on the preprocessing since a simple skin color
filter was employed to perform the segmentation. Another
approach which also focused on skin color pixels was proposed
by [16], in which static gestures of VSL are classified by a
neural network. Although such mentioned solutions provided
promising experimental results, the preprocessing for hand
segmentation was significantly affected by the brightness of
environment as well as the background texture. Fig. 1. Bounding box of the object in a depth frame. B. Preprocessing Besides,
background pixels in the frame is changed into the intensity of
255, in order to reduce the effect of background on the spatial-
temporal volume representing the sequence of depth images. A 5 × 5 median filter is also used before thresholding for
smoothing the depth image as well as noise removal. Although
this filter may slightly change the information on each pixel,
the thresholding could be performed more effective. This paper proposes a technique for extracting gesture
features and classifying them using SVM. An experiment on
HMM was also performed in order to provide a discussion. Since input of this approach is depth image, the mentioned
drawbacks of previous works, which are related to sensor and
color image, could be overcome. A. Microsoft Kinect Camera Kinect is a product manufactured by Microsoft. There are two versions of Kinect which used different tech-
niques for estimating depth information. The proposed system
uses a Kinect version 2 which contains many components
inside, including a color image acquisition device with a high-
resolution up to 1920×1080 pixels, the depth sensor consisting
of an infrared emitter and an infrared receiver which provide
depth images at 512 × 424 pixels image at real-time rate. The
depth map, which is calculated based on the infrared signals,
plays an important role in extracting and recognizing objects
since the changes in brightness almost have no impact on
the received depth information of Kinect. Nowadays, many
researches who are working on the field of sign language
recognition [18], [20]–[23] use Kinect to extract objects of
interest based on color information, depth as well as joint
coordinates provided in the SDK. In the proposed approach,
the depth image is captured frame by frame, and each dynamic
gesture is represented by a sequence of such images. C. Feature extraction Finally, each block
is represented by a single value corresponding with the average
of elements. The result is an array Z with the size of z3, which
is much smaller than the original array C. Figure 3 illustrates a
1D and 2D representations of array Z, in which z is assigned
to 4. Each array shape corresponds to an input of the used
machine learning models, which support classifying gestures. A(h, w, d) →B(n, n, d)
(1) (1) Next, array B is then processed from column 1st to nth, in
which every 2D array of n × d is resized to n × n to obtain a
3D array with the size of n × n × n. B(n, n, d) →C(n, n, n)
(2) (2) In this work, the process of resizing array is executed by
using bicubic interpolation [25] because this method could
give smooth results and is used by most of image processing
software, digital cameras and printers. In this technique, a new
pixel value is calculated based on the mean value of 16 nearest
original pixel, i.e. a neighborhood with size of 4 × 4. C. Feature extraction Feature extraction is an important step, which has a great
influence on the effectiveness of the process of automatic
model training. The featured values are extracted from the
sequences of depth image to effectively distinguish between a
gesture and another one. An overview of the feature extraction
is shown in Fig. 2. Let d is the number of frames in the sequence, h × w is
size of the smallest bounding box that was mentioned in the
previous section, these frames are combined together along the
time axis in order to form a three-dimensional array A with
the size of h×w ×d. The goal of this step is to normalize the
size of such arrays to a same resolution of n × n × n where
n is a predefined whole number. First, the array A is considered along the depth, i.e. time,
direction. Each two-dimensional array h×w is resized to n×n. www.ijacsa.thesai.org 416 | P a g e (IJACSA) International Journal of Advanced Computer Science and Applications,
Vol. 8, No. 3, 2017 Fig. 2. The diagram of extracting feature for a sequence of depth images corresponding to a gesture. Fig. 2. The diagram of extracting feature for a sequence of depth images corresponding to a gesture. The results after performing on d arrays are a 3D array B with
the size of n × n × d. The results after performing on d arrays are a 3D array B with
the size of n × n × d. different sequences of depth images. Next, the new array C
is divided into a 3D grid with the size of z × z × z in which
each cell is a block of normalized elements. Finally, each block
is represented by a single value corresponding with the average
of elements. The result is an array Z with the size of z3, which
is much smaller than the original array C. Figure 3 illustrates a
1D and 2D representations of array Z, in which z is assigned
to 4. Each array shape corresponds to an input of the used
machine learning models, which support classifying gestures. different sequences of depth images. Next, the new array C
is divided into a 3D grid with the size of z × z × z in which
each cell is a block of normalized elements. D. Support Vector Machine Support vector machine (SVM) is a supervised learning
method which is popularly used for classification and regres-
sion analysis. Given a set of training data which was divided
into two classes, the SVM algorithm tries to build a binary
classification model to separate the input patterns into two
defined classes corresponding to the positive class and negative
class. Visually, a SVM model builds a super plane to separate
input data points in the training set so that the distance from
it to nearest points of the two classes is maximized. The obtained array of size n × n × n is not directly used
to represent the feature vector of the corresponding gesture
because of the large number of data dimensions and possible
noise pixels inside. Therefore, this 3D array is divided into
blocks in order to reduce the dimensionality of data as well
as the impact of noise since noise level in each block, i.e. the
ratio of noise pixels over all elements, is expected to be low. Each block is then converted into a scalar value. In order to create a multi-class support vector machine,
one of these two strategies including one-against-all and one-
against-one was usually used. In this study, the latter one is
selected because of its efficiency and stability. Specifically, a
collection of k(k −1)/2 binary SVM classifiers, where k is
the number of gestures, is built. Each classifier is trained based
on data extracted from two classes. In summary, multi-class
classification problem is solved by an ensemble of binary SVM
classifiers in this work. First of all, the elements in the whole array C are aligned
based on the mean value m. The new value of each element
in the array is then recalculated by performing a subtraction
on m. The sum of obtained elements in the new array is thus
normalized to be zero in order to reduce the impact of the
deviation of distance between the performer and Kinect in 417 | P a g e 417 | P a g e www.ijacsa.thesai.org (IJACSA) International Journal of Advanced Computer Science and Applications,
Vol. 8, No. 3, 2017 Fig. 3. Low-dimensional array Z and different representations for various training models. Fig. 3. Low-dimensional array Z and different representations for various training models. Fig. 4. Examples of some words in our dataset containing depth sequences. E. Hidden Markov Model Hidden Markov Model (HMM) is a statistical model in
which the system being modeled is assumed to be a Markov
process with unobserved (hidden) states. This technique was
proposed and developed in [26]. With a system involving N
states which are numbered in order from 1 to N, HMM is
characterized by following elements: •
N is the number of states •
N is the number of states •
S = {s1, s2, ..., sN} is the set of states •
S = {s1, s2, ..., sN} is the set of states
•
M is the number of distinct observations
•
V = {v1, v2, ..., vM} is the set of observations
•
A = {aij} is the set of transition probabilities
•
aij = P(qt+1 = sj|qt = si), in which 1 ≤i, j ≤N,
qt is the actual state at time t •
M is the number of distinct observations •
B is the set of output probability distribution •
B is the set of output probability distribution •
π is the initial state distribution, i.e. πi = P(q1 = si) •
λ = (A, B, π) is the compact notation of a HMM •
λ = (A, B, π) is the compact notation of a HMM The objective of HMM related problems includes determin-
ing the probability which a sequence of observations is gener-
ated from a HMM model in case of testing, and approximating
a HMM based on a training set of series of observations in case
of training. This technique is selected to perform a comparison
because it was employed to solve many problems related to
temporal information (e.g. gait assessment [27], [28]). Fig. 4. Examples of some words in our dataset containing depth sequences. Fig. 4. Examples of some words in our dataset containing depth sequences. B. Experimental results [4]
V. E. Kosmidou and L. J. Hadjileontiadis*, “Sign language recognition
using intrinsic-mode sample entropy on semg and accelerometer data,”
IEEE Transactions on Biomedical Engineering, vol. 56, no. 12, pp. 2879–2890, Dec 2009. Figure 5 and 6 show the accuracy with different exper-
iments, using HMM and SVM approach, respectively. It is
obvious to see that the SVM method with the 3D grid size
4×4×4 gives the highest result, which is about 95%, compared
with other ones. [5]
T. D. Bui and L. T. Nguyen, “Recognizing postures in vietnamese sign
language with mems accelerometers,” IEEE Sensors Journal, vol. 7,
no. 5, pp. 707–712, May 2007. [6]
T. Kuroda, Y. Tabata, A. Goto, H. Ikuta, M. Murakami, and T. Limited,
“Consumer price data-glove for sign language recognition,” in In: Proc. of 5th Intl Conf. Disability, Virtual Reality Assoc. Tech, 2004, pp. 253–
258. In order to perform a comparison with a state-of-the-
art approach, the method proposed in [29] was applied on
the dataset in section IV-A. Differently to the preprocessing
in [29] where the stage of hand segmentation is performed
on color images, the built-in hand detector of the Kinect was
employed to determine the hand silhouette in this experiment. The resulting average accuracy was 93%, which is lower than
the best one (95%) of the proposed method. This is because
the employed dataset focuses on motion trajectory of the hand
while the hand geometry is more difficult to be described
compared with the dataset in [29]. The classification accuracies
of the proposed approach with different sizes of grid and the
method [29] are shown in Table I. [7]
S. A. Mehdi and Y. N. Khan, “Sign language recognition using
sensor gloves,” in Neural Information Processing, 2002. ICONIP ’02. Proceedings of the 9th International Conference on, vol. 5, Nov 2002,
pp. 2204–2206 vol.5. [8]
H. Brashear, V. Henderson, K.-H. Park, H. Hamilton, S. Lee, and
T. Starner, “American sign language recognition in game development
for deaf children,” in Proceedings of the 8th International ACM
SIGACCESS Conference on Computers and Accessibility, ser. Assets
’06. New York, NY, USA: ACM, 2006, pp. 79–86. [Online]. Available: http://doi.acm.org/10.1145/1168987.1169002 [9]
K. Assaleh and M. Al-Rousan, “Recognition of arabic sign language
alphabet using polynomial classifiers,” EURASIP J. Appl. Signal
Process., vol. 2005, pp. 2136–2145, Jan. 2005. [Online]. Available:
http://dx.doi.org/10.1155/ASP.2005.2136 REFERENCES [1]
Y. Zhu, Z. Yang, and B. Yuan, “Vision based hand gesture recognition,”
in Service Sciences (ICSS), 2013 International Conference on. IEEE,
2013, pp. 260–265. Fig. 6. Accuracy of different machine learning techniques on 30 gestures
with different values of z. [2]
K. K. Jung, J. W. Kim, H. K. Lee, S. B. Chung, and K. H. Eom, “Emg
pattern classification using spectral estimation and neural network,” in
SICE Annual Conference 2007, Sept 2007, pp. 1108–1111. set is formed by 1800 samples corresponding to 3 subjects,
and the remaining is used for testing stage. This experiment
was performed with different grid sizes z as mentioned in
section III-C. [3]
X. Zhang, X. Chen, W.-h. Wang, J.-h. Yang, V. Lantz, and K.-q. Wang, “Hand gesture recognition and virtual game control based
on 3d accelerometer and emg sensors,” in Proceedings of the 14th
International Conference on Intelligent User Interfaces, ser. IUI ’09. New York, NY, USA: ACM, 2009, pp. 401–406. [Online]. Available:
http://doi.acm.org/10.1145/1502650.1502708 A. Dataset to 600 sequences of depth images. Each depth image is created
at 30 fps with the resolution of 512 × 424 pixels. Figure 4
illustrates some gestures in the recorded dataset. The dataset that was used in the experiments was built
from 5 volunteers with the average distance between each one
and the camera is about 2.5m. Each volunteer performed 30
predefined gestures with 20 times for each one, corresponding In total 3000 patterns recorded by 5 volunteers, the training 418 | P a g e 418 | P a g e www.ijacsa.thesai.org (IJACSA) International Journal of Advanced Computer Science and Applications,
Vol. 8, No. 3, 2017 (IJACSA) International Journal of Advanced Computer Science and Applications,
Vol. 8, No. 3, 2017 TABLE I. CLASSIFICATION ACCURACIES OF PROPOSED APPROACH
AND THE METHOD [29]
Method
HMM
SVM
[29]
Grid size
4
16
32
4
16
32
Accuracy
0.45
0.67
0.48
0.95
0.83
0.80
0.93 TABLE I. CLASSIFICATION ACCURACIES OF PROPOSED APPROACH
AND THE METHOD [29] Fig. 5. The result of SVM, HMM when the grid size z is assigned to 4 and
16, respectively. data collected from a Kinect camera. The experimental result
on 3000 gestures has confirmed the classification ability of this
approach on VSL since the highest accuracy is up to 95%. With such promising results, we intend to expend the
experiment with more words as well as complicated gestures,
e.g. combining the hands with motion of other body parts such
as head and shoulder, and also to build a system supporting
communication between hard-of-hearing people, which focus
on the deaf in the context of VSL. Fig. 5. The result of SVM, HMM when the grid size z is assigned to 4 and
16, respectively. Fig. 6. Accuracy of different machine learning techniques on 30 gestures
with different values of z. ACKNOWLEDGMENT The authors would like to thank Trong-Nguyen Nguyen,
DIRO, University of Montreal, for his helpful comments. This work was supported by the Polytechnic Computer Vision
Group (PCVG), University of Science and Technology, The
University of Danang. V.
CONCLUSION [10]
X. Li, “Gesture recognition based on fuzzy c-means clustering algo-
rithm,” Department Of Computer Science The University Of Tennessee
Knoxville, 2003. This paper propose an approach for performing feature
extraction and recognizing of hand gesture in VSL with the 419 | P a g e 419 | P a g e www.ijacsa.thesai.org (IJACSA) International Journal of Advanced Computer Science and Applications,
Vol. 8, No. 3, 2017 [11]
S. Mitra and T. Acharya, “Gesture recognition: A survey,” IEEE
Transactions on Systems, Man, and Cybernetics, Part C (Applications
and Reviews), vol. 37, no. 3, pp. 311–324, May 2007. in 2015 International Conference on Advanced Technologies for Com-
munications (ATC), Oct 2015, pp. 279–284. in 2015 International Conference on Advanced Technologies for Com-
munications (ATC), Oct 2015, pp. 279–284. [21]
Z. Zafrulla, H. Brashear, T. Starner, H. Hamilton, and P. Presti,
“American sign language recognition with the kinect,” in Proceedings
of the 13th International Conference on Multimodal Interfaces, ser. ICMI ’11. New York, NY, USA: ACM, 2011, pp. 279–286. [Online]. Available: http://doi.acm.org/10.1145/2070481.2070532 [12]
V. Athitsos and S. Sclaroff, Database Indexing Methods for 3D Hand
Pose Estimation. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004,
pp. 288–299. [13]
R. Bowden, D. Windridge, T. Kadir, A. Zisserman, and M. Brady, A
Linguistic Feature Vector for the Visual Interpretation of Sign Language. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004, pp. 390–401. [22]
S. Lang, M. Block, and R. Rojas, Sign Language Recognition Using
Kinect. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012, pp. 394–
402. [14]
A. C. Kak, “Purdue rvl-slll asl database for automatic recognition of
american sign language,” in Proceedings of the 4th IEEE International
Conference on Multimodal Interfaces, ser. ICMI ’02. Washington, DC,
USA: IEEE Computer Society, 2002, pp. 167–. [Online]. Available:
http://dx.doi.org/10.1109/ICMI.2002.1166987 [23]
X. Chai, G. Li, Y. Lin, Z. Xu, Y. Tang, X. Chen, and M. Zhou, “Sign
language recognition and translation with kinect,” in IEEE Conf. on
AFGR, 2013. [24]
N. Otsu, “A threshold selection method from gray-level histograms,”
IEEE Transactions on Systems, Man, and Cybernetics, vol. 9, no. 1,
pp. 62–66, Jan 1979. [15]
D. V. Hieu and S. Nitsuwat, “Image preprocessing and trajectory feature
extraction based on hidden markov models for sign language recogni-
tion,” in 2008 Ninth ACIS International Conference on Software En-
gineering, Artificial Intelligence, Networking, and Parallel/Distributed
Computing, Aug 2008, pp. 501–506. [25]
R. V.
CONCLUSION Keys, “Cubic convolution interpolation for digital image process-
ing,” IEEE Transactions on Acoustics, Speech, and Signal Processing,
vol. 29, no. 6, pp. 1153–1160, Dec 1981. [16]
T.-N. Nguyen, H.-H. Huynh, and J. Meunier, “Static hand gesture
recognition using artificial neural network,” Journal of Image and
Graphics, vol. 1, no. 1, pp. 34–38, 2013. [26]
A. A. Markov, “An example of statistical investigation in the text
of ‘Eugene Onyegin’ illustrating coupling of ‘tests’ in chains,” in
Proceedings of the Academy of Sciences, vol. 7 of VI, St. Petersburg,
1913, pp. 153–162. [17]
Z. Ren, J. Yuan, and Z. Zhang, “Robust hand gesture recognition based
on finger-earth mover’s distance with a commodity depth camera,” in
Proceedings of the 19th ACM International Conference on Multimedia,
ser. MM ’11. New York, NY, USA: ACM, 2011, pp. 1093–1096. [Online]. Available: http://doi.acm.org/10.1145/2072298.2071946 [27]
T.-N. Nguyen, H.-H. Huynh, and J. Meunier, “Skeleton-based abnormal
gait detection,” Sensors, vol. 16, no. 11, 2016. [Online]. Available:
http://www.mdpi.com/1424-8220/16/11/1792 [28]
L. Tao, A. Paiement, D. Damen, M. Mirmehdi, S. Hannuna, M. Cam-
plani, T. Burghardt, and I. Craddock, “A comparative study of pose
representation and dynamics modelling for online motion quality as-
sessment,” Computer vision and image understanding, vol. 148, pp. 136–152, 2016. [18]
Y. Li, “Hand gesture recognition using kinect,” in 2012 IEEE Interna-
tional Conference on Computer Science and Automation Engineering,
June 2012, pp. 196–199. [19]
X. Liu and K. Fujimura, “Hand gesture recognition using depth data,”
in Sixth IEEE International Conference on Automatic Face and Gesture
Recognition, 2004. Proceedings., May 2004, pp. 529–534. [29]
D.-H. Vo, H.-H. Huynh, and T.-N. Nguyen, “Modeling dynamic hand
gesture based on geometric features,” in 2014 International Conference
on Advanced Technologies for Communications (ATC 2014), Oct 2014,
pp. 471–476. [20]
D. H. Vo, T. N. Nguyen, H. H. Huynh, and J. Meunier, “Recognizing
vietnamese sign language based on rank matrix and alphabetic rules,” 420 | P a g e www.ijacsa.thesai.org
|
https://openalex.org/W2025631100
|
https://zenodo.org/records/2393868/files/article.pdf
|
English
| null |
Report on Instruments and Methods of Radiometry*
|
Journal of the Optical Society of America
| 1,921
|
public-domain
| 3,596
|
*Section of 1920 Report of Standards Committee on Spectroradionetry,
W. W.
Coblentz, Chairman. REPORT ON INSTRUMENTS AND METHODS OF
RADIOMETRY* BY
W. W. COBLENTZ I. INTRODUCTORY
STATEMENT Under this caption a brief outline is given of the most important
radiometric instruments for present day laboratory work in
thermal radiation. The measurement of (1) solar, sky, nocturnal
and stellar radiation, and (2) the study of polarization phenomena
by means of spectroradiometry, require special apparatus which
is described in separate reports on this subject. Radiometric
instruments
are used for two classes of work:
(1) the measurement of total radiation and (2) the measurement
of thermal radiation intensities in the spectrum. The latter
requires auxiliary apparatus including a spectrometer and prisms
of quartz, rock salt, etc. The calibration of the spectroradiometer,
the precautions necessary for eliminating the effect of stray
radiation, etc., are described in a separate paper on transmission
and refraction data of prism and lens material with special
reference to spectroradiometry. 8
More specific information
on
various types of spectroradiometers for investigations in absorp-
tion, emission and reflection spectra, in the ultra-violet, visible,
and infrared is given in the classified bibliography at the end
of this report. Various details on the construction and operation
of bolometers, thermopiles, etc., are given in papers by Coblentz'
on "Instruments
and Methods of Radiometry."
A concise exposi-
tion of the whole subject of radiometry and spectroradiometry is
given in Nutting's "Outlines of Applied Optics."2 One of the chief complaints
of workers in radiometry
is the
uncertainty of the observations caused by unsteadiness of atmos-
pheric conditions. Radiometers are essentially of small heat
capacity and as a consequence are greatly affected by air currents. In planning a research, it is therefore desirable to place the 259 260 W. W. COBLENT [J.O.S.A., V [J.O.S.A., V radiometer in a container that can be evacuated, or to make the
observations on dull, cloudy, windstill days, or in the summer
when the air is more uniformly heated within and without the
laboratory. The loss of heat by convection is very great. The sensitivity
of a modern thermopile is doubled and that of a thermocouple
of fine (0. 01 mm) wire is quadrupled, by placing it in an evacu-
ated enclosure. Most of the radiometers to be discussed are non-selective in
their response to thermal radiation of all wave lengths, and this
sometimes causes difficulties. Hence in investigations employing
ultra-violet radiations, (for example, ultra-violet transmission
and reflection measurements) it is sometimes advisable to use a
selective radiometer such as, for example, a potassium-hydride
photoelectric
cell. II. THERMOPILES Thermopiles are constructed of fine wires of different kinds
of metal as for example copper and constantan. They function
by generating an electric current when the alternate junctures
of these two metals are heated by absorption of thermal radiation. The thermopile is therefore less affected by air currents than a
bolometer which is slightly warmer than the air as a result of the
electric current constantly flowing through the circuit. Improve-
ments introduced during the past few years have made the
thermopile a close competitor with the bolometer in sensitivity. It is not so quick in response as is a bolometer, requiring three to
five seconds to attain a maximum. However, there are but few
everyday problems requiring instantaneous action. The theory of thermopile design has been worked out by
Altenkirch'4 and by Johansen.6
The latter finds that (1) the
resistance of the thermopile should equal that of the galvanometer,
(2) the radii of the two wires of the element should be so chosen
that the ratio between the heat conductivity and the electrical
resistance is the same in both, (3) the heat loss by conduction
through the wires should equal the heat loss by radiation from
the junctions, (4) the radiation sensitivity is proportional to the May, 1921] May, 1921] THERMAL RADIOMETRY 261 square root of the exposed surface. In an iron-constantan couple
the theory required the use of iron wire 0.023 mm and constantan
wire 0.045 mm diameter; and for a Bi-Fe couple, iron wire 0. 024
mm and bismuth wire 0.075 mm diameter. If the diameter of
both wires were twice as great, theory indicates that the sensitivity
would be only 0. 8 the maximum sensitivity. He used a single
long junction consisting of a constantan wire 0.03 mm and an
iron wire 0. 015 mm diameter soldered to a strip of silver 10 by 0. 2
by 0.015 mm. The earlier form of Ruben's 13 thermopile has been modified by
Paschen, 5 who constructed
a thermopile of iron 0. 1 mm and of
constantan 0.08 mm in diameter. The constantan wire was
4 mm long. The wires were mounted end to end and fused with a
little borax and silver solder. The junctions and wires were
then rolled to 0. 002 mm thickness. The maximum temperature
was attained in four seconds and 98 per cent of the increase in
two seconds. II. THERMOPILES The sensitivity was about the same as that of
a bolometer strip 0.001 mm thickness but was only about one-half
that of his best bolometers on high battery current; its manipu-
lation, however, was easier. Reinkober' constructed a vacuum thermopile of 14 junctidns
of iron-constantan, of wires 0.05 mm diameter and having a
resistance of 14 ohms. It was 3 times as sensitive as the old form
of Rubens pile with wires 0. 15 mm in diameter. In vacuo it was
1. 6 times as sensitive as in air. He made also a thermopile (of
wires 0.021 mm thickness, hammered thin) of only four elements,
since the resistance was 18 ohms. In air, this was twice as
sensitive as the old form, and in vacuo 10 times as sensitive as
the commercial Rubens instrument. Hefoundthatits
sensitivity
was only one-half that of a vacuum bolometer. The technique of rapid construction of thermopiles of bismuth
and silver is given in papers by Coblentz.18
In a separate paper"
various modifications of the thermopiles having a continuous
absorbing surface are described, suitable for physical photometers,
for physiological investigations, for the measurement of nocturnal
radiation, etc. The construction of thermo-couples for measuring
heat from stars20 requires considerable skill and special technique. 262- W. W. COBLENTZ [J.O.S.A., V For ordinary laboratory work Bi wire 0. 1 mm in thickness and
Ag wire 0.035 to 0.04 mm, with receivers of tin (2 by 1 by 0.02
mm) are used. After completion the silver wire is given a thin
coating of shellac. Such thermopiles are strong and can be
shipped without breakage. Symmetry of construction is important in a thermopile. To
attain this end all the junctures should be suspended freely in
the air which becomes warmed by the incident radiation. Ther-
mopiles in which the "cold" (unexposed) junctions are soldered
to metal supports invariably cause a drifting of the galvanometer
as a result of warming of the air surrounding the "hot" junction. This can be neutralized by having a thermocouple of low e.m.f. (e.g. iron-copper) in the circuit. By slightly heating one of the
junctures of this couple, the zero position of the galvanometer
reading is brought back on the scale. The radiation sensitivity of a thermopile is doubled by placing
it in a vessel evacuated to 0.02 mm pressure. The radiation
sensitivity of thermopiles of fine (0. II. THERMOPILES 02 mm diam.) wire is increased
4 to 5 times in a vacuum. IV. RADIOMICROMETERS The radiomicrometer is essentially a moving coil galvanometer
having a single loop of wire with a thermojunction
at the end. This instrument was invented independently by d'Arsonval30
and by Boys."
Coblentz3 4 has devised a vacuum radiometer which
combined the principle of the radiomicrometer and the Nichols
radiometer. One of the most noteworthy radiomicrometers was
constructed by Schmidt35 in the laboratory of Prof. Rubens. The instrument has undergone modifications by the latter36
and, judging from published work, is practically the only one in
use. The commendable feature of the radiomicrometer is its
freedom from magnetic disturbances. However, it is not portable,
and to attain a high sensitivity requires a long period. III. BOLOMETERS The electrical connections of a bolometer and its auxiliary
galvanometer are the same as that of a Wheatstone bridge. The latter is constructed of resistances having a negligible tem-
perature coefficient. It is therefore misleading to speak of the
bolometer as being "simply a Wheatstone bridge." In a bolometer
two branches of the bridge are made of thin strips of metal having
a high temperature coefficient of resistance. These strips, called
receivers, are made as thin as possible in order to reduce the heat
capacity. They are usually made of thin (0. 001 mm) platinum,
though iron23 and nickel have also been used. They are blackened
to increase the absorption of radiation. Two strips are used for
symmetry. The remaining two branches of the bridge are usually
made of manganin wire having 3 to 4 times the resistance22 of the
receivers. It will be understood that the bolometer functions as a result
of a change in resistance of one of these thin blackened strips May, 1921] May, 1921] 263 THERMAL RADIOMETRY when it is exposed to radiation. The resulting galvanometer
deflection is proportional to the temperature rise of the exposed
receiver and hence of the intensity of the thermal radiation
stimulus. Convection currents of air cause great unsteadiness in a
bolometer. It is therefore necessary in practically all work to
place the receivers in a vessel from which the air can be evacuated
to a pressure of less than 0. 01 mm.27
The vacuum bolometer2 6 28,29
is much more sensitive than a bolometer in air. However, there
are many complications and disturbances, and recent improve-
ments in the sensitivity of thermopiles have made it possible to
substitute the latter for the bolometer in most radiometric work. V. NICHOLS RADIOMETERS The torsion radiometer by Crookes37 as improved by Nichols39
consists essentially of two similar, thin vanes of blackened mica
or platinum, attached to a horizontal arm and suspended, by
means of a fine quartz fiber, in a vessel which is evacuated. The
vanes are about 3 mm from a window. The radiation
to be
measured falls upon one of the vanes which becomes warmed and
repelled from the window. A small mirror is attached to a glass
staff which supports the vanes. The deflection is measured
by means of a telescope and scale. The device is free from V. W. CODLENTZ 264 [J.O.S.A.,
T [J.O.S.A.,
T [J.O.S.A.,
T [J.O.S.A.,
T magnetic disturbances but to attain high sensitivity it requires
a long period, say 30 to 60 seconds as compared with a thermopile
and Thomson galvanometer which requires 5 seconds. In its
time it was very useful, but at present it is being replaced by
vacuum thermopiles and iron-clad galvanometers. VI. GALVANOMETERS One of the most important adjuncts to a radiometric laboratory
is a magnetically well-shielded astatic galvanometer. The
bolometer and the thermopile require an auxiliary galvano-
meter. Much radiometric work can be done with a thermopile
and a sensitive d'Arsonval galvanometer. Such galvanometers,
now constructed by Leeds and Northrup and by Weston, have a
sensitivity of i= 1X 10-9 ampere. They are designed to fit a
bismuth-silver
thermopile" 9 having a resistance of 10 to 12 ohms. In other words they are designed to be critically damped on an
external resistance of 12 ohms and a single swing of 8 to 10 seconds. Recent great advances in radiometry have resulted from
imbedding the coils of a Thomson galvanometer in soft iron52 55
and providing laminated shields of transformer iron. Tests by
Coblentz55 showed that while the inner shields of laminated iron
greatly reduced the magnetic disturbances, imbedding the coils
in blocks of soft iron, reduced still further the effects of air currents
and magnetic perturbations. Whether there is a further gain by
making the inner shields of transformer iron regularly separated
by thin paper, as described by Wente,56 or by wrapping iron wire
upon cardboard, as described by Esmarch53 remains undecided. These like other refinements (as for example the older method of
not having slots in the shields, for viewing the mirror) are usually
negligible by an experimenter when he is anxious to get things
done. For example, judging from published work, not until within
recent years did Paschen54 devise and use a special iron-clad
mounting. The galvanometer should be permanently mounted upon a
substantial pier. Local tremors are sometimes avoided by
shifting the position of the galvanometer. Serious earth tremors May, 1921] May, 1921] THERMAL RADIOMETRY 265 may be avoided by suspending the galvanometer as described by
Julius.57 A good shield from the magnetic disturbances of the average
laboratory is obtained by imbedding the coils in blocks of soft
(Norway) iron, over which is placed a laminated
shield of soft
iron. The latter is made of 20 or more pieces of transformer iron
(which is in strips about 75 cm (2 .5 ft.) in length and 18 cm wide)
and weighing 9 to 10 lbs. It is well to provide additional shields
of black wrought iron welded pipe of "extra strong" quality in
sizes 5, 7, 9, and 11, (See Kent's Mech. Eng. VI. GALVANOMETERS Pocketbook)
and
cut in lengths of 25 or to 30 cm. Researches
61 not requiring the
highest radiometric sensitivity have been made successfully by
using simply the iron-clad mounting and laminated cylinder
just described, and one additional shield which consisted of an
8-inch black wrought-iron pipe inside of which was placed a
series of laminations of transformer iron which practically doubled
the thickness. A cover of pieces of transformer iron adds to the
shielding effect5 and keeps out dust. VIII.
SOURCES OF RADIATION
FOR SPECTRORADIOMETRY VIII. SOURCES OF RADIATION
FOR SPECTRORADIOMETRY The difficulties experienced by earlier workers in spectroradiom-
etry are gradually being overcome by the development and
application of apparatus suited for the purpose. It is essential
to use spectrometers of high light-gathering power, as described
in a separate report published elsewhere in this journal.8 1. ULTRA-VIOLET For transmission and reflection measurements in the ultra-
violet between 0.18,q and 0. 28,g we have the strong emission
lines 58 from the spark spectra of Al, Cd, Mg, and Zn.59
8 6 The emission spectrum of the mercury in quartz arc lamps, 8'6'
is a source of powerful emission lines at 0. 25g to 1iu. Equipped
with a Cooper-Hewitt 600-watt quartz-glass, mercury-vapor
lamp the experimenter is now able to make measurements, at
certain wave lengths in the ultra-violet, with as great ease and
accuracy as in the infra-red. Owing to the generation of ozone and nitrous oxide fumes this
lamp should be operated in a closed metal box provided with a
ventilator. Deep brown-colored glasses should be worn when
exposed to the lamp, otherwise painful and perhaps permanent
injurious effects will occur to the eyes. BUREAU OF STANDARDS, WASHINGTON, D. C. VII.
VACUUM MAINTENANCE The most efficient device for easily maintaining
a vacuum is
metallic calciuml9 2 0 in a quartz or porcelain tube which is ce-
mented to the thermopile container. Heavy pyrex tubing is
useful but is likely to collapse on heating. At the beginning, the
thermopile container is thoroughly evacuated by means of an
oil pump and the stop cock is closed. The metallic calcium should be free from carbide, and should
be heated to a dull red before closing the stop cock. After this
the vacuum is maintained by heating the calcium to a dull red
by means of an alcohol lamp, a gas flame, or by electric means. The vacuum stellar thermocouples20 have been heated but twice
in 6 years to remove the gases liberated from the cell walls. On
the other hand a laboratory thermopile which has always leaked
badly has had its vacuum maintained for the past 4 years by
frequently heating the calcium. 266 W. W. COBLENTZ [J.O.S.A., V May, 1921] May, 1921] May, 1921] THERMAL RADIOMETRY IX. BIBLIOGRAPHY INSTRUMENTS AND METHODS OF RADIOMETRY INSTRUMENTS AND METHODS OF RADIOMETRY 1. Coblentz, B. S. Bulletin, 4, p. 391, 1907; 9, p. 7, 1912; 11, p. 131, 1914; 13, p. 423,
1916; 14, 507, 1918. 1. Coblentz, B. S. Bulletin, 4, p. 391, 1907; 9, p. 7, 1912; 11, p. 131, 1914; 13, p. 423,
1916; 14, 507, 1918. 2. Nutting, Outlines of Applied Optics, Chapter 9. 2. Mirror-spectrometers for I 2. Mirror-spectrometers for Infra-red R 9. Coblentz, B. S. Bulletin, 10, p. 1; 1913. 10. Gorton, Phys. Rev., (2) 7, p. 66; 1916. THERMOPILES 13. Rubens, Zs. Instrk., 18, p. 65; 1898. 14. Altenkirch, Phys. Zs., 10, p. 560; 1909. 15. Paschen, Ann. der. Phys., 33, p. 736; 1910. 16. Johansen, Ann. d. Phys. (4), 33, p. 517; 1910. 16. Johansen, Ann. d. Phys. (4), 33, p. 517; 1910. 16. Johansen, Ann. d. Phys. (4), 33, p. 517; 1910. 17 Reinkober
Ann
der Phys
(4) 34 p 349 1911; Phys
Zs
14 p 998; 1913 17. Reinkober, Ann. der Phys., (4) 34, p. 349, 1911; Phys. Zs., 14, p. 998; 1913. . Reinkober, Ann. der Phys., (4) 34, p. 349, 19 18. Coblentz, B. S. Bulletin 4, p. 400, 1908; 9, p. 15, 1912. 19. Coblentz, B. S. Bulletin, 11, p. 141; 1914. 20. Coblentz, B. S. Bulletin 11, p. 613; 1915. 3. Vacuum Spectrometers 11. Trowbridge, Phil. Mag., (6) 20, p. 768; 1910. 12. McCauley, Astrophys. Jour., 37, p. 164; 1913. BOLOMETERS 21. Langley, Proc. Amer. Acad. Sci., 16, p. 342; 1881. 22. Abbot, Astrophys. Jour., 18, p. 1; 1903. 22. Abbot, Astrophys. Jour., 18, p. 1; 1903. 23. Rubens, Ann. der Phys., (3) 37, p. 255, 1889; 45, p. 238, 1892. 24. Paschen, Ann. der Phys., 48, p. 272; 1893. 25. Ingersoll, Phil. Mag. (6) 11, p. 41; 1906. 26. Warburg, Leithauser and Johansen, Ann. der Phys., (4) 2 27. Coblentz, B. S. Bulletin, 4, p. 415, 1908; 9, p. 34, 1912. 28. Liembach, Ann. der Phys., (4) 33, p. 308; 1910. 29. Buchwald, Ann. der Phys., (4) 35, p. 928; 1910. 2. VISIBLE
AND
INFRA-RED Transmission and reflection measurements in the visible and
in the infra-red to 4 are now easily made by using a gas-filled
tungsten lamp60
(500 watt, "Mazda C," stereoptican type is
recommended). This type of lamp is easily calibrated for an equal
energy spectrum such as is used in studying the photoelectric
sensitivity of substances.62
For investigations in the infra-red
of long wave lengths the ordinary gas-mantle63 is a useful source
of radiation. The Nernst glower is also useful, but it is easily
affected by air currents. BUREAU OF STANDARDS, WASHINGTON, D. C. 267 SPECTRORADIOMETERS 1. Lens Spectrometers for Ultra-violet Radiometry 1. Lens Spectrometers for Ultra-violet Radiometry 3. PflUiger, Ann. der Phys., (4) 13, p. 890; 1904. 3. PflUiger, Ann. der Phys., (4) 13, p. 890; 1904. 4. Coblentz, B. S. Bulletin, 7, p. 245; 1911. 5. Coblentz, B. S. Bulletin, 10, p. 38 (Fig. 5); 1903. 6. Coblentz, and Kahier, B. S. Bulletin, 16, p. 233; 1920. 7. Pfund, Phys. Rev., (2) 7, p. 289; 1916. 7. Pfund, Phys. Rev., (2) 7, p. 289; 1916. 8. Coblentz, Jour. Opt. Soc. Am., Vol. 4, No. 6 and B. S. Sci. Paper No. 401; 1920. 8. Coblentz, Jour. Opt. Soc. Am., Vol. 4, No. 2. Mirror-spectrometers for Infra-red Radiometry RADIOMICROMETERS 30. d'Arsonval, Soc. Franc. de Phys., pp. 30 and 77; 1886. 31. Boys, Proc. Roy. Soc., 42, p. 189, 1887; Phil. Mag. 180A, p. 159, 1889. 32. Paschen, Ann. der Phys., (3) 48, p. 275; 1893. 33. Lewis, Astrophys. Jour., 2, p. 1; 1895. 34. Coblentz, B. S. Bulletin, 2, p. 479, 1906; 7, p. 243, 1911. [J.O.S.A., V 268 W. W. COBLENTZ 35. Schmidt, Ani. der Phys., (4) 29, p. 1003; 1909. 36. Rubens and Hollnagel, Sitzber Akad. Wiss., 4, p. 26; 1910. NICHOLS RADIomETERS 37. Crookes, Phil. Trans. (II) 66, p. 325; 1876. 38. Pringsheim, Ann. der Phzys., (3) 18, p. 32; 1883. 39. Nichols, Pizys. Rev., 4, p. 297; 1897. 40. Nichols, Astrophys. Jour., 13, p. 101; 1901. 41. Stewart, Pizys. Rev., 13, p. 257; 1901. 42. Drew, Phzys. Rev., 17, p. 321; 1903. 43. Porter, Astrophys. Jour., 22, p. 229; 1905. 44. Coblentz, Publ. No. 35, Carnegie Inst. of Washington, 1905. 45. Coblentz, B. S. Bulletin 4, p. 404; 1908. GALVANOMETERS AND MAGNETIC SHIELDING 46. Dubois and Rubens, Annt. der Plzys., (4) 2 p. 84; 1900. 47. Mendenhall and Waidner, Amner. Jour. Sci., 27, p. 249; 1907. 47. Mendenhall and Waidner, Amner. Jour. Sci., 48. Abbott, Astropitys. Jour., 18, p. 1; 1903. 49. Wills, Phys. Rev., 24, p. 243; 1907. 50. Nichols and Williams, Phys. Rev., 27, p. 250; 1908. 51. Coblentz, B. S. Bulletin 4, p. 431; 1908. 52. Coblentz, B. S. Bulletin 9, p. 60; 1911. 53. Esmarch, Ant. der Phys., (4) 39, p. 1540; 1912. 54. Paschen, Pitys. Zs., 14, p. 521; 1913 55. Coblentz, B. S. Bulletin 13, p. 423; 1916. 56. Wente, Pllys. Rev., (2) 16, p. 137; 1920. 57. Julius, Ant. der Plzys., (3), 56, p. 151; 1895. SOURCES OF RADIATION FOR SPE SOURCES OF RADIATION FOR SPECTRORADIOAIETR 58. PflUger, Ann. der Plzys., (4), 13, p. 890; 1904. 59. Coblentz, Jalzrb. Radiovaktivitdt und Elektronik, 8, p. 177; 1910. 60. Coblentz, B. S. Bulletin, 14, p. 115; 1917. 61
C bl
t
E
d L
B S B ll i
15 60. Coblentz, B. S. Bulletin, 14, p. 115; 1917. 61. Coblentz, Emerson, and Long, B. S. Bulletin, 15, p. 1; 19 61. Coblentz, Emerson, and Long, B. S. Bulleti 62. Coblentz and Kahler, B. S. Bulletin 15, p. 121; 1919. 63. Rubens, Ann. der Phys. (4), 18, p. 725, 1905; 20, p. 593, 1906.
|
https://openalex.org/W2150622190
|
https://europepmc.org/articles/pmc1201568?pdf=render
|
English
| null |
Regulation of mouse hepatic genes in response to diet induced obesity, insulin resistance and fasting induced weight reduction
|
Nutrition & metabolism
| 2,005
|
cc-by
| 10,342
|
Published: 28 June 2005 Published: 28 June 2005 Nutrition & Metabolism 2005, 2:15
doi:10.1186/1743-7075-2-15 This article is available from: http://www.nutritionandmetabolism.com/content/2/1/15 © 2005 Raab 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. BioMed Central BioMed Central BioMed Central Nutrition & Metabolism Open Access Open A
Research
Regulation of mouse hepatic genes in response to diet induced
obesity, insulin resistance and fasting induced weight reduction
R Michael Raab1, John Bullen2, Joanne Kelleher3, Christos Mantzoros2 and
Gregory Stephanopoulos*1 Address: 1Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA, 2Beth-Israel Deaconess Medical
Center, Harvard Medical School, Boston, MA, USA and 3Department of Physiology, The George Washington School of Medicine and Health
Sciences, Washington, DC, USA Email: R Michael Raab - rmraab@mit.edu; John Bullen - jbullen@caregroup.harvard.edu; Joanne Kelleher - jkk@mit.edu;
Christos Mantzoros - cmantzor@caregroup.harvard.edu; Gregory Stephanopoulos* - gregstep@mit.edu
* Corresponding author * Corresponding author Received: 25 April 2005
Accepted: 28 June 2005 Methods
Animals In the liver, hepatic glucose output (HGO) increases dur-
ing insulin resistance and several key molecules contribut-
ing to this phenotype have been widely studied [3-6]. Despite these extensive efforts, the genes identified thus
far do not alone account for all of the variability in HGO. Further insight may be obtained by conducting genome
wide transcriptional studies during diet induced obesity
(DIO) and its associated insulin resistant physiological
state. This approach is a critical step towards further defin-
ing the molecular processes that regulate the phenotype
and thereby augment the discovery of new potential ther-
apeutic targets. Three to five week old C57/BL/6J mice were obtained
from Jackson Laboratories (Bar Harbor, ME). All animals
were allotted a seven day acclimation period with access
to food and water ad libitum, and were maintained at
25°C with a 12-hour light/ dark cycle (lights on from
06:30–18:30) for the duration of the study. A normal
chow (Purina Rodent Chow; Harlan Teklad #5008; 6.5%
fat, 49% carbohydrate, 23% protein, 3.5 kcal/g) and high-
fat diet (Harlan Teklad #TD88137, 42.16% fat, 42.81%
carbohydrate, 15.02% protein, 4.53 kcal/g) were fed to
respective mice, as outlined below. C57/BL/6J mice fed a high-fat diet become obese, hyperg-
lycemic, and hyperinsulinemic, reflecting an insulin
resistant metabolic state [7-11] that resembles the human
condition. Although it has been demonstrated that short-
term caloric restriction can improve insulin resistance
[12], the regulatory pathways that control hepatic metab-
olism during DIO and associated insulin resistance, and
the improvement of insulin resistance with caloric restric-
tion, are the focus of intense research efforts. The molecu-
lar mechanisms underlying these pathways rely upon
alterations in gene transcription [13], which can be mon-
itored using DNA microarrays [14,15]. This report explored alterations in hepatic gene mRNA
levels in C57/BL/6J mice fed either a control or high-fat
diet for 10 weeks, as well as alterations in mRNA levels of
C57/BL/6J mice fasted for 48 hours following 10 weeks of
high-fat feeding. Fasted animals were allowed access to
water during the fasting period. All animals were sacri-
ficed by CO2 asphyxiation, followed by immediate collec-
tion of liver tissue, which were stored at -80°C as
previously described [16]. The control group consisted of C57/BL/6J mice fed nor-
mal chow diet for 10 weeks. The experimental group con-
sisted of C57/BL/6J mice fed a high-fat diet for 10 weeks
(n = 9/group). Background was fed the same high-fat diet for ten weeks followed
immediately by 48 hours of fasting, returning their
weights to baseline levels prior to tissue harvest. Fasting/
weight reduction data provides further differentiation
among genes that not only respond to DIO and insulin
resistance, but are also normalized by caloric restriction. g
Obesity is a growing concern in the industrialized world. It is estimated that over 61% of adult Americans are over-
weight or obese [1] and an alarming number of children
and adolescents are following suit [2]. Of primary concern
are the associated complications stemming from obesity's
growing prevalence, among which type 2 diabetes is
reaching epidemic proportions. An extensive bioinformatics analysis led to the identifica-
tion of 41 discriminatory genes participating in key
molecular pathways in DIO, insulin resistance, and fast-
ing/ weight reduction. The implicated pathways involve
signal transduction and protein metabolism and secre-
tion. In addition, the 41 genes identified can accurately
classify the three groups of mice ("control", "high-fat",
and "fasted/ weight reduce"), and importantly, they repre-
sent a set of candidate genes that may influence hepatic
function during periods of insulin resistance and
sensitivity. The aetiology of type 2 diabetes is complex because of its
heterogeneous origins that result in the commonly
observed hyperglycemia and hyperinsulinemia, which are
characteristic of insulin resistance. While an enormous
number of investigations have resulted in identifying
some of the relevant molecular pathways, particularly in
muscle and adipose tissue, more research is required to
fully understand genetic susceptibility to type 2 diabetes
and insulin resistance. http://www.nutritionandmetabolism.com/content/2/1/15 Nutrition & Metabolism 2005, 2:15 http://www.nutritionandmetabolism.com/content/2/1/15 Abstract Background: Obesity is associated with insulin resistance that can often be improved by caloric
restriction and weight reduction. Although many physiological changes accompanying insulin resistance
and its treatment have been characterized, the genetic mechanisms linking obesity to insulin resistance are
largely unknown. We used DNA microarrys and RT-PCR to investigate significant changes in hepatic gene
transcription in insulin resistant, diet-induced obese (DIO)-C57/BL/6J mice and DIO-C57/BL/6J mice
fasted for 48 hours, whose weights returned to baseline levels during these conditions. Results: Transcriptional profiling of hepatic mRNA revealed over 1900 genes that were significantly
perturbed between control, DIO, and fasting/weight reduced DIO mice. From this set, our bioinformatics
analysis identified 41 genes that rigorously discriminate these groups of mice. These genes are associated
with molecular pathways involved in signal transduction, and protein metabolism and secretion. Of
particular interest are genes that participate in pathways responsible for modulating insulin sensitivity. DIO
altered expression of genes in directions that would be anticipated to antagonize insulin sensitivity, while
fasting/ weight reduction partially or completely normalized their levels. Among these discriminatory
genes, Sh3kbp1 and RGS3, may have special significance. Sh3kbp1, an endogenous inhibitor of PI-3-kinase,
was upregulated by high-fat feeding, but normalized to control levels by fasting/weight reduction. Because
insulin signaling occurs partially through PI-3-kinase, increased expression of Sh3kbp1 by DIO mice may
contribute to hepatic insulin resistance via inhibition of PI-3-kinase. RGS3, a suppressor of G-protein
coupled receptor generation of cAMP, was repressed by high-fat feeding, but partially normalized by
fasting/weight reduction. Decreased expression of RGS3 may augment levels of cAMP and thereby
contribute to increased, cAMP-induced, hepatic glucose output via phosphoenolpyruvate carboxykinase
(PCK1), whose mRNA levels were also elevated. Conclusion: These findings demonstrate that hepatocytes respond to DIO and weight reduction by
controlling gene transcription in a variety of important molecular pathways. Future studies that
characterize the physiological significance of the identified genes in modulating energy homeostasis could
provide a better understanding of the mechanisms linking DIO with insulin resistance. Page 1 of 13
(page number not for citation purposes) Page 2 of 13
(page number not for citation purposes) Methods
Animals The ten week high-fat dietary treatment has
been demonstrated to be long enough for C57/BL/6J mice
to develop insulin resistance and a condition that resem-
bles type 2 diabetes [7,8]. Two days before tissue harvest,
the C57/BL/6J mice on the high-fat diet were divided into
two groups, with one group remaining on the high-fat diet
(n = 5; to be used in the first study) and one group fasting
for the final 48 hours (n = 4; to be used in the second
study). Mouse weights were recorded two days prior to, To investigate hepatic gene regulation in response to DIO
and insulin resistance, whole genome microarrays con-
taining 17,280 gene probes were used to examine tran-
scription in two groups of C57/BL/6J mice : 1) the
"control mice" received a normal diet for 10 weeks, 2) the
"high-fat mice" received a high-fat diet for 10 weeks. In
addition, to assess hepatic gene regulation in response to
caloric restriction, which is a commonly recommended
treatment for DIO and insulin resistance, a third group of
mice was used, the "fasted/ weight reduced mice", which Page 2 of 13
(page number not for citation purposes) Page 2 of 13
(page number not for citation purposes) Nutrition & Metabolism 2005, 2:15 http://www.nutritionandmetabolism.com/content/2/1/15 http://www.nutritionandmetabolism.com/content/2/1/15 http://www.nutritionandmetabolism.com/content/2/1/15 5'-CAGAGAGACACAGTGCCCATCC-3', and 5'-AAGTC-
CTCTTCCGACATCCAGC-3'; for malic enzyme 5'-GCCA-
GAGGATGTCGTCAAGG-3',
and
5'-
ATTACAGCCAAGGTCTCCCAAG-3', respectively. These
primers each gave specific fragments of the correct length
when viewed upon a 4% agarose gel (data not shown). As
an internal control β-Actin mRNA levels were also meas-
ured. The sense and antisense sequences were 5'-
AATAAGTGGTTACAGGAAGTC-3' and 5'-ATGAAGTAT-
TAAGGCGGAAG-3', respectively. 5'-CAGAGAGACACAGTGCCCATCC-3', and 5'-AAGTC-
CTCTTCCGACATCCAGC-3'; for malic enzyme 5'-GCCA-
GAGGATGTCGTCAAGG-3',
and
5'-
ATTACAGCCAAGGTCTCCCAAG-3', respectively. These
primers each gave specific fragments of the correct length
when viewed upon a 4% agarose gel (data not shown). As
an internal control β-Actin mRNA levels were also meas-
ured. The sense and antisense sequences were 5'-
AATAAGTGGTTACAGGAAGTC-3' and 5'-ATGAAGTAT-
TAAGGCGGAAG-3', respectively. and on the day of tissue harvest. All animals were handled
in accordance with the principles and guidelines estab-
lished by the National Institutes of Health. The protocol
was approved by the Institutional Review Board at Beth
Israel Deaconess Medical Center, Boston, MA. Array validation Microarray protocols have been extensively validated in
our laboratory as described previously [17]. For valida-
tion, we prepared arrays containing an approximately
13,000 gene sub-set of our oligonucleotide mouse library,
printed in triplicate. Total RNA from skeletal muscle and
brain tissue were used for validation comparisons, and
each sample was analyzed in duplicate and prepared and
processed as described above. Matlab was used to calcu-
late basic statistics. RT-PCR analysis of IL6st, PTP4a2, G6P, PCK1, and malic
enzyme Preparation of total RNA and cDNA for microarray
hybridization Total RNA was purified from liver tissue samples using
STAT-60 (Tel-Test, Inc., Friendswood, TX) according to the
manufacturer's instructions, and stored at -80°C. Labeled
control cDNA was made from Total RNA control samples
(Universal Mouse Reference RNA, catalog #740100, Strat-
agene) using Cy3 dCTP (Perkin-Elmer), and labeled liver
cDNA was made from total RNA experimental samples
using Cy5 dCTP (Perkin-Elmer) during reverse transcrip-
tion, as described previously [17]. Gene specific standards were developed by amplifying the
entire mRNA coding sequence of each gene by PCR, gel
purifying the resulting band, and then diluting it to con-
centrations from 104 µg/µL to 10 9 µg/µL. The R2 value of
the standard curve, relating the threshold cycle to the
amount of standard template, was always greater than
0.97. The mRNA levels of β-actin measured were not sig-
nificantly (p > 0.05) different between the dietary treat-
ments for any of the groups. Microarrays were prepared using GAPS glass slides (Corn-
ing) and a Virtek arrayer (Bio-Rad). Arrays contained
17,280 features, printed from a synthesized oligonucle-
otide mouse library (Operon) as described previously
[17]. RT-PCR analysis of IL6st, PTP4a2, G6P, PCK1, and malic
enzyme y
A two-step RT-PCR protocol was performed to confirm
the mRNA levels of several genes. In this procedure the
cDNA synthesis was performed as detailed previously [17]
except the Cy-labeled nucleotides were replaced with
unlabeled nucleotides such that all dNTPs were at the
same final concentration during the reaction. PCR was
conducted in 94-well plates using the iQ SYBR Green
Supermix Kit (Bio-Rad), according to the manufacturer's
instructions on an iCycler RT-PCR machine (Bio-Rad). Briey, 1 µL of the final, diluted cDNA template was mixed
with 19 µL of RNase free water, 25 µL of Bio-Rad RT-PCR
Supermix (Bio-Rad), 2 µL of sense and antisense primers,
and 1 µL of 12.5 mM dNTPs. The final primer concentra-
tion was 0.25 µM. The PCR cycle used a single three
minute hot-start at 95°C, followed by 50 cycles of 30 sec-
onds at 95°C, one minute at 60°C, and two minutes at
72°C during which time the reaction fluorescence was
measured. Each mouse sample was measured in either
triplicate or quadruplicate. The sense and antisense
primer sequences were: for interleukin 6 signal transducer
IL6st 5'-GCGGCTCGAACTTCACTGC-3', and 5'-CACGAT-
GTAGCTGGCATTCACG-3'; for protein tyrosine phos-
phatase 4a2 PTP4a2 5'-TTTCTGCTGCGGAACATTTCAAG-
3', and 5'-GCGTGCGTGTGTGAGTGTG-3'; for regulator
of g-protein signalling 3 RGS3 5'-GCACATCCCGCATTC-
CAGTTAC-3', and 5'-AGGGAACACCAGGACTTTAGGG-
3'; for glucose-6-phosphatase G6P 5'-GTGATTGCTGAC-
CTGAGGAACG-3', and 5'-TGCCACCCAGAGGAGATT-
GATG-3'; for phosphoenolpyruvate carboxykinase PCK1 The arrays' ability to detect differential transcription
between muscle and brain RNA was evaluated by two dif-
ferent methods. In the first, we examined the number of
genes that were up- or down-regulated by a factor greater
than two (i.e., whose mean ratio was either greater than
two, or less than 0.5) in the muscle versus muscle and the
muscle versus brain RNA comparisons. This criterion has
been used as a basis for assessing differential transcription
in a number of studies [18-20]. In the second method, we
defined a threshold for differential expression by using
the 95% confidence interval determined from the muscle
versus muscle control arrays. Table 1 summarizes the
results, where the p-values reported were from two-tailed
student t-tests. Although there are only about 370 genes exceeding the
threshold in the muscle versus muscle arrays, more than
1000 genes were differentially expressed in the muscle
versus brain arrays. This result supports the assertion that
the assaying method and selection criterion are signifi-
cantly more likely to identify differentially expressed
genes. RT-PCR analysis of IL6st, PTP4a2, G6P, PCK1, and malic
enzyme Page 3 of 13
(page number not for citation purposes) http://www.nutritionandmetabolism.com/content/2/1/15 Nutrition & Metabolism 2005, 2:15 Table 1: Differential gene transcription validation data. This table summarizes the results of the array validation with respect to the
study of differential expression. Array Condition
# of Probes Detected
# of Genes >2-Fold Different
Differentially Genes at the
Expressed 95% Confidence Level
Muscle vs. Muscle
7574
438
429
Muscle vs. Muscle
6417
314
302
Average
6996
376
366
Muscle vs. Brain
7143
1201
1161
Muscle vs. Brain
8318
981
931
Average
7731
1091
1046
P-value
0.47
0.03
0.03 Table 1: Differential gene transcription validation data. This table summarizes the results of the array validation with respect to the
study of differential expression. on validation data. This table summarizes the results of the array validation with respect to the transcription validation data. This table summarizes the results of the array validation with respect to the
sion erential gene transcription validation data. This table summarizes the results of the array validation with r
rential expression. Table 1: Differential gene transcription validation data. This table summarizes the results of the array
study of differential expression. The coefficient of variation, CV, was calculated for each
replicated gene expression and the distribution across all
genes is plotted in Figure 1. For the muscle versus muscle
control arrays, the median CV across all probes was
10.2%. For the muscle versus brain arrays the median
coefficient of variation across all probes was 9.8%. This
indicates that for a gene transcription ratio of 1, we might
expect the true value to lie between 0.9 and 1.1; similarly
for a gene transcription ratio of 3, we might expect the true
value to lie between 2.7 and 3.3. Although the median CV
across all probes for the muscle versus muscle control
arrays was 10.2%, the median CV for the 314 genes com-
mon to both muscle versus muscle arrays that had a fold
difference greater than two, was 24.7%. Because of their
increased CV and high fold change, none of these genes
were included in our subsequent analysis. for uncovering patterns and structure in microarray data
that might have otherwise been difficult to detect through
manual inspection and intuition alone [22,23]. Applying
statistics and data mining methods to microarray data in
unison enables rapid and reliable analysis without a priori
assumptions that may bias expectations about the data
set. RT-PCR analysis of IL6st, PTP4a2, G6P, PCK1, and malic
enzyme A t-test [24] was used to evaluate whether a gene exhibited
statistically significant expression differences in pairwise
comparisons between the control, high-fat, and fasting/
weight reduced groups. The t-test results showed that
1981 genes had at least one statistically significant (p <
0.05) change between the treatments. Wilks-λ based rank-
ing [25] was used to identify discriminatory genes that dif-
ferentiated the three groups. This technique is particularly
appropriate for multi-class comparisons, ranking genes on
the basis of their within group, and between group vari-
ances. Thus, a gene exhibiting a small variation within
each of the three groups, but a large variation between
groups would rank highly; conversely, a gene that had a
high level of variation within each group and a low level
of variation among the groups would be ranked low. The
Wilks-λ score can be transformed into an F statistic, which
can be compared with the F distribution to assess the sta-
tistical significance of the observation [25]. In this analy-
sis a Wilks-λ threshold value of 0.47 was used, which is
equivalent to a p value of 0.05. From the 1981 genes
selected by the p < 0.05 cutoff, we retained the 1169 genes
that had a Wilks-λ value below 0.47. In duplicate arrays, 76% of the genes observed on one
muscle versus muscle array were also observed on the
duplicate; likewise 77% of the genes found on one muscle
versus brain array were conserved on the duplicate. These
data demonstrate the inter-array reproducibility by show-
ing the majority of genes are reproducibly found in multi-
ple replicate arrays. RT-PCR was also used to verify the array results for IL6st,
PTP4a2, and RGS3. The variation in the ratios of the
mRNA levels was less than 30% for each of these genes
whether measured using the arrays or RT-PCR as shown in
Table 2. Computational methods Fischer Discriminant Analysis [26] (FDA) was used to
identify not just individual genes, but combinations of
genes whose expression levels are capable of correctly clas-
sifying the control mice, high-fat mice, and fasting/ weight
reduced mice. FDA is based on linear combinations of gene
expressions and considers the discriminatory power of gene
groups as opposed to individual genes. Samples are A combination of statistical and data mining methods
were used to extract information from the microarray
data. Statistical methods rigorously quantify the reliability
of differences in the microarray data [21] and can objec-
tively evaluate changes in gene transcription ratios and
derivative quantities. Data mining is particularly useful Page 4 of 13
(page number not for citation purposes) Page 4 of 13
(page number not for citation purposes) http://www.nutritionandmetabolism.com/content/2/1/15 http://www.nutritionandmetabolism.com/content/2/1/15 Nutrition & Metabolism 2005, 2:15 Distribution of the coefficient of variation for DNA microarrays
Figure 1
Distribution of the coefficient of variation for DNA microarrays. The coefficient of variation was calculated for every gene in
the experiment, and plotted for the muscle versus muscle and muscle versus brain. Distributio
Figure 1 Distribution of the coefficient of variation for DNA microarrays
Figure 1
Distribution of the coefficient of variation for DNA microarrays. The coefficient of variation was calculated for every gene in
the experiment, and plotted for the muscle versus muscle and muscle versus brain. cessful classification afforded by the FDA projection, dis-
criminatory genes were selected using the magnitude of
the loading coefficients. Principle Component Analysis
[27] was used as an unsupervised classification procedure
to complement FDA. The results of the PCA analysis
largely mirrored the FDA results (data not shown). cessful classification afforded by the FDA projection, dis-
criminatory genes were selected using the magnitude of
the loading coefficients. Principle Component Analysis
[27] was used as an unsupervised classification procedure
to complement FDA. The results of the PCA analysis
largely mirrored the FDA results (data not shown). scored based on the weighted contribution of each gene's
expression level to a newly defined metric called a "canon-
ical variable" (CV). Because each gene's contribution to a
sample's score is weighted by a coefficient called a "load-
ing," genes with very small loadings do not significantly
contribute to the sample's score and classification, and
can therefore be eliminated from further consideration. This technique can be used as a tool to visualize the gene
transcription results in a lower dimensional space defined
by the canonical variables. As shown in Figure 2, using
expression data of the selected gene combinations allows
accurate classification of the dietary treatments suggesting
that the genes in Table 3 (See Additional file: 1) are dis-
criminatory of the conditions examined when sample
classification is used as a criterion. On the basis of the suc- Methods used here, along with the data set, are available
for public use at our laboratory's web-site [28]. The entire
data set is also available through the National Center for
Biotechnology Information's Gene Expression Omnibus
database [29]. Page 5 of 13
(page number not for citation purposes) http://www.nutritionandmetabolism.com/content/2/1/15 Nutrition & Metabolism 2005, 2:15 Table 2: Comparison of array results and RT-PCR results for selected genes. Gene expression percentages are reported relative to the
control values. F/ WR: Fasting Weight Reduction. Genes
Assay
High Fat vs. Control
F/ WR vs. The effect of 10 weeks of high-fat feeding and 48 hours of
caloric restriction on body weight in C57/BL/6J mice The effect of 10 weeks of high-fat feeding and 48 hours of
caloric restriction on body weight in C57/BL/6J mice C57/BL/6J mice significantly increased their body weight
by 32% after 10 weeks of high-fat feeding (p < 0.001;
Table 4). After 48 hours of fasting, their weights returned
to baseline levels and were not significantly different from
the control mice, but were significantly less than mice
maintained on the high-fat diet (p < 0.001; Table 4). The 41 discriminating genes contributed to the classifica-
tion observed in Figure 2. In Figure 2, each sample is given
a canonical variable (CV) score, based on the weighted
sum of its gene expression values. The genes with the larg-
est contributions to CV1 and CV2 are given in Table 3 (See
Additional file: 1), suggesting these genes underlie the
biological differences between the samples. Figure 2
shows that 10 weeks of high-fat feeding altered the tran-
scriptional levels of genes composing CV1 and CV2 so as
to separate the control and high-fat mice in the CV1 and
CV2 space. However, while 48 hours of fasting/ weight
reduction normalized many of the genes contributing to
CV2, resulting in a return to control levels for that
variable, the genes contributing to CV1 remained
perturbed, resulting in the observed separation between
the fasted/ weight reduced mice and control mice. This
suggests that while some genes, and their associated path-
ways that differentiate DIO and insulin resistance from
normal physiology, return to control levels as weight is
reduced, other genes remain perturbed, reflecting further
physiological adaptations that occur during these treat-
ments. To show individual gene responses to the dietary
treatments, the 41 genes were clustered according to
changes in the p-values from pairwise comparisons
between the control mice, the high-fat fed mice, and the
fasting/ weight reduced mice. This classification arranges
the genes according to their transcript levels during the
physiological states examined. For example, Group A in Distributio
Figure 1 Control
IL6st
Array
154 ± 21%*
144 ± 21%*†
RT-PCR
167 ± 19%*
185 ± 15%*†
PTP4a2
Array
71 ± 4%*
89 ± 3%*
RT-PCR
75 ± 16%
94 ± 18%
RGS3
Array
35 ± 5%*
54 ± 8%*
RT-PCR
38 ± 9%*
59 ± 8%*
G6P
RT-PCR
476 ± 72%
769 ± 216%*
PCK1
RT-PCR
132 ± 28%
217 ± 80%*
Malic Enzyme
RT-PCR
9.1 ± 1.5%*
0.1 ± 0.1%*
*Indicates that the measurements were significantly different from control values at P < 0.01. †Indicates that the measurements made on the micro array were significantly different from the RT-PCR measurement at P < 0.05. Table 2: Comparison of array results and RT-PCR results for selected genes. Gene expression percentages are reported relative to the
control values. F/ WR: Fasting Weight Reduction. results and RT-PCR results for selected genes. Gene expression percentages are reported relative to the
Weight Reduction. *Indicates that the measurements were significantly different from control values at P < 0.01. †Indicates that the measurements made on the micro array were significantly different from the RT-PCR measurement at P < 0.05. Component Analysis (PCA) loading coefficients [27],
resulting in the 41 genes reported in Table 3 (See Addi-
tional file: 1). Component Analysis (PCA) loading coefficients [27],
resulting in the 41 genes reported in Table 3 (See Addi-
tional file: 1). Page 6 of 13
(page number not for citation purposes) Microarray analysis of hepatic genes after 10 weeks of
high-fat feeding and 48 hours of fasting/ weight reduction
in C57/BL/6J mice Employing statistical and data mining methods we
searched the transcription data set for hepatic genes that
direct the biological response during DIO, associated
insulin resistance, and fasting/ weight reduction. We used
the t-test to determine the statistical significance of every
pairwise gene difference between the treatments. The t-test
showed that 1981 genes had at least one statistically sig-
nificant (p < 0.05) change between the treatments. Within
this gene set, 113 genes were significantly changed
between the high-fat fed mice and the control mice, 169
genes were significantly changed between the fasting/
weight reduced mice and the control mice, and 260 genes
were significantly changed between the high-fat fed and
fasting/ weight reduced mice, all at p < 0.01. From the
1981 genes selected by the p < 0.05 cutoff, we retained the
1169 genes that had a Wilks-λ value below our cutoff cri-
terion of 0.47, which is equivalent to a p-value of less than
0.05 [25]. From these genes we selected those with the
greatest Fisher Discriminant Analysis (FDA) and Principle Page 6 of 13
(page number not for citation purposes) Page 6 of 13
(page number not for citation purposes) http://www.nutritionandmetabolism.com/content/2/1/15 Nutrition & Metabolism 2005, 2:15 her discriminant analysis plot of mouse liver samples
gure 2
her discriminant analysis plot of mouse liver samples. Samples were scored according to the canonical variables determined
Fisher Discriminant Analysis (FDA). Each canonical variable is defined as a weighted sum of 100 specific genes, including each
the 41 genes contained in Table 3 (See Additional file: 1). To score a sample, the gene expression value is multiplied by an
DA coefficient, called a loading, and the products from the 100 genes used in the analysis are summed to give the canonical
riable score for the sample. F/ WR: Fasting/ Weight Reduced. Microarray analysis of hepatic genes after 10 weeks of
high-fat feeding and 48 hours of fasting/ weight reduction
in C57/BL/6J mice -10
-9
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
10
-10
-9
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
10
Circles = Control mice
Squares = High–Fat mice Triangles = F/WR mice
Canonical Variable 1
Canonical Variable 2 -10
-9
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
9
10
-10
-9
-8
-7
-6
-5
-4
-3
-2
-1
0
1
2
3
4
5
6
7
8
Canonical Variable 1
Canonical Variable 2 Canonical Variable 1 Fisher discriminant analysis plot of mouse liver samples
Figure 2
Fisher discriminant analysis plot of mouse liver samples. Samples were scored according to the canonical variables determined
by Fisher Discriminant Analysis (FDA). Each canonical variable is defined as a weighted sum of 100 specific genes, including each
of the 41 genes contained in Table 3 (See Additional file: 1). To score a sample, the gene expression value is multiplied by an
FDA coefficient, called a loading, and the products from the 100 genes used in the analysis are summed to give the canonical
variable score for the sample. F/ WR: Fasting/ Weight Reduced. Discussion Diet induced obesity (DIO) in C57/BL/6J mice is a com-
monly used animal model for the development of insulin
resistance in humans [7-11], which results in simultane-
ous hyperglycemia and hyperinsulinemia. Although
short-term caloric restriction and weight loss can improve
insulin resistance [12,30,31], the regulatory mechanisms
in the liver that lead to insulin resistance in response to
DIO, as well as the improvement of insulin sensitivity in
response to short-term caloric restriction and weight
reduction, remain largely unknown. To identify genes
involved in hepatic physiology during DIO and short-
term caloric restriction, we used DNA microarrays to
measure genome-wide transcript abundance. Fisher disc
Figure 2 Table 3 (See Additional file: 1) comprises genes that were
significantly elevated or repressed (p < 0.05) by high-fat
feeding, but then normalized to (insignificant, p > 0.05)
control levels by fasting and weight reduction. Similarly,
group B genes were significantly elevated or repressed (p <
0.05) by high-fat feeding and partially normalized to con-
trol levels by fasting/ weight reduction: the expression dif-
ferences are still significant (p < 0.05) when comparing
both the high-fat and control mice with the fasted/ weight
reduced mice. The genes of each group along with their
normalized expression levels are given in Table 3 (See
Additional file: 1). Among the 41 discriminatory genes identified in this
study, interleukin 6 signal transducer (IL6st), protein tyro-
sine phosphatase 4a2 (PTP4a2), SH3-domain kinase
binding protein 1 (Shk3bp1), and regulator of g-protein
signaling 3 (RGS3) are of special interest because, based
on known biology, they may contribute to the physiolog-
ical changes that accompany DIO, insulin resistance, and
increased insulin sensitivity due to fasting/ weight reduc-
tion. Both IL6st and Sh3kbp1 are significantly upregulated
after 10 weeks of high-fat feeding (p < 0.001), but only
Sh3kbp1 is normalized to baseline levels after 48 hours of
fasting and weight reduction (Table 3: See Additional file:
1). Both PTP4a2 and RGS3 are significantly downregu-
lated after 10 weeks of high-fat feeding (p < 0.01), and
both are partially normalized after 48 hours of fasting/
weight reduction (p < 0.01 for fasted/ weight reduced ver-
sus high-fat and fasted/ weight reduced versus control;
Table 3: See Additional file: 1). Fisher disc
Figure 2 Fisher discriminant analysis plot of mouse liver samples
Figure 2
Fisher discriminant analysis plot of mouse liver samples. Samples were scored according to the canonical variables determined
by Fisher Discriminant Analysis (FDA). Each canonical variable is defined as a weighted sum of 100 specific genes, including each
of the 41 genes contained in Table 3 (See Additional file: 1). To score a sample, the gene expression value is multiplied by an
FDA coefficient, called a loading, and the products from the 100 genes used in the analysis are summed to give the canonical
variable score for the sample. F/ WR: Fasting/ Weight Reduced. Table 4: Experimental treatments and mouse weights. Diet
Feeding Regimen
Weight 48 hours Prior to Harvest
(Average ± St. Dev., n)
Weight at Harvest (Average ± St. Dev., n)
Normal Chow
Ad libitum
35.6 ± 1.8, 9
35.6 ± 1.5, 9
High-Fat
Ad libitum
47.1 ± 5.8*, 9
51.7 ± 4.4*†,5
High-Fat
Restricted
37.3 ± 2.6,4
*Indicates that the weight was statistically different from the control at P < 0.001. † Indicates that the weight of the high-fat and fasted mice was different at P < 0.001. Table 4: Experimental treatments and mouse weights. *Indicates that the weight was statistically different from the control at P < 0.001. † Indicates that the weight of the high-fat and fasted mice was different at P < 0.001. Page 7 of 13
(page number not for citation purposes) http://www.nutritionandmetabolism.com/content/2/1/15 http://www.nutritionandmetabolism.com/content/2/1/15 http://www.nutritionandmetabolism.com/content/2/1/15 Nutrition & Metabolism 2005, 2:15 Although several commonly studied genes, such as glu-
cose-6-phosphatase (G6P), phosphoenolpyruvate carbox-
ykinase (PCK1), and malic enzyme, did not make it into
our bioinformatics analysis, we evaluated their expression
by RT-PCR because of their considerable effects on hepatic
glucose output. G6P and PCK1 were upregulated follow-
ing 10 weeks of high-fat feeding, but only the change
observed in G6P achieved statistical significance (p = 0.09
for PCK1 and p < 0.01 for G6P in the high-fat versus con-
trol comparison; Table 2). Fasting/ weight reduction
resulted in even larger increases in mRNA levels for both
G6P and PCK1 (p < 0.01 versus controls; Table 2). In con-
trast, malic enzyme exhibited significant underexpression
following 10 weeks of high-fat feeding, with further
down-regulation following fasting/ weight reduction
(Table 2). Page 8 of 13
(page number not for citation purposes) RT-PCR analysis of IL6st, PTP4a2, RGS3, G6P, PCK1, and
malic enzyme These differences include
elevated concentrations of serum triglycerides, leptin, and
tumor necrosis factor-α, as well as changes in the levels of
other factors that have been previously demonstrated to
play a physiological role during DIO in C57/BL/6J mice Page 8 of 13
(page number not for citation purposes) Page 8 of 13
(page number not for citation purposes) http://www.nutritionandmetabolism.com/content/2/1/15 Nutrition & Metabolism 2005, 2:15 Inhibition of PI-3-Kinase signaling by Sh3kbp1
Figure 3
Inhibition of PI-3-Kinase signaling by Sh3kbp1. In this figure, insulin, I, binds to its receptor, activating the receptor's tyrosine
kinase activity. Insulin receptor substrates, IRS, are activated by phosphorylation. IRS phosphorylates PI-3-kinase, which
migrates to the cell membrane where it generates phosphatidylinositol, PI, second messengers, which alters physiological proc-
esses. Shown here, Sh3kbp1 is capable of binding the regulatory subunit of PI-3-kinase, inhibiting its ability to generate PI sec-
ond messengers, and thereby attenuating insulin signaling. Inhibition of PI-3-Kinase signaling by Sh3kbp1
Figure 3
Inhibition of PI-3-Kinase signaling by Sh3kbp1. In this figure, insulin, I, binds to its receptor, activating the receptor's tyrosine
kinase activity. Insulin receptor substrates, IRS, are activated by phosphorylation. IRS phosphorylates PI-3-kinase, which
migrates to the cell membrane where it generates phosphatidylinositol, PI, second messengers, which alters physiological proc-
esses. Shown here, Sh3kbp1 is capable of binding the regulatory subunit of PI-3-kinase, inhibiting its ability to generate PI sec-
ond messengers, and thereby attenuating insulin signaling. Inhibition of PI 3 Kinase signaling by Sh3kbp1
Figure 3
Inhibition of PI-3-Kinase signaling by Sh3kbp1. In this figure, insulin, I, binds to its receptor, activating the receptor's tyrosine
kinase activity. Insulin receptor substrates, IRS, are activated by phosphorylation. IRS phosphorylates PI-3-kinase, which
migrates to the cell membrane where it generates phosphatidylinositol, PI, second messengers, which alters physiological proc-
esses. Shown here, Sh3kbp1 is capable of binding the regulatory subunit of PI-3-kinase, inhibiting its ability to generate PI sec-
ond messengers, and thereby attenuating insulin signaling. [7-9,11,32]. Notably, Group A and B genes are either com-
pletely (Group A, Table 3: See Additional file: 1) or par-
tially (Group B, Table 3: See Additional file: 1)
normalized following 48 hours of fasting/ weight reduc-
tion, when insulin sensitivity has increased, suggesting
they may be important to the development of hepatic
insulin resistance during DIO. RT-PCR analysis of IL6st, PTP4a2, RGS3, G6P, PCK1, and
malic enzyme The 41 most discriminating genes determined by our bio-
informatics analysis lie essentially within two large groups
(Table 3: See Additional file: 1): 1) Genes that are signifi-
cantly induced or repressed by 10 weeks of high-fat feed-
ing and completely (Group A) or partially (Group B)
normalized by 48 hours of fasting/ weight reduction, 2)
Genes that are significantly induced or repressed by 10
weeks of high-fat feeding, but are not normalized by 48
hours of fasting/ weight reduction (Group D). Both of
these groups contain genes involved in signal transduc-
tion pathways, as well as protein metabolism and secre-
tion, highlighting the importance of these molecular
pathways in the hepatic response to DIO and fasting/
weight reduction. We compared the transcript levels measured by RT-PCR
with the ratios measured using DNA microarrays by divid-
ing RT-PCR expression values observed in high-fat fed
mice and fasted/ weight reduced mice by the expression
values measured in the control mice. Liver mRNA levels
for each mouse in the study were determined by RT-PCR
for IL6st, PTP4a2, and RGS3. The values measured by RT-
PCR were not significantly different from the results
observed by hepatic microarray analysis (p > 0.05; Table
2) for all genes except IL6st between the fasting/ weight
reduced mice and control mice. Notably, in this single
case, both microarray analysis and RT-PCR show signifi-
cant increases (p < 0.001) in the levels of IL6st mRNA,
demonstrating similar qualitative changes between the
measurement methods. The close agreement between the
micoarray results and RT-PCR results thus validates the
specificity and accuracy of our microarray measurements. The difference in the ratios between the values determined
by RT-PCR and those determined by microarray analysis
was less than 30% for each of these genes (Table 2). Because genes in Group A and B (Table 3: See Additional
file: 1) were perturbed by DIO, their expression levels cor-
relate with observed physiological differences that
develop during this condition. Page 9 of 13
(page number not for citation purposes) RT-PCR analysis of IL6st, PTP4a2, RGS3, G6P, PCK1, and
malic enzyme IL6st forms homo- and het-
erodimers with other signal transducing subunits in
response to binding by an assortment of ligands including
IL-6, IL-11, LIF, CT-1, CNTF, and OSM [55]. Among these,
IL-6 knockout mice develop mature-onset obesity [56],
and treatment of hepatocytes with IL-6 reduces the
expression of PCK1 [6], thus implicating IL-6 in the regu-
lation of hepatic glucose output. There are at least four dif-
ferent Jaks (Jak1, Jak2, Jak3, and Tyk2) and seven different
STAT factors (STAT1, 2, 3, 4, 5a, 5b, and 6) that can inter-
act with IL6st. Of particular relevance to DIO and insulin
resistance is STAT3. The liver-specific STAT3 knockout
mouse is insulin resistant and develops glucose intoler-
ance when fed a high-fat diet, due in part to increased
expression of PCK1 and G6P [57]. Adenoviral mediated
reconstitution of STAT3 signaling ameliorated glucose
intolerance in both L-ST3KO and Lepr-/- mice [57] by low-
ering PCK1 and G6P levels, demonstrating the impor-
tance of STAT3 signalling to hepatic glucose output. Because IL6st is significantly upregulated (p < 0.001) by
10 weeks of high-fat feeding and 48 hours of fasting/
weight reduction, when PCK1 and G6P were also induced
relative to control levels (Table 2), it may be that IL6st per-
forms a sensitizing function that contributes to feedback
control of hepatic glucose output via IL6 and STAT3 sign-
aling. In addition to the cellular signaling pathways that
contained differentially expressed genes identified in this
study, a number of genes involved in protein metabolism
and secretion were also identified. Although a direct link
between protein metabolism/ secretion and DIO/ insulin
resistance is not as well established, in other insulin sensi-
tive tissues the release of hormones and trafficking of
receptors clearly plays a role in regulating tissue specific
responses to insulin and glucose. Group A and B genes
involved in protein metabolism and secretion pathways While genes in Group D (Table 3: See Additional file: 1)
were also significantly induced or repressed following 10
weeks of high-fat feeding, unlike genes in Group A and B,
they do not respond to 48 hours of fasting/ weight reduc-
tion. Therefore hepatic regulation of Group D genes may
not be as directly linked to changes resulting from DIO
and insulin resistance and sensitivity. RT-PCR analysis of IL6st, PTP4a2, RGS3, G6P, PCK1, and
malic enzyme A definitive role
for many PTPs in glucose homeostasis and insulin signal-
ing has not been established, however, PTP1B knock-out
mice have enhanced insulin sensitivity and are resistant to
DIO [40]. Therefore if PTP4a2 also negatively regulates
insulin signaling, its significant downregulation (p < 0.01)
following 10 weeks of high-fat feeding may be a physio-
logical adaptation that protects hepatocytes against insu-
lin resistance, which is normalized by fasting/ weight
reduction. FosB is a member of the AP-1 family of transcription fac-
tors [51]. These molecules are considered immediate early
genes, because they initiate responses to environmental
stimuli [52]. The Fos family of transcription factors form
either homodimers with one another, or heterodimers
with the Jun family of transcription factors, which then
bind DNA to alter gene transcription [53]. Because insulin
affects the expression of members of the AP-1 family of
transcription factors [54], it is not surprising that during
DIO and fasting/ weight reduction, conditions that per-
turb insulin signaling, significantly increase transcription
of FosB. RGS3 (Regulator of G-protein coupled receptor (GPCR)
signaling 3) has been primarily studied in neurons [41-
43] and cells in culture [44,45]. RGS proteins bind Gα
subunits and generally increase the GTPase activity [46]. We found that hepatic RGS3 mRNA levels are significantly
decreased (p < 0.01) after 10 weeks of high-fat feeding, but
partially normalized by fasting/ weight reduction. These
findings are particularly relevant because hepatocytes
express a truncated form of RGS3 that has been shown to
directly inhibit Gsα stimulated cAMP production and Gqα
stimulated IP production [47], in addition to interacting
with, Giα [48]. Glucagon signals via a GPCR that stimu-
lates adenyl cyclase and increases cAMP levels [49]. Because the truncated form of RGS3 inhibits cAMP
production, lowering RGS3 concentration may augment
basal cAMP levels and thereby promote hepatic glucose
output resulting from cAMP induced phosphoenolpyru-
vate carboxykinase (PCK1) expression and cAMP
repressed glucokinase transcription. Although glucoki-
nase expression levels were not measured, PCK1 mRNA
levels were increased by both 10 weeks of high-fat feeding
and fasting/ weight reduction (Table 2). IL6st (Interleukin 6 signal transducing subunit, also called
gp130) is a key component in cytokine signal transduc-
tion that occurs during inflammation through the JAK
(Janus kinase)/ STAT (signal transducers and activators of
transcription) pathway. RT-PCR analysis of IL6st, PTP4a2, RGS3, G6P, PCK1, and
malic enzyme Several relevant signal
transduction pathways are influenced by the genes within
Group A and B (Table 3: See Additional file: 1), particu-
larly Sh3kbp1, PTP4a2, and RGS3. While Sh3kbp1 and
PTP4a2 may be directly involved with insulin signaling,
by respectively binding PI-3-kinase and dephosphorylat-
ing protein tyrosine residues, RGS3 interacts directly with
G-proteins and some evidence suggests RGS family mem-
bers may also indirectly affect proteins in the MAPK signal
transduction pathways [33] as well as certain tyrosine
phosphatases [34]. signaling occurs via phosphorylation of insulin receptor
substrates (IRSs) that interact with signal transduction
molecules including PI-3-kinase, Grb2, nck, and SHP2
[36]. Sh3kbp1 has been shown to directly inhibit PI-3-
kinase signaling by binding the p85α regulatory subunit
in vivo and in vitro, and interacts with Grb2 in vitro [37]. Therefore, increased levels of Sh3kbp1 mRNA in the high-
fat fed mice relative to both the control and fasted/ weight
reduced mice, suggests that Sh3kbp1 may mediate DIO
associated insulin resistance in hepatocytes via a mecha-
nism described in Figure 3. PTP4a2 (Protein tyrosine phosphatase 4a2) dephosphor-
ylates tyrosine residues in proteins. When insulin binds its
receptor it activates the receptor's tyrosine kinase activity
[38], leading to autophosphorylation and subsequent
tyrosine phosphorylation of molecules containing Src
homology 2 (SH2) or phosphotyrosine binding (PTB)
domains. Therefore PTPs can in fluence insulin signaling
by dephosphorylating protein tyrosine residues. Although
it would be anticipated that PTPs would attenuate insulin
signaling, they have been implicated in both positive and Sh3kbp1 (SH3-domain kinase binding protein, also called
Ruk) belongs to the CD2AP/CMS family of adapter-type
proteins, which mediate a number of different cellular
mechanisms including signal transduction [35]. Insulin Page 9 of 13
(page number not for citation purposes) Page 9 of 13
(page number not for citation purposes) Nutrition & Metabolism 2005, 2:15 http://www.nutritionandmetabolism.com/content/2/1/15 http://www.nutritionandmetabolism.com/content/2/1/15 required to determine the effects of BMP2 upregulation in
mice following these dietary treatments. negative regulation of this pathway [39]. A definitive role
for many PTPs in glucose homeostasis and insulin signal-
ing has not been established, however, PTP1B knock-out
mice have enhanced insulin sensitivity and are resistant to
DIO [40]. Therefore if PTP4a2 also negatively regulates
insulin signaling, its significant downregulation (p < 0.01)
following 10 weeks of high-fat feeding may be a physio-
logical adaptation that protects hepatocytes against insu-
lin resistance, which is normalized by fasting/ weight
reduction. negative regulation of this pathway [39]. Page 10 of 13
(page number not for citation purposes) Additional file 1 Additional file 1
Table 3
Table 3
Click here for file
[http://www.biomedcentral.com/content/supplementary/1743-
7075-2-15-S1.pdf] Additional file 1
Table 3
Table 3
Click here for file
[http://www.biomedcentral.com/content/supplementary/1743-
7075-2-15-S1.pdf] Table 3
Table 3
Click here for file
[http://www.biomedcentral.com/content/supplementary/1743-
7075-2-15-S1.pdf] Acknowledgements We thank Dr. Depi Sanoudo at the Harvard Medical School for her insight-
ful comments and review of the manuscript. This work was supported by a
grant from the National Institutes of Health Bioengineering research part-
nership, DK-585331. The Virtek arrayer was generously provided by
Virtek, and supported by Bio-Rad. While the link between many of these genes and DIO will
require further investigations, their identification here is
an important contribution to understanding how the
hepatic response to DIO and fasting/ weight reduction is
mediated through a variety of molecular pathways. These
genes all share a consistent set of attributes that made
them stand out in the data set. They demonstrate signifi- Conclusion Using DNA microarrays we have investigated the effects of
DIO and fasting/ weight reduction on liver gene transcrip-
tion. We have analyzed this data set using four computa-
tional methods that represent a rigorous approach to
analysis requiring no a priori assumptions about the data. This has enabled us to infer the importance of any given
gene change among a multitude of gene differences result-
ing from DIO and fasting/ weight reduction. Our results
lead us to focus on 41, out of an initial 1981 genes. Authors' contributions RMR helped with the tissue harvest, conducted the RNA
purification, prepared the DNA microarrays, conducted
the sample labeling and hybridization, conducted the RT-
PCR, conducted the data analysis, and wrote the manu-
script. JB handled the animals used in the study, helped
conduct the tissue and RNA harvests, and helped write the
manuscript. JK consulted on the project and reviewed the
manuscript. CM helped design the experiment and set-up
the animal handling procedures. GS organized the
project, helped design the experiments, and helped write
the manuscript. Note Table 3: (See Additional file: 1) Percent control expression
of genes found common to all analysis methods. Included
are genes identified using t-test, Wilks ranking, fisher dis-
criminate analysis, and principle component analysis. These genes are organized by their pairwise t-test results,
and the relation between their expression levels. F/ WR:
Fasting/ Weight Reduced. Although many of the genes resulting from our analysis
have not yet been studied extensively in the context of
energy homeostasis, several are related to important
molecular pathways that have been previously identified
in the literature. Those pathways include different signal
transduction cascades, as well as pathways involved in
protein metabolism and secretion. Given the diverse func-
tions of the liver, identifying genes involved in signaling
and protein metabolism pathways in response to DIO and
fasting/ weight reduction is not surprising. Among the
genes involved in signaling are Sh3kbp1, Rgs3, PTP4a2,
BMP2, IL6st, Fosb, Gabrr1, and possibly Rab3c. Genes
implicated in protein metabolism and secretion pathways
include Crym, Serpina5, Eif4a2, Ctrl, Snrpg, Kcnk8, Copz2,
and Rab3c. Competing interests p
g
The author(s) declare that they have no competing
interests. RT-PCR analysis of IL6st, PTP4a2, RGS3, G6P, PCK1, and
malic enzyme Despite this, it is
interesting that a number of Group D genes are also
implicated in several signal transduction pathways that
may be activated by DIO. These genes include BMP2, Fosb,
Gabrr1, IL6st, and 4833414G15Rik. BMP2 (Bone morphogenetic protein 2), is a highly con-
served member of the transforming growth factor-β (TGF-
β) gene family. BMP2 is related to BMP9, which was the
first reported hepatic factor shown to decrease blood glu-
cose levels by increasing insulin release and decreasing
food intake [50]. While these mechanisms may be a
compensating response to DIO, they oppose the physio-
logical adaptations that accompany 48 hours of fasting/
weight reduction, and therefore additional studies are Page 10 of 13
(page number not for citation purposes) http://www.nutritionandmetabolism.com/content/2/1/15 http://www.nutritionandmetabolism.com/content/2/1/15 Nutrition & Metabolism 2005, 2:15 include Kcnk8, Pmm1, Serpina5, and Eif4a2. Group D
genes that were identified include Copz2, Rab3c, and
4933432M07Rik. cant differences between the dietary treatments, are indi-
vidually discriminatory of each treatment, and are
members of a set that classifies each sample using both
supervised and unsupervised algorithms. Genes that
satisfy all of these criteria represent good candidates for
influencing the liver's response to DIO and fasting/ weight
reduction,
and
therefore
warrant
more
detailed
investigations. Serpina5, encodes a serine protease inhibitor. Serine pro-
tease inhibitors represent a family of glycoproteins that
are known to inactivate serine proteases by forming stoi-
chiometric enzyme-inhibitor complexes. Among the pro-
teases known to be inhibited by Serpins are trypsin,
chymotrypsin, the sperm protease acrosin, and a variety of
proteases involved in hemostasis [58]. Copz2 encodes a
vesicle coating protein that helps to mediate vesicle traf-
ficking, while Rab3c is a member of the Ras oncogene fam-
ily that encodes a monomeric GTP-binding protein that is
implicated in regulated exocytosis and vesicle transport,
and has been suggested to play a role in GLUT4 transloca-
tion in rat cardiac muscle cells [59]. Hence, Copz2 and
Rab3c may synergistically influence protein trafficking in
response to 10 weeks of high-fat feeding and 48 hours of
fasting/ weight reduction. References J
y
13. O'Brien RM, Granner DK: Regulation of Gene Expression by
Insulin. Physiological Reviews 1996, 76(4):1109-1161. y
g
( )
14. Jr AWF, Thearle M, Liao T, Leibel RL: Effects of Leptin Deficiency
and Short-term Repletion on Hepatic Gene Expression in
Genetically Obese Mice. Diabetes 2001, 50(10):2268-2278. 38. Cheng A, Dube N, Gu F, Tremblay ML: Coordinated Action of
Protein
Tyrosine
Phosphatases
in
Insulin
Signal
Transduction. European
Journal
of
Biochemistry
2002,
269:1050-1059. y
(
)
15. Tobe K, Suzuki R, Aoyama M, Terauchi Y: Increased Expression of
SREBP-1 Gene in IRS-2(-/-) Mice Liver. Diabetes 2001, 50(Sup-
plement 2):A324-A324. 39. Asante-Appiah E, Kennedy BP: Protein Tyrosine Phosphatases:
The quest for negative regulators of insulin action. American
Journal
of
Physiology,
Endocrinology
and
Metabolism
2003,
284:E663-E670. 16. Ziotopoulou M, Mantzoros C, Hileman S, Flier J: Differential
Expression of Hypothalamic Neuropeptides in the Early
Phase of Diet-Induced Obesity in Mice. American Journal of Phys-
iology: Endocrinology and Metabolism 2000, 279(4):E838-E845. 40. Elchebly M, Payette P, Michaliszyn E, Cromlish W, Collins S, Loy A,
Normandin D, Cheng A, Himms-Hang J, Chan C, Ramachandran C,
Gresser M, Tremblay M, Kennedy B: Increased Insulin Sensitivity
and Obesity Resistance in Mice Lacking the Protein Tyrosine
Phosphatase-1B Gene. Science 1999, 283:1544-1548. gy
gy
( )
17. Bullen JW Jr, Ziotopoulou M, Ungsunan L, Misra J, Alevizos I, Kokko-
tou E, Maratos-Flier E, Stephanopoulos G, Mantzoros CS: Short-
term Resistance to Diet-Induced Obesity in A/ J Mice is Not
Associated with Regulation of Hypothalamic Neuropeptides. American Journal of Physiology: Endocrinology and Metabolism 2004 in
press. 41. Arshavsky V, Jr EP: Lifetime Regulation of G Protein-Effector
Complex: Immerging Importance of RGS Proteins. Neuron
1998, 20:11-14. 18. Jelinsky S, Samson L: Global Response of Saccharomyces cerevi-
siae to an Alkylating Agent. Proceedings of the National Academy of
Sciences – USA 1999, 96:1486-1491. 42. Jeong S, Ikeda S: Endogenous Regulator of G-Protein Signalling
Proteins Modify N-type Calcium Channel Modulation in Rat
Sympathetic
Neurons. Journal
of
Neuroscience
2000,
20:4489-4496. 19. Wang Y, Rea T, Bian J, Gray S, Sun Y: Identification of the Genes
Responsive to Etoposide-induced Apoptosis: Application of
DNA Chip Technology. FEBS Letters 1999, 445:269-273. 43. Sinnarajah S, Dessauer CW, Srikumar D, Chen J, Yuen J, Yilma S, Den-
nis JC, Morrison EE, Vodyanoy V, Kehrl JH: RGS2 Regulates Signal
Transduction in Olfactory Neurons by Attenuating Activa-
tion of Adenylyl Cyclase III. Nature 2001, 409:1051-1055. 20. References Keller K, Lemberg L: Obesity and the Metabolic Syndrome. American Journal of Critical Care 2003, 12(2):167-170. 1. Keller K, Lemberg L: Obesity and the Metabolic Syndrome. American Journal of Critical Care 2003, 12(2):167-170. Page 11 of 13
(page number not for citation purposes) Nutrition & Metabolism 2005, 2:15 http://www.nutritionandmetabolism.com/content/2/1/15 http://www.nutritionandmetabolism.com/content/2/1/15 2. Goran MI, Ball GD, Cruz ML: Obesity and Risk of Type 2 Diabe-
tes and Cardiovascular Disease in Children and Adolescents. Journal of Clinical Endocrinology and Metabolism 2003, 88(4):1417-1427. tially Expressed Genes using Genomic Expression Profiles. Genome Research 2001, 11:1227-1236. 25. Hwang D, Schmitt WA, Stephanopoulos G, Stephanopoulos G:
Determination of Minimum Sample Size and Discriminatory
Expression Patterns. Bioinformatics 2002, 18:1184-1193. J
gy
( )
3. youn Kim S, il Kim H, Park SK, Im SS, Li T, Cheon HG, ho Ahn Y:
Liver Glucokinase can be Activated by Peroxisome Prolifer-
ator-Activated Receptor-gamma. Diabetes 2004, 53(Supple-
ment 1):S66-S70. 26. 26. Stephanopoulos G, Hwang D, Schmitt WA, Misra J, Stephanopoulos
G: Mapping Physiological States from Microarray Expression
Measurements. Bioinformatics 2002, 18(8):1054-1063. )
4. Kerstein S, Desvergne B, Wahli W: Roles of PPARs in Health and
Disease. Nature 2000, 405:421-424. f
( )
27. Dillon WR, Goldstein M: Multivariate Analysis: Methods and Applications
New York: John Wiley & Sons; 1984. Disease. Nature 2000, 405:421-424. 5. Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray
HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI,
Young RA: Control of Pancreas and Liver Gene Expression by
HNF Transcription Factors. Nature 2004, 303:1378-1381. J
y
28. Bioinformatics and Metabolic Engineering Laboratory at
MIT [http://web.mit.edu/bamel/index.shtml] 29. Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus:
NCBI Gene Expression and Hybridization Array Data
Repository. Nucleic Acids Research 2002, 30:207-210. 6. Christ B, Yazici E, Nath A: Phosphatidylinositol 3-kinase and
Protein Kinase C Contribute to the Inhibition by Interleukin
6 of Phosphoenolpyruvate Carboxykinase Gene Expression
in Cultured Hepatocytes. Hepatology 2000, 31:461-468. 30. Escalante-Pulido M, Escalante-Herrera A, Milke-Najar M, Alpizar-Sala-
zar M: Effects of Weight Loss on Insulin Secretion and in vivo
Insulin Sensitivity in Obese Diabetic and Non-diabetic
Subjects. Diabetes Nutrition and Metabolism 2003, 16:277-283. p
y
p
gy
,
7. Surwit R, Kuhn C, Cochrane C, McCubbin J, Feinglos M: Diet-
induced Type II Diabetes in C57BL/6J Mice. Diabetes 1988,
37(9):1163-1167. j
31. Heilbronn LK, Ravussin E: Calorie Restriction and Aging:
Review of the literature and implications for studies in
humans. References American Journal of Clinical Nutrition 2003, 78:361-369. ( )
8. Parekh P, Petro A, Tiller J, Feinglos M, Surwit R: Reversal of Diet-
induced Obesity and Diabetes in C57BL/6J Mice. Metabolism
1998, 47(9):1089-1096. Ahima RS, Prabakaran D, Mantzoros C, Qu D, Lowell B, Mara
E Fl
JS R l
f L
i
i
h
N
d
i
R 32. Ahima RS, Prabakaran D, Mantzoros C, Qu D, Lowell B, Maratos-Flier
E, Flier JS: Role of Leptin in the Neuroendocrine Response to
Fasting. Nature 1996, 383:250-252. ( )
9. Frederich R, Hamann A, Anderson S, Lollmann B, Flier J: Leptin Lev-
els Reflect Body Lipid Content in Mice: Evidence for Diet-
Induced Resistance to Leptin Action. Nature Medicine 1995,
1:1311-1314. 33. Koch W, Hawes B, Allen L, Lefkowitz R: Direct Evidence that Gi-
Coupled Receptor Stimulation of Mitogen-Activated Protein
Kinase is Mediated by Gβγ Activation of p21ras. Proceedings of the
National Academy of Sciences: U S A 1994, 91:12706-12710. 10. El-Haschimi K, Pierroz D, Hileman S, Bjorbaek C, Flier J: Two
Defects Contribute to Hypothalamic Leptin Resistance in
Mice with Diet-Induced Obesity. Journal of Clinical Investigation
2000, 105:1827-1832. 34. Kullander K, Klein R: Mechanisms and Functions of EPH and
EPHRIN Signalling. Nature Reviews Molecular Cell Biology 2002,
3:475-486. 11. Lin S, Thomas T, Storlien L, Huang X: Development of High Fat
Diet-Induced Obesity and Leptin Resistance in C57Bl/6J
Mice. International Journal of Obesity and Related Metabolic Disorders
2000, 24:639-646. 35. Verdier F, Valovka T, Zhyvoloup A, Drobot LB, Buchman V, Water-
fiedl M, Gout I: Ruk is Ubiquitinated but not Degraded by the
Proteasome. European Journal of Biochemistry 2002, 269:3402-3408. 35. Verdier F, Valovka T, Zhyvoloup A, Drobot LB, Buchman V, Water-
fiedl M, Gout I: Ruk is Ubiquitinated but not Degraded by the
Proteasome. European Journal of Biochemistry 2002, 269:3402-3408. 36. White MF, Jr MGM: Diabetes Mellitus, Carbohydrate Metabolism, and
Lipid Disorders Canada: Harcourt Canada; 2000. p
J
y
36. White MF, Jr MGM: Diabetes Mellitus, Carbohydrate Metabolism, and
Lipid Disorders Canada: Harcourt Canada; 2000. 12. Belfiore F, Ianneloo S, Rabuazzo A, Campione R: Metabolic Effects
of Short-Term Fasting in Obese Hyperglycaemic Humans
and Mice. International Journal of Obesity 1987, 11:631-640. 37. Gout I, Middleton G, Adu J, Ninkina NN, Drobot LB, Filonenko V,
Matsuka G, Davies AM, Waterfield M, Buchman VL: Negative Reg-
ulation of PI 3-kinase by Ruk, a Novel Adaptor Protein. EMBO Journal 2000, 19(15):4015-4025. References Hirsch J, Zhang L, Lazard Y, Fischer C, Barber MC, Ma ZD, Zhang YQ, vey P, Zhong L, Teng B, Sanyal I, Ruben SM, Blondel O, Birse An Integrated Functional Genomics Screening Program
Reveals a Role for BMP-9 in Glucose Homeostasis. Nature
Biotechnology 2003, 21:294-301. gy
51. Angel P, Imagawa M, Chiu R, Stein B, Imbra R, Rahmsdorf H, Jonat C,
Herrlich P, Karin M: Phorbol Ester-inducible Genes Contain a
Common cis Element Recognized by a TPA-modulated
trans-acting Factor. Cell 1987, 49:729-739. g
52. Segal R, Greenberg M: Intracellular Signalling Pathways Acti-
vated by Neurotrophic Factors. Annual Reveiws in Neuroscience
1996, 19:463-489. 53. Nakabeppu Y, Nathans D: A Naturally Occurring Truncated for
of FosB that Inhibits Fos/Jun Transcriptional Activity. Cell
1991, 64:751-759. 54. O'Brien RM, Granner DK: Regulation of Gene Expression by
Insulin. Biochemistry Journal 1991, 278:609-619. 55. Heinrich PC, Behrmann I, Muller-Newen G, Schaper F, Graeve L:
Interleukin-6-type Cytokine Signalling through the gp130/
Jak/STAT Pathway. Biochemistry Journal 1998, 334:297-314. J
y
y J
56. Wallenius V, Wallenius K, Ahren B, Rudling M, Carlsten H, Dickson
S, Ohlsson C, Jansson J: Interleukin-6-deficient Mice Develop
Mature-Onset Obesity. Nature Medicine 2002, 8:75-79. 57. Inoue H, Ogawa W, Ozaki M, Haga S, Matsumoto M, Furukawa K,
Hashimoto N, Kido Y, Mori T, Sakaue H, Teshigawara K, Jin S, Iguchi
H, Hiramatsu R, LeRoith D, Takeda K, Akira S, Kasuga M: Role of
STAT-3 in Regulation of Hepatic Gluconeogenic Genes and
Carbohydrate Metabolism in vivo. Nature Medicine 2004,
10(2):168-174. ( )
58. Zechmeister-Machhart M, Hufnagl P, Uhrin P, Korschineck I, Binder
B, Geiger M: Molecular Cloning and Sequence Analysis of the
Mouse Protein C Inhibitor Gene. Gene 1997, 186:61-66. 59. Uphues I, Chern Y, Eckel J: Insulin-dependent Translocation of
the Small GTP-binding Protein RAB3C in Cardiac Muscle:
Studies on Insulin-Resistant Zucker Rats. FEBS Letters 1995,
377(2):109-112. References Ruan H, Hacohen N, Golub TR, Parijs LV, Lodish HF: Tumor
Necrosis Factor-α Suppresses Adipocyte-Specific Genes and
Activates Expression of Preadipocyte Genes in 3T3-L1
Adipocytes. Diabetes 2002, 51:1319-1336. 44. Chan R, Otte C: Isolation and Genetic Analysis of Saccharomy-
ces cerevisiae Mutants Supersensitive to G1 Arrest by a Fac-
tor and α-factor Pheromones. Molecular Cellular Biology 1982,
2:11-20. p
21. Nadon R, Shoemaker J: Statistical Issues with Microarrays:
Processing
and
Analysis. TRENDS
in
Genetics
2002,
18(5):265-271. ( )
22. Quackenbush J: Computational Analysis of Microarray Data. Nature Reviews Genetics 2001, 2(6):418-427. 45. Vries LD, Zheng B, Fischer T, Elenko E, Farquhar M: The Regulator
of G Protein Signalling Family. Annual Reviews in Pharmacology
and Toxicology 2000, 40:235-271. 23. Kuruvilla FG, Park PJ, Schreiber SL: Vector Algebra in the Analy-
sis of Genome-wide Expression Data. Genome Biology 2002,
3(3):0011.1-0011.11. gy
46. Siderovski D, Strockbine B, Behe C: Whither goest the RGS pro-
teins? Critical Reviews in Biochemistry and Molecular Biology 1999,
34:215-251. ( )
24. Thomas JG, Olson JM, Tapscott SJ, Zhao LP: An Efficient and
Robust Statistical Modeling Approach to Discover Differen- Page 12 of 13
(page number not for citation purposes) Page 12 of 13
(page number not for citation purposes) Nutrition & Metabolism 2005, 2:15 http://www.nutritionandmetabolism.com/content/2/1/15 http://www.nutritionandmetabolism.com/content/2/1/15 http://www.nutritionandmetabolism.com/content/2/1/15 47. Chatterjee TK, Eapen AK, Fisher RA: A Truncated Form of RGS3
Negatively Regulates G Protein-coupled Receptor Stimula-
tion of Adenylyl Cyclase and Phosphoinositide Phospholi-
pase
C. The
Journal
of
Biological
Chemistry
1997,
272(24):15481-15487. (
)
48. Neubig RR, Siderovski DP: Regulators of G-Protein Signalling as
New Central Nervous System Drug Targets. Nature Reviews
Drug Discovery 2002, 1:187-197. g
y
49. Berne RM, Levy MN: Physiology fourth edition. St. Louis, MO: Mosby;
1998. 50. Chen C, Grzegorzewski KJ, Barash S, Zhao Q, Schneider H, Wang Q,
Si
h M P k
L B ll AC D
R C l
T D tt
A Ch
S 50. Chen C, Grzegorzewski KJ, Barash S, Zhao Q, Schneider H, Wang Q,
Singh M, Pukac L, Bell AC, Duan R, Coleman T, Duttaroy A, Cheng S,
Hirsch J, Zhang L, Lazard Y, Fischer C, Barber MC, Ma ZD, Zhang YQ,
Reavey P, Zhong L, Teng B, Sanyal I, Ruben SM, Blondel O, Birse CE:
An Integrated Functional Genomics Screening Program
Reveals a Role for BMP-9 in Glucose Homeostasis. Nature
Biotechnology 2003, 21:294-301. References Publish with BioMed Central and every
scientist can read your work free of charge
"BioMed Central will be the most significant development for
disseminating the results of biomedical research in our lifetime."
Sir Paul Nurse, Cancer Research UK
Your research papers will be:
available free of charge to the entire biomedical community
peer reviewed and published immediately upon acceptance
cited in PubMed and archived on PubMed Central
yours — you keep the copyright
Submit your manuscript here:
http://www.biomedcentral.com/info/publishing_adv.asp
BioMedcentral
Page 13 of 13
(page number not for citation purposes) Publish with BioMed Central and every
scientist can read your work free of charge
"BioMed Central will be the most significant development for
disseminating the results of biomedical research in our lifetime."
Sir Paul Nurse, Cancer Research UK
Your research papers will be:
available free of charge to the entire biomedical community
peer reviewed and published immediately upon acceptance
cited in PubMed and archived on PubMed Central
yours — you keep the copyright
Submit your manuscript here:
http://www.biomedcentral.com/info/publishing_adv.asp
BioMedcentral Publish with BioMed Central and every
scientist can read your work free of charge
"BioMed Central will be the most significant development for
disseminating the results of biomedical research in our lifetime."
Sir Paul Nurse, Cancer Research UK
Your research papers will be:
available free of charge to the entire biomedical community
peer reviewed and published immediately upon acceptance
cited in PubMed and archived on PubMed Central
yours — you keep the copyright
Submit your manuscript here:
http://www.biomedcentral.com/info/publishing_adv.asp
BioMedcentral Publish with BioMed Central and every
scientist can read your work free of charge Page 13 of 13
(page number not for citation purposes)
|
https://openalex.org/W4229699304
|
https://ojs.tdmu.edu.ua/index.php/here/article/download/1701/1646
|
Ukrainian
| null |
ВИКОРИСТАННЯ ПРИНЦИПІВ МЕДИЧНОЇ ОНТОЛОГІЇ ДЛЯ ПОБУДОВИ СЦЕНАРНИХ МОДЕЛЕЙ ПІСЛЯДИПЛОМНОГО НАВЧАННЯ ЛІКАРІВ І ПРОВІЗОРІВ
|
Medična ìnformatika ta ìnženerìâ
| 2,013
|
cc-by
| 3,135
|
МЕДИЧНА ІНФОРМАТИКА
ТА ІНЖЕНЕРІЯ УДК61:007:002.6:681.31:614.252.2:615.1:378.2 УДК61:007:002.6:681.31:614.252.2:615.1:378.2 ВИКОРИСТАННЯ ПРИНЦИПІВ МЕДИЧНОЇ ОНТОЛОГІЇ ДЛЯ ПОБУДОВИ
СЦЕНАРНИХ МОДЕЛЕЙ ПІСЛЯДИПЛОМНОГО НАВЧАННЯ ЛІКАРІВ І
ПРОВІЗОРІВ Описуються підходи, засоби та технології формування персоніфікованих електронних майданчиків управління
знаннями в навчально-інформаційному середовищі. Розглянуті онтологічні аспекти побудови моделі е-сценарію
супроводу процесу навчання/перепідготовки лікаря з використанням мережевих систем знань. Це припускає ви-
рішення актуальних проблем підвищення ефективності навчання лікарів на основі застосування сучасних мере-
жевих технологій дистанційного доступу до розподілених систем знань. Ключові слова: онтологія медичних знань, персоніфікований електронний майданчик, інформаційні джерела
формування знань, онтологічна модель е-сценарію процесу супроводу навчального процесу. О. П. Минцер, А. Е. Стрижак1, С. В. Денисенко
Национальная
медицинская
академия
последипломного
образования
имени П. Л. Шупика
Национальный центр
«Малая академия наук Украины»1 Национальная Описываются подходы, средства и технологии формирования персонифицированных электронных площадок
управления знаниями в учебно-информационной среде. Рассмотрены онтологические аспекты построения мо-
дели е-сценария сопровождения процесса обучения/переподготовки врача с использованием сетевых систем
знаний. Это предполагает решение актуальных проблем повышения эффективности обучения врачей на основе
применения современных сетевых технологий дистанционного доступа к распределенным системам знаний. Ключевые слова: онтология, онтология медицинских знаний, персонифицированная электронная площадка,
информационные источники формирования знаний, онтологическая модель е-сценария процесса сопровожде-
ния учебного процесса. МЕДИЧНА ІНФОРМАТИКА
ТА ІНЖЕНЕРІЯ МЕДИЧНА ІНФОРМАТИКА
ТА ІНЖЕНЕРІЯ О О. П. Мінцер, О. Є. Стрижак, С. В. Денисенко МЕДИЧНА ІНФОРМАТИКА
ТА ІНЖЕНЕРІЯ вчання, при якому учасники й організатори навчаль-
ного процесу здійснюють переважно індивідуалізо-
вані взаємодії як асихронно, так і синхронно в часі,
використовуючи електронні транспортні системи по-
стачання навчальних матеріалів і інших інформацій-
них об'єктів, комп'ютерні мережі Інтернет/Інтранет,
ІКТ [3]. Одним із завдань діяльності в цьому сере-
довищі є надання умов ефективного використання
інформаційних ресурсів усіма учасниками навчаль-
ного процесу в медичній установі для освоєння ліка-
рями нових знань в галузі діагностики та лікування
захворювань. Для цього створюються засоби фор-
малізації навчальних інформаційних джерел форму-
вання знань, що враховують специфіку лікувального
процесу. Вступ. Сучасні досягнення комп'ютерних наук у
сфері освіти привели до спільного використання да-
них у багатьох різних сховищах. Використання
інформаційно-комунікаційних технологій (ІКТ) сумо-
вою забезпечення новаторської альтернативи тради-
ційному навчанню, створюючи можливості для пер-
сонального навчання, інтерактивного заняття та ко-
лективної роботи в комп'ютерній мережі незалежно
від місця розташування слухача. Світ стає цифро-
вим і ефективне використання цифрових технологій
у різних галузях економіки, включаючи освіту, науку
та бізнес, стає непорушною умовою існування. Оче-
видно, що ключовим моментом стає доступ до інфор-
маційних джерел формування знань, що розміщують-
ся у відповідних середовищах і доступних із будь-
якого місця та у будь-який час [10]. За допомогою програмно-інформаційних компо-
нентів ІКТ забезпечується створення та використання
баз навчальних і наукових джерел, на основі яких ре-
алізується освітній процес для конкретної особи. При
застосуванні програмно-інформаційних засобів ІКТ
у лікувальній практиці лікаря повинен враховуватися
той факт, що обсяг і різноманітність даних і повідом-
лень із різних профілів медичних знань нині настільки
величезні, що виникає необхідність їх класифікації з
точки зору належності до конкретної предметної об-
ласті. Йдеться не лише про дані, що зберігаються в
спеціалізованих базах або інформаційних сховищах,
але й про динамічні повідомлення, генеровані певни-
ми джерелами при необхідності. При розробці корпоративних систем управління
інформаційними джерелами в завданнях витягання,
трансферу та використання знань основною пробле-
мою є забезпечення цілеспрямованого пошуку, фор-
мулювання, формування, структуризації та представ-
лення даних і повідомлень, із яких надалі формують-
ся знання. Корпоративна інформаційно-юмунікаційна
система (ІКС) в сучасному світогляді є складовою
освітніх організаційних структур (ООС). Саме вона
забезпечує ефективну реалізацію корпоративних ІКТ
- процесів, в якій збір і оброблення даних здійснюється
автоматизовано за допомогою відповідних засобів
комп'ютерної техніки та ІКТ. Засоби та технології
корпоративної ІКС утворюють в ООС адаптивне,
інтегроване інформаційно-освітнє середовище, що
розвивається й активно здійснює визначальний вплив
на формування в ООС найбільш сприятливих (інфор-
маційно-комфортних) умов для ефективного здійснен-
ня його функцій [ 1 ]. USE OF PRINCIPLES OF MEDICAL ONTOLOGY FOR CONSTRUCTION OF
SCENARIO MODELS OF POST-GRADUATE EDUCATION OF DOCTORS AND
PHARMACISTS
O. P. Mintser, O. Ye. Stryzhak1, S. V. Denysenko
National Medical Academy of Post-Graduate
Education
by P.
L.
Shupyk
National center
Minor Academy of Sciences of Ukraine1 Approaches, facilities and technologies of forming of the personalized electronic grounds of management in the educational-
informative environment knowledge are described. The ontological aspects of model scenario construction in doctor's
education
post-graduate training accompaniment are considered with the use of the network systems of knowledge. It
supposes the decision of increasing of efficiency medical educating of doctors on application of modern network technologies
of the distance access to the distributed knowledge systems. Key words: ontology, ontology of medical knowledge, personalized electronic basis, informative sources of knowledge
forming and ontological model of e-scenario of process of educational process accompaniment. О О. П. Мінцер, О. Є. Стрижак, С. В. Денисенко Медична інформатика та інженерія, № 2, 2013 18 МЕДИЧНА ІНФОРМАТИКА
ТА ІНЖЕНЕРІЯ бути, ролі), стосунки між концептами (залежності,
функції) та додаткові обмеження, що визначаються
аксіомами. Концептом може бути опис завдання,
функції, дії, стратегії, процесу міркування, хід здійснен-
ня дослідження і так далі [4]. При цьому увага спря-
мована на формалізацію етапів побудови, структу-
ризації та представлення інформаційних джерел фор-
мування знань дозволяє слухачам ефективніше
засвоювати лекційний матеріал у поєднанні з прак-
тичними завданнями. В свою чергу, ефективна реа-
лізація вказаних етапів і отримання кінцевого резуль-
тату (бібліотеки онтологічних баз інформаційних
джерел формування знань) неможлива без проведен-
ня системно-онтологічного аналізу заданої сукупності
інформаційних навчальних ресурсів [6]. - забезпечення можливості оперативного пошуку
слухачами джерела необхідних інформаційних ре-
сурсів стосовно конкретної предметної області [7]. Основою формування корпоративного персоніфіко-
ваного комп'ютерно-інтегрованого навчального се-
редовища є накопичення не розрізнених даних, а
структуровані, формалізовані закономірності та прин-
ципи, що дозволяють вирішувати реальні завдання
при виконанні освітньої діяльності слухачами. Онто-
логічний підхід до проектування персоніфікованих
корпоративних ІКС якраз і дозволяє створювати си-
стеми, в яких інформаційні джерела формування знань
стають доступними для всіх учасників навчального
процесу. Можна виділити такі основні переваги под-
ібного підходу: - онтологічний підхід надає користувачеві цілісний,
системний погляд на певну предметну область; Поняття онтології й онтологічного аналізу увійшли
до процедур і стандартів моделювання корпоратив-
них ІКС навчального призначення. Адже описом та-
ких систем є структуризація інформаційних джерел
формування знань. Реалізація вказаних технологій
вимагає обліку різних формально-методологічних
вимог, критеріїв і оцінок. Основні з них: - інформаційні джерела про предметну область
представлені однотипно, що спрощує їх сприйняття; - інформаційні джерела про предметну область
представлені однотипно, що спрощує їх сприйняття;
- побудова онтології дозволяє відновити бракуючі
логічні зв'язки предметної області. - побудова онтології дозволяє відновити бракуючі
логічні зв'язки предметної області. Важливість онтологічного підходу в створенні пер-
соніфікованих корпоративних ІКС навчального при-
значення обумовлена також тим, що, якщо інфор-
маційні джерела формування знань не описати та не
тиражувати, вони, в підсумку, застарівають і стають
неактуальними. Інформаційні ж джерела формуван-
ня знань, що поширюються та використовуються,
можуть бути використані для генерування нового
знання. 1. Побудова інформаційної і функціональної моде-
лей. 2. Необхідність структуризації термінів і понять. 3. Правила формування достовірних тверджень і
висновків, що описують терміни та поняття [6]. На початковому етапі побудови онтологічної мо-
делі мають бути виконані такі завдання: - створення та документування словника термінів; Онтологічний підхід дозволяє подавати терміни,
поняття у такому вигляді, що вони стають придатни-
ми для комп'ютерного оброблення. Він об'єднує круг
питань, починаючи від сфери застосування, формаль-
ного опису компонентів предметних областей. МЕДИЧНА ІНФОРМАТИКА
ТА ІНЖЕНЕРІЯ При цьому зростають вимоги до
підвищення продуктивності ІКТ. їх надійності при по-
стійному збільшенні обсягів оброблених даних. Застосування програмно-інформаційних засобів
ІКТ орієнтоване на вирішення таких завдань: Застосування програмно-інформаційних засобів
ІКТ орієнтоване на вирішення таких завдань: - забезпечення можливості оперативної організації
доступу до інформаційних джерел формування знань,
що стосуються однієї предметної області або об'-
єднаних схожими інтересами сфер діяльності; - підтримка взаємодії всіх учасників навчального
процесу в рамках неодиничної безлічі предметних
областей із можливістю розширення цієї великої
кількості; Мета роботи - представлення онтологічних ас-
пектів побудови моделі е-сценарію супроводу про-
цесу навчання/перепідготовки лікаря з використан-
ням мережевих систем знань. - забезпечення можливості розширення списку
джерел і споживачів різнорідних інформаційних дже-
рел формування знань у рамках певної предметної
області або сфери інтересів; Результати та їх обговорення. Використання
програмно-інформаційних засобів ІКТ в освітньому
просторі Національної медичної академії післядип-
ломної освіти імені П. Л. Шупика забезпечує побу-
дову персоніфікованого корпоративного комп'ютер-
но-інтегрованого навчального середовища, в якому
підтримуються режими безперервної електронної
дистанційної взаємодії між лікарями-практиками та
викладачами різних кафедр, і зокрема супроводи кур-
су лікування. Дистанційне навчання є різновидом на- - обмеження доступу до інформаційних ресурсів
навчального призначення рамками конкретної пред-
метної області або сфери інтересів у зв'язку з мож-
ливістю вирішення попереднього завдання; - забезпечення кожному суб'єкту освітнього про-
цесу можливості використання інформаційних ре-
сурсів навчального призначення декількох предмет-
них областей; - забезпечення кожному суб'єкту освітнього про-
цесу можливості використання інформаційних ре-
сурсів навчального призначення декількох предмет-
них областей; (Ім'я об'єкту 1)... (ім'я ознаки п),
(Ім'я об'єкту 2)... (ім'я ознаки j) виконання. Тому виникає необхідність створення си-
стеми електронної дистанційної підтримки виконан-
ня прийняття рішень лікарями при обгрунтуванні кур-
су лікування за певною методикою. Одним із
підходів, що забезпечить ефективне функціонування
такої системи, є побудова онтологічної моделі е-сце-
нарію супроводу процесу лікування. Він є системою
формалізації лікувальних процедур за допомогою
онтологічного підходу її побудови, операційно, покро-
ково відтворюючи маршрут лікування. При цьому
передбачається використання інформаційної підтрим-
ки лікаря шляхом об 'єднання різних засобів Інтернет
- технологій і програмних модулів (мережеві елект-
ронні наукові та навчально-методичні ресурси, бази
даних, сервісно-функціональні й аналітичні програмні
модулі тощо), котрі формуються з певної галузі знань
і безлічі цілей лікувального курсу. Ці ресурси не лише
істотно урізноманітнюють змістовну складову е-
методичних систем підтримки медичної діяльності,
але й ураховують специфіку реалізації всього проце-
су навчання [2]. (Ім'я об'єкту m) ... (ім'я ознаки к). (Ім'я об'єкту m) ... (ім'я ознаки к). Онтологічна модель супроводу процесу курсу ліку-
вання (е-сценарій) була створена за допомогою вка-
заного комп'ютерного засобу. Загальна формула формалізації цієї онтологічної
моделі: S = {Оа {Pb {Td {Ее {Cq {Mv {Zg} Rh
{Zg}}}}}}},де - суб'єкти лікувального курсу: В = {Оа}, а = 1,2,3,
... т ; - суб'єкти лікувального курсу: В = {Оа}, а = 1,2,3,
... т ; - кластери лікувального курсу: Р = {Оа {Pb}} b =
al, а2, а3,..., An; - система діагнозів лікувального курсу: Т = {Pb
{Td}} d = bl,b2,bЗ,..., Bn; - етапи лікувального курсу: Е = {Td {Ее}} е = dl,
d2, d3,..., Dn; - мета лікувального курсу: С = {Ее {Cq}} q = el,
e2, еЗ,..., En; - мета лікувального курсу: С = {Ее {Cq}} q = el,
e2, еЗ,..., En; - засоби лікувального курсу: Z = {Cq {Zg}} g = ql,
q2, q3,... ,Qn; Процес формування онтологічної моделі е-сцена-
рію супроводу процесу курсу лікування полягає в
тому, що маючи опис певних понять, можна погод-
жено представляти їх у вигляді об'єктів засобами
побудови онтології [9]. Для візуалізації створення он-
тологічних моделей нами використана комп'ютерна
програма "Трафсдитор". Початковими даними для
неї служили описи об'єктів, представлені безліччю
їх ознак. Початкові дані можуть бути представлені у
вигляді текстового файлу. Структура текстового
файлу в цьому випадку така: - маршрут лікувального курсу: M = {Cq {Mv
{Zg}}},v = gl,g2,g3,...,Gn; " - оцінювання результатів: R = {Cq {Rh {Zg} } } h =
vl, v2, v3,..., Hn. МЕДИЧНА ІНФОРМАТИКА
ТА ІНЖЕНЕРІЯ На
формальному рівні, онтологія - система, що скла-
дається з безлічі термінів, тверджень про ці поняття,
на основі яких можна будувати класи, об 'єкти, зв' яз-
ки, функції і теорії. Комп'ютерну онтологію деякої
предметної дисципліни можна розглядати як загаль-
нозначущу, відкриту базу інформаційних джерел фор-
мування знань, представлену загальноприйнятою
(формальною) мовою специфікації. У онтолого-кла-
сифікаційній схемі засобів і методів штучного інте-
лекту онтологічний підхід трактується як різновид
системного підходу, ґрунтованого на формуванні
знань. Онтологічний підхід забезпечує ефективне
проектування компонентів будь-якої знання-орієнто-
ваної інформаційної системи [5,11,12]. - опис правил, згідно з якими на базі введеної тер-
мінології формуються достовірні твердження, що
характеризують стан системи; - побудова моделі, за допомогою якої на основі існу-
ючих тверджень можна формувати необхідні додат-
кові твердження [4]. Онтологічна система характе-
ризується єдністю, логічним взаємозв'язком і несу-
перечністю використовуваних понять. Візуальні методи проектування онтологій сприяють
швидкому та повному розумінню структури знань
предметної області [9], що особливо цінно для лікарів,
які освоюють нові методики лікування. При виконанні
персональних навчальних програм перед слухачем
виникає необхідність оперативного спілкування з вик-
ладачами. При цьому об'єктивні обставини - час і
місце спілкування, не завжди співпадають із можли-
востями слухача та викладача. Також навчальна
програма, яку виконує слухач, не завжди повною
мірою відображає процес проведення курсу лікуван-
ня, консультаційної взаємодії й оцінку результатів, а
містить тільки загальні методичні рекомендації з її Практично всі моделі онтології містять певні кон-
цепти (поняття, класи), властивості концептів (атри- Медична інформатика та інженерія, № 2, 2013 20 МЕДИЧНА ІНФОРМАТИКА
ТА ІНЖЕНЕРІЯ (Ім'я об'єкту 1)... (ім'я ознаки п),
(Ім'я об'єкту 2)... (ім'я ознаки j) виконання. Тому виникає необхідність створення си-
стеми електронної дистанційної підтримки виконан-
ня прийняття рішень лікарями при обгрунтуванні кур-
су лікування за певною методикою. Одним із
підходів, що забезпечить ефективне функціонування
такої системи, є побудова онтологічної моделі е-сце-
нарію супроводу процесу лікування. Він є системою
формалізації лікувальних процедур за допомогою
онтологічного підходу її побудови, операційно, покро-
ково відтворюючи маршрут лікування. При цьому
передбачається використання інформаційної підтрим-
ки лікаря шляхом об 'єднання різних засобів Інтернет
- технологій і програмних модулів (мережеві елект-
ронні наукові та навчально-методичні ресурси, бази
даних, сервісно-функціональні й аналітичні програмні
модулі тощо), котрі формуються з певної галузі знань
і безлічі цілей лікувального курсу. Ці ресурси не лише
істотно урізноманітнюють змістовну складову е-
методичних систем підтримки медичної діяльності,
але й ураховують специфіку реалізації всього проце-
су навчання [2]. (Ім'я об'єкту 1)... (ім'я ознаки п),
(Ім'я об'єкту 2)... (ім'я ознаки j) (Ім'я об'єкту 1)... (ім'я ознаки п),
(Ім'я об'єкту 2)... (ім'я ознаки j) Формалізована структура онтологічної моделі е-сце-
нарію супроводу курсу лікування певного захворюван-
ня представлена в таблиці 1, а на рисунку 1 зображе-
на загальна графорієнтована структура онтологічної
моделі е-сценарію супроводу навчального процесу з
вивчення нової методики лікування лікарями. Таблиця 1. Загальна формалізована структура онто ічної моделі е-сценарію супроводу курсу лікування ічної моделі е-сценарію супроводу курсу лікування Таблиця 1. Загальна формалізована структура онто
ічної моделі е-сценарію супроводу курсу лікування
*) Умови ідентифікації ознаки: {х | F (х)} - визначає множину всіх х таких, що вірно F (х). Приклад: {kKa | k<5] = {1,2, 3,4}. МЕДИЧНА ІНФОРМАТИКА
ТА ІНЖЕНЕРІЯ МЕДИЧНА ІНФОРМАТИКА
ТА ІНЖЕНЕРІЯ Рис. 1. Загальна графорієнтована структура онтологічної моделі е-сценарію супроводу навчального
процесу з вивчення нової методики лікування лікарями. альна графорієнтована структура онтологічної моделі е-сценарію супроводу навчального
процесу з вивчення нової методики лікування лікарями. знань. Природним при цьому є створення онтологіч-
них описів і моделювання подій, що визначають курс
діагностики і лікування захворювань. Висновки. Одним із перспективних напрямів для
подальшого вдосконалення освітніх організаційних
структур у медицині є розроблення методологічних,
онтологічних і логічних основ конструювання баз
інформаційних джерел формування знань. Онтології
грають вирішальну роль у моделі опису формування
таких систем. Це припускає рішення актуальних про-
блем підвищення ефективності безперервного про-
фесійного розвитку лікарів і провізорів на основі зас-
тосування сучасних мережевих технологій дистан-
ційного доступу до розподілених систем формування знань. Природним при цьому є створення онтологіч-
них описів і моделювання подій, що визначають курс
діагностики і лікування захворювань. Використання запропонованого методу побудови
онтологічної моделі е-сценарію супроводу лікуваль-
ного процесу дозволяє зробити цей процес більш пер-
соніфікованим. Іншими словами, підвищення якості
передавання знань досягається за рахунок того, що
лікар має можливість використати свій власний
досвід, будувати свої моделі формування та викори-
стання знань. 9. Применение методов и средств онтологического анали-
за для управления образовательной деятельностью /
В. В. Мартынов, В. И. Рыков, Е. И. Филосова, Ю. В. Шаро-
нова // Вестник УГАТУ Управление в социальных и эконо-
мических системах.-Уфа: УГАТУ 2012.-Т. 16.-№3 (48).
-С. 230-234.
10. Морзе Н. В. Інформатичні компетентності професора
- міф чи реальність? [Електронний ресурс] / Н. В. Морзе //
Електронний депозитарій. Національний педагогічний ун-
іверситет імені М. П. Драгоманова. - Вип. 9. - Режим дос-
тупу: http://enpuir.npu.edu.ua/handle/123456789/691/
browse?type=author&order=ASC&rpp=20&value= Література 1. Биков В. Ю. Технології хмарних обчислень, ІКТ-аутсорсінг
та нові функції ІКТ-підрозділів навчальних закладів і науко-
вих установ [Електроннийресурс] /В. Ю. Биков//Інфор-
маційно-юмунікаційні технології в освіті: зб. наук, праць. -Херсон: ХДУ 2011. -Вип. 10. - Режим доступу : http://
ite.ksu.ks.ua/2011/випуск-10. 1. Биков В. Ю. Технології хмарних обчислень, ІКТ-аутсорсінг
та нові функції ІКТ-підрозділів навчальних закладів і науко-
вих установ [Електроннийресурс] /В. Ю. Биков//Інфор-
маційно-юмунікаційні технології в освіті: зб. наук, праць. -Херсон: ХДУ 2011. -Вип. 10. - Режим доступу : http://
ite.ksu.ks.ua/2011/випуск-10. 6. Дем'яненко В. Б. Комп'ютерні онтології-технологічна
основа формування освітянських інформаційних ресурсів
[Електронний ресурс] /В. Б. Дем'яненко, О. Є. Стрижак//
Інформаційні технології і засоби навчання. - 2011. - Том
22. - № 2. - Режим доступу: http://journal.iitta.gov.ua/
index.php/itlt/article/view/419. 2. Биков В. Ю. Електронна педагогіка та сучасні інструмен-
ти систем відкритої освіти [Електронний ресурс] /
В. Ю. Биюв, І. В. Мушка// Інформаційні технології і засоби
навчання. - 2009.-№5(13).- Режим доступу до журналу
: http://www.ime.edu-ua.net/em.html. 2. Биков В. Ю. Електронна педагогіка та сучасні інструмен-
ти систем відкритої освіти [Електронний ресурс] /
В. Ю. Биюв, І. В. Мушка// Інформаційні технології і засоби
навчання. - 2009.-№5(13).- Режим доступу до журналу
: http://www.ime.edu-ua.net/em.html. 7. Стрижак О. Є. Інформаційно-технологічні рішення фор-
мування операційного простору діяльності обдарованої
особистості [Електронний ресурс] / [Г. Востров, С. Каль-
ной, О. Павлов та ін.]. - Режим доступу: http://
archive.nbuv.gov.ua/portaVSoc_Gum/Nivoo/2010_4/22.pdf. 8. Мананникова Н. Н. Учебно-исследовательская работа
учащихся: методические рекомендации для учащихся и
педагогов [Электронный ресурс] / Н. Н. Мананникова. -
Режим
доступу:
http://nsportal.ru/blog/shkola/
obshcheshkolnaya-tematika/nauchno-issledovatelskaya-
rabota-uchashchikhsya. 3. Биков В. Ю. Моделі організаційних систем відкритої осві-
ти: монографія/В.Ю.Биков,-К.: Атіка,2008.-684с. :іл. 4. Гладун А. Я. Онтологии в корпоративных сетях [Элект-
ронный ресурс] / А. Я. Гладун, Ю. В. Рогушина // Корпора-
тивные информационные системы. - 2006. - № 1. - Режим
доступу: littp://www.mamgement.com.ua/ims/ims 115 .html. 3. Биков В. Ю. Моделі організаційних систем відкритої осві-
ти: монографія/В.Ю.Биков,-К.: Атіка,2008.-684с. :іл. 4. Гладун А. Я. Онтологии в корпоративных сетях [Элект-
ронный ресурс] / А. Я. Гладун, Ю. В. Рогушина // Корпора-
тивные информационные системы. - 2006. - № 1. - Режим
доступу: littp://www.mamgement.com.ua/ims/ims 115 .html. 5. Гладун В. П. Процессы формирования новых знаний / Медична інформатика та інженерія, № 2, 2013 22 10. Морзе Н. В. Інформатичні компетентності професора
- міф чи реальність? [Електронний ресурс] / Н. В. Морзе //
Електронний депозитарій. Національний педагогічний ун-
іверситет імені М. П. Драгоманова. - Вип. 9. - Режим дос-
тупу: http://enpuir.npu.edu.ua/handle/123456789/691/
browse?type=author&order=ASC&rpp=20&value= D0%9D%D0%92.
11. Палагин А. В. К проектированию онтологоуправляемой
информационной системы с обработкой естественно-язы-
ковых объектов / А. В. Палагин, Н. Г. Петренко // Математи-
ческие машины и системы. - 2008. -№ 2. - С. 14-23.
12. СтрижакО. Є. Комп'ютерні тезауруси як технологічна
платформа створення авторських методик викладання пред-
метних дисциплін/О. Є. Стрижак//Актуальні проблеми
психології: Психологічна теорія і технологія навчання / за
ред. С. М Максименко, М. JI Смульсон. - К.: НПУ імені
М. П. Драгоманова 2009. - Т. 8. - Вип. 6. - С. 259-266. %D0%9C%D0%BE%Dl%80%D0%B7%D0%B5%2C+%
D0%9D%D0%92. %D0%9C%D0%BE%Dl%80%D0%B7%D0%B5%2C+%
D0%9D%D0%92. %D0%9C%D0%BE%Dl%80%D0%B7%D0%B5%2C+%
D0%9D%D0%92. 11. Палагин А. В. К проектированию онтологоуправляемой
информационной системы с обработкой естественно-язы-
ковых объектов / А. В. Палагин, Н. Г. Петренко // Математи-
ческие машины и системы. - 2008. -№ 2. - С. 14-23. 12. СтрижакО. Є. Комп'ютерні тезауруси як технологічна
платформа створення авторських методик викладання пред-
метних дисциплін/О. Є. Стрижак//Актуальні проблеми
психології: Психологічна теорія і технологія навчання / за
ред. С. М Максименко, М. JI Смульсон. - К.: НПУ імені
М. П. Драгоманова 2009. - Т. 8. - Вип. 6. - С. 259-266.
|
https://openalex.org/W2131581112
|
https://ricerca.uniba.it/bitstream/11586/148105/2/NanomatNanotech_Carlucci2015.pdf
|
English
| null |
Properties of Aluminosilicate Refractories with Synthesized Boron-Modified TiO<sub>2</sub> Nanocrystals
|
Nanomaterials and nanotechnology.
| 2,015
|
cc-by
| 4,329
|
DOI: 10.5772/60204 © 2015 The Author(s). Licensee InTech. 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. Abstract ture was analysed by Scanning Electron Microscopy
(SEM) and energy dispersion spectroscopy (EDS). The
bricks obtained with nanoadditives presented improved
mechanical characteristics with respect to the typical
aluminosilicates, presumably because of a better compac‐
tion during the raw materials’ mixing stage. An efficient microwave supported synthesis, with a
reaction time of only one and a half minute, to prepare
boron-modified titania nanocrystals TiO2:(B), was
developed. The nanocrystals were obtained by hydroly‐
sis of titanium tetraisopropoxide (TTIP) together with
benzyl alcohol and boric acid, and the approach did not
need surfactants use and a final calcination step. The
produced TiO2:(B) nanocrystals were characterized in
detail by low magnification Transmission Electron
Microscopy (TEM), Inductively Coupled Plasma-Atomic
Emission Spectroscopy (ICP-AES), X-Ray Diffractometry
(XRD), and a Micro Raman Spectroscopy. One of the
obtained samples was then tested as an additive in
various amounts in a typical aluminosilicate refractory
composition. The effects of these additions in bricks were
evaluated, according to UNI EN 196/2005, in terms of
thermo-physical and mechanical properties: diffusivity,
bulk density, apparent density, open and apparent
porosity and cold crushing strength. Bricks’ microstruc‐ Keywords TiO2, Anatase, Boron, Aluminosilicate, Nano‐
crystals, Refractories Regular Paper Claudia Carlucci1, Francesca Conciauro2, Barbara Federica Scremin2, Antonio Graziano Antico2,
Marco Muscogiuri4, Teresa Sibillano3, Cinzia Giannini3, Emanuela Filippo4, Caterina Lorusso4,
Paolo Maria Congedo4* and Giuseppe Ciccarella2* 1 Chemistry Department, University of Bari, Via Orabona 4, 70126 Bari, Italy
2 National Nanotechnology Laboratory (NNL), Nanoscience Institute—CNR, Via Arnesano, 73100 Lecce, Italy
3 Institute of Crystallography (IC)—CNR, Via Giovanni Amendola, 122/O, 70126 Bari, Italy
4 Department of Engineering for Innovation, University of Salento, via Monteroni, Lecce I-73100, Italy
* Corresponding author(s) E-mail: giuseppe.ciccarella@unisalento.it; paolo.congedo@unisalento.it 1 Chemistry Department, University of Bari, Via Orabona 4, 70126 Bari, Italy gy
y
3 Institute of Crystallography (IC)—CNR, Via Giovanni Amendola, 122/O, 70126 Bari, Italy 4 Department of Engineering for Innovation, University of Salento, via Monteroni, Lecce I-73100, Italy
* Corresponding author(s) E-mail: giuseppe.ciccarella@unisalento.it; paolo.congedo@unisalento.it Received 21 November 2014; Accepted 06 February 2015 ARTICLE ARTICLE Nanomaterials and Nanotechnology Nanomaterials and Nanotechnology 1. Introduction Aluminosilicate bricks have been used as refractory in
industrial furnaces in constructing and restoring, in coke
ovens, glass melting furnaces, and hot blast furnaces [1, 2]. The high temperature volume stability and creep features
of aluminosilicate bricks [2] are the unique properties of the
heavy-duty refractory products. The conventional silica
bricks generally exhibit some disadvantages such as 1 Nanomater Nanotechnol, 2015, 5:8 | doi: 10.5772/60204 <10 ppb) (HNO3 70% (Hg ≤0.0000005%) were purchased
from Aldrich. The reagents were employed as received
without additional purification. degradation [1, 3], low refractoriness [4], and thermal
expansion due to their poor alkali content and thermal
resistance [5, 6, 7]. The incorporation of nano-metal oxides,
such as TiO2, enhances the physico-chemical and thermo-
mechanical properties of refractories and their composites
[8, 9, 10]. In a typical preparation, TTIP (1 mL, 3.36 mmol) was added
to boric acid dispersed in benzyl alcohol (10 mL, 96.4
mmol), while stirring in a Teflon vessel. The reaction vessel
was sealed and maintained at 200° C for 1 minute and 30
seconds, without the requirement of a post-synthetic
calcination treatment of the nanocrystals [12]. The micro‐
wave-assisted synthesis took place in a single and quick
step, by using a microwave digestion system [13, 14, 15]. The system uses 2.45 GHz microwaves and it is controlled
in both temperature (200 °C) and pressure (300 psi). The
reaction vessel has been connected to a pressure transducer
that monitors and controls the pressure during synthesis. The resulting milky suspension was centrifuged; the white
precipitate was twice washed with diisopropylether and
dried overnight at room temperature. Different TTIP:
H3BO3 molar ratios (1:1, 1:2, 1:3, 1:4, 1:5) were tested and
samples were named BT1, BT2, BT3, BT4, and BT5, respec‐
tively. The processing of nanomaterials for the construction
industry is complex in nature and requires careful moni‐
toring to achieve the required performances. In the case of
nanocomposites a major difficulty lies in the tendency of
nanoparticles to aggregate into micrometer-sized crystal‐
line forms in the attempt to reduce their surface free energy. The present investigation deals with the eco-friendly
production of nanoscale boron-modified TiO2 particles and
their application in aluminosilicate refractories. It is
necessary, however, that the nanoparticles arrange uni‐
formly in the matrix to effectively contribute to the com‐
posite’s final properties; the nanoparticles’ shape,
moreover, may be important in increasing the compound
mechanical strength according to preferential directions. 2
Nanomater Nanotechnol, 2015, 5:8 | doi: 10.5772/60204 2.3 Nanocrystals’ characterization Finally, the open pore distribution and their size were
estimated by mercury porosimetric analysis supporting the
results from thermal and mechanical characterization. The
refractories with and without additive (standard) were
compared to highlight the changes in the composites’
behaviour. Microstructure study was performed with
SEM-EDS analysis. Morphological characterizations of the TiO2:(B) nanopow‐
ders were performed using a JEOL JEM 1011 Transmission
Electron Microscope (TEM). Inductively Coupled Plasma-
Atomic Emission Spectroscopy (ICP-AES) was performed
on a Varian Vista AX ICP-AES instrument, with samples
digested using a mixture of HNO3 and HF 1:1. The ICP-AES
measurements were accomplished by calibration using
aqueous standards of Ti and B after appropriate dilution;
the calibration ranges were selected according to the
expected concentrations of the elements of interest. 2.2 Preparation of aluminosilicate bricks The BT2 nanocrystals were tested as bricks’ additives. They
were prepared in three different suspensions of benzyl
alcohol in concentration percentages of 0.5 wt.%, 1 wt.%,
and 2 wt.%. In this paper concerned with improving thermal/insulating
quality, resistance, and lifetime of standard concrete,
boron-modified titanium dioxide nanoparticles were
added to aluminosilicate specimens and the resultant
thermo-physical and mechanical characterizations are
presented. Tests were conducted also using anatase
titanium dioxide nanocrystals synthesized in our previous
works [11] but the results with boron modified anatase
nanocrystals of the present study gave better results in
terms of bricks’ properties. The bricks were obtained mixing 2.2 kg of commercial
refractory material (Al2O3 55 wt.% and SiO2 42 wt.%) with
water at 6 wt.% in which the additive suspensions were
emulsified previously. The mixture was "thrown" in the
mould in two different phases spaced by a compaction
process and placed in the curing chamber at 20 °C, exposed
to not less than 90% relative humidity for 24 hours; then
each brick was carried out of the mould, and put back in
the chamber to mature for 28 days, as described in UNI EN
196/2005. Later all the specimens were fired at 1300 °C for
24 hours. Physical properties, such as thermal diffusivity, apparent
porosity, water absorption, and density were measured
and compression mechanical resistance has been studied. 2.3 Nanocrystals’ characterization 1. Introduction Knowledge of the thermo-mechanical properties of
nanocrystals modified in an aluminosilicate refractory is
relatively limited, and potentially of great importance,
because such materials in service are typically subjected to
constant stress over long periods, and therefore a design
that ensures components’ optimal performance over time
requires a careful estimation of their lifetime. 2.1 Synthesis 3. Results and discussion TEM images of the boron-modified titania nanoparticles
are reported in Figure 1. TEM images of the boron-modified titania nanoparticles
are reported in Figure 1. TEM analysis, reported in Table 1, revealed that the axes’
average lengths were comparable in all the samples, with
an estimated average length for the short axis of about 5–6
nm, and of 7–8 nm for the long axis. 2. Materials and methods The penetration pressure relates directly to the pores’
size according to the Washburn equation [17]: R
2 cos
/ Pc
g
q
= - R
2 cos
/ Pc
g
q
= - 2. The phase composition of the samples was determined
by fitting the XRD patterns with the crystal structure
models of tetragonal TiO2 anatase (space group I41/
amd; cell parameters: a = b = 3.7835430 Å and c =
9.614647 Å; α = β = γ = 90°). The weight percentage
accuracy of the estimation was determined to be 5–7%
w/w. where γ is the mercury surface tension (generally 0.480 N/
m), θ is the contact angle between the mercury and the solid
(in average 140°), Pc is the penetration pressure, and R the
pore radius. The hypothesis of the Washburn equation is
that of cylindrical pores. 3. The inhomogeneous peak broadening of the anatase
TiO2 reflections was described by a phenomenological
model based on the modified Scherrer formula [11–15]. The refinement procedure allowed the calculation of
the coherent crystal apparent domain size along each
reciprocal lattice vector (h,k,l) direction. Other refina‐
ble parameters were the unit cell parameters, whereas
the background was linearly interpolated and unre‐
fined. 2. Materials and methods The Raman spectra were acquired with a Renishaw inVia
Raman microscope, with 633 nm excitation wavelength, a
50X microscope objective giving a spot diameter of 2μm, a
resolution of 4 cm-1, and a power of about 0.8 mW. Powders Ti(IV)-isopropoxide (Ti(OPri)4 or TTIP, 97%), benzyl
alcohol (C6H5CH2OH or BzOH, ≥99%), boric acid (H3BO3
99.5%), nitric acid, and hydrofluoric acid (HF 47-51% Hg Ti(IV)-isopropoxide (Ti(OPri)4 or TTIP, 97%), benzyl
alcohol (C6H5CH2OH or BzOH, ≥99%), boric acid (H3BO3
99.5%), nitric acid, and hydrofluoric acid (HF 47-51% Hg 2
Nanomater Nanotechnol, 2015, 5:8 | doi: 10.5772/60204 of the prepared samples were placed on a glass slide, and
spectra were collected at room temperature. force (UNI EN 196/2005); prismatic specimens were used
(4x4x4 cm) and a 65-L12G2 Controls programmed control
press was employed. The load was increased uniformly at
a speed of 2400 N / s until specimen failure, which is of the
brittle type. Powder X-ray diffraction (XRD) for phase analysis of the
nanocrystals was performed on a Rigaku diffractometer in
Bragg-Brentano reflection geometry, using filtered Cu Kα
radiation. The XRD patterns were recorded in the range of
2Θ = 20° - 90° by step scanning, using 2Θ increments of 0.03°
and a fixed counting time of 2 s/step. The bricks’ microstructure was analysed through Scanning
Electron Microscopy with a JEOL 5410 LV SEM microscope
equipped for energy dispersion spectroscopy (EDS). EDS
allows detecting X-photons emitted by the sample in
response to the incident electrons from the SEM microscope
giving evidence about the specimen elemental composi‐
tion. The samples were fractured under liquid nitrogen and
successively metalized to ensure a good electrical conduc‐
tivity. The XRD patterns revealed only the presence of the anatase
phase and were analysed by using a whole-profile Riet‐
veld-based fitting program [16] according to the following
procedure, fully described elsewhere [11–15]: 1. The instrumental resolution function (IRF) was
evaluated by fitting the XRD pattern of a LaB6 NIST
standard recorded under the same experimental
conditions as those used for measuring the samples. The IRF data file was provided separately to the
program in order to allow subsequent refinement of
the XRD patterns of the samples. Porosimetry measurements were accomplished with a
Pascal 140 and 240 Thermo Finnigan mercury porosime‐
ters. g
Properties of Aluminosilicate Refractories with Synthesized Boron-Modified TiO2 Nanocrystals Claudia Carlucci, Francesca Conciauro, Barbara Federica Scremin, Antonio Graziano Antico, Marco
Muscogiuri, Teresa Sibillano, Cinzia Giannini, Emanuela Filippo, Caterina Lorusso, Paolo Maria
Congedo and Giuseppe Ciccarella:
Properties of Aluminosilicate Refractories with Synthesized Boron-Modified TiO2 Nanocrystals 2.4 Aluminosilicate bricks’ characterization Mean value ± standard deviation σ; statistics on about 60 particles (nm), e Calculated long axis: short axis ratio. Table 1. Details of boron-modified TiO2 nanocrystals samples Figure 3. Raman spectra of nanocrystalline TiO2:(B) samples. Figure 3. Raman spectra of nanocrystalline TiO2:(B) samples. XRD was carried out to investigate the crystal structure of
boron-modified TiO2 nanoparticles and the corresponding
XRD patterns are shown in Figure 2. Figure 2. XRD patterns of TiO2:(B) Figure 3. Raman spectra of nanocrystalline TiO2:(B) samples. Micro Raman spectra were collected on TiO2:(B) samples
and are reported in Figure 3. All the detected peaks in
Raman spectra belong to the anatase TiO2 phase and lie in
the region 100–700 cm-1: Fig. 3 shows Eg(1) around 144cm-1,
Eg(2) at 197 cm-1, B1g(1) at 400 cm-1, A1g(1) and B1g(2) at 520
cm-1, and Eg(3) at 640 cm-1. Figure 2. XRD patterns of TiO2:(B) Table 3 shows the data for unmodified and modified bricks,
obtained varying suspensions weight percentages (from
0.5 wt.% to 2 wt.%). Tests have shown that nanocrystals
increasing additions, under the error left the bulk density
and the apparent density, water absorption and the
apparent porosity were left almost unchanged. The
resulting bulk densities were a little higher in respect to the
reference brick. Bending failure tests were conducted on
three points at room temperature, using a programmed
press. Each dried specimen was placed horizontally
between two supports distanced by 100 mm, and divided
into two half prisms. Compression breakage tests were
conducted according to standard regulations: the two
prisms settled previously for the bending test were used,
and in this case a press with a programmed control was also
employed. The load was uniformly increased at a speed of
2400 N/s, until the specimen failure. The failure mode
denoted fragile composites. Sample
a.s.r.a
Tib
Ob
004c
200c
a=b [Å-1]d
c [Å-1]d
BT1
1.04
1.07
2.49
5.07
5.29
3.785
9.492
BT2
1.22
0.99
2.44
4.60
5.63
3.786
9.492
BT3
1.39
0.98
2.42
4.90
6.84
3.786
9.492
BT4
1.41
0.99
2.26
4.32
6.08
3.785
9.481
BT5
1.52
1.00
2.10
4.66
7.09
3.785
9.478
a Aspect size ratio, b Occupancy, c Apparent size along the indicated
directions (nm), d Anatase unit cell lattice parameters. Table 2. XRD parameters of TiO2:(B) nanocrystals Table 2. Nanomater Nanotechnol, 2015, 5:8 | doi: 10.5772/60204 2.4 Aluminosilicate bricks’ characterization Figure 1. TEM images of the TiO2:(B) nanoparticles synthesized with
different TIIP:H3BO3 ratios. Undoped TiO2 (a); BT1 (b); BT2 (c), BT3 (d), BT4
(e), and BT5 (f). All bricks were characterized by different techniques. Density, apparent porosity, and water absorption were
measured by the Archimedes method using water. Thermal diffusivity was determined using the Hot Disk
technique: a disk sensor was placed between two pieces
of the sample material, then heated by a constant
electrical current for about 40 s. The generated heat,
dissipated from the sensor into the surrounding un‐
known sample material, causes a temperature variation
both in the sensor and in the surrounding material. The
sensor average transient temperature is simultaneously
measured monitoring a change in its electrical resist‐
ance. The sensor resistivity change correlates with the
corresponding change in temperature through a temper‐
ature coefficient of resistivity. Figure 1. TEM images of the TiO2:(B) nanoparticles synthesized with
different TIIP:H3BO3 ratios. Undoped TiO2 (a); BT1 (b); BT2 (c), BT3 (d), BT4
(e), and BT5 (f). The calculated aspect ratios were comparable under the
error in all the samples, thus boron addition did not
influence appreciably the size of the resultant nanocrystals. Boron content evaluated by ICP-AES increased with the
nominal increment of TiO2: B ratio (Table 1). The refractory mechanical performances were estimated by
compression breaking tests, according to the Standard in Sample
Boric Acid (mmol) a
TiO2: B Ratio b
B: Ti c
Long axis (nm) d
Short axis (nm) d
Aspect Ratio e
BT1
3.36
1:1
0.007
6.6 ± 1.0
5.0 ± 0.8
1.3 ± 0.3
BT2
6.72
1:2
0.020
7.0 ± 0.9
5.6 ± 0.7
1.2 ± 0.2
BT3
10.1
1:3
0.027
7.3 ± 1.1
6.1 ± 0.9
1.2 ± 0.3
BT4
13.4
1:4
0.079
7.1 ± 1.1
5.3 ± 0.7
1.3 ± 0.3
BT5
16.8
1:5
0.239
7.8 ± 2.5
5.0 ± 0.8
1.6 ± 0.5
a Boric acid amount (mmol) used in the preparations, b Nominal TiO2 : H3BO3 ratios, c B : Ti measured molar ratios, obtained by ICP-AES measurements, d
TEM measurements. Mean value ± standard deviation σ; statistics on about 60 particles (nm), e Calculated long axis: short axis ratio. Table 1. Details of boron-modified TiO2 nanocrystals samples a Boric acid amount (mmol) used in the preparations, b Nominal TiO2 : H3BO3 ratios, c B : Ti measured molar ratios, obtained by ICP-AES measurements, d
TEM measurements. 2.4 Aluminosilicate bricks’ characterization XRD parameters of TiO2:(B) nanocrystals Table 2 summarizes the relevant data extracted from
Rietveld analysis: titanium and oxygen lattice site occu‐
pancy, which were found to deviate slightly from the
stoichiometric values of Ti = 1 and O = 2, the apparent size
along the crystallographic [004] and [200] directions,
respectively, along the rod length and the base diameter,
from which the aspect size ratio was determined. The
refined anatase lattice parameters, evidenced a c-axis
contraction for high nominal boron concentrations, for high
nominal boron concentrations as expected from results
reported in previous papers [12, 18]. The breaking strength (Table 3) increased appreciably with
the nanoadditive concentrations with respect to the
reference brick. Thermal Diffusivity, determined by the hot
disk method slightly decreased with nanofillers amount
(Table 3). 4
Nanomater Nanotechnol, 2015, 5:8 | doi: 10.5772/60204 4 Sample
Nanoadditive
(wt.%)
Bulk density
(g/cm3)
Apparent density
(g/cm3)
Apparent porosity
(%)
Water
Absorption
(%)
Breaking
strength
(MPa)
Diffusivity
(mm2/s)
Commercial
composition brick
2.70± 0.05
2.28± 0.05
18.5± 0.5
8.1± 0.2
80.00± 0.01
1.06± 0.01
TiO2 :(B) modified
brick
0.5
2.81± 0.05
2.28± 0.05
19.0± 0.5
8.2± 0.2
86.55± 0.01
1.00± 0.01
1
2.80± 0.05
2.30± 0.05
18.0± 0.5
7.8± 0.2
90.40± 0.01
0.88± 0.01
2
2.78± 0.05
2.29± 0.05
17.7± 0.5
7.7± 0.2
97.60± 0.01
0.84± 0.01
Table 3. Thermo-physical and mechanical properties of aluminosilicate bricks showing only bands corresponding to the anatase TiO2 Raman modes, as
described in the text. Table 3. Thermo-physical and mechanical properties of aluminosilicate bricks showing only bands corresponding to the anatase TiO2 R
described in the text. Sample
Nanoadditive
(wt.%)
Cumulative volume
(cc/g)
Surface area
(m2/g)
Pores size
(μm)
Open Porosity
(%)
Commercial
composition
brick
0.098± 0.005
1.04± 0.01
0.35± 0.02
20.84± 0.06
TiO2 :(B)
modified
brick
0.5
0.083± 0.005
1.49± 0.01
0.36± 0.02
19.77± 0.06
1
0.085± 0.005
1.53± 0.01
0.45± 0.02
19.82± 0.06
2
0.086± 0.005
1.57± 0.01
0.50± 0.02
19.94± 0.06
Table 4. Surface areas, total volume, pore dimensions, and open porosity of commercial composition versus nanocrystals modified bricks. Results reported in Table 4 show that the cumulative
volume, which is indicative of the matrix compactness,
does not correlate with the nanocrystals’ amounts and is
only slightly lower than in the reference brick. 5
Claudia Carlucci, Francesca Conciauro, Barbara Federica Scremin, Antonio Graziano Antico, Marco
Muscogiuri, Teresa Sibillano, Cinzia Giannini, Emanuela Filippo, Caterina Lorusso, Paolo Maria
Congedo and Giuseppe Ciccarella:
Properties of Aluminosilicate Refractories with Synthesized Boron-Modified TiO2 Nanocrystals 5. Acknowledgements In the low magnification mode, large aggregates with
smooth surfaces could be observed in both samples;
however, in the refractory without nanoparticles there are
areas with clear internal defects and larger micropores. The
addition of TiO2:(B) nanoparticles causes some differences
in the microstructures: the microcracks’ and micropores’
sizes were greatly reduced. High magnification SEM
images confirmed a denser microstructure with fewer
voids in TiO2:(B) modified refractory (Fig. 4: c and d). Moreover, EDS through the elemental analysis evidenced
that in nanocrystals-modified specimens the fillers were
present along the entire scanned surface. This work was partially supported by the FIRB 2009/2010
project “Rete integrata per la Nano Medicina (RINAME)” This work was partially supported by the FIRB 2009/2010
project “Rete integrata per la Nano Medicina (RINAME)”
— RBAP114AMK_006. Giuseppe Chita and Giovanni
Filograsso are acknowledged for their technical and This work was partially supported by the FIRB 2009/2010
project “Rete integrata per la Nano Medicina (RINAME)” This work was partially supported by the FIRB 2009/2010
project “Rete integrata per la Nano Medicina (RINAME)”
— RBAP114AMK_006. Giuseppe Chita and Giovanni
Filograsso are acknowledged for their technical and
administrative support. — RBAP114AMK_006. Giuseppe Chita and Giovanni
Filograsso are acknowledged for their technical and
administrative support. PO FESR 2007-2013 - Regione Puglia Aiuti a sostegno dei
partenariati regionali per l’innovazione NAno / MIcro
STrutturazione nei materiali per l’Edilizia ed altri settori
produttivi (NAMISTE). Cod. 2Y6DME5. PON, Avviso prot. n. 84/Ric. del 2 marzo 2012 NAnoMA‐
teriali per l'edilizia SosTEnibile (NAMASTE) prot. PON04a3_00107 CUP: B35I12000100005. PON 254/Ric. Potenziamento del “CENTRO RICERCHE PER LA SAL‐
UTE DELL'UOMO E DELL'AMBIENTE” Cod. PO‐
Na3_00334. CUP: F81D11000210007. To explain SEM results and the overall increase in the
breaking strength with nanocrystals’ additions it is to be
assumed that nanoadditives possibly induced a better
particles’ aggregation, through a thickening effect during
the formation of the liquid phase. Previous literature
studies [19] demonstrated that anatase containing boron, at
least at the surface of the nanocrystals, has peculiar
characteristics in bricks: boron favours the persistence of
the anatase phase when thermal treatments are performed
[19]. It can qualitatively explain the higher compression
breaking resistance with the nanofillers obtained in the
present study. 2.4 Aluminosilicate bricks’ characterization The surface
areas increased as well as the calculated pores’ size, while
the calculated open porosity was lower than in the refer‐ ence brick (which is in agreement with results reported in
Table 3). To study the mechanism improving the breaking
strength, SEM analysis of refractory bricks has been
conducted and the microstructures at low and high
magnification are shown in Fig. 4. Figure 4. SEM images of bricks: (a), (c) without, and (b), (d) with TiO2:(B) (2% wt) nanoparticles’ addition. Figure 4. SEM images of bricks: (a), (c) without, and (b), (d) with TiO2:(B) (2% wt) nanoparticles’ addition. 6. References [1] Balkevich VL, Medvedovskaya EI, Popov ON,
Orlova VN (1984) Contact interaction of bacor and
silica refractories. Refractories and Industrial
Ceramics 25:118–121. [2] Arahori T, Suzuki T (1987) Transformation of
tridymite to cristobalite below 1470° C in silica
refractories. J Mater Sci 22:2248–2252. [3] Brown JT, Wosinski JF, Alkali resistant silica
refractory. (2001) US Patent 6, 313, 057. [4] Chrzan ES, Petrie EC, Swain SM (1952) Study of
silica brick from a glass tank crown. J American
Ceramic Society 35:173–181. 5. Acknowledgements The results of the SEM analysis are in
contradiction with results collected in Table 4, where an
increase in the pore radii calculated in bricks with modified
nanocrystals is observed: we speculate that it may be
because of a failure of the hypothesis of the Washburn
equation, which is valid for cylindrical pores. 4. Conclusions In the present work, a microwave-assisted synthesis of
boron-modified TiO2 anatase nanocrystals with about one
minute and a half of reaction time was developed. The
effective boron content was tuned by the addition of boric
acid and increased with its nominal amount. It was found
that boron addition does not influence appreciably the
nanocrystals’ size and morphology. One of the obtained
samples was tested as additive in various quantities in a
typical aluminosilicate refractory composition. The effects
of nanocrystals’ addition on bricks were evaluated accord‐
ing to UNI EN 196/2005 in terms of thermophysical,
mechanical properties, and microstructure. The thermal
conductivity decreases and breaking strength increases
with the nanofillers’ addition. According to SEM images
the TiO2:(B) nanoparticles’ addition reduced the micro‐
cracks’ and micropores’ sizes. [5] Coler SS (1930) Thermal expansion of silica brick
and mortars. Journal of the American Ceramic
Society 13:437–446. [6] Houldsworth HS, Cobb JW (1923) The reversible
thermal expansion of refractory materials. J Ameri‐
can Ceramic Society 6:645–662. [7] Austin JB, Pierce RHH (1933.) Constitution and
thermal expansion of silica cokeoven brick after
service. J Am Ceramic Soc 16:102–106. [8] Yang Y, Wang Y, Tian W, Wang Z-Q, Zhao Y, Wang
Y, Bian H-M (2009) Reinforcing and toughening
alumina/titania ceramic composites with nano-
dopants from nanostructured composite powders. Mat Sci Engineering A 508:161–166. [9] Manivasakan P, Rajendran V, Rauta P R, Sahu B B,
Sahu P, Panda B K, Valiyaveettill S, Jegadesan S
(2010) Effect of TiO2 nanoparticles on properties of
silica refractory. J American Ceramic Society
93:2236–2243. SEM-EDS spectroscopy confirmed the presence of nano
fillers along the scanned surfaces. Possibly, nanoadditives
induced better particles’ aggregation, through a thickening
effect during the formation of the liquid phase; in this way
the nanocrystals-modified bricks presented improved
mechanical characteristics due to a better compaction of the
components. [10] Huang C-L, Wang J-J, Huang C-Y (2007) Microwave
dielectric properties of sintered alumina using
nano-scaled powders of α alumina and TiO2. J
American Ceramic Society 90:1487–1493. 6
Nanomater Nanotechnol, 2015, 5:8 | doi: 10.5772/60204 (2014) Synthesis of ultrafine anatase titanium
dioxide TiO2 nanocrystals by the microwave-
solvothermal method. J Nanoeng Nanomanufact
4:28–32. [11] Carlucci C, Scremin BF, Sibillano T, Giannini C,
Filippo E, Perulli P, Capodilupo AL, Corrente GA,
Ciccarella G (2014) Microwave-assisted synthesis of
boron-modified
TiO2
nanocrystals.Inorganics
2:264–277. [16] FULLPROF Refinement of powder (Rietveld) and
single-crystal diffraction data Accessed 22 Septem‐
ber 2014 http://www.ill.eu/sites/fullprof. 7
Claudia Carlucci, Francesca Conciauro, Barbara Federica Scremin, Antonio Graziano Antico, Marco
Muscogiuri, Teresa Sibillano, Cinzia Giannini, Emanuela Filippo, Caterina Lorusso, Paolo Maria
Congedo and Giuseppe Ciccarella:
Properties of Aluminosilicate Refractories with Synthesized Boron-Modified TiO2 Nanocrystals 4. Conclusions [12] Xu H, Picca RA, De Marco L, Carlucci C, Scrascia A,
Papadia P, Scremin BF, Carlino E, Giannini C,
Malitesta C, Mazzeo M, Gigli G, Ciccarella G (2013)
Nonhydrolytic route to boron-doped TiO2 nano‐
crystals. Eur J of Inorg Chem 3: 364–374. [17] Washburn EW (1921) The dynamics of capillary
flow. Phys Rev 17:273–283. [18] Chen D, Yang D, Wang Q, Jiang Z (2006) Effects of
Boron Doping on Photocatalytic Activity and
Microstructure of Titanium Dioxide Nanoparticles. Industrial & Engineering Chemistry Research 45:
4110–4116. [13] Carlucci C, Xu H, Scremin BF, Giannini C, Altamura
D, Carlino E, Videtta V, Conciauro F, Gigli G,
Ciccarella G (2014) Selective synthesis of TiO2
nanocrystals with morphology control with the
microwave-solvothermal
method. Cryst
Eng
Comm 16:1817–1824. [19] Imteyaz Ahmad Md, Bhattacharya SS, Hahn H
(2009), Thermal stability, and optical properties of
boron modified nanocrystalline anatase prepared
by chemical vapor synthesis. Journal of Applied
Physics 105:113526–113534. [14] Carlucci C, Xu H, Scremin BF, Giannini C, Sibillano
T, Carlino E, Videtta V, Gigli G, Ciccarella G (2014)
Controllable One-Pot Synthesis of Anatase TiO2
Nanorods
with
the
Microwave-Solvothermal
Method. Sci Adv Mater 6:1668–1675. [15] Xu H, Carlucci C, Scremin BF, Giannini C, Sibillano
T, Scrascia A, Capodilupo AL, Gigli G, Ciccarella G
|
https://openalex.org/W2988769880
|
https://www.jvolcanica.org/ojs/index.php/volcanica/article/download/54/53
|
English
| null |
The eruption of Timor in 1638: 350 years of plagiarism, embellishments and misunderstandings
|
Volcanica
| 2,019
|
cc-by
| 16,956
|
†It seems unlikely that the Jesuits had direct information about
Timor. Before the 1630s the nearest Catholic missionaries were Do-
minicans located on Solor. Their fort was taken over by the Dutch
in 1613 and the Dominicans moved to Flores and had some success
in Timor in the 1640s. Although the Portuguese had a presence on
Timor there was no fixed establishment until 1663. In Ternate and
Tidore the Portuguese, Spanish and Dutch traded power in the early
17th century; by the 1630s the Dutch were dominant everywhere ex-
cept for small enclaves (the Portuguese in Oecussi (Timor) and the
English in Macassar [Bassett 1958]). However, the Jesuits had a strong
presence in the Philippines and Japan and no doubt travelled on nu-
merous routes in the region. The Eruption of Timor in 1638:
350 years of plagiarism, embellishments and misunderstandings Russell Blong∗
Risk Frontiers, 8/33 Chandos St., St Leonards, NSW 2065, Australia. Abstract In 1665 Athanasius Kircher included a short paragraph in his Mundus Subterraneus about a flamy spire and the
collapse and disappearance of a high mountain following a ‘horrible earthquake’ on Timor in 1638. Although Timor
has been known to have no volcanoes for at least the last century, Kircher’s story has been repeated for 350 years,
generally without acknowledgement, and often with the addition of embellishments and/or errors. This study
traces the various accounts and the ways in which the story has morphed, particularly in the early 19th century,
when the emphasis in Kircher’s story changes from a ‘flamy spire’, a ‘horrible earthquake’, and the collapse of the
volcano into a continuing Stromboli-like eruption with no mention of an earthquake. Strangely, the fiction that the
flamy spire could be seen from a distance of 300 miles is maintained and other embellishments added up to the
present day. Keywords: Timor; Volcanic eruption; Earthquake; Kircher; History; Archives 1
Introduction polymath. Mundus Subterraneus was published first in
Latin in 1665, and then a partial translation appeared
in English in 1669 as: In the early 1970s I came across the Phil Trans Royal So-
ciety paper on “The Dust Veil Index” by the renowned
English meteorologist H. H. Lamb [Lamb 1970]. I no-
ticed that an eruption on Timor was recorded for the
year 1638. I had been to Timor-Leste (at that time Por-
tuguese Timor) in 1972 and was fairly certain that there
were no volcanoes on the island of Timor (c.f., Neu-
mann van Padang [1951] and van Bemmelen [1949]∗). Lamb gave as his reference the “List of principal ascer-
tained volcanic eruptions from 1500 to 1886” in the
Royal Society report of 1888 on the 1883 eruption of
Krakatoa (now Krakatau) [Symons et al. 1888]. I wrote
to him and he graciously confirmed that he knew no
more than was recorded in the 1888 Royal Society re-
port; that is, there was no reference to an earlier source. Thus began a search that has intrigued me, on and off,
for nearly fifty years. The
Volcano’s:
or,
Burning
and
Fire-
vomiting Mountains, Famous in the world:
With their Remarkables. Colleed for the
moõ part out of Kircher’s Subterraneous
World; And expos’d to more general view in
English, upon the Relation of the late Won-
derful and Prodigious Eruptions of Aetna. Thereby to occasion greater admirations of the
Wonders of Nature (and of the God of Nature)
in the mighty Element of Fire. The
Volcano’s:
or,
Burning
and
Fire-
vomiting Mountains, Famous in the world:
With their Remarkables. Colleed for the
moõ part out of Kircher’s Subterraneous
World; And expos’d to more general view in
English, upon the Relation of the late Won-
derful and Prodigious Eruptions of Aetna. Thereby to occasion greater admirations of the
Wonders of Nature (and of the God of Nature)
in the mighty Element of Fire. Page 13 in the 1669 version (identical in this section to
the 1665 Latin version), states: g
g
g
∗Interestingly, none of the great Dutch volcanologists and geolo-
gists working in Indonesia (R. D. M. Verbeek, H. A. Brouwer, Reinout
Willem van Bemmelen, Herman Th. Verstappen, and M. Neumann
van Padang among others) from the 1880s to the early 1950s appear
to even mention the eruption of Timor. ∗Corresponding author: rblong43@gmail.com 2
Athanasius Kircher (1602–1680) In about 1618 Athanasius Kircher was enrolled to study
at the Jesuit college in Mainz; by 1633, at the age of 32,
he was in Rome. He had personal experience of the Cal-
abrian earthquake in 1638, the eruption of Etna and,
in the same year, climbed into the crater of Vesuvius. These journeys awakened his interest in “the incredi-
ble power of Nature working in subterranean burrows
and passages” [Glassie 2012, p94]. For the next few
years he worked on all manner of natural philosophy
subjects [Glassie 2012, p99]. Jesuits and others in his
network of correspondents around the world sent him
astronomical observations, reports of unusual phenom-
ena, specimens of flowers, animals, and shells [Glassie
2012, p113]. Stephen Jay Gould, in a work demonstrating Kircher’s
contribution to the study of fossils, notes [I]n spending so much time reading the
Mundus Subterraneus and other works by
Kircher, I have developed enormous respect,
not so much for the power of his insights and
assertions, but for the quality of his doubts, and
for his willingness to grope and struggle with
material that he understood only poorly by his
own admission [Gould 2004, p235]. Waddell argues Kircher’s aim was not necessarily to
codify facts as expected by Royal Society experimen-
talists and others but to create probable imitations of
Nature’s secret realms and forces which, by extension,
were controlled by Kircher and the Jesuits (and God?)
[Waddell 2006, p4]. Mundus Subterraneus—a two volume tome of atlas-
like proportions and ten years in the making [Bald-
win 2004, p67]—was published in Amsterdam in 1665
[Glassie 2012, p183]. Another one of his many major
works, China Illustrated, was published in 1667. It was
not limited to China but was drawn primarily from re-
ports of missionaries who had been travelling to the
east since the 1570s; Glassie [2012, p201] described the
book as “probably the single most important written
source for shaping the Western understanding of China
and its neighbours”. Kircher was the most prolific Je-
suit author (at least 30 books) of the mid-seventeenth
century [Siebert 2004, p94]. As Glassie [2012, p272], one of Kircher’s biographers,
summarised [I]t’s clear that the modern perspective is sim-
ply not the right one to take when it comes
to Kircher and to the entire Kircherian enter-
prise. Page 13 in the 1669 version (identical in this section to
the 1665 Latin version), states: The Mountain Pico in the Iôand Timor, of such
an height, that a flamy Spire or Pyramid was seen
for three hundred miles in the Sea. This in the
year , had its very foundations shaken, by
an horrible Earthquake; and was wholly swal-
low’d up, together with the Iôand, leaving noth-
ing behind it, but an huge mighty Lake. So the
Annals of the Jesuites Society relate.† Within a year or two I had found George Adams’
1912 paper in the Philippines Journal of Science. Adams,
a professor of geology in Tientsin, China, asserted that
there were no active or recently active volcanoes on
Timor and traced the source of the information about
the 1638 eruption, via various intermediaries, back
to a 1671 publication by Thomae Ittig, a Jesuit priest
[Adams 1912; Ittig 1671]. Later, I found what appears
to be the initial published source, Mundus Subterraneus
by Anthanasius Kircher, a prolific Jesuit author and Blong, 2019 The Eruption of Timor in 1638 As a general rule Kircher never ruined a good
story with facts. . . . he was also known for
a tendency to embellish on his own behalf. (The other frequent complaint about him was
more like the opposite: people said he was
inclined to believe any spectacular story he
heard) [Glassie 2012]. As a general rule Kircher never ruined a good
story with facts. . . . he was also known for
a tendency to embellish on his own behalf. (The other frequent complaint about him was
more like the opposite: people said he was
inclined to believe any spectacular story he
heard) [Glassie 2012]. A more recent reference to the eruption of Timor is
that from the wonderfully named Pessimist’s Guide to
History: an irresistible compendium of catastrophes, bar-
barities, massacres, and mayhem – from 14 billion years
ago to 2007 [Flexner and Flexner 2008, p77]: 1638: Indonesian Volcano Explodes. Located
on the island of Timor in modern-day Indone-
sia, the 10,500 foot volcano peak blew itself
apart in a cataclysmic eruption, killing hun-
dreds of people in the area. Or as an American historian, John Ferguson, wrote in
1906 “his works in number, bulk and uselessness are
not surpassed in the whole field of learning” [Glassie
2012]. In 1643 René Descartes noted “The Jesuit is
quite boastful; he is more of a charlatan than a scholar”
[Glassie 2012, p108]. ∗A separate account which attempts to trace whether or not such
an eruption may have occurred somewhere in the east, and an exam-
ination of the several possible locales is being prepared. Appendix B
briefly introduces some of the possibilities. Page 13 in the 1669 version (identical in this section to
the 1665 Latin version), states: Another scholar suggested he of-
ten entered in “full plagiaristic mode” for pages and
pages at a time [Glassie 2012, p141]. Kircher’s original statement contains both details of
dubious veracity and a problem with the logic of an is-
land disappearing to leave behind nothing but a lake,
but it is clear the story has shifted somewhat in 350
years. Such negative views are countered by those of numer-
ous others scholars: Our present concern is only with the 350-year
progress of the account of the 1638 eruption of Timor
through volcanological and other literature and the
ways in which details have been added or changed∗. Each publication demonstrated his dizzying
array of linguistic, paleographic, historical,
and scientific skills, and each advertised his
myriad inventions, possessions of strange and
exotic artifacts, and mysterious manuscripts
[Findlen 2004, p2]. 3
Methodology I first came across the account in Lamb’s 1970 paper on
the dust veil index and in the 1888 Krakatoa committee
report. It seemed obvious (to me) that the information
was incorrect and I was intrigued that the prestigious
Royal Society of London had been wrong twice! At first
I was curious as to how and where the story had begun. Later I was surprised that the story had persisted for
so long and captivated by the ways in which the story
had changed. Throughout, I hoped that I might be able
to pinpoint just where the ‘eruption of Timor’ had oc-
curred; while I have been unsuccessful in this endeav-
our Appendix B sets out some of the events I see as pos-
sibilities. Five types of Jesuit letter can be distinguished (Lach
[1965, p317–318], Correia-Afonso [1969, p9–10]): 1. those meant for the superiors of the Order–these
are the most explicit and illuminating; they are the
most realistic and detailed; 2. those meant for the members of the Society in
general–these are more discreet in style, yet are
written with a good deal of freedom and affection-
ate regard. They supply details regarding social
life and customs and missionary work abroad; My exploration of the available literature on the
1638 eruption of Timor was not driven by any for-
mal methodology. In effect, the available literature was
searched for (i) sources that mentioned the 1638 erup-
tion of Timor; and (ii) sources that might corroborate
Kircher’s account. In pre-internet days this included
searches in various libraries (including those in Sydney,
Cambridge, London, Seattle, Honolulu and Washing-
ton D.C) and requests for inter-library loans, not always
successful and often available only on microfilm. The
search was erratic and discontinuous, one source lead-
ing to another and another . . . intermittently for nearly
five decades†. In the last decade or two when ‘keyword’
searches were possible ‘Timor 1638’ and ‘Timor erup-
tion’ were the most fruitful, but worthwhile finds di-
minished in number. Despite the length of this search
we can assume that only a limited proportion of the
accounts of the 1638 eruption of Timor have been un-
covered, particularly as sources in languages other than
English have been inadequately sampled. 3. those addressed to the public at large–these letters
are more studied in style and their contents more
carefully checked and edited; 4. †In 2006 a presentation ‘An eruption in Timor in 1638 – sepa-
rating fact from fiction’ was made in Quito, Ecuador at the Cities on
Volcanoes conference. This failed to elicit any new leads (though, in-
terestingly, R W Johnson of Geoscience Australia (GA) reported that
after the Boxing Day 2004 Aceh tsunami GA received reports, inter
alia, of volcanoes erupting in Timor – about 3500 km from the earth-
quake epicentre). ∗Siebert [2004] provides an interesting account of Kircher’s issues
with Jesuit censorship of his writings 2
Athanasius Kircher (1602–1680) There’s something to be said for his ef-
fort to know everything and to share every-
thing he knew, for asking a thousand ques-
tions about the world around him, and for get-
ting so many others to ask questions about
his answers; for stimulating, as well as con-
founding and inadvertently amusing, so many
minds; for having been a source of so many
ideas – right, wrong, half right, half-baked,
ridiculous, beautiful, and all-encompassing. The views below provide a range of assessments of
the importance of Kircher as a scholar: Presses universitaires de rasbourg Page 192 2(2): 191 – 210. doi: 10.30909/vol.02.02.191210 Volcanica While this background provides a variety of possible
contexts, none of it helps with establishing the origin or
veracity of Kircher’s comment on the eruption of Timor. with an apologetical and apostolic rather than an his-
torical end in view, so the letters from the east were
touched up, or summarised, or enlarged, or embel-
lished [Correia-Afonso 1969, p35]. Even forgeries were
put on the market [Correia-Afonso 1969, p159]. Kircher gives his source as the Annals of the Jesuit So-
ciety. Jesuit letters, one of the main information sources
in the vast Archivum Romanum Societatis Iesu (ARSI),
grew out of an early recognition that it was essential to
secure union among its members and close contact be-
tween subjects and superiors. The aim of letters was
edification of members of the society and their guid-
ance [Correia-Afonso 1969, p1–2]. Thus, it is not clear that the event described by
Kircher ever actually happened, if it occurred where
it might have happened, or whether it had been em-
bellished even before it came to Kircher’s attention. A
three-day search of the vast Archivum Romanum So-
cietatis Iesu (ARSI) failed to identify Kircher’s source. Nonetheless, versions of his account, with the source
seldom acknowledged, have survived for more than 350
years. Letters could take 5 or even more years to reach the
addressee and return [Correia-Afonso 1969, p28]. From
1517 it was decided that a Provincial report should be
sent yearly to the Society’s headquarters, comprising
accounts of the various houses of the Province. Extracts
from these letters were gathered together, making up
the history of the Society for that year [Correia-Afonso
1969, p6]. Presses universitaires de rasbourg 4
Location of Kircher’s Timor who referred to ‘Timor, most easterly of these islands’,
the following year [Ponton 1872]. Kircher [1665; 1669] clearly refers to the eruption being
located on the island Timor, an island that we locate to-
day at about 9 °S, 125 °E (Figure 1). Kircher, if he was
even interested, probably had only a vague idea where
Timor was located. However, Diego Ribero’s map of the
world of 1529 shows the Spice Islands and Lesser Sun-
das as far east as Timor and an “astoundingly accurate
Southeast Asian mainland” [Suárez 1999, p102]. The
Blaeu maps of the first half of the 17th century also
show Timor in approximately the correct position to
the east of Sumatra and Java and south of the equator. Timor had been visited by European navigators as early
as 1514 when Antonio Pigafetta was the first European
to describe the island. Earlier, in 1511, Abreu and Ro-
driques coasted along the interlocked group of islands
comprising Wetar, Timor, Alor, and Solor but it is un-
clear whether they sighted Timor. The island in Maluku which Varenius et al. [1683]
call Timor, Varenius also calls Motir (a transposition of
Timor), Motil, Motill, and Mothir. Varenius describes
the isle as five or six leagues† in circuit (p322). This
island is also named as ‘Timor or Motir’ on the Willem
Janszoon Blaeu map of 1630, and similarly named on a
1764 French map (Figure 2). Astonishingly, Pigafetta in
1514 gave the latitude of Motir as exactly 0 °, correct to
within about 40 km [Suárez 1999, p145]. Today the island is known as Pulau Moti (0.5 °N,
127.4 °E) (Figures 1 and 2). As the spice islands of Ter-
nate and/or Tidore, less than 40 km to the north, were
populated by Europeans from 1578 [Lach 1965, p500],
and as no Holocene activity from this volcano (Volcano
Number 268063) have been recorded in the Smithso-
nian database‡, it is unlikely that Moti is the source vol-
cano or island in Kircher’s story. y
A third possibility for the location of Kircher’s Timor
also deserves consideration. Pires [1944, p203–204]
notes that by the "Islands of Timor" is meant the great
Timor Island and Sumba or Sandalwood Island. He
also notes “All the islands from Java onwards are called
Timor, for ‘timor’ means ‘east’ in the language of the
country, as if they were saying the islands of the east”
(Figure 1). †The Shorter OED describes a league as “an itinerary measure of
distance, varying in different countries but usually estimated at about
3 miles”. ∗The exact authorship of this statement is unclear. There appear
to be three possibilities: Bernhardus Varenius, noted as an author and
a major figure in mid-17th century geography, died in 1650. Nicolas
Sanson, also identified as making additions to the manuscript and
a prominent French cartographer, died in 1667. Richard Blome, an
English engraver, cartographer and publisher is not acknowledged
on the title page. See full title in the References. ‡The Global Volcanism database at the Smithsonian Institution
in Washington DC is the global repository for information about vol-
canic activity.
The database records every known eruption in the
world in the last 10,000 years. See http://volcano.si.edu/search_
volcano.cfm 4
Location of Kircher’s Timor Tibbets [1981, p501], examining Arab nav-
igation in the Indian Ocean before the coming of the
Portuguese, wrote: “The term Timor . . . according to
the texts includes the whole of the islands to the south-
east of J¯awa but what is actually meant is all the islands
south and east of Sumbawa and Sumba. Whether or not
Flores is included it is impossible to tell”. Despite this knowledge it is apparent that Timor was
not on the main route used by Europeans from Malacca
to the Spice Islands with ships generally following the
course Java – Batu Tara – Buru – then either to Banda
or the Moluccas [Pires 1944, p204] (see Figure 1). How-
ever, Arab, Indonesian, and Chinese traders were also
active in the area during the early part of the 17th cen-
tury and Kircher’s information could have been derived
(probably indirectly) from any of these. While modern gazetteers (and Google Earth™) list
only the one Timor, Varenius et al. [1683, p321] refers
to two distinct Timors: I Comprehend under the name of the Moluc-
coes, not only the Iôes of Ternate, Tidore,
Motill or Timor, Machian, and Bachian,
which are particularly called the Moluccoes;
but likewise those of Gilolo, of the Land of Pa-
pous, which lie on the Eaõ; of Celebes, which
are on their Weõ; of them of Ceram, of Flores,
and Timor, which are towards their South, and
several others thereabouts∗. Thus, it appears that there are (at least) three possi-
bilities for the location of Kircher’s Island Timor: 1. The island that we call Timor today located at 9 °S,
125 °E, with the eastern part forming the indepen-
dent country of Timor-Leste, and the western part
a portion of the Indonesian province of Nusa Teng-
gara Timur (as shown on Figure 1); 2. The small Pulau Moti, west of Halmahera and
south of Pulau Tidore in Provinsi Maluku Utara (as
shown on Figures 1 and 2); It seems that Varenius et al. [1683] regard both
the Timors described as located under the name ‘the
Moluccas’; today, we use ‘Maluku’ to refer to the Moluc-
cas (Figure 1) but delineating a much more limited area
than that described by Varenius. 3. 3
Methodology letters addressed to personal friends within or out-
side the Society–contain interesting information
about the author and his environment; sometimes
published; 5. allied documents–not strictly letters; studies of life
and customs of particular tribes, accounts of par-
ticular expeditions, history of noted stations etc. The superiors of the Society insisted on accuracy and
fidelity to truth on the part of their chroniclers∗. Sensa-
tional effect was not what was wanted, but objectivity
and reliability [Correia-Afonso 1969, p7]. Original let-
ters from the east were usually in Portuguese, Spanish
or Latin [Correia-Afonso 1969, p108]. It was quite com-
mon for three or more transcripts of the one letter to be
sent separately to Europe as a precaution against loss at
sea [Correia-Afonso 1969, p24]. The system of transcription by hand (as letters were
passed around Europe) involved many delays and was
likely to be the source of many inaccuracies [Correia-
Afonso 1969, p33]. Jesuit letters were edited in Europe Presses universitaires de rasbourg Page 193 The Eruption of Timor in 1638 Blong, 2019 Presses universitaires de rasbourg 4
Location of Kircher’s Timor A location somewhere in the island chain stretch-
ing from Sumbawa to Timor and beyond to Pu-
lau Yamdena (Provinsi Nusa Tenggara Barat, Nusa
Tenggara Timur, and the southern part of Provinsi
Maluku) (as shown on Figure 1). Confusion as to which of the two Timors known at
the time Kircher was writing about was maintained by
Robert Hooke’s [1705] reference to “Timor, one of the
Moluccas” (Table 1), a reference continued by Georg
Hartwig in 1871, and compounded by Mungo Ponton Presses universitaires de rasbourg Page 194 2(2): 191 – 210. doi: 10.30909/vol.02.02.191210 Volcanica Figure 1: Eastern Indonesia showing Maluku the modern name for the Moluccas, with the islands of Provinsi
Maluku Utara outlined in blue and those of Provinsi Maluku outlined in pink. The two Maluku provinces exclude
Timor and Timor-Leste, West Papua/New Guinea, Sulawesi/Celebes, and Pantar and Alor which lie east of Flores
(and north of Timor). Figure 1: Eastern Indonesia showing Maluku the modern name for the Moluccas, with the islands of Provinsi
Maluku Utara outlined in blue and those of Provinsi Maluku outlined in pink. The two Maluku provinces exclude
Timor and Timor-Leste, West Papua/New Guinea, Sulawesi/Celebes, and Pantar and Alor which lie east of Flores
(and north of Timor). ficult to determine [Lach 1965, p604]. A fourth possibility—that Kircher was writing about
a volcano called Timor—seems unlikely; Siebert et al. [2010]) include a gazetteer of thousands of volcano
names and synonyms but none resemble “Timor”. Secondly, as early as 1793, Raspe pointed out that
quite a lot of mistakes were made by authorities in
translating unfamiliar names [Raspe 1970]∗. As Pires
[1944, p202] noted describing the ways names have
changed from map to map: “All this shows once more
how the cartographers, copying from map to map
names they did not know, could disfigure them until
they became almost unrecognizable and even meaning-
less”. Further, as Suárez [1999, p133] wrote: However, two additional points deserve considera-
tion. Firstly, during the 16th and 17th centuries there
was intense competition for access to the Spice Islands
(in particular Ternate, Tidore, Banda) in order to corner
the market for pepper, cloves, mace and nutmeg. Span-
ish and Portuguese sources were often contradictory on
the exact location of the Moluccas and the Philippines
[Lach 1965, p501]; misinformation played an impor-
tant part in this game, and it is possible that the in-
formation Kircher received was deliberately incorrect. ∗Reference is to translation of 1793 edition 4
Location of Kircher’s Timor On the other hand, for example, Pigafetta’s estimate of
the longitude of the Moluccas was markedly superior to
the longitude that he assigned the Philippines – an il-
lustration of the fact that although the direction of lon-
gitude was almost certainly politically influenced the
fact that the figure was inaccurate was not necessarily
deliberate. What we, in hindsight, might see as politi-
cally motivated deception of longitude may in fact have
been simply the temptation to opt for the most advanta-
geous figure within the range of possible truths. Errors
in position stood for long periods–Varenius et al. [1683,
p321], for example, gave the co-ordinates of the Isles of
Moluccoes as straddling the Equator at 168 °E longi-
tude, whereas 128 °E is more correct. Whether such
‘errors’ were deliberate or represent a selection most
advantageous to a particular colonial power is now dif- First-hand observers sometimes mistook part
of an island to be a separate island altogether,
while the map makers who plotted their data
sometimes misconstrued distinct islands as
different regions of a single island, or vice-
versa. Finally, explorers who searched for spe-
cific islands discovered and named by their
predecessors often reached different islands
but erroneously deemed them to be the orig-
inal landfall, and then mapped the new island
under the original name. 5
Subsequent accounts of the eruption of
Timor 5 5.1
Post-Kircher views on the location Although we can’t be certain at this distance in time
just which location Kircher’s account actually refers to,
subsequent writers rarely expressed any doubt. While
we can judge it most likely that Kircher’s story was re-
ferring to the Timor south of the Equator, 19th century
authorities become even more specific. Earl in 1845
locates an eruptive centre—not necessarily Kircher’s
‘flamy spire’, on the north-east extreme of Timor—but
then retracts in 1852 stating there are no active volca-
noes in the eastern (Portuguese-controlled) part of the
island∗. In 1857 the Javanasche Courant places an erup-
tion in the western (Dutch-controlled) half in 1856 at
the mountain Iloen Bano, noting that “the account from
which we are borrowing these details is all the more re-
markable since it is the first notice of an eruption of
a volcano in Timor, or at least the western part of the
island” [as reported by Adams 1912]. Figure 2: “Carte Particuliere des Îsles Moluques”, by
[Bellin 1765]. Published in Prévost L’Histoire Générale
des Voyages. The stratovolcano on Mothir/ Moti/
Timor rises to a height of 927m above sea level. As , p286–287 has shown the accounts of the 1856
and 1857 eruptions on Timor refer to one or more mud
volcanoes, which have nothing to do with Kircher’s
original story. Bonney [1899, p230] also expresses the
doubt that volcanoes exist in Timor, and doesn’t men-
tion the eruption of 1638, but says there must be a few
volcanoes “for one in the western part of the island is
said to have been in eruption in 1856 and in the follow-
ing year”, noting there are also some mud volcanoes,
“but nothing calling for special attention”. Figure 3: Moti drawn from the south [Verbeek 1908]. W = West, O = East [Oost]. Figure 3: Moti drawn from the south [Verbeek 1908]. W = West, O = East [Oost]. Figure 3: Moti drawn from the south [Verbeek 1908]. W = West, O = East [Oost]. Mercalli, writing in 1907, pulls all the information
together referring to the 1638 eruption and providing
some details about the violent explosion at Floen-Bano
[sic] in the western part of Timor on 26 December, 1856
and at Volcano Bibulito in May 1857. He then goes on to
write: “Probably all these eruptions should be referred
to one volcano which bears different names”. ∗Details for each example cited here are given in Appendix A. 5 All known accounts of the eruption of Timor have
been collected in the Appendix A. Verbatim accounts Presses universitaires de rasbourg Page 195 Page 195 The Eruption of Timor in 1638 Blong, 2019 Figure 2: “Carte Particuliere des Îsles Moluques”, by
[Bellin 1765]. Published in Prévost L’Histoire Générale
des Voyages. The stratovolcano on Mothir/ Moti/
Timor rises to a height of 927m above sea level. by subsequent authors. In most, but not all, cases
subsequent editions of an author’s work have been ig-
nored. Blue cells in accounts later than 1665 identify
new items of information additional to those supplied
by Kircher. The second last row illustrates just how few
authors provided a source for their information. Some
of the main items in these accounts are considered in
more detail below. 5.1
Post-Kircher views on the location are given together, where appropriate, with transla-
tions into English. Translations have been performed
by friends, colleagues and, in more than one case, by
Google Translate (https://translate.google.com). The translations should be regarded as reasonably cor-
rect rather than perfect. Schneider [1911] follows Mercalli, incorrectly nam-
ing the volcano Floen-Bano, and giving the dates of
eruption as 1638, 1856, and 1857. Although Mercalli
stated the volcano was located in the western part of the
island, Schneider locates it in the eastern part, shows
the location on a map (his Figure 32), places the volcano
at 126 °30’E, 8 °50’S and states the height of the volcano
as 2400m. This location is near the south coast about
110 km ESE of Dili, the capital of Timor–Leste, whereas
Schneider’s map shows the volcano located near the
north coast about 130km east of Dili. Table 1 summarises the information content of each
of the 30 or so accounts contained in Appendix A under
the major headings: Location, Height of the Peak, the
year of the event, reference to an earthquake, the na-
ture of volcanic activity, and the reported consequences
of the event. Comparison of Table 1 with Appendix A
shows that it is not always easy to ‘categorize’ an au-
thor’s view. In the third column [Kircher 1665] cells
marked in blue indicate the ‘original’ information items
that stem from Kircher’s account. Pink cells in columns
to the right indicate that these items were also reported Presses universitaires de rasbourg Page 196 2(2): 191 – 210. doi: 10.30909/vol.02.02.191210 Volcanica Table 1 – A summary of the main features included in each account as detailed in Appendix A. Blue cells = new
information added at this time. Pink cells = this item is included in the account published in this year. Clear
cells = no information about this item included in the account published in this year. Table 1 – A summary of the main features included in each account as detailed in Appendix A. Blue cells = new
information added at this time. Pink cells = this item is included in the account published in this year. Clear
cells = no information about this item included in the account published in this year. p
y
cells = no information about this item included in the account published in this year. 5.2
The Mountain Pico, seen for 300 miles in the sea 5.2
The Mountain Pico, seen for 300 miles in the sea Kircher [1665; 1669] reported that “a flamy Spire or
Pyramid was seen for three hundred miles in the Sea”. If we use a simplified equation illustrating the effect of
the curvature of the earth on distant observations∗, for
a flamy spire to be just seen at a distance of 300 nautical
miles, Pico would have to be nearly 20,000 metres high. If the 300 miles refers to statute miles instead of nauti-
cal miles, the necessary height reduces to about 15,000
metres. As Mount Everest is about 8,850 metres high,
either would seem to be a significant exaggeration. Rin-
jani on Lombok, the second highest volcanic mountain
in east Asia, reaches an elevation of 3726 m†. Subsequent writers until the publication of Lamb’s
work in 1970, for example, Sapper [1917] and Wich-
mann [1918], repeat at least part of Kircher’s account
but are inclined to the view that there have been no vol-
canic eruptions on Timor. It is easy to understand how many of the errors and
misunderstandings listed above occurred. Timor was
on the other side of the world for most authors and
finding and verifying sources was often no easy mat-
ter in pre-internet days. Nonetheless, that in no way
excuses the majority of authors from failing to state
where their information came from. Table 1 shows just
how few authors bothered to state their sources, and
often borrowed almost verbatim chunks from earlier
works without acknowledgement. The only author be-
fore Adams who provides first-hand information is Earl
[1845; 1852] who lived in Timor, made observations,
and then corrected them. In the decades before Kircher was writing, Pico de
Teido on Tenerife in the Canary Islands, was believed
by many, including many Jesuits, to be the highest
mountain in the world‡. Hooke [1705] compares the
height of Pico, in the Moluccas, to that of Tenariff. The
volcano on Tenerife has a height of 3715 m. If the sighting refers to a reflection of a fiery erup-
tion on the cloud base, 15,000 m seems possible as high
clouds in the tropics range about 6,000–18,000 m above
sea level. As Table 1 shows, 16 of the 30 authors included in
this survey describe the peak as a ‘high mountain’ or
‘colossal cone’. ‡Jesuit Fathers wrote on the "pico" of Canarias, island of Tener-
ife, in 1556 [Wicki 1954, p494], as the highest or nearly so, moun-
tain of the world; again in 1566 [Wicki 1960, p787]; also Fr Thomas
Stephens, in 1579 [Wicki 1970, p683]. I am grateful to the late Fr
Joseph Wicki, SJ, Jesuit Historical Institute, Rome, for this informa-
tion. Interestingly, Varenius et al. [1683, p49] wrote: “El Pico in Tener-
iff, esteemed the highest in the whole World, whose top is conspicuous
at Sea 60 miles”. He also notes that Pico de St George in the Azores is
reported to have “an equal Altitude with the Mountain of Teneriff”. 5.2
The Mountain Pico, seen for 300 miles in the sea Seventeen authors, usually the same
ones, describe the peak as being seen at a distance of
300 miles. Two other distances at which the peak could
be seen are mentioned: Wilson [1906] suggests 270
miles, and Mercalli [1907] allows 450 km (roughly 280
statute miles). Flexner and Flexner [2008]) opt for a
height of 10,500 ft (~3200 m). The one author referenced in Table 1 but left out of
the above discussion is Alfred Russel Wallace, in a sense
co-founder of the theory of evolution, resident of Timor
for some months in 1861, an explorer, naturalist and
resident in the area between Malaysia and westernmost
New Guinea from April 1854 to January 1862, and au-
thor of The Malay Archipelago 1869. Despite Wallace’s
all-consuming focus (at this stage of his life) on the va-
riety of species of animals and insects and his famil-
iarity with Maluku landscapes and ecology, he too be-
lieved that Timor had a volcano, near the centre of the
island. At the same time he recognised that Timor con-
sisted of “ancient stratified rocks” [Wallace 1869, p18]
and noted “it seems to form the termination of the great
range of volcanic islands which begins with Sumatra,
more than two thousand miles to the west” [Wallace
1869, p184]. He continues: “In no other part of Timor
do there appear to be any recent igneous rocks, so that
it can hardly be classed as a volcanic island. Indeed
its position is just outside of the great volcanic island,
which extends from Flores through Ombay and Wetter
[Alor and Wetar: see Figure 1] to Banda”. †Gunung Kerinci in Sumatra is the highest volcano in Indonesia
at about 3800 m.
‡ ∗h1 = 0.228(D - 5)2 where h1 is the cut-offheight and D is the
total distance in nautical miles from a ship to Pico [Blong et al. 2016]. 5.1
Post-Kircher views on the location 1665
1669
1671
1692
1705
1761
1825
1826
1830
1841
1848
Timor
Island/Isle
One of/In the Moluccas
Near centre of island
Eastern coast
Western half
Latitude/Longitude given
Pico/Peak
High Mountain/Colossal cone/vast height
visible ≥300 miles
Equal height of Tenariff
2400 metre high
10,500 feet high
270 miles
1638
1637
Earthquake
Foundations shaken/shattered
Terrifying Earthquake
Catastrophe
Catastrophe
Flamy spire/flaming summit
Continually active
Like Stromboli
Like a lighthouse
Violent/paroxysmal/great eruption
Blown up/top blown off
Since been quiescent
Swalled up
Together with (almost all of the) island
Entirely destroyed
Absorbed/engulfed
Replaced by a concavity
Replaced by an abyss/enormous void
Lake/Large lake
Replaced by a crater lake
Disappeared
Killed hundreds
Nothing left behind
Source cited
Kircher
Kircher
Ittig
Bottoni
Hooke
Montbéliard
Scrope
Daubeny
Forbes
Hitchcock
Daubeny
Consequence
Activity
In Eruption
Location
Height
Year of event
Earthquake
1858
1862
1868
1869
1871
1872
1879
1885
1888
1893
1906
1907
1911
1917
1918
1970
1985
2008
2010s
Perrey
Scrope
Z & M
Wallace
Hartwig
Ponton
Wallace
Balfour
Roy. Soc. Hartwig
Wilson
Mercalli
Schneider
Sapper
Wichmann
Lamb
CDIC
Flexner
Gluedideas
Presses universitaires de rasbourg Presses universitaires de rasbourg Page 197 The Eruption of Timor in 1638 Blong, 2019 read works of George Julius Poulett Scrope (first pub-
lished in 1825) which led him to follow more than 200
years of misrepresentation about an eruption in Timor. Worcester [1914–1915], a professor of zoology, pro-
vides a review of Adams [1912] and follows Adams in
believing that Scrope obtained his information from It-
tig’s 1671 work and that the eruption was likely on a
neighbouring island. However, he then finds Adam’s
view that there are no volcanoes on Timor a sweeping
statement as he (Worcester) is “cognisant of the fact
that there were eruptions from Timor as recently as
1856 and 1857”. It appears either Worcester failed to
read Adams’ work carefully or that he believes that an
eruption from a mud volcano is, in fact, a volcanic erup-
tion. 5.3
Volcanic activity Only six authorities refer to a ‘flamy spire’ or ‘flaming
summit’ : the four publications by Jesuits in the 17th
century, Perrey writing in 1858a who also cites a Jesuit
source, and Ponton [1872] who gives no source for his
information. Scrope [1825] extends the notion of a ‘flamy spire’ We do not know why Wallace in his 1869 Malay
Archipelago thought Timor had a central volcanic peak
despite his own observations and instincts. However,
Wallace also edited and extended the 1879 edition of
Stanford’s Compendium of Geography and Travel, and
there he makes it quite clear it was one of the widely Presses universitaires de rasbourg Page 198 2(2): 191 – 210. doi: 10.30909/vol.02.02.191210 Volcanica to ‘continually active’; perhaps there is an implication
in Kircher that the flamy spire had been seen more than
once, but Scrope’s account represents a significant esca-
lation in volcanic activity. This theme is continued by
five more authors in the 19th century, while Daubeny
[1826] extends the metaphor further introducing ‘like
a lighthouse’ and ‘like Stromboli’. Daubeny is also the
first to use the word ‘volcano’, though the volcanic na-
ture of the Pico of Timor is implied in Kircher’s ‘flamy
spire’. to ‘continually active’; perhaps there is an implication
in Kircher that the flamy spire had been seen more than
once, but Scrope’s account represents a significant esca-
lation in volcanic activity. This theme is continued by
five more authors in the 19th century, while Daubeny
[1826] extends the metaphor further introducing ‘like
a lighthouse’ and ‘like Stromboli’. Daubeny is also the
first to use the word ‘volcano’, though the volcanic na-
ture of the Pico of Timor is implied in Kircher’s ‘flamy
spire’. just an expression for the sea. If we compared this event
with the minor eruption of Ritter Island in the Bis-
marck Sea in 1888 and the associated debris avalanche
which left just a small sliver of the island remaining
above sea level [Johnson 1987; Micallef et al. 2017],
Kircher’s description seems less incredible or unimag-
inable. Of course, if Kircher was referring to the mod-
ern island of Timor south of the equator, the descrip-
tion is fanciful. 5.3
Volcanic activity The part of Kircher’s description which has most cap-
tured the imagination of subsequent writers is the ref-
erence to the huge lake; 19 of the 28 later writers re-
fer to this lake (Table 1), while many fewer authors use
expressions such as “disappeared” or “nothing left be-
hind” or “entirely destroyed”. Scrope [1825] attempts
to avoid any illogicality by referring to “replaced by a
concavity” but he abandons this too in later editions. Wallace [1869] is the first author to mention no conse-
quences. No authors mention a tsunami, a quite prob-
able consequence of a sudden earthquake or eruption-
induced collapse of a large “flamy spire” on an island. Scrope [1825] and Daubeny [1826] also enlarge the
volcanic nature of the Pico, the former reporting that
it was “blown up” (and a “catastrophe”), the latter re-
ferring to a “violent eruption”. One or other of these
themes is continued by almost all 19th century re-
porters up to and including Mercalli [1907]. Wallace
[1869], fortified by his personal knowledge of Timor, is
able to report that Timor Peak was “blown up” in the
1638 eruption “and has since been quiescent”. While very few authors cite the source of their infor-
mation, Table 1 indicates the authors who introduced
new information to Kircher’s saga (blue cells) and those
that continued reporting specific elements of the story
(pink cells). Only Flexner and Flexner [2008] considers conse-
quences for humans, reporting that the cataclysmic
eruption killed hundreds of people in the area. While
this consequence seems based entirely on imagination,
perhaps owing something to the 2004 Aceh (Sumatra)
earthquake and tsunami, it makes reasonable sense;
one wonders why earlier authors had not thought to
mention consequences for humans. 5.6
Year of the event Almost all accounts assume the eruption of Timor, fol-
lowing Kircher [1665; 1669], occurred in the year 1638. However, Daubeny [1826] introduced the idea that the
eruption occurred in 1637. Whether this was an acci-
dental error or a view including information from an
additional source unknown to us we cannot discern. It is possible that Daubeny thought that Kircher’s
Catholic source in the Annals of the Society of Jesus
would have used a Gregorian calendar date, a calen-
dar not adopted by England until 1752. It is also possi-
ble that Daubeny had information suggesting the ‘erup-
tion’ occurred in the first three months of the year, a pe-
riod (1st January–25th March) that formed part of the
previous year until England switched from the Julian
calendar to the Gregorian, again in 1752. It is also pos-
sible that Daubeny’s information, from a source we are
unaware of, had already switched the date from 1638 to
1637, and that Daubeny himself knew nothing of this
change. This change in emphasis from earthquake to erup-
tion appears to begin with Scrope [1825] and Daubeny
[1826] and indicates that most subsequent accounts
probably relied on one or other of these widely-read
popular authors for their unsubstantiated information. ∗Wichmann [1918, p31] appears not to really believe the account
and notes that he has been unable to source the original 17th century
German accounts which he relied on. I have not found these accounts
either. 5.4
Earthquake The volcanic emphasis of all the 19th century and later
accounts is all the more remarkable in that Kircher’s
and subsequent early accounts are focused on the earth-
quake, rather than the eruption; as Kircher [1669]
noted Pico “had its very foundations shaken, by an hor-
rible Earthquake”. All 17th and 18th century accounts
describe the earthquake as “terrifying” or “shaking/
shattering” the foundations of the Pico/ Peak. The only
subsequent accounts that mention an earthquake are
those of Perrey [1858a] and Wichmann [1918], both of
whom cite Jesuit sources∗. 5.5
Consequences Kircher [1665; 1669] makes clear that the foundations
of the Pico on the island Timor were severely shaken;
the mountain was “wholly swall’ed up, together with
the iôand, leaving nothing behind it, but an huge
mighty lake”. In other words, the mountain and the
island disappeared beneath the sea. It seems illogical
to refer to a mighty lake remaining, but perhaps this is However, it seems much more likely that Daubeny
made a simple error in ascribing the event to 1637
and that this ‘error’ was repeated in the 1848 edi-
tion of his A description of active and extinct volcanos,
or earthquakes, and of thermal springs, copied by Pon-
ton in 1872, and continued in the
Royal Society re-
port on the Krakatau eruption of 1883 [Symons et al. ∗Wichmann [1918, p31] appears not to really believe the account
and notes that he has been unable to source the original 17th century
German accounts which he relied on. I have not found these accounts
either. Presses universitaires de rasbourg Page 199 The Eruption of Timor in 1638 Blong, 2019 1826, has been through 43 editions in English and Ger-
man, with the most recent in 2014 (http://worldcat. org/identities/lccn-no89017152/). While the num-
ber of editions of George Poulett Scrope’s Considera-
tions on volcanos . . . [1825] and Volcanoes . . . [1862]
is not known, his less popular The geology and extinct
volcanos of central France [1858] has been published
in 35 editions (http://worldcat.org/identities/
lccn-n84074013/). Both the Scrope and Daubeny
books of interest here are still in print. Their contri-
bution to the story of the eruption of Timor has been
far larger than the analysis here suggests, and it is pos-
sible that their published works are still contributing to
21st century versions of the eruption of Timor in 1638. 1888], and Lamb’s major work on the Dust Veil Index
[Lamb 1970]. However, both the 1888 and 1970 reports
give the date as 1637–1638, suggesting they used more
than one source for their information. Interestingly, the
1985 Carbon Dioxide Information Center (Oak Ridge
National Laboratory) version of Lamb’s 1970 Royal So-
ciety paper reverts to just the 1637 date. While this 1637 ‘error’ in dating the Timor event is
of little consequence, it does establish a chain of un-
acknowledged plagiarism from Daubeny [1826] to the
Royal Society [Symons et al. 8
Conclusions Table 1 suggests that Kircher’s accounts contain 14 in-
formation items (1665, blue cells). The dotted line in
Figure 4 shows the proportion of these 14 items that
have been repeated in the various accounts over the
last 350 years. Only once in the mid-18th century,
once in the mid-19th century, and in Wichmann’s early
20th century version [Wichmann 1918] have accounts
contained more than 50% of these items. The solid
line in Figure 4 indicates the total number of informa-
tion items in each account as a proportion of those in
Kircher’s accounts; thus, it is possible for an account to
exceed 100 % if all of Kircher’s items were included and
a few new details added. No account achieves this, but
the dubious honour of producing the biggest ‘gaps’ be-
tween the original and the current account is achieved
by Scrope [1825] who introduced four new items, and
Daubeny [1826] who added six new items. Kircher’s account of the eruption of Timor was repeated
in a few other publications by Jesuits in the 17th cen-
tury. A search of the literature, with all its limita-
tions, suggests there were few reports in the 18th cen-
tury. Then in the 19th century there is an outpouring
of accounts with numerous embellishments, the for-
mer likely reflecting the romanticism of nature com-
mon at that time. These additions turn the story of a
flamy spire into a continuing Stromboli-like eruption,
and imply that an eruption, possibly seen only once, be-
came a lighthouse for navigators. At the same time that
the story is ‘improved’ by an enhanced understanding
of the way some volcanoes erupt more or less contin-
uously, the fiction that the eruption can be seen from
a distance of 300 miles is maintained. At the same
time, Kircher’s emphasis on a ‘horrible earthquake’ is
neglected and the new focus is on a violent or paroxys-
mal eruption or the volcano being blown up. 5.5
Consequences 1888], with subsequent au-
thors acknowledging the 1888 source. Acknowledgements of Kircher’s account of the eruption of Timor, appears
to stem from these two writers. While these two au-
thors popularised, and ‘modernised’ the eruption story
to some extent with references to Stromboli, “like a
lighthouse”, “blown up”, and “violent eruption”, like
so many others they failed to indicate their sources of
information. As my interest in the 1638 eruption of Timor has ex-
tended for nearly five decades, I am indebted to many
scholars for assistance and thoughtful advice. With the
passage of time, many of them are no longer with us:
Fr Joseph Wicki, S.J., Jesuit Historical Institute, Rome;
Fr Hubert Jacobs, S.J., Jesuit Historical Institute, Rome;
Professor C R Boxer, Little Gaddesden, Herts., UK.;
Professor Anthony Disney, La Trobe University; Profes-
sor C R de Silva, University Park, Sri Lanka; Professor
Dauril Alden, University of Washington; Professor Jim
Fox, ANU; and Professor Jack Golson, ANU – the lat-
ter for his role as a sounding board in so many things
volcanic and archaeological. As Correia-Afonso [1969, pxxii], noted: Much of the perverted history of the past owes
its origin to the unscholarly if time-saving
device of passing on statements obtained at
second- or third-hand, without checking them
even when this could be done with ease, and
often without mentioning their purloined ori-
gin. I am also deeply indebted to Lucinda Coates for in-
numerable ferreting forays to the Macquarie University
library, and to a large number of anonymous librari-
ans at Macquarie University, University of Washington
(Seattle), the Mitchell Library (Sydney), the British Mu-
seum Library (London), and at the University of Cam-
bridge, and the Australian National Library (Canberra). My thanks also to Camilla Russell and her colleagues
who introduced me to the Archivum Romanum Soci-
etatis Iesu (ARSI) in Rome. This plea is all too true, but would the course of
Kircher’s story about an eruption on Timor in 1638
have been very different over the last 350 years if
sources had been quoted? The story would probably
have continued much as it did–embellished and mis-
understood. A story, possibly true, about a horrible
earthquake on a flamy spire and the disappearance of
a colossal cone would still have become a story about
a paroxysmal eruption of a Stromboli-like, continually-
active, volcano that collapsed. 7
Limitations In the late 19th and early 20th centuries some com-
mentators know enough about Timor to dismiss the
story, confidently stating that there are no volcanoes on
Timor, though there are still doubters adding dubious
locations for the 1638 eruption and creating histories
that combine a 1638 event with later ‘explosions’ from
mud volcanoes. Possibly it is unfair to suggest that Scrope, Daubeny and
others have shown the most imagination in adding to or
diverging from Kircher’s account. Some authors may
have found new sources of information (which they
have failed to acknowledge), or more precise (or likely)
terminology was introduced due to advanced under-
standing of volcanic eruptions. Nonetheless the 1883 eruption of Krakatau and the
associated global atmospheric phenomena lead to the
compilation of a list of the principal volcanic eruptions
between 1500 and 1886 by the Royal Society. This in-
cluded the 1637–1638 eruption of Timor and led to a
new phase of interest in dust veil indices and extended
reports of the eruption until at least 1985, albeit with-
out any of the details of a flamy spire, horrible earth-
quake, “swall’ed up”, engulfed, or a large lake. This overview is also unfair in that it probably down-
plays the role of several authors in spreading elements
of Kircher’s story and/ or in disseminating diverging
information about the eruption of Timor. In Table 1,
Appendix A and Figure 4 we have, at the most, in-
cluded only two editions of each author’s work. This
almost certainly undervalues the broad influence of
Scrope and Daubeny as extremely popular authors on
volcanology. For example, Charles Daubeny’s A de-
scription of active and extinct volcanos: with remarks on
their origin, their chemical phænomena, and the charac-
ter of their products, as determined by the condition of the
earth during the period of their formation: being the sub-
stance of some lectures delivered before the University of
Oxford, with much additional matter, first published in While the evidence is at best slender, the 19th cen-
tury interest in volcanic eruptions probably owes much
to the writings of Scrope and Daubeny and the nu-
merous editions of their popular books which remain
in print even today. As Table 1 indicates most of the
additional/new misinformation, indeed the corruption Presses universitaires de rasbourg Presses universitaires de rasbourg Page 200 2(2): 191 – 210. 7
Limitations doi: 10.30909/vol.02.02.191210 Volcanica Figure 4: The dotted line indicates the proportion of Kircher’s original information items retained in each account
during the following 350 years. The solid line compares the number of information items in the account, with
the number in Kircher’s account. Thus, the difference between the two lines shows the proportion of the account
that owes nothing to Kircher. Figure 4: The dotted line indicates the proportion of Kircher’s original information items retained in each account
during the following 350 years. The solid line compares the number of information items in the account, with
the number in Kircher’s account. Thus, the difference between the two lines shows the proportion of the account
that owes nothing to Kircher. Presses universitaires de rasbourg References Adams, G. (1912). “Timor Island; its supposed volcano
and its probable tectonic relations”. Philippines Jour-
nal of Science 7A.4, pp. 283–289. Baldwin, M. (2004). “Reverie in Time of Plague:
Athanasius Kircher and the Plague Epidemic of
1656”. The last man who knew everything. . . or did
he?: Athanasius Kircher, SJ (1602-80) and His World. Ed. by P. Findlen. London: Routledge, pp. 63–77. Earl, G. W. (1845). “On the Physical Structure and Ar-
rangement of the Islands of the Indian Archipelago”. Journal of the Royal Geographical Society of London 15,
p. 358. doi: 10.2307/1797916. p
– (1852). “Contributions to the physical geography of
south-eastern Asia and Australia”. The Journal of the
Indian Archipelago and Eastern Asia 6.5, pp. 243–277. Balfour, E. (1885). The Cyclopædia of India and of East-
ern and Southern Asia: Commercial, Industrial and Sci-
entific, Products of the Mineral, Vegetable, and Animal
Kingdoms, Useful Arts and Manufactures. Vol. 3. Lon-
don: B. Quartitch. Findlen, P. (2004). “Introduction”. The last man who
knew everything. . . or did he?: Athanasius Kircher, SJ
(1602-80) and His World. Ed. by P. Findlen. London:
Routledge, pp. 1–48. Barnes, R. H. (1982). “The Majapahit dependency
Galiyao”. Bijdragen tot de Taal-, Land-en Volkenkunde
4, pp. 407–412. Flexner, D. and S. B. Flexner (2008). The Pessimist’s
Guide to History: An Irresistible Compendium of Catas-
trophes, Barbarities, Massacres, and Mayhem—from 14
Billion Years Ago to 2007. 3rd. Harper Collins. Bassett, D. K. (1958). “English trade in Celebes, 1613-
1667”. Journal of the Malayan Branch of the Royal Asi-
atic Society 31.1, pp. 1–39. Î Forbes, J. D. (1830). “Physical Notices on the Bay of
Naples:—No. 6. the Bay of Baja”. The Edinburgh Jour-
nal of Science 2, pp. 75–102. Bellin, J. N. (1765). Carte Particuliere des Îsles Moluques. Paris. [Scale 1: 620,000 ]. Blong, R., S. Fallon, R. Wood, C. McKee, K. Chen, C. Magill, and P. Barter (2018). “Significance and tim-
ing of the mid-17th-century eruption of Long Island,
Papua New Guinea”. The Holocene 28.4, pp. 529–544. doi: 10.1177/0959683617735589. Glassie, J. (2012). A man of misconceptions: the life of an
eccentric in an age of change. New York: Penguin. GluedIdeas.com (n.d.). Volcanoes. url: http :
/ / gluedideas . com / content - collection /
cyclopedia-of-india-3/Volcanoes_P5.html (vis-
ited on 11/11/2019). [Free Resource of Historical In-
formation: Cyclopedia of India, Volume 3]. Blong, R., J. Kemp, and K. Chen (2016). Acknowledgements Essential as citations are
in modern scholarship it seems difficult to assume that
the plagiarism, embellishments, and misunderstand-
ings that have characterised the 350-year history of the
1638 eruption of Timor would have been any fewer if
every author had provided a source. I am most grateful to Laurie Drake, S.J., Ron Pa-
ton, Sandra Schuster, and Michael Barkhausen for var-
ious translations and to Rosemary Saul and Belinda
Chambers who typed and retyped my vast notes on the
eruption of Timor as the word processing art changed
over several decades last century. My sincere thanks to
Qianyang Chen who can do things with spreadsheets
that I can only dream about. Our best chance of understanding more about the
‘eruption of Timor in 1638’ probably lies in the
Archivum Romanum Societatis Iesu (ARSI) in Rome. While opinions about Athanasius Kircher range from
‘charlatan’ to ‘genius’ he did provide a source for his
information about the eruption. But did he report his
source accurately, embellish the information, or misun-
derstand it? This report has benefited enormously from the edi-
torial process. Alison Jolley, for Volcanica, has provided
friendly, positive comment and suggestions as has an
anonymous reviewer. Finally, I would like to thank
most seriously Kenneth L. Taylor, Emeritus Professor
in the Department of History of Science, University of Presses universitaires de rasbourg Page 201 Blong, 2019 The Eruption of Timor in 1638 on theRoebuck”. Terrae Incognitae 48.2, pp. 139–159. doi: 10.1080/00822884.2016.1211354. on theRoebuck”. Terrae Incognitae 48.2, pp. 139–159. doi: 10.1080/00822884.2016.1211354. Oklahoma, for his kindly, encouraging, insightful com-
ments that have not only enhanced the paper but also
markedly improved my understanding of Athanasius
Kircher and seventeenth century science. I am also ex-
tremely grateful to Jamie Farquharson for producing
Figure 1, and to those who made sense of the partial ref-
erences I provided for a number of early manuscripts. Bonney, T. G. (1899). “Volcanoes: their Structure and
Significance”. Nature 60.1541, pp. 27–28. doi: 10. 1038/060027b0. Bottoni, D. (1692). Pyrologia topographica, id est De
igne dissertatio Juxta loca cum eorum descriptionibus. Napoli: In publico Neapolitino Gymnasio Primarii
Philosophi{ae. [In Latin]. This work has not been supported by any funding
bodies. Boxer, C. R. (1947). The topasses of Timor. 24. Amster-
dam: Indisch Instituut. Data availability Correia-Afonso, J. (1969). “Jesuit letters and Indian his-
tory, 1542-1773”. Studies in Indian history and culture
of the Heras Institute of Bombay. 2nd. Vol. 20. Bombay:
Oxford University Press. All necessary data are included in Appendix A. y
Daubeny, C. (1826). A description of active and extinct
volcanos: with remarks on their origin, their chemical
phænomena, and the character of their products. Lon-
don: Philips and Parker. – (1848). A Description of Active and Extinct Volcanos, of
Earthquakes, and of Thermal Springs. London: Richard
and John E. Taylor. Daubeny, C. (1826). A description of active and extinct
volcanos: with remarks on their origin, their chemical
phænomena, and the character of their products. Lon-
don: Philips and Parker. Copyright notice © The Author(s) 2019. This article is distributed un-
der the terms of the Creative Commons Attribution 4.0
International License, which permits unrestricted use,
distribution, and reproduction in any medium, pro-
vided you give appropriate credit to the original au-
thor(s) and the source, provide a link to the Creative
Commons license, and indicate if changes were made. – (1848). A Description of Active and Extinct Volcanos, of
Earthquakes, and of Thermal Springs. London: Richard
and John E. Taylor. de Montbéliard, G. (1761). “Liste chronologique des
Éruptions de Volcans, des tremblements de terre,
de quelques faits météorologiques les plus remar-
quables, des cometes, des maladies pestilentielles,
&c. jusqu’en 1760. tirée des Mémoires des Académies
de l’Europe, des Ouvrages périodiques des Histoires
générales & des Relations particulières”. Collection
académique composée des mémoires, actes ou Journaux
des plus célébres Académies, pp. 488–681. [In French]. References Leipzig: Joh. Wittigau. [In Latin]. pp
[
]
– (1858b). “Deuxième note sur les phénomènes seis-
miques à Timor”. Nouvelles Annales des Voyages, de la
Géographie, de l’Histoire, et de l’Archéologie 6.4. Ed. by
A. Bertrand, pp. 303–305. [In French]. Johnson, R. W. (1987). “Large-scale volcanic cone col-
lapse: The 1888 slope failure of Ritter volcano, and
other examples from Papua New Guinea”. Bulletin
of Volcanology 49.5, pp. 669–679. doi: 10 . 1007 /
bf01080358. Pires, T. (1944). “The Suma Oriental of Tomé Pires: An
Account of the East, from the Red Sea to Japan, writ-
ten in Malacca and India in 1512—1515, and The
Book of Francisco Rodrigues, Rutter of a Voyage in
the Red Sea, Nautical Rules, Almanack and Maps,
Written and Drawn in the East before 1515.” Works
issued by the Hakluyt Society. Ed. by A. Cortesão. Vol. 2. 90. New York: Routledge. Kircher, A. (1665). Mundus Subterraneus. Amsterdam:
Joannem Janssonium & Elizeum Weyerstraten. [In
Latin]. ]
– (1669). The Volcano’s: or, Burning and Fire-vomiting
Mountains, Famous in the world: With their Remark-
ables. Colleed for the moõ part out of Kircher’s Sub-
terraneous World; And expos’d to more general view
in English, upon the Relation of the late Wonderful
and Prodigious Eruptions of Aetna. Thereby to occasion
greater admirations of the Wonders of Nature (and of the
God of Nature) in the mighty Element of Fire. London:
J. Darby for John Allen. Ponton, M. (1872). Earthquakes and Volcanoes: Their His-
tory, Phenomena, and Probable Causes. London: T. Nel-
son and Sons. Raspe, R. E. (1970). An introduction to the natural his-
tory of the terrestrial sphere, principally concerning new
islands born from the sea, and Hooke’s hypothesis of the
earth, on the origin of mountains and petrified bodies,
to be further established from accurate descriptions and
observations. Latin and English. Ed. and trans. by
A. N. Iversen and A. V. Carozzi. New York: Hafner
Press Publishing Co. [Translation of Specimen histo-
riae naturalis globi terraquei [1763]. Includes facsimile
of 1783 edition.] Kuenen, P. H. (1937). “Geological results”. Scientific
results of the Snellius Expedition in the eastern part of
the Netherlands East Indies, 1929-1930. Ed. by P. H. Kuenen, P. M. van Riel, J. P. H. Perks, F. Pinke, and H. Boschma. Lleiden: Brill. Lach, D. F. (1965). Asia in the making of Europe, I: The
century of discovery, Book 2. References “Dating
the Last Major Eruption of Long Island, Papua New
Guinea: The Evidence From Dampier’s 1700 Voyage Presses universitaires de rasbourg Page 202 Page 202 2(2): 191 – 210. doi: 10.30909/vol.02.02.191210 Volcanica Gould, S. J. (2004). “Father Athanasius on the Isthmus
of a Middle State: Understanding Kircher’s Paleon-
tology”. The last man who knew everything. . . or did
he?: Athanasius Kircher, SJ (1602-80) and His World. Ed. by P. Findlen. London: Routledge, pp. 207–237. – (1985). Volcanic Loading, the Dust Veil Index. Tech. rep. Oak Ridge National Laboratory, TN. Mennis, M. R. (1981). “Yomba Island: a real or mythical
volcano?” Cooke-Ravian Volume of Volcanological Pa-
pers. Geological Survey of Papua New Guinea Memoir
10, pp. 95–99. y P. Findlen. London: Routledge, pp. 207–237. – (2005). Yomba Island (Hankow Reef) : Atlantis of the
South Pacific : fact or fiction? Brisbane: Lalong Enter-
prises. Longmans, Green and Co. – (1887). Volcanoes and Earthquakes: A Popular Descrip-
tion of the Movements in the Earth’s Crust: from "The
Subterranean World". London: Longmans, Green and
Co. Mercalli, G. (1907). I vulcani attivi della terra:
morfologia-dinamismo-prodotti-distribuzione
geografica-cause. Milan: Ulrico Hoepli. [In Ital-
ian]. Hitchcock, E. (1841). Elementary Geology. New York:
Dayton and Saxton. Micallef, A., S. Watt, C. Berndt, M. Urlaub, S. Brune,
I. Klaucke, C. Böttner, J. Karstens, and J. Elger
(2017). “An 1888 Volcanic Collapse Becomes a
Benchmark for Tsunami Models”. Eos. doi: 10.1029/
2017eo083743. HMSO (1920). Dutch Timor and the lesser Sunda Islands. London: His Majesty’s Stationery Office. [Handbook
prepared under the direction of the historical section
of the Foreign Office, No 86]. Hooke, R. (1705). Lectures and discourses of eathquakes
and subterranean eruptions. Explicating the causes of
the rugged and uneven face of the Earth, and what rea-
sons may be given for the frequent finding of shells and
other sea and land petrified substances, scattered over the
whole terrestrial superficies. Ed. by R. Waller. London. [2nd ed., with a new introduction by T .M. Brown of
Princeton University]. Neumann van Padang, M. (1951). “Catalogue of the
active volcanoes of Indonesia, Part I”. Catalogue of the
active volcanoes of the world including solfatara fields. Napoli: International Volcanological Association. Perrey, M. A. (1858a). “Sur le Bibiluto: Volcan de LÎle
de Timor”. Nouvelles Annales des Voyages, de la Géo-
graphie, de l’Histoire, et de l’Archéologie 6.3. Ed. by A. Bertrand, pp. 129–136. [In French]. Ittig, M. T. (1671). De Montium Incendiis. References Volcanos: the Character of Their Phenomena,
Their Share in the Structure and Composition of the
Surface of the Globe, and Their Relation to Its Internal
Forces. With a Descriptive Catalogue of All Known Vol-
canos and Volcanic Formations. 2nd. London: Long-
man, Green, Longmans, and Roberts. g
– (1872). Über Vulkane. Der Charakter ihrer Phänomene,
ihre Rolle in dem Bau und in der Zusammenfeßung der
Erdoberfläche und iihre Beziehung zu den Kräften des
Inneren. Berlin: Robert Oppenheim. [In German]. Vatter, E. (1932). Ata kiwan, unbekannte bergvölker im
tropischen Holland. Leipzig: Bibliographisches Insti-
tut. [In German]. Siebert, H. (2004). “Kircher and His Critics: Censorial
Practice and Pragmatic Disregard in the Society of
Jesus”. The last man who knew everything. . . or did
he?: Athanasius Kircher, SJ (1602-80) and His World. Ed. by P. Findlen. London: Routledge, pp. 79–104. Verbeek, R. D. M. (1908). Rapport sur les Moluques:
Reconnaissances géologiques dan la partie orientale de
l’Archipel des Indes Orientales Néerlandaises. Vol. 1. 37. Batavia: Imprimerie de l’état. [Edition francaise du
Jahrboek van het Mijnwegen in Nederlandsch Oost-
Indië, 37, partie scientifique.] [In French]. Siebert, L., T. Simkin, and P. Kimberly (2010). Volca-
noes of the World. 3rd. Berkely–Los Angeles–London:
University of California Press. Waddell, M. A. (2006). “The World, As It Might Be:
Iconography and Probabilism in the Mundus sub-
terraneus of Athanasius Kircher”. Centaurus 48.1,
pp. 3–22. doi: 10.1111/j.1600-0498.2006.00038. x. Silver, E., S. Day, S. Ward, G. Hoffmann, P. Llanes,
N. Driscoll, B. Appelgate, and S. Saunders (2009). “Volcano collapse and tsunami generation in the Bis-
marck Volcanic Arc, Papua New Guinea”. Jour-
nal of Volcanology and Geothermal Research 186.3-4,
pp. 210–222. doi: 10.1016/j.jvolgeores.2009. 06.013. Wallace, A. R. (1869). The Malay Archipelago: The Land
of the Orang-utan, and the Bird of Paradise. A narra-
tive of travel, with studies of Man and Nature. London:
Macmillan and Co. St. John, H. S. R. (1853). The Indian archipelago: its his-
tory and present state. Vol. 2. London: Longman,
Brown, Green, and Longmans. Wallace, A. R. (1879). “Australasia”. Stanford’s Com-
pendium of Geography and Travel. Ed. by A. R. Wal-
lace. Trans. by A. H. Kean. London: Edward Stanford. [Based on Hellwald’s ‘Die Erde und Ihre Völker]. g
Suárez, T. (1999). Early mapping of Southeast Asia: the
epic story of seafarers, adventurers, and cartographers
who first mapped the regions between China and India. Singapore: Periplus Editions. Watt, S. F. et al. (2019). References Chicago and London: The
University of Chicago Press. Sapper, K. (1917). “Katalog der geschichtlichen
Vulkanausbrüche”. Schriften der Wissenschaftlichen
Gesellschaft in Strassburg 27, pp. iii–358. [In German]. – (1927). Vulkankunde. Vol. 3. Stuttgart: J. Engelhorns. [In German]. Lamb, H. H. (1970). “Volcanic dust in the atmosphere;
with a chronology and assessment of its meteorolog-
ical significance”. Philosophical Transactions of the
Royal Society of London. Series A, Mathematical and
Physical Sciences 266.1178, pp. 425–533. [
]
Schneider, K. (1911). Die vulkanischen Erscheinungen
der Erde. Berlin: Gebrüder Borntraeger. Presses universitaires de rasbourg Page 203 Page 203 The Eruption of Timor in 1638 Blong, 2019 Varenius, B., N. Sanson, R. Blome, and F. Lamb (1683). Cosmography and Geography, in Two Parts: The First,
Containing the General and Absolute Part of Cosmog-
raphy and Geography, Being a Translation From That
Eminent and Much Esteemed Geographer, Varenius. Wherein Are at Large Handled All Such Arts as Are Nec-
essary to Be Understood, for the True Knowledge Thereof. To Which Is Added the Much Wanted Schemes, Omit-
ted by the Author. The Second Part, Being a Geographi-
cal Description of the World, Taken From the Notes and
Works of the Famous Monsieur Sanson, Late Geographer
to the French King. To Which Are Added About an Hun-
dred Cosmographical, Geographical and Hydrographical
Tables of Several Kingdoms and Isles in the World, With
Their Chief Cities, Seaports, Bays, &c. Drawn From the
Maps of the Said Sanson. London: Samuel Roycroft. Scrope, G. P. (1825). Considerations on Volcanos: The
Probable Causes of Their Phenomena, the Laws which
Determine Their March, the Disposition of Their Prod-
ucts and Their Connexion with the Present State and
Past History of the Globe; Leading to the Establishment
of a New Theory of the Earth London: W Phillips Scrope, G. P. (1825). Considerations on Volcanos: The
Probable Causes of Their Phenomena, the Laws which
Determine Their March, the Disposition of Their Prod-
ucts and Their Connexion with the Present State and
Past History of the Globe; Leading to the Establishment
of a New Theory of the Earth London: W Phillips y f
g
of a New Theory of the Earth. London: W. Phillips. – (1858). The geology and extinct volcanos of central
France. London: J. Murray. – (1858). The geology and extinct volcanos of central
France. London: J. Murray. – (1862). Daubeny [1826, p322]: In the Island of Timor, the volcano of the peak
served, like that of Stromboli, as a sort of light-
house, seen at more than 300 miles distance. In 1637, this mountain, during a violent erup-
tion disappeared entirely: a lake at present
takes its place. ∗Kircher began work on Mundus Subterraneus perhaps a decade
before 1665. In November 1657 he published Iter ecstaticum ii (Sec-
ond Ecstatic Journey), a forerunner of Subterranean World [p67 Bald-
win 2004]. I have been unable to find a copy of this book–possibly it
refers to the eruption of Timor. Ittig [1671, p120]: There was also, in the island of Timor, a moun-
tain so high that its flaming summit was said
to be visible three hundred miles at sea. In the
year 1638 when its foundations were shattered
by a terrible earthquake, together with the is-
land, it was absorbed, leaving only a great lake
in its place, as the annals of the Society of Je-
sus record. (translated from the Latin in Per-
rey [1858a] provided by Adams [1912, p287]). There was also, in the island of Timor, a moun-
tain so high that its flaming summit was said
to be visible three hundred miles at sea. In the
year 1638 when its foundations were shattered
by a terrible earthquake, together with the is-
land, it was absorbed, leaving only a great lake
in its place, as the annals of the Society of Je-
sus record. (translated from the Latin in Per-
rey [1858a] provided by Adams [1912, p287]). de Montbéliard [1761, p564]: Le Pic de l’Isle Timor étoit si haut, qu’on voy-
ait à la distance de 300 milles les flammes qu’il
vomissoit; il fut englouti avec presque toute
l’Isle, et ne laissa en sa place qu’un grand lac. [in Sapper 1917, p198]. Kircher [1665, p181]: Erat & alius in Timor Insula Mons Picus
nomine, tantae altitudinus, ut per mil-
liaria
flammeus
in
mari
vertex
fe
con-
spiciendium praeberet; hic anno con-
cuffis per horrendum terraemotum funda-
mentis una cum Insula absorptus, nil praeter
ingentem lacum poõ fe reliquit. Ita referunt
Annales Soc. Jesu∗. [The Peak of Isle Timor was so high that the
flames it vomited were visible at a distance of
300 miles; it was engulfed with almost all the
Isle, and left in its place only a large lake]. Forbes [1830, p84]: In 1638, an island had also been formed off
St Michael’s, and this year was rather remark-
able for the occurrence of volcanic explosions. Not only this island was elevated, but we have
already noticed that an eruption of pumice
took place at the island of Santorini, and the
Peak, a very lofty volcanic mountain in the is-
land of Timor, one of the Moluccas, had its top
blown offby an explosion the same year, and
replaced by a lake. Hooke [1705, p307]: The Pico in the Moluccas, accounted of equal
height with that of Tenariff, was by a late
Earthquake quite swallow’d into the Earth,
and left a Lake in its Place. References “From catastrophic col-
lapse to multi-phase deposition: Flow transforma-
tion, seafloor interaction and triggered eruption fol-
lowing a volcanic-island landslide”. Earth and Plane-
tary Science Letters 517, pp. 135–147. doi: 10.1016/
j.epsl.2019.04.024. Symons, G. J., J. W. Judd, S. R. Strachey, W. J. L. Whar-
ton, F. J. Evans, F. A. R. Russell, D. Archibald, and
G. M. Whipple (1888). The eruption of Krakatoa, and
subsequent phenomena. London: Trübner & Co. Wichmann, A. (1918). The earthquakes of the Indian
Archipelago until the year 1857. Vol. 20. 4. Ams-
terdam. The Royal Geographical Society (1913). “Tectonic Re-
lations of Timor”. The Geographical Journal 41.4,
pp. 385–386. [with the Institute of British Geogra-
phers]. “Documenta Indica III (1553-1557)” (1954). Monu-
menta Historica SI 3. Ed. by I. Wicki. [In Latin]. Tibbets, G. R. (1981). Arab Navigation in the Indian
Ocean before the Coming of the Portuguese. Vol. 42. London: Royal Asiatic Society of Great Britain and
Ireland. [Translation of Kit¯ab al-faw¯aidfı us¯ul al-
bahr wa’l-qaw¯a’id of Ahmad b. M¯ajid al-Najdı]. “Documenta Indica VI (1563-1566)” (1960). Monu-
menta Historica SI 6. Ed. by I. Wicki. [In Latin]. “Documenta Indica XI (1577–1580)” (1970). Monu-
menta Historica SI 11. Ed. by I. Wicki. [In Latin]. Wilson, J. R. (1906). San Francisco’s Horror of Earth-
quake and Fire: Terrible Devastation and Heart-rending
Scenes... to which is Added Graphic Accounts of the
Eruptions of Vesuvius and Many Other Volcanoes, Ex-
plaining the Causes of Volcanic Eruptions and Earth-
quakes. Memorial Publishing Company. van Bemmelen, R. W. (1949). The Geology of Indonesia,
Volume 1A, General Geology of Indonesia and Adjacent
Archipelagoes. The Hague: Government Printing Of-
fice. Presses universitaires de rasbourg Page 204 Page 204 2(2): 191 – 210. doi: 10.30909/vol.02.02.191210 Volcanica Worcester, D. C. (1914–1915). “Review of recent vul-
canological literature”. Zeitschrift für Vulkanologie
1.1, pp. 126–127. [Includes review of The Royal
Geographical Society article in Geographical Journal
[1913], Vol. 41, pages 385–386]. afforbuit, lacusque folus remanfit, mirabilique
evétu mare in terram conversum eft. [The peak of the island Timor, conspicuous for
300 miles at sea, was absorbed after a terrify-
ing earthquake; leaving only a lake, the mirac-
ulous event turned the land into the sea]. Zurcher, F. and E. Margollé (2012). Volcanoes and earth-
quakes, ancient and modern. Trans. by W. Lockyer. Cambridge: Cambridge University Press. doi: 10 . 1017/cbo9781139226806. [Translation of 1868 edi-
tion published by Blackie and Son, London.] Kircher [1669, p13]: Such a catastrophe destroyed in the year 1638,
a colossal cone called the Peak, in the isle of
Timor, one of the Moluccas. The whole moun-
tain, which was before this continually active,
and so high that its light was visible, it is said,
three hundred miles off, was blown up and re-
placed by a concavity now containing a lake. The Mountain Pico in the Iôand Timor, of such
an height, that a flamy Spire or Pyramid was seen
for three hundred miles in the Sea. This in the
year , had its very foundations shaken, by
an horrible Earthquake; and was wholly swal-
low’d up, together with the Iôand, leaving noth-
ing behind it, but an huge mighty Lake. So the
Annals of the Jesuites Society relate. A
Appendix 1 Direct quotations from the named sources are inset. Inset items in [ ] are translations of the quotations. Paragraphs that are not inset are generally commen-
taries provided by the named authors. ∗According to Sapper [1917, p198], Daubeny was thinking of Fire
Mt, near Wetar. This inference, perhaps correct, seems to be based on
the juxtaposition of two sentences. Daubeny [1848, p402]: In the island of Timor itself the volcano of the
peak served, like that of Stromboli, as a sort of
lighthouse, seen at more than 300 miles dis-
tance. In 1637 this mountain∗, during a vio-
lent eruption, disappeared entirely; a lake at
present takes its place. †Repeated in Scrope [1872] Über Vulkane. The wording differs a
little in the various editions of Scrope’s books. See also Adams [1912,
p284]. p
]
‡Reference is to translation of 1868 edition
§ §Supporting comments are made on p17 and p210. Statements
similar to that above are also made in subsequent editions. Earl [1852, p264]: In the first half of this paper, reprinted from the
Transactions of the Royal Geographical Society [Earl
1845, p358] Earl refers to an active volcano near the
east end of Timor and refers to the chain of islands
extending from Java to Timor as being of the same
volcanic character. However, his accompanying map
shows no active volcanoes on Timor and shows Timor
as being amongst his "areas of upheaval" rather than
amongst his "volcanic formations". Wallace [1869, p193]: Wallace [1869, p193]: It
differs,
however,
very
remarkably-
textcitepp[][p
from
all
the
other
islands
of the chain in not possessing any active
volcanoes, with the one exception of Timor
Peak near the centre of the island, which was
formerly active, but was blown up during
an eruption in 1638 and has since been
quiescent.§ It
differs,
however,
very
remarkably-
textcitepp[][p
from
all
the
other
islands
of the chain in not possessing any active
volcanoes, with the one exception of Timor
Peak near the centre of the island, which was
formerly active, but was blown up during
an eruption in 1638 and has since been
quiescent.§ Hitchcock [1841]: The 26th or 27th of December, 1856, the
mountain Iloen Bano in the western part of
Timor erupted causing the death of two per-
sons struck by stones which the volcano threw
out. The account from which we are borrow-
ing these details is all the more remarkable
since it is the first notice of eruption of a vol-
cano in Timor, or at least in the western part
of the island. In 1638, the Pic, a volcano in the Island of
Timor, so high as to be visible 300 miles, dis-
appeared, and in its place is now a lake. Perrey [1858a]: There was also, in the island of Timor, a moun-
tain so high that its flaming summit was said
to be visible three hundred miles at sea. In the
year 1638 when its foundations were shattered
by a terrible earthquake, together with the is-
land, it was absorbed, leaving only a great lake
in its place, as the annals of the Society of Jesus
record [in Adams 1912, p287. Perrey, writing
in Latin, cites Ittig as his source]. Bottoni [1692, p239]: Bottoni [1692, p239]: Insulam Timor mons Picus per mill. in
mari conspicuus poõ horribilem terremotum Insulam Timor mons Picus per mill. in
mari conspicuus poõ horribilem terremotum Presses universitaires de rasbourg Presses universitaires de rasbourg Page 205 Page 205 The Eruption of Timor in 1638 Blong, 2019 Zurcher and Margollé [2012, p133-134]: Zurcher and Margollé [2012, p133-134]: Zurcher and Margollé [2012, p133-134]: In 1638, the colossal cone, called the Peak, in
the Isle of Timor, disappeared entirely, and
was replaced by an abyss now containing a
lake. Until then this volcano, in continual ac-
tivity, served as a lighthouse to mariners. ‡ Wallace [1869, p193]: Scrope [1862, p463]: The great peak of Timor once served, like
Stromboli, as a lighthouse to mariners, being,
from its vast height, visible at a distance of 300
miles. In 1638 a prodigious eruption blew off
the greater part of the cone and replaced it by
a large lake. It will be remarked that this is an
event of frequent occurrence among the pow-
erful volcanos of this quarter of the globe. (1st
edition)† In my essay of 1845 I have pronounced the
peaked mountain at the north-east extreme of
Timor to be in a state of activity, having been
induced to do so by the reports of natives of
the adjacent island Kissa, and from my having
on two several occasions seen the summit of
the mountain in a state of ignition, but I have
since been informed by gentlemen connected
with the Portuguese settlements in Timor, that
there are no active volcanoes in the eastern
part of the island. I must therefore have been
deceived by the burnings of the jungle which
the natives make toward the close of the year,
for the purpose of clearing new lands for cul-
tivation. Ponton [1872, p231]: In 1638, the summit of the peak of Timor,
which might be seen like a light-house from a
distance of 270 miles, exploded, and blew up
into the air, and the water collecting, formed
a lake in the enormous void caused by the ex-
plosion. In Timor, the most easterly of these islands,
there was once a mountain named the Peak,
which used to be a volcano in constant activ-
ity, like Stromboli. It served as a lighthouse to
mariners in those seas, being visible at a dis-
tance of 300 miles. During a great eruption
in 1637, however, the mountain disappeared
bodily, leaving a lake in its place. St. John [1853, p20]: With reference to Timor: “No volcanoes are
found, and no traces of their action: conse-
quently there is, in the aspect of the country,
little to attract”. With reference to Timor: “No volcanoes are
found, and no traces of their action: conse-
quently there is, in the aspect of the country,
little to attract”. Javasche Courant, May 9, 1857 [in Adams 1912, p287]: Javasche Courant, May 9, 1857 [in Adams 1912, p287]: Presses universitaires de rasbourg Page 206 Page 206 Volcanica 2(2): 191 – 210. doi: 10.30909/vol.02.02.191210 ‡The source given by Mercalli for Perrey’s publication is different
to that given here. Mercalli [1907, p313]: Il vulcano dell’isola Timor fece una grande
eruzione esplosiva nel 1638: altra violentis-
sima eruziona esplosiva avenne al vulcano
Floen-Bano, nella parta occidentale di Timor,
il 26 dicembre 1856; infine una terza eruzione
ebbe luogo al vulcano di Bibiluto nel maggio
1857 (Perrey). Hartwig [1871, p68]: The Javan line is continued from Soumbava by
Sangeang, another Stromboli, through the Flo-
res Islands to Timor, in which the existence of
volcanoes has been doubted; there must, how-
ever, be a very few, for one in the western part
of the island is said to have been in eruption in
1856 and in the following year; there are also
some mud volcanoes, but nothing calling for
special attention. In the year 1638 a colossal cone called the
Peak, in the Isle of Timor, one of the Moluc-
cas, was entirely destroyed by a paroxysmal
explosion. The whole mountain, which was
before this continually active, and so high that
its light was visible, it is said, three hundred
miles off, was blown up and replaced by a con-
cavity now containing a lake.∗ Mercalli also quotes Scrope and notes further (p313): Nel 1856, due persone vennero uccise dalle
pietre che lanciava il volcano di Timor. La
eruzione del 1857 venne accompagnata da ter-
remoti fortissimi e da sprofondamenti dell
suolo che fecero perire 36 persone (Perrey). -
Probablimenta tutte quests eruzioni sono da
riferirsi a uno stesso volcano che porta diversi
nomi. Wallace [1879, p429]: It is generally considered that there are no
volcanoes in Timor, and none were known
to Mr Crawfurd when he compiled his valu-
able Dictionary. Mr. Scrope, however, in his
work on volcanoes, speaks of Timor Peak as
a mountain of great height, continually active
before the year 1638, when it was blown up
during an eruption, and replaced by a crater-
formed lake. Previous to this eruption the
mountain was said to be visible 300 miles off,
and was therefore probably the loftiest in the
archipelago. Gunong Allas, about the mid-
dle of the south coast, is marked on the latest
Dutch maps as being 11,500 feet high†. [The volcano of the island of Timor made a
grand explosive eruption in 1638, another vi-
olent explosive eruption occurred at the vol-
cano Floen-Bano in the Western part of Timor
the 26th of December, 1856; finally a third
eruption took place in the Volcano Bibuluto
in May 1857 (Perrey)‡ – translation in Adams
[1912, p285]]. Mercalli also quotes Scrope and notes further (p313): Balfour [1885]: [Timor] has only one active Volcano, Timor
Peak, near the centre of the island, which was
blown up during an eruption in 1638, and has
since been quiescent. p
, p
†The above is repeated with minor differences in earlier editions.
The source given by Mercalli for
to that given here. ∗Repeated verbatim in 1887, p86–87.
† ∗Repeated verbatim in 1887, p86–87.
†The above is repeated with minor differences in earlier editions.
‡The source given by Mercalli for Perrey’s publication is different
to that given here. †The above is repeated with minor differences in earlier editions. ∗, p286 points out that this event occurred on Pulo Camby, a
small island north of Timor. However, Wichmann [1918, p173–174]
reports an earthquake around 10.30am on May 13, 1857 felt severely
in Dili (the centre of government in Portuguese Timor) which also led
to an eruption of the mud volcano at Bibiluto and to a tsunami. Later
on the same morning on Pulu Kambing “23 men, 13 women and an
indeterminate amount of children departed this life”. Cambing or
Kambing are synonyms for the island of Artauro, a few km north of
Dili. §Cambing or Kambing are synonyms for the island of Ar-
tauro, a few km north of Dili, the capital of East Timor [Boxer
1947; Kuenen 1937].
Alternatively, this could also be a refer-
ence to Pulau Komba, also known as Pulu Komba and Batu Tara
some 50 km north of Lomblen.
However, the only known erup-
tion of this island, a small eruption, was from 1847 to August
1852.
No fatalities are recorded in the Smithsonian catalogue
(http://volcano.si.edu/volcano.cfm?vn=264260). The Royal Geographical Society [1913, p385–386]: The Royal Geographical Society [1913, p385–386]: Schneider’s catalogue of volcanoes gives Floen-Bano
as the name of the volcano in Timor, its longitude and
latitude are stated as 126 °30’E, 8 °50’S and its location
is given on a map (p190) as being in the eastern part of
the island even though Mercalli had stated that Floen
Bano is in the western part. The dates of the eruption
of this volcano are given as 1638? 1856 and 1857. The height of the volcano is given as 2400m [see also
Adams 1912, p286]. Prof. George I Adams ... has come to the con-
clusion that Timor must be definitely struck
offthe list of volcanic islands (Philippine Jour-
nal of Science, vol. 7, Sect. A, No. 4,
1912). The current misconception seems to
have been due principally to a statement in
Scrope’s well-known work on volcanoes to the
effect that in 1638 a colossal cone in Timor
was entirely destroyed by a volcanic catastro-
phe. This has been repeated by others, who
have also referred to supposed eruptions of
later date. The only basis for the idea seems to
be the existence of a so-called "mud-volcano",
which Prof. Adams visited. In his view its
activity, with other supposed manifestations
of volcanic force, has been a result of earth-
quake shocks. The original source of Scrope’s
statement appears to be Iltig’s [sic] "De Mon-
tium Incendiis" (Leipzig, 1671), the Jesuit an-
nals being there given as the authority; and it
may be suggested that there was here a confu-
sion between Timor and some other island of
the archipelago. Prof. Adams makes no refer-
ence to Kotó’s memoir on the geologic struc-
ture of the Malay Archipelago (Journ. Tokyo
Coll. Sci., vol. 11, part 2)[1899], in which the
same conclusion as to the non-volcanic char-
acter of Timor is arrived at. †However, St. John [1853, p20] noted, regarding Timor: “No vol-
canoes are found, and no traces of their action”. See also, Earl [1852].
‡Adams [1912, p284] cites Scrope: “Such a catastrophe destroyed
in the year 1638 a colossal cone, called the Peak, in the Isle of Timor,
one of the Moluccas. The whole mountain, which was before this
continually active and so high that its light was visible, it is said, three
hundred miles off, was blown up and replaced by a concavity now
containing a lake”. Adams does not cite a year or other details for
the reference to Scrope’s book though we know that many editions
appeared. †However, St. John [1853, p20] noted, regarding Timor: “No vol-
canoes are found, and no traces of their action”. See also, Earl [1852]. Symons et al. [1888, p385]: In the List of principal ascertained volcanic erup-
tions from 1500 to 1886, one item says simply “Timor
1637–38”. There is no entry in the adjacent “List of
unusual atmospheric phenomena, such as blue suns,
dry fogs, and red twilights, and general remarks.” Bonney [1899, p230]: Bonney [1899, p230]: Presses universitaires de rasbourg Page 207 Page 207 The Eruption of Timor in 1638 Blong, 2019 [In 1856 two people were killed by stones
hurled out by the volcanos of Timor. The
eruption of 1857 was accompanied by a strong
earthquake and a fissuring of the ground
which caused the death of 36 people (Per-
rey)∗. Probably all these eruptions should be
referred to one volcano which bears different
names. – translation in Adams [1912, p285]]. Portuguese governor of Timor describing earthquakes
was sufficient proof of the existence of volcanic activity. He further notes that the 36 people reported killed in
1857 were on Pulo-Cambay [Pulau Kambing?] a small
island to the north of Timor§. Adams surmises that
Perrey overlooked the fact that "Pulo" means "island". He describes a visit to a mud volcano near Viqueque
[8°52’ S, 126°22’ E] and believes that this is the volcano
referred to by Perrey. Portuguese governor of Timor describing earthquakes
was sufficient proof of the existence of volcanic activity. He further notes that the 36 people reported killed in
1857 were on Pulo-Cambay [Pulau Kambing?] a small
island to the north of Timor§. Adams surmises that
Perrey overlooked the fact that "Pulo" means "island". He describes a visit to a mud volcano near Viqueque
[8°52’ S, 126°22’ E] and believes that this is the volcano
referred to by Perrey. Schneider [1911, p241]: Schneider [1911, p241]: Presses universitaires de rasbourg Worcester [1914–1915, p127]: der Nachtricht von 1638 eine Verwechslung
vorliegt, wie schon Daubeny und neuerdings
Adams vermutete. Daubeny (der allerdings
1637 schrieb) dachte an den Goenoeng Api bei
Wetar. ∗ der Nachtricht von 1638 eine Verwechslung
vorliegt, wie schon Daubeny und neuerdings
Adams vermutete. Daubeny (der allerdings
1637 schrieb) dachte an den Goenoeng Api bei
Wetar. ∗ Professor George S. Adams recently made
a
visit
to
the
island
of
Timor,
Malay
Archipelago, and from observations he states
that the volcanic character of the island (i.e. as far as active volcanoes are concerned), has
been misconcepted. He alludes to the erup-
tion, mentioned by Scrope in his work on Vol-
canoes, of 1638, whom he says seems to have
obtained this information from Iltigs [sic.] "De
Montium Incendis" (Leipzig, 1671) which has
probably been confounded from an eruption
on a neighbouring island. Furthermore admit-
ting the existence of a "mud volcano", which
Prof. Adams visited the traveller comes to
the conclusion that in the linear Volcanic belt,
which extends through the east Idian [sic.] Is-
lands, the island of Timor should be dropped
out. This appears to be a sweeping statement,
as the writer of this review is cognisant of the
fact that there were eruptions from Timor as
recently as 1856 and 1857. Therefore a more
satisfactory explanation would be required to
"fully" substantiate the statement made by
Prof. Adams. [1638. The peak of Timor island is so high,
that one can see it from a distance of 300 miles
the flames which it vomits out; almost all of
the island was engulfed leaving in its place a
great lake. 1856, 26/27 Eruption of the Iloen-Bano in
west Timor. Two were killed by stones. 1857, May Eruption of Bibiluto. Perrey spoke
from official Portuguese reports of the numer-
ous shocks from the 15th May of this year and
a strong sinking whereby the villages of Mac-
dadi with 36 people disappeared; also a part
of the Rainha de Viqueque was destroyed. G. S. Worcester [1914–1915, p127]: [sic] Adams has now put forward another
point of view, that there are no true volca-
noes in Timor, so I turned to the person who
had the best knowledge of the island, my dear
friend G A F Molengroff, who stated, that no
volcano occurs in the island of Timor, but only
mud volcanoes, which however according to
Rotti and Saman, “often have considerable
eruptions and besides gas hurl forth much
mud and pieces of rock”. Of such eruptions
are all reports of 1856 referred to, on the ef-
fect of this shock, during by the news of 1638 a
confusion is put forward; as already Daubeny
and more recently Adams surmised. Daubeny
(who certainly writing of 1637) thought of Fire
Mt. near Wetar (Gunung Api)]. Adams [1912]: Adams’ paper, entitled "Timor Island;
its supposed
volcano and its probable tectonic relations" was the
first to argue that there was no volcano on Timor†. He cites Scrope’s book (a different edition to the one
cited above)‡ and the quotations noted above from
Bonney [1899], Mercalli [1907], and Schneider [1911]. Adams traces the source of the error concerning a
1638 eruption to Ittig [1671]. He traces information
concerning the supposed 1856 and 1857 eruptions to
Perrey [1858a; 1858b] whose original source for the
1856 account seems to have been the May 9, 1857
Javasche Courant. Adams [1912, p286–287] believes that the 1856 ac-
count stems from the misinterpretation of earthquake
phenomena that are then attributed to a volcanic
eruption. He also notes that the mountain is called
Iloen Bano and not Floen Bano as written by Mercalli
and those who followed him. He also believes that
Perrey was misled by assuming that the incidental
mention of "volcanoes" in a non-technical report by the Presses universitaires de rasbourg Page 208 2(2): 191 – 210. doi: 10.30909/vol.02.02.191210 Volcanica ∗Sapper [1927, p330] is quite different to the above. Sapper [1917, p198]: Fur die ausserhalb der eigentlichen Vulkan-
zone der kleinen Sunda-Inseln liegende Insel
Timor gibt es mehrere Ausbruchnachrichten
in de Literatur: 1638 [Here Sapper quotes the French source,
de Montbéliard [1761]] 1638 [Here Sapper quotes the French source,
de Montbéliard [1761]] 1856, [no month given] 26./27., Ausbruch des
Iloen-Bano in West-Timor. Zwei Menschen
durch Steine gettet. 1856, [no month given] 26./27., Ausbruch des
Iloen-Bano in West-Timor. Zwei Menschen
durch Steine gettet. Flexner and Flexner [2008, p77]: Flexner and Flexner [2008, p77]: 1638: Indonesian Volcano Explodes. Located
on the island of Timor in modern-day Indone-
sia, the 10,500 foot volcano peak blew itself
apart in a cataclysmic eruption, killing hun-
dreds of people in the area” Even more remarkably, 165 km west north west of
Ritter Island, Mary Mennis [1981; 2005] has collected
dozens of oral histories about a volcano called Yomba
that erupted, created a large tsunami, and entirely
disappeared beneath the waves a generation or two
before the VEI 6 eruption of nearby Long Island (fairly
securely dated to 1651–1671 C.E. – Blong et al. [2018]). The location of Yomba has never been accurately deter-
mined but it is generally believed to be at Hankow Reef
(4.88 °S, 146.72 °E) and, somewhat surprisingly, Yomba
has been assigned a volcano number in the GVP cata-
logue (http://volcano.si.edu/volcano.cfm?vn=251041). GluedIdeas.com [n.d.]: Timor, in violent eruption 1638, and a lake
formed and peak disappeared. Timor, in violent eruption 1638, and a lake
formed and peak disappeared. und Ober-Kaufmanns-Dienste.
Stulzbach-
Nürnberg 1686, p. 93-97.] und Ober-Kaufmanns-Dienste. Stulzbach-
Nürnberg 1686, p. 93-97.] und Ober-Kaufmanns-Dienste. Stulzbach-
Nürnberg 1686, p. 93-97.] und Ober-Kaufmanns-Dienste. Stulzbach-
Nürnberg 1686, p. 93-97.] p204]. While none of these island volcanoes have
eruptions in the relevant timeframes recorded in the
Smithsonian catalogue there are eruptions recorded
in the accounts of early navigators in the area that
need to be sorted out. Other possibilities include the
1538 eruption of Gamalama (on Ternate), or to another
eruption in Indonesia or even further afield which has
so far escaped our notice. In each case some or other
details of Kircher’s account seem to be at odds with
eruption characteristics we might expect, though this
need not necessarily imply that the story is fanciful. HMSO [1920, p2]: It is not now believed that there are any vol-
canoes, but there are numerous mud geysers,
perhaps the sign of former volcanic activity. Lamb [1985, p9]: Lamb [1985, p9]: Lamb [1985, p9]: No
iven 1637. A reprint and update of Lamb [1970]. N
further details are provided, but the date is now giv
as 1637. 1637. A reprint and update of Lamb [1970]. N
further details are provided, but the date is now giv
as 1637. B
Appendix 2 Could Kircher’s eruption be like the eruption of
Yomba? Could Yomba be Kircher’s eruption, even
though it is about 2300 km east of Timor? That is
fanciful–unless we can find accounts of unknown (Eu-
ropean?) navigators that not only ventured along the
north coast of mainland Papua New Guinea between
the voyages of Schouten and Le Maire in 1616 and
Abel Tasman in 1642 but also corresponded (directly
or indirectly) with Jesuits in Rome. My personal views of Kircher’s story are complex. I am
intrigued by the possibility that such an eruption may
have occurred. While I am sure there are no volcanoes
on Timor I find it hard to conclude that his account
is entirely fanciful. Kircher’s story could refer to the
1638 eruption of Raung (east Java), to one or more
eruptions of Gunungapi Wetar (about 200 km north
of Timor in the Banda Sea), Banda Api, or even Batu
Tara on Komba Island, about 50 km north of Lembata
(Figure 1). All three of these volcanoes are on early
European sea routes to the Spice Islands [Pires 1944, Our best chance of finding out more about Kircher’s
1638 eruption of Timor probably lies in the Jesuit
archives. Presses universitaires de rasbourg Wichmann [1918, p31]: (no date). Timor. The fear of the moun-
tain and the other on the Island, named Pi-
cus, elevation so great that it was visible, and
fiery in this case, to the top from 300 miles
in the sea; the year 1638 an earthquake shook
the foundations together with the island was
swallowed up by a horrible thing, that had left
behind nothing but a huge lake. Thus refer-
ence Annals Soc. Jesus 6) 1857, Mai, Ausbruch des Bibiluto. Per-
rey spricht nach offiziellen portugiesischen
Berichten von zaheeichen Beben seit dem
15. Mai d. J. und einer starken Senkung,
wodurch das Dorf Macdadi mit 36 Personen
verschwand; auch ein teill van Rainha de
Viqueque wurde zerstrt. 1857, Mai, Ausbruch des Bibiluto. Per-
rey spricht nach offiziellen portugiesischen
Berichten von zaheeichen Beben seit dem
15. Mai d. J. und einer starken Senkung,
wodurch das Dorf Macdadi mit 36 Personen
verschwand; auch ein teill van Rainha de
Viqueque wurde zerstrt. Da nun aber G.S. Adams die Ansicht ver-
tritt, dass es echte Vulkane auf Timor nicht
gibt, so wandte ich mich um Auskunft an den
besten Kenner dieser Insel, meinen verehrten
Freund G.A.F. Molengroff, der mir bestätigte,
dass auf der Insel Keine Vulkane vorkom-
men,
sundern nur Schlamm-vulkane,
die
ebenso wie die von Rotti und Saman "oft
heftige Eruptionen haben und nebst Gas viel
Schlamm und Gesteinsstcke ausschleudern". Auf solche Ausbruche sind jedenfalls die
Nachtrichen von 1856 zurűcksufűhren, die
von 1857 auf Bebenwirkungen, während bei Despite many-fold attempts it has not been
possible to procure for myself the volumes of
Litterae annuae taken into account, in order to
understand the original relation. I can thus
only repeat 7) that the record sounds very im-
probable, as there is no volcano known on
Timor. Despite the exaggeration 8) it is still
possible that this is a case of a mix-up. [All
these footnotes refer to: Joh. Sigmund Wurff-
bain. Vierzehn Jährige Ost-Indianische Krieg- Presses universitaires de rasbourg Page 209 The Eruption of Timor in 1638 Blong, 2019 Blong, 2019 Lamb [1970, p502]: Lamb [1970, p502]: 1637–8 Timor. 9-10 °S 124-7 °E. No estimate
of the Dust Veil Index are given. Royal Soci-
ety Krakatoa Volume 1888 “List of principal
ascertained volcanic eruptions from 1500 to
1886” is given as the source. Could the account instead refer to the subsidence of
an area between Lembata and Pantar for which Barnes
[1982] records a patchy oral history and which Vatter
[1932] thought occurred mid- or late-17th century? In 1888, about 2500 km to the east of Timor, Ritter
Island in the Bismarck Sea to the north of mainland
Papua New Guinea collapsed producing a small erup-
tion, a large tsunami, and leaving just a sliver of the
original island remaining above sea level [Johnson
1987; Micallef et al. 2017; Silver et al. 2009; Watt
et al. 2019]. Does this type of event sound more like
Kircher’s eruption of Timor? Repeated verbatim from Balfour [1885, p1033]. Repeated verbatim from Balfour [1885, p1033]. Presses universitaires de rasbourg Page 210 Page 210
|
https://openalex.org/W2134412337
|
https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1000163&type=printable
|
English
| null |
Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq
|
PLOS genetics
| 2,008
|
cc-by
| 18,559
|
Abstract Funding: This work was supported by the core strategic grant of the BBSRC to the Hinton lab, and funds from the DFG Priority Program SPP1258 Sensory and
Regulatory RNAs in Prokaryotes to the Vogel lab. Funding: This work was supported by the core strategic grant of the BBSRC to the Hinton lab
Regulatory RNAs in Prokaryotes to the Vogel lab. Competing Interests: The authors have declared that no competing interests exist. Competing Interests: The authors have declared that no competing interests exist. Competing Interests: The authors have declared that no competing interests exist. * E-mail: jay.hinton@bbsrc.ac.uk (JCDH); vogel@mpiib-berlin.mpg.de (JV) * E-mail: jay.hinton@bbsrc.ac.uk (JCDH); vogel@mpiib-berlin.mpg.de (JV) Abstract Recent advances in high-throughput pyrosequencing (HTPS) technology now allow a thorough analysis of RNA bound to
cellular proteins, and, therefore, of post-transcriptional regulons. We used HTPS to discover the Salmonella RNAs that are
targeted by the common bacterial Sm-like protein, Hfq. Initial transcriptomic analysis revealed that Hfq controls the
expression of almost a fifth of all Salmonella genes, including several horizontally acquired pathogenicity islands (SPI-1, -2, -
4, -5), two sigma factor regulons, and the flagellar gene cascade. Subsequent HTPS analysis of 350,000 cDNAs, derived from
RNA co-immunoprecipitation (coIP) with epitope-tagged Hfq or control coIP, identified 727 mRNAs that are Hfq-bound in
vivo. The cDNA analysis discovered new, small noncoding RNAs (sRNAs) and more than doubled the number of sRNAs
known to be expressed in Salmonella to 64; about half of these are associated with Hfq. Our analysis explained aspects of
the pleiotropic effects of Hfq loss-of-function. Specifically, we found that the mRNAs of hilD (master regulator of the SPI-1
invasion genes) and flhDC (flagellar master regulator) were bound by Hfq. We predicted that defective SPI-1 secretion and
flagellar phenotypes of the hfq mutant would be rescued by overexpression of HilD and FlhDC, and we proved this to be
correct. The combination of epitope-tagging and HTPS of immunoprecipitated RNA detected the expression of many
intergenic chromosomal regions of Salmonella. Our approach overcomes the limited availability of high-density microarrays
that have impeded expression-based sRNA discovery in microorganisms. We present a generic strategy that is ideal for the
systems-level analysis of the post-transcriptional regulons of RNA-binding proteins and for sRNA discovery in a wide range
of bacteria. Citation: Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, et al. (2008) Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global
Post-Transcriptional Regulator, Hfq. PLoS Genet 4(8): e1000163. doi:10.1371/journal.pgen.1000163
Editor: William F. Burkholder, Stanford University, United States of America
Received May 8, 2008; Accepted July 14, 2008; Published August 22, 2008 Received May 8, 2008; Accepted July 14, 2008; Published August 22, 2008 Received May 8, 2008; Accepted July 14, 2008; Published August 22, 2008 Copyright: 2008 Sittka 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. Deep Sequencing Analysis of Small Noncoding RNA and
mRNA Targets of the Global Post-Transcriptional
Regulator, Hfq Alexandra Sittka1, Sacha Lucchini2, Kai Papenfort1, Cynthia M. Sharma1, Katarzyna Rolle1, Tim T. Binnewies3, Jay C. D. Hinton2*, Jo¨ rg Vogel1* 1 Max Planck Institute for Infection Biology, RNA Biology, Berlin, Germany, 2 Institute of Food Research, Norwich Research Park, Norwich, United Kingdom, 3 Center for
Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark PLoS Genetics | www.plosgenetics.org Transcriptomic Profiling Reveals a Large Hfq Regulon in
Salmonella Transcriptomic Profiling Reveals a Large Hfq Regulon in
Salmonella The past decade has seen small regulatory RNA become an
important new mediator of bacterial mRNA regulation. This study describes a rapid way to identify novel sRNAs
that are expressed, and should prove relevant to a variety
of bacteria. We purified the epitope-tagged RNA-binding
protein, Hfq, and its bound RNA by immunoprecipitation
from the model pathogen, Salmonella enterica serovar
Typhimurium. This new strategy used Next Generation
pyrosequencing to identify 727 Hfq-bound mRNAs. The
numbers of sRNAs expressed in Salmonella was doubled to
64; half are associated with Hfq. We defined the exact
coordinates of sRNAs, and confirmed that they are
expressed at significant levels. We also determined the
Hfq regulon in Salmonella, and reported the role of Hfq in
controlling transcription of major pathogenicity islands,
horizontally acquired regions, and the flagellar cascade. Hfq is reported to be a global regulator that affects the
expression of almost a fifth of all Salmonella genes. Our
new approach will allow sRNAs and mRNAs to be
characterized from different genetic backgrounds, or from
bacteria grown under particular environmental conditions. It will be valuable to scientists working on genetically
tractable bacteria who are interested in the function of
RNA-binding proteins and the identification of sRNAs. To detect genes that are, directly or indirectly, regulated by Hfq
the transcriptomic mRNA profile of the Salmonella wild-type and of
mutant strain JVS-0255 (Dhfq) was determined. We used two
different conditions for the comparison; aerobic growth in L-broth
to early stationary phase (ESP; OD600 of 2) was chosen because the
hfq mutation causes drastic protein pattern changes in ESP
Salmonella [32], and overnight growth in high-salt medium under
oxygen
limitation
(SPI-1-inducing
conditions)
to
specifically
activate the Salmonella virulence genes required for host cell
invasion [39]. Hfq-dependent mRNAs that showed statistically
significant changes ($2-fold) were identified, and we discovered
that 734 genes were differentially expressed in the Dhfq strain
grown to ESP (279 up-regulated genes, 455 down-regulated genes,
Figure 2 and Table S1). Of the 71 proteins known to be Hfq-
dependent (as determined by protein levels on 2D gels; [32]), 50%
were regulated by Hfq at the transcriptional level (Table S1). Consequently, Hfq controls the expression of 17% of all Salmonella
genes at ESP (based on the 4425 annotated ORFs; [40]). Growth
under SPI-1 inducing conditions revealed 164 differentially
expressed genes in Dhfq (91 up-, 73 down-regulated; Table S2). Transcriptomic Profiling Reveals a Large Hfq Regulon in
Salmonella 69% of these genes overlapped with the changes seen in ESP. Taken together, Hfq affects at least 785 genes, or 18% of the
Salmonella genome. Loss of Hfq function also results in a non-motile phenotype for
Salmonella and the deregulation of .70 abundant proteins,
including the accumulation of outer membrane proteins (OMPs);
the latter is accompanied by a chronic activation of the sE (s24)-
mediated envelope stress response [32,34]. Hfq has also been
implicated in the control of Salmonella gene expression changes
induced
by
the
low
gravity
condition
experienced
during
spaceflight [35]. g
Classification of the genes deregulated at ESP (Table 1)
showed that Hfq impacted upon 26 of the 107 functional groups
annotated for Salmonella [41]; in seven groups $50% of all genes
were
misregulated. In
four
of
the
five
major
Salmonella
pathogenicity islands (i.e., SPI-1, -2, -4, -5), and in the flagellar
and chemotaxis pathways, .60% of genes were down-regulated,
which explains the previously observed invasion and motility
phenotypes of Dhfq [32]. Because Hfq affects the mRNAs of sS
(RpoS) and sE (RpoE) [25,26,34,42], two major alternative
stress s factors of enterobacteria, we quantified the expression of
these sigma factors in Salmonella at the mRNA level (ESP) and at
the protein level (ESP and SPI-1 inducing conditions). sE
mRNA and protein levels were strongly elevated in Dhfq under
both conditions tested (Figure S1), confirming the previously
observed chronic induction of the envelope stress response. Levels of rpoS mRNA were slightly increased, yet RpoS protein
levels were strongly decreased. This reflects the poor translation
of rpoS mRNA in the absence of Hfq (Figure S1 and [25,26]). We
used published lists of sE- and sS-dependent genes of Salmonella
[43,44] to determine how the Hfq-dependent changes we
observed were related to the sE and/or sS regulons. We
discovered that 55% (41/75) and 73% (54/74) of sE- and sS-
dependent
genes
were
also
Hfq-dependent. Therefore,
a
proportion
of
the
Hfq-dependent
gene
expression
changes
observed at ESP and under SPI-1 inducing conditions were
indirect effects caused by modulation of sS and sE levels by
Hfq. Understanding how Hfq controls Salmonella gene expression at
the post-transcriptional level requires the identification of its sRNA
and mRNA ligands. In a pioneering global study in E. coli, Zhang
et al. (2003) used co-immunoprecipitation (coIP) with Hfq-specific
antisera and direct detection of the bound RNAs on genomic high-
density oligonucleotide microarrays. Introduction and Gram-positive species, and at least one archaeon, encode an
Hfq homologue [10,11]. Hfq interacts with regulatory sRNAs and
mRNAs, and much of its post-transcriptional function is caused by
the facilitation of the generally short and imperfect antisense
interactions of sRNAs and their targets [12,13,14,15,16,17]. However, Hfq can also act alone as a translational repressor of
mRNA [18,19], and can modulate mRNA decay by stimulating
polyadenylation [20,21]. In addition, roles of Hfq in tRNA
biogenesis have recently been described [22,23]. Until now, global gene expression control studies have generally
focussed on the transcriptional regulation exerted by the specific
action of DNA binding proteins, and on the post-translational
regulation governed by specific protein–protein interactions. In
comparison, little is known about how RNA binding proteins
facilitate the global control of gene expression at the post-
transcriptional level. However, the latest discoveries of many small
noncoding RNAs (sRNAs) in both pro- and eukaryotes have
shown that the interaction of RNA with proteins plays a
prominent role in the regulation of cellular processes. In bacteria,
the majority of the sRNAs basepair with target mRNAs to regulate
their translation and/or decay [1,2,3], and these regulatory events
commonly require the bacterial Sm-like protein, Hfq [4,5]. The pleiotropy of an hfq deletion mutation was first apparent
from the multiple stress response-related phenotypes in E. coli [24],
and partly reflects the reduced efficiency of translation of rpoS
mRNA, encoding the major stress sigma factor, sS [25,26]. However, Hfq clearly impacts on bacterial physiology in a much
broader
fashion,
including
the
sS-independent
control
of
virulence factors in pathogenic bacteria (e.g., [27,28,29,30,
31,32,33]). Specifically, deletion of hfq attenuates the ability of
the model pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) to infect mice, to invade epithelial cells, to secrete
virulence factors and to survive inside cultured macrophages [32]. Hfq is one of the most abundant RNA-binding proteins in
bacteria [6,7,8]. First identified in Escherichia coli as a host factor
required for phage Qb RNA replication ,40 years ago [9], Hfq is
now known to have an important physiological role in numerous
model bacteria [5]. Almost half of all sequenced Gram-negative August 2008 | Volume 4 | Issue 8 | e1000163 1 Hfq and Deep Sequencing PLoS Genetics | www.plosgenetics.org August 2008 | Volume 4 | Issue 8 | e1000163 Transcriptomic Profiling Reveals a Large Hfq Regulon in
Salmonella Although this method proved
highly effective for detecting diverse sRNAs and mRNAs in E. coli,
the requirement for high-density microarrays and specialized
antibodies has hampered similar studies in other bacteria. An
alternate approach identified individual abundant Hfq-associated
RNAs by cDNA cloning or direct sequencing [29,36]; however,
these methods are not appropriate for large-scale analyses. pp
p
g
y
To overcome these limitations for the global identification of
Hfq targets in Salmonella, we have now used high-throughput
pyrosequencing (HTPS, a.k.a. deep sequencing) of RNA associ-
ated with an epitope-tagged Hfq protein (Figure 1). We show that
this approach recovers Hfq-binding sRNAs with high specificity,
and identifies their boundaries with unprecedented resolution. We
report the discovery of novel Salmonella sRNA genes, detect the
expression of many conserved enterobacterial sRNA genes, and
provide a set of potential mRNA targets in this model pathogen. Comparison with the transcriptomic profile of an hfq mutant
showed that Hfq mediates its pleiotropic effects by regulating the
master transcription factors of complex regulons, and explained
how Hfq is required for Salmonella virulence. In microbiology, deep
sequencing has been used extensively for genome sequencing,
either of individual microbial species [37] or of bacterial
communities [38]. This study is the first report that describes the
use of deep sequencing to study protein-bound mRNA from
bacteria, and to discover bacterial noncoding RNAs. The S. Typhimurium genome contains about 444 genes
acquired by horizontal gene transfer (HGT; [45]). 122 or 17 of
these HGT genes were Hfq-dependent under ESP or SPI-1
inducing conditions, respectively (16 genes being Hfq-dependent
under both conditions; Tables S1, S2). In other words, Hfq
regulates 28% of the HGT genes, significantly more than the 18%
regulated when using the entire Salmonella genome for calculation. This may indicate a role of Hfq in the acquisition of DNA from
foreign sources, by regulating expression of newly acquired genes
at the RNA level. August 2008 | Volume 4 | Issue 8 | e1000163 August 2008 | Volume 4 | Issue 8 | e1000163 2 Hfq and Deep Sequencing Figure 1. Strategy to identify Hfq targets. RNA was co-immunoprecipitated with Hfq in extracts from ESP-grown Salmonella cells (wild-type and
chromosomal hfqFLAG strain) using an anti-FLAG antibody. The extracted RNA was converted to 59 monophosphate RNA, and subsequently into
cDNA, followed by direct pyrosequencing. Our approach was validated by hybridization of cDNA to high density oligo microarrays. Transcriptomic Profiling Reveals a Large Hfq Regulon in
Salmonella In addition, total
RNA of the wild-type strain and its hfq deletion mutant was used for transcriptomic analysis using Salmonella SALSA microarrays. doi:10.1371/journal.pgen.1000163.g001 Figure 1. Strategy to identify Hfq targets. RNA was co-immunoprecipitated with Hfq in e
chromosomal hfqFLAG strain) using an anti-FLAG antibody. The extracted RNA was converte Figure 1. Strategy to identify Hfq targets. RNA was co-immunoprecipitated with Hfq in extracts from ESP-grown Salmonella cells (wild-type and
chromosomal hfqFLAG strain) using an anti-FLAG antibody. The extracted RNA was converted to 59 monophosphate RNA, and subsequently into
cDNA, followed by direct pyrosequencing. Our approach was validated by hybridization of cDNA to high density oligo microarrays. In addition, total
RNA of the wild-type strain and its hfq deletion mutant was used for transcriptomic analysis using Salmonella SALSA microarrays. doi:10.1371/journal.pgen.1000163.g001 PLoS Genetics | www.plosgenetics.org UTRs, with a few antisense transcripts to tRNAs, rRNAs, and
sRNAs (0.1%; Figure 3B). UTRs, with a few antisense transcripts to tRNAs, rRNAs, and
sRNAs (0.1%; Figure 3B). The variety of transcriptional regulons that showed Hfq-
dependent expression patterns could either be mediated by the
binding of certain regulatory sRNAs or of specific mRNAs by Hfq. To identify the direct Hfq targets we co-immunoprecipitated RNA
with the chromosomally FLAG epitope-tagged Hfq protein
expressed by a Salmonella hfqFLAG strain [46]. CoIP was performed
in extracts
prepared
from ESP-grown
bacteria. The Hfq-
associated RNA was converted to cDNA, and a total of 176,907
cDNAs pooled from two independent biological experiments was
then characterised by high-throughput pyrosequencing [37]. The
resulting sequences, from here on referred to as ‘‘Hfq cDNAs’’,
ranged in length from 1 to 145 bp, and 92% were $18 bp
(Figure 3A). Disregarding small cDNAs (,18 bp), 122,326
sequences were unequivocally mapped to the Salmonella genome
by WU-BLAST searches (http://blast.wustl.edu/; Figure 2). About half of the mapped cDNAs (57,529) were derived from
rRNA, tRNA, and housekeeping RNAs (tmRNA, M1 RNA, and
SRP RNA; Figure 3B). Of the remaining 64,797 sequences, the
majority corresponded to mRNA regions (53% matched the sense
strand of protein-coding regions), followed by known/predicted
conserved sRNAs (18%; [47]; for distribution see Figure 3C),
predicted Salmonella-specific sRNAs (1%; [46]) and sequences that
were antisense to ORF regions (3%). The remaining 25% of
cDNAs mostly represented intergenic regions (IGRs) and 59/39 To confirm that our procedure did effectively enrich Hfq-
associated RNAs, we analyzed 175,142 cDNAs from a control
coIP using wild-type Salmonella (expressing untagged Hfq). Of these
‘‘Control cDNAs’’ which ranged in length from 1 to 290 bp
(Figure 3A), 145,873 sequences were $18 bp in size and could be
correlated to the Salmonella chromosome. Most of the inserts (91%)
were abundant rRNA, tRNA, and housekeeping RNA transcripts
(Fig 3B). The remaining 13,725 sequences were used to calculate
the level of enrichment of Hfq-bound RNA (see below). Visualizing Hfq-Dependent RNAs at the Nucleotide Level Visualizing Hfq-Dependent RNAs at the Nucleotide Level
Upon WU-BLAST matching, the number of cDNA hits for
each nucleotide position for either strand of the Salmonella
chromosome was calculated, and visualized using the Integrated
Genome Browser (IGB, Affymetrix). This browser allows the visuali-
zation of both whole genomes and individual genomic regions. Figure 4 shows the distribution of cDNA sequences over a
subsection of the genome, i.e. the ,40 kb SPI-1 virulence region,
for which we observed strong enrichment of Hfq cDNAs over the
Control cDNAs. As well as the 35 mRNAs of protein-coding
genes, SPI-1 encodes the Hfq-dependent InvR sRNA [46]. Enrichment of InvR by coIP with FLAG-tagged Hfq was
previously demonstrated by Northern blot analysis [46], and this August 2008 | Volume 4 | Issue 8 | e1000163 3 PLoS Genetics | www.plosgenetics.org Hfq and Deep Sequencing Figure 2. Correlation between HTPS, coIP-on-chip and transcriptomic data upon the S. Typhimurium chromosome. The data obtained
from transcriptomic, cDNA sequencing and coIP-on-chip analyses of ESP-grown bacteria were mapped onto the Salmonella chromosome for direct
comparison. The outer (1st) ring displays changes in gene expression in the Dhfq strain compared to the parental SL1344 strain. Genes that are down-
regulated in the Dhfq strain are shown as blue; genes that are up-regulated are shown as red. The next three circles show regions coding for Hfq-
associated RNA identified by deep sequencing (2nd ring shows positive strand, and 3rd ring shows negative strand) or coIP-on-chip (4th ring). Ring 5
shows the location of coding sequences on the positive strand (CDS+), on the negative strand (CDS2), and the tRNA and rRNA genes. GC-skew [110]
is shown in ring 6; purple and blue regions have a GC skew that is below or above the genomic average, respectively. AT-content is shown in ring 7;
blue and red regions have an AT-content that is below or above the genomic average, respectively. Numbers on the inside of the innermost circle are
the location relative to position zero measured in millions of base-pairs (Mbp) of the Salmonella LT2 genome. The location of the SPI-1 to SPI-5 is
indicated. An invaluable zoomable version of this atlas is available online at http://www.cbs.dtu.dk/services/GenomeAtlas/suppl/zoomatlas/
?zpid = Styphimurium_LT2_Atlas ; click on the region of interest to accurately visualize the data at the level of individual genes. doi:10.1371/journal.pgen.1000163.g002
Hfq and Deep Sequencing Figure 2. Correlation between HTPS, coIP-on-chip and transcriptomic data upon the S. PLoS Genetics | www.plosgenetics.org Visualizing Hfq-Dependent RNAs at the Nucleotide Level Typhimurium chromosome. The data obtained
from transcriptomic, cDNA sequencing and coIP-on-chip analyses of ESP-grown bacteria were mapped onto the Salmonella chromosome for direct
comparison. The outer (1st) ring displays changes in gene expression in the Dhfq strain compared to the parental SL1344 strain. Genes that are down-
regulated in the Dhfq strain are shown as blue; genes that are up-regulated are shown as red. The next three circles show regions coding for Hfq-
associated RNA identified by deep sequencing (2nd ring shows positive strand, and 3rd ring shows negative strand) or coIP-on-chip (4th ring). Ring 5
shows the location of coding sequences on the positive strand (CDS+), on the negative strand (CDS2), and the tRNA and rRNA genes. GC-skew [110]
is shown in ring 6; purple and blue regions have a GC skew that is below or above the genomic average, respectively. AT-content is shown in ring 7;
blue and red regions have an AT-content that is below or above the genomic average, respectively. Numbers on the inside of the innermost circle are
the location relative to position zero measured in millions of base-pairs (Mbp) of the Salmonella LT2 genome. The location of the SPI-1 to SPI-5 is
indicated. An invaluable zoomable version of this atlas is available online at http://www.cbs.dtu.dk/services/GenomeAtlas/suppl/zoomatlas/
?zpid = Styphimurium_LT2_Atlas ; click on the region of interest to accurately visualize the data at the level of individual genes. doi:10.1371/journal.pgen.1000163.g002 result is confirmed by the strong cDNA peak seen at the invR locus
located at the right-hand SPI-1 border (Figure 4). equal numbers in the Hfq and Control cDNAs (CsrB, 67/69;
CsrC, 63/64; Table 2). Moreover, cDNAs of the abundant yet
Hfq-independent 6S RNA [49] were found in smaller numbers in
the Hfq than in the control library (451 versus 836; Table 2). equal numbers in the Hfq and Control cDNAs (CsrB, 67/69;
CsrC, 63/64; Table 2). Moreover, cDNAs of the abundant yet
Hfq-independent 6S RNA [49] were found in smaller numbers in
the Hfq than in the control library (451 versus 836; Table 2). Hfq-Dependent sRNAs Are Highly Associated with Hfq Figure 5 illustrates the distribution of cDNAs of the three
predominant Hfq-bound RNAs and of the Hfq-independent 6S
RNA. cDNAs of both the InvR (89 nt; [46]) and SroB (84 nt; [50])
sRNAs mapped along the entire RNA coding sequence from the
transcriptional start site to the Rho-independent terminator. SraH,
which is transcribed as an unstable 120 nt precursor and processed
into an abundant ,58 nt RNA species (39 part of SraH; [17,51]),
was almost exclusively recovered as the processed sRNA. Notably,
the borders of the cDNA clusters were in perfect agreement with
previous 59 and/or 39 end mapping data of the four sRNAs
[46,50,51,52]. In other words, our cDNA sequencing approach
not only detects association with Hfq, but also identifies the
termini of expressed sRNAs at nucleotide-level resolution. Inspection of the cDNA libraries revealed that a major class
were derived from sRNA regions. These sRNAs, as well as their
enrichment by Hfq coIP, are listed in Tables 2 and S3. The three
most abundant sRNAs, according to the numbers of Hfq cDNA
sequences are InvR, SraH (a.k.a. RyhA) and SroB (RybC), and are
known to be strongly bound by Hfq [17,46]; coIP of Hfq enriched
these three sRNAs by 30- to 57-fold, in comparison to the control
reaction. For example, InvR, which binds Hfq with a kD of 10 nM
[46], was represented by 3,236 Hfq cDNAs and 113 Control
cDNAs (Table 2). In contrast, other sRNAs not expected to be
Hfq-dependent were found in equal numbers in the two samples. For example, the CsrB or CsrC sRNAs which target the conserved
RNA-binding protein, CsrA [48], were represented by almost August 2008 | Volume 4 | Issue 8 | e1000163 PLoS Genetics | www.plosgenetics.org 4 Hfq and Deep Sequencing Table 1. Pathway clustering of Hfq-dependent genes at ESP. Identification of Expressed Salmonella sRNAs summarized in Table 2 (the whole set of candidates tested is shown
in Table S3); including the 26 previously detected Salmonella
sRNAs [34,46,55,58,59,60,61,62,63], a total of 64 Salmonella
sRNAs can now be considered to be experimentally validated. summarized in Table 2 (the whole set of candidates tested is shown
in Table S3); including the 26 previously detected Salmonella
sRNAs [34,46,55,58,59,60,61,62,63], a total of 64 Salmonella
sRNAs can now be considered to be experimentally validated. To evaluate the sRNA expression profile of Salmonella more
extensively, we analyzed three classes of sRNA candidate loci for
coverage by the Hfq and Control cDNAs. First, cDNAs of E. coli
sRNA candidate loci with predicted conservation in Salmonella
were
inspected
[17,47,49,50,51,53,54]. Second,
we
counted
cDNAs of Salmonella-specific sRNAs predicted in two recent global
screens [46,55]. Third, we manually inspected cDNAs from a
third of the Salmonella chromosome (first 1.6 Mb) and all major five
pathogenicity islands for expression patterns of IGRs indicative of
new sRNA genes, and for possible enrichment by Hfq coIP. Using
criteria similar to [49], our evaluation of these loci considered
orphan promoter/terminator signals, and possible conservation in
bacteria other than E. coli. Of the latter two classes of candidates
(summarized in Table S3), those with an Hfq enrichment factor
$10 and/or candidates showing strong promoter/terminator
predictions were selected for Northern blot analysis. To assess
sRNA expression under relevant environmental conditions, we
probed RNA from five stages of growth in standard L-broth from
exponential to stationary phases, and from two conditions known
to strongly induce the expression of the major SPI-1 [39,56] or
SPI-2 [57] virulence regions. The results of this analysis are We used Northern blots to detect 10 of the 31 newly identified
Salmonella sRNAs under the environmental conditions that were
tested (Figure 6, Tables 2 and S3). These sRNAs yielded stable
transcripts, predominantly in the 50 to 100 nt range (Figure 6A
and B). Faint bands of larger transcripts were observed for
STnc150 (150 nt), and STnc400 (190 nt), resembling certain E. coli
sRNAs such as SraH whose precursor is rapidly degraded whilst
the processed form accumulates [51]. The STnc150, 400, and 560
sRNAs are almost constitutively expressed, whereas STnc500, 520
and 540 are only expressed in certain environmental conditions. Intriguingly, STnc580 can only be detected under SPI-1 inducing
conditions that mimic the environment Salmonella encounters in
the host intestine. Hfq-Dependent sRNAs Are Highly Associated with Hfq pathwaya
genes in pathwayb
% upc
% downd
% genes regulated
Flagellar system
53
0
87
87
Chemotaxis
19
0
84
84
Fimbrial proteins
24
0
20
20
SPI1
39
0
90
90
SPI2
40
0
72.5
72.5
SPI3
29
0
14
14
SPI4
6
0
100
100
SPI5
8
0
62.5
62.5
ABC transporter
188
11
7
28
Cyanoamino acid metabolism
10
20
10
30
Cystein metabolism
15
20
0
20
Fatty acid metabolism & biosynthesis
20
15
15
30
Fructose & mannose metabolism
64
2
11
13
Glutamate metabolism
29
7
7
14
Lipopolysaccharidee biosynthesis
28
3.5
3.5
7
Glycerophospholipid metabolism
24
17
12.5
29.5
Glycine, serine & threonine metabolism
35
31.5
3
34.5
Glycolysis/Gluconeogenesis
28
3
21
24
Nitrogen metabolism
33
15
6
21
Pentose phosphate pathway
32
12.5
19
31.5
Purine metabolism
73
11
4
15
Pyrimidine metabolism
49
10
0
10
Pyruvate metabolism
49
12
0
12
Ribosome
78
35
0
35
Selenoamino acid, sulfur metabolism
18
33
17
50
Starch & sucrose metabolism
31
3
26
29
Hfq-dependent genes in ESP-grown Salmonella are shown in Table S1. aPathway classification according to KEGG (http://www.genome.jp/kegg/; [21]). Pathways in which $50% of genes are Hfq-regulated are shadowed. bNumber of genes involved in pathway (acc. KEGG). c,dNumbers in percent of genes that were up- or down-regulated in Dhfq compared to wt, (Table S1). doi:10.1371/journal.pgen.1000163.t001 Identification of Expressed Salmonella sRNAs PLoS Genetics | www.plosgenetics.org August 2008 | Volume 4 | Issue 8 | e1000163 Identification of Expressed Salmonella sRNAs Generally, only candidates represented by $20
cDNAs in a cDNA pool yielded a signal on Northern blots
(Tables 2 and S3). While this suggests some correlation between
intracellular abundance and cDNA frequency, we note the case of
STnc150, for which a single cDNA was recovered yet a strong
signal was obtained on Northern blots. In contrast, several 5 August 2008 | Volume 4 | Issue 8 | e1000163 August 2008 | Volume 4 | Issue 8 | e1000163 Hfq and Deep Sequencing ranging in size from 500 to 2000 nucleotides (STnc180, Stnc190,
STnc330, STnc470, STnc610, and STnc640; Figure S2 and
Table S3), and are likely to be processed mRNA species. Figure 3. Statistical analysis of the cDNA sequencing results of
Hfq-associated RNA. (A) The pyrosequencing results were analyzed
by plotting the number of cDNA reads over the read length in bp. The
length distribution of all resulting sequences is shown. (B) Pie diagram
showing the relative proportions of the different RNA species contained
in all sequences that mapped to the Salmonella genome. The rRNA,
tRNA and housekeeping RNAs are shown in grey. Left panel: Hfq coIP,
right panel: control coIP. (C) Pie diagram showing the relative
proportions of all Hfq-associated sequences that unequivocally mapped
to known sRNA sequences. The names of the six most frequently
recovered sRNAs are given. doi:10 1371/journal pgen 1000163 g003 )
y
p
p
Three sRNAs expressing stable transcripts of ,85 to 90 nts
originate from close to, or within, IS200 transposable elements
(Figure 6B). STnc290 and STnc440 are expressed just upstream of
tnpA_4 and tnpA_6, respectively, whereas STnc490 is antisense to
the translational start site of the IS200 transposase ORF. IS200
elements generally posses two stem-loop structures, one of which is
a Rho-independent transcription terminator that prevents read-
through from genes located upstream of the integration site [64]. Given their location, the STnc290 sRNA could originate from
processing of the STM3033 transcripts reading into the tnpA_4
terminator structure; by analogy, STnc440 would be derived from
STM4310 transcripts. If so, this would constitute interesting cases
in which transposon insertion has created stable sRNAs. The other
IS200
stem-loop
functions
as
a
translational
repressor
by
sequestering the start codon of the transposon ORF [64]; STnc490
overlaps with this structure on the opposite strand, and by acting
as an antisense RNA may function as an additional repressor of
IS200. Identification of Expressed Salmonella sRNAs (C) Pie diagram showing the relative
proportions of all Hfq-associated sequences that unequivocally mapped
to known sRNA sequences. The names of the six most frequently
recovered sRNAs are given. doi:10.1371/journal.pgen.1000163.g003 PLoS Genetics | www.plosgenetics.org Identification of Expressed Salmonella sRNAs We determined whether 8 of the new Salmonella sRNAs showed
an Hfq-dependent pattern of transcript abundance that correlated
with Hfq binding (Figure 6C). The STnc290, 440, 490, 520, 540
and 560 sRNAs were all enriched by Hfq coIP (Table 2), by factors
up to 51-fold (STnc440). The expression of the four sRNAs with
the highest enrichment factors (STnc290, 440, 520, 560) was
strongly reduced in Dhfq, and so classified as Hfq-dependent; in
contrast, the accumulation of STnc150, STnc490 and STnc540
($1.0-, 5.1-, and 3.3-fold enrichment, respectively) was unaffected
in the absence of Hfq. STnc500, which is only detected in samples
originating from cultures at OD600 of 1, and STnc580, which
seems to be specifically expressed under the SPI-1 inducing
condition, were not detected on these blots. In addition to the sRNAs listed above, the cDNAs included two
loci predicted to encode small peptides, i.e. shorter than the 34
amino acid cut-off used to define ORFs in the current Salmonella
genome annotation [40]. These are referred to as STnc250 and
STnc570 in Table 2, and correspond to the predicted small ypfM
and yneM mRNA-encoding genes of E. coli [49]. Probing of the
Salmonella loci yielded signals of stable short mRNAs which are
expressed in a growth phase-dependent manner (Figure S3). Figure 3. Statistical analysis of the cDNA sequencing results of
Hfq-associated RNA. (A) The pyrosequencing results were analyzed
by plotting the number of cDNA reads over the read length in bp. The
length distribution of all resulting sequences is shown. (B) Pie diagram
showing the relative proportions of the different RNA species contained
in all sequences that mapped to the Salmonella genome. The rRNA,
tRNA and housekeeping RNAs are shown in grey. Left panel: Hfq coIP,
right panel: control coIP. (C) Pie diagram showing the relative
proportions of all Hfq-associated sequences that unequivocally mapped
to known sRNA sequences. The names of the six most frequently
recovered sRNAs are given. doi:10.1371/journal.pgen.1000163.g003 Figure 3. Statistical analysis of the cDNA sequencing results of
Hfq-associated RNA. (A) The pyrosequencing results were analyzed
by plotting the number of cDNA reads over the read length in bp. The
length distribution of all resulting sequences is shown. (B) Pie diagram
showing the relative proportions of the different RNA species contained
in all sequences that mapped to the Salmonella genome. The rRNA,
tRNA and housekeeping RNAs are shown in grey. Left panel: Hfq coIP,
right panel: control coIP. Hfq-Associated mRNAs We tested 14 of such
candidates which had the appropriate orientation to flanking
mRNA genes to be UTR-derived; six of these showed signals August 2008 | Volume 4 | Issue 8 | e1000163 August 2008 | Volume 4 | Issue 8 | e1000163 6 Hfq and Deep Sequencing Figure 4. Visualization of pyrosequencing data for the Salmonella pathogenicity island 1 (SPI-1) with the Integrated genome
Browser (Affymetrix). The upper panel shows an extraction of the screenshot of the Integrated Genome Browser, with the mapped Control and
Hfq cDNAs of the SPI-1 region. Shown are the annotations for the ‘‘+’’ and ‘‘–’’ strand (blue), the cDNA sequence distribution from the Hfq coIP for the
‘‘+’’ and ‘‘–’’ strand (red), the cDNA-clone distribution for the control coIP for the ‘‘+’’ and ‘‘–’’ strand (black), and the genome coordinates in the center
for the entire SPI-1. The annotation for SPI-1 and the Hfq coIP peaks for hilD and the sRNA InvR in the Hfq coIP are indicated. Note, that the clone
numbers per nucleotide are scaled to a maximum of 250 for the Hfq and the control coIP, which truncates the high peak for InvR in the Hfq coIP
library (.3000 cDNAs). The lower panel shows a close up of the invR locus and its adjacent genes. doi:10.1371/journal.pgen.1000163.g004 Figure 4. Visualization of pyrosequencing data for the Salmonella pathogenicity island 1 (SPI-1) with the Integrated genome
Browser (Affymetrix). The upper panel shows an extraction of the screenshot of the Integrated Genome Browser, with the mapped Control and
Hfq cDNAs of the SPI-1 region. Shown are the annotations for the ‘‘+’’ and ‘‘–’’ strand (blue), the cDNA sequence distribution from the Hfq coIP for the
‘‘+’’ and ‘‘–’’ strand (red), the cDNA-clone distribution for the control coIP for the ‘‘+’’ and ‘‘–’’ strand (black), and the genome coordinates in the center
for the entire SPI-1. The annotation for SPI-1 and the Hfq coIP peaks for hilD and the sRNA InvR in the Hfq coIP are indicated. Note, that the clone
numbers per nucleotide are scaled to a maximum of 250 for the Hfq and the control coIP, which truncates the high peak for InvR in the Hfq coIP
library (.3000 cDNAs). The lower panel shows a close up of the invR locus and its adjacent genes. doi:10.1371/journal.pgen.1000163.g004 Genome annotations of protein-coding genes are generally
limited to the mRNA coding regions (CDS). Hfq-Associated mRNAs To determine which of the 34,136 cDNAs were derived from
Hfq-bound mRNAs and represented genuine mRNA targets, a
stringent cutoff was used. An mRNA coding region (CDS) was
required to be represented by $10 cDNAs to be considered
significant, which identified 727 Hfq-bound mRNAs (cistrons) for
further analysis. Table 3 lists the top 42 mRNAs with at least 100
cDNAs in the Hfq coIP library (Table S4 lists all 727 mRNAs). In
the genome browser, many of these enriched mRNAs were readily
visible as a distinct cDNA cluster, e.g., the ompD mRNA (encoding
the major Salmonella outer membrane protein) shown in Figure 7A. A survey of the transcriptomic data revealed that 33% of the Hfq-
bound mRNAs showed an Hfq-dependent pattern of gene
expression (Table S1). The reciprocal analysis showed that 32%
of the Hfq-dependent mRNAs were bound to Hfq (Table S1). We
attribute the observed partial overlap of the Hfq coIP and the
transcriptomic data (33%) to three major factors. First, Hfq
regulates transcription factors, de-regulation of which alters the
expression of downstream genes. In other words, not every gene
deregulated in the Dhfq strain is necessarily a ‘‘direct’’ Hfq target,
i.e. its mRNA bound by Hfq. Second, there may be a considerable Figure 3. Statistical analysis of the cDNA sequencing results of
Hfq-associated RNA. (A) The pyrosequencing results were analyzed
by plotting the number of cDNA reads over the read length in bp. The
length distribution of all resulting sequences is shown. (B) Pie diagram
showing the relative proportions of the different RNA species contained
in all sequences that mapped to the Salmonella genome. The rRNA,
tRNA and housekeeping RNAs are shown in grey. Left panel: Hfq coIP,
right panel: control coIP. (C) Pie diagram showing the relative
proportions of all Hfq-associated sequences that unequivocally mapped
to known sRNA sequences. The names of the six most frequently
recovered sRNAs are given. doi:10 1371/journal pgen 1000163 g003 doi:10.1371/journal.pgen.1000163.g003 candidates with .20 cDNAs failed the Northern blot validation
(Table S3). We speculated that the corresponding cDNAs were
derived from 59 or 39 UTRs of larger mRNA transcripts, and
tested this on Northern blots of agarose gels. PLoS Genetics | www.plosgenetics.org August 2008 | Volume 4 | Issue 8 | e1000163 Hfq-Associated mRNAs Whilst Tables 3 and
S4 list absolute hit numbers in annotated CDS, the detailed
analysis of cDNA distribution over a given mRNA gene often
revealed a more complex picture. For example, the number of
ompA cDNAs does not drastically differ in the two libraries (Hfq
coIP, 102; control coIP, 77), which would question whether ompA
is an Hfq-bound mRNA. However, up to 12-fold enrichment is
seen in some sections of the ompA mRNA, e.g., around the AUG
and in the central CDS (Figure 7B). Note that the availability of
cDNA hit numbers for every single nucleotide of the Salmonella
chromosome offers the possibility to also analyze 59 and 39 UTRs
of mRNAs, which are not included in Tables 3 and S4, but could
also be targeted by Hfq. number of Hfq-associated mRNAs below our very stringent cut-off
for Hfq-association; increasing sequencing depth will overcome
this problem. Third, the precise borders of most 59/39 UTRs are
unknown in Salmonella (and any other bacterial genome sequence);
consequently, calculations of Hfq enrichment were limited to the
CDS of an mRNA. As outlined further below (Figure 7B), this can
skew the overall enrichment factor. To validate our cDNA sequencing approach for the detection of
Hfq-bound mRNAs by the conventional approach, we hybridized
the
RNA
obtained
from
Hfq and
control
coIP to
a
S. Typhimurium oligonucleotide microarray. Analysis of this coIP-
on-Chip experiment with SAM-software (Statistical Analysis of
Microarrays; FDR,0.01) identified 365 enriched mRNAs. Nearly
half (45%) of these mRNAs corresponded to regions identified by
the deep sequencing approach (Table S5; P,10e-10). The overlap
increased to 67% when genes that showed enrichment values
above 5 were taken into consideration. Although coIP-on-Chip
displays a lower sensitivity than deep sequencing these two
independent methods do generate comparable results for the
identification of mRNA-protein interactions. Figure 8A further illustrates the complex enrichment patterns of
diverse mRNAs, some of which may be explained by previous data
obtained for these transcripts, as discussed below. i) cDNAs of
Hfq-bound mRNAs of hilD (encoding a key transcription factor of
the Salmonella invasion gene island, SPI-1), fliC (which encodes a
major flagellin), or flhDC (encoding the major transcription factor PLoS Genetics | www.plosgenetics.org 7 August 2008 | Volume 4 | Issue 8 | e1000163 August 2008 | Volume 4 | Issue 8 | e1000163 Hfq and Deep Sequencing Table 2. Compilation of expressed Salmonella sRNAs and their enrichment by Hfq coIP. Hfq-Associated mRNAs sRNAa
Alternative IDs b
Identification c
Adjacent genes d
Orientation e
59 end f
39 end f
cDNA reads
control coIP g
cDNA reads Hfq coIP h
Enrichment i
Northern j
sgrS
ryaA
I
yabN/leuD
r R r
128574
128812
3
61
20.3
isrA
-
II
STM0294.ln/STM0295
R R R
339338
339760
0
0
sroB
rybC
I
ybaK/ybaP
r R r
556005
556085
27
1530
56.7
sroC
-
I
gltJ/gltI
r r r
728913
728761
26
898
34.5
rybB
p25
III
STM0869/STM0870
R r r
942632
942554
3
103
34.3
STnc490k
-
IV
clpA/tnpA_1
R r R
1024975
1025165
75
385
5.1
,85 nt
isrB-1
-
II
sbcA/STM1010
r R r
1104179
1104266
2
4
2.0
STnc500
-
IV
STM1127/STM1128
r r r
1216157
1216440
7
84
12.0
,65 nt
STnc150
-
V
icdA/STM1239
R r R
1325914
1325649
0
1
$1.0
,90 nt
isrC
-
II
envF/msgA
r R r
1329145
1329432
0
1
$1.0
STnc520
-
IV
STM1248/STM1249
R r r
1332809
1334044
12
100
8.3
,80 nt
isrD
-
II
STM1261/STM1263
R r R
1345788
1345738
0
0
ryhB-2
isrE
II
STM1273/yeaQ
R r R
1352987
1352875
0
0
STnc540
-
IV
himA/btuC
R R R
1419369
1419570
7
23
3.3
,85 nt
rprA
IS083
I
ydik/ydil
r r r
1444938
1444832
37
286
7.7
rydB
tpe7, IS082
I
ydiH/STM1368
R R r
1450415
1450519
4
10
2.5
STnc570l
yneM ORF
IV
ydeI/ydeE
R r r
1593723
1594413
2
21
10.5
,190 nt
STnc560
IV
ydeI/ydeE
R R r
1593723
1594413
10
290
29.0
,90 nt
isrF
-
II
STM1552/STM1554
R r r
1630160
1629871
1
0
rydC
IS067
I
STM1638/cybB
R R r
1729673
1729738
5
245
49.0
micC
IS063, tke8
III
nifJ/ynaF
R r R
1745786
1745678
0
15
$15.0
STnc580
-
IV
dbpA/STM1656
r r r
1749662
1750147
11
311
28.3
,100 nt
ryeB
tpke79
I
STM1871/STM1872
R r r
1968155
1968053
24
653
27.2
dsrA
-
I
yodD/yedP
R r R
2068736
2068649
6
149
24.8
rseX
-
I
STM1994/ompS
r R R
2077175
2077269
0
3
$3.0
ryeC
tp11
I
yegD/STM2126
R R R
2213871
2214016
42
72
1.7
cyaR
ryeE
III
yegQ/STM2137
R R R
2231130
2231216
31
659
21.3
isrG
-
II
STM2243/STM2244
r R R
2344732
2345013
0
0
micF
-
III
ompC/yojN
r R R
2366913
2367005
0
11
$11.0
isrH-2
-
II
glpC/STM2287
R r R
2394582
2394303
0
0
isrH-1
-
II
glpC/STM2287
R r R
2394753
2394303
0
0
STnc250l
ypfM ORF
V
acrD/yffB
R r R
2596882
2596789
6
24
4.0
,220 nt
ryfA
tp1
I
STM2534/sseB
R R r
2674934
2675228
3
6
2.0
glmY
tke1, sroF
I
yfhK/purG
r r r
2707847
2707664
20
92
4.6
isrI
-
II
STM2614/STM2616
R r r
2761576
2761329
0
2
$2.0
PLoS Genetics | www plosgenetics org
8
August 2008 | Volume 4 | Issue 8 | e1000163 e 2. Hfq-Associated mRNAs Compilation of expressed Salmonella sRNAs and their enrichment by Hfq coIP. Hfq-Associated mRNAs 8 Hfq and Deep Sequencing sRNAa
Alternative IDs b
Identification c
Adjacent genes d
Orientation e
59 end f
39 end f
cDNA reads
control coIP g
cDNA reads Hfq coIP h
Enrichment i
Northern j
isrJ
-
II
STM2614/STM2616
R r r
2762031
2761957
1
0
isrK
-
II
STM2616/STM2617
r r r
2762867
2762791
0
0
isrB-2
-
II
STM2631/sbcA
R r R
2770965
2770872
0
0
isrL
-
II
smpB/STM2690
R r R
2839399
2839055
0
0
isrM
-
II
STM2762/STM2763
r R R
2905050
2905378
0
0
isrN
-
II
STM2764/STM2765
r R r
2906925
2907067
0
0
micA
sraD
I
luxS/gshA
r R r
2966853
2966926
1
128
128.0
invR
STnc270
III
invH/STM 2901
R R R
3044924
3045014
113
3236
28.6
csrB
-
III
yqcC/syd
r r r
3117059
3116697
69
67
gcvB
IS145
III
gcvA/ygdI
r R r
3135317
3135522
12
402
33.5
omrA
rygB
III
aas/galR
r r R
3170208
3170122
0
51
$51.0
omrB
t59, rygA, sraE
III
aas/galR
r r R
3170408
3170322
1
52
52.0
STnc290
-
V
tnpA_4/STM3033
r r r
3194996
3194914
2
72
36.0
,85 nt
isrO
-
II
STM3038/STM3039
r R R
3198380
3198580
0
0
ssrS
-
I
ygfE/ygfA
R R R
3222098
3222280
836
451
rygC
t27
I
ygfA/serA
R R r
3222913
3223065
14
17
1.2
rygD
tp8, C0730
I
yqiK/rfaE
R r r
3362474
3362327
17
104
6.1
sraF
tpk1, IS160
I
ygjR/ygjT
R R R
3392069
3392261
0
25
$25.0
sraH
ryhA
I
yhbL/arcB
r R r
3490383
3490500
55
2292
41.7
ryhB-1
sraI, IS176
I
yhhX/yhhY
r r R
3715495
3715401
0
2
$2.0
istR-1
VI
ilvB/emrD
r r R
3998147
3998018
0
0
,75 nt
istR-2
VI
ilvB/emrD
r r R
3998147
3998018
0
0
,140 nt
STnc400
-
V
STM3844/STM3845
R R R
4051145
4051340
112
42
,55 nt
glmZ
k19, ryiA, sraJ
I
yifK/hemY
R R r
4141650
4141854
20
196
9.8
Spf
spf
I
polA/yihA
R R r
4209066
4209175
2
33
16.5
csrC
sraK, ryiB, tpk2
III
yihA/yihI
r R R
4210157
4210400
63
64
isrP
-
II
STM4097/STM4098
r R r
4306719
4306866
0
2
$2.0
oxyS
-
I
argH/oxyR
R r R
4342986
4342866
0
10
$10.0
sraL
ryjA
III
soxR/STM4267
R r R
4505010
4504870
0
0
STnc440
-
V
STM4310/tnpA_6
R R R
4559193
4559277
9
456
50.7
,85 nt
isrQ
-
II
STM4508/STM4509
r R R
4762997
4763158
0
0
aGene names of Salmonella sRNAs that have been experimentally proven here, and in previous studies. August 2008 | Volume 4 | Issue 8 | e1000163 Hfq-Associated mRNAs lSTnc250 and STnc570 contain small ORFs annotated as ypfM or yneM, respectively, in E. coli (Wassarman et al., 2001). doi:10 1371/journal pgen 1000163 t002 of the Salmonella flagellar genes) were distributed over the entire
length of the relevant gene, including the ,300 nt 39 UTR in the
case of hilD. Either Hfq does target such a large number of sites on
these three mRNAs, or alternatively, given that Hfq is a ribosome-
bound protein, these cDNAs may derive from polysome-bound
mRNAs. ii) cDNAs of ompD were also distributed over the entire
ompD locus, and abruptly ended 50 nt downstream of the ompD
stop codon, at the predicted Rho-independent terminator; a major
cDNA cluster was observed around the ompD AUG start codon,
i.e. the 270 to +19 region (for separate display of control coIP,
Hfq coIP, and enrichment curves see Figure 7A). Intriguingly, this
particular region binds Hfq with high affinity in vitro (kD#1 nM;
[32]). Binding of Hfq to the ompD AUG region may control
translation initiation analogous to the Hfq-mediated repression of
the E. coli ompA mRNA [18]. Similarly, cDNAs representing dppA
clustered at the 59 end of this mRNA, from the transcriptional +1
site into the N-terminal (signal peptide) coding region. The Hfq-
dependent sRNA, GcvB, is known to target the dppA 59 UTR [58],
and our data suggest that Hfq-binding to this dppA region could
enhance GcvB action. iii) cDNA clones of the ,10kb flgBCDEF-
GHIJKL mRNA (flagellar components) were almost exclusively
derived from the terminal, 80 nt region downstream of the flgL
stop codon which includes the terminator. It is possible that Hfq
controls flagellar operon mRNA expression through modulation of
mRNA decay initiating at the 39 end. iv) Almost all of the 48
cDNAs of the dicistronic glmUS mRNA mapped in two clusters to
the glmUS IGR (188 nt). cDNAs of the upstream cluster start with
the adenosine of the glmU UGA stop codon and span the first 73 nt
of the IGR. In E. coli, glmUS mRNA undergoes RNaseE-
dependent
cleavage
within
the glmU
UGA to
generate a
monocistronic glmS mRNA [65,66]; the glmS mRNA is activated
by the GlmZ sRNA, which binds Hfq [49] and the glmUS IGR
[19]. As mentioned for GcvB/dppA, Hfq is likely to aid the binding
of GlmZ to the glmUS mRNA in the region of the two clusters of
cDNAs. Hfq-Associated mRNAs It is worth noting that the extended steps of lysate preparation
and antibody incubation involved in the Hfq coIP protocol do
cause some mRNA degradation [17]. Our Northern blots did not
detect full-length mRNA in the RNA samples from the Salmonella
Hfq coIP (data not shown). We believe that the sequenced cDNAs
were synthesized from a mixture of shorter cDNA fragments,
rather than from intact transcripts of several kb in length. The
short cDNAs that were prepared from Hfq coIP have the
advantage of favoring the primary Hfq binding region. To confirm that Hfq bound to enriched mRNA regions,
corresponding fragments of the dppA, glmUS, flhD and hilD mRNAs
were in vitro-synthesized, and analyzed in gel mobility shift assays
(Figure 8B). These RNA fragments were fully shifted by addition
of #50 nM Hfq hexamer, which suggested significantly stronger
binding than to the previously tested, non-specific metK mRNA
(kD$250 nM; [32]) which is not regulated by Hfq and was not
recovered by Hfq coIP (Tables S1 and S4). Thus, the cDNA
sequences appear to represent high-affinity, primary binding sites
of Hfq on mRNAs. Hfq-Associated mRNAs eOrientation of sRNA candidate (middle) and flanking genes (R and r denote location of a gene on the clockwise or the counterclockwise strand of the Salmonella chromosome). fGenomic location of sRNA candidate gene according to the Salmonella typhimurium LT2 genome. For STnc470 through STnc640 start and end of the entire intergenic region are given. gOut of 145,873 sequences in total. hOut of 122,326 sequences in total. iEnrichment factor calculated by the number of blastable reads from Hfq coIP over control coIP. jDenotes verification on Northern blot in this study for new RNA transcripts; the estimated size is given in nucleotides. kThe cDNA reads map antisense internally of the IS200 element. Based on sequence identity they map to all IS200 elements (tnpA_1 to tnpA_6). lSTnc250 and STnc570 contain small ORFs annotated as ypfM or yneM, respectively, in E. coli (Wassarman et al., 2001). doi:10 1371/journal pgen 1000163 t002 (III) sRNA previously validated on Northern blots in Salmonella (Altier et al., 2000; Figueroa-Bossi et al., 2006; Fortune et al., 2006; Papenfort et al., 2006; Papenfort et al., 2008; Pfeiffer et al., 2007; Sharma et al., 2007; Viegas et al.,
2007). (IV) sRNA predicted through cDNA sequencing and validated by Northern blot analysis in this study. (V) sRNA previously predicted by (Pfeiffer et al., 2007) is recovered in cDNA sequences and validated by Northern blot analysis in this study. (VI) IstR sRNAs (Vogel et al., 2004) were not recovered in cDNA sequences but their expression in Salmonella validated by Northern blot analysis in this study (Figure S5). dFlanking genes of the intergenic region in which the sRNA candidate is located. eOrientation of sRNA candidate (middle) and flanking genes (R and r denote location of a gene on the clockwise or the counterclockwise strand of the Salmonella chromosome). fGenomic location of sRNA candidate gene according to the Salmonella typhimurium LT2 genome. For STnc470 through STnc640 start and end of the entire intergenic region are given. gOut of 145,873 sequences in total. hOut of 122,326 sequences in total. iEnrichment factor calculated by the number of blastable reads from Hfq coIP over control coIP. jDenotes verification on Northern blot in this study for new RNA transcripts; the estimated size is given in nucleotides. kThe cDNA reads map antisense internally of the IS200 element. Based on sequence identity they map to all IS200 elements (tnpA_1 to tnpA_6). Hfq-Associated mRNAs Method of identification is given in the third column. sRNA names follow Salmonella and/or E. coli nomenclature referenced in
(Hershberg et al., 2003; Padalon-Brauch et al., 2008; Papenfort et al., 2008), except STnc490, 500, 520, 540, 560, 570, 580, which have been newly predicted in this study (see Supplementary Table S3). bAlternative sRNA IDs. References in (Hershberg et al., 2003; Padalon-Brauch et al., 2008; Papenfort et al., 2008). cEvidence for sRNAs in Salmonella. (I) Conserved sRNA found in Salmonella cDNA libraries, and previously shown to be expressed in E. coli (relevant ref. in (Papenfort et al., 2008); Table 1). (II) sRNA previously predicted and validated on Northern blots in Salmonella by (Padalon-Brauch et al., 2008). Hfq and Deep Sequencing
PLoS Genetics | www.plosgenetics.org
9
August 2008 | Volume 4 | Issue 8 | e1000163 aGene names of Salmonella sRNAs that have been experimentally proven here, and in previous studies. Method of identification is given in the third column. sRNA names follow Salmonella and/or E. coli nomenclature referenced in
(Hershberg et al., 2003; Padalon-Brauch et al., 2008; Papenfort et al., 2008), except STnc490, 500, 520, 540, 560, 570, 580, which have been newly predicted in this study (see Supplementary Table S3). bAlternative sRNA IDs. References in (Hershberg et al., 2003; Padalon-Brauch et al., 2008; Papenfort et al., 2008). cEvidence for sRNAs in Salmonella. (I) Conserved sRNA found in Salmonella cDNA libraries, and previously shown to be expressed in E. coli (relevant ref. in (Papenfort et al., 2008); Table 1). (II) sRNA previously predicted and validated on Northern blots in Salmonella by (Padalon-Brauch et al., 2008). August 2008 | Volume 4 | Issue 8 | e1000163 9 Hfq and Deep Sequencing (III) sRNA previously validated on Northern blots in Salmonella (Altier et al., 2000; Figueroa-Bossi et al., 2006; Fortune et al., 2006; Papenfort et al., 2006; Papenfort et al., 2008; Pfeiffer et al., 2007; Sharma et al., 2007; Viegas et al.,
2007). (IV) sRNA predicted through cDNA sequencing and validated by Northern blot analysis in this study. (V) sRNA previously predicted by (Pfeiffer et al., 2007) is recovered in cDNA sequences and validated by Northern blot analysis in this study. (VI) IstR sRNAs (Vogel et al., 2004) were not recovered in cDNA sequences but their expression in Salmonella validated by Northern blot analysis in this study (Figure S5). dFlanking genes of the intergenic region in which the sRNA candidate is located. Mechanisms of Pleiotropic Hfq Effects in Virulence and
Flagellar Pathways The earlier shotgun-
cloning studies in bacteria [50,54,71] and many other organisms
(reviewed
in
[72,73])
were
limited
by
costly
Sanger-type
sequencing of individual cDNA inserts from plasmid vectors. The deep sequencing approach described here avoids a cloning
step, and is able to detect small RNAs with unparalleled sensitivity
by defining the 59 and 39 ends of transcripts at basepair resolution. p
p
In an analogous situation, 87% of the flagellar genes were
down-regulated in the Dhfq mutant, yet Hfq primarily bound to
the fhlDC (class I genes), flgMN, flgKL, fliAZ, fliD, fliI and fliP
mRNAs (class II genes) and fliC mRNA (class III gene; Tables S1,
S4 and Figure S4). fhlDC encodes the key transcription factor of
the flagellar gene cascade, and we predicted that loss of this
mRNA would account for much of the flagellar defect of Dhfq,
which is associated with strongly reduced levels of the major
flagellin, FliC (Figure 9B). Ectopic expression of flhDC restored the
levels of FliC to almost wild-type levels in the Dhfq strain carrying
the pBAD-flhDC plasmid (Figure 9B). We note, however, that the
previously reported non-motile phenotype of Dhfq on swim agar
plates [32] was not rescued by flhDC overexpression (data not
shown), presumably because the FlhD2C2-independent chemo-
taxis genes required for full motility are also down-regulated in the
absence of Hfq (Table 1). Deep sequencing of cDNAs has identified the small RNA
component of eukaryotic transcriptomes (e.g., [74,75]), and new
classes of noncoding RNAs associated with eukaryotic RNA-
binding proteins [76,77]. These studies primarily focussed on the
class of 20–30 nucleotide long microRNAs and siRNAs, and
typically included size-fractionation steps. Bacterial riboregulators
are considerably larger (80-250 nucleotides), and we show that
even without prior size fractionation, deep sequencing can capture
and define the termini of these large sRNAs. Our analysis extends the tally of confidently identified sRNAs to
64 in the model pathogen, S. Typhimurium (Table 2). Thirty eight
of these are conserved sRNAs that were initially identified in E. coli, but only a few of their homologues have previously been
shown
to
be
expressed
in
other
enteric
bacteria
[58,59,60,61,62,63,78,79]. A recent study of the widely conserved
DsrA and RprA sRNAs [80] failed to validate their expression
and/or function in Salmonella [81]. Mechanisms of Pleiotropic Hfq Effects in Virulence and
Flagellar Pathways Thus, by identifying the hilD mRNA
as a direct Hfq target, we have revealed the mechanism of part of
the pleiotropic virulence defect of the Dhfq strain. of SPI-1 genes (hilC, hilD, invFGAC, sicA, sip operon, prgHK, and orgB;
Tables S1, S4 and Figures 4, S4). Of these, hilD encodes the
primary transcriptional activator of the SPI-1 region [67]. We
hypothesized that loss of Hfq-association with hilD mRNA in Dhfq
causes loss of HilD protein synthesis, and thereby one of the
strongest hfq phenotypes, i.e. loss of SPI-1 activation and virulence
factor (effector protein) secretion. If so, ectopic HilD overexpres-
sion should restore SPI-1 effector secretion to Dhfq. As predicted,
overproduction of HilD from a PBAD expression plasmid restored
SPI-1 effector secretion to almost wild-type levels in the absence of
Hfq (Figure 9A; compare lanes 1 and 4), and also rescued
expression of the PrgI needle protein indicative of a functional
SPI-1 secretion apparatus (data not shown). In contrast, ectopic
production of HilA, the SPI-1 transcription factor that acts
downstream of HilD, failed to influence the secretion defect of
Dhfq. Preliminary data from gentamicin protection assays that
assess epithelial cell invasion of Salmonella, suggests that overex-
pression of HilD increased the invasion rate of the Dhfq strain by a
factor of ten (data not shown). Thus, by identifying the hilD mRNA
as a direct Hfq target, we have revealed the mechanism of part of
the pleiotropic virulence defect of the Dhfq strain. cellular proteins [68]. Epitope-tagging of the yeast La homolog
was successfully used for global coIP analysis [69]. However, the
requirement for custom high-density microarrays and/or species-
specific antibodies has impeded similar studies in other organisms. It is now apparent that the ideal sRNA discovery approach would
not only detect sRNAs, but would also define their exact sequence. Given the typical genome size of model bacteria (,5 Mb), a high-
density oligonucleotide microarray with ,10 million oligonucle-
otide probes would be required to achieve single basepair
resolution. Such arrays do not exist for any organism, and even
today’s high-density arrays (with 0.5 million features) come with
extraordinarily high set-up and printing costs, and are available for
very few bacteria. Our strategy remedies these technical and
financial limitations. The identification of Hfq-associated RNAs in Salmonella is based
upon a powerful chromosomal epitope-tagging approach [70],
followed by coIP with a commercially-available antibody, and
sequencing of hundreds of thousands cDNAs. Mechanisms of Pleiotropic Hfq Effects in Virulence and
Flagellar Pathways Our analyses revealed an intriguing relationship between the
transcriptomic and deep sequencing data; the genes belonging to
some regulons were consistently down-regulated in the Dhfq
mutant, yet Hfq only associated with a few of the relevant mRNAs. For example, the transcriptomic data showed that the entire SPI-1
pathogenicity island was down-regulated in the Dhfq mutant, but
the Hfq coIP only showed a strong enrichment for a small subset August 2008 | Volume 4 | Issue 8 | e1000163 PLoS Genetics | www.plosgenetics.org 10 Figure 5. Visualization of the clone distribution of exemplar Hfq dependent and independent sRNAs in Salmonella. Clone distribution
for sequences mapped to InvR, SroB, SraH, or 6S sRNAs (red: Hfq coIP, black: control coIP). The vertical axis indicates the number of cDNA sequences
that were obtained. A bent arrow indicates each sRNA promoter, a circled ‘‘T’’ its transcriptional terminator. doi:10.1371/journal.pgen.1000163.g005
Hfq and Deep Sequencing Figure 5. Visualization of the clone distribution of exemplar Hfq dependent and independent sRNAs in Salmonella. Clone distribution
for sequences mapped to InvR, SroB, SraH, or 6S sRNAs (red: Hfq coIP, black: control coIP). The vertical axis indicates the number of cDNA sequences
that were obtained. A bent arrow indicates each sRNA promoter, a circled ‘‘T’’ its transcriptional terminator. doi:10.1371/journal.pgen.1000163.g005 of SPI-1 genes (hilC, hilD, invFGAC, sicA, sip operon, prgHK, and orgB;
Tables S1, S4 and Figures 4, S4). Of these, hilD encodes the
primary transcriptional activator of the SPI-1 region [67]. We
hypothesized that loss of Hfq-association with hilD mRNA in Dhfq
causes loss of HilD protein synthesis, and thereby one of the
strongest hfq phenotypes, i.e. loss of SPI-1 activation and virulence
factor (effector protein) secretion. If so, ectopic HilD overexpres-
sion should restore SPI-1 effector secretion to Dhfq. As predicted,
overproduction of HilD from a PBAD expression plasmid restored
SPI-1 effector secretion to almost wild-type levels in the absence of
Hfq (Figure 9A; compare lanes 1 and 4), and also rescued
expression of the PrgI needle protein indicative of a functional
SPI-1 secretion apparatus (data not shown). In contrast, ectopic
production of HilA, the SPI-1 transcription factor that acts
downstream of HilD, failed to influence the secretion defect of
Dhfq. Preliminary data from gentamicin protection assays that
assess epithelial cell invasion of Salmonella, suggests that overex-
pression of HilD increased the invasion rate of the Dhfq strain by a
factor of ten (data not shown). Mechanisms of Pleiotropic Hfq Effects in Virulence and
Flagellar Pathways Our observation of 149 (DsrA)
and 286 (RprA) cDNAs in the Hfq coIP libraries (versus 6/37 in
the control library), unequivocally confirmed that these important
stress response regulators are both expressed and Hfq-associated. The finding, from this and other studies, that highly-conserved
sRNAs are commonly expressed at the transcriptional level should
prove useful to researchers working in other bacterial systems. PLoS Genetics | www.plosgenetics.org August 2008 | Volume 4 | Issue 8 | e1000163 Discussion Whereas ORF identification in such islands has
become routine, island-specific sRNAs are more difficult to
recognize by bioinformatic-based approaches. these, invR exemplifies a sRNA gene that was likely horizontally
acquired with the SPI-1 virulence region, early in Salmonella
evolution [46]. Intriguingly, InvR is the most frequently recovered
sRNA (.3,000 cDNAs in the Hfq coIP library), which shows that
our approach is not only effective for detecting conserved, but also
species-specific sRNAs of recently acquired pathogenicity regions. Horizontal transfer of virulence islands is a driving force in the
evolution of bacterial pathogens [82], and knowledge of the Besides confirming InvR, the present study found evidence for
the expression of five of the 47 Salmonella sRNA candidate loci
listed by Pfeiffer et al. [46], who predicted orphan promoter/
terminator pairs in IGRs (Table S3 and Figure 2). One of these,
i.e. STnc250, has turned out as a small mRNA gene (see above). While this study was in progress, others reported the discovery of
18 Salmonella expressed sRNA loci [55]. We recovered cDNAs of 8
of these sRNAs (isrB-1, C, E, I-L, and P; Table 2). The fact that 10
of these sRNAs were not recovered probably reflects their low-
level expression under the growth condition used here [55]. This
observation suggests an improvement that could be made to our
method. RNomics- or microarray-based sRNA discovery methods
require sRNAs to be expressed under the chosen assay condition,
unlike bioinformatics-aided approaches that score for orphan
transcription
signals
and
primary
sequence
conservation
[49,51,83,84] or for conservation of RNA structure [53]. Thus,
future studies combining several different growth conditions with
increasing sequencing depth are likely to identify even more novel
sRNAs. Figure 7. Comparison of Hfq and Control coIP cDNA distribu-
tions at the ompD and ompA loci. Extract of the screenshot of the
Integrated Genome Browser, showing the mapped Hfq and Control
cDNAs, and the enrichment curve (ratio of reads of Hfq coIP over
control coIP) for (A) the ompD and (B) ompA transcripts. Shown are
(from top to bottom) the annotations for the ‘‘+’’ strand (blue), the
enrichment curve (grey), the cDNA distributions on the ‘‘+’’ strand for
the Hfq coIP (red) and the control coIP (black), the genome coordinates,
and the annotations for the ‘‘–’’ strand (blue). In panel A, the annotation
of the ompD coding region and the flanking genes, yddG and STM1573,
are indicated. Discussion For ompA, the CDS, -10 and -35 boxes, as well as the
ribosome binding site (RBS) and a CRP binding site are indicated by
black arrows. doi:10.1371/journal.pgen.1000163.g007 Regarding the sensitivity of our approach, it is remarkable that
RyeB sRNA was found in 653 Hfq cDNAs and 24 Control cDNAs
(Table 2); RyeB is late stationary phase-specific [49,50], and barely
detectable by probing of Salmonella RNA from the coIP assay
condition by Northern blot (unpublished results). Moreover, the 24
cDNAs recovered from the control library, i.e. without Hfq coIP,
suggest the exciting possibility that deep sequencing of total RNA,
without prior enrichment or size-fractionation, will prove to be a
successful approach for sRNA discovery. Like any other global
method for RNA identification [85,86], our approach is likely to
show certain biases, e.g., caused by cross-hybridization in the
immunoprecipitation step, or from the limited ability of reverse
transcriptase to deal with stable RNA structures in cDNA
synthesis, and these will need to be studied in more detail. However, it is clear that deep sequencing resolved the termini of
many expressed and/or Hfq-bound sRNAs at basepair resolution
(Figure 5), which has not been achieved by other methods. (
g
)
y
The combination of HTPS of co-immunoprecipitated sRNAs
and mRNAs with transcriptomics partly explains how Hfq acts as
a pleiotropic regulator of Salmonella gene expression. Transcrip-
tome analysis under two different growth conditions suggests that
Hfq regulates the expression of nearly a fifth of all Salmonella genes. This proportion of Hfq-dependent genes is similar to Pseudomonas
aeruginosa (,15% of all genes; [87]), but bigger than for E. coli
(6.3%; [42]), or Vibrio cholerae (5.6%; [30]). However, the different
growth conditions and scoring parameters used for these other
organisms preclude a direct comparison with our Salmonella data. Nonetheless, the strong impact of Hfq on the sS and sE stress
regulons that we observed is consistent with the findings in E. coli
[42] and in part in V. cholerae (sE; [30]), and expands the previous
work
on
Salmonella
sS
and
sE
regulated
genes Figure 7. Comparison of Hfq and Control coIP cDNA distribu-
tions at the ompD and ompA loci. Extract of the screenshot of the
Integrated Genome Browser, showing the mapped Hfq and Control
cDNAs, and the enrichment curve (ratio of reads of Hfq coIP over
control coIP) for (A) the ompD and (B) ompA transcripts. Discussion To understand how bacterial RNA binding proteins such as Hfq
mediate the control of global gene expression at the post-
transcriptional level, direct targets need to be identified. The first
approach that was used to do this in a global fashion involved
detection
of
RNA
co-immunoprecipitated
with
Hfq-specific
antibodies on high-density oligonucleotide microarrays, and
identified new E. coli sRNAs and interesting properties of Hfq
[17]. Similarly, microarray-based detection following co-immuno-
precipitation of eukaryotic mRNA–protein complexes (mRNPs)
identified endogenous organization patterns of mRNAs and A significant number of the Hfq-associated cDNAs correspond
to sRNA loci that are absent from E. coli ([46,55] and Table 2). Of PLoS Genetics | www.plosgenetics.org 11 August 2008 | Volume 4 | Issue 8 | e1000163 August 2008 | Volume 4 | Issue 8 | e1000163 Hfq and Deep Sequencing PLoS Genetics | www.plosgenetics.org
12
August 2008 | Volume 4 | Issue 8 | e1000163 PLoS Genetics | www.plosgenetics.org August 2008 | Volume 4 | Issue 8 | e1000163 12 Hfq and Deep Sequencing Hfq and Deep Sequencing Hfq and Deep Sequencing Figure 6. Expression of 10 new Salmonella sRNAs over growth. Total RNA was isolated from Salmonella at seven different growth stages and/
or conditions and subjected to Northern blot analysis. (A) Blots showing the detection of stable transcripts for seven new sRNAs. The lanes refer to
the following samples (from left to right): aerobic growth of the wild-type strain in L-broth to an OD600 of 0.5, 1 or 2; growth continued after the
culture reached OD600 of 2 for 2 or 6 hours, respectively; SPI-1 inducing condition; SPI-2 inducing condition. (B) Northern blots of three sRNAs
encoded in close proximity (STnc290, STnc440) or antisense (STnc490) to IS200 elements. A schematic presentation of the position of the sRNAs
according to the IS200 element is shown to the right. The upper drawing indicates the two stem-loop structures, start codon, and stop codon of the
transposase-encoding mRNA of the IS200 elements. The three detected sRNAs are indicated by black arrows. Growth conditions as Panel A. (C) RNA
abundance of selected new sRNAs in wild-type (+) versus hfq mutant (2) Salmonella cells at ESP (OD600 of 2). The enrichment factor of each of these
sRNAs in the coIP experiment is given below the blots for comparison. doi:10.1371/journal.pgen.1000163.g006 functional elements of these islands is key to understanding
pathogenesis. August 2008 | Volume 4 | Issue 8 | e1000163 Discussion ORF length is given for each gene, for the overlapping ORFs of flhDC, or for the
intergenic region in the case of glmUS mRNA. Numbers in parentheses below each gene name denote number of cDNA sequences obtained from
Hfq coIP. Promoters and terminators are indicated as above. (B) The binding of Hfq to four mRNA fragments was confirmed by gel mobility shift
assay. 32P-labeled RNA fragments of dppA, glmUS, flhD, or hilD, respectively, were incubated with increasing amounts of Hfq protein (concentrations
of the hexamer are given in nM above the lanes). The lollipops on the left of the gel panels show the position of the unshifted mRNA fragment
Following 10 minutes incubation at 37uC, samples were resolved on native 6% polyacrylamide gels, autoradiographs of which are shown. doi:10.1371/journal.pgen.1000163.g008 Figure 8. Distribution patterns of cDNAs of Hfq-associated mRNA species and confirmation of binding to Hfq. (A) Different mRNAs are
shown with marked open reading frame, promoter and terminator (where known). Start and stop codons are indicated. The clone distribution is
represented by a stairstep diagram of fold enrichment in Hfq coIP vs control coIP per nucleotide below each mRNA. The vertical axis indicates the
enrichment factor in the Hfq coIP calculated over the control coIP. ORF length is given for each gene, for the overlapping ORFs of flhDC, or for the
intergenic region in the case of glmUS mRNA. Numbers in parentheses below each gene name denote number of cDNA sequences obtained from
Hfq coIP. Promoters and terminators are indicated as above. (B) The binding of Hfq to four mRNA fragments was confirmed by gel mobility shift
assay. 32P-labeled RNA fragments of dppA, glmUS, flhD, or hilD, respectively, were incubated with increasing amounts of Hfq protein (concentrations
of the hexamer are given in nM above the lanes). The lollipops on the left of the gel panels show the position of the unshifted mRNA fragment. Following 10 minutes incubation at 37uC, samples were resolved on native 6% polyacrylamide gels, autoradiographs of which are shown. doi:10.1371/journal.pgen.1000163.g008 Figure 8. Distribution patterns of cDNAs of Hfq-associated mRNA species and confirmation of binding to Hfq. (A) Different mRNAs are
shown with marked open reading frame, promoter and terminator (where known). Start and stop codons are indicated. The clone distribution is
represented by a stairstep diagram of fold enrichment in Hfq coIP vs control coIP per nucleotide below each mRNA. PLoS Genetics | www.plosgenetics.org Discussion The vertical axis indicates the
enrichment factor in the Hfq coIP calculated over the control coIP. ORF length is given for each gene, for the overlapping ORFs of flhDC, or for the
intergenic region in the case of glmUS mRNA. Numbers in parentheses below each gene name denote number of cDNA sequences obtained from
Hfq coIP. Promoters and terminators are indicated as above. (B) The binding of Hfq to four mRNA fragments was confirmed by gel mobility shift
assay. 32P-labeled RNA fragments of dppA, glmUS, flhD, or hilD, respectively, were incubated with increasing amounts of Hfq protein (concentrations
of the hexamer are given in nM above the lanes). The lollipops on the left of the gel panels show the position of the unshifted mRNA fragment. Following 10 minutes incubation at 37uC, samples were resolved on native 6% polyacrylamide gels, autoradiographs of which are shown. doi:10.1371/journal.pgen.1000163.g008 subsequently identified as CyaR in Salmonella [63]. Tables 2 and 3
confirm that both ompX mRNA and CyaR strongly associate with
Salmonella Hfq (22.8-fold and 21.2-fold enrichment, respectively). Our current data set comprises several hundred such candidate
mRNAs (Table S4); this catalogue contains many experimentally
confirmed targets of Salmonella sRNAs, e.g., the dppA, fadL, ompD,
or oppA mRNAs [34,46,58,59]. Integrating the score for Hfq-
association deduced from our experiments, and–where applicable–
from the available E. coli data [17] into available algorithms such
as TargetRNA [92] could significantly improve target predictions
for the large class of Hfq-dependent sRNAs. [34,43,44,88,89,90,91]
to
a
global
level. Importantly,
our
combined transcriptomic and coIP data revealed that Hfq exerts
a direct role in gene expression through the control of specific
check-points in other well-defined transcriptional regulons, such as
HilD in the SPI-1 virulence regulon, and FlhD2C2 in the flagellar
gene expression cascade. Transcriptomic profiling by itself is clearly unable to differen-
tiate between transcriptional and post-transcriptional effects of
Hfq. In contrast, enrichment of a regulated mRNA in the Hfq
library has successfully hinted at post-transcriptional regulation by
sRNAs. For example, the observation of OmpX overproduction in
Salmonella Dhfq, combined with ompX mRNA enrichment by Hfq
coIP in E. coli [17], led to the prediction that OmpX synthesis is
repressed by an Hfq-dependent antisense sRNA; this sRNA was Such predictions bring new understanding to the pleiotropic
phenotypes caused by the absence of Hfq in Salmonella [32]. Discussion Shown are
(from top to bottom) the annotations for the ‘‘+’’ strand (blue), the
enrichment curve (grey), the cDNA distributions on the ‘‘+’’ strand for
the Hfq coIP (red) and the control coIP (black), the genome coordinates,
and the annotations for the ‘‘–’’ strand (blue). In panel A, the annotation
of the ompD coding region and the flanking genes, yddG and STM1573,
are indicated. For ompA, the CDS, -10 and -35 boxes, as well as the
ribosome binding site (RBS) and a CRP binding site are indicated by
black arrows. doi:10.1371/journal.pgen.1000163.g007 13 PLoS Genetics | www.plosgenetics.org Figure 8. Distribution patterns of cDNAs of Hfq-associated mRNA species and confirmation of binding to Hfq. (A) Different mRNAs are
shown with marked open reading frame, promoter and terminator (where known). Start and stop codons are indicated. The clone distribution is
represented by a stairstep diagram of fold enrichment in Hfq coIP vs control coIP per nucleotide below each mRNA. The vertical axis indicates the
enrichment factor in the Hfq coIP calculated over the control coIP. ORF length is given for each gene, for the overlapping ORFs of flhDC, or for the
intergenic region in the case of glmUS mRNA. Numbers in parentheses below each gene name denote number of cDNA sequences obtained from
Hfq coIP. Promoters and terminators are indicated as above. (B) The binding of Hfq to four mRNA fragments was confirmed by gel mobility shift
assay. 32P-labeled RNA fragments of dppA, glmUS, flhD, or hilD, respectively, were incubated with increasing amounts of Hfq protein (concentrations
of the hexamer are given in nM above the lanes). The lollipops on the left of the gel panels show the position of the unshifted mRNA fragment. Following 10 minutes incubation at 37uC, samples were resolved on native 6% polyacrylamide gels, autoradiographs of which are shown. doi:10.1371/journal.pgen.1000163.g008
Hfq and Deep Sequencing Hfq and Deep Sequencing Figure 8. Distribution patterns of cDNAs of Hfq-associated mRNA species and confirmation of binding to Hfq. (A) Different mRNAs are
shown with marked open reading frame, promoter and terminator (where known). Start and stop codons are indicated. The clone distribution is
represented by a stairstep diagram of fold enrichment in Hfq coIP vs control coIP per nucleotide below each mRNA. The vertical axis indicates the
enrichment factor in the Hfq coIP calculated over the control coIP. Discussion The
fact that the Salmonella hfq mutant is attenuated for virulence can August 2008 | Volume 4 | Issue 8 | e1000163 PLoS Genetics | www.plosgenetics.org August 2008 | Volume 4 | Issue 8 | e1000163 14 Hfq and Deep Sequencing Figure 9. Rescue of complex Dhfq phenotypes by overexpression of identified Hfq target mRNAs. SDS-PAGE analysis (12% gels stained
with Coomassie) of (A) secreted proteins upon overexpression of the SPI-1 transcription factors, HilA and HilD from pCH-112 and pAS-0045 (lanes 3
and 4) in Salmonella Dhfq. Lanes 1 and 2 show the secreted protein profile of Salmonella wild-type and Dhfq bacteria carrying a control vector, pKP8-
35. (B) Whole cell and secreted proteins upon overexpression of the flagellar transcription factor, FlhD2C2. The left hand three lanes show total protein
samples, and the right hand three lanes show secreted proteins. Genetic background and plasmids are indicated above the lanes; FlhDC was
expressed from plasmid pAS-0081. FliC was also analyzed on a Western blot using a specific antibody (lower panel). FliC protein levels are shown (in
%), in comparison to wild-type Salmonella, which was set to 100% for either the total protein or secreted protein lanes. doi:10.1371/journal.pgen.1000163.g009 Figure 9. Rescue of complex Dhfq phenotypes by overexpression of identified Hfq target mRNAs. SDS-PAGE analysis (12% gels stained
with Coomassie) of (A) secreted proteins upon overexpression of the SPI-1 transcription factors, HilA and HilD from pCH-112 and pAS-0045 (lanes 3
and 4) in Salmonella Dhfq. Lanes 1 and 2 show the secreted protein profile of Salmonella wild-type and Dhfq bacteria carrying a control vector, pKP8-
35. (B) Whole cell and secreted proteins upon overexpression of the flagellar transcription factor, FlhD2C2. The left hand three lanes show total protein
samples, and the right hand three lanes show secreted proteins. Genetic background and plasmids are indicated above the lanes; FlhDC was
expressed from plasmid pAS-0081. FliC was also analyzed on a Western blot using a specific antibody (lower panel). FliC protein levels are shown (in
%), in comparison to wild-type Salmonella, which was set to 100% for either the total protein or secreted protein lanes. doi:10.1371/journal.pgen.1000163.g009 mRNA and noncoding RNA genes. In addition, the available data
sets should help to discover whether Hfq controls the expression of
cis-antisense sRNAs that overlap with mRNA coding regions [54],
or whether certain Salmonella tRNAs are selectively associated with
this protein [22,23]. Discussion now be explained by the requirement of Hfq for the expression of
all but one key pathogenicity islands of Salmonella (SPI-3). In the
SPI-1 invasion gene island, HilD acts at the top of a transcription
factor cascade to activate SPI-1 genes, and to mediate secretion of
effector proteins by the SPI-1 type III secretion system (reviewed
in [67,93]). The levels of hilD mRNA were sevenfold reduced in
Dhfq, but the unchanged activity of a hilD promoter fusion in this
background (unpublished data) argues against direct transcrip-
tional control by Hfq. Rather, the 7.5-fold enrichment of hilD
cDNAs by Hfq coIP (Table S4) suggests that hilD is post-
transcriptionally activated in a Hfq-dependent process, presum-
ably involving an unknown sRNA. Our demonstration that SPI-1
virulence factor secretion is fully restored by HilD overproduction
in Dhfq raises the exciting possibility that post-transcriptional hilD
activation could be key event in Salmonella invasion of epithelial
cells. Bacterial genomes encode a large number of RNA binding
proteins [102], including globally acting proteins such as the
CsrA/RsmA [48] and Csp families [103]. Our generic method will
identify the RNA targets of these proteins in any genetically
tractable bacterium. Bacterial Strains, Plasmids, and Oligodeoxynucleotides This type of
sequence is also recognized by the major endoribonuclease, RNase
E, and Hfq has been shown to protect certain RNAs by
competitive binding to RNase E sites [97,98]. It is tempting to
speculate that Hfq could reduce the impact of DNA from foreign
sources by controlling expression of newly acquired AT-rich genes
at the RNA level, similar to the role of the H-NS DNA-binding
protein in controlling such genes at the DNA level [99,100,101]. PLoS Genetics | www.plosgenetics.org Bacterial Strains, Plasmids, and Oligodeoxynucleotides Bacterial Strains, Plasmids, and Oligodeoxynucleotides
The Salmonella enterica serovar Typhimurium strains used in this
study were: JVS-0255 (Dhfq::CmR, [32]), JVS-1338 (hfqFLAG, [46]),
and the isogenic wild-type strain SL1344 [104]. Plasmid pKP8-35
[59] served as a pBAD control plasmid. The SPI-1 transcription
factor, HilA, was expressed from pCH-112 [105], and HilD from
plasmid pAS-0045 (which carries a hilD PCR fragment obtained
with primer pair JVO-686/-687 amplified from Salmonella DNA,
inserted into plasmid pLS-119 [106] by NcoI/EcoRI cloning). The
FlhDC
expression
plasmid,
pAS-0081,
was
constructed
by
inserting a PCR fragment obtained with primers JVS-2152/-
2153 into plasmid pBAD/Myc-His A (Invitrogen) by NcoI/XhoI
cloning. All cloning procedures where carried out in E. coli strain
Top10 (Invitrogen). Table S6 lists the sequences of oligodeox-
ynucleotides used in this study for cloning and T7 transcript
generation. We expect Hfq to have further roles in SPI-1 expression since
the protein seems to bind to many mRNAs encoded by this
pathogenicity island (Figures 4 and S4). Interestingly, SPI-1 has a
significantly
higher
AT
content
than
the
rest
of
the
S. Typhimurium chromosome [40], predicting that SPI-1 mRNAs
are AU-rich. Coincidently, Hfq primarily recognizes AU-rich
single-stranded regions in RNAs [12,94,95,96]. This type of
sequence is also recognized by the major endoribonuclease, RNase
E, and Hfq has been shown to protect certain RNAs by
competitive binding to RNase E sites [97,98]. It is tempting to
speculate that Hfq could reduce the impact of DNA from foreign
sources by controlling expression of newly acquired AT-rich genes
at the RNA level, similar to the role of the H-NS DNA-binding
protein in controlling such genes at the DNA level [99,100,101]. Collectively, the present study provides the first picture of the
impact of Hfq on Salmonella gene expression at both the
transcriptional and post-transcriptional level. We believe that
more detailed inspection of this freely available data set, in
particular of the remaining ,60% of the chromosome that
remains to be fully analyzed, as well as sampling under different
growth conditions, will expand the gamut of Salmonella small We expect Hfq to have further roles in SPI-1 expression since
the protein seems to bind to many mRNAs encoded by this
pathogenicity island (Figures 4 and S4). Interestingly, SPI-1 has a
significantly
higher
AT
content
than
the
rest
of
the
S. Typhimurium chromosome [40], predicting that SPI-1 mRNAs
are AU-rich. Coincidently, Hfq primarily recognizes AU-rich
single-stranded regions in RNAs [12,94,95,96]. August 2008 | Volume 4 | Issue 8 | e1000163 Materials and Methods Bacterial Strains, Plasmids, and Oligodeoxynucleotides Bacterial Growth and L-arabinose Induction Collectively, the present study provides the first picture of the
impact of Hfq on Salmonella gene expression at both the
transcriptional and post-transcriptional level. We believe that
more detailed inspection of this freely available data set, in
particular of the remaining ,60% of the chromosome that
remains to be fully analyzed, as well as sampling under different
growth conditions, will expand the gamut of Salmonella small Growth in Lennox (L) broth (220 rpm, 37uC) or on L-plates at
37uC
was
used
throughout
this
study. Antibiotics
(where
appropriate) were used at the following concentrations: 50 mg/
ml ampicillin, 30 mg/ml chloramphenicol. For early stationary
phase (ESP) cultures, 30 ml L-broth in 100 ml flasks were
inoculated 1/100 from overnight cultures and incubated at August 2008 | Volume 4 | Issue 8 | e1000163 15 Hfq and Deep Sequencing Table 3. mRNAs represented by $100 cDNAs in the pyrosequencing data. Bacterial Growth and L-arabinose Induction STM number Gene namea
Number of inserts in control
coIPb
Number of inserts in Hfq
coIPc
Enrichmentd
Producte
STM4261
254
1042
4.1
putative inner membrane protein
STM2665
yfiA
72
648
9.0
ribosome stabilization factor
STM1377
lpp
168
608
3.6
murein lipoprotein
STM4087
glpF
40
570
14.3
glycerol diffusion
STM1959
fliC
248
547
2.2
flagellar biosynthesis protein
STM2874
prgH
73
415
5.7
needle complex inner membrane protein
STM2267
ompC
63
385
6.1
outer membrane protein C precursor
STM2882
sipA
36
354
9.8
secreted effector protein
STM2885
sipB
126
335
2.7
translocation machinery component
STM4326
aspA
79
328
4.2
aspartate ammonia-lyase
STM2925
nlpD
30
300
10.0
lipoprotein
STM4086
glpK
115
278
2.4
glycerol kinase
STM2883
sipD
34
269
7.9
translocation machinery component
STM0739
sucD
14
261
18.6
succinyl-CoA synthetase alpha subunit
STM1572
ompD
76
246
3.2
putative outer membrane porin precursor
STM2898
invG
16
226
14.1
outer membrane secretin precursor
STM2879
sicP
6
224
37.3
secretion chaparone
STM2283
glpT
30
221
7.4
sn-glycerol-3-phosphate transport protein
STM1091
sopB
23
216
9.4
secreted effector protein
STM1732
ompW
28
206
7.4
outer membrane protein W precursor
STM0451
hupB
14
198
14.1
DNA-binding protein HU-beta
STM2871
prgK
46
198
4.3
needle complex inner membrane lipoprotein
STM2884
sipC
96
192
2.0
translocation machinery component
STM4406.S
ytfK
6
191
31.8
putative cytoplasmic protein
STM2867
hilC
3
187
62.3
invasion regulatory protein
STM2869
orgB
8
182
22.8
needle complex export protein
STM2878
sptP
20
177
8.9
protein tyrosine phosphatase/GTPase
activating protein
STM2894
invC
14
175
12.5
type III secretion system ATPase
STM2875
hilD
23
174
7.6
invasion protein regulatory protein
STM2284
glpA
57
149
2.6
sn-glycerol-3-phosphate dehydrogenase
large subunit
STM3526
glpD
39
147
3.8
sn-glycerol-3-phosphate dehydrogenase
STM2886
sicA
23
146
6.3
secretion chaperone
STM3138
19
143
7.5
putative methyl-accepting chemotaxis
protein
STM2896
invA
19
142
7.5
needle complex export protein
STM0833
ompX
6
137
22.8
outer membrane protein X
STM2899
invF
18
129
7.2
invasion regulatory protein
STM2924
rpoS
19
129
6.8
RNA polymerase sigma factor
STM0629
cspE
9
125
13.9
cold shock protein E
STM2285
glpB
33
119
3.6
anaerobic glycerol-3-phosphate
dehydrogenase subunit B
STM0736
sucA
42
110
2.6
2-oxoglutarate dehydrogenase
STM2445
ucpA
5
105
21.0
short chain dehydrogenase
STM1070
ompA
77
102
1.3
putative hydrogenase membrane
component precurosr
aGene names according to ColiBase (Chaudhuri et al., 2004)
bBased on 145,873 sequences
cBased on 122,326 sequences
dEnrichment factor calculated by the number of blastable reads from Hfq coIP over control coIP. August 2008 | Volume 4 | Issue 8 | e1000163 coIP and Sequence Analysis y
Strains SL1344 and JVS-1338 (hfqFLAG) were grown in L-broth
under normal aeration at 37uC to ESP. Co-immunoprecipitation
was carried out using the protocol published in [46]. For
pyrosequencing and coIP-on-Chip experiments, samples of two
independent pull down experiments were used. cDNA cloning and
pyrosequencing was performed as described for the identification
of eukaryotic microRNA [109] but omitting size-fractionation of
RNA prior to cDNA synthesis. Microarrays used for the coIP-on-
Chip experiments were designed and produced by Oxford Gene
Technology (Kidlington, UK). They consist of 21,939 60-mer
oligonucleotides tiled throughout the S. Typhimurium SL1344
NCTC13347 genome and 636 control oligonucleotides. The
SL1344 sequence
was obtained
from the Sanger Institute
(Hinxton, UK) website (http://www.sanger.ac.uk/Projects/Sal-
monella/). As this genome is not yet fully annotated, the
oligonucleotides were associated with corresponding S. Typhimur-
ium LT2 genes or intergenic regions, if conserved in both
organisms. Full description of the microarray and protocols used
for generating and analysing the data are associated with the
dataset deposited in the GEO data repository (http://www.ncbi. nlm.nih.gov/geo/) under accession number GSE10149. For
detailed description of data analysis using the Integrated Genome
Browser see the Supplementary Text S1. In brief, cDNA reads
$18 nt were mapped to the Salmonella chromosome and hits per
nucleotide were calculated along the entire genome. To calculate
enrichment factors for Hfq coIP, the Hfq cDNA number was divided
by Control cDNA number at each position of the genome,
following normalization to the total number of mapped reads. Upon upload of the Salmonella genome sequence and annotation
from Genbank (NC_003197.fna and NC_003197.gff), the two
graphs for each library were loaded into the Integrated Genome
Browser (IGB) of Affymetrix (version IGB-4.56), which can be
directly launched by Java Web Start at http://www.affymetrix. com/support/developer/tools/download_igb.affx or downloaded
from http://genoviz.sourceforge.net/. RNA Isolation and Northern Blot Analysis RNA was prepared by hot phenol extraction [108], followed by
DNase I treatment. After separation on 5% polyacrylamide (PAA)
gels containing 8.3 M Urea, or agarose gels, respectively, RNA
was transferred onto Hybond-XL membrane (Amersham). 5 or
10 mg (PAA gels) or 20 mg (agarose gels) RNA was loaded per
sample. For detection of new transcripts c-ATP end-labeled
oligodeoxyribonucleotides were used (see Table S7). Gel Mobility Shift Assay of In Vitro RNA
DNA templates carrying a T7 promoter sequence were
generated by PCR using genomic DNA and primers as listed in
Table
S6. For
dppA
oligonucleotides
JVO-1034/1035
(the
fragment covers the dppA region from positions 2163 to +73
relative to the start codon) were used. For the PCR of the
intergenic region of glmUS primer JVO-2471/2472 were used,
resulting in a product starting 38 nucleotides upstream of the glmU
stop codon and extending to nucleotide 113 in the intergenic
region. For flhD, oligonucleotides JVO-2284/-2285 were used, to
yield a fragment that covers flhD from position 259 to +38
relative to the start codon. The hilD fragment (oligonucleotides
JVO-2286/-2287) spans region +400 to +600 relative to the start
codon. Bacterial Growth and L-arabinose Induction August 2008 | Volume 4 | Issue 8 | e1000163 16 Hfq and Deep Sequencing 10 min at 37uC complexes were separated on 6% native PAA gels
at 4uC. Signals were detected with a Fuji PhosphorImager. 37uC, 220 rpm to an optical density of 2. For SPI-1 induced
cultures, 5 ml L-broth containing NaCl (final concentration
0.3 M) was inoculated from single colonies; incubation was carried
out for 12 hours at 37uC, 220 rpm in tightly closed 15 ml Falcon
tubes. For SPI-2 induced cultures, 70 ml SPI-2 medium [107] in
250 ml flasks were inoculated 1/100 from overnight cultures
grown in the same medium. Bacteria were grown at 37uC,
220 rpm until the culture reached an OD of 0.3. For HilA, HilD,
and FlhDC expression from pBAD-derived plasmids, growth
media were supplemented with 0.1% L-arabinose. PLoS Genetics | www.plosgenetics.org Transcriptomic Experiments Strain SL1344 and JVS-0255 (Dhfq) were grown in L-broth
either to an OD600 of 2 (ESP aerobic growth), or for 12 hours
under SPI-1 inducing conditions. RNA extraction and data
generation were carried out as described with SALSA microarrays
[59]. The complete dataset is available at GEO under accession
number GSE8985. SDS PAGE and Western Blot for Protein Quantification
Proteins were resolved by SDS PAGE (12% gels). For
Coomassie stain or Western analysis, proteins equivalent to 0.1
OD or 0.05 OD, respectively, were loaded per lane. For FliC
detection, strains SL1344 and JVS-0255 carrying the indicated
plasmids were grown to an OD of 1, and induced with L-
arabinose. Growth continued for one hour, and whole cell and
secreted protein fractions were analyzed as described in [32]. FliC
was detected using a monoclonal FliC antibody (BioLegend). Supporting Information Figure S1
Expression levels of RpoE and RpoS in wild-type and
Dhfq cells. Samples were taken from wild-type and Dhfq strains
grown under standard conditions to early stationary phase (OD600
of 2) or for 12 hours under SPI-1 inducing conditions, respectively. (A) Analysis of mRNA level by real time PCR for rpoE, degP, and
rpoS mRNA. (B) Whole cell proteins were separated by 12% SDS
PAGE and sigma factors detected via Western blot. Expression
levels of each protein were determined by densitometry and are
given as a percentage of the wild-type level of expression below
each gel. Found at: doi:10.1371/journal.pgen.1000163.s001 (0.29 MB TIF) Found at: doi:10.1371/journal.pgen.1000163.s001 (0.29 MB TIF) In vitro transcription was performed using the MEGAscript High
Yield Transcription Kit (Ambion, #1333), followed by DNase I
digestion (1 unit, 15 min, 37uC). Following extraction with
phenol:chloroform:isopropanol (25:24:1 v/v), the RNA was pre-
cipitated overnight at -20uC with 1 vol of isopropanol. RNA
integrity was checked on a denaturing polyacrylamide gel. RNA
was 59 end-labeled and purified as described in [59]. Figure S2
Northern detection of Hfq bound mRNAs. Total
RNA was isolated from Salmonella at OD600 of 2. Northern blots
based on agarose gel for detection of long transcripts showing the
detection of six mRNAs. Found at: doi:10.1371/journal.pgen.1000163.s002 (1.29 MB TIF) Found at: doi:10.1371/journal.pgen.1000163.s002 (1.29 MB TIF) Figure S3
Expression levels of small peptide encoding mRNAs
in Salmonella. RNA samples were either taken from wild-type or hfq
mutant Salmonella at different growth stages (as in Figure 6 in the
main manuscript), and probed for STnc250 and STnc570 over
growth (A) or at early stationary phase (B). Gel mobility shift assays were carried out as described in [32]. In brief, labeled RNA was used in 10 ml reactions at a final
concentration of 4 nM. Hfq was added to a final concentration in
the range of 1.25 to 150 nM of the hexamer. After incubation for August 2008 | Volume 4 | Issue 8 | e1000163 17 Hfq and Deep Sequencing Table S4
mRNAs in Hfq CoIP identified by $10 of 170,000
inserts in pyrosequencing data. Found
at:
doi:10.1371/journal.pgen.1000163.s009
(0.81
MB
DOC) Found at: doi:10.1371/journal.pgen.1000163.s003 (0.99 MB TIF) Found at: doi:10.1371/journal.pgen.1000163.s003 (0.99 MB TIF) Figure S4
Hfq binds significantly to a few but not all mRNAs of
the SPI-1 and the flagellar regulon. Shown are all genes belonging
to the SPI-1 and the flagellar regulon. References 16. Lease RA, Woodson SA (2004) Cycling of the Sm-like protein Hfq on the DsrA
small regulatory RNA. J Mol Biol 344: 1211–1223. 1. Majdalani N, Vanderpool CK, Gottesman S (2005) Bacterial small RNA
regulators. Crit Rev Biochem Mol Biol 40: 93–113. 2. Vogel J, Wagner EG (2007) Target identification of regulatory sRNAs in
bacteria. Curr Opin Microbiol 10: 262–270. 17. Zhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, et al. (2003)
Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50:
1111–1124. 3. Storz G, Altuvia S, Wassarman KM (2005) An abundance of RNA regulators. Annu Rev Biochem 74: 199–217. 18. Vytvytska O, Moll I, Kaberdin VR, von Gabain A, Bla¨si U (2000) Hfq (HF1)
stimulates ompA mRNA decay by interfering with ribosome binding. Genes
Dev 14: 1109–1118. 4. Aiba H (2007) Mechanism of RNA silencing by Hfq-binding small RNAs. Curr
Opin Microbiol 10: 134–139. 5. Valentin-Hansen P, Eriksen M, Udesen C (2004) The bacterial Sm-like protein
Hfq: a key player in RNA transactions. Mol Microbiol 51: 1525–1533. 19. Urban JH, Vogel J (2008) Two seemingly homologous noncoding RNAs act
hierarchically to activate glmS mRNA translation. PLoS Biol 6: e64. 6. Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A (1999) Growth phase-
dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181: 6361–6370. y
g
20. Hajnsdorf E, Regnier P (2000) Host factor Hfq of Escherichia coli stimulates
elongation of poly(A) tails by poly(A) polymerase I. Proc Natl Acad Sci U S A
97: 1501–1505. J
7. Kajitani M, Kato A, Wada A, Inokuchi Y, Ishihama A (1994) Regulation of the
Escherichia coli hfq gene encoding the host factor for phage Q beta. J Bacteriol
176: 531–534. 21. Mohanty BK, Maples VF, Kushner SR (2004) The Sm-like protein Hfq
regulates polyadenylation dependent mRNA decay in Escherichia coli. Mol
Microbiol 54: 905–920. 8. Franze de Fernandez MT, Hayward WS, August JT (1972) Bacterial proteins
required for replication of phage Q ribonucleic acid. Pruification and
properties of host factor I, a ribonucleic acid-binding protein. J Biol Chem
247: 824–831. 22. Lee T, Feig AL (2008) The RNA binding protein Hfq interacts specifically with
tRNAs. Rna 14: 514–523. 23. Scheibe M, Bonin S, Hajnsdorf E, Betat H, Mo¨rl M (2007) Hfq stimulates the
activity of the CCA-adding enzyme. BMC Mol Biol 8: 92. 9. Author Contributions Conceived and designed the experiments: AS SL JCDH JV. Performed the Conceived and designed the experiments: AS SL JCDH JV. Performed the Conceived and designed the experiments: AS SL JCDH JV. Performed the
experiments: AS SL KP KR. Analyzed the data: AS SL KP CMS JCDH
JV. Contributed reagents/materials/analysis tools: CMS TTB. Wrote the
paper: AS JCDH JV. Table S3
Coverage of known and candidate Salmonella sRNA
loci in pyrosequencing data. Found
at:
doi:10.1371/journal.pgen.1000163.s008
(0.26
MB
DOC) Table S3
Coverage of known and candidate Salmonella sRNA
loci in pyrosequencing data. Supporting Information The level of Hfq-dependent
gene regulation is shown as fold-change below each gene (taken
from the transcriptomic dataset; Table S1). Representation of
cDNAs in pyrosequencing is indicated by different colours (green:
1–10 clones, turquoise: 11–100 clones, orange: 101–500 clones,
magenta: $501 clones). Found at: doi:10.1371/journal.pgen.1000163.s004 (0.41 MB TIF) Table S5
Genes that were significantly enriched in coIP-on-
Chip and were identified by pyrosequencing. Found
at:
doi:10.1371/journal.pgen.1000163.s010
(0.32
MB
DOC) Table S6
Oligodeoxynucleotides used in this study. Found
at:
doi:10.1371/journal.pgen.1000163.s011
(0.06
MB
DOC) Figure S5
Expression of IstR-1 and IstR-2 in Salmonella. Northern analysis of istR transcripts. Total RNA was extracted
from of E. coli K12 and Salmonella Typhimurium SL1344 cells
grown to an OD600 of 2, exposed to Mitomycin C (0.5 mg/ml) for
30 min as described by [2]. Length is indicated according to
marker sizes in nt. Full-length IstR-1 and IstR-2 are indicated by
arrows. Table S7
Oligodeoxynucleotides used for Northern detection. Found
at:
doi:10.1371/journal.pgen.1000163.s012
(0.05
MB
DOC) Text S1
Supplementary material and methods. Found
at:
doi:10.1371/journal.pgen.1000163.s013
(0.31
MB
DOC) d at: doi:10.1371/journal.pgen.1000163.s005 (0.28 MB TI Table S1
Deregulated genes in Dhfq at ESP. Found
at:
doi:10.1371/journal.pgen.1000163.s006
(0.95
MB
DOC) Table S1
Deregulated genes in Dhfq at ESP. Acknowledgments We thank R. Reinhart and B. Timmermann for pyrosequencing and vertis
Biotechnology AG for cDNA construction. Table S2
Deregulated genes in Dhfq after 12 hrs SPI-inducing
conditions. Found
at:
doi:10.1371/journal.pgen.1000163.s007
(0.21
MB
DOC) References Franze de Fernandez MT, Eoyang L, August JT (1968) Factor fraction
required for the synthesis of bacteriophage Qbeta-RNA. Nature 219: 588–590. 24. Tsui HC, Leung HC, Winkler ME (1994) Characterization of broadly
pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli
K-12. Mol Microbiol 13: 35–49. 10. Sun X, Zhulin I, Wartell RM (2002) Predicted structure and phyletic
distribution of the RNA-binding protein Hfq. Nucleic Acids Res 30:
3662–3671. 25. Muffler A, Fischer D, Hengge-Aronis R (1996) The RNA-binding protein HF-
I, known as a host factor for phage Qbeta RNA replication, is essential for rpoS
translation in Escherichia coli. Genes Dev 10: 1143–1151. 11. Nielsen JS, Boggild A, Andersen CB, Nielsen G, Boysen A, et al. (2007) An
Hfq-like protein in archaea: Crystal structure and functional characterization of
the Sm protein from Methanococcus jannaschii. Rna 13: 2213–2223. 26. Brown L, Elliott T (1996) Efficient translation of the RpoS sigma factor in
Salmonella typhimurium requires host factor I, an RNA-binding protein
encoded by the hfq gene. J Bacteriol 178: 3763–3770. p
j
12. Møller T, Franch T, Hojrup P, Keene DR, Bachinger HP, et al. (2002) Hfq: a
bacterial Sm-like protein that mediates RNA-RNA interaction. Mol Cell 9:
23–30. y
q g
J
27. Sharma AK, Payne SM (2006) Induction of expression of hfq by DksA is
essential for Shigella flexneri virulence. Mol Microbiol 62: 469–479. 13. Kawamoto H, Koide Y, Morita T, Aiba H (2006) Base-pairing requirement for
RNA silencing by a bacterial small RNA and acceleration of duplex formation
by Hfq. Mol Microbiol 61: 1013–1022. 28. Sonnleitner E, Hagens S, Rosenau F, Wilhelm S, Habel A, et al. (2003)
Reduced virulence of a hfq mutant of Pseudomonas aeruginosa O1. Microb
Pathog 35: 217–228. 14. Zhang A, Wassarman KM, Ortega J, Steven AC, Storz G (2002) The Sm-like
Hfq protein increases OxyS RNA interaction with target mRNAs. Mol Cell 9:
11–22. 29. Christiansen JK, Nielsen JS, Ebersbach T, Valentin-Hansen P, Sogaard-
Andersen L, et al. (2006) Identification of small Hfq-binding RNAs in Listeria
monocytogenes. Rna 12: 1383–1396. 15. Mikulecky PJ, Kaw MK, Brescia CC, Takach JC, Sledjeski DD, et al. (2004)
Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and
poly(A) RNAs. Nat Struct Mol Biol 11: 1206–1214. 30. Ding Y, Davis BM, Waldor MK (2004) Hfq is essential for Vibrio cholerae
virulence and downregulates sigma expression. Mol Microbiol 53: 345–354. References August 2008 | Volume 4 | Issue 8 | e1000163 PLoS Genetics | www.plosgenetics.org 18 Hfq and Deep Sequencing Hfq and Deep Sequencing 31. Nakao H, Watanabe H, Nakayama S, Takeda T (1995) yst gene expression in
Yersinia enterocolitica is positively regulated by a chromosomal region that is
highly homologous to Escherichia coli host factor 1 gene (hfq). Mol Microbiol
18: 859–865. 59. Papenfort K, Pfeiffer V, Mika F, Lucchini S, Hinton JC, et al. (2006) sigma(E)-
dependent small RNAs of Salmonella respond to membrane stress by
accelerating global omp mRNA decay. Mol Microbiol 62: 1674–1688. g g
p
y
60. Fortune DR, Suyemoto M, Altier C (2006) Identification of CsrC and
characterization of its role in epithelial cell invasion in Salmonella enterica
serovar Typhimurium. Infect Immun 74: 331–339. 32. Sittka A, Pfeiffer V, Tedin K, Vogel J (2007) The RNA chaperone Hfq is
essential for the virulence of Salmonella typhimurium. Mol Microbiol 63:
193–217. 61. Viegas SC, Pfeiffer V, Sittka A, Silva IJ, Vogel J, et al. (2007) Characterization
of the role of ribonucleases in Salmonella small RNA decay. Nucleic Acids Res
35: 7651–7664. 33. Robertson GT, Roop RM Jr (1999) The Brucella abortus host factor I (HF-I)
protein contributes to stress resistance during stationary phase and is a major
determinant of virulence in mice. Mol Microbiol 34: 690–700. 62. Altier C, Suyemoto M, Ruiz AI, Burnham KD, Maurer R (2000)
Characterization of two novel regulatory genes affecting Salmonella invasion
gene expression. Mol Microbiol 35: 635–646. 34. Figueroa-Bossi N, Lemire S, Maloriol D, Balbontin R, Casadesus J, et al. (2006)
Loss of Hfq activates the sigma-dependent envelope stress response in
Salmonella enterica. Mol Microbiol 62: 838–852. 63. Papenfort K, Pfeiffer V, Lucchini S, Sonawane A, Hinton JC, et al. (2008)
Systematic deletion of Salmonella small RNA genes identifies CyaR, a
conserved CRP-dependent riboregulator of OmpX synthesis. Mol Microbiol in
press. 35. Wilson JW, Ott CM, Zu Bentrup KH, Ramamurthy R, Quick L, et al. (2007)
Space flight alters bacterial gene expression and virulence and reveals a role for
global regulator Hfq. Proc Natl Acad Sci U S A 104: 16299–16304. g
g
q
36. Antal M, Bordeau V, Douchin V, Felden B (2005) A small bacterial RNA
regulates a putative ABC transporter. J Biol Chem 280: 7901–7908. 64. Beuzon CR, Marques S, Casadesus J (1999) Repression of IS200 transposase
synthesis by RNA secondary structures. Nucleic Acids Res 27: 3690–3695. References 65. Kalamorz F, Reichenbach B, Marz W, Rak B, Go¨rke B (2007) Feedback
control of glucosamine-6-phosphate synthase GlmS expression depends on the
small RNA GlmZ and involves the novel protein YhbJ in Escherichia coli. Mol
Microbiol 65: 1518–1533. 37. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005)
Genome sequencing in microfabricated high-density picolitre reactors. Nature
437: 376–380. 38. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, et al. (2007) The
Sorcerer II Global Ocean Sampling expedition: expanding the universe of
protein families. PLoS Biol 5: e16. 66. Joanny G, Le Derout J, Brechemier-Baey D, Labas V, Vinh J, et al. (2007)
Polyadenylation of a functional mRNA controls gene expression in Escherichia
coli. Nucleic Acids Res 35: 2494–2502. 39. Lee CA, Falkow S (1990) The ability of Salmonella to enter mammalian cells is
affected by bacterial growth state. Proc Natl Acad Sci U S A 87: 4304–4308. 67. Ellermeier JR, Slauch JM (2007) Adaptation to the host environment:
regulation of the SPI1 type III secretion system in Salmonella enterica serovar
Typhimurium. Curr Opin Microbiol 10: 24–29. 40. McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, et al. (2001)
Complete genome sequence of Salmonella enterica serovar Typhimurium
LT2. Nature 413: 852–856. 68. Tenenbaum SA, Lager PJ, Carson CC, Keene JD (2002) Ribonomics:
identifying mRNA subsets in mRNP complexes using antibodies to RNA-
binding proteins and genomic arrays. Methods 26: 191–198. 41. Goto S, Bono H, Ogata H, Fujibuchi W, Nishioka T, et al. (1997) Organizing
and computing metabolic pathway data in terms of binary relations. Pac Symp
Biocomput. pp 175–186. 69. Inada M, Guthrie C (2004) Identification of Lhp1p-associated RNAs by
microarray analysis in Saccharomyces cerevisiae reveals association with
coding and noncoding RNAs. Proc Natl Acad Sci U S A 101: 434–439. p
pp
42. Guisbert E, Rhodius VA, Ahuja N, Witkin E, Gross CA (2007) Hfq modulates
the sigmaE-mediated envelope stress response and the sigma32-mediated
cytoplasmic stress response in Escherichia coli. J Bacteriol 189: 1963–1973. 70. Uzzau S, Figueroa-Bossi N, Rubino S, Bossi L (2001) Epitope tagging of
chromosomal genes in Salmonella. Proc Natl Acad Sci U S A 98:
15264–15269. 43. Skovierova H, Rowley G, Rezuchova B, Homerova D, Lewis C, et al. (2006)
Identification of the sigmaE regulon of Salmonella enterica serovar
Typhimurium. Microbiology 152: 1347–1359. 71. References Willkomm DK, Minnerup J, Huttenhofer A, Hartmann RK (2005)
Experimental RNomics in Aquifex aeolicus: identification of small non-coding
RNAs and the putative 6S RNA homolog. Nucleic Acids Res 33: 1949–1960. yp
gy
44. Bang IS, Frye JG, McClelland M, Velayudhan J, Fang FC (2005) Alternative
sigma factor interactions in Salmonella: sigma and sigma promote antioxidant
defences by enhancing sigma levels. Mol Microbiol 56: 811–823. 72. Hu¨ttenhofer A, Brosius J, Bachellerie JP (2002) RNomics: identification and
function of small, non-messenger RNAs. Curr Opin Chem Biol 6: 835–843. 45. Garcia-Vallve S, Guzman E, Montero MA, Romeu A (2003) HGT-DB: a
database of putative horizontally transferred genes in prokaryotic complete
genomes. Nucleic Acids Res 31: 187–189. 73. Hu¨ttenhofer A (2005) Experimental RNomics: A Global Approach to Identify
Non-coding RNAs in Model Organisms. In: Hartmann R, Bindereif A,
Scho¨n A, Westhof E, eds (2005) Handbook of RNA Biochemistry. Weinheim,
Germany: WILEY-VCH Verlag GmbH. pp 643–654. 46. Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, et al. (2007) A small
non-coding RNA of the invasion gene island (SPI-1) represses outer membrane
protein synthesis from the Salmonella core genome. Mol Microbiol 66:
1174–1191. 74. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, et al. (2005) Elucidation
of the small RNA component of the transcriptome. Science 309: 1567–1569. 47. Hershberg R, Altuvia S, Margalit H (2003) A survey of small RNA-encoding
genes in Escherichia coli. Nucleic Acids Res 31: 1813–1820. 75. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, et al. (2006) Large-scale
sequencing reveals 21U-RNAs and additional microRNAs and endogenous
siRNAs in C. elegans. Cell 127: 1193–1207. 48. Babitzke P, Romeo T (2007) CsrB sRNA family: sequestration of RNA-binding
regulatory proteins. Curr Opin Microbiol 10: 156–163. 76. Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, et al. (2006)
A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442:
203–207. 49. Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001)
Identification of novel small RNAs using comparative genomics and
microarrays. Genes Dev 15: 1637–1651. 77. Girard A, Sachidanandam R, Hannon GJ, Carmell MA (2006) A germline-
specific class of small RNAs binds mammalian Piwi proteins. Nature 442:
199–202. y
50. Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG, et al. (2003)
RNomics in Escherichia coli detects new sRNA species and indicates parallel
transcriptional output in bacteria. References Nucleic Acids Res 31: 6435–6443. 78. Bossi L, Figueroa-Bossi N (2007) A small RNA downregulates LamB
maltoporin in Salmonella. Mol Microbiol 65: 799–810. transcriptional output in bacteria. Nucleic Acids Res 31: 6435–6443. 51. Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, et al. (2001)
Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 11: 941–950. 79. Julio SM, Heithoff DM, Mahan MJ (2000) ssrA (tmRNA) plays a role in
Salmonella enterica serovar Typhimurium pathogenesis. J Bacteriol 182:
1558–1563. 52. Brownlee GG (1971) Sequence of 6S RNA of E. coli. Nat New Biol 229:
147–149. 80. Repoila F, Majdalani N, Gottesman S (2003) Small non-coding RNAs, co-
ordinators of adaptation processes in Escherichia coli: the RpoS paradigm. Mol
Microbiol 48: 855–861. 53. Rivas E, Klein RJ, Jones TA, Eddy SR (2001) Computational identification of
noncoding RNAs in E. coli by comparative genomics. Curr Biol 11:
1369–1373. 81. Jones AM, Goodwill A, Elliott T (2006) Limited role for the DsrA and RprA
regulatory RNAs in rpoS regulation in Salmonella enterica. J Bacteriol 188:
5077–5088. 54. Kawano M, Reynolds AA, Miranda-Rios J, Storz G (2005) Detection of 59- and
39-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia
coli. Nucleic Acids Res 33: 1040–1050. 82. Dobrindt U, Hochhut B, Hentschel U, Hacker J (2004) Genomic islands in
pathogenic and environmental microorganisms. Nat Rev Microbiol 2:
414–424. 55. Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
et al. (2008) Small RNAs encoded within genetic islands of Salmonella
typhimurium show host-induced expression and role in virulence. Nucleic
Acids Res. 83. Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, et al. (2002) A
bioinformatics based approach to discover small RNA genes in the Escherichia
coli genome. Biosystems 65: 157–177. 56. Song M, Kim HJ, Kim EY, Shin M, Lee HC, et al. (2004) ppGpp-dependent
stationary phase induction of genes on Salmonella pathogenicity island 1. J Biol
Chem 279: 34183–34190. 84. Livny J, Brencic A, Lory S, Waldor MK (2006) Identification of 17
Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in
10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids
Res 34: 3484–3493. 57. Deiwick J, Nikolaus T, Erdogan S, Hensel M (1999) Environmental regulation
of Salmonella pathogenicity island 2 gene expression. Mol Microbiol 31:
1759–1773. 85. Hu¨ttenhofer A, Vogel J (2006) Experimental approaches to identify non-coding
RNAs. Nucleic Acids Res 34: 635–646. 58. References Sharma CM, Darfeuille F, Plantinga TH, Vogel J (2007) A small RNA
regulates multiple ABC transporter mRNAs by targeting C/A-rich elements
inside and upstream of ribosome-binding sites. Genes Dev 21: 2804–2817. 86. Altuvia S (2007) Identification of bacterial small non-coding RNAs:
experimental approaches. Curr Opin Microbiol 10: 257–261. PLoS Genetics | www.plosgenetics.org August 2008 | Volume 4 | Issue 8 | e1000163 19 Hfq and Deep Sequencing Hfq and Deep Sequencing 99. Lucchini S, Rowley G, Goldberg MD, Hurd D, Harrison M, et al. (2006) H-NS
mediates the silencing of laterally acquired genes in bacteria. PLoS Pathog 2:
e81. 87. Sonnleitner E, Schuster M, Sorger-Domenigg T, Greenberg EP, Blasi U (2006)
Hfq-dependent alterations of the transcriptome profile and effects on quorum
sensing in Pseudomonas aeruginosa. Mol Microbiol 59: 1542–1558. g
g
88. Rhodius VA, Suh WC, Nonaka G, West J, Gross CA (2006) Conserved and
variable functions of the sigmaE stress response in related genomes. PLoS Biol
4: e2. 100. Navarre WW, Porwollik S, Wang Y, McClelland M, Rosen H, et al. (2006)
Selective silencing of foreign DNA with low GC content by the H-NS protein
in Salmonella. Science 313: 236–238. 89. Fang FC, Chen CY, Guiney DG, Xu Y (1996) Identification of sigma S-
regulated genes in Salmonella typhimurium: complementary regulatory
interactions between sigma S and cyclic AMP receptor protein. J Bacteriol
178: 5112–5120. 101. Doyle M, Fookes M, Ivens A, Mangan MW, Wain J, et al. (2007) An H-NS-like
stealth protein aids horizontal DNA transmission in bacteria. Science 315:
251–252. 102. Anantharaman V, Koonin EV, Aravind L (2002) Comparative genomics and
evolution of proteins involved in RNA metabolism. Nucleic Acids Res 30:
1427–1464. 90. Robbe-Saule V, Coynault C, Ibanez-Ruiz M, Hermant D, Norel F (2001)
Identification of a non-haem catalase in Salmonella and its regulation by RpoS
(sigmaS). Mol Microbiol 39: 1533–1545. 103. Yamanaka K, Fang L, Inouye M (1998) The CspA family in Escherichia coli:
multiple gene duplication for stress adaptation. Mol Microbiol 27: 247–255. g
91. Ibanez-Ruiz M, Robbe-Saule V, Hermant D, Labrude S, Norel F (2000)
Identification of RpoS (sigma(S))-regulated genes in Salmonella enterica
serovar typhimurium. J Bacteriol 182: 5749–5756. 104. Hoiseth SK, Stocker BA (1981) Aromatic-dependent Salmonella typhimurium
are non-virulent and effective as live vaccines. Nature 291: 238–239. 92. Tjaden B, Goodwin SS, Opdyke JA, Guillier M, Fu DX, et al. (2006) Target
prediction for small, noncoding RNAs in bacteria. August 2008 | Volume 4 | Issue 8 | e1000163 References Nucleic Acids Res 34:
2791–2802. 105. Lostroh CP, Bajaj V, Lee CA (2000) The cis requirements for transcriptional
activation by HilA, a virulence determinant encoded on SPI-1. Mol Microbiol
37: 300–315. 93. Jones BD (2005) Salmonella invasion gene regulation: a story of environmental
awareness. J Microbiol 43 Spec No. pp 110–117. 106. Schechter LM, Lee CA (2001) AraC/XylS family members, HilC and HilD,
directly bind and derepress the Salmonella typhimurium hilA promoter. Mol
Microbiol 40: 1289–1299. p
pp
94. Sledjeski DD, Whitman C, Zhang A (2001) Hfq is necessary for regulation by
the untranslated RNA DsrA. J Bacteriol 183: 1997–2005. 107. Lober S, Jackel D, Kaiser N, Hensel M (2006) Regulation of Salmonella
pathogenicity island 2 genes by independent environmental signals. Int J Med
Microbiol 296: 435–447. 95. Senear AW, Steitz JA (1976) Site-specific interaction of Qbeta host factor and
ribosomal protein S1 with Qbeta and R17 bacteriophage RNAs. J Biol Chem
251: 1902–1912. 108. Mattatall NR, Sanderson KE (1996) Salmonella typhimurium LT2 possesses
three distinct 23S rRNA intervening sequences. J Bacteriol 178: 2272–2278. 96. Zhang A, Altuvia S, Tiwari A, Argaman L, Hengge-Aronis R, et al. (1998) The
OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I)
protein. Embo J 17: 6061–6068. 109. Berezikov E, Thuemmler F, van Laake LW, Kondova I, Bontrop R, et al. (2006) Diversity of microRNAs in human and chimpanzee brain. Nat Genet
38: 1375–1377. 97. Folichon M, Arluison V, Pellegrini O, Huntzinger E, Regnier P, et al. (2003)
The poly(A) binding protein Hfq protects RNA from RNase E and
exoribonucleolytic degradation. Nucleic Acids Res 31: 7302–7310. 110. Lobry JR (1996) Asymmetric substitution patterns in the two DNA strands of
bacteria. Mol Biol Evol 13: 660–665. 98. Moll I, Afonyushkin T, Vytvytska O, Kaberdin VR, Blasi U (2003) Coincident
Hfq binding and RNase E cleavage sites on mRNA and small regulatory
RNAs. Rna 9: 1308–1314. August 2008 | Volume 4 | Issue 8 | e1000163 PLoS Genetics | www.plosgenetics.org 20
|
https://openalex.org/W3017550957
|
https://www.frontiersin.org/articles/10.3389/fnana.2020.00013/pdf
|
English
| null |
Anatomy and Connectivity of the Subthalamic Nucleus in Humans and Non-human Primates
|
Frontiers in neuroanatomy
| 2,020
|
cc-by
| 22,004
|
Anatomy and Connectivity of the
Subthalamic Nucleus in Humans and
Non-human Primates Aron Emmi1, Angelo Antonini2, Veronica Macchi1, Andrea Porzionato1* and
Raffaele De Caro1 1 Institute of Human Anatomy, Department of Neuroscience, University of Padua, Padua, Italy, 2 Parkinson and Movement
Disorders Unit, Neurology Clinic, Department of Neuroscience, University of Padua, Padua, Italy The Subthalamic Nucleus (STh) is an oval-shaped diencephalic structure located
ventrally to the thalamus, playing a fundamental role in the circuitry of the basal ganglia. In addition to being involved in the pathophysiology of several neurodegenerative
disorders, such as Huntington’s and Parkinson’s disease, the STh is one of the
target nuclei for deep brain stimulation. However, most of the anatomical evidence
available derives from non-human primate studies. In this review, we will present the
topographical and morphological organization of the nucleus and its connections to
structurally and functionally related regions of the basal ganglia circuitry. We will also
highlight the importance of additional research in humans focused on validating STh
connectivity, cytoarchitectural organization, and its functional subdivision. Edited by:
Yoland Smith, Edited by:
Yoland Smith,
Emory University, United States REVIEW
published: 22 April 2020
doi: 10.3389/fnana.2020.00013 REVIEW
published: 22 April 2020
doi: 10.3389/fnana.2020.00013 1The abbreviation “STh,” as seen in G. Paxinos’s texts, is preferred over the more widely used “STN,” as it may be confused
for an abbreviation of Solitary Tract Nucleus. INTRODUCTION Emory University, United States Emory University, United States
Reviewed by:
Adriana Galvan,
Emory University, United States
Martin Parent,
Laval University, Canada
*Correspondence:
Andrea Porzionato
andrea.porzionato@unipd.it Reviewed by:
Adriana Galvan,
Emory University, United States
Martin Parent,
Laval University, Canada The Subthalamic Nucleus (STh)1, also known as Corpus Luysii, is an oval-shaped diencephalic
structure located ventrally to the thalamus (Allheid et al., 1990; Parent and Hazrati, 1995; Joel
and Weiner, 1997), playing a fundamental role in the circuitry of the basal ganglia. Described
for the first time by Jules Bernard Luys (1865) (1828–1897), its functions remained largely
unknown until 1927, when J. P. Martin reported the first case of hemichorea following lesion
of the STh (Martin, 1927). As a key structure involved in the pathophysiology of several
neurological disorders (e.g., Fedio et al., 1979; Martin and Gusella, 1986; Reiner et al., 1988;
Albin et al., 1989b, 1990a,b; Alexander et al., 1990; Bahatia and Marsden, 1994; Ferrante
et al., 1994; Lozano et al., 2002; Temel et al., 2006a; Temel and Visser-Vandewalle, 2006;
Hardman et al., 1997), the STh has also become a target for deep brain stimulation (DBS) in
Parkinson’s Disease (PD) to modulate its firing patterns and improve clinical manifestations
(Ranck, 1975; Lozano et al., 2002). In PD, the progressive loss of dopaminergic neurons in the
substantia nigra pars compacta causes an alteration of the striatopallidal and pallidosubthalamical
pathways in the basal ganglia, resulting in an abnormal burst-firing pattern in STh neurons
(Magill et al., 2000; Urbain et al., 2002; Temel et al., 2005). DBS modulates STh firing, *Correspondence:
Andrea Porzionato
andrea.porzionato@unipd.it Received: 07 December 2019
Accepted: 13 March 2020
Published: 22 April 2020
Citation:
Emmi A, Antonini A, Macchi V,
Porzionato A and De Caro R (2020)
Anatomy and Connectivity of the
Subthalamic Nucleus in Humans
and Non-human Primates. Front. Neuroanat. 14:13. doi: 10.3389/fnana.2020.00013 Received: 07 December 2019
Accepted: 13 March 2020
Published: 22 April 2020 Keywords: subthalamic nucleus, Parkinson, anatomy, connectivity, topography Keywords: subthalamic nucleus, Parkinson, anatomy, connectivity, topography Citation: Emmi A, Antonini A, Macchi V,
Porzionato A and De Caro R (2020)
Anatomy and Connectivity of the
Subthalamic Nucleus in Humans
and Non-human Primates. Front. Neuroanat. 14:13. doi: 10.3389/fnana.2020.00013 April 2020 | Volume 14 | Article 13 1 Frontiers in Neuroanatomy | www.frontiersin.org Anatomy of the Subthalamic Nucleus Emmi et al. resulting in improvement in motor and non-motor disability as
well as quality of life (Grill and Mcintyre, 2001; Dostrovsky and
Lozano, 2002; Grill et al., 2004; Mcintyre et al., 2004). However,
adverse side effects of the treatment are not to be underestimated
(Saint-Cyr et al., 2000; Berney et al., 2002; Kulisevsky et al.,
2002; Temel et al., 2006a,b): in a recent review Temel et al. (2006a,b) reported that out of 1389 patients who underwent
bilateral STh DBS, 41% presented cognitive dysfunctions and
decline in executive functions, 8% exhibited major depression
symptoms and further 4% showed signs of hypomania. Even
though the authors evidenced no association between the surgical
approach to STh DBS and the side effects of the treatment,
a possible explanation for cognitive and affective dysfunctions
following DBS may reside in the functional subdivision of the
STh, which is known to project to different circuits of the basal
ganglia in primates (Carpenter et al., 1981b; Smith et al., 1990;
Shink et al., 1996; Joel and Weiner, 1997). Thus, the stimulation
of specific areas of the nucleus may modulate connectivity within
associative and limbic circuits of the basal ganglia (Vergani et al.,
2007; Dafsari et al., 2016, 2018a,b; Fabbri et al., 2017; Hamel et al.,
2017; Antonini and Obeso, 2018; Petry-Schmelzer et al., 2019). In the following review we critically assess the available literature
on STh morphology, morphometry and structural connectivity. With respect to other reviews in literature, we present a detailed
description of the topographical organization of STh connectivity
by comparing non-human primate tracing studies and human
fiber tracking studies, evidencing similarities and differences
between humans and non-human primates and methodological
approaches used. The evolution of STh functional subdivision
models is also briefly assessed and compared to progress achieved
in human and non-human primate connectivity studies. Hence,
our aim is to summarize the available anatomical evidence
regarding connections and functional subdivisions of the STh,
while suggesting aspects that require further investigation. Citation: the base of the cerebral peduncle in the mesencephalon, while
the most caudal part of the STh is situated atop the rostral
extent of the substantia nigra (Allheid et al., 1990), in particular
the dorsolateral aspect of the pars reticulata (Figures 2B,C). Dopaminergic nigrostriatal fibers pass dorsomedially to the STh
through the medial forebrain bundle, where they enter the Fields
of Forel and ascend to the striatum (Parent et al., 2000). The STh is characterized by rich iron deposits (Rutledge
et al., 1987) which can be evidenced through Perl’s stain in
histological sections (Massey and Yousry, 2010; Massey et al.,
2012); furthermore, these deposits are known to accentuate in
pathological conditions, such as PD (Kosta et al., 2006). The
vascular supply of the STh derives mainly from the perforating
branches of the anterior choroidal artery and the posterior
communicating artery, originating from the internal carotid
artery, and posteromedial choroidal arteries, which derive from
the superior cerebellar artery, hence from the vertebrobasilar
circulation (Hamani et al., 2004). From a cytoarchitectonical perspective, the STh of rodents,
non-human primates and humans is largely characterized by
the presence of excitatory glutamatergic neurons (Type I Grey
Neurons), even though a small population of γ-aminobutyric
acid interneurons (Type II Grey Neurons) has been identified
(Iwahori, 1987; Albin et al., 1989a; Parent and Hazrati, 1995;
Shink et al., 1996; Clarke et al., 1997; Kearney and Albin, 2000;
Wang et al., 2000; Tai et al., 2001; Levesque and Parent, 2005;
Marani et al., 2008). In rodents Kita et al. (1983) evidenced two
morphologically diverse subpopulations of projection neurons in
the STh through horseradish peroxidase labeling: 1. Type I STh Neurons, characterized by (a) axon collaterals
contacting STh neurons at a local level, and by (b)
dense dendritic arborizations, especially in proximity
of the perykarion. 2. Type II STh Neurons, which possess no axon collaterals
at a local level and present fewer dendrites at a
proximal level. Frontiers in Neuroanatomy | www.frontiersin.org ANATOMY OF THE SUBTHALAMIC
NUCLEUS Both neuron types found in the rodent STh possess, however,
a fundamental common feature which consists in a main axon
dividing into two opposite-facing branches; the first branch
ascends toward the lenticular nucleus, contacting mainly, but
not exclusively, the globus pallidus; the second branch descends
toward the mesencephalon and contacts the neurons of the
substantia nigra pars compacta and pars reticulata (Gerfen et al.,
1982; Kita et al., 1983; Kita and Kitai, 1987; Groenewegen and
Berendse, 1990), as seen in Figure 3. As a diencephalic structure, the STh has a close topographical
relationship with the nuclei of the basal ganglia and with the
structures of the mesencephalon (Figures 1, 2A). Dorsally,
the STh confines with the zona incerta (ZI); the Field H2
of Forel, in particular the lenticular fasciculus, defines the
dorsolateral margin of the nucleus, while the Field H1 of
Forel, constituted mainly by the thalamic fasciculus, delineates
part of its dorsomedial margin. The latter originates from the
conjunction of the ansa lenticularis and part of the adjoining
fibers of the lenticular fasciculus (Williams and Warwick, 1980),
which separates the STh from the nucleus of the zona incerta. The ventromedial margin of the STh is delimitated by the ansa
lenticularis, a white matter bundle originating from the ventral
aspect of the lenticular nucleus which then joins the lenticular
fasciculus to form the thalamic fasciculus, circumnavigating the
medial aspect of the STh, as seen in Figures 2B,C. In
primates,
glutamatergic
neurons
in
the
STh
are
characterized by a large oval-shaped perykarion with a transverse
diameter variable between 25 and 40 µm, whilst possessing
wide dendritic arborizations which extend up to 400 µm from
the soma; interneurons are more sparse, with fewer dendritic
arborizations and generally smaller somata (Rafols and Fox,
1976; Yelnik and Percheron, 1979). Sato et al. (2000b) evidenced
a branching pattern which varies in relationship to the target of
the neurons: neurons contacting both the substantia nigra and
the pallidal complex bifurcate in rostral and caudal branches Ventrally, the rostral regions of the STh confine with the
dorsomedial aspect of the internal capsule as it continues into April 2020 | Volume 14 | Article 13 2 Emmi et al. Anatomy of the Subthalamic Nucleus FIGURE 1 | Coronal macrosection of the human brain at the level of the mammillary bodies. Human specimen from the body donation program of the Institute of
Human Anatomy of the University of Padua. ANATOMY OF THE SUBTHALAMIC
NUCLEUS The STh (Subthalamic Nucleus) appears as the slightly dark area dorsal to the Substantia Nigra and ventral to the Zona
Incerta. FIGURE 1 | Coronal macrosection of the human brain at the level of the mammillary bodies. Human specimen from the body donation program of the Institute of
Human Anatomy of the University of Padua. The STh (Subthalamic Nucleus) appears as the slightly dark area dorsal to the Substantia Nigra and ventral to the Zona
Incerta. Levesque and Parent (2005) studied the morphological
characteristics of GABAergic interneurons within the STh
compared to the main population projection neurons. The
interneurons were identified by a distinct glutamic acid
decarboxylase (GAD) immunoreactivity and presented smaller
somata than projection neurons (12 versus 24 µm) with thinner
and less numerous dendrites. According to the authors, these
neurons appear similar to the interneurons identified in non-
human primates by Rafols and Fox (1976) through Golgi
silver impregnation. Another interesting aspect identified by
Levesque and Parent (2005) is the lack of parvalbumin (PV)
and calretinin (CR) immunoreactivity of human GABAergic
interneurons within the STh; in fact, only projection neurons
appear to be immunoreactive for these calcium binding proteins. Furthermore PV + neurons appear more abundant dorsolaterally
within the STh, while CR + neurons were predominant in the
ventromedial STh. similarly to the neurons identified in rodents by Kita et al. (1983),
while neurons projecting only to the striatum or the pallidal
complex present a single branch which bifurcates in proximity
of its target; in particular, the authors identified five subtypes
of subthalamic neurons in non-human primates based on their
axon branching patterns: (1) neurons projecting to the SNr, GPi,
and GPe (21.3%); (2) neurons projecting to the SNr and GPe
(2.7%); (3) neurons projecting to the GPi and GPe (48%); (4)
neurons projecting to the GPe (10.7%); (5) neurons projecting
to the striatum (17.3%). It appears evident that, compared to
rodents, non-human primates present a more diverse population
of subthalamic neurons with different axon branching patterns. The typical axonal bifurcation encountered in rodents by Kita
et al. (1983; Kita and Kitai, 1987) is present only in a small
portion of primate STh neurons (type I and II STh neurons
according to Sato et al. (2000b) accounting only for the 24%
of the total population identified by Sato et al. (2000b). The
remaining neurons present a branching pattern that has no direct
correspondence in rodents. Frontiers in Neuroanatomy | www.frontiersin.org ANATOMY OF THE SUBTHALAMIC
NUCLEUS Through stereology, Hardman et al. (2002) compared the
neuronal population of the STh in rodents, non-human
primates and humans. While the number of neurons was
proportional to the cross-sectional area of the STh across species,
the proportional amount of neurons expressing parvalbumin
(a calcium binding protein) was significantly lower in rodents
compared to non-human primates and humans. Considering Even though the morphology of subthalamic neurons has been
adequately studied in rodents, primates, and even in minipigs
(Larsen et al., 2004), only few studies have examined human
specimen (Levesque and Parent, 2005), thus representing a
potential field for further investigations. April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 3 Anatomy of the Subthalamic Nucleus Emmi et al. FIGURE 2 | (A) Horizontal section of the human brain at the level of the mesencephalon (A). Klüver-Barrera Stain. 1.25× Magnification, scale bar = 500 µm. STh,
subthalamic nucleus; CP, cerebral peduncle; RN, Red Nucleus. (B) Coronal section of the brain passing through the Subthalamic Nucleus, posteriorly to the anterior
commissure. Luxol Fast Blue Stain. 1.25× Magnification, scale bar = 500 µm. STh, subthalamic nucleus; CP, cerebral peduncle; AL, ansa lenticularis; LF, lenticular
fasciculus; SN, substantia nigra; ZI, zona incerta. Human specimen from the body donation program of the Institute of Human Anatomy of the University of Padua. (B) Coronal section passing through the postcommissural basal ganglia and the subthalamic nucleus, Weigert-Pal Stain. Human specimen from the body donation
program of the Institute of Human Anatomy of the University of Padua. 1, Caudate nucleus; 2, Insular cortex; 3, Putamen; 4, Claustrum; 5, Ventral regions of the
putamen, in relationship with the substantia innominata; 6, External Globus Pallidus; 7, Internal Globus Pallidus; 8, Substantia Nigra; 9, Subthalamic Nucleus; 10,
Zona Incerta; 11, Lateral and medial thalamic nuclei; 12, Anterior dorsal nucleus of the thalamus. A, Internal capsule; B, External capsule; C, Extreme Capsule; D,
Optic tract; E, Cerebral peduncle; F, Ansa lenticularis; G, Lenticular Fasciculus. (C) Digital schematization of a coronal section passing through the postcommissural
basal ganglia, similar to the section seen in panel (B). STh, Subthalamic Nucleus; SN, Substantia Nigra; GPi, Internal Globus Pallidus. GPe, External Globus Pallidus;
Pu, Putamen; Th, thalamus; Ant. Dors Th, Anterior Dorsal nuclei of the Thalamus; Cau, Caudate nucleus; L. Vent., Lateral Ventricle; CC, Corpus Callosum; IC,
Internal Capsule; Opt, Optic Tract; LF, Lenticular Fasciculus; AL, Ansa Lenticularis. ANATOMY OF THE SUBTHALAMIC
NUCLEUS FIGURE 2 | (A) Horizontal section of the human brain at the level of the mesencephalon (A). Klüver-Barrera Stain. 1.25× Magnification, scale bar = 500 µm. STh,
subthalamic nucleus; CP, cerebral peduncle; RN, Red Nucleus. (B) Coronal section of the brain passing through the Subthalamic Nucleus, posteriorly to the anterior
commissure. Luxol Fast Blue Stain. 1.25× Magnification, scale bar = 500 µm. STh, subthalamic nucleus; CP, cerebral peduncle; AL, ansa lenticularis; LF, lenticular
fasciculus; SN, substantia nigra; ZI, zona incerta. Human specimen from the body donation program of the Institute of Human Anatomy of the University of Padua. (B) Coronal section passing through the postcommissural basal ganglia and the subthalamic nucleus, Weigert-Pal Stain. Human specimen from the body donation
program of the Institute of Human Anatomy of the University of Padua. 1, Caudate nucleus; 2, Insular cortex; 3, Putamen; 4, Claustrum; 5, Ventral regions of the
putamen, in relationship with the substantia innominata; 6, External Globus Pallidus; 7, Internal Globus Pallidus; 8, Substantia Nigra; 9, Subthalamic Nucleus; 10,
Zona Incerta; 11, Lateral and medial thalamic nuclei; 12, Anterior dorsal nucleus of the thalamus. A, Internal capsule; B, External capsule; C, Extreme Capsule; D,
Optic tract; E, Cerebral peduncle; F, Ansa lenticularis; G, Lenticular Fasciculus. (C) Digital schematization of a coronal section passing through the postcommissural
basal ganglia, similar to the section seen in panel (B). STh, Subthalamic Nucleus; SN, Substantia Nigra; GPi, Internal Globus Pallidus. GPe, External Globus Pallidus;
Pu, Putamen; Th, thalamus; Ant. Dors Th, Anterior Dorsal nuclei of the Thalamus; Cau, Caudate nucleus; L. Vent., Lateral Ventricle; CC, Corpus Callosum; IC,
Internal Capsule; Opt, Optic Tract; LF, Lenticular Fasciculus; AL, Ansa Lenticularis. FIGURE 2 | (A) Horizontal section of the human brain at the level of the mesencephalon (A). Klüver-Barrera Stain. 1.25× Magnification, scale bar = 500 µm. STh,
subthalamic nucleus; CP, cerebral peduncle; RN, Red Nucleus. (B) Coronal section of the brain passing through the Subthalamic Nucleus, posteriorly to the anterior
commissure. Luxol Fast Blue Stain. 1.25× Magnification, scale bar = 500 µm. STh, subthalamic nucleus; CP, cerebral peduncle; AL, ansa lenticularis; LF, lenticular
fasciculus; SN, substantia nigra; ZI, zona incerta. Human specimen from the body donation program of the Institute of Human Anatomy of the University of Padua. (B) Coronal section passing through the postcommissural basal ganglia and the subthalamic nucleus, Weigert-Pal Stain. Cytoarchitectonics: Further Investigation The number of estimated neurons and the neuronal density
in the STh varied significantly among studies. In the case of
Salvesen et al. (2015), the values reported (900 × 103) refer to
the bilateral number of neurons obtained by multiplying by two
the estimated number of neurons; hence, the mean unilateral
value corresponds to 450 × 103, and was reported as such in
Table 1 (no standard deviation or variance was reported). The
studies by Zwirner et al. (2017) and Salvesen et al. (2015) were
conducted on more subjects compared to previous studies (14
versus 10, respectively) and reported more concordant values
for the estimated amount of neurons (431 ± 72 × 103 versus
450 × 103, respectively); also, as stated by Zwirner et al. (2017)
their reported morphometrical parameters also appeared to be
concordant with Hardman et al. (2002) (561 ± 30), but not with
Levesque and Parent (2005) (239.5 ± 31.9). This could be related
to tissue processing, subject variability and age. Cytoarchitectonics: Further Investigation
The morphological characterization of Human STh represents
one of the main areas which requires further investigation. In
humans, technical limitations determined by silver impregnation
techniques, such as the incomplete impregnation of fine
structures
like
axons
and
smaller
dendrites
in
formalin
fixed
tissue,
do
not
allow
for
a
complete
visualization
of axonal branching patterns. However, features such as
somata size and shape, number of dendrites and dendritic
branching
pattern
could
help
in
the
identification
of
morphologically distinct neuronal subpopulations in humans. Another point of interest is the topographical distribution
of
the
morphologically
defined
neuronal
subpopulations
within the structure: for example, what is the dendritic
branching pattern of neurons found in the ventromedial
STh compared to neurons in the dorsolateral STh? Does
the
neuronal
morphology
reflect
the
type
of
afferences
received? Is
there
a
relationship
between
morphological
characteristics of STh neurons and functional territories within
the structure? p
g
j
y
g
According to Levesque and Parent (2005), the neuronal
density of the STh displays a decreasing gradient from the
posterior to the anterior aspect of the nucleus, whilst displaying
an increasing gradient from the dorsal to the ventral part of
the structure; this is also confirmed by Zwirner et al. (2017). Furthermore, the authors evidenced how the ventral aspect, and
in particular the medial and posterior thirds of the nucleus,
displayed the highest neuronal density of the entire structure. Cytoarchitectonics: Further Investigation This appears to be coherent with the tripartite subdivision of the
STh, as a higher density of projection neurons and interneurons
is a typical feature of associative/limbic areas and is thought
to reflect the complex integrative activity of these regions (Wu
and Parent, 2000; Levesque and Parent, 2005), thus supporting
the role of ventral (medial and lateral) aspects of the nucleus in
associative/limbic circuitry. ANATOMY OF THE SUBTHALAMIC
NUCLEUS 50 ± 22.5 years; Salvesen et al. (2015): 69 years (60–75 range);
Zwirner et al. (2017) 82 ± 10 years. different populations of neurons within the STh. Given that
the expression of calcium binding proteins is related to
different firing properties of neurons (Hardman et al., 2002),
a combined morphological and molecular characterization of
neuronal populations within the STh could improve our
understanding of the physiology of STh’s efferences and how
external afferences are processed. Tissue processing was also variable: in the case of Hardman
et al. (2002) and Levesque and Parent (2005) the specimen
were fixed in paraformaldehyde (PFA), cryoprotected in sucrose
enriched phosphate-buffered saline (PBS) and cut with a cryostat. Lange et al. (1976), Salvesen et al. (2015) and Zwirner et al. (2017) employed paraffin embedding following formalin fixation. Due to the extensive dehydration of specimen during paraffin-
embedding, significant shrinkage occurs and must be accounted
for when estimating the volume of structures (Porzionato et al.,
2015). While Zwirner et al. (2017) explicitly described shrinkage
correction for volume estimation, the other two authors did not
explicitly mention it in the manuscript. Unlike non-human primates, the morphology of human
STh neurons has not yet been investigated through silver
impregnation techniques. Morphologically different classes of
STh neurons could represent functional subpopulations within
the structure, possibly connected to different basal ganglia and
cortical circuits. Frontiers in Neuroanatomy | www.frontiersin.org ANATOMY OF THE SUBTHALAMIC
NUCLEUS Human specimen from the body donation
program of the Institute of Human Anatomy of the University of Padua. 1, Caudate nucleus; 2, Insular cortex; 3, Putamen; 4, Claustrum; 5, Ventral regions of the
putamen, in relationship with the substantia innominata; 6, External Globus Pallidus; 7, Internal Globus Pallidus; 8, Substantia Nigra; 9, Subthalamic Nucleus; 10,
Zona Incerta; 11, Lateral and medial thalamic nuclei; 12, Anterior dorsal nucleus of the thalamus. A, Internal capsule; B, External capsule; C, Extreme Capsule; D,
Optic tract; E, Cerebral peduncle; F, Ansa lenticularis; G, Lenticular Fasciculus. (C) Digital schematization of a coronal section passing through the postcommissural
basal ganglia, similar to the section seen in panel (B). STh, Subthalamic Nucleus; SN, Substantia Nigra; GPi, Internal Globus Pallidus. GPe, External Globus Pallidus;
Pu, Putamen; Th, thalamus; Ant. Dors Th, Anterior Dorsal nuclei of the Thalamus; Cau, Caudate nucleus; L. Vent., Lateral Ventricle; CC, Corpus Callosum; IC,
Internal Capsule; Opt, Optic Tract; LF, Lenticular Fasciculus; AL, Ansa Lenticularis. FIGURE 3 | Neuron types in the STh according to rodent studies by Kita et al. (1983). (A) Type I STh neuron, characterized by local axon collaterals and dense
proximal dendritic arborizations. (B) Type II STh neuron, with only two axon ramifications and less dense dendrites at a proximal level. GP, Globus Pallidus; SN,
Substantia Nigra. FIGURE 3 | Neuron types in the STh according to rodent studies by Kita et al. (1983). (A) Type I STh neuron, characterized by local axon collaterals and dense
proximal dendritic arborizations. (B) Type II STh neuron, with only two axon ramifications and less dense dendrites at a proximal level. GP, Globus Pallidus; SN,
Substantia Nigra. compared to rodents (Sato et al., 2000b), one point of further
investigation could be related to the expression of calcium
binding proteins, such as parvalbumin, in the morphologically that the amount of PV + neurons increases in primates
compared to rodents (Hardman et al., 2002) and that primate
STh neurons present different axonal branching patterns that the amount of PV + neurons increases in primates
compared to rodents (Hardman et al., 2002) and that primate
STh neurons present different axonal branching patterns April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 4 Anatomy of the Subthalamic Nucleus Emmi et al. 50 ± 22.5 years; Salvesen et al. (2015): 69 years (60–75 range);
Zwirner et al. (2017) 82 ± 10 years. SUBTHALAMIC NUCLEUS
CONNECTIVITY: FUNCTIONAL
SUBDIVISIONS OF BASAL GANGLIA
CIRCUITRY AND METHODS OF
INVESTIGATION The
connectivity
and
functional
subdivision
of
nervous
structures can be effectively studied through different means
of investigation. In non-human primates, the elective method to study the
connectivity of subcortical structures such as the basal ganglia
and the STh is represented by retrograde, anterograde or
bidirectional tracing (Carpenter et al., 1981b; Smith et al., 1990;
Joel and Weiner, 1997, 2000; Haynes and Haber, 2013; Coudé
et al., 2018) and autoradiography (Nauta and Cole, 1978). Axonal
tracing is currently considered the gold standard for studying
anatomical connectivity in non-human primates. Through
iontophoretic injection, bidirectional or anterograde tracers such
as PHA-L (phaseolus vulgaris leucoagglutinin) and biotinylated
dextran amine (Coudé et al., 2018) or retrograde tracers such
as Fluoro-Gold (FG) and cholera toxin B (CTb) are injected in
targeting sites through stereotaxic surgery, whilst animals are
allowed to survive between 48 h and 14 days post-injection. The
brains are then removed from the subjects and either postfixed
in order to be processed for immunohistochemistry, or processed
for autoradiography or confocal imaging; other tracing methods,
such as the Marchi method (Whittier and Mettler, 1949) and
silver techniques (Knook, 1965) were particularly popular in
earlier studies, but are rarely found in recent literature. According to literature, the STh is characterized by several
functional and regional subdivisions, with each region of the STh
being structurally connected to either the sensomotor, cognitive
or limbic circuit of the basal ganglia (Kita and Kitai, 1987; Smith
et al., 1990; Parent and Hazrati, 1995; Joel and Weiner, 1997,
2000; Temel et al., 2006a). While several subdivisions of the
basal ganglia have been proposed (Albin et al., 1989b), the most
influential model of the organization of these structures views
them as components of circuits connecting distinct thalamic,
cortical and subcortical areas in a parallel manner, giving rise
to relatively segregated connections, both anatomically and
functionally (Alexander et al., 1986, 1990; Parent and Hazrati,
1995; Joel and Weiner, 1997, 2000). More recently, however,
the structural segregation of the circuits of the basal ganglia
has been questioned by several authors (Percheron et al., 1987,
1994; Reiner et al., 1988; Percheron and Fillon, 1991), providing
evidence on the convergence of different afferent projections on
dendritic fields in neurons of these subcortical structures (Smith
et al., 1990, 1995; Shink et al., 1996). According to the classical
tripartite organization proposed by Alexander et al. Morphometry of the STh Morphometry: Further Investigation
Ultra-high field MRI should be employed in conjuncti
unbiased stereology to accurately estimate STh volume. and age related
ariations in
olume neuronal populat Morphometry: Further Investigation
Ultra-high field MRI should be employed in conjunction with
unbiased stereology to accurately estimate STh volume. Gender
and age related variations in volume, neuronal population and
neuron density should also be taken into consideration. Globus Pallidus (GPi); the medial regions of the
substantia nigra and the ventral tegmental area of the
mesencephalon; the parvocellular part of the ventral
anterior nucleus and the magnocellular part of the
dorsomedial nucleus of the thalamus. Frontiers in Neuroanatomy | www.frontiersin.org Morphometry of the STh Few
authors
have
approached
the
human
STh
from
a
morphometrical perspective and through the aid of unbiased
stereology (Lange et al., 1976; Hardman et al., 2002; Levesque and
Parent, 2005; Salvesen et al., 2015; Zwirner et al., 2017). We have
reported stereology based studies on subjects with no clinical
or pathological evidence in Table 1. Studies focused exclusively
on subjects with clinical or pathological features were excluded,
while only the values of healthy controls were included in the
case of comparative studies between clinical and non-clinical
populations (Salvesen et al., 2015). As for the volume, three out of five studies found in literature
displayed similar values (ranging from 114 to 144 mm3), while
the remaining two displayed higher values, ranging from 174 to
240 mm3 (Hardman et al., 2002; Levesque and Parent, 2005). As previously stated, the difference may be attributable to the
employment of formalin fixation and paraffin embedding by
the three studies reporting lower values, even though shrinkage
correction was applied in most cases. Zwirner et al. (2017)
combined post-mortem 3 Tesla MRI volume estimation with
unbiased stereology, with highly consistent results. To date,
this is the only study which has compared STh volumes
through both methods. From a methodological aspect, it must be noted that the
stereological design varied notably across studies. Some authors
(Hardman et al., 2002; Levesque and Parent, 2005) performed
counting on 50–55 µm thick sections sampled at low ratio (1/20)
with approximately 6–9 total sections evaluated, while other
authors performed counting on 20 µm-thick paraffin-embedded
sections sampled at higher ratio (1/10) (Zwirner et al., 2017). The age of the subjects included in the studies was also variable
within and across studies (range is reported when standard
deviation is missing): Lange et al. (1976): 50 years (24–99 range);
Hardman et al. (2002): 74 ± 10 years; Levesque and Parent (2005): April 2020 | Volume 14 | Article 13 5 (mm
3
20.4 ection
nterval
Number of
sections
Stereological
method
Number of
neurons (103)
Volume (mm
NS
NS
NS
286–306
134–144
1/20
6
Optical fractionator
561 ± 30
240 ± 23
1/20
6–9
Optical disector
239.5 ± 31.9
174.5 ± 20.4
1/4
NS
Optical disector
450 (SD not
available)
114.4 (SD no
available)
1/10
NS
Optical fractionator
431 ± 72
131.58 ± 19. Anatomy of the Subthalamic Nucleus Emmi et al. SUBTHALAMIC NUCLEUS
CONNECTIVITY: FUNCTIONAL
SUBDIVISIONS OF BASAL GANGLIA
CIRCUITRY AND METHODS OF
INVESTIGATION effectively and accurately only through recordings in DBS
patients, given the subcortical localization of the structure. on the connections which arise from the different brain regions
conjoining with the aforementioned functional circuits. Thus, a
peculiar region of the STh is defined mainly by the connections
it forms with other cortical and subcortical structures and their
relationship with the functional circuitry of the basal ganglia,
while its intrinsic cytoarchitecture remains a current topic
of investigation. However, while electrophysiological recordings in DBS
patients have greatly improved our understanding of the STh’s
electrophysiological properties, measurements derive from an
invasive approach requiring neurosurgery that allows recording
only from patients with medical need for DBS (Alkemade et al.,
2015). Hence, translation to normal STh physiology appears to be
difficult, as it can be investigated in humans only in pathological
states. Furthermore, the anatomical accuracy of these methods
can not be compared to non-human primate fiber tracing and
human MRI derived fiber tracking; while compelling results were
provided by some authors (Fogelson et al., 2006) suggesting
functional sub-loops between the STh and the motor areas of the
cortex, the spatial resolution was too low to establish whether or
not the recordings actually derived from the subthalamic area. Among the very first to extensively review STh connectivity
in non-human primates, although without considering its
functional subdivision, Whittier and Mettler (1949) evidenced
that out of 44 authors, 22 reported connections between the
STh and the globus pallidus, while fewer reported projections
to other areas, such as the mesencephalic tegmentum, putamen,
substantia nigra, caudate nucleus, red nucleus, thalamus and
commissural connections with the controlateral STh. As for
afferent projections, extensive input appeared to originate mainly
from the GPe (Ranson and Berry, 1941; Ranson et al., 1941; Nauta
and Mehler, 1966). Successive studies further confirmed the
importance of pallido-subthalamic projections, whilst expanding
the STh circuitry by evidencing cortico-subthalamic, reticulo-
subthalamic and thalamo-subthalamic afferences (Nauta and
Cole, 1978; Smith et al., 1990; Parent and Hazrati, 1995; Shink
et al., 1996). SUBTHALAMIC NUCLEUS
CONNECTIVITY: FUNCTIONAL
SUBDIVISIONS OF BASAL GANGLIA
CIRCUITRY AND METHODS OF
INVESTIGATION Basing on non-human primate tracing studies,
a functional subdivision of the nucleus has been proposed by
Parent and Hazrati (1995) and expanded by Joel and Weiner
(1997): according to the authors, the medial third of the rostral
two-thirds of the STh is connected mainly, but not exclusively,
to the limbic circuit; the dorsolateral aspect of the rostral two
thirds and most of the caudal third of the STh is connected
mainly with the motor circuit; the ventrolateral aspect of the
rostral two thirds and a small ventromedial region of the caudal
third of the STh is connected with the associative circuit, as
seen in Figure 4. This gives rise to a functional tripartition
of the structure, which represents the main trend in classical
literature on STh regionalization and connectivity, and has layed
the ground for investigations on STh functional subdivision and
connectivity in humans. Considering
the
advantages
and
limitations
of
the
aforementioned methods of investigation, anatomical evidence
deriving from different sources should be integrated in order to
generate an accurate representation of axonal pathways arising
from and directed to the human STh. Recently, Petersen et al. (2019) developed an holographic
interface that allows the reconstruction of axonal pathways
within the human brain by integrating different anatomical
data deriving both from humans and non-human primates. In particular, the authors focused on the subthalamic region,
with particular regard to STh connectivity. Data deriving from
the vast array of non-human primate axon tracing studies was
implemented within the interface and integrated with human
histological and structural MRI studies. The holographic nature
of the developed interface allowed for shared group sessions in
which expert neuroanatomists reconstructed axonal pathways
within the human subthalamic region basing on multifaceted
anatomical evidence. According to the authors, the generated
pathway atlas integrates anatomical detail regarding the STh in a
manner that exceeds by far the capabilities of currently available
tractography algorithms. As for STh connectivity in humans, Aravamuthan et al. (2007) were among the first authors to employ diffusion MRI
(1.5 Tesla) to study STh connectivity in living subjects through
probabilistic tractography. The authors identified several regions
with high probability of connection to the STh; these included
the dorsal premotor cortex, the supplementary motor area, and
the primary motor area for the lower limbs, trunk, arm and
forearm, while the probable subcortical connections of the STh
included the thalamus, pallidal complex, substantia nigra, and
pedunculopontine nucleus. SUBTHALAMIC NUCLEUS
CONNECTIVITY: FUNCTIONAL
SUBDIVISIONS OF BASAL GANGLIA
CIRCUITRY AND METHODS OF
INVESTIGATION A topographical organization of the
STh was also reported, with the motor cortical regions being
connected to the dorsal STh and the associative cortical regions
being connected to the inferior and medial STh. It must be
noted, however, that the authors defined a single voxel based on
surrounding landmarks that they were confident fell within the
STh (Lambert et al., 2012); hence, results must be considered with
caution, as the STh was not actually anatomically identified. While the construction of the pathway atlas by Petersen
et al. (2019) represents an important advance in modeling STh
connectivity in humans, with important educational, clinical
and research applications, limitations must also be considered. In fact, most connections reconstructed in the human pathway
atlas derived from non-human primate studies. According to the
authors, this requires inter-species assumptions on (a) the exact
origin and termination points of fibers and (b) the maintenance
of the somatotopic organization of the projections. Hence, non-
human primate data should be integrated with other sources of
anatomical evidence in humans, such as ultra-high field MRI
(7 Tesla), to further enhance the accuracy of reconstructions. SUBTHALAMIC NUCLEUS
CONNECTIVITY: FUNCTIONAL
SUBDIVISIONS OF BASAL GANGLIA
CIRCUITRY AND METHODS OF
INVESTIGATION (1986), the
basal ganglia can be subdivided into a motor and oculomotor
circuit (forming together the general sensory-motor circuit of the
basal ganglia); a dorsolateral prefrontal and lateral orbitofrontal
circuit (forming the associative circuit); and an anterior cingulate
circuit (also known as the limbic circuit). In humans, structural and diffusion imaging techniques
represent an important non-invasive tool for investigating STh
connectivity both in vivo and ex vivo, even though important
limitations must be considered. As far as DWI is concerned, the
anatomical accuracy of brain connections derived from diffusion
MRI tractography appears to be inherently limited (Jones et al.,
2013; Thomas et al., 2014). According to Thomas et al. (2014)
the anatomical accuracy of fiber reconstructions deriving from
diffusion MRI appears to be highly dependent upon parameters
of the tractography algorithm, with different optimal values for
mapping different pathways. Tractography presents an inherent
limitation in determining long-range anatomical projections
based on voxel-averaged estimates of local fiber orientation
obtained from DWI data. Furthermore, directionality of fibers
can not be inferred, while the values regarding the connection
strength between structures must be interpreted with care. • The motor circuit comprises mainly the primary,
supplementary and pre-motor cortex; the dorsolateral
part of the caudal putamen (postcommissural) and of the
head of the caudate nucleus; the ventrolateral two thirds
of the pallidal complex and part of the lateral substantia
nigra; the ventrolateral, vental anterior and centromedian
nucleus of the thalamus. • The associative circuit comprises mainly the dorsolateral
and ventrolateral prefrontal cortex; the rostral regions of
the striatum (precommissural); the dorsomedial regions
of the pallidal complex and most of the substantia
nigra; the parvocellular part of the dorsomedial nucleus
of the thalamus. According to numerous authors (e.g., Jones et al., 2013;
Thomas
et
al.,
2014;
Petersen
et
al.,
2019)
it
appears
necessary
to
complement
tractography
with
histological
and electrophysiological data in order to accurately map
structural connectivity. In the case of STh research, MRI
derived tractography should be based on the anatomical
evidence derived by non-human primate tracing studies, as
the electrophysiological properties of the STh can be studied • The limbic circuit comprises the orbitofrontal cortical
regions and the anterior cingulate; the nucleus accumbens
and the ventral pallidum; the rostral External Globus
Pallidus (GPe) and the rostral ventromedial Internal April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 7 Anatomy of the Subthalamic Nucleus Emmi et al. STh Functional Subdivision: Tripartite
Hypothesis As a fundamental part of the basal ganglia circuitry, the STh
is also connected to the circuits of the basal ganglia and
presents, according to classical literature, a relatively distinct
functional subdivision. The subdivision of the STh is founded ,
y
y
On the other hand, Lambert et al. (2012) were the first
to employ a data driven method with DWI (in living human
subjects) that evidenced three distinct clusters within the STh April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 8 Emmi et al. Anatomy of the Subthalamic Nucleus FIGURE 4 | Functional subdivision of the STh according to the classical tripartite hypothesis. Redrawn from various sources (Parent and Hazrati, 1995; Hamani
et al., 2004). FIGURE 4 | Functional subdivision of the STh according to the classical tripartite hypothesis. Redrawn from various sources (Parent and Hazrati, 1995; Hamani
et al., 2004). division of the STh according to the classical tripartite hypothesis. Redrawn from various sources (Parent and Hazrati, 1995; Haman GURE 4 | Functional subdivision of the STh according to the classical tripartite hypothesis. Redrawn from various sources (Parent
al
2004) et al., 2004). supporting the idea of functionally overlapping regions within
the STh (Lambert et al., 2015). based on brain connectivity profiles, largely corresponding to
the functional tripartition hypothesized in non-human primates. The authors sub-parcellated the STh into the aforementioned
functional territories and evidenced connections between the STh
and subcortical structures that were coherent with the tripartite
hypothesis; most cortical regions, on the other side, possessed
some connections to all of the defined STh territories. Probabilistic tractography, employed by both groups albeit
with significantly different methodologies, presents inherent
limitations, as it estimates the probability of connection between
seed and target regions. As stated by Lambert et al. (2012),
seed and target region size, distance of tracking, regions
with dense crossing fibers, MRI artifact and noise are all
factors which can greatly influence fiber tracking. Again, results
deriving from tractography must be interpreted with care and
require complementary validation by histology and non-human
primate studies. • The posterior aspect of the STh was identified as the motor
region and showed connections with the posterior insula,
posterior putamen and GPe, mid-caudate and ventro-
lateral thalamic nuclei. • The anterior STh was defined as the limbic region and
was connected to the baso-lateral amygdala, mid-inferior
putamen, mid-GPe and ventral-anterior thalamus. Frontiers in Neuroanatomy | www.frontiersin.org Non-human Primate Studies Recently, Haynes and Haber (2013) conducted an extensive
study on the cortical projections to the STh in non-human
primates, evidencing the following connections: the dorsal
anterior cingulate cortex appears to be connected to the medial
tip of the STh (limbic circuit); the dorsal prefrontal cortex
(Brodmann area 9 and 46) projects to the medial half of the
STh; the rostral dorsal prefrontal cortex (rostral Brodmann
area 6) projects to the medial half of the caudal STh; the
caudal dorsal prefrontal motor cortex (caudal Brodmann area
6) projects to the ventrolateral STh, while the primary motor
cortex shows connections to the dorsolateral regions of the STh
(thus part of the motor circuit). No clear connections between
the ventromedial prefrontal cortex and the STh were evidenced. These results were further confirmed by Ishida et al. (2016) and
Coudé et al. (2018) which revealed that the ventral premotor
cortex is connected mainly to the caudal dorsolateral STh and
rostral ventrolateral STh, and that the projections arising from
the motor cortex originate from the V layer (deep pyramidal
cell layer). Interestingly, Coudé et al. (2018) evidenced how
the cortico-subthalamic fibers are actually axon collaterals of
corticofugal fibers that in most cases also project to the zona
incerta and the red nucleus. Hence, in accordance to these
results, the hyperdirect pathway from the cortex is not exclusively
devoted to the STh, but projects also to other subcortical nuclei. In conclusion, controversy on STh subdivision location,
boundaries and circuit segregation remains a topic of current
debate between research groups, and further confirmation is
needed by combining ultra-high field MRI, histology and
cytoarchitectonics (Alkemade et al., 2015). With particular regard to the projections arising from the
primary motor cortex (M1), a somatotopic organization is
reported (Parent and Hazrati, 1995; Hamani et al., 2004): the
leg, arm and orofacial structures appear to be represented in the
medial, lateral and dorsolateral portions of the STh, respectively. According to Nambu et al. (1996, 1997, 2000) the lateral portion
of the STh receives projections from the primary motor cortex
and presents a medial to lateral representation of the leg, arm
and face, while the medial portion of the nucleus receives fibers
from the supplementary motor area, dorsal and ventral premotor
cortex and presents an inverse somatotopic distribution. The
somatotopic organization of M1 projections to STh has been
confirmed in Miyachi et al.’s study (2006), in accordance to
Nambu et al. Non-human Primate Studies As summarized by Alkemade and Forstmann (2014), evidence
points toward a topographical organization of the STh without
defined anatomical borders, with at least partial overlap
between functional subregions within the structure; furthermore,
according to the authors, the extent of functional overlap
within STh subregions is still unclear and represents a point of
further investigation. The very first authors to report cortico-subthalamic projections
were Kunzle and Akert (1977), evidencing diffuse projections to
the STh originating from Brodmann area 8. Further investigation
by Von Monakow et al. (1978) evidenced a peculiar topography of
the connections arising from the frontal cortex: Brodmann area 4
appears to be connected with the dorsolateral regions of the STh;
Brodmann area 6 appears to be connected to the central third of
the STh, while Brodmann area 8 appears to be connected to the
ventral regions of the STh. The authors were unable to identify
any projections arising from Brodmann areas 9 and 3,1,2. g
On the other hand, numerous tracing studies aimed to identify
the connections between the STh and other brain structures
without considering their intrinsic functional subdivision. In fact,
distribution of tracers is related to (a) injection site and (b)
diffusion of the tracer within the injected structure; numerous
studies, especially early tracing studies prior to the 1980s, did
not consider the functional subdivision of the injection sites
(Kim et al., 1976; Nauta and Cole, 1978; Smith and Parent, 1986;
Parent and Smith, 1987). This is also related to the difficulty of
selectively injecting small brain structures and to the intrinsic
diffusion of the tracer within the site, along with the issue
related to tracer diffusion to unrelated fibers passing within or
close by large injection site. Furthermore, other studies only
considered the connection between specific structures (such as
the brainstem nuclei) and the STh (Lavoie and Parent, 1994c;
Rico et al., 2010), which may or may not be related to the
functional subdivision of the basal ganglia. Confirmation for
the classical tripartite hypothesis has been recently provided by
the very large tracing study carried out by Haynes and Haber
(2013), indicating topographically organized projections arising
from cortical areas directed to specific regions within the STh
compatible with the subdivision proposed by previous authors
(Parent and Hazrati, 1995; Joel and Weiner, 1997). Non-human Primate Studies (1996, 2000). In the following paragraphs, the connectivity of the STh will be
studied considering mainly non-human primate tracing studies,
whilst also integrating information coming from the few available
human fiber tracking studies through DTI and DWI both in vivo
and ex vivo, in order to highlight aspects which require further
investigation in humans. For an extensive revision of non-human
primate in vivo tracing studies involving the STh, refer to Table 2. Challenges to the Tripartite Hypothesis Challenges to the Tripartite Hypothesis
A recent review by Keuken et al. (2012) has evidenced how
variability across non-human primate tracing studies is not to
be underestimated, with many authors disagreeing on both the
number of STh subdivisions and on the localization of such
subregions. Keuken et al. (2012) also advance the hypothesis of
more than three functional subdivisions within the STh, with
regard to Alexander et al. (1990) aforementioned hypothesis of
five parallel loop circuits within the basal ganglia (sensorimotor,
oculomotor, dorsolateral prefrontal, orbitofrontal, and anterior
cingulate circuits). • The associative STh was defined as a region with
connections to both limbic and motor circuits which
represented more of a functional gradient between motor
and limbic territories rather than a distinct subregion. It must be noted that, even though Lambert et al.’s
(2012)
study
seems
to
support
the
tripartite
hypothesis
basing on the STh subparcellization, the authors clearly
state that the STh territory commonly defined as associative
actually represents an overlapping and topographically arranged
transition between the limbic and motor territories, thus Another critical point in the classical tripartite hypothesis of
the STh is the segregation of anatomo-functional circuits; while April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 9 Anatomy of the Subthalamic Nucleus Emmi et al. earlier studies suggested relatively segregated and defined STh
subdivisions, more recent evidence points toward overlapping
subregions and converging axonal afferents on large dendritic
fields of neuronal populations of the structure (Percheron et al.,
1987, 1994; Reiner et al., 1988; Smith et al., 1990, 1995; Percheron
and Fillon, 1991,; Shink et al., 1996; Haynes and Haber, 2013;
Alkemade et al., 2015). Von Monakow et al., 1978; Parent and Hazrati, 1995; Haynes
and Haber, 2013; Ishida et al., 2016; Coudé et al., 2018), with few
studies investigating the pathway also in humans through DTI
and DWI. This pathway is also referred to as the “hyperdirect
pathway” of the basal ganglia, in regards to the direct and indirect
pathway subdivision. Cortical Connections With the STh The
existence
of
cortico-subthalamic
projections
is
well
documented in non-human primates (Kunzle and Akert, 1977; To date, no studies reported subthalamo-cortical projections. April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 10 nced
Th
h
h
h
udal
h Technique
Tracing agent
PI.T.*
Injection site(s)
Connection(s) evidenc
Anterograde tracing
(Autoradiography)
[3H]- aminoacids
(L-leucine, L-proline,
L-lysine)
68 h–22 days
Rostrolateral SN
Whole extent of the STh
Caudolateral SN
No connections to STh
evidenced
Rostromedial SN
Medial STh
Central SN
No connections to STh
evidenced
Anterograde tracing
(Autoradiography)
[3H]- aminoacids
(L-leucine, L-proline,
L-lysine)
5–28 days
GPi
No connections to STh
evidenced
GPe
Whole STh except cauda
and medial regions
Putamen
No connections to STh
evidenced
Anterograde tracing
(Autoradiography)
3H-proline
2–3 days
Brodmann area 8
Subthalamic nucleus (no
topography specified)
Anterograde tracing
(Autoradiography)
Tritiated aminoacids (NS)
7–13 days
STh
1. Pallidal complex
2. SN
3. Ventral lateral and ventra
anterior thalamic nuclei
4. PPT (pars compacta)
5. Putamen
Anterograde tracing
(Autoradiography)
Radioactive labels: arginine,
leucine and proline. 2–8 days
Brodmann area 4
Dorsal and lateral STh
Brodmann area 6
Central STh
Brodmann area 8
Ventral STh
Brodmann area 9
No connections to STh
Brodmann area 3,1,2
No connections to STh
Retrograde tracing
Horseradish peroxidase
48–65 h
GPi
Central and ventromedia
STh
Retrograde tracing
Horseradish peroxidase
24–72 h
Outer portion of the GPi
(rostral and dorsal regions)
Ventral and medial thirds
the caudal third of the ST
Central GPi
Medial third of the cauda
third of the STh
Apical GPi
Medial third of the cauda
two thirds of the STh
Rostral division of the GPe
Medial third of the middle
third of the nulceus
Central division of the GPe
Whole rostral third of the
STh; central and dorsal
regions of the caudal
two-thirds of the STh
(Continu L lysine)
evidenced
Rostromedial SN
Medial STh
Central SN
No connections to ST
evidenced
nterograde tracing
Autoradiography)
[3H]- aminoacids
(L-leucine, L-proline,
L-lysine)
5–28 days
GPi
No connections to ST
evidenced
GPe
Whole STh except cau
and medial regions
Putamen
No connections to ST
evidenced
nterograde tracing
Autoradiography)
3H-proline
2–3 days
Brodmann area 8
Subthalamic nucleus (
topography specified)
nterograde tracing
Autoradiography)
Tritiated aminoacids (NS)
7–13 days
STh
1. Pallidal complex
2. SN
3. Ventral lateral and ve
anterior thalamic nuc
4. PPT (pars compacta)
5. Putamen
nterograde tracing
Autoradiography)
Radioactive labels: arginine,
leucine and proline. Cortical Connections With the STh 2–8 days
Brodmann area 4
Dorsal and lateral STh
Brodmann area 6
Central STh
Brodmann area 8
Ventral STh
Brodmann area 9
No connections to ST
Brodmann area 3,1,2
No connections to ST
etrograde tracing
Horseradish peroxidase
48–65 h
GPi
Central and ventrome
STh
etrograde tracing
Horseradish peroxidase
24–72 h
Outer portion of the GPi
(rostral and dorsal regions)
Ventral and medial thir
the caudal third of the
Central GPi
Medial third of the cau
third of the STh
Apical GPi
Medial third of the cau
two thirds of the STh
Rostral division of the GPe
Medial third of the mid
third of the nulceus
Central division of the GPe
Whole rostral third of t
STh; central and dors
regions of the caudal
two-thirds of the STh
(Cont chnique
Tracing agent
PI.T.*
Injection site(s)
Connection(s) evide
terograde tracing
utoradiography)
3H-aminoacids (NS)
NS
GPi
No connections evide
STh
Rostral division of the GPe
Medial two-thirds of t
third of the STh; Cent
the middle third of the
Central division of the GPe
Lateral third of the ST
trograde tracing
Horseradish peroxidase
48 h
Subthalamic nucleus
1. GPe, regions adjace
lateral medullary lam
2. SN (pars compacta
reticulata)
3. PPT
4. Dorsal nucleus of ra
terograde tracing
utoradiography)
L-leucine + L-proline
5–8 days
Subthalamic nucleus
1. Pallidal complex (wit
dorsoventral topogra
2. Substantia nigra
3. Ventral anterior, vent
and dorsomedial nuc
thalamus
Substantia Nigra
Subthalamic nucleus
topography specified
terograde tracing
utoradiography)
L-proline + L-leucine + L-
lysine
48–65 h
Internal Globus Pallidus
Uncertain connection
External Globus Pallidus
Whole STh
directional tracing
Wheat germ agglutinin –
horseradish peroxidase
conjugate (WGA-HRP)
48 h
Putamen
Dorsolateral STh
Caudate nucleus
Ventromedial STh
Motor and premotor cortex
No connections evide
STh
terograde tracing
• Wheat germ agglutinin –
horseradish peroxidase
conjugate (WGA-HRP)
• Nuclear yellow
• Fast blue
18–48 h
Putamen
Rostral dorsolateral tw
of the STh
Caudate nucleus
Rostral ventromedial
Substantia nigra
Ventromedial STh
Globus pallidus
Whole STh, more evid
dorsolateral STh
Pedunculopontine nucleus
Central regions of the
( Anterograde tracing
Phaseolus
vulgaris-leucoagglutinin
10–12 days
STh
1. Pallidal complex
2. Striatum (middle third of the
putamen and caudate
nucleus)
3. SN pars compacta
4. SN pars reticulata
5. Cortical Connections With the STh Mesencephalic and pontine
tegmentum (PPT and
periacqueductal gray)
Anterograde tracing
Phaseolus
vulgaris-leucoagglutinin
12–14 days
Centromedian nucleus
Dorsolateral STh
Parafascicular nucleus
Medial and rostral STh
Anterograde tracing
Phaseolus
vulgaris-leucoagglutinin;
Biocytin
2–12 days
Putamen
No connections investigated to
the STh
STh
Globus pallidus (no topography
specified)
Anterograde tracing
Phaseolus
vulgaris-leucoagglutinin;
[H]leucine
6–12 days
PPT
Whole extent of the STh
Anterograde tracing
Biotin dextran amine
7–10 days
Pallidal complex (both
segments) – different
injection sites
Inverse dorsoventral
topography of STh connections
(i.e., dorsal pallidal regions are
connected with ventral STh
regions, and vice-versa)
GPi – different injection
sites
Phaseolus
vulgaris-leucoagglutinin
7–10 days
GPe – different injection
sites
Anterograde tracing
Biotin dextran amine
10 days
Peri- and retrorubral area
(cathecolaminergic cell
group A8)
Whole extent of the STh
SN pars compacta
(cathecolaminergic cell
group A9)
Anteromedial STh
Retrograde tracing
Fluoro-gold
10 days
STh
Whole mesencephalon
Anterograde tracing
Biotin dextran amine
48–72 h
GPe
Medial GPe is connected to
Medial STh
Dorsal GPe is connected to
Ventral STh
Ventral GPe is connected to
Dorsal STh
Anterograde tracing
Biotin dextran amine
48–72 h
STh
1. SN pars reticulata
2. GPe
3. GPi
4. Striatum
(Continued Technique
Tracing agent
PI.T.*
Injection site(s)
Connection(s) eviden
Anterograde tracing
Autoradiography)
[H]-leucine
5–7 days
Different cortical areas
No connections invest
the STh
Retrograde tracing
Wheat germ agglutinin –
horseradish peroxidase
conjugate (WGA-HRP)
48 h
Nucleus reticularis tegmenti
pontis
STh (topography not s
Retrograde tracing
Rabies virus
4 days
Primary motor area (M1)
3rd Order neurons with
dorsolateral STh
Brodmann area 46
3rd Order neurons with
rostral ventromedial ST
Retrograde tracing
Wheat germ agglutinin –
horseradish peroxidase
conjugate (WGA-HRP)
3 days
Motor GPe
Associative GPe
Limbic GPe
Motor GPe is connecte
posterior and dorsal re
the STh
Assocative GPe is con
to anterior central and
ventrolateral STh
Limbic GPe is connect
anterior medioventral S
Anterograde tracing
Biotin dextran amine
10 days
Motor GPe
Associative GPe
Limbic GPe
Retrograde tracing
Fluoro-gold
10 days
Subthalamic Nulceus
Parafascicular nulceus
Retrograde tracing
Rabies virus
4 days
Somatotopically defined
regions of the primary
motor cortex (M1)
Orofacial M1 is connec
ventrolateral STh; Hind
is connected to dorsom
STh; Forelimb M1 is co
to the two aforementio
regions. Human Tractography Studies Connectivity between the cortex and the STh has been
investigated in humans using DTI and DWI in both controls
and PD patients (Aravamuthan et al., 2007; Lambert et al., 2012;
Petersen et al., 2017; Isaacs et al., 2018; Plantinga et al., 2018). The
studies by Aravamuthan et al. (2007) and Lambert et al. (2012)
were discussed previously and will be briefly summarized with
regard to cortical connections to the STh. Through probabilistic
tractography Aravamuthan et al. (2007) evidenced connections
between the motor cortical areas and the dorsal STh, while
associative regions of the cortex were connected to the inferior
and medial STh. Lambert et al. (2012), on the other hand,
evidenced how most cortical regions possessed at least some
connections to all of the functional territories identified within
the STh, without a precise topographical organization. Petersen
et al. (2017) investigated cortico-subthalamic projections in PD
patients and controls, using both probabilistic and deterministic
tractography; projections to the STh derived mainly from
the motor cortex, with particular regard to BA6 and BA4. The probabilistic method further identified a larger portion
of projections connecting BA6 to the STh, compared to the
projections from the BA4 to the STh. As for the target STh
regions, the authors identified the dorsolateral aspect of the
nucleus as the main site of projection of cortical fibers; this
appears to be coherent with the tripartite hypothesis of the STh,
where the dorsolateral aspect represents the motor subregion of
the structure. Isaacs et al. (2018) studied the projections arising
from the cortex and directed to the STh and the striatum by
employing DWI and resting-state functional MRI. The cortical
areas of interest were identified basing on primate tracing
studies. Comparatively, the striatum appeared to receive more
projections from the cortex when compared to the STh, with
the exception of the orbitofrontal cortex and the ventromedial
prefrontal cortex, whose tract strength were stronger for the STh. Both structures received strong projections from the cingulate
motor area and from the supplementary motor area. The study
did not assess the topographical organization of the projections,
but rather focused on tract strengths between cortical areas
and subcortical targets. However, several limitations to the
estimation of connection strengths must be noted. As stated by
the authors, the exact identification of white matter “entrance
points” within the cortex appears particularly challenging,
giving rise to what is generally referred as “gyral biases”
(Isaacs et al., 2018). Cortical Connections With the STh Retrograde tracing
Cholera toxin B
14 days
Ventral anterior and ventral
lateral nuclei of the
thalamus
Mainly medial STh
Retrograde Tracing
Rabies virus
42 h
Crus IIp and lobule VIIb of
the cerebellum
Controlateral STh; Cru
presents more connec
the rostral STh and mo
ventromedially, while lo
presents more connec
the caudal STh
Anterograde + Bidirectional
racing
Lucifer Yellow, Fluororuby
or Fluorescin coniugated
with dextran amine or
tritiated amino acids. 12–14 days
Orbitofrontal
cortex/ventromedial
prefrontal cortex
Uncertain (mostly outs
medial border of STh)
(C Emmi et al. Anatomy of the Subthalamic Nucleus TABLE 2 | Continued
Author(s)
Species
Technique
Tracing agent
PI.T.*
Injection site(s)
Connection(s) evidenced
Dorsal Anterior Cingulate
Cortex
Medial tip of the STh
Dorsal prefrontal cortex
(B.A. 9–46)
Medial half of the STh
Rostral dorsal prefrontal
cortex (rostral B.A. 6)
Medial half of the STh, mainly
caudal. Caudal dorsal prefrontal
cortex (caudal B.A. 6)
Ventrolateral STh
Primary motor cortex
Dorsolateral STh
shida et al. (2016)
Macaca fuscata
Retrograde tracing
Rabies virus
3–4 days
Ventral premotor cortex
Caudal dorsolateral STh and
rostral ventrolateral STh
Coudé et al. (2018)
Macaca fascicularis
Anterograde tracing
Biotin dextran amine
8–10 days
Layer V of primary motor
cortex
Dorsolateral STh
PI.T.: Post injection time, i.e., period between tracer injection and sacrifice. STh, Subthalamic Nucleus; GPe, External Globus Pallidus; GPi, Internal Globus Pallidus; SN, Substantia Nigra; PPT, pedunculopontine
egmental nucleus; B.A., Brodmann area. From a cytoarchitectural and chemoarchitectural perspective,
the cortico-subthalamic pathway utilizes glutamate as main
neurotransmitter, and the terminals of the projections contact
mainly small dendrites; in particular, projections arising from
the motor cortex appear to contact mainly, but not exclusively,
distal dendrites and other afferent axons directed toward the STh
(Coudé et al., 2018). Human Tractography Studies Furthermore, the term “tract strength”
is referred to the amount of streamlines originating from the
seed region (i.e., the cortex) and terminating on the target
area (i.e., subcortical structures, including the STh), but does
not quantify the actual number of white matter fibers, and its
values are related to the size of the target structure. Hence, Connectivity between the cortex and the STh has been
investigated in humans using DTI and DWI in both controls
and PD patients (Aravamuthan et al., 2007; Lambert et al., 2012;
Petersen et al., 2017; Isaacs et al., 2018; Plantinga et al., 2018). The
studies by Aravamuthan et al. (2007) and Lambert et al. (2012)
were discussed previously and will be briefly summarized with
regard to cortical connections to the STh. Through probabilistic
tractography Aravamuthan et al. (2007) evidenced connections
between the motor cortical areas and the dorsal STh, while
associative regions of the cortex were connected to the inferior
and medial STh. Lambert et al. (2012), on the other hand,
evidenced how most cortical regions possessed at least some
connections to all of the functional territories identified within
the STh, without a precise topographical organization. Petersen
et al. (2017) investigated cortico-subthalamic projections in PD
patients and controls, using both probabilistic and deterministic
tractography; projections to the STh derived mainly from
the motor cortex, with particular regard to BA6 and BA4. The probabilistic method further identified a larger portion
of projections connecting BA6 to the STh, compared to the
projections from the BA4 to the STh. As for the target STh
regions, the authors identified the dorsolateral aspect of the
nucleus as the main site of projection of cortical fibers; this
appears to be coherent with the tripartite hypothesis of the STh,
where the dorsolateral aspect represents the motor subregion of
the structure. Isaacs et al. (2018) studied the projections arising
from the cortex and directed to the STh and the striatum by
employing DWI and resting-state functional MRI. The cortical
areas of interest were identified basing on primate tracing
studies. Comparatively, the striatum appeared to receive more
projections from the cortex when compared to the STh, with
the exception of the orbitofrontal cortex and the ventromedial
prefrontal cortex, whose tract strength were stronger for the STh. Both structures received strong projections from the cingulate
motor area and from the supplementary motor area. Human Tractography Studies The study
did not assess the topographical organization of the projections,
but rather focused on tract strengths between cortical areas
and subcortical targets. However, several limitations to the
estimation of connection strengths must be noted. As stated by
the authors, the exact identification of white matter “entrance
points” within the cortex appears particularly challenging,
giving rise to what is generally referred as “gyral biases”
(Isaacs et al., 2018). Furthermore, the term “tract strength”
is referred to the amount of streamlines originating from the
seed region (i.e., the cortex) and terminating on the target
area (i.e., subcortical structures, including the STh), but does
not quantify the actual number of white matter fibers, and its
values are related to the size of the target structure. Hence, April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org Frontiers in Neuroanatomy | www.frontiersin.org 15 Anatomy of the Subthalamic Nucleus Emmi et al. results related to tract strengths should not be over interpreted
(Jones et al., 2013). authors were unable to confirm any commissural connection
between the STh of each hemisphere. According to Carpenter
et al. (1981a,b); Carpenter and Jayaraman (1990) projections
from the STh possess a topographical organization. Subthalamo-
pallidal (efferent) projections directed toward the GPe are
organized as follows: the rostral third of the STh projects to the
central part of the GPe; the central third of the STh projects
to the rostral part of the GPe; the caudal third, especially the
lateral surface, projects toward the caudal GPe. Subthalamo-
pallidal (efferent) projections directed toward the GPi originate
mainly from the medial third of the caudal STh. According to
the authors, the rostral regions of the STh do not project to the
GPi. A common characteristic of subthalamo-pallidal projections
evidenced by both Nauta and Cole (1978) and Carpenter et al. Carpenter et al. (1981a,b); Carpenter and Jayaraman (1990) is
the inverse dorsoventral topography of the fibers, i.e., the dorsal
regions of the STh project to the ventral regions, while the
ventral regions of the STh project to the dorsal regions of the
pallidal complex. These findings were further confirmed and
extended by Shink et al. (1996) and Smith et al. (1990, 1995),
who also evidenced a convergence at a synaptic level: many
STh neurons projecting to the GPi received synaptic input from
GPe collaterals, whose neurons were originally directed to the
same area of the GPi. Future Perspectives To date, the presence of cortico-subthalamic fibers has been
evidenced in humans only through tractography. Histological
studies present inherent technical limitations in reconstructing
fiber pathways from the cortex to the STh due to the conspicuous
length of the fibers. Within this context, post-mortem MRI-
derived tractography could be employed to further characterize
the connections between the cortex and the STh, similarly to
Plantinga et al.’s (2016) study on STh connections to the GPe
and SN. The higher resolution achievable through longer scan
times could provide useful information on the characterization
of connections between the cortex and the STh. p
j
g
A more detailed description of the subthalamo-pallidal
topography has been proposed by Joel and Weiner (1997) by
integrating the findings of Nauta and Cole (1978); Carpenter and
Jayaraman (1990), Shink et al. (1996) and Smith et al. (1990,
1995): the medial third of the rostral two-thirds of the STh
projects mainly to the rostral GPe (associative circuit), to the
ventral pallidum (limbic circuit) and to the rostral-ventromedial
GPi (associative and limbic circuits); the lateral two thirds of
the rostral two thirds of the STh project mainly to the central
and caudal GPe and GPi; in particular, the dorsolateral two-
thirds of this region project to the ventrolateral GPe and GPi
(motor circuit), while the ventrolateral third projects to the
dorsomedial third of the GPe and GPi (associative circuit). The caudal STh projects mainly to the ventrolateral GPe and
GPi (thus converging on the motor circuit) apart of a small
ventromedial portion projecting toward the associative circuit
(dorsomedial GPe and GPi). This organization appears to be
coherent with the hypothesis of the functional tripartition of
the STh. Figure 5 shows a schematic representation of the
aforementioned topography. Another point of further investigation is related to the
overlap between functional territories within the STh. As recent
literature suggests (Alkemade and Forstmann, 2014; Lambert
et al., 2015), the associative territories of the STh could represent
a transition gradient between motor and limbic regions, rather
than an anatomically distinct area with defined boundaries. The high resolution achieved through Ultra-High field MRI on
ex vivo human specimen could shed more light on the precise
topography of cortical connections with the STh. Pallidal (GPe and GPi) Connections With
the STh Subthalamo-Pallidal Projections
Non-human Primate Studies Human Tractography Studies Similarly, GPe neurons projecting to the
GPi received input from axon collaterals of STh neurons mainly
projecting to the same areas of the GPi. Plantinga et al. (2018) studied the connectivity between
cortical areas and the STh with regards to the parcellation of
the structure in PD patients using 7 Tesla MRI. The authors
evidenced connections between the motor areas of the cortex
(Primary motor, supplementary motor and premotor cortex)
and the posterior dorsolateral aspect of the STh, the associative
areas of the cortex and the central region of the STh, partially
overlapping with the motor area, and the limbic areas of the
cortex (hippocampus, amygdala, cingulate gyrus, orbitofrontal
cortex) with the anterior ventromedial aspect of the STh; the
authors also identified volumetric differences between the areas,
with the 55.3 ± 14%, 55.6 ± 15.9% and 20.3 ± 16.3% of the
total volume of the nucleus being occupied by the posterior
dorsolateral motor region, central associative region and anterior
ventromedial limbic region, respectively. This subdivision seems
to confirm, along with the other human tracing studies, the
classical tripartite hypothesis. Frontiers in Neuroanatomy | www.frontiersin.org Subthalamo-Pallidal Projections
Non-human Primate Studies On both segments, the subthalamo-pallidal efferents terminate
in the form of dense elongated bands that lie parallel to the
medullary laminae (Parent and Hazrati, 1995). The target pallidal
cells present an elongated dendritic domain parallel to the
medullary laminae and are organized in rostrocaudally oriented
cell layers, with each subthalamo-pallidal band contacting several
pallidal cells. These bands are formed by thick non-varicose
axons coursing in a caudorostral direction and giving rise to
multiple thin and varicose axon collaterals forming a dense
network around the dendrites and soma of pallidal neurons
(Parent and Hazrati, 1995). This organization appears to be Through autoradiography, Nauta and Cole (1978) confirmed the
existence of a highly organized subthalamo-pallidal projection
which, originating from the STh, traverses the internal capsule
and ends on the pallidal complex (both segments) describing a
route identical, but with opposite directionality, to the second
division of the ansa lenticularis. In particular, the medial part
of the rostral third of the STh projects to the rostral GPe and
ventromedial GPi, including the ventral pallidum, while the
dorsal regions of the caudal STh project toward the ventrolateral
two thirds of the caudal pallidal complex. Furthermore, the April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 16 Anatomy of the Subthalamic Nucleus Emmi et al. FIGURE 5 | (A) Schematic topography of the Subthalamo-pallidal efferents. Red regions: motor circuits; Green regions: associative circuit; Yellow regions: limbic
circuit. (B) Schematic topography of the pallido-subthalamic afferents. Red regions: motor circuit; Green regions: exclusively associative circuit; Yellow regions:
associative and limbic circuit. STh, Subthalamic Nucleus; SN, Substantia Nigra; GPi, Internal Globus Pallidus. GPe, External Globus Pallidus; Pu, Putamen; Th,
thalamus; Ant. Dors Th, Anterior Dorsal nuclei of the Thalamus; Cau, Caudate nucleus; CC, Corpus Callosum; IC, Internal Capsule; Opt, Optic Tract; LF, Lenticular
Fasciculus; AL, Ansa Lenticularis (for representation purposes, the topographical relationship between structures within the anteroposterior levels were simplified and
depicted with the same schematic). FIGURE 5 | (A) Schematic topography of the Subthalamo-pallidal efferents. Red regions: motor circuits; Green regions: associative circuit; Yellow regions: limbic
circuit. (B) Schematic topography of the pallido-subthalamic afferents. Red regions: motor circuit; Green regions: exclusively associative circuit; Yellow regions:
associative and limbic circuit. STh, Subthalamic Nucleus; SN, Substantia Nigra; GPi, Internal Globus Pallidus. GPe, External Globus Pallidus; Pu, Putamen; Th,
thalamus; Ant. Subthalamo-Pallidal Projections
Non-human Primate Studies Dors Th, Anterior Dorsal nuclei of the Thalamus; Cau, Caudate nucleus; CC, Corpus Callosum; IC, Internal Capsule; Opt, Optic Tract; LF, Lenticular
Fasciculus; AL, Ansa Lenticularis (for representation purposes, the topographical relationship between structures within the anteroposterior levels were simplified and
depicted with the same schematic). the whole extent of the pallidal complex, the striato-pallidal
projections present a more heterogeneous arborization pattern
and an opposite directionality. Furthermore, the proximal part
of the striatal axons contacts the soma of the pallidal neurons very similar to the vertically oriented terminal bands formed
by striato-pallidal fibers, with the main difference being the
distribution of the efferent arborizations: while the subthalamo-
pallidal efferents present a quite uniform arborization throughout April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 17 Anatomy of the Subthalamic Nucleus Emmi et al. ganglia, conveying striatal information to the STh and GPi
(Parent and Hazrati, 1995). while the terminal portion of the axon branches in order to
entwine the dendrites of a more caudally located pallidal neuron;
conversely, the subthalamic axons send numerous collaterals
which entwine the dendrites and soma of several pallidal neurons,
with the main axon continuing its caudorostral course (Parent
and Hazrati, 1995). This indicates that the STh exerts a relatively
widespread influence on the pallidal segments, contacting vast
fields of pallidal neurons. Human Histology and Tractography Studies gy
g
p y
Lambert et al. (2012) evidenced a topographical organization of
GPe connections with the STh: the posterior GPe is connected
to the posterior STh (motor regions), while the middle GPe is
connected to the anterior STh. This appears to be coherent with
the functional subdivision of the GPe and with data deriving from
non-human primate tracing studies. Pujol et al. (2017) explored
the connectivity between the STh and the GP in vivo using fiber
tracking. The fibers connecting the STh and the GPe crossed the
anterior two-thirds of the posterior limb of the internal capsule
and connected to the mediodorsal and medioventral aspects of
the GPe. Connections between the STh and the GPi were found
within the ventromedial aspect of the STh, while no topography
of the projections on the GPi was reported. Plantinga et al. (2016) employed Ultra-high field MRI (7T) on a human ex vivo
specimen to study the structural connectivity between the STh,
the GP and the SN. Non-human Primate Tracing Studies One of the main afferent pathways to the STh is represented by
the pallido-subthalamic fibers, which originates exclusively from
the GPe (Parent and Hazrati, 1995; Joel and Weiner, 1997, 2000;
Sato et al., 2000a; Hamani et al., 2004). To date, no afferences
from the GPi have been described; hence, the term pallido-
subthalamic afferences refers to axons arising from the GPe. The
majority of pallidal terminals within the STh exhibited numerous
varicosities reminiscent of boutons en passant or boutons
terminaux and displayed GAD and GABA immunoreactivity,
forming synapses predominantly with proximal dendrites and
less frequently with the soma and the distal dendrites (Parent and
Hazrati, 1995; Sato et al., 2000a). Rostral GPe (associative and supposedly limbic circuit)
projects to the medial two-thirds of the rostral STh and to
the central third of the middle STh, and to a lesser extent
to the medial third of the central STh. Central GPe can be
divided into two parts: (1) the dorsal two thirds, part of the
associative circuit, project to the lateral two thirds of the central
regions of the STh; (2) the ventral third of the GPe, part of the
motor circuit, projects along with the whole caudal third of the
GPe to the lateral and caudal regions of the STh. The ventral
pallidum (part of the limbic circuit) appears to be reciprocally
connected to the limbic STh. There also appears to be an
inverse dorsoventral topography, with dorsal regions of the GPe
projecting more ventrally, and ventral regions projecting more
dorsally in the STh. Recently, Alho et al. (2019) employed histological sections,
ultra-high field MRI and connectome analysis to describe a
bundle of fibers connecting the anterior and medial STh to
the ventral GPi in humans. This bundle of fibers, known as
ansa subthalamica, appears to be distinct from other bundles
connecting the STh to the pallidal complex such as the ansa
lenticularis, and constitutes a fundamental anatomical pathway
for the limbic circuit of the basal ganglia. According to
the authors this bundle could represent an interesting target
for stereotactic surgery in psychiatric disorders, as it may
play a crucial role within the fronto-striato-subthalamo-pallidal
network engaged in goal-directed behaviors (Alho et al., 2019). More recently, Karachi et al. (2005) studied the pallido-
subthalamic pathway with particular regard to recent evidence on
the functional subdivision of the GPe. Subthalamo-Pallidal Projections
Non-human Primate Studies The authors evidenced distinct connections
with anteromedial aspect of the STh; these fibers circled around
the internal capsule and connected to the anterior and inferior
margins of the GPi, following a course compatible with the ansa
lenticularis. The STh connections with the GPe, on the other
hand, coursed either anteriorly around the internal capsule, in
a bundle dorsal to the fibers connected to the GPi, or could be
found running through the internal capsule and connected to the
medial border of the GPe. Non-human Primate Tracing Studies According to the authors,
the motor GPe is connected to the posterior and dorsal regions
of the STh; the associative GPe is connected to the anterior
central and posterior ventrolateral STh, while the Limbic GPe is
connected with the anterior medioventral STh. These findings are
coherent with the functional tripartite hypothesis of the STh and
in accordance with previous literature. Frontiers in Neuroanatomy | www.frontiersin.org Further Perspective
h l
h While the connections between the GPe and STh have been
extensively studied in non-human primates, data deriving
from human subjects is still scarce. The connections between
functional territories of the STh and functional territories of
the GPe require more investigation in humans, and must be
guided by the large amount of anatomical evidence deriving from
non-human primate studies. Figure
5
evidences
the
aforementioned
topography. Comparing the afferent projections to the efferent projections
exposed in the previous paragraph, a correspondence between
the GPe terminal field in the STh and the area of the nucleus
projecting to the corresponding region of the GPi was evidenced,
but appeared not to be absolute. Furthermore, the associative
GPe appears to be reciprocally connected with the STh, but
also projects to the dorsolateral regions of the central STh
which are primarily connected to the motor pallidum. The
pallido-subthalamic
projection
is
thus
considered
as
the
essential component of the indirect pathway of the basal Human Fiber Tracking Studies According to Lambert et al. (2012) the posterior putamen is
connected to the motor STh, in particular the posterior parts of
the nucleus, while the mid-inferior putamen is connected to the
limbic STh, in particular the anterior regions of the nucleus. The dopaminergic fibers arising from the substantia nigra
appear to be characterized by numerous axon varicosities; some
axons branch extensively within the STh in order to contact
numerous target neurons, while other axons selectively target
very few neurons within the structure (Lavoie et al., 1989;
François et al., 2000; Hamani et al., 2004). Nigro-Subthalamical Projections Smith and Parent (1986; Parent and Smith, 1987), projections to
the putamen arise mainly from the dorsolateral STh (part of the
motor circuit), while projections to the caudate nucleus arise
mainly from the ventromedial associative and limbic regions of
the STh. According to Sato et al. (2000b), approximately 17% of
the STh neurons labeled present a single axon projecting toward
the striatum. However, the terminal arborizations of these labeled
neurons could not be visualized in this study. Smith and Parent (1986; Parent and Smith, 1987), projections to
the putamen arise mainly from the dorsolateral STh (part of the
motor circuit), while projections to the caudate nucleus arise
mainly from the ventromedial associative and limbic regions of
the STh. According to Sato et al. (2000b), approximately 17% of
the STh neurons labeled present a single axon projecting toward
the striatum. However, the terminal arborizations of these labeled
neurons could not be visualized in this study. The nigro-subthalamical pathway appears to be less prominent
in primates than in rodents (Parent and Hazrati, 1995). While the
nucleus appears to be surrounded by several dopaminergic fiber
systems, only few appear to contact its neurons by entering the
mediodorsal regions. According to tracing studies in rodents, the
nigro-subthalamical projection arises mainly from the substantia
nigra pars compacta, while the STh projects mainly to the pars
reticulata (Brown et al., 1979). Subthalamo-striatal fibers are characterized by long, varicose
axons with few collaterals, scattered throughout wide areas of
both striatal components (Smith and Parent, 1986; Parent and
Smith, 1987; Parent and Hazrati, 1995). According to Parent and
Hazrati (1995), these projections likely exert an en passant type
of excitatory influence on vast populations of striatal cells. No
striato-subthalamical projections have been evidenced in non-
human primates so far. In non-human primates, François et al. (2000) evidenced
extensive projections arising from dopaminergic areas A8,
A9, and A10 in the mesencephalon. Through anterograde
tracing, the authors confirmed projections arising from the
mesencephalon and targeting the STh. The dopaminergic nature
of these afferences was confirmed through positivity for tyrosine
hydroxylase. In particular, the labeled axons originating from the
mediodorsal part of area A9 project to the anteriomedial STh,
while the fibers originating from area A8 project to the whole
extent of the STh. Further Perspectives Literature on STh connections with the Striatum in both non-
human primates and humans appears scarce and requires
further investigation. Considering the functional subdivision
of the striatum and the morphofunctional difference between
striosomes and matrix, it could be interesting to define if,
and how, these territories are connected with the functional
subdivisions of the STh. Striatal Connections to the STh
Subthalamo-Striatal Projections
Non-human Primate Tracing Studies Subthalamic projections to the Striatum, both Caudate nucleus
and Putamen, are scarce compared to other subthalamic
targets (Nauta and Cole, 1978; Smith and Parent, 1986;
Parent and Smith, 1987; Sato et al., 2000b). According to April 2020 | Volume 14 | Article 13 18 Anatomy of the Subthalamic Nucleus Emmi et al. Frontiers in Neuroanatomy | www.frontiersin.org Human Tractography Studies Connections between the STh and the SN were reported in a post-
mortem human specimen by Plantinga et al. (2016) using DWI. The authors evidenced connections between the inferolateral
border of the STh and the superior border of the SN. The
connection with the SNc is located more anteriorly within the
STh compared to the connections with the SNr. According to the
authors, the connection with the SNc appears to be significantly
larger than the connection with the SNr. Further Perspectives
d
h
dd a starting point for the morphofunctional characterization of
extrastriatal dopaminergic innervations in humans. unlike Pelzer et al. (2013), the authors identified an ipsilateral
connection between the STh and the cerebellar cortex. a starting point for the morphofunctional characterization of
extrastriatal dopaminergic innervations in humans. Wang et al. (2020) employed high definition fiber tractography
to
identify
cortico-subthalamo-cerebellar
connections. According to the authors, fibers connecting the STh and
the cerebellum pass through the cerebral peduncle along the
course of the cortico-cerebellar fibers. At the level of the pons
they connect in two opposite directions to join the middle
cerebellar pedicle on both sides. Most fibers connected bilaterally
to Crus I in the cerebellum, while the remaining fibers crossed
the midline and connected to Crus II. Interestingly, the authors
evidenced a positive correlation between the numbers of fibers
connecting mesial BA8 to the STh and the number of fibers
connecting the STh with Crus I. Since the hyperdirect pathway
between BA8 and the STh seems to be involved in decision
making (Wang et al., 2020), the fibers connecting the STh to
Crus I and II could represent a continuation of such pathway and
also contribute to higher cognitive functions. Non-human Primate Tracing Studies Recently, indirect connections between the STh and the
cerebellum have been identified by Bostan et al. (2010). Through
the injection of rabies virus (retrograde tracer) in the cerebellum
of non-human primates, the authors identified a disynaptic
pathway connecting the STh to the pontine nuclei, which in turn
projected toward the controlateral cerebellar cortex. In particular,
injections within the Crus IIp of the cerebellum displayed
numerous labeled neurons within the rostral and ventromedial
STh, while injections within the lobule VIIb displayed numerous
labeled neurons within the caudal STh. According to the authors,
modulation of the subthalamo-cerebellar pathway could be
provided by the nucleus reticularis tegmenti pontis and other
pontine nuclei, which are also structurally connected to the STh
(Giolli et al., 2001). Further Perspectives While
human
fiber
tracking
studies
provide
compelling
information on the subthalamo-cerebellar circuitry, more data
deriving from non-human primate tracing studies is required
to further characterize these connections. In fact, it must be
considered that Bostan et al. (2010) tracing study is based on the
observation of only two subjects and two main injection sites. Cerebellar Connections With the STh Even though indirect connections arising from and terminating
on the STh were not considered within this review, the
recent discovery and the morphofunctional relevance of indirect
connections between the STh and the Cerebellum could represent
an important stimulus to functional and connectivity research,
along with their clinical implications, within the network of basal
ganglia circuits, and will therefore briefly discussed. The identification of second order neurons and mediating
nuclei, along with the topographical organization of subthalamo-
cerebellar projections represent aspects that require further
clarification: is there a topographically organized projection
arising from the motor areas of the STh that maintains the
somatotopic representation of cortical afferences? What is the
role of deep cerebellar nuclei, such as the dentate nucleus, in the
subthalamo-cerebellar pathway? Hopefully, more non-human
primate tracing studies will provide information on these aspects. Thalamic Connections With the STh
Non-human Primate Tracing Studies The
thalamo-subthalamic
pathway
arises
mainly
from
the parafascicular nucleus of the thalamus and from the
centromedian nuclei (Sadikot et al., 1992; Tandé et al., 2006). The
centromedian nucleus appears to project mainly to the motor
division of the STh, in particular to the dorsolateral regions of the
nucleus. The parafascicular nucleus innervates mainly the medial
and rostral regions of the STh, constituting the limbic/associative
territories of the nucleus. The axon terminals of this pathway
appear to contact mainly the dendrites of the STh cells, displaying
glutamatergic immunoreactivity (Hamani et al., 2004). More recently, bidirectional connections with the ventral
anterior and ventral lateral thalamus have been described (Rico
et al., 2010). These fibers connect mainly the medial STh to the
aforementioned thalamic nuclei, playing a role in both motor and
associative control. Further Perspectives
d
h
dd The substantia nigra represents one of the main targets of the
STh (Carpenter et al., 1981b; Parent and Smith, 1987; Smith et al.,
1990; François et al., 2000). These fibers enter the substantia nigra
pars reticulata (SNr) mainly by coursing through the cerebral
peduncle, arborizing along the basis of the SNr and forming
several distinct terminal plexuses (Carpenter et al., 1981b; Parent
and Hazrati, 1995). Even though most fibers terminate at the level
of the reticulate part, some fibers ascend along the dopaminergic
cell columns of the substantia nigra pars compacta (SNc),
thus influencing both dopaminergic and non-dopaminergic cells
(Smith et al., 1990). The subthalamo-nigral pathway appears to
arise from neurons mainly in the ventromedial regions of the
STh, displaying an approximate mediolateral topography (Smith
et al., 1990). At the level of the substantia nigra, these fibers form
several terminal fields consisting of networks of axon collaterals
showcasing both en passant and terminal boutons (Smith et al.,
1990); prominent perisomatic arborization has been highlighted,
but appears to be inconsistent throughout different studies. These
terminals showcase certain similarities to the subthalamo-pallidal
terminals, suggesting that both projections arise from the same
neuronal population (Parent and Hazrati, 1995). Few studies have addressed the structural connectivity between
the STh and the substantia nigra in non-human primates and
in humans. Aspects such as the precise termination of SN
projections to the STh remain to be clearly determined. From
a functional perspective, the dopaminergic innervation of the
STh may play a fundamental role in the regulation of STh
afferences, such as corticosubthalamic fibers (Mathai and Smith,
2011). From an anatomical perspective, the exact identification
and subcellular localization of dopaminergic synapses within
the human STh could significantly improve our understanding
of the dopaminergic modulation of the STh. Considering the
topographical vicinity between the STh and the SN, ex vivo
tracing methods could be employed to study the connections
between the SN and the STh without incurring in significant
technical difficulties related to tracer transport over long
distances (i.e., from the cortex to subcortical structures) within
ex vivo human brain tissue. While this information does not
resolve most of the questions posed by Mathai and Smith (2011)
regarding the physiological and pathological implications of
dopaminergic modulation of STh afferences, it could represent April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 19 Anatomy of the Subthalamic Nucleus Emmi et al. Brainstem Connections to the STh
Non-human Primate Tracing Studies The STh appears to be connected to several brainstem nuclei,
such as the pedunculopontine tegmental nucleus (PPT), the
ventral tegmental area of the mesencephalon, the periacqueductal
gray and the dorsal raphe nucleus (Nauta and Cole, 1978;
Carpenter et al., 1981b; Parent and Smith, 1987; Smith et al., 1990;
Lavoie and Parent, 1994a,b,c). The PPT projects conspicuously to
the whole extent of the STh, representing the main cholinergic
input to the nucleus (Lavoie and Parent, 1994c). These fibers
appear to modulate the activity of neurons in the STh and other
basal ganglia structures. A minor pathway arising from the STh
and directed toward the PPT has also been identified, which is
thought to relay basal ganglia information to the lower brainstem
and spinal cord via the mesencephalic locomotor region (Parent
and Hazrati, 1995), in particular through the activation of the
nucleus reticular gigantocellularis, which regulates the activity
of spinal interneurons through the reticulospinal tract (Pahapill
and Lozano, 2000; Hamani et al., 2004). Thus, the circuit appears
to be involved in the facilitation of locomotion and in the
regulation of cardiorespiratory activity during motor exercise Frontiers in Neuroanatomy | www.frontiersin.org Human Fiber Tracking Studies Based on Bostan et al.’s (2010) results, Pelzer et al. (2013)
identified connections between the STh and the cerebellar cortex
in living humans through DTI. According to the authors, the STh
was connected to both regions identified by Bostan et al. (2010),
but appeared to also be connected to lobule VIII and IX. These
fibers crossed the midline at the level of the pons and entered the
cerebellum passing through the middle cerebellar peduncle. Milardi et al. (2016) extensively examined the connections
between the basal ganglia and the cerebellum, confirming
and expanding the findings of previous authors. However, April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 20 Emmi et al. Anatomy of the Subthalamic Nucleus (Eldridge et al., 1985). According to Lavoie and Parent (1994c),
the terminals of the PPT-STh projection form contacts with
the soma and proximal dendrites of STh neurons; however,
these information seem to derive from rodent and feline studies
(Morizumii et al., 1987). Information on these terminals in non-
human primates seems to be lacking. and proximal dendrites of STh cells (Parent and Hazrati, 1995;
Sato et al., 2000a). Human Fiber Tracking Studies Through DTI, Muthusamy et al. (2007) and Aravamuthan et al. (2007) were the first to identify the connection between the
PPT and the STh in humans. In particular, the two structures
appeared to be connected at the level of the medial, posterior
and superior eight of the PPT and at the level of the medial
and inferior STh (Aravamuthan et al., 2007). Again, results
deriving from diffusion based approaches should be interpreted
with care: even though the connections evidenced largely match
those found in animal studies, all non-human primate axon
tracing studies known to us identify projections arising from
the PPT with diffuse terminations and extensive branching
throughout the whole extent of the STh, and do not describe an
inferomedial termination of afferences (Nauta and Cole, 1978;
Carpenter et al., 1981b; Parent and Smith, 1987; Smith et al., 1990;
Lavoie and Parent, 1994a,b,c). Interestingly, Lavoie and Parent
(1994c) evidenced that PPT fibers enter the STh from its medial
tip and dorsal surface and arborize profusely and uniformly
throughout the nucleus; considering the technical limitations of
DTI, it could be speculated that Aravamuthan et al.’s (2007)
study reconstructed PPT projections to the STh entering the
nucleus from its medial tip, in accordance to animal studies,
without being able to reconstruct the arborization of these fibers
within the structure. More evidence from human fiber tracking
studies, possibly with higher spatial resolution, could help to
clarify this aspect. However, the functional segregation initially proposed appears
to be only partially confirmed: segregation seems to be
maintained with regard to the associative subregions of the
striatum (associative regions being contacted exclusively by other
associative regions), but not at the level of the motor circuits
(motor regions being contacted by other functional division, in
particular the associative ones). Two possible hypotheses arise: Two possible hypotheses arise: 1. The associative and motor circuit project to the same
neurons of the motor STh, which integrates the
information originating from both circuits and redirects
them to the motor GPi. FUNCIONAL SEGREGATION OR
FUNCTIONAL CONVERGENCE?
ANATOMICAL EVIDENCE OF STH OPEN
AND CLOSED-LOOP CIRCUITS The dorsal raphe nucleus appears to consistently innervate
the STh through widespread 5-HT immunoreactive fibers, even
though their physiological activity remains controversial (Rinvik
et al., 1979; Carpenter et al., 1981b; Mori et al., 1985). The previous paragraphs highlighted the intricate network of
connections directed to and originating from the STh. Given
the tripartite division of the striatum, pallidum and STh, the
parallel segregated principle predicts the existence of indirect
pathways connecting functionally corresponding subregions of
the striatum, GPe, GPi and STh. In particular, it has been
evidenced that efferents originating from the GPe contact STh
neurons projecting to GPi and SNr, thus providing an anatomical
support for the existence of an indirect pathway (Joel and
Weiner, 1997). Initially the original hypothesis was rejected
by Parent and Hazrati (1995) due to lack of firm anatomical
evidence for the existence of the indirect pathway, as previous
studies were unable to confirm GPe connections to the STh
territory containing neurons projecting toward the GPi/SNr. According to the authors, an indirect pathway connecting the
GPe to the output structures of the basal ganglia (i.e., GPi and
SNr) required either direct connections between the GPe and
the aforementioned nuclei, or an indirect GPe-STh-GPi/SNr
projection, which in turn relied on the existence of a link
between the dorsolateral STh (receiving GPe input) and the
ventromedial STh (giving rise to GPi/SNr projections) (Parent
and Hazrati, 1995). Supporting data was subsequently provided
by Shink et al. (1996), identifying the connection between
GPe fibers and STh neurons projecting to the GPi through
electron microscopy. Several other nuclei projecting to the STh have been identified,
even though the organization and the functional role of these
projections remains unclear; these include: the reticular nucleus
of the thalamus, the hypothalamus, the amygdaloid nuclei, the
locus coeruleus, the zona incerta and the parabrachial nuclei
(Rinvik et al., 1979; Canteras et al., 1990). Synaptic Contacts of the Major Afferents
to the Subthalamic Nucleus Table 3 shows the distribution and cellular localization of
synaptic contacts at the level of STh cells. Fibers originating from
the motor cortex (in particular area M1 and PMC), centromedian
and parafascicular nuclei of the thalamus, substantia nigra
pars compacta, pedunculopontine tegmental nucleus and dorsal
raphe nucleus contact STh neurons mainly at the level of
distal dendrites (Rinvik et al., 1979; Carpenter et al., 1981b;
Mori et al., 1985; Morizumii et al., 1987; Smith et al., 1990;
François et al., 2000; Tandé et al., 2006; Rico et al., 2010; Coudé
et al., 2018), whilst pallidal fibers contact mainly the soma 2. The associative circuit and the motor circuit project
to different subpopulations of neurons within the STh. These subpopulation would differ only for the afferences
received, whilst projecting on the same neurons at the
level of the motor GPi. However, regardless of whether the projections from the
motor and associative GPe remain segregated in the motor STh
or converge on the same neurons, information is still transferred
from the associative striatum through associative GPe and motor April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 21 Anatomy of the Subthalamic Nucleus Emmi et al. TABLE 3 | Localization of subcellular afferences to monkey STh. Afferent structure
Principal neurotransmitter
Localization of main synaptic
contacts
References
Motor cortex
Glutamate
Distal dendrites and spines
Coudé et al., 2018
GPe
GABA
Cell body and proximal dendrites
Parent and Hazrati, 1995; Sato et al.,
2000a
Thalamus
Glutamate
Distal dendrites
Tandé et al., 2006; Rico et al., 2010
SNc
Dopamine
Dendrites
Smith et al., 1990; Parent and
Hazrati, 1995; François et al., 2000
PPT (Tegmentum)
ACh
Distal dendrites and soma
Rodent and feline studies (Morizumii
et al., 1987); confirmation required
from non-human primate studies. Dorsal Raphe
5-HT
Distal dendrites
Rinvik et al., 1979; Carpenter et al.,
1981b; Mori et al., 1985 TABLE 3 | Localization of subcellular afferences to monkey STh. STh to the motor GPi (Joel and Weiner, 1997). The consequences
of this anatomical organization will be discussed further. to the authors, this connection could represent the anatomical
demonstration in primates for an open-loop circuit between the
limbic circuit and the motor circuit of the basal ganglia. Synaptic Contacts of the Major Afferents
to the Subthalamic Nucleus According to Joel and Weiner’s hypothesis (1997), two types of
indirect pathways can be identified in regard to the topographical
organization of STh afferent and efferent projections: g
g
More recently, a study on rodents (Aoki et al., 2019) has
provided some interesting insight on the anatomo-functional
organization of closed and open loop circuits within the rat
basal ganglia. By combining genetic and viral approaches, the
authors mapped the limbic and motor circuits between the
cortex, the basal ganglia and the thalamus in rodents. Despite
evidencing largely closed loops within each functional domain,
the authors discovered an unidirectional influence of the limbic
over the motor loop via ventral striatum-substantia nigra (SNr)-
motor thalamus circuitry; furthermore, activity within the ventral
striatum of the rat seems to modulate the activity of the primary
motor cortex. These results appear to be in line with Kelly and
Strick’s (2004) findings in non-human primates. Interestingly,
this pathway seems to form synapses with the SNr, rather than
the GPi. Kelly and Strick (2004) did not report any retrogradely
labeled neurons within the SNr, but only in the GPi. Therefore,
it could be speculated that the non-human primate open loop
circuit connecting the ventral putamen to the motor cortex passes
through the GPi, rather than the SNr. According to Hardman
et al. (2002), the SNr plays a much more important role as an
output structure of the basal ganglia in rodents compared to non-
human primates, while the opposite seems to be true for the GPi. 1. Closed indirect pathway: this pathway terminates in the
same GPi/SNr subregion as the direct pathway arising
from the corresponding striatal subregion. This leads
to the connection of functionally related regions of the
striatum, pallidal complex and STh according to the
parallel segregation scheme. The closed indirect pathway
contributes to the processing of information within the
basal ganglia-thalamocortical circuits. 2. Open
indirect
pathway:
this
pathway
terminates
in a different subregion of the GPi/SNr than the
direct pathway, thus connecting functionally non-
corresponding subregions of the striatum, pallidal
complex and STh. The open indirect pathway contributes
to the connection between circuits of the basal ganglia. Thus, three possible closed pathways can be hypothesized,
each one connecting the corresponding functional regions of the
striatum, pallidal complex, STh and SNr. Synaptic Contacts of the Major Afferents
to the Subthalamic Nucleus On the other hand,
among the open indirect pathways it is possible to identify the
one linking the associative striatum to the motor GPi passing
through the associative GPe and motor STh (one further open
indirect pathway is the one connecting the associative regions to
the ventral pallidum and the limbic circuit; for more information,
consult Joel and Weiner, 1997). Considering the increasing importance of the STh in
processing different types of information through phylogenesis
(Hardman et al., 2002), the definition of the STh’s role
in
open
versus
closed loop
circuits
could
represent an
important aspect regarding information processing within the
human basal ganglia. Empirical evidence for the open versus closed loop circuits
hypothesis in non-human primates and humans remains
controversial. Kelly and Strick (2004) employed rabies virus
retrograde tracing to define closed and open loop circuits within
the primate cortico-basal ganglia-thalamo-cortical circuits. Even
though the authors evidenced mostly closed-loop circuits
between motor and limbic areas, an open-loop circuit connecting
(indirectly) the ventral putamen to M1 has also been identified. The ventral putamen belongs to the limbic circuit of the basal
ganglia (Parent and Hazrati, 1995), and seems to be connected
to limbic structures such as the amygdala (Parent and Hazrati,
1995; Joel and Weiner, 1997; Kelly and Strick, 2004). According Frontiers in Neuroanatomy | www.frontiersin.org Connectivity A general overview of the axonal and dendritic network within
the STh can be further investigated through the aid of the
Cajal-De Castro photographic silver techniques, allowing for the
impregnation not only of formalin fixed bulks of tissue, but also
of paraffin embedded sections. y
Currently, the connectivity of the STh has been investigated in
non-human primates through in vivo tracing studies, and in
humans in both in vivo and ex vivo specimen through MRI,
specifically through DTI and DWI. Conversely, the connectivity
of the human STh has never been investigated through post-
mortem tracing methods, such as Carbocyanine tracing or Neuro
Vue Dyes. These tracers allow for the anterograde and retrograde
tracing of axons even in formalin fixed human specimens
(Heilingoetter and Jensen, 2017), and could be employed to
study the connectivity between the STh and closely related
structures, such as the substantia nigra, the globus pallidus,
and the nucleus of the zona incerta. For long distance tracing,
complications may arise due to the very long incubation times
required (from several months to years) and due to technical
difficulties with the cryostat-sectioning of macrosections. Even
though these techniques may present inherent limitations, such
as long incubation periods and possible tracer diffusion during
sectioning, they also appear to be significantly more accurate
than in vivo tracing studies (Heilingoetter and Jensen, 2017);
furthermore, given the increasingly important role of the STh
through phylogenesis (Hardman et al., 2002), these tracing
techniques could identify a different organization of afferent and
efferent projections in humans compared to monkeys, whilst also
expanding on the topography of STh connections. Immunohistochemistry should be employed to characterize
the
distribution
of
different
receptors
or
molecules
of
interest; it must be noted, however, that the quality of
Immunohistochemistry depends on the method and time of
fixation: specimen fixed for longer periods (>1 year) in formalin
yield generally worse results than fresh and appropriately fixed
specimen. The definition of neuronal populations expressing
specific proteins or receptors, as well as their distribution
within the structure, should be investigated through the aid of
unbiased stereology in both health and disease, with particular
regard to movement disorders and α-sinucleopathies. The
chemoreceptorial characterization of STh neurons could help
define fundamental functional aspects of the structure. AUTHOR CONTRIBUTIONS AA conceived the review. AE drafted the manuscript and
designed the figures. AE, RD, AP, and VM revised the manuscript. All authors contributed to the final manuscript. CONCLUSION AND FUTURE
PERSPECTIVES Even though the STh represents a topic of interest in current
neuroscience research, most anatomical data available derives
from histological and tracing studies in non-human primates. Data on humans is limited to very few studies employing
mostly MRI in combination with unbiased stereology applied to April 2020 | Volume 14 | Article 13 22 Anatomy of the Subthalamic Nucleus Emmi et al. histological sections. According to our perspective, it is possible
to identify three main points of interest within human STh
research which require further and detailed investigation:
connectivity,
cytoarchitectural
and
chemoarchitectural
organization, and functional subdivision. of metallic silver, if not appropriately pre-treated. On the other
hand, fresh tissue can be impregnated using osmic acid as a
fixative (Golgi-Cox variation), after isolating the STh in a freshly
cut hemisphere. Otherwise, carbocyanines and Neuro Vue dyes
can also be employed to evidence the morphology of single
neurons and, unlike silver impregnation techniques, also allow
for the visualization of synaptic contacts in traced neurons. Cytoarchitectonics and
Chemoarchitectonics While the cellular morphology and different cellular populations
have been identified in rodents, cats and primates, there are
no conclusive studies in humans. The morphology of human
subthalamic neurons can be studied through Golgi silver
impregnation techniques, such as the Golgi-Cox and Golgi-De
Bubenaite methods, even though formalin fixed human tissue
generally leads to artifact formation and incomplete precipitation Connectivity Hence, both cytoarchitectonics and chemoarchitectonics
could provide evidence for different subpopulations of neurons
within the STh, receiving and processing different types
of informations, with particular regard to the functional
subdivision hypothesis. Albin, R. L., Young, A. B., and Penney, J. B. (1989b). The functional anatomy of
basal ganglia disorders. Trends Neurosci. 12, 366–375.
Albin, R. L., Reiner, A., Anderson, K. D., Penney, J. B., and Young, A. B.
(1990a). Striatal and nigral neuron subpopulations in rigid Huntington’s
disease: implications for the functional anatomy of chorea and rigidity-akinesia.
Ann. Neurol. 27, 357–365. doi: 10.1002/ana.410270403 Functional Subdivision Post-mortem tracing techniques can be used in conjunction
with ultra high field MRI, DTI and DWI of ex vivo specimens
to confirm the anatomo-radiological findings and to expand on
several aspects of connectivity which are still unclear, such as the
topography of projections, eventual subpopulations of target cells
and the type of synapse formed (e.g., axo-axonic, axo-somatic, or
axo-dendritic synapses). This aspect remains one of the most crucial in STh research. The identification of functional subdivisions within the nucleus,
and their clear definition in terms of topography, connectivity,
cell population, and receptor and protein expression could
provide novel insights on how different types of information are
processed within the basal ganglia. Furthermore, considering the
fundamental role played by the STh in DBS, the identification
of functional divisions of the structure which are both safe
to stimulate and easy to target could significantly improve
treatment outcome. REFERENCES “Mechanisms of neural
degeneration in Huntington’s disease,” in The Basal Ganglia IV: New Ideas and
Data on Structure and Function, eds G. Percheron, J. S. McKenzie, and J. Feger
(New York, NY: Plenum Press), 149–161. Bostan, A. C., Dum, R. P., and Strick, P. L. (2010). The basal ganglia communicate
with the cerebellum. Proc. Natl. Acad. Sci. U.S.A. 107, 8452–8456. doi: 10.1073/
pnas.1000496107 Fogelson, N., Williams, D., Tijssen, M., van Bruggen, G., Speelman, H., and
Brown, P. (2006). Different functional loops between cerebra.l cortex and the
subthalamic area in Parkinson’s disease. Cereb. Cortex 16, 64–75 doi: 10.1093/
cercor/bhi084 Brown, L. L., Markman, M. H., Wolfson, L. I., Dvorkin, B., Warner, C., and
Karzman, R. (1979). A direct role of dopamine in the rat subthalamic nucleus
and an adjacent intrapeduncular area. Science 206, 1416–1418. doi: 10.1126/
science.505015 François, C., Savy, C., Jan, C., Tande, D., Hirsh, E. C., and Yelnik, J. (2000). Dopaminergic innervation of the subthalamic nucleus in the normal state, in
MPTP-treated monkeys, and in Parkinson’s disease patients. J. Comp. Neurol. 425, 121–129. doi: 10.1002/1096-9861(20000911)425:1<121::aid-cne10>3.0. co;2-g Canteras, N. S., Shammah-Lagnado, S. J., Silva, B. A., and Ricardo, J. A. (1990). Afferent connections of the subthalamic nucleus; a combined retrograde
and anterograde horse radish peroxidase study in the rat. Brain Res. 513,
43–59. Gerfen, C. R., Staines, W. A., Arbuthnott, G. W., and Fibiger, H. C. (1982). Crossed
connections of the substantia nigra in the rat. J. Comp. Neurol. 207, 283–303. doi: 10.1002/cne.902070308 Carpenter, M. B., Batton, R. R., Carleton, S. C., and Keller, J. T. (1981a). Interconnections and organization of pallidal and subthalamic nucleus neurons
in the monkey. J. Comp. Neurol. 197, 579–603. doi: 10.1002/cne.90197
0404 Giolli, R. A., Gregory, K. M., Suzuki, D. A., Blanks, R. H., Lui, F., and Betelak, K. F. (2001). Cortical and subcortical afferents to the nucleus reticularis tegmenti
pontis and basal pontine nuclei in the macaque monkey. Vis. Neurosci. 18,
725–740. doi: 10.1017/s0952523801185068 Carpenter, M. B., Carleton, S. C., Keller, J. T., and Conte, P. (1981b). Connections
of the subthalamic nucleus in the monkey. Brain Res. 224, 1–29. doi: 10.1016/
0006-8993(81)91113-6 Grill, W. M., and Mcintyre, C. (2001). Extracellular excitation of central neurons:
implications for the mechanism of deep brain stimulation. Thalamus Relat. Syst. 1, 269–277. doi: 10.1016/s1472-9288(01)00025-5 Carpenter, M. B., and Jayaraman, A. (1990). “Subthalamic nucleus afferents:
anatomical and immunocytochemical features,” in The Basal Ganglia III, Vol. 1991, eds G. Bernardi, M. REFERENCES An autoradiographic study of efferent
connections of the globus pallidus in Macaca Mulatta. Exp. Brain Res. 46,
107–117. doi: 10.1007/bf00238104 Alkemade, A., Schnitzler, A., and Forstmann, B. U. (2015). Topographic
organization of the human and non-human primate subthalamic nucleus. Brain
Struct. Funct. 220, 3075–3078. doi: 10.1007/s00429-015-1047-2 DeVito, J. L., Anderson, M. E., and Walsh, K. E. (1980). A horseradish peroxidase
study of afferent connections of the globus pallidus in Macaca mulatta. Exp. Brain Res. 38, 65–73. Allheid, G. F., Heimer, L., and Switzer, R. C. (1990). “Basal ganglia,” in The Human
Nervous System, ed. G. Paxinos (San Diego, CA: Academic Press). heid, G. F., Heimer, L., and Switzer, R. C. (1990). “Basal ganglia,” ervous System, ed. G. Paxinos (San Diego, CA: Academic Press). Dostrovsky, J. O., and Lozano, A. M. (2002). Mechanisms of deep brain
stimulation. Mov. Disord. 17(Suppl. 3), S63–S68. Antonini, A., and Obeso, J. A. (2018). DBS for Parkinson’s disease with behavioural
disturbances. Lancet Neurol. 17, 195–197. doi: 10.1016/s1474-4422(18)30044-9 Eldridge, F. L., Millhorn, D. E., Kiley, J. P., and Waldrop, T. G. (1985). Stimulation by central command of locolmotion, respiration and circulation
during exercise. Respir. Physiol. 59, 313–337. doi: 10.1016/0034-5687(85)90
136-7 Aoki, S., Smith, J. B., Li, H., Yan, X., Igarashi, M., Coulon, P., et al. (2019). An
open cortico-basal ganglia loop allows limbic control over motor output via the
nigrothalamic pathway. eLife 8:e49995. doi: 10.7554/eLife.49995 Fabbri, M., Coelho, M., Guedes, L. C., Rosa, M. M., Abreu, D., Gonçalves, N.,
et al. (2017). Acute response of non-motor symptoms to subthalamic deep brain
stimulation in Parkinson’s disease. Parkinsonism Relat. Disord. 41, 113–117. doi: 10.1016/j.parkreldis.2017.05.003 Aravamuthan, B. R., Muthusamy, K. A., Stein, J. F., Aziz, T. Z., and Johansen-
Berg, H. (2007). Topography of cortical and subcortical connections of the
human pedunculopontine and subthalamic nuclei. Neuroimage 37, 694–705. doi: 10.1016/j.neuroimage.2007.05.050 Bahatia, K. P., and Marsden, C. D. (1994). The behavioral and motor consequences
of focal lesions of the basal ganglia in man. Brain 117, 859–876. doi: 10.1093/
brain/117.4.859 Fedio, P., Cox, C. S., Neophytides, A., Conal-Frederick, G., and Chase, T. N. (1979). Neuropsychological profile of Huntington’s disease: patients and those at risk. Adv. Neurol. 23, 239–255. Berney, A., Vingerhoets, F., and Perrin, A. (2002). Effect on mood of subthalamic
DBS for Parkinson’s disease: a consecutive series of 24 patients. Neurology 59,
1427–1429. doi: 10.1212/01.wnl.0000032756.14298.18 Ferrante, R. J., Beal, M. F., and Kowall, N. W. (1994). REFERENCES Albin, R. L., Aldridge, J. W., Young, A. B., and Gliman, S. (1989a). Feline
subthalamic nucleus neurons contain glutamate-like but not GABA-like or
glycine-like immunoreactivity. Brain Res. 491, 185–188. doi: 10.1016/0006-
8993(89)90103-0 Albin, R. L., Aldridge, J. W., Young, A. B., and Gliman, S. (1989a). Feline
subthalamic nucleus neurons contain glutamate-like but not GABA-like or
glycine-like immunoreactivity. Brain Res. 491, 185–188. doi: 10.1016/0006-
8993(89)90103-0 April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 23 Emmi et al. Anatomy of the Subthalamic Nucleus Albin, R. L., Young, A. B., Penney, J. B., Handelin, B., Balfour, K. D., Markel, D. S.,
et al. (1990b). Abnormalities of striatal projection neurons and N-methyl-d-
aspartate receptors in perisymptomatic Huntington’s disease. N. Engl. J. Med. 322, 1293–1298. doi: 10.1056/nejm199005033221807 Coudé, D., Parent, A., and Parent, M. (2018). Single-axon tracing of the
corticosubthalamic hyperdirect pathway in primates. Brain Struct. Funct. 223,
3959–3973. doi: 10.1007/s00429-018-1726-x Dafsari, H. S., Petry-Schmelzer, J. N., Ray-Chaudhuri, K., Ashkan, K., Weis, L.,
Dembek, T. A., et al. (2018a). Non-motor outcomes of subthalamic stimulation
in Parkinson’s disease depend on location of active contacts. Brain Stimul. 11,
904–912. doi: 10.1016/j.brs.2018.03.009 Alexander, G. E., Crutcher, M. D., and Delong, M. R. (1990). Basal ganglia
thalamocortical circuits: parallel substrates for motor, oculomotor, prefrontal
and limbic functions. Prof. Brain Res. 85, 119–146. doi: 10.1016/s0079-6123(08)
62678-3 Dafsari, H. S., Weiß, L., Silverdale, M., Rizos, A., Reddy, P., Ashkan, K., et al. (2018b). Short-term quality of life after subthalamic stimulation depends on
non-motor symptoms in Parkinson’s disease. Brain Stimul. 11, 867–874. doi:
10.1016/j.brs.2018.02.015 Alexander, G. E., Delong, M. R., and Stick, P. L. (1986). Parallel organization of
functionally segregated circuits linking basal ganglia and cortex. Annu. Rev. Neurosci. 9, 357–381. doi: 10.1146/annurev.ne.09.030186.002041 Dafsari, H. S., Reddy, P., Herchenbach, C., Wawro, S., Petry-Schmelzer, J. N.,
Visser-Vandewalle, V., et al. (2016). Beneficial effects of bilateral subthalamic
stimulation on non-motor symptoms in Parkinson’s Disease. Brain Stimul. 9,
78–85. doi: 10.1016/j.brs.2015.08.005 Alho, E. J. L., Alho, A. T. D. L., Horn, A., Martin, M., da, G. M., Edlow, B. L., et al. (2019). The ansa subthalamica: a neglected fiber tract. Mov. Disord. 35, 75–80. doi: 10.1002/mds.27901 78–85. doi: 10.1016/j.brs.2015.08.005 Alkemade, A., and Forstmann, B. (2014). Do we need to revise the tripartite
subdivision hypothesis of the human subthalamic nucleus (STN)? Neuroimage
95, 326–329. doi: 10.1016/j.neuroimage.2014.03.010 DeVito, J. L., and Anderson, M. E. (1982). REFERENCES doi: 10.1002/cne.901820303 Lavoie, B., and Parent, A. (1994c). Pedunculopontine nucleus in the squirrel
monkey: projections to the basal ganglia as revealed by anterograde tract-
tracing methods. J. Comp. Neurol. 344, 2010–2031. Joel, D., and Weiner, I. (1997). The connections of the primate subthalamic
nucleus: indirect pathways and the open-interconnected scheme of basal
ganglia-thalamocortical circuitry. Brain Res. Brain Res. Rev. 23, 62–78. doi:
10.1016/s0165-0173(96)00018-5 Lavoie, B., Smith, Y., and Parent, A. (1989). Dopaminergic innervation of the
basal ganglia in the squirrel monkey, as revealed by tyrosine hydroxylase
immunohistochemistry. J. Comp. Neurol. 289, 36–52. doi: 10.1002/cne. 902890104 Joel, D., and Weiner, L. (2000). The connections of the dopaminergic system with
the striatum in rats and primates: an analysis with respect to the functional
and compartmental organization of the striatum. Neuroscience 96, 451–474. doi: 10.1016/s0306-4522(99)00575-8 Levesque, J. C., and Parent, A. (2005). GABAergic interneurons in human
subthalamic nucleus. Mov. Disord. 20, 574–584. doi: 10.1002/mds.20374 Jones, D. K., Knösche, T. R., and Turner, R. (2013). White matter integrity, fiber
count, and other fallacies: the do’s and don’ts of diffusion MRI. Neuroimage 73,
239–254. doi: 10.1016/j.neuroimage.2012.06.081 Lozano, A. M., Dostrovsky, J., Chen, R., and Ashby, P. (2002). Deep brain
stimulation for Parkinson’s disease: disrupting the disruption. Lancet Neurol. 1, 225–231. doi: 10.1016/s1474-4422(02)00101-1 Karachi, C., Yelnik, J., Tandé, D., Tremblay, L., Hirsch, E. C., and François,
C. (2005). The pallidosubthalamic projection: an anatomical substrate for
nonmotor functions of the subthalamic nucleus in primates. Mov. Disord. 20,
172–180. doi: 10.1002/mds.20302 Luys, J. (1865). Recherches sur le systeme nerveux cerebro-spinal: sa structure, ses
fonctions et ses maladies. Paris: Bailliere. Magill, P., Bolam, J., and Bevan, M. (2000). Relationship of activity in the
subthalamic nucleus-globus pallidus network to cortical electroencephalogram. J. Neurosci. 20, 820–833. doi: 10.1523/jneurosci.20-02-00820.2000 Kearney, J. A., and Albin, R. L. (2000). Intrasubthalamic nucleus metabotropic
glutamate receptor activation: a behavioral, Fos immunohistochemical and
[14C]2-deoxyglucose autoradiographic study. Neuroscience 95, 409–416. doi:
10.1016/s0306-4522(99)00439-x Marani, E., Heida, T., Lakke, E. A., and Usunoff, K. G. (2008). The subthalamic
nucleus. Part I: development, cytology, topography and connections. Adv. Anat. Embryol. Cell. Biol. 198, 1–113. Kelly, R. M., and Strick, P. L. (2004). Macro-architecture of basal ganglia loops with
the cerebral cortex: use of rabies virus to reveal multisynaptic circuits. Prog. Brain Res. 143, 449–459. Martin, J. D., and Gusella, J. F. (1986). Huntington’s disease: pathogenesis and
management. N. Eng. J. Med. 315, 1267–1276. Keuken, M. C., Uylings, H. REFERENCES J. Comp. Neurol. 173, 147–164. Lambert, C., Zrinzo, L., Nagy, Z., Lutti, A., Hariz, M., Foltynie, T., et al. (2012). Confirmation of functional zones within the human subthalamic nucleus:
patterns of connectivity and sub-parcellation using diffusion weighted imaging. Neuroimage 60, 83–94. doi: 10.1016/j.neuroimage.2011.11.082 Haynes, W. I., and Haber, S. N. (2013). The organization of the prefrontal-
subthalamic inputs in primates provides an anatomical substrate for both
functional specificity and integration: implications for basal ganglia models and
deep brain stimulation. J. Neurosci. 33, 4804–4814. doi: 10.1523/JNEUROSCI. 4674-12.2013 Lambert, C., Zrinzo, L., Nagy, Z., Lutti, A., Hariz, M., Foltynie, T., et al. (2015). Do we need to revise the tripartite subdivision hypothesis of the
human subthalamic nucleus (STN)? Response to Alkemade and Forstmann. Neuroimage 110, 1–2. doi: 10.1016/j.neuroimage.2015.01.038 Hazrati, L. N., and Parent, A. (1992). Convergence of subthalamic and striatal
efferents at pallidal level in primates: an anterograde double-labeling study
with biocytin and PHA-L. Brain Res. 569, 336–340. doi: 10.1016/0006-8993(92)
90648-s Lange, H., Thorner, G., Hopf, A., and Schroder, K. F. (1976). Morphometric
studies of the neuropathological changes in choreatic diseases. J. Neurol. Sci. 28, 401–425. doi: 10.1016/0022-510x(76)90114-3 Heilingoetter, C. L., and Jensen, M. B. (2017). Histological methods for ex vivo axon
tracing: a systematic review. Neurol. Res. 38, 561–569. doi: 10.1080/01616412. 2016.1153820 Larsen, M., Bjarkam, C. R., Østergaard, K., West, M. J., and Sørensen, J. C. (2004). The anatomy of the porcine subthalamic nucleus evaluated with
immunohistochemistry and design-based stereology. Anat. Embryol. 208,
239–247. Isaacs, B. R., Forstmann, B. U., Temel, Y., and Keuken, M. C. (2018). The connectivity fingerprint of the human frontal cortex, subthalamic
nucleus and striatum. Front. Neuroanat. 12:60. doi: 10.3389/fnana.2018.0
0060 Lavoie, B., and Parent, A. (1994a). Pedunculopontine nucleus in the squirrel
monkey: cholinergic and glutamatergic projections to the substantia nigra. J. Comp. Neurol. 344, 232–241. doi: 10.1002/cne.903440205 Ishida, H., Inoue, K., Takada, M., and Hoshi, E. (2016). Origins of multisynaptic
projections from the basal ganglia to the forelimb region of the ventral premotor
cortex in macaque monkeys. Eur. J. Neurosci. 43, 258–269. doi: 10.1111/ejn. 13127 Lavoie, B., and Parent, A. (1994b). Pedunculopontine nucleus in the squirrel
monkey: distribution of cholinergic and monoaminergic neurons in the
mesopontine tegmentum with evidence for the presence of glutamate in
cholinergic neurons. J. Comp. Neurol. 344, 190–209. doi: 10.1002/cne. 903440203 Iwahori, N. (1987). A Golgi study on the subthalamic nucleus of the cat. J. Comp. Neurol. 182, 383–397. REFERENCES B. Carpenter, G. Di Chiara, M. Morelli, and P. Stanzione (New York, NY: Plenum Press), 109–117. doi: 10.1007/978-1-4684-
5871-8_12 Grill, W. M., Snyder, A. N., and Miocinovic, S. (2004). Deep brain stimulation
creates an informational lesion of the stimulated nucleus. Neuroreport 15,
1137–1140. doi: 10.1097/00001756-200405190-00011 Carpenter, M. B., Nakano, K., and Kim, R. (1976). Nigrothalamic projections in
the monkey demonstrated by autoradiographic technics. J. Comp. Neurol. 165,
401–415. doi: 10.1002/cne.901650402 Groenewegen, H. J., and Berendse, H. W. (1990). Connections of the
subthalamic nucleus with ventral striatopallidal parts of the basal ganglia
in the rat. J. Comp. Neurol. 294, 607–622. doi: 10.1002/cne.90294
0408 Clarke, N. P., Bevan, M. D., Cozzari, C., Hartman, B. K., and Bolam, J. P. (1997). Glutamate-enriched cholinergic synaptic terminals in the entopeduncular
nucleus and subthalamic nucleus of the rat. Neuroscience 81, 371–385. doi:
10.1016/s0306-4522(97)00247-9 Hamani, C., Saint-Cyr, J. A., Fraser, J., Kaplitt, M., and Lozano, A. M. (2004). The
subthalamic nucleus in the context of movement disorders. Brain 127, 4–20. doi: 10.1093/brain/awh029 April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 24 Anatomy of the Subthalamic Nucleus Emmi et al. Hamel, W., Köppen, J. A., Alesch, F., Antonini, A., Barcia, J. A., Bergman, H.,
et al. (2017). Targeting of the subthalamic nucleus for deep brain stimulation:
a survey among Parkinson Disease specialists. World Neurosurg. 99, 41–46. doi: 10.1016/j.wneu.2016.11.012 Knook, H. L. (1965). The Fibre-Connections of the Forebrain. thesis. Van Gorcum
and Co. N. V. Leiden. Kosta, P., Argyropoulou, M. I., and Markoula, S. (2006). MRI evaluation of
the basal ganglia size and iron content in patients with Parkinson’s disease. J. Neurol. 253, 26–32. doi: 10.1007/s00415-005-0914-9 Hardman, C. D., Halliday, G. M., McRitchie, D. A., and Morris, J. G. (1997). The
subthalamic nucleus in Parkinson’s disease and progressive supranuclear palsy. J. Neuropathol. Exp. Neurolol. 56, 132–142. Kulisevsky, J., Berthier, M. L., and Gironell, A. (2002). Mania following deep brain
stimulation for Parkinson’s disease. Neurology 59, 1421–1424. doi: 10.1212/wnl. 59.9.1421 Hardman, C. D., Henderson, J. M., Finkelsen, D. I., Horne, M. K., Paxinos, G., and
Halliday, G. M. (2002). Comparison of the basal ganglia in rats, marmosets,
macaques, baboons and humans: volume and neuronal number for the output,
internal relay and striatal modulating nuclei. J. Comp. Neurol. 445, 238–255. doi: 10.1002/cne.10165 Kunzle, H., and Akert, K. (1977). Efferent connections of cortical area 8 (frontal
eye field) in Macaca Fascicularis. a reinvestigation using the autoradiographic
technique. REFERENCES Ultra-High field MRI post mortem structural connectivity of the
Human Subthalamic Nucleus, Substantia Nigra, and Globus Pallidus. Front. Neuroanat. 10:66. doi: 10.3389/fnana.2016.00066 Miyachi, S., Lu, X., Imanishi, M., Sawada, K., Nambu, A., and Takada, M. (2006). Somatotopically arranged inputs from putamen and subthalamic nucleus to
primary motor cortex. Neurosci. Res. 56, 300–308. Mori, S., Takino, T., Yamada, H., and Sano, Y. (1985). Imunohistochemical
demonstration of serotonin nerve fibers in the subthalamic nucleus of the rat,
cat and monkey. Neurosci. Lett. 62, 305–309. Plantinga, B. R., Temel, Y., Duchin, Y., Uludag, K., Patriat, R., Roebroeck, A., et al. (2018). Individualized parcellation of the subthalamic nucleus in patients with Plantinga, B. R., Temel, Y., Duchin, Y., Uludag, K., Patriat, R., Roebroeck, A., et al. (2018). Individualized parcellation of the subthalamic nucleus in patients with
Parkinson’s Disease with 7T MRI. Neuroimage 168, 403–411. Morizumii, T., Nakamura, Y., Kitao, Y., and Kudo, M. (1987). Ultrastructural
anlyses of afferent terminals in the subthalamic nucleus of the cat with a
combined degeneration and horseradish peroxidase tracing method. J. Comp. Neurol. 265, 159–174. Porzionato, A., Macchi, V., Zaramella, P., Sarasin, G., Grisafi, D., Dedja, A., et al. (2015). Effects of postnatal hyperoxia exposure on the rat dentate gyrus and
subventricular zone. Brain Struct. Funct. 220, 229–247. doi: 10.1007/s00429-
013-0650-3 Muthusamy, K. A., Aravamuthan, B. R., Kringelbach, M. L., Jenkinson, N.,
Voets, N. L., Johansen-Berg, H., et al. (2007). Connectivity of the human
pedunculopontine nucleus region and diffusion tensor imaging in surgical
targeting. J. Neurosurg. 107, 814–820. Pujol, S., Cabeen, R., Sébille, S. B., Yelnik, J., François, C., Fernandez Vidal, S., et al. (2017). In vivo Exploration of the connectivity between the subthalamic nucleus
and the globus pallidus in the human brain using multi-fiber tractography. Front. Neuroanat. 10:119. doi: 10.3389/fnana.2016.00119 Nambu, A., Takada, M., Hamada, I., Kita, H., Imanishi, M., Akazawa, T., et al. (2000). Excitatory cortical inputs to pallidal neurons via the subthalamic
nucleus in the monkey. J. Neurophysiol. 84, 289–300. Rafols, J. A., and Fox, C. A. (1976). The neurons in the primate subthalamic
nucleus: A Golgi and electron microscopic study. J. Comp. Neurol. 168, 75–112. Ranck, J. B. (1975). Which elements are excited in electrical stimulation of
mammalian central nervous system: a review. Brain Res. 98, 417–440. Nambu, A., Takada, M., Inase, M., and Tokuno, H. (1996). REFERENCES B., Geyer, S., Schäfer, A., Turner, R., and Forstmann,
B. U. (2012). Are there three subdivisions in the primate subthalamic nucleus? Front. Neuroanat. 6:14. doi: 10.3389/fnana.2012.00014 Martin, J. P. (1927). Hemichorea resulting from a local lesion of the brain (the
syndrome of the body of Luys). Brain 50, 637–651. Massey, L. A., Miranda, M. A., Zrinzo, L., Al-Helli, O., Parkes, H. G., Thornton,
J. S., et al. (2012). High resolution MR anatomy of the subthalamic nucleus:
imaging at 9.4 T with histological validation. Neuroimage 59, 2035–2044. doi:
10.1016/j.neuroimage.2011.10.016 Kim, R., Nakano, K., Jayaraman, A., and Carpenter, M. B. (1976). Projections of
the globus pallidus and adjacent structures: an autoradiographic study in the
monkey. J. Comp. Neurol. 169, 263–290. Kita, H., Chang, H. T., and Kitai, S. T. (1983). The morphology of intracellularly
labeled rat subthalamic neurons: a light microscopic analysis. J. Comp. Neurol. 215, 245–257. doi: 10.1002/cne.902150302 Massey, L. A., and Yousry, T. A. (2010). Anatomy of the substantia nigra and
subthalamic nucleus on MR imaging. Neuroimaging Clin. N. Am. 20, 7–27. doi: 10.1016/j.nic.2009.10.001 Kita, H., and Kitai, S. T. (1987). Efferent projections of the subthalamic nucleus
in the rat: light and electron microscopic analysis with the PHA-L method. J. Comp. Neurol. 260, 435–452. doi: 10.1002/cne.902600309 Mathai, A., and Smith, Y. (2011). The corticostriatal and corticosubthalamic
pathways: two entries, one target. So what? Front. Syst. Neurosci. 1:64. doi:
10.3389/fnsys.2011.00064 April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 25 Anatomy of the Subthalamic Nucleus Emmi et al. Mcintyre, C. C., Grill, W. M., Sherman, D. L., and Thakor, N. V. (2004). Cellular
effects of deep brain stimulation: model-based analysis of activation and
inhibition. J. Neurophysiol. 91, 1457–1469. Petersen, M. V., Mlakar, J., Haber, S. N., Parent, M., Smith, Y., Strick, P. L., et al. (2019). Holographic reconstruction of axonal pathways in the human brain. Neuron 104, 1056–1064. doi: 10.1016/j.neuron.2019.09.030 Milardi, D., Arrigo, A., Anastasi, G., Cacciola, A., Marino, S., Mormina, E., et al. (2016). Extensive direct subcortical cerebellum-basal ganglia connections in
human brain as revealed by constrained spherical deconvolution tractography. Front. Neuroanat. 10:29. doi: 10.3389/fnana.2016.00029 Petry-Schmelzer, J. N., Krause, M., Dembek, T. A., Horn, A., Evans, J., Ashkan,
K., et al. (2019). Non-motor outcomes depend on location of neurostimulation
in
Parkinson’s
disease. Brain
142,
3592–3604. doi:
10.1093/brain/
awz285 Plantinga, B. R., Roebroeck, A., Kemper, V. G., Uludað, K., Melse, M., Mai, J.,
et al. (2016). REFERENCES Dual somatotopical
representations in the primate subthalamic nucleus: evidence for ordered
but reversed body-map transformations from the primary motor cortex and
supplementary motor area. J. Neurosci. 16, 2671–2683. Ranson, S. W., and Berry, C. (1941). Observations on monkeys with bilateral
lesions of the globus pallidus. Arch. Neurol. Psychat. 46, 504–508. Ranson, S. W., Ranson, S. W. Jr., and Ranson, M. (1941). Fiber connections of
the corpus striatum as seen in Marchi preparations. Arch. Neurol. Psychat. 46,
230–249. Nambu, A., Tokuno, H., Inase, M., and Takada, M. (1997). Corticosubthalamic
input zones from forelimb representations of the dorsal and ventral divisions of
the premotor cortex in the macaque monkey: comparison with the input zones
from the primary motor cortex and the supplementary motor area. Neurosci. Lett. 239, 13–16. Reiner, A., Albin, R. L., Anderson, K. D., D’Amato, C. J., Penney, J. B., and Young,
A. B. (1988). Differential loss of striatal projection neurons in Huntington’s
disease. Proc. Nat. Acad. Sci. U.S.A. 85, 5733–5737. Nauta, H. J. W., and Cole, M. (1978). Efferent projections of the subthalamic
nucleus: an autoradiographic study in monkey and cat. J. Comp. Neurol. 180,
1–16. Rico, A. J., Barroso Chinea, P., Conte-Perales, L., Roda, E., Gomez-Bautista, V.,
Gendive, M., et al. (2010). A direct projection from the subthalamic nucleus to
the ventral thalamus in monkeys. Neurobiol. Dis. 39, 381–392. Nauta, W. J., and Mehler, W. R. (1966). Projections of the lentiform nucleus in the
monkey. Brain Res. 1, 3–42. Rinvik, E., Grofova, I., Hammond, C., Féger, J., and Deniau, J. M. (1979). A study
of the afferent connections of the subthalamic nucleus in the monkey and the
cat using the HRP technique. Adv. Neurol. 24:53. Pahapill, P. A., and Lozano, A. M. (2000). The pedunculopontine nucleus and
Parkinson’s disease. Brain 123, 1767–1783. Rutledge, J. N., Hilal, S. K., and Silver, A. J. (1987). Study of movement disorders
and brain iron by MR. Am. J. Roentgenol. 149, 365–379. Parent, A., and Hazrati, L. N. (1995). Functional anatomy of the basal ganglia. II. The place of subthalamic nucleus and external pallidum in basal ganglia
circuitry. Brain Res. Brain Res. Rev. 20, 128–154. circuitry. Brain Res. Brain Res. Rev. 20, 128–154. Sadikot, A. F., Parent, A., and François, C. (1992). Efferent connections of the
centromedian and parafascicular talami nuclei in the squirrel monkey: a PHA-L
study of subcortical projections. J. Comp. Neurol. 315, 137–159. REFERENCES Parent, A., Sato, F., Wu, Y., Gauthier, J., Levesque, M., and Parent, M. (2000). Organization of the basal ganglia: the importance of axonal collateralization. Trends Neurosci. 23 (10 suppl.), S20–S27. Saint-Cyr, J. A., Trepanier, L. L., Kumar, R., Lozano, A. M., and Lang, A. E. (2000). Neuropsychological consequences of chronic bilateral stimulation of the
subthalamic nucleus in Parkinson’s disease. Brain 123, 2091–2108. Parent, A., and Smith, Y. (1987). Organization of efferent projections of the
subthalamic nucleus in the squirrel monkey as revealed by retrograde labeling
methods. Brain Res. 436, 296–310. Salvesen, L., Ullerup, B. H., Sunay, F. B., Brudek, T., Lokkegaard, A., Agander, T. K.,
et al. (2015). Changes in total cell numbers of the basal ganglia in patients with
multiple system atrophy – A stereological study. Neurobiol. Dis. 74, 104–113. doi: 10.1016/j.nbd.2014.11.008 Pelzer, E. A., Hintzen, A., Goldau, M., von Cramon, D. Y., Timmermann, L., and
Tittgemeyer, M. (2013). Cerebellar networks with basal ganglia. Feasibility for
tracking cerebello-pallidal and subthalamo-cerebellar projections in the human
brain. Eur. J. Neurosci. 38, 3106–3114. doi: 10.1111/ejn.12314 brain. Eur. J. Neurosci. 38, 3106–3114. doi: 10.1111/ejn.12314 Sato, F., Lavallée, P., Lévesque, M., and Parent, A. (2000a). Single-axon tracing
study of neurons of the external segment of the globus pallidus in primate. J. Comp. Neurol. 417, 17–31. Percheron, G., Filion, M., and Yelnik, J. (1987). “Spatial organization and
information processing in the core of the basal ganglia,” in The Basal Ganglia
II: Structure and Function – Currecnt Concepts, eds M. B. Carpenter and A. Jayraman (New York, NY: Plenum Press), 205–226. Sato, F., Parent, M., Levesque, M., and Parent, A. (2000b). Axonal branching
pattern of neurons of the subthalamic nucleus in primates. J. Comp. Neurol. 424, 142–152. Percheron, G., and Fillon, M. (1991). Parallel processing in the basal ganglia: up to
a point. Trends Neurosci. 14, 55–56. Shink, E., Bevan, M. D., and Bolam, J. P. (1996). The subthalamic nucleus and the
external pallidum: two tightly interconnected structures that control the output
of the basal ganglia in the monkey. Neuroscience 73, 335–357. Percheron, G., Francois, C., Yelnik, J., Fenelon, G., and Talbi, B. (1994). “The basal
ganglia related systems of primates: definition, description and informational
analysis,” in The Basal Ganglia IV: New Ideas and Data on Structure and
Function, eds G. Percheron, J. S. McKenzie, and J. Feger (New York, NY: Plenum
Press), 3–20. of the basal ganglia in the monkey. Neuroscience 73, 335–357. REFERENCES Smith, Y., Hazrati, L. N., and Parent, A. (1990). Efferent projections of the
subthalamic nucleus in the squirrel monkey as studied by the PHA-L
anterograde tracing method. J. Comp. Neurol. 294, 306–323. Smith, Y., and Parent, A. (1986). Differential connections of caudate nucleus
and putamen in the squirrel monkey (Saimiri sciureus). Neuroscience 18,
347–371. Petersen, M. V., Lund, T. E., Sunde, N., Frandsen, J., Rosendal, F., Juul, N., et al. (2017). Probabilistic versus deterministic tractography for delineation of the
cortico-subthalamic hyperdirect pathway in patients with Parkinson disease
selected for deep brain stimulation. J. Neurosurg. 126, 1657–1668. doi: 10.3171/
2016.4.JNS1624 Smith, Y., Shink, E., Bevan, M. D., and Bolan, J. P. (1995). The subthalamic
nucleus and the external pallidum: two tightly interconnected structures that April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 26 Anatomy of the Subthalamic Nucleus Emmi et al. control the output of the basal ganglia in primates. Brain Res. Ass. Abstr. 12:89. Wang, X. S., Ong, W. Y., Lee, H. K., and Huganir, R. L. (2000). A light and electron
microscopic study of glutamate receptors in the monkey subthalamic nucleus. J. Neurocytol. 29, 743–754. control the output of the basal ganglia in primates. Brain Res. Ass. Abstr. 12:89. Tai, L. S., Ng, T. K., Mak, N. K., and Yung, K. K. (2001). Co-localization of AMPA-
type glutamate receptor immunoreactivity in neurons of the rat subthalamic
nucleus. Brain Res. 895, 95–103. Wang, Z. M., Wei, P. H., Shan, Y., Han, M., Zhang, M., Liu, H., et al. (2020). Identifying and characterizing projections from the subthalamic nucleus to
the cerebellum in humans. Neuroimage 210:116573. doi: 10.1016/j.neuroimage. 2020.116573 Tandé, D., Féger, J., Hirsch, E. C., and François, C. (2006). Parafascicular nucleus
projection to the extrastriatal basal ganglia in monkeys. Neuroreport 17,
277–280. Whittier, J. R., and Mettler, F. A. (1949). Studies on the subthalamus of the rhesus
monkey. I. Anatomy and fiber connections of the subthalamic nucleus of Luys. J. Comp. Neur. 90, 281–318. Temel, Y., Blokland, A., Steinbusch, H. W., and Visser-Vandewalle, V. (2005). The
functional role of the subthalamic nucleus in cognitive and limbic circuits. Prog. Neurobiol. 76, 393–413. Williams, P. L., and Warwick, R. (1980). “The ventral thalamus or subthalamus,”
in Gray’s Anatomy, 36th Edn, eds P. L. Williams and R. Warkick (Edinburgh:
Churchill Livingstone), 963–965. Temel, Y., Kessels, A., Tan, S., Topdag, A., Boon, P., Visser-Vandewalle, V.,
et al. (2006a). REFERENCES Behavioural changes after bilateral subthalamic stimulation in
advanced Parkinson disease a systematic review. Parkinsonism Relat. Disord. 12, 265–272. Wu, Y., and Parent, A. (2000). Striatal interneurons expressing calretinin,
parvalbumin or NADPH- diaphorase: a comparative study in the rat, monkey
and human. Brain Res. 863, 182–191. Temel, Y., Visser-Vandewalle, V., Kaplan, S., Kozan, R., Daemen, M. A., Blokland,
A., et al. (2006b). Protection of nigral cell death by bilateral subthalamic nucleus
stimulation. Brain Res. 1120, 100–105. Yelnik, J., and Percheron, G. (1979). Subthalamic neurons in primates: a
quantitative and comparative analysis. Neuroscience 4, 1717–1743. Temel, Y., and Visser-Vandewalle, V. (2006). Targets for deep brain stimulation in
Parkinson’s Disease. Expert. Opin. Ther. Targets 10, 355–362. doi: 10.5137/1019-
5149.JTN.25028-18.3 Zwirner, J., Mobius, D., Bechmann, I., Arendt, T., Hoffmann, K. T., Jager, C.,
et al. (2017). Subthalamic nucleus volumes are highly consistent but decrese
age-dependently – a combined magnetic resonance imaging and stereology
approach in humans. Hum. Brain Mapp. 38, 909–922. doi: 10.1002/hbm. 23427 Thomas, C., Ye, F. Q., Ifranoglu, M. O., Modi, P., Saleem, K. S., Leopold, D. A.,
et al. (2014). Anatomical accuracy of brain connections derived from diffusion
MRI tractography is inherently limited. Proc. Natl. Acad. Sci. U.S.A. 111,
16574–16579. doi: 10.1073/pnas.1405672111 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. Urbain, N., Rentero, N., Gervasoni, D., Renaud, B., and Chouvet, G. (2002). The
switch of subthalamic neurons from an irregular to a bursting pattern does not
solely depend on their GABAergic inputs in the anesthetic-free rat. J. Neurosci. 22, 8665–8675. Copyright © 2020 Emmi, Antonini, Macchi, Porzionato and De Caro. 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. Vergani, F., Landi, A., Antonini, A., Parolin, M., Cilia, R., Grimaldi, M., et al. (2007). Anatomical identification of active contacts in subthalamic deep brain
stimulation. Surg. Neurol. 67, 140–146. Von Monakow, K. H., Akert, K., and Kuzle, H. (1978). Frontiers in Neuroanatomy | www.frontiersin.org Copyright © 2020 Emmi, Antonini, Macchi, Porzionato and De Caro. 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. REFERENCES Projections of the precentral
motor cortex and other cortical areas f the frontal lobe to the subthalamic
nucleus in the monkey. Exp. Brain. Res. 33, 395–403. April 2020 | Volume 14 | Article 13 Frontiers in Neuroanatomy | www.frontiersin.org 27
|
https://openalex.org/W3003143547
|
https://nottingham-repository.worktribe.com/preview/2216452/Development%20of%20an%20Extended%20RAMS%20Framework%20for%20Railway%20Networks.pdf
|
English
| null |
Development of an Extended RAMS Framework for Railway Networks
|
Proceedings of the 29th European Safety and Reliability Conference (ESREL)
| 2,019
|
cc-by
| 6,918
|
1. Introduction The earliest examples of Reliability, Maintain-
ability, Availability (RAM) analysis can be found
in the nuclear industry, Cleveland et al. (1985). Further examples of RAM analysis can be found
in the aerospace industry, Cole (1998), plant in-
dustry, Rotab Khan and Zohrul Kabir (1995), and
telecoms industry, Hamersma and Chodos (1992). In some early case studies it was referred to as
ARM. This paper proposes a new assessment framework
for railway asset managers. It is an extension of
RAMS (Reliability, Maintainability, Availability
and Safety) analysis. It provides a means of
assessing the network, identifying areas which
are performing differently and potentially allow
comparison between different railway networks. The framework allows asset managers to make
decisions regarding design, maintenance and op-
eration of the railway. In the nuclear industry, safety studies were per-
formed as early as the 1950s, Beckerley (1957),
and by 1970 comprehensive safety reports were
produced, US Nuclear Regulatory Commission
(1975). Towards the end of the 20th century,
following a spate of accidents such as Flixborough
[1974], Three Mile Island [1975] and Chernobyl
[1986], safety assessments were no longer per-
formed by the industry but by independence safety
bodies. This resulted in stricter safety guidelines
and a desire to avoid similar accidents. y
RAMS analysis is a well-established frame-
work used to assess a system or component. RAMS analysis is well suited to systems where
the failure modes are well understood. However,
in railway systems, while failure modes tend to
be well known due to a long history of operation,
the consequences of a given failure can be very
different depending on the part of the network in
which it occurs. The aim of this paper is to apply
RAMS analysis to railway networks and explore
how traditional RAMS analysis can be adapted for
use in the railway industry. This paper aims to, as
much as possible, use International Standards to
define terms. However, for a number of the ad-
ditional parameters considered no internationally
recognized definition exists, for these parameters
this paper presents a novel means to calculate
them. Safety and reliability analysis did not develop
as a unified discipline, but have merged as a
result of integrating a number of activities such
as reliability modelling (Smith (2017)). This
caused RAM analysis to evolve into RAMS anal-
ysis. Proceedings of the 29th European Safety and Reliability Conference.
Edited by Michael Beer and Enrico Zio
Copyright c⃝2019 by ESREL2019 Organizers. Published by Research Publishing, Singapore
ISBN: 981-973-0000-00-0 :: doi: 10.3850/981-973-0000-00-0 esrel2019-paper May 6, 2019
16:12
RPS/Trim Size: 221mm x 173mm for Proceedings/Edited Book May 6, 2019
16:12
RPS/Trim Size: 221mm x 173mm for Proceedings/Edited Book esrel2019-paper Keywords: Asset Management, Performance, Railway, RAMS, RAMSSHEeP. Keywords: Asset Management, Performance, Railway, RAMS, RAMSSHEeP. Safety, Technical and Engineering Directorate, Network Rail, United Kingdom. Railway asset managers have finite resources which requires them to make strategic decisions on where, when
and how the available budget will be spent on the railway, while ensuring safety limits are maintained and a high
level of performance is delivered for customers. The purpose of this research is to develop a suitable framework,
which can be used by railway asset managers, to quantify asset performance in a way that enables comparisons
between different parts of the railway and enables the asset manager to make key decisions on how the railway can
be improved. A frequently used assessment tool is RAMS (Reliability, Availability, Maintainability and Safety)
analysis. In recent years RAMS analysis has been extended to include additional parameters such as: security,
health, environment, economics and politics (SHEeP). This research proposes an extended RAMS framework,
which considers 12 parameters in a four level hierarchy, specifically for use on railway networks by railway asset
managers. Development of an Extended RAMS Framework for Railway Networks Jack Litherland, Gareth Calvert, John Andrews
Resilience Engineering Research Group, University of Nottingham, United Kingdom. E-mail: jack.litherland@nottingham.ac.uk Jack Litherland, Gareth Calvert, John Andrews
Resilience Engineering Research Group, University of Nottingham, United Kingdom. E-mail: jack.litherland@nottingham.ac.uk Jack Litherland, Gareth Calvert, John Andrews and Andy Kirwan 2 Jack Litherland, Gareth Calvert, John Andrews and Andy Kirwan as opposed to the standard, safety (Zoeteman
and Braaksma (2001); Breemer (2009)). How-
ever, there is now universal agreement in the ‘S’
being safety; the industry standard for railway
RAMS BS EN 50126 (British Standards Institu-
tion (2017)) recognizes the ‘S’ as safety. ‘Asset Condition’ considers the factors that influ-
ence ‘Reliability’ and ‘Maintainability’. Three
metrics are considered to assess the ‘Asset Con-
dition’; ‘Condition’, ‘Remaining Life’ and ‘Uti-
lization’. The third level of the hierarchy ‘Asset
Performance’ is as in BS EN 50126. The second
level of the hierarchy, ‘Service Performance’, con-
siders the ‘Environment’ and ‘Train Performance’
in addition to ‘Safety and ‘Availability’. There is a
directly flow between levels two, three and four of
the hierarchy; ‘Asset Condition’ will directly ef-
fect ‘Asset Performance’ which in turn influences
‘Service Performance’. (
))
g
y
Although RAMS normally gives a complete
picture of the system in some cases it may be
necessary to consider additional parameters. Wag-
ner and Van Gelder (2013) worked on expanding
the traditional RAMS framework; RAMS was
extended to RAMSSHE, RAMS+ security health
and environment,
and finally RAMSSHEeP
(RAMSSHE+ economics and politics). This pa-
per aims to introduce an alternative extension of
a RAMS framework, for specific use on railway
networks. The top level of the hierarchy ‘Service Offer-
ing’ contains three high level metrics to assess
performance; ‘Capacity’, ‘Journey Time’ and ‘Ca-
pability’. These values are not directly influenced
by the factors below, but are critical to railway
performance and are normally set at the design
stage or when a franchise is issued. 3. Preferred Subset of Parameters Upon
review
it
became
apparent
that
the
RAMSSHEeP framework does not provide a
complete assessment of a railway network. There-
fore in this research an extended framework con-
sisting of 12 parameters, organized in a four level
hierarchy is presented as shown in Figure 2. Railway RAMS
Safety
Availability
(Train Delays)
Operations &
Maintenance
Reliability &
Maintainability
Figure 1. Interaction between reliability, availability, mainte-
nance and safety (British Standards Institution (2017)) y
p
g
As RAM parameters are integral to system per-
formance they will be considered in the analysis. ‘Safety’ will also be considered as it is funda-
mental to any railway network. Currently the
data on the UK network does not fully support
a RAMSSHEeP analysis, at this stage the only
SHEeP parameter considered directly is ‘Envi-
ronment’. The environmental impact is consid-
ered due to the importance of climate change and
green energy; currently train travel is one of the
most low carbon means to transport people and
goods (International Energy Agency (2009)). Figure 1. Interaction between reliability, availability, mainte-
nance and safety (British Standards Institution (2017)) Environmental
Safety
Availability
Maintainability
Reliability
Capacity
Journey Time
Capability
Train
Performance
Condition
Remaining
Life
Service
Offering
Service
Performance
Asset
Performance
Asset
Condition
Utilization
1
2
3
4
5
6
7
8
9
12
11
10
Figure 2. Extended RAMS Framework Environmental
Safety
Availability
Maintainability
Reliability
Capacity
Journey Time
Capability
Train
Performance
Condition
Remaining
Life
Service
Offering
Service
Performance
Asset
Performance
Asset
Condition
Utilization
1
2
3
4
5
6
7
8
9
12
11
10
Figure 2. Extended RAMS Framework ‘Security’ will not be considered as a param-
eter in its own right. However, delay minutes
that can be attributed to security incidents will
be considered in train performance. ‘Health’ will
not be considered at this stage, as it is unclear
how health performance can be measured and
there is insufficient data. ‘Economics’ will not be
considered at this stage, as to fully quantify eco-
nomics a life-cycle cost (LCC) analysis is needed
and this is, currently, beyond the scope of this
study. ‘Politics’ is not considered as currently it
is impossible to define in any meaningful way the
political performance of the railway. Figure 2. Extended RAMS Framework 1. Introduction Initially there was some debate on what
the ‘S’ should represent with some arguing it
should be survivability, Hamersma and Chodos
(1992), while others argued supportability would
be more appropriate, Markeset and Kumar (2003), 1 May 6, 2019
16:12
RPS/Trim Size: 221mm x 173mm for Proceedings/Edited Book esrel2019-paper aRevenue services and shunting operations to and from depots
and IM’s working traffic. Development of an Extended RAMS Framework for Railway Networks 3 Development of an Extended RAMS Framework for Railway Networks to calculate these parameters, textbook definitions
and NR definitions were also consulted. The 12
parameters are defined as: to calculate these parameters, textbook definitions
and NR definitions were also consulted. The 12
parameters are defined as: ing points with less than or equal to five
minutes delay’, where; y
(b) Robustness is defended as ‘Average delay
minutes caused by asset failures on main
track according to UIC CODE 450-2, num-
bers 20-25 and 28-29’. • Capacity:
There are a range of definitions
for capacity in International Standards how-
ever none are specific to railway networks and
defining the capacity of a railway is nontrivial. PRIME (2018b) assesses capacity based on a
number of key indicators; • Safety: Safety is defined as; ‘freedom from un-
acceptable risk’ (International Electrotechnical
Commission (2013)) A more specific railway
definition can be found in PRIME (2018b):
‘Safety is the primary focus of the manage-
ment of a railway IM and a prerequisite in
any framework of management indicators. It is
the most important and essential element in the
performance of an IM, and affects customers,
stakeholders, the reputation of the IM, the rail-
way and society at large. Safety should be con-
sidered with a holistic perspective, including
as well as the fundamental task of providing
a stable, safe and secure network for the user
and the IM’s staff, wider aspects of safety such
as suicide prevention and minimizing trespass
events’. PRIME defines the following key per-
formance indicators (KPIs) to assess the safety
performance: • Safety: Safety is defined as; ‘freedom from un-
acceptable risk’ (International Electrotechnical
Commission (2013)) A more specific railway
definition can be found in PRIME (2018b):
‘Safety is the primary focus of the manage-
ment of a railway IM and a prerequisite in
any framework of management indicators. It is
the most important and essential element in the
performance of an IM, and affects customers,
stakeholders, the reputation of the IM, the rail-
way and society at large. Safety should be con-
sidered with a holistic perspective, including
as well as the fundamental task of providing
a stable, safe and secure network for the user
and the IM’s staff, wider aspects of safety such
as suicide prevention and minimizing trespass
events’. 4. Defining Parameters A range of sources were reviewed in order to de-
fine the parameters considered in this study. The
sources were reviewed in a hierarchical manner;
International Standards were considered first, EU
frameworks were reviewed next, and then text-
book definitions and finally Network Rail (NR)
definitions were used. When defining parame-
ters International Standards and the PRIME (Plat-
form of Railway Infrastructure Manager in Eu-
rope) European framework (PRIME (2018a,b))
were sufficient to provide quantification. However
when applied to railway networks the calculation
procedures given in International Standards and
PRIME were not always sufficient. Therefore, It was concluded that RAMSE parameters alone
were not sufficient to give asset managers a com-
plete picture of the railway. Therefore, seven ad-
ditional parameters were added to create a frame-
work consisting of 12 parameters in a four level
hierarchy as shown in Figure 2. The parameters
were organized in a hierarchical structure based
on the International Standard BS EN 50126 (see
Figure 1). The hierarchy was increased from three
to four levels. The bottom level of the hierarchy May 6, 2019
16:12
RPS/Trim Size: 221mm x 173mm for Proceedings/Edited Book esrel2019-paper Development of an Extended RAMS Framework for Railway Networks PRIME defines the following key per-
formance indicators (KPIs) to assess the safety
performance: (a) Possession and possession utilization (b) Time lost due to temporary and permanent
speed restrictions p
(c) Congested
tracks
and
congested
nodes
where congestion is defined according to Ar-
ticle 47(1) of Directive 2012/34/EU (Euro-
pean Commission (2012)) In this study, capacity will be assessed based
on (b) and (c), as possessions are more aligned
with ‘Availability’ and ‘Maintainability’. The
existing definition of congestion of nodes is
qualitative. To obtain a quantitative value, con-
gestion will assessed by calculating the min-
imum time to travel between adjacent timing
points. The largest value of these minima will
be used to describe the capacity of the consid-
ered route. (a) Significant accidents
(b)
i
l i j (b) Persons seriously injured and killed
( ) S i id
d
d
i id • Journey Time: A journey can be defined as
‘Movement of a person who is traveling be-
tween two locations’ (International Standards
Organisation (2015b)). In this study locations
will be stations and the journey time will be
defined as the time taken to travel between two
stations. (c) Suicides and attempted suicides
d
kf
f (d) Workforce safety • Environment: There is no internationally rec-
ognized means to quantify the environmental
impact of the railway. It is common practice
to only consider the environmental impact and
consequence of failures. This can be assessed
as ‘the number of environmental incidents’. The
majority of environmental incidents will be due
to freight train spillages or derailments such as
the incident in Stewarton, UK (Rail Accident
Investigation Branch (RAIB) (2010)). The en-
vironmental impact of an operational railway
is determined by a range of factors. PRIME
(2018b) proposes assessing the rolling stock
traction typea: • Capability: There is no international definition
of railway capability. PRIME (2018b) states
that; ‘Asset capability describes the function-
ality of the infrastructure manager’s (IM) rail-
way network. It provides the overview of the
capability of the network and specifically the
extent to which the network meets the TEN-T
(Trans-European Transport Network,European
Commission (2019)) requirements’. In this study, the capability will be assessed
based on a range of factors that limit the number
and/or type of trains that can run. • Capability: There is no international definition
of railway capability. Development of an Extended RAMS Framework for Railway Networks PRIME (2018b) states
that; ‘Asset capability describes the function-
ality of the infrastructure manager’s (IM) rail-
way network. It provides the overview of the
capability of the network and specifically the
extent to which the network meets the TEN-T
(Trans-European Transport Network,European
Commission (2019)) requirements’. (
))
q
In this study, the capability will be assessed
based on a range of factors that limit the number
and/or type of trains that can run. (i) ‘Total diesel train kilometers operated.’
(ii) ‘Total electric train kilometers operated.’ 5.1. Capacity There is no standard way to calculate the capacity
of a railway network. The route capacity is nor-
mally limited by certain network attributes such
as; (
))
• Condition: Assessing the condition of a rail-
way network can be difficult, there is no in-
ternationally recognized definition of condition. The condition is often assessed based on the
normal condition ‘Condition in which all means
for project against hazards are intact’ (Interna-
tional Standards Organisation (2011)). How-
ever in railway networks the condition of rail-
way assets is usually determined based on a
condition index. In the UK, NR uses BCMI
(Bridge Condition Marking Index) and TCMI
(Tunnel Condition Marking Index) (Network
Rail Standards (2009)) to assess the condition
of bridges and tunnels, the condition index is
also used to determine the remaining life of
assets. PRIME assesses asset condition based
on the number of asset failures subdivided into
the following asset groups; (
))
• Condition: Assessing the condition of a rail-
way network can be difficult, there is no in-
ternationally recognized definition of condition. The condition is often assessed based on the
normal condition ‘Condition in which all means
for project against hazards are intact’ (Interna-
tional Standards Organisation (2011)). How-
ever in railway networks the condition of rail-
way assets is usually determined based on a
condition index. In the UK, NR uses BCMI
(Bridge Condition Marking Index) and TCMI
(Tunnel Condition Marking Index) (Network
Rail Standards (2009)) to assess the condition
of bridges and tunnels, the condition index is
also used to determine the remaining life of
assets. PRIME assesses asset condition based
on the number of asset failures subdivided into
the following asset groups; (i) Number of Running Lines
(ii) Junctions
(iii) Signal Separation
(iv) Sidings/Loops
(v) Number of Platforms (i) Number of Running Lines ( )
g
(ii) Junctions
(iii) Signal Separation
(iv) Sidings/Loops
(v) Number of Platforms ( )
g
(ii) Junctions
(iii) Signal Separation
(iv) Sidings/Loops
(v) Number of Platforms In this research the capacity will be calculated
based on the time to travel between timing points. The minimum possible time to travel between
timing points will be calculated as, t = D
S ,
(1) (1) where D is the distance between the timing points
and S is the line speed. 4
Jack Litherland, Gareth Calvert, John Andrews and Andy Kirwan • Availability: The availability (of an item) is
defined as; ‘ability to be in a state to perform as
required’ (International Electrotechnical Com-
mission (2015)). • Availability: The availability (of an item) is
defined as; ‘ability to be in a state to perform as
required’ (International Electrotechnical Com-
mission (2015)). issued, these values tend to remain constant unless
a major enhancement project is undertaken. These
metrics will be assessed based on the adherence
to these targets. The remaining parameters will
be monitored in real time and used to assess the
current performance of the network. (
))
• Maintainability: The maintainability (of an
item) is defined as; ‘ability to be retained
in, or restored to a state to perform as re-
quired, under given conditions of use and main-
tenance’ (International Electrotechnical Com-
mission (2015)). (
))
• Maintainability: The maintainability (of an
item) is defined as; ‘ability to be retained
in, or restored to a state to perform as re-
quired, under given conditions of use and main-
tenance’ (International Electrotechnical Com-
mission (2015)). 5.1. Capacity In the UK, NR assesses the volume
of traffic according to EMGTPA (Equivalent
million gross tonnes per annum), this is an
alternative measure of utilization. Figure 3. Example route section for capacity calculation 5.2. Journey Time In this study, the journey time will be assessed
based on the journey time index, J. Which will be
calculated as, In this study, the journey time will be assessed
based on the journey time index, J. Which will be
calculated as, J = α · A
N ,
(2) (2) (i) ‘Total diesel train kilometers operated.’
(ii) ‘Total electric train kilometers operated.’ Asset managers have little control over the op-
erational environmental impact of the railway. In this study, only ‘the number of environmen-
tal incidents’ will be considered as these are
more directly influenced by asset management
decisions. • Train Performance: Train performance is very
railway specific. A range of metrics are used
in the UK; at NR, public performance measure
(PPM) and delay minutes are used. Whereas,
at Transport for London, lost customer hours
is the primary metric Transport for London
(2018). In this study, performance will be
defined according to PRIME (2018b), which
states that, ‘Performance is made up of punc-
tuality and robustness’ • Train Performance: Train performance is very
railway specific. A range of metrics are used
in the UK; at NR, public performance measure
(PPM) and delay minutes are used. Whereas,
at Transport for London, lost customer hours
is the primary metric Transport for London
(2018). In this study, performance will be
defined according to PRIME (2018b), which
states that, ‘Performance is made up of punc-
tuality and robustness’ • Reliability: The reliability (of an item) is de-
fined as; ‘ability to perform as required, with-
out failure, for a given time interval, under
given conditions’ (International Electrotechni-
cal Commission (2015)). (a) Train punctuality is defined as; ‘the per-
centage of national and international pas-
senger and freight trains (excluding works
trains) which arrive at all strategic measur- May 6, 2019
16:12
RPS/Trim Size: 221mm x 173mm for Proceedings/Edited Book esrel2019-paper 5.1. Capacity The capacity will be
assessed as the maximum, of the minimum time
between timing points, for a given route section. (a) Signalling
(b) Telecom
(c) Power Supply
(d) Track
(e) Structure
(f) Other
and the total number of permanent and tempo- g p
g
Figure 3 shows an example route consisting of
six nodes, the distance in meters and speed limit
in kph between each node is shown. It can be
seen that the maximum time of 38 seconds, occurs
between timing points four and five. This section
will cause bottlenecks, the capacity of the route is
indicated by this value. and the total number of permanent and tempo-
rary speed restrictions (PRIME (2018a)). and the total number of permanent and tempo-
rary speed restrictions (PRIME (2018a)). and the total number of permanent and tempo-
rary speed restrictions (PRIME (2018a)). • Remaining Life:
Another useful measure
of asset condition is remaining life defined
as;‘remaining time before system health falls
below a defined failure threshold’ (International
Standards Organisation (2015a)). • Remaining Life:
Another useful measure
of asset condition is remaining life defined
as;‘remaining time before system health falls
below a defined failure threshold’ (International
Standards Organisation (2015a)). x
x
x
x
x
2300
2100
2005
950
1325
250
250
250
90
150
Distance (m):
Speed (kph):
Time(s):
33.12
30.24
28.87
38.00
31.80
x
Inter-City
12 5
1
2
3
4
5
6
Figure 3. Example route section for capacity calculation g
• Utilization: A final measure of asset condi-
tion is utilization. There is no internation-
ally recognized definition of railway utiliza-
tion. PRIME assesses utilization based on;
degree of utilization of passenger trains, defined
as; ‘Average daily passenger train-km on main
track (revenue service only, no shunting, and no
work trains) related to main track- km’ PRIME
(2018a). In the UK, NR assesses the volume
of traffic according to EMGTPA (Equivalent
million gross tonnes per annum), this is an
alternative measure of utilization. • Utilization: A final measure of asset condi-
tion is utilization. There is no internation-
ally recognized definition of railway utiliza-
tion. PRIME assesses utilization based on;
degree of utilization of passenger trains, defined
as; ‘Average daily passenger train-km on main
track (revenue service only, no shunting, and no
work trains) related to main track- km’ PRIME
(2018a). 5.7. Reliability The reliability of a component is well defined and
can be calculated mathematically using the fail-
ure/hazard rate, λ(t) (Andrews and Moss (2002)). It can be shown that the failure rate is related to the
reliability according to the following equation; Robustness will be calculated as defined in
PRIME, as delay minutes per asset failure. The as-
set failures can be categorized into the same asset
groups listed under condition in Section 4. More-
over, an additional category could be included for
delay minutes caused by security incidents. R(t) = e−
R t
0 λ(τ)dτ. (3) (3) If the failure rate is constant the reliability is
calculated as; R(t) = e−λt. (4) (4) Alternatively, if the failure rate is thought to be
non-constant, a range of other distributions can
be used to model reliability, including; Weibull,
Gamma and Log-normal. If the component
is repairable the Mean Time Between Failures
(MTBF) can be expressed as, Development of an Extended RAMS Framework for Railway Networks Development of an Extended RAMS Framework for Railway Networks Development of an Extended RAMS Framework for Railway Networks 5 route criticality. In the future it is hoped that a
more universal definition of α can be determined. and ‘Precursor Indicator Model’ to calculate the
probability of ‘Top Event’ and the subsequent
number of injuries and fatalities. These models
will be used to assess the safety performance of
the network in this study. 5.4. Train Performance There is no standard way of calculating the envi-
ronmental impact of the railway. In this study the
environmental performance will be assessed ac-
cording to the ‘number of rail related environmen-
tal incidents with major and significant impact or
effect’ (PRIME (2018b)). There is currently no standard way of calculating
train performance on the railway. In this study
punctuality will be assessed using the NR’s PPM
metric, which is defined as; ‘The percentage of
scheduled trains which successfully run their en-
tire planned route, calling at all timetabled sta-
tions, and arrive at their terminating station ‘on
time’, where ‘on time’ means within five minutes
of the scheduled destination arrival time for Lon-
don and South East and regional operators, or
within ten minutes for long-distance operators’
(Network Rail (2017)). 5.3. Capability In this study capability will be determined based
on the six factors given in PRIME (2018b) y
Another consideration in a safety metric is sui-
cides. In 2016/17 there were 237 suicides on the
overground rail network in the UK. Unfortunately
suicide prevention is influenced by factors largely
outside the control of asset managers. Nonethe-
less some measures such as; platform edge doors
and additional fencing can be implemented to re-
duce suicide risk. However significantly reducing
suicides requires long term strategies to reduce
the underlying causes, to this end NR are work-
ing closely with the Samaritans. As suicides are
largely out of the asset manager’s control they will
not be considered in this study. (i) Axle Load
(ii) Gauge
(iii) Line Speed
(iv) Train Length
(v) Electrification
(vi) Extent of ERTMS (European Rail Traffic
Management System) (i) Axle Load
(ii) Gauge
(iii) Line Speed
(iv) Train Length
(v) Electrification
(vi) Extent of ERTMS (European Rail Traffic
Management System) (iv) Train Length (v) Electrification
( i)
f (vi) Extent of ERTMS (European Rail Traffic
Management System) These values can be used to compare between
routes, and can be used to determine assets that
limit capability. 5. Calculating Parameters The following sections will explore how the pa-
rameters are calculated based on the definitions
in the previous section. The ‘Capacity’, ‘Jour-
ney time’ and ‘Capability are generally decided
in the design stage or when a new franchise is where A is the average timetabled time to travel
between the two stations of interest, N is the dis-
tance between the two stations and α is a scaling
factor based on the number of passengers that use
the route. In this study α is chosen based on NR’s May 6, 2019
16:12
RPS/Trim Size: 221mm x 173mm for Proceedings/Edited Book esrel2019-paper esrel2019-paper 5.5. Safety There is no standard definition of safety on the
railway, so defining a metric is difficult. There are
a range of direct and indirect safety elements to
be encapsulated in the safety metric. A common
measure of safety performance on the UK railway
is Fatalities and Weighted Injuries (FWI). How-
ever, fatalities on the railway are extremely rare, in
2016-17 there were 15 passenger fatalities on the
UK railway network, of which seven were due to a
tram derailment (Office of Road and Rail (2017)). As these events are so infrequent accurately pre-
dicting them can be difficult. Accident precur-
sors, Kyriakidis et al. (2012), are a commonly
used means of assessing railway safety risk. For
example, the ‘Top Event’ derailment will be influ-
enced by a number of precursors such as; signal
passed at danger (SPAD), signal failure or broken
rail. NR and the Rail Safety and Standards Board
(RSSB) have developed the ‘Safety Risk Model’ Total Time −Total Down Time (5) 5.10. Condition Maintainability is a measure of how easily a sys-
tem can be repaired following a failure and how
much downtime results from the failure. The
more easily the system can be repaired, the faster
such repairs may be carried out and hence the
smaller the downtime. The calculation procedure
for maintainability as given by Andrews and Moss
(2002) is; ‘The probability that a failed item is
repaired in the time interval (0, t)’. This definition
can be difficult to apply to real world systems and
maintainability is commonly approximated using
the following expression (Barringer (1997)); NR assesses the condition of their assets using
state based condition indexes such as BCMI and
TCMI. In this study the asset condition was as-
sessed based on NR condition indexes. The assets
were grouped into the six categories defined by
PRIME and listed in the ‘Condition’ definition in
Section 4. A =
MTTF
MTTF + MTTR.
(8) (8) However in this analysis as the maintainabil-
ity has not been calculated in the standard way,
Eq. 8 cannot be used. An alternative measure
of availability is required for railway networks. The availability metric in this study will be; ‘the
percentage of time it is not possible to run a full
service on the network’. This can be calculated by
summing downtime for all assets, this approach
was used to determine predictions for Crossrail
availability and performance (King and Gugala
(2018)). Figure 4. Maintenance actions during unplanned and planned
processes. (i) Independent
ii
l (i) Independent p
(ii) Cause complete failure of the system Unlike reliability, calculating the maintainabil-
ity of a railway network using standard techniques
generally is not possible. Therefore to express
the maintainability of a railway network a non-
standard means is required. In this study the
maintainability will be expressed as the number of
hours spent on each of the planned and unplanned
maintenance tasks shown in Figure 4. If these two assumptions are made than the
railway network can be modelled as a combination
of assets in series with no redundancy and the reli-
ability can be calculated using standard techniques
according to Eq. 6. As the system is made up of
many components in series it is difficult to achieve
a high level of reliability on a railway network. n where n is the number of failures. A railway
network is made up of numerous components
therefore reliability analysis needs to be extended
to system level. The reliability of a system of com-
ponents in series and parallel is well documented
(Elsayed (2012)). If components are assumed to
be independent the system reliability for n com-
ponents in series can be calculated according to; where n is the number of failures. A railway
network is made up of numerous components
therefore reliability analysis needs to be extended
to system level. The reliability of a system of com-
ponents in series and parallel is well documented
(Elsayed (2012)). If components are assumed to
be independent the system reliability for n com-
ponents in series can be calculated according to; Rs
sys(t) =
n
Y
i=1
Ri(t). (6) (6) May 6, 2019
16:12
RPS/Trim Size: 221mm x 173mm for Proceedings/Edited Book esrel2019-paper 6 5.8. Availability Fault occurs
Fault revealed
Correct cause of fault
determined
Team on site
Spares, equipment and
Engineers to site
Repair Completed
Test system
Handback
Scheduling
Cyclic maintenance due
Schedule
Resources and engineers to site
Repair Completed
Test system
Handback
Key
Possession
Safety measure
imposed
Unplanned Mainteance
Planned Maintenance
Figure 4. Maintenance actions during unplanned and planned
processes. In a traditional RAMS analysis once the mean
time to failure (MTTF) and mean time to repair
(MTTR) have been calculated from the ‘Reliabil-
ity’ and ‘Maintainability’, the ‘Availability’ can be
calculated as; A =
MTTF
MTTF + MTTR. (8) Jack Litherland, Gareth Calvert, John Andrews and Andy Kirwan Jack Litherland, Gareth Calvert, John Andrews and Andy Kirwan For n components in parallel, the system reliabil-
ity can be calculated according to; For n components in parallel, the system reliabil-
ity can be calculated according to; Railway networks comprise many components
each of which are maintained under different
regimes. The downtime during the maintenance
process is made up of a number of parts as shown
in Figure 4. The maintenance process can be
analyzed to determine which parts of the pro-
cess contribute the largest amount of downtime. Hence, allowing asset managers to make decisions
on how the downtime can be reduced. An example
of this is; handbacks at full line speed without
needing a period of running at reduced speed, the
100th high speed handover in the UK took place in
December 2018 (Network Rail (2019)). Rp
sys(t) = 1 −
n
Y
i=1
(1 −Ri(t)). (7) (7) In this study the reliability of a railway network is
calculated based on the number of service affect-
ing failures (SAFs) that occur. In this study SAFs
are assumed to be; (i) Independent M(t) = 1 −e
−t
MTTR .
(9) Acknowledgements John Andrews is the Royal Academy of Engi-
neering and Network Rail Professor of Infrastruc-
ture Asset Management. He is also Director of
the Lloyd’s Register Foundation (LRF) Resilience
Engineering Research Group at the University of
Nottingham. Jack Litherland is a Research As-
sociate in Railway Infrastructure Asset Manage-
ment. Gareth Calvert is conducting a research
project funded by Network Rail and EPSRC grant
reference EP/N50970X/1. Andy Kirwan is the
Head of Advanced Analytics at Network Rail. They gratefully acknowledge the support of these
organizations. 𝜆1
𝜆2
𝜆3
S1 :New
S2:Good
S3:Poor
S4:Failed
Figure 5. State based condition index 𝜆1
𝜆2
𝜆3
S1 :New
S2:Good
S3:Poor
S4:Failed
Figure 5. State based condition index Development of an Extended RAMS Framework for Railway Networks Development of an Extended RAMS Framework for Railway Networks Development of an Extended RAMS Framework for Railway Networks 7 north of England and, if successful, will be rolled
out to other parts of the network. The framework
is built as far as possible around internationally
recognized standards and definitions. However,
a number of parameters are calculated using UK
specific metrics, which will be revisited in future
work. consider ‘Remaining Life’ as it can have a signifi-
cant impact on parameters higher up the hierarchy
and needs to be taken into account when assessing
the overall performance, as older assets would be
expected to perform worse. As discussed it is common practice to assess
condition using a state based condition index. Fig-
ure 5 shows a simple four state condition index. For each state there is a deterioration rate, λi,
these values can be used to determine the remain-
ing life, RL, (the time to the ‘failed’ (absorbing
state)) according to; As future work, the authors would also like
to undertake a LLC analysis to allow economics
to be considered in the framework. Additionally
there are likely to be dependencies between some
of the metrics, once results are obtained from the
TransPennine route it is hoped that these depen-
dencies can be explored in more detail. The results
from TransPennine will also be used to validate
the assumptions made in the framework, to see if
any revisions are required. p
For each state there is a deterioration rate, λi,
these values can be used to determine the remain-
ing life, RL, (the time to the ‘failed’ (absorbing
state)) according to; RL =
d−n
X
i=1
1
λd−i
,
(10) (10) where d is the total number of states (in the case
of Figure 5, d=4) and n is the current number state
of the asset. In the UK NR make assessments
of the remaining life of all their assets based on
condition indexes and engineering judgment. References (11) Andrews, J. D. and T. R. Moss (2002). Reliability
and Risk Assessment (2nd ed.). Bury St
Edmunds: Professional Engineering
Publishing. (12) g
Barringer, H. P. (1997). Availability, Reliability,
Maintainability, and Capability. Technical
report, Texus. where ¯P is the average daily passenger train miles
on main track (revenue service only, no shunting
and no work trains), ¯F is the average daily freight
train miles on main track (revenue service only, no
shunting and no work trains) and L is the length in
kilometers of the given route. where ¯P is the average daily passenger train miles
on main track (revenue service only, no shunting
and no work trains), ¯F is the average daily freight
train miles on main track (revenue service only, no
shunting and no work trains) and L is the length in
kilometers of the given route. Beckerley, J. G. (1957). Safety Aspects of
Nuclear Reactors. New York: D Van Nostrand. Breemer, J. (2009). RAMS and LCC in the
Design Process of Infrastructural Construction
Projects: an Implementation Case. Master’s
thesis, University of Twente. 5.12. Utilization It this study the passenger utilization, Up, and
freight utilization, Fp, was calculated according
to the PRIME definitions: Up =
¯P
L ,
(11)
Uf =
¯F
L ,
(12) Up =
¯P
L ,
(11)
Uf =
¯F
L ,
(12) Up =
¯P
L ,
(11)
Uf =
¯F
L ,
(12) 5.11. Remaining Life Remaining life is a common way to determine
‘Asset Condition’. The remaining life of assets is
usually based on their condition. It is important to M(t) = 1 −e
−t
MTTR . (9) (9) May 6, 2019
16:12
RPS/Trim Size: 221mm x 173mm for Proceedings/Edited Book esrel2019-paper esrel2019-paper Jack Litherland, Gareth Calvert, John Andrews and Andy Kirwan Jack Litherland, Gareth Calvert, John Andrews and Andy Kirwan 8 and Development Work Processes: A Case
Study. A case study. Journal of Quality in
Maintenance Engineering 9(4), 393–410. and Development Work Processes: A Case
Study. A case study. Journal of Quality in
Maintenance Engineering 9(4), 393–410. Cole, G. K. (1998). Practical Issues Relating to
Statistical Failure Analysis of Aero Gas
Turbines. Proceedings of the Institution of
Mechanical Engineers, Part G: Journal of
Aerospace Engineering 212(3), 167–176. g
g
Network Rail (2017). Railway Performance -
Network Rail. https://www.networkrail.co.uk/who-we-
are/how-we-work/performance/railway-
performance/ Last accessed:
25/02/2019. p
g
g
( )
Elsayed, E. A. (2012). Reliability engineering
(2nd ed.). John Wiley & Sons. European Commission (2012). Directive
2012/34/EU of the European Parliament and of
the Council establishing a single European
railway area. Technical report, Brussels:
2012/34/EU. Network Rail (2019). Engineers deliver 100th
high-speed handback of the year. https://www.networkrail.co.uk/engineers-
deliver-100th-high-speed-handback-of-the-
year/ Last accessed:
25/02/2019. European Commission (2019). TEN-T Project. https://ec.europa.eu/inea/en/ten-t/ten-t-
projects, Last Accessed:
14/02/2019. Network Rail Standards (2009). NR/L3/CIV/0006/4C Handbook for the
examination of Structures Part 4C : Recording
of Tunnel examinations and condition marking
index score. Technical Report 1. Hamersma, B. and M. S. Chodos (1992). Availability and Maintenance Considerations
in Telecommunications Network Design and
The Use of Simulation Tools. In AFRICON’92
Proceedings., 3rd AFRICON Conference, pp. 267–270. IEEE. Office of Road and Rail (2017). Rail Safety
Statistics: 2016-17 Annual Statistical Release. Technical report, London: Office of Road and
Rail. International Electrotechnical Commission
(2013). IEC 60050-903:2013 International
Electrotechnical Vocabulary. Risk assessment. Technical report, Geneva, Switzerland. PRIME (2018a). Good Practice Benchmarking of
the Rail Infrastructure Managers. Technical
report. International Electrotechnical Commission
(2015). IEC 60050-192:2015. International
Electrotechnical Vocabulary - Part 192:
Dependability: International Electrotechnical
Commission. Technical report, Geneva,
Switzerland. p
PRIME (2018b). Key Performance Indicators For
Performance Benchmarking. Technical Report
2.1. Rail Accident Investigation Branch (RAIB)
(2010). Derailment of a freight train near
Stewarton, Ayrshire. Technical report,
Department for Transport, Derby. International Energy Agency (2009). Transport
Energy and CO2 : Moving Towards
Sustainability. Paris: OECD Publishing. Rotab Khan, M. R. and A. B. Zohrul Kabir
(1995). Availability Simulation of an
Ammonia Plant. Reliability Engineering and
System Safety 48(3), 217–227. International Standards Organisation (2011). EN
ISO 22734-2:2011 Hydrogen Generators
Using Water Electrolysis Process — Part 2:
Residential Applications. Technical report,
Geneva, Switzerland. y
f y
Smith, D. J. (2017). Reliability, Maintainability
and Risk: Practical Methods for Engineers
(9th ed.). Butterworth-Heinemann: Elsevier. International Standards Organisation (2015a). 6. Conclusion British Standards Institution (2017). BS EN
50126-1:2017 Railway Applications - The
Specification and Demonstration of Reliability,
Availability, Maintainability and
Safety(RAMS). Technical report, London:
BSI. This paper proposes an assessment tool for use by
railway asset managers. The assessment frame-
work proposed is an extension of a traditional
RAMS analysis that considers eight additional pa-
rameters. The research established that reliability
was the only parameter that could be calculated
using traditional techniques. For each of the re-
maining parameters this paper presents a metric to
calculate them based on EU frameworks and NR
definitions. The methodology is being trialed on
the TransPennine route, a major rail corridor in the Cleveland, J. W., T. R. Regenie, and R. J. Wilson
(1985). Nuclear Power Generating Station
Operability Assurance Reliability, Availability,
and Maintainability Application for
Maintenance Management. IEEE transactions
on power apparatus and systems 4, 785–789. May 6, 2019
16:12
RPS/Trim Size: 221mm x 173mm for Proceedings/Edited Book esrel2019-paper Jack Litherland, Gareth Calvert, John Andrews and Andy Kirwan EN ISO 13381-1:2015 Condition Monitoring
and Diagnostics of Machines — Prognostics
— Part 1: General Guidelines. Technical
report, Geneva, Switzerland. Transport for London (2018). Underground
services performance. https://tfl.gov.uk/corporate/publications-and-
reports/underground-services-performance,
Last accessed: 21/01/2019. International Standards Organisation (2015b). EN ISO 19147:2015 Geographic Information
— Transfer Nodes. Technical report, ISO
19147:2015, Geneva, Switzerland. US Nuclear Regulatory Commission (1975). Reactor Safety Study. Wash 1400. Technical
report, Washington, DC. Wagner, W. and P. H. A. J. M. Van Gelder (2013). Applying RAMSSHEEP Analysis for
Risk-driven Maintenance. In Proceedings of
the 22nd European Safety and Reliability
Conference” Safety, Reliability and Risk
Analysis: Beyond the Horizon”, Amsterdam. CRC Press/Balkema-Taylor & Francis Group. King, J. and O. Gugala (2018). Crossrail
Learning Legacy Effective Reliability,
Availability, Maintainability(RAM) and
Safety(S), Principles and Guidelines for Large
Subsurface Metro and Main Line Projects. Technical report, Crossrail, London. Kyriakidis, M., R. Hirsch, and A. Majumdar
(2012). Metro Railway Safety : An Analysis of
Accident Precursors. Safety Science 50(7),
1535–1548. CRC Press/Balkema Taylor & Francis Group. Zoeteman, A. and E. Braaksma (2001). An
approach to Improving the Performance of
Rail Systems in a Design Phase. World
Congress on Railway Research, 1–9. Markeset, T. and U. Kumar (2003). Integration of
RAMS and Risk Analysis in Product Design
|
https://openalex.org/W2116874502
|
https://hal.archives-ouvertes.fr/hal-03796156/file/file.pdf
|
English
| null |
The Absence of CYP3A5*3 Is a Protective Factor to Anticonvulsants Hypersensitivity Reactions: A Case-Control Study in Brazilian Subjects
|
PloS one
| 2,015
|
cc-by
| 6,644
|
RESEARCH ARTICLE The Absence of CYP3A53 Is a Protective
Factor to Anticonvulsants Hypersensitivity
Reactions: A Case-Control Study in Brazilian
Subjects Luciana Kase Tanno1☯*, Daniel Shikanai Kerr2,5☯, Bernardo dos Santos4, Leda
Leme Talib2,5, Célia Yamaguti3, Helcio Rodrigues3, Wagner Farid Gattaz2,5, Jorge Kalil1,3 a1111 1 Clinical Immunology and Allergy Division, University of São Paulo, São Paulo, Brazil, 2 Laboratory of
Neuroscience - LIM-27 Institute of Psychiatry, University of São Paulo, São Paulo, Brazil, 3 Laboratory of
Immunology - LIM-19 Clinical Immunology and Allergy Division, University of São Paulo, São Paulo, Brazil,
4 Nursing School of the University of São Paulo, São Paulo, Brazil, 5 Center for Interdisciplinary Research
on Applied Neurosciences (NAPNA), University of São Paulo, São Paulo, Brazil ☯These authors contributed equally to this work. * luciana.tanno@gmail.com * luciana.tanno@gmail.com Abstract Citation: Tanno LK, Kerr DS, dos Santos B, Talib LL,
Yamaguti C, Rodrigues H, et al. (2015) The Absence
of CYP3A53 Is a Protective Factor to
Anticonvulsants Hypersensitivity Reactions: A Case-
Control Study in Brazilian Subjects. PLoS ONE 10(8):
e0136141. doi:10.1371/journal.pone.0136141 Although aromatic anticonvulsants are usually well tolerated, they can cause cutaneous
adverse drug reactions in up to 10% of patients. The clinical manifestations of the antiepilep-
tics-induced hypersensitivity reactions (AHR) vary from mild skin rashes to severe cutaneous
drug adverse reactions which are related to high mortality and significant morbidity. Genetic
polymorphisms in cytochrome P450 genes are associated with altered enzymatic activity and
may contribute to the risk of AHR. Here we present a case-control study in which we geno-
typed SNPs of CYP2C19, 2C9 and 3A5 of 55 individuals with varying severities of AHR, 83
tolerant, and 366 healthy control subjects from São Paulo, Brazil. Clinical characterization
was based on standardized scoring systems and drug patch test. All in vivo investigation fol-
lowed the ENDA (European Network of Drug Allergy) recommendations. Genotype was
determined by real time PCR using peripheral blood DNA as a template. Of all 504 subjects,
65% were females, 45% self-identified as Afro-American, 38% as Caucasian and 17% as
having non-African mixed ascendancy. Amongst 55 subjects with AHR, 44 had severe cuta-
neous drug adverse reactions. Of the 46 drug patch tests performed, 29 (63%) were positive. We found a strong association between the absence of CYP3A5*3 and tolerant subjects
when compared to AHR (p = 0.0002, OR = 5.28 [CI95% 2.09–14.84]). None of our groups
presented positive association with CYP2C19 and 2C9 polymorphisms, however, both SNPs
contributed to separation of cases and tolerants in a Classification and Regression Tree. Our
findings indicate that drug metabolism genes can contribute in the tolerability of antiepileptics. CYP3A5*3 is the most prevalent CYP3A5 allele associated with reduced enzymatic function. The current study provides evidence that normal CYP3A5 activity might be a protective factor
to aromatic antiepileptics-induced hypersensitivity reactions in Brazilian subjects. Editor: Marie-Pierre Dubé, Universite de Montreal,
CANADA CANADA
Received: April 2, 2015
Accepted: July 30, 2015
Published: August 20, 2015
Copyright: © 2015 Tanno 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. Introduction Aromatic anticonvulsants (ARA) are important drugs effective in the treatment of epilepsy, tri-
geminal neuralgia, and bipolar disorder [1,2]. Although well tolerated by the majority, they can
cause cutaneous adverse drug reactions (ADRs) in up to 10% of patients [1]. The clinical manifes-
tations of the antiepileptics-induced hypersensitivity reactions (AHR) vary from mild skin rashes
to severe cutaneous drug adverse reactions (SCARs), such as Stevens—Johnson syndrome (SJS),
toxic epidermal necrolysis (TEN) and drug reaction with eosinophilia and systemic symptoms
(DRESS) [3]. These SCARs are related to high mortality and significant morbidity. The most fre-
quently associated ARA are phenobarbital (PB), phenytoin (PHT), and carbamazepine (CBZ) [4]. q
y
p
(
) p
y
(
)
p
(
) [ ]
The mechanisms of aromatic anticonvulsant-induced SCARs are not fully understood, but
evidences suggest an immune-mediated etiology. The discovery of drug-specific T-cells in
hypersensitive individuals is consistent with this hypothesis [5]. Drug patch tests (PTs) can
reproduce delayed T-cell mediated hypersensitivity to drugs and are useful on determining the
offending drug [5,6]. Family and twins studies suggest a genetic predisposition to these reac-
tions [7]. Metabolism of ARA to reactive metabolites is thought to be involved in the pathogen-
esis of SCARs [8]. The detoxification of ARA occurs mostly in the liver where they are
converted in more soluble end products which can usually be secreted by the kidneys. Cyto-
chrome P450 enzymes, such as CYP2C19, CYP2C9 and CYP3A5, are the main enzymes in the
hydroxylation of ARA and are expressed mainly in the liver as well as extra-hepatic tissues
including the skin [9–13] However, in these metabolic pathways, some reactive intermediate
metabolites, such as arene-oxides, can be formed [14,15]. Several Single Nucleotide Polymor-
phisms (SNPs) have major consequences in the expression and activity of these enzymes, how-
ever the results are still not comparable in different populations worldwide [16–18]. These
informations are particularly relevant for pharmacogenetics strategies, in which the knowledge
of CYP genotype may lead to individualized drug dosing and improved therapeutics. The association between the CYP2C19, CYP2C9 and CYP3A5 allele frequencies and aro-
matic anticonvulsant—induced SCARs has not been studied in Brazilian subjects yet. The
CYP2C19 and CYP2C9 variants have been described as being risk factors for the development
of SCARs in Thai and Japanese populations [16,17]. Abstract Received: April 2, 2015
Accepted: July 30, 2015
Published: August 20, 2015
Copyright: © 2015 Tanno 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. Published: August 20, 2015 Published: August 20, 2015 Copyright: © 2015 Tanno 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: Data are available as a
supplementary table. Further inquiries should be
addressed to the authors. Funding: This work received funding from Fundação
de Amparo à Pesquisa do Estado de São Paulo
(FAPESP - http://fapesp.br/) under the grant number
2011/22748-1. 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. 1 / 11 PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 Absence of CYP3A5*3 Is a Protective Factor to AHR Ethics statement The study was reviewed and approved by the ethic local committee. All participating subjects
were informed about the contents and the aims of the study and gave their written consent. After written informed consent signed, genomic DNA was extracted from peripheral blood,
according to the established protocols. Introduction The CYP3A53/3 genotype was associ-
ated with increased half-life of CBZ in African-Americans, but no significant association was
observed in Caucasians [18,19]. In addition, recent studies have demonstrated the utility of
PTs as a method for the identification of both SJS/TEN and DRESS induced by ARA [20,21]. Therefore, the major goal of this study was to analyze the association between aromatic anti-
convulsant—induced hypersensitivity reactions and polymorphisms of CYP2C19, CYP2C9
and CYP3A5 in Brazilian subjects and explore the clinical characteristics and results of PTs of
patients with SCARs due to PB, PHT and CBZ. Subjects All the 504 subjects were recruited from the University of São Paulo Faculty of Medicine Clin-
ics Hospital, being 55 cases, 83 tolerants, and 366 healthy control subjects. Case subjects were 2 / 11 PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 Absence of CYP3A5*3 Is a Protective Factor to AHR patients with a diagnosis of hypersensitivity reactions due to PB, PHT and CBZ within 1–8
week after the drug intake, including SJS, TEN and DRESS. We excluded subjects from the
same family or with history of consanguinity. All the subjects were from São Paulo, Brazil, and
the ethnicity of each participant was inferred from self-reported data about their four grand-
parents ancestry utilizing Brazilian Institute of Geography and Statistics—IBGE—classification
(White, Black, Brown, Indian and Yellow). Accordingly, we classified each individual by his/
her ancestry in African-American (at least one grandparent identified as Black), Caucasian or
others (non-African descendant mixed population). Case subjects The DRESS group consisted of 32 patients and SJS group of 12, defined by the RegiSCAR [22–
25]. We recruited 11 cases of maculopapular exanthema (MPE), defined as rash without sys-
temic symptoms, which required the discontinuation of CBZ within 3 months after the initia-
tion of drug therapy [23]. Control subjects Tolerants group consisted of 83 subjects taking ARA for at least 6 months with no clinical or
biochemical signs of hypersensitivity. All the subjects were from São Paulo, Brazil. We included samples from 366 of healthy volunteers. We did not screen either set of popu-
lation controls for carbamazepine-related adverse drug reactions. Drug Patch Test The PTs were performed 6 weeks to 6 months after complete healing of the adverse drug reac-
tion, and at least 1 month after discontinuation of systemic corticosteroids. PTs were applied
on the upper back, using Finn Chambers with culprit ARA. The concentrations, readings and
interpretation were performed according to the European Network of Drug Allergy recom-
mendations [26,27]. The test was also performed in 10 control subjects, all resulted negative. The medications or conditions that could affect the interpretation of the test followed the
guidelines of the International Contact Dermatitis Group. PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 Genotyping DNA was extracted from peripheral blood by salting-out [28]. SNPs characterizing
CYP2C192, CYP2C193, CYP2C1917, CYP2C92, CYP2C93 and CYP3A53 alleles
(Table 1) were genotyped using TaqMan allele-specific polymerase chain reactions (Life Tech-
nologies). Amplification reactions were as follow: TaqMan PCR Mastermix 1x/μL, TaqMan
SNP genotyping assay 1x/μL, genomic DNA 1ng/μL, ultrapure water to complete 7μL volume. rs12248560 required 500mM of Betaine (Sigma Aldrich) in the final reaction. Allele discrimination was evaluated in a Line Gene 9600 (BIOER Technology CO.) compar-
ing amplification curves and fluorescence levels before and after amplification (45 cycles of 15
seconds at 95°C and 1min at 60°C). The candidate CYP genes were chosen according to the described association to the aro-
matic anticonvulsant-reactions [14,15,18,19,29] in different populations and the importance in
the metabolism of these drugs (Table 1). According to the alleles presented, each subject was classified with normal (EM), decrease
(IM/PM) or increased (UM) function for each enzyme (Table 2). 3 / 11 PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 Absence of CYP3A5*3 Is a Protective Factor to AHR Table 1. Candidate CYP genes, alleles, polymorphisms identification and enzymatic activity. CYP2C19
Allele
Ref SNP ID
Enzymatic activity
*2
rs4244285
Null
*3
rs4986893
Null
*17
rs12248560
Increased
*17
rs11188072
Increased
CYP2C9
*2
rs1057910
Decreased
*3
rs1799853
Decreased
CYP3A5
*3
rs776746
Decreased
doi:10.1371/journal.pone.0136141.t001 Table 1. Candidate CYP genes, alleles, polymorphisms identification and enzymatic activity. doi:10.1371/journal.pone.0136141.t001 Statistical Analysis The data is available as a supporting information table (S1 Table). Descriptive statistical meth-
ods (mean, median, and frequency) were applied to analyze the demographic data. Analyses of
the difference in frequencies across groups (sex and clinical manifestation) were performed
with the chi-squared test or analysis of variance. CYP phenotypes were compared between
diagnostic groups (Healthy, Tolerant and Cases) with Pearson's Chi-squared test. Significance
was set at p<0.05. The CYP phenotypes were also entered in a Classification and Regression
Tree (CART) model to predict tolerant cases. Variable selection was based on Gini impurity
index and pruning was conducted based on 10-fold cross-validation to avoid over fitting. All
analyses were conducted with the aid of the R software version 3.2.0. PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 On the basis of this result, the absence of CYP3A53 has a putative sensitivity of
81 1% as a protective factor to aromatic antiepileptics hypersensitivity reactions whereas the
Table 3. Demographic data of cases and controls subjects. Variables
Cases (N = 55)
Tolerants (N = 85)
Healthy Controls (N = 366)
Total (506)
Categorical Variables
N (%)
N (%)
N (%)
N (%)
Gender
Female
42 (76)
47 (55)
293 (80)
382 (75)
Male
13 (24)
38 (45)
73 (20)
124 (25)
Age
Young adults (18–40 years)
23 (42)
26 (30)
147 (40)
196 (39)
Adults (40–60 years)
25 (46)
44 (52)
179 (49)
248 (49)
Elderly(> 61 years)
7 (12)
15 (18)
40 (11)
62 (12)
Ethnicity
Caucasian
14 (26)
20 (24)
161 (44)
195 (38)
Afro-American
29 (53)
41 (48)
154 (42)
224 (45)
Others
12 (21)
24 (28)
51 (14)
87 (17)
doi:10.1371/journal.pone.0136141.t003
Absence of CYP3A5*3 Is a Protective Factor to AHR Absence of CYP3A5*3 Is a Protective Factor to AHR Table 3. Demographic data of cases and controls subjects. Variables
Cases (N = 55)
Tolerants (N = 85)
Healthy Controls (N = 366)
Total (506)
Categorical Variables
N (%)
N (%)
N (%)
N (%)
Gender
Female
42 (76)
47 (55)
293 (80)
382 (75)
Male
13 (24)
38 (45)
73 (20)
124 (25)
Age
Young adults (18–40 years)
23 (42)
26 (30)
147 (40)
196 (39)
Adults (40–60 years)
25 (46)
44 (52)
179 (49)
248 (49)
Elderly(> 61 years)
7 (12)
15 (18)
40 (11)
62 (12)
Ethnicity
Caucasian
14 (26)
20 (24)
161 (44)
195 (38)
Afro-American
29 (53)
41 (48)
154 (42)
224 (45)
Others
12 (21)
24 (28)
51 (14)
87 (17)
doi:10.1371/journal.pone.0136141.t003 Table 3. Demographic data of cases and controls subjects. The severities of cutaneous manifestation of the reactions varied from MPE to exfoliative
dermatitis. As shown in Table 4, 32 patients were validated as DRESS, 12 as SJS and 11 as MPE. CBZ was involved in 82% of the reactions, both mild and SCARs. The late onset of the reaction
was important in cases of DRESS, but happened in low proportion in SJS. No MPE happened
after 4 weeks of drug intake. SCARs showed to be systemic reactions with internal organ
involvement requiring long-term hospitalization, mainly in DRESS cases but also in SJS
(Table 4). Most of the cases, both mild and severe, were treated with systemic corticosteroids
and anti-histamines. Intravenous immunoglobulin (IgIV) was exclusively indicated to SJS
cases. We found no association between ethnicity and clinical status (p = 0.231). Of all 46 PTs, 29 (63%) were positive and 63% of positive results were in DRESS. The PTs
was not performed in 9 cases due to the difficulties on the clinical follow-up or if the patient
had contraindications to the procedure. Apparently grade of positivity of PTs did not corre-
lated with the intensity of reaction nor the internal organ involvement, however, positive reac-
tions occurred in the more severe cases. There was no association between positivity of the
tests and skin color or reported ethnicity. None of the patients presented adverse reactions dur-
ing the in vivo procedure. Results Clinical characteristics of aromatic anticonvulsant—induced
hypersensitivity reactions patients and control subjects There were no significant differences in the demographic data between groups as shown in
Table 3. Table 2. Candidate CYP genes, corresponding predicted phenotype and enzymatic activity according
to the allele combination (EM = normal metabolizers, IM and PM = decrease function, UM and
UMH = increase function). Table 2. Candidate CYP genes, corresponding predicted phenotype and enzymatic activity according
to the allele combination (EM = normal metabolizers, IM and PM = decrease function, UM and
UMH = increase function). Table 2. Candidate CYP genes, corresponding predicted phenotype and enzymatic activity according
to the allele combination (EM = normal metabolizers, IM and PM = decrease function, UM and
UMH = increase function). Gene
Predicted Phenotype
Enzymatic activity of allele combination
CYP2C19
EM
Normal+Normal; Increased+Decreased
IM
Normal+Decreased
UM
Increased+Increased
UM heterozygote
Increased+Normal
PM
Decreased+Decreased
CYP2C9
EM
Normal+Normal
IM
Normal+Decreased
PM
Decreased+Decreased
CYP3A5
EM
Normal+Normal
IM
Normal+Decreased
PM
Decreased+Decreased
doi:10.1371/journal.pone.0136141.t002 PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 4 / 11 The severities of cutaneous manifestation of the reactions varied from MPE to exfoliative
dermatitis. As shown in Table 4, 32 patients were validated as DRESS, 12 as SJS and 11 as MPE. CBZ was involved in 82% of the reactions, both mild and SCARs. The late onset of the reaction
was important in cases of DRESS, but happened in low proportion in SJS. No MPE happened
after 4 weeks of drug intake. SCARs showed to be systemic reactions with internal organ
involvement requiring long-term hospitalization, mainly in DRESS cases but also in SJS
(Table 4). Most of the cases, both mild and severe, were treated with systemic corticosteroids
and anti-histamines. Intravenous immunoglobulin (IgIV) was exclusively indicated to SJS
cases. We found no association between ethnicity and clinical status (p = 0.231). Of all 46 PTs, 29 (63%) were positive and 63% of positive results were in DRESS. The PTs
was not performed in 9 cases due to the difficulties on the clinical follow-up or if the patient
had contraindications to the procedure. Apparently grade of positivity of PTs did not corre-
lated with the intensity of reaction nor the internal organ involvement, however, positive reac-
tions occurred in the more severe cases. There was no association between positivity of the
tests and skin color or reported ethnicity. None of the patients presented adverse reactions dur-
ing the in vivo procedure. CYP3A5, CYP2C9 and CYP2C19 genotyping and aromatic
anticonvulsant—induced hypersensitivity reactions
On the basis of our hypothesis that the polymorphisms of CYP2C19, CYP2C9 and CYP3A5
are associated with aromatic anticonvulsant—induced hypersensitivity reactions, we genotyped
the CYP2C192, CYP2C193, CYP2C1917, CYP2C92, CYP2C93 and CYP3A53 alleles in
all subjects included in the study (Tables 1 and 2). The allele frequencies and its distribution
among the enzymatic phenotype and the studied groups are shown in Table 5. We showed a strong association between the absence of CYP3A53 and tolerant subjects
when compared to cases (p = 0.0002, OR = 5.28 [CI95% 2.09–14.84]). However, we observed
homogeneous distribution of variants of CYP2C19 and 2C9 in our case and control groups
(Table 5). The classification and regression tree showed that non-decreased function of
CYP3A5 (absence of 3 allele; EM), was the most important factor to classify tolerant individu-
als (Fig 1). PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 CYP3A5, CYP2C9 and CYP2C19 genotyping and aromatic
anticonvulsant—induced hypersensitivity reactions On the basis of our hypothesis that the polymorphisms of CYP2C19, CYP2C9 and CYP3A5
are associated with aromatic anticonvulsant—induced hypersensitivity reactions, we genotyped
the CYP2C192, CYP2C193, CYP2C1917, CYP2C92, CYP2C93 and CYP3A53 alleles in
all subjects included in the study (Tables 1 and 2). The allele frequencies and its distribution
among the enzymatic phenotype and the studied groups are shown in Table 5. We showed a strong association between the absence of CYP3A53 and tolerant subjects
when compared to cases (p = 0.0002, OR = 5.28 [CI95% 2.09–14.84]). However, we observed
homogeneous distribution of variants of CYP2C19 and 2C9 in our case and control groups
(Table 5). The classification and regression tree showed that non-decreased function of
CYP3A5 (absence of 3 allele; EM), was the most important factor to classify tolerant individu-
als (Fig 1). On the basis of this result, the absence of CYP3A53 has a putative sensitivity of
81.1% as a protective factor to aromatic antiepileptics-hypersensitivity reactions, whereas the
presence of IM or PM phenotypes is split in 54.32% cases and 45.67% tolerants. 5 / 11 PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 Absence of CYP3A5*3 Is a Protective Factor to AHR nticonvulsant-induced reactions and demographic characteristics (DRESS = Drug Reaction with eosino-
Stevens-Johnson Syndrome, MPE = Maculopapular exanthema, IgIV = Intravenous immunoglobulin). Table 4. Clinical patterns of aromatic anticonvulsant-induced reactions and demographic characteristics (DRESS = Drug Reaction with eosino-
philia and systemic symptoms, SJS = Stevens-Johnson Syndrome, MPE = Maculopapular exanthema, IgIV = Intravenous immunoglobulin). Table 4. Clinical patterns of aromatic anticonvulsant-induced reactions and demographic characteristics (DRESS = Drug Reaction with eosino-
philia and systemic symptoms, SJS = Stevens-Johnson Syndrome, MPE = Maculopapular exanthema, IgIV = Intravenous immunoglobulin). Table 4. Clinical patterns of aromatic anticonvulsant-induced reactions and demographic characteristics (DRESS = Drug Reaction with eosino-
philia and systemic symptoms, SJS = Stevens-Johnson Syndrome, MPE = Maculopapular exanthema, IgIV = Intravenous immunoglobulin). CYP3A5, CYP2C9 and CYP2C19 genotyping and aromatic
anticonvulsant—induced hypersensitivity reactions DRESS (N:32)
SJS (N:12)
MPE (N:11)
TOTAL (N:55)
Mean age
49.7
48.3
47.7
43.6
Sex (M/F)
26/6
7/5
9/2
42/13
Onset of the reaction
< 4 weeks (%)
13 (40)
11 (92)
11 (100)
35 (64)
> 4 weeks (%)
19 (60)
1 (8)
0 (0)
20 (36)
Drug involved
Phenobarbital
4 (13)
2 (17)
1 (9)
7 (13)
Phenytoin
2 (6)
1 (8)
0 (0)
3 (5)
Carbamazepine
26 (81)
9 (75)
10 (91)
45 (82)
Clinical manifestations
Cutaneous (%)
32 (100)
12 (100)
11 (100)
55 (100)
Gastrointestinal (%)
32 (100)
6 (50)
0 (0)
38 (69)
Respiratory (%)
5 (15)
4 (34)
0 (0)
9 (16)
Fever (%)
32 (100)
11 (91)
2 (18)
45 (82)
Mean time of hospitalization (days)
20
12
0
24
Treatment
Anti-histamines (%)
32 (100)
8 (67)
11 (100)
51 (93)
Systemic corticosteroids (%)
32 (100)
12 (100)
8 (72)
52 (95)
IgIV (%)
0 (0)
5 (41)
0 (0)
5 (9)
Drug patch test (N: 46)
Positive
18 (72)
7 (58)
4 (45)
29 (63)
Negative
7 (28)
5 (42)
5 (55)
17 (37)
Not Done
7
0
2
9 (16)
doi:10.1371/journal.pone.0136141.t004 Given the fact that CYP2C19, CYP2C9 and CYP3A5 enzymes are expressed in the skin, we
analyzed the association between genotype and the results of PT. Even without statistically sig-
nificant associations, we observed a predominance of low function phenotype of CYP3A5, nor-
mal function of CYP2C9, and increased function of CYP2C19 in positive results. Table 5. Phenotipic frequencies for cytochrome P450 (CYP) 2C9, 2C19 and 3A5 in healthy controls, cases and tolerants (EM = normal metaboli-
zers, IM and PM = decrease function, UM and UMH = increase function) as predicted by SNP genotype. Gene (SNP)
Enzymatic Phenotype
Group
Phenotypic Frequency (%)
P Value
Healthy controls
(%)
Cases
(%)
Tolerants
(%)
CYP2C9 (rs1057910, rs1799853)
EM
251 (71.1)
43 (81.1)
54 (65.9)
IM
97 (27.5)
8 (15.1)
25 (30.5)
0.083
PM
5 (1.4)
2 (3.8)
3 (3.7)
CYP2C19 (rs4244285, rs4986893, rs12248560,
rs11188072)
EM
163 (48.4)
24 (47.1)
41 (51.3)
IM/PM
79 (23.4)
12 (23.5)
20 (25)
0.945
UM/UMH
95 (28.2)
15 (29.4)
19 (23.8)
CYP3A5 (rs776746)
EM
37 (10.6)
8 (14.8)
38 (46.3)
IM
122 (34.9)
23 (42.6)
19 (23.2)
0.0005
OR = 4.9
PM
191 (54.6)
23 (42.6)
25 (30.5)
doi:10.1371/journal.pone.0136141.t005 Table 5. CYP3A5, CYP2C9 and CYP2C19 genotyping and aromatic
anticonvulsant—induced hypersensitivity reactions Phenotipic frequencies for cytochrome P450 (CYP) 2C9, 2C19 and 3A5 in healthy controls, cases and tolerants (EM = normal metaboli-
zers, IM and PM = decrease function, UM and UMH = increase function) as predicted by SNP genotype. Table 5. Phenotipic frequencies for cytochrome P450 (CYP) 2C9, 2C19 and 3A5 in healthy controls, cases and tolerants (EM = normal metaboli-
zers, IM and PM = decrease function, UM and UMH = increase function) as predicted by SNP genotype. rome P450 (CYP) 2C9, 2C19 and 3A5 in healthy controls, cases and tolerants (EM = normal metaboli-
nd UMH = increase function) as predicted by SNP genotype. henotipic frequencies for cytochrome P450 (CYP) 2C9, 2C19 and 3A5 in healthy controls, cases and tolerant
d PM = decrease function, UM and UMH = increase function) as predicted by SNP genotype. 6 / 11 Absence of CYP3A5*3 Is a Protective Factor to AHR Fig 1. Classification and regression tree: CYP3A5 phenotype discriminates between cases and
tolerants (EM = normal metabolizers, IM and PM = decrease function, UM and UMH = increase
function). d i 10 1371/j
l
0136141 001 Fig 1. Classification and regression tree: CYP3A5 phenotype discriminates between cases and
tolerants (EM = normal metabolizers, IM and PM = decrease function, UM and UMH = increase
function). PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 Discussion This study is the first and most broad case-control study ever conducted towards the associa-
tion of CYP alleles and aromatic antiepileptics-induced hypersensitivity reactions in Brazilian
subjects. Our data add to the growing evidence of different CYP alleles role in immune-medi-
ated ADRs, such as drug-induced hypersensitivity [5,6]. Genetic variation in genes involved in
their metabolism may result in the increase of arene oxide, which potentially initiates immune
responses [8]. On the other hand, the immune response to CBZ in AHR has been associated
with the drug itself and not its metabolites [6]. Genetic polymorphisms of CYP2C19 are highly present in Asian population and the most
common variant resulting in poor metabolism are CYP2C192 and CYP193 [16,30]. The
allele frequency of CYP2C92 and CYP2C93 vary among different populations, but seems to
be more frequent in Caucasians. The CYP3A5 gene is highly polymorphic and the allele
CYP3A53 is the most prevalent related to the loss of activity. The prevalence of this allele
appears to be higher in Caucasians when compared to African Americans. The CYP3A53/3
genotype was associated with increased half-life of CBZ in African-Americans, but no signifi-
cant association was observed in Caucasians [16,29,31]. We found that the absence of the CYP3A53 is an important protective factor of the full
spectrum of aromatic antiepileptics-induced hypersensitivity reactions in Brazilian subjects. The CYP3A53 has been shown to be related to the decreased function of this enzyme. The
association of drug tolerance with normal activity of CYP3A5 supports previous works indicat-
ing that immune response to CBZ in AHR is due to the drug itself and not its metabolytes 7 / 11 PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 Absence of CYP3A5*3 Is a Protective Factor to AHR [6,32,33]. Whereas we demonstrated that the absence of this allele is related with increased tol-
erability of these drugs, the similar proportion of CYP3A53 in both cases and controls with
IM/PM phenotypes underlined that it cannot be considered an isolated risk factor for the
development of antiepileptic hypersensitivity reactions. However, the presence of the CYP3A53 allele is neither necessary nor sufficient for the
development of these reactions. Although CYP3A53 is the most prevalent CYP3A5 allele with
reduced function, it is not the only one [19]. Thus, it remains to be evaluated if cases in our
sample that were considered with normal CYP3A5 function (EM) are actually carriers of rarer
non-functional alleles. Discussion Most studies published in the last years, which have been searching for
genetic risk factors for the development of drug-induced hypersensitivity reactions, showed the
predictive value of HLA alleles [34,35]. The current study now provides evidence suggesting
that the absence of the CYP3A53 is a protective factor to aromatic antiepileptics-induced
hypersensitivity reactions in Brazilian subjects. The worldwide distribution of CYP3A53 pro-
vides a remarkable example of population diversity, with allele frequencies ranging from 0.14
among sub-Saharan Africans to 0.95 in European populations [18]. The Brazilian population,
in excess of 195 million people, has major ancestral roots in Europe, Africa and America, nev-
ertheless, we didn’t found significant association between ethnicity and clinical status. It has
been recently reported that the genetic background of the Brazilian population is less heteroge-
neous than previously believed, with a high percentage (60–77%) of caucasian background
[36]. This study is the first to show the association between CYP3C53 and aromatic anticon-
vulsant—induced reactions in subjects from São Paulo, Brazil. CYP3C53 may have a potential
role in future screening before prescribing aromatic anticonvulsant, especially CBZ. Since we
do not know the responsiveness of the healthy population to anticonvulsants we calculated
negative (NPV) and positive predictive value (PPV) for the absence of CYP3A53 to predict
tolerability considering cases and tolerants subjects. In this scenario it shows a NPV of 51%
and PPV of 82%. According to our data, testing would prevent 4 cases of adverse reaction in
every 5 prescriptions of anticonvulsants (NNT = 4 [2.1–5.5]). We did not found association between CYP2C19 and CYP2C9 variants and cases in our
study. The CYP2C9 and CYP2C19 variants have been described as risk factors for the develop-
ment of SCARs in Thai and Japanese populations [16,17]. In addition, CYP2C9 has been
shown to be associated with PHT metabolism and elimination, but not with PB or CBZ and
CYP2C19 may be the major metabolic pathway of PB [15]. Most cases of this study were
SCARs due to CBZ in a Brazilian cohort of mixed ethnic background, which might explain the
discrepancies with the literature. Patch Tests are the only in vivo diagnostic method available
to SCARs up to now, with positive reactions in 60–100% of the cases studied [20,21]. Neverthe-
less, the reactivity depends on the type of the cutaneous adverse drug reactions. PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 Discussion The positivity
of PTs in our study varied according to the clinical pattern, being more positive (72%) in cases
of DRESS. The CYP2C9, CY2C19 and CYP3A5 enzymes have been described as being
expressed in human skin [37]. Here, we hypothesized that they can influence in the positivity
of the ARA patch test, however we found no association between functional CYP3A5 genotype
in individuals with positive PTs. CYP activation is a possible mechanism for allergic contact
dermatitis (ACT), a complex syndrome representing immunological responses to cutaneous
and/or systemic exposure to protein-reactive chemicals. Recently, many drug-induced hyper-
sensitivity reactions such as DRESS and SJS have been classified in a similar pathophysiologic
scenario as the ACT. We are aware that the current findings may not be taken as isolated genetic factors to deter-
mine lower risk on developing AHR. Considering the ongoing knowledge on the specific HLA
alleles as risk factors for SCARs, we would expect that combined analysis of CYP and HLA
data could help identify subjects with higher or lower risk of developing AHR. HLA-A3101 8 / 11 PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 Absence of CYP3A5*3 Is a Protective Factor to AHR has been associated with AHR in European population while HLA-B1502 in Chinese. Given
the relative rarity of those two alleles in the Brazilian population [38] and the ethnic specificity
they present we do not believe that they would substantially modify the present analysis. How-
ever, further studies are necessary in order to rule out this possibility. Some limitations of the present study are similar to the majority of the association studies
linking genetic factors and antiepileptics-induced cutaneous adverse reactions, such as the lim-
ited number of cases, the population included were exclusively of subjects living in São Paulo
and the ancestry was based on self-identification. Due to the self-identified admixed ancestry
in our cohort, we believe that the current data may require replication by future multicentric
multinational collaborations with accurate phenotypic characterization studies in populations
of other ancestry subjects. We therefore suggest that consideration be given to the absence of CY3A53 as a genetic
preventive marker of aromatic anticonvulsants hypersensitivity reactions. Supporting Information S1 Table. Data utilized in this study in a CSV format file. Ethnicity (AA—afro american, C
—caucasian, O—others), Clinical_Pattern (0 –Healthy, 1 –Case, 2 –Tolerant), Clinical_Pat-
tern_Severity (0 –Healthy, 1 –Severe Reaction, 2 –Tolerant, 3 –Mild reaction), Type_Of_Reac-
tion (0 –Healthy, 2 –Tolerant, 3 –Mild reaction, 4 –DRESS, 5 –Steven Johnson), Contact (P—
Positive, N—Negative, ND—Not Done). (CSV) Acknowledgments This study had a financial support provided by FAPESP (Fundação de Amparo à Pesquisa do
Estado de São Paulo), under the grants number 2011/22748-1 and 2013/01352-8. Author Contributions Conceived and designed the experiments: LKT JK DSK. Performed the experiments: LKT CY
DSK. Analyzed the data: LKT BS DSK. Contributed reagents/materials/analysis tools: LKT CY
HR JK DSK WFG LLT. Wrote the paper: LKT DSK BS LLT CY HR WFG JK. Designed the
study, analyzed and interpreted the data, and wrote the manuscript: LKT. Designed the study,
analyzed the data and reviewed the paper: JK. Designed the study, proceeded the experimental
analysis and wrote the paper: DSK. Was responsible for the statistical analysis and reviewed the
paper: BS. Helped in the interpretation of the data and with the revision of the manuscript:
LLT CY HR WFG. PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 References 1. Marson AG, Al-Kharusi AM, Alwaidh M, Appleton R, Baker GA, Chadwick DW, et al. The SANAD study
of effectiveness of valproate, lamotrigine, or topiramate for generalised and unclassifiable epilepsy: an
unblinded randomised controlled trial. Lancet. 2007; 369: 1016–1026. doi: 10.1016/S0140-6736(07)
60461-9 PMID: 17382828 2. Wiffen PJ, Derry S, Moore RA, McQuay HJ. Carbamazepine for acute and chronic pain in adults. Cochrane Database Syst Rev Rev. 2011;Issue 1: . Available: http://www.mrw.interscience.wiley.com/
cochrane/clsysrev/articles/CD005451/frame.html 3. Roujeau JC, Stern RS. Severe adverse cutaneous reactions to drugs. N Engl J Med. 1994; 331: 1272–
85. doi: 10.1056/NEJM199411103311906 PMID: 7794310 4. Roujeau JC, Kelly JP, Naldi L, Rzany B, Stern RS, Anderson T, et al. Medication use and the risk of Ste-
vens-Johnson syndrome or toxic epidermal necrolysis. N Engl J Med. 1995; 333: 1600–7. doi: 10.1056/
NEJM199512143332404 PMID: 7477195 PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 9 / 11 Absence of CYP3A5*3 Is a Protective Factor to AHR 5. Posadas SJ, Pichler WJ. Delayed drug hypersensitivity reactions—new concepts. Clin Exp Allergy. 2007; 37: 989–999. doi: 10.1111/j.1365-2222.2007.02742.x PMID: 17581192 6. Naisbitt DJ, Britschgi M, Wong G, Farrell J, Depta JPH, Chadwick DW, et al. Hypersensitivity reactions
to carbamazepine: characterization of the specificity, phenotype, and cytokine profile of drug-specific T
cell clones. Mol Pharmacol. 2003; 63: 732–41. Available: http://www.ncbi.nlm.nih.gov/pubmed/
12606784 PMID: 12606784 7. Edwards SG, Hubbard V, Aylett S, Wren D. Concordance of primary generalised epilepsy and carba-
mazepine hypersensitivity in monozygotic twins. Postgraduate medical journal. 1999. pp. 680–681. doi: 10.1136/pgmj.75.889.680 PMID: 10621883 8. Spielberg S, Gordon G, Blake D, Mellits E, Bross D. Anticonvulsant toxicity in vitro: possible role of
arene oxides. J Pharmacol Exp Ther. 1981; 217: 386–389. Available: http://jpet.aspetjournals.org/
content/217/2/386.short PMID: 7229980 9. Green VJ, Pirmohamed M, Kitteringham NR, Gaedigk A, Grant DM, Boxer M, et al. Genetic analysis of
microsomal epoxide hydrolase in patients with carbamazepine hypersensitivity. Biochem Pharmacol. 1995; 50: 1353–1359. doi: 10.1016/0006-2952(95)02009-8 PMID: 7503783 10. Madden S, Maggs JL, Park BK. Bioactivation of carbamazepine in the rat in vivo: Evidence for the for-
mation of reactive arene oxide(s). Drug Metab Dispos. 1996; 24: 469–479. PMID: 8801063 11. Lertratanangkoon K, Horning MG. Metabolism of carbamazepine. Drug Metab Dispos. 1982; 10: 1–10. PMID: 6124375 12. Gaedigk A, Spielberg SP, Grant DM. Characterization of the microsomal epoxide hydrolase gene in
patients with anticonvulsant adverse drug reactions. Pharmacogenetics. 1994; 4: 142–153. PMID:
7920694 13. Baron JM, Wiederholt T, Heise R, Merk HF, Bickers DR. References Expression and function of cytochrome p450-
dependent enzymes in human skin cells. Curr Med Chem. 2008; 15: 2258–2264. doi: 10.2174/
092986708785747535 PMID: 18781947 14. Thorn CF, Leckband SG, Kelsoe J, Leeder JS, Müller DJ, Klein TE, et al. PharmGKB summary: carba-
mazepine pathway. Pharmacogenet Genomics. 2011; 21: 906–10. PMID: 21738081 15. Thorn CF, Whirl-Carrillo M, Leeder JS, Klein TE, Altman RB. PharmGKB summary: phenytoin pathway. Pharmacogenet Genomics. 2012; 22: 466–70. PMID: 22569204 16. Ozawa S, Soyama A, Saeki M, Fukushima-Uesaka H, Itoda M, Koyano S, et al. Ethnic differences in
genetic polymorphisms of CYP2D6, CYP2C19, CYP3As and MDR1/ABCB1. Drug Metab Pharmacoki-
net. 2004; 19: 83–95. doi: 10.2133/dmpk.19.83 PMID: 15499174 17. Goldstein JA, Ishizaki T, Chiba K, de Morais SM, Bell D, Krahn PM, et al. Frequencies of the defective
CYP2C19 alleles responsible for the mephenytoin poor metabolizer phenotype in various Oriental,
Caucasian, Saudi Arabian and American black populations. Pharmacogenetics. 1997; 7: 59–64. PMID:
9110363 18. International HapMap Project [Internet]. 2014. Available: http://hapmap.ncbi.nlm.nih.gov/ 19. Hustert E, Haberl M, Burk O, Wolbold R, He YQ, Klein K, et al. The genetic determinants of the
CYP3A5 polymorphism. Pharmacogenetics. 2001; 11: 773–779. PMID: 11740341 20. Barbaud A, Collet E, Milpied B, Assier H, Staumont D, Avenel-Audran M, et al. A multicentre study to
determine the value and safety of drug patch tests for the three main classes of severe cutaneous
adverse drug reactions. Br J Dermatol. 2013; 168: 555–562. doi: 10.1111/bjd.12125 PMID: 23136927 21. Santiago F, Gonçalo M, Vieira R, Coelho S, Figueiredo A. Epicutaneous patch testing in drug hypersen-
sitivity syndrome (DRESS). Contact Dermatitis. 2010; 62: 47–53. doi: 10.1111/j.1600-0536.2009. 01659.x PMID: 20136879 22. Mockenhaupt M. The RegiSCAR Project. In: Inclusion Criteria [Internet]. 2014. Available: http://www. regiscar.org/pdf/inclusioncriteriaforscar.pdf 23. Pirmohamed M, Friedmann PS, Molokhia M, Loke YK, Smith C, Phillips E, et al. Phenotype standardi-
zation for immune-mediated drug-induced skin injury. Clin Pharmacol Ther. 2011; 89: 896–901. doi: 10. 1038/clpt.2011.79 PMID: 21562486 24. Lonjou C, Thomas L, Borot N, Ledger N, de Toma C, LeLouet H, et al. A marker for Stevens-Johnson
syndrome. . .: ethnicity matters. Pharmacogenomics J. 2006; 6: 265–8. doi: 10.1038/sj.tpj.6500356
PMID: 16415921 25. Auquier-Dunant A, Mockenhaupt M, Naldi L, Correia O, Schröder W, Roujeau J-C. Correlations
between clinical patterns and causes of erythema multiforme majus, Stevens-Johnson syndrome, and
toxic epidermal necrolysis: results of an international prospective study. Arch Dermatol. 2002; 138:
1019–24. Available: http://www.ncbi.nlm.nih.gov/pubmed/12164739 PMID: 12164739 26. 26.
Demoly P, Adkinson NF, Brockow K, Castells M, Chiriac AM, Greenberger PA, et al. International Con-
sensus on drug allergy. Allergy. 2014; 69: 420–37. doi: 10.1111/all.12350 PMID: 24697291 PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 References Demoly P, Adkinson NF, Brockow K, Castells M, Chiriac AM, Greenberger PA, et al. International Con-
sensus on drug allergy. Allergy. 2014; 69: 420–37. doi: 10.1111/all.12350 PMID: 24697291 PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 10 / 11 Absence of CYP3A5*3 Is a Protective Factor to AHR 27. Brockow K, Garvey LH, Aberer W, Atanaskovic-Markovic M, Barbaud A, Bilo MB, et al. Skin test con-
centrations for systemically administered drugs—An ENDA/EAACI Drug Allergy Interest Group position
paper. Allergy Eur J Allergy Clin Immunol. 2013; 68: 702–712. doi: 10.1111/all.12142 28. Laitinen J, Samarut J, Holtta E. A nontoxic and versatile protein salting-out method for isolation of DNA. Biotechniques. 1994; 17: 316, 318, 320–2. Available: http://www.ncbi.nlm.nih.gov/pubmed/7980935
PMID: 7980935 29. Sim SC, Ingelman-Sundberg M. The Human Cytochrome P450 (CYP) Allele Nomenclature website: a
peer-reviewed database of CYP variants and their associated effects. Hum Genomics. 2010; 4: 278–
81. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3525213&tool =
pmcentrez&rendertype = abstract PMID: 20511141 30. Xie HG, Prasad HC, Kim RB, Stein CM. CYP2C9 allelic variants: Ethnic distribution and functional sig-
nificance. Advanced Drug Delivery Reviews. 2002. pp. 1257–1270. doi: 10.1016/S0169-409X(02)
00076-5 PMID: 12406644 31. Suarez-Kurtz G, Vargens DD, Santoro AB, Hutz MH, De Moraes ME, Pena SDJ, et al. Global pharma-
cogenomics: Distribution of CYP3A5 polymorphisms and phenotypes in the Brazilian population. PLoS
One. 2014; 9. doi: 10.1371/journal.pone.0083472 32. Wu Y, Sanderson JP, Farrell J, Drummond NS, Hanson A, Bowkett E, et al. Activation of T cells by car-
bamazepine and carbamazepine metabolites. J Allergy Clin Immunol. 2006; 118: 233–41. doi: 10. 1016/j.jaci.2006.03.005 PMID: 16815161 33. Lee A-Y, Choi J, Chey W-Y. Patch testing with carbamazepine and its main metabolite carbamazepine
epoxide in cutaneous adverse drug reactions to carbamazepine. Contact Dermatitis. 2003; 48: 137–9. Available: http://www.ncbi.nlm.nih.gov/pubmed/12755726 PMID: 12755726 34. McCormack M, Alfirevic A, Bourgeois S, Farrell JJ, Kasperavičiūtė D, Carrington M, et al. HLA-A*3101
and carbamazepine-induced hypersensitivity reactions in Europeans. N Engl J Med. 2011; 364: 1134–
1143. doi: 10.1056/NEJMoa1013297 PMID: 21428769 35. Hung S-I, Chung W-H, Jee S-H, Chen W-C, Chang Y-T, Lee W-R, et al. Genetic susceptibility to carba-
mazepine-induced cutaneous adverse drug reactions. Pharmacogenet Genomics. 2006; 16: 297–306. PMID: 16538176 36. Pena SDJ, Di Pietro G, Fuchshuber-Moraes M, Genro JP, Hutz MH, Kehdy F de SG, et al. The genomic
ancestry of individuals from different geographical regions of Brazil is more uniform than expected. PLoS One. 2011; 6: e17063. doi: 10.1371/journal.pone.0017063 PMID: 21359226 37. PLOS ONE | DOI:10.1371/journal.pone.0136141
August 20, 2015 References Nishimura M, Yaguti H, Yoshitsugu H, Naito S, Satoh T. Tissue distribution of mRNA expression of
human cytochrome P450 isoforms assessed by high-sensitivity real-time reverse transcription PCR. Yakugaku Zasshi. 2003; 123: 369–375. PMID: 12772594 38. González-Galarza FF, Takeshita LY, Santos EJ, Kempson F, Maia MH, da Silva AL,et. al. Allele fre-
quency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reac-
tion associations. Nucleic Acids Res. 2015 Jan; 43(Database issue):D784–8. doi: 10.1093/nar/
gku1166 PMID: 25414323 11 / 11
|
https://openalex.org/W2233934372
|
http://eprints.whiterose.ac.uk/119003/1/A%20Personalized%20Self-Management%20Rehabilitation%20System%20with%20an%20Intelligent%20Shoe%20for%20Stroke%20Survivors%3A%20A%20Realist%20Evaluation.pdf
|
English
| null |
A Personalized Self-Management Rehabilitation System with an Intelligent Shoe for Stroke Survivors: A Realist Evaluation
|
JMIR rehabilitation and assistive technologies
| 2,016
|
cc-by
| 9,016
|
Corresponding Author: Corresponding Author:
Susan Mawson, BSc (Hons), PhD
Rehabilitation and Assistive Technology Research Group
School of Health and Related Research
University of Sheffield
Innovation Centre
217 Portobello Road
Sheffield, S14DP
United Kingdom
Phone: 44 114 2265518
Fax: 44 114 2265595
Email: s.mawson@sheffield.ac.uk Corresponding Author:
Susan Mawson, BSc (Hons), PhD
Rehabilitation and Assistive Technology Re
School of Health and Related Research
University of Sheffield
Innovation Centre
217 Portobello Road
Sheffield, S14DP
United Kingdom
Phone: 44 114 2265518
Fax: 44 114 2265595
Email: s.mawson@sheffield.ac.uk JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES Mawson et al Original Paper JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.1
(page number not for citation purposes) A Personalized Self-Management Rehabilitation System with an
Intelligent Shoe for Stroke Survivors: A Realist Evaluation Susan Mawson1*, BSc (Hons), PhD; Nasrin Nasr1*, BSc (Hons), MSc, PhD; Jack Parker1*, BSc (Hons), PhD; Richard
Davies2*, B Eng (Hons); Huiru Zheng2*, BEng, MSc, PgCHET, PhD; Gail Mountain1*, DipCOT, MPhil, PhD 1Rehabilitation and Assistive Technology Research Group, School of Health and Related Research, University of Sheffield, Sheffield, United Kingdom
2Computer Science Research Institute, School of Computing and Mathematics, Ulster University, County Antrim, United Kingdom
*all authors contributed equally (JMIR Rehabil Assist Technol 2016;3(1):e1) doi:10.2196/rehab.5079 http://rehab.jmir.org/2016/1/e1/ Abstract Background: In the United Kingdom, stroke is the most significant cause of adult disability. Stroke survivors are frequently
left with physical and psychological changes that can profoundly affect their functional ability, independence, and social
participation. Research suggests that long-term, intense, task- and context-specific rehabilitation that is goal-oriented and
environmentally enriched improves function, independence, and quality of life after a stroke. It is recommended that rehabilitation
should continue until maximum recovery has been achieved. However, the increasing demand on services and financial constraints
means that needs cannot be met through traditional face-to-face delivery of rehabilitation. Using a participatory design methodology,
we developed an information communication technology–enhanced Personalized Self-Managed rehabilitation System (PSMrS)
for stroke survivors with integrated insole sensor technology within an “intelligent shoe.”. The intervention model was based
around a rehabilitation paradigm underpinned by theories of motor relearning and neuroplastic adaptation, motivational feedback,
self-efficacy, and knowledge transfer. Objective: To understand the conditions under which this technology-based rehabilitation solution would most likely have an
impact on the motor behavior of the user, what would work for whom, in what context, and how. We were interested in what
aspects of the system would work best to facilitate the motor behavior change associated with self-managed rehabilitation and
which user characteristics and circumstances of use could promote improved functional outcomes. Methods: We used a Realist Evaluation (RE) framework to evaluate the final prototype PSMrS with the assumption that the
intervention consists of a series of configurations that include the Context of use, the underlying Mechanisms of change and the
potential Outcomes or impacts (CMOs). We developed the CMOs from literature reviews and engagement with clinicians, users,
and caregivers during a series of focus groups and home visits. These CMOs were then tested in five in-depth case studies with
stroke survivors and their caregivers. Results: While two new propositions emerged, the second importantly related to the self-management aspects of the system. The study revealed that the system should also encourage independent use and the setting of personalized goals or activities. Conclusions: Information communication technology that purports to support the self-management of stroke rehabilitation
should give significant consideration to the need for motivational feedback that provides quantitative, reliable, accurate,
context-specific, and culturally sensitive information about the achievement of personalized goal-based activities. (JMIR Rehabil Assist Technol 2016;3(1):e1) doi:10.2196/rehab.5079 KEYWORDS ; self-management; design; realist evaluation; sensor technology; equipment design; telehealth; self-care stroke; self-management; design; realist evaluation; sensor technology; equipment design; telehealth; self-care conditions through an iterative, user-centered design
methodology focused on health and social care [13]. Three
conditions were chosen for the study—chronic pain, chronic
heart failure, and stroke—with the intent of exploring how a
multimodular system could support the three areas, with a
proposition that other long-term conditions could be integrated
into the system at a later stage. The intervention model for the
stroke system was based around a rehabilitation paradigm
underpinned by theories of motor relearning and neuroplastic
adaptation, motivational feedback, self-efficacy, and knowledge
transfer [14-17]. (JMIR Rehabil Assist Technol 2016;3(1):e1) doi:10.2196/rehab.5079 JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.1
(page number not for citation purposes) http://rehab.jmir.org/2016/1/e1/ XSL•FO
RenderX JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES Mawson et al JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.2
(page number not for citation purposes) Introduction In the United Kingdom, stroke is the most significant cause of
adult disability. Stroke survivors are frequently left with physical
and psychological changes that can profoundly affect their
functional ability [1], independence [2], and social participation
[3-6]. With the global incidence of stroke set to escalate from
15.3 million to 23 million by 2030 [7] and the decrease in
mortality and rise in morbidity, more stroke survivors will be
living with long-term disability [8]. Research suggests that long-term, intense, task-specific,
context-specific, goal-oriented, variable rehabilitation that is
goal-oriented and environmentally enriched improves function,
independence, and quality of life after a stroke [9]. Over recent
years, there has been a contextual shift in service delivery from
hospital-based rehabilitation to the community. It is
recommended that rehabilitation should continue until maximum
recovery has been achieved [9,10]; however, the increasing
demand on services and financial constraints mean that needs
cannot be met through traditional face-to-face delivery of
rehabilitation. Radical innovation and the adoption of a
self-management paradigm need to be considered as a way to
deliver home-based rehabilitation, thereby meeting the
challenges faced in health care. The SMART interdisciplinary research team applied a mix of
health, social sciences, and user-centered design methods to
develop the Personalized Self-Management Rehabilitation
System (PSMrS) for stroke survivors [18]. The PSMrS is a
prototype ICT system integrated with home hub sensor
technology—the intelligent shoe—developed to enable stroke
survivors to self-manage their rehabilitation to achieve identified
life goals specific to them (Figures 1-3). While other wearable
devices are available, the sensored insole was deemed to be the
most appropriate as walking re-education and foot placement
are key components of a stroke rehabilitation program. Data
from the sensors give feedback to users through screens (Figure
3) designed with stroke survivors to depict balance and heel
strike as a percentage of normal values. The aim of this final
aspect of the research program was to understand the conditions
under which this technology-based rehabilitation solution would
most likely have an impact (outcome) on the motor behavior of
the user, what would work for whom, in what context, and in
what way. In 2007, the SMART consortium began a program of research
to develop and evaluate an Information Communication
Technology (ICT) enhanced Personalized Self-Managed System
for people with complex long-term conditions [11,12]. The
program aimed to deepen our understanding of the potential for
technology to support self-management of long-term chronic Figure 1. JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.3
(page number not for citation purposes) Introduction The PSMrS home hub for stroke survivors with insole and data logger providing walking feedback through the PSMrS. JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.2
http://rehab.jmir.org/2016/1/e1/
(page number not for citation purposes)
L•FO
derX Figure 1. The PSMrS home hub for stroke survivors with insole and data logger providing walking feedback through the PSM home hub for stroke survivors with insole and data logger providing walking feedback through the PSMrS. http://rehab.jmir.org/2016/1/e1/ http://rehab.jmir.org/2016/1/e1/ XSL•FO
RenderX Mawson et al JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES Figure 2. Screenshots of the PSMrS user interface. Methods
In order to enhance and strengthen our previous research, we
used a Realist Evaluation (RE) approach [19] to evaluate the
final prototype of PSMrS, prior to a feasibility pilot study, in
order to explore in depth the value, usability, and potential
impact such technology could have on an individual’s ability
to self-manage their rehabilitation following a stroke. Realist evaluation is a well-recognized methodology with its
roots in philosophy, social sciences, and evaluation methods. To conduct realist evaluation, it is necessary to assume that the
program (or in this case the PSMrS intervention) consists of a
series of configurations that include the context, the underlying
mechanisms of change, and the potential outcomes or impacts. Realist evaluation is underpinned by theory described as a set
of prepositions about the nature of change that is predicted, as
well as the hypothesis that change can be maintained by the
action of particular mechanisms within particular contexts (eg,
the proposition that a simple touch-screen computer interface
can motivate people even with low or no computer literacy to
use the system for monitoring their health in the context of their
home). This methodology also tries to explain those contexts that are
“conducive” or “resistant” to change [20]. Any realist evaluation
must fully engage stakeholders, clinicians, stroke survivors, and
caregivers in the generation of theories to be tested through the
evaluation and the identification of subsequent working
hypotheses that then drive the evaluation process. An overview
of the realist evaluation plan adopted in this research is
summarized in Figure 4. The overall evaluation questions for this research were what
works, for whom, why, in what way, and under what
circumstances? Introduction In the case of the PSMrS, we were interested
in what aspects of the system would work best to facilitate the
motor behavior change associated with self-managed
rehabilitation and which stroke user characteristics and
circumstances of use could promote improved functional
outcomes. Mawson et al
JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES Figure 2. Screenshots of the PSMrS user interface. i
l
i h l
li ure 2. Screenshots of the PSMrS user interface. Figure 2. Screenshots of the PSMrS user interface. Methods can motivate people even with low or no computer literacy to
use the system for monitoring their health in the context of their
home). Methods Methods In order to enhance and strengthen our previous research, we
used a Realist Evaluation (RE) approach [19] to evaluate the
final prototype of PSMrS, prior to a feasibility pilot study, in
order to explore in depth the value, usability, and potential
impact such technology could have on an individual’s ability
to self-manage their rehabilitation following a stroke. In order to enhance and strengthen our previous research, we
used a Realist Evaluation (RE) approach [19] to evaluate the
final prototype of PSMrS, prior to a feasibility pilot study, in
order to explore in depth the value, usability, and potential
impact such technology could have on an individual’s ability
to self-manage their rehabilitation following a stroke. This methodology also tries to explain those contexts that are
“conducive” or “resistant” to change [20]. Any realist evaluation
must fully engage stakeholders, clinicians, stroke survivors, and
caregivers in the generation of theories to be tested through the
evaluation and the identification of subsequent working
hypotheses that then drive the evaluation process. An overview
of the realist evaluation plan adopted in this research is
summarized in Figure 4. Realist evaluation is a well-recognized methodology with its
roots in philosophy, social sciences, and evaluation methods. To conduct realist evaluation, it is necessary to assume that the
program (or in this case the PSMrS intervention) consists of a
series of configurations that include the context, the underlying
mechanisms of change, and the potential outcomes or impacts. Realist evaluation is underpinned by theory described as a set
of prepositions about the nature of change that is predicted, as
well as the hypothesis that change can be maintained by the
action of particular mechanisms within particular contexts (eg,
the proposition that a simple touch-screen computer interface The overall evaluation questions for this research were what
works, for whom, why, in what way, and under what
circumstances? In the case of the PSMrS, we were interested
in what aspects of the system would work best to facilitate the
motor behavior change associated with self-managed
rehabilitation and which stroke user characteristics and
circumstances of use could promote improved functional
outcomes. http://rehab.jmir.org/2016/1/e1/ XSL•FO
RenderX Mawson et al JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES ure 3. User feedback for symmetry and heel strike data from insole. Mawson et a
IR REHABILITATION AND ASSISTIVE TECHNOLOGIES Figure 3. User feedback for symmetry and heel strike data from insole. JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.4
(page number not for citation purposes) http://rehab.jmir.org/2016/1/e1/ Methods to which technology can facilitate a shift in responsibility for
the management of care from the professional to the stroke
survivor. The theories to be validated through the realist evaluation
process were generated through literature reviews together with
empirical data collected in the earlier work [18,21,22]. These
theories were then validated or refuted through individual and
focus group interviews conducted with patients/caregivers and
health professionals as described below. There were a number
of theories that we wished to explore in this aspect of the
evaluation;
for
example,
the
theoretical
models
of
self-management
rehabilitation
that
are
amenable
to
technological solutions, the implications of motor behavior
change mechanisms such as neuroplasticity and how they can
be taken into account in technology development, and the extent The theories to be validated through the realist evaluation
process were generated through literature reviews together with
empirical data collected in the earlier work [18,21,22]. These
theories were then validated or refuted through individual and
focus group interviews conducted with patients/caregivers and
health professionals as described below. There were a number
of theories that we wished to explore in this aspect of the
evaluation;
for
example,
the
theoretical
models
of
self-management
rehabilitation
that
are
amenable
to
technological solutions, the implications of motor behavior
change mechanisms such as neuroplasticity and how they can
be taken into account in technology development, and the extent The theories generated a number of hypotheses/propositions,
to be explored rather than tested: 1. Specific elements of self-management can be successfully
promoted through the use of technology designed for this
purpose. 2. This technology can help individuals relearn motor behavior
by encouraging achievement of personal functional goals
and repetition of key motor activities within those goals. XSL•FO
RenderX Mawson et al JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.5
(page number not for citation purposes) JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES 3. The technology facilitates partnership working between the
user and others to achieve self-management. of this through real-time feedback on performance, users
develop confidence (self-efficacy) that then leads to a more
active role in the management of their condition. 4. The stroke PSMrS gives users the opportunity to perform
exercises as much as they can through repetition and
provides them with tailored feedback. Both these attributes
can promote motor relearning and neuroplastic adaptation. In accordance with the realist evaluation methodology, the
process of hypothesis validation and generation were followed
by operationalization of the hypotheses into mechanism, context,
and outcome configurations (CMOCs). These were explored,
refined, developed, and tested through practitioner and
participant engagement. p
g
p
p
5. The technology can enable users to interpret physiological
data through motivational feedback screens. 6. By
mastering
(mastery)
the
tasks
involved
in
self-management programs and being provided evidence 6. By
mastering
(mastery)
the
tasks
involved
in
self-management programs and being provided evidence Figure 4. An overview of the realist evaluation plan. Recruitment and Participant Involvement
All participants were recruited via health services and deemed
to be fit to join the study by the referring physiotherapist. Ethics
approval was obtained through the Leeds Ethics committee
(08/H1306/46), and informed consent was obtained before the
system was deployed to participants’ homes. All participants
had to be able to comprehend written English, not have
significant cognitive impairment, and be clinically stable. The
stroke survivors needed to be willing and able to use the
equipment and report back on their experiences to the
team. Specific inclusion criteria for participants were
did not have any communication problems tha
significantly impede comprehension or have severe he
to the extent that they were not able to get up out of
independently. Participants’ demographic characteristics and baselin
data were recorded at the outset (see Table 1). Th
survivors were also interviewed qualitatively before
h
i d f i
ll i
b
h i
i
d Figure 4. An overview of the realist evaluation plan. Figure 4. An overview of the realist evaluation plan. Recruitment and Participant Involvement
All participants were recruited via health services and deemed
to be fit to join the study by the referring physiotherapist. Ethics
approval was obtained through the Leeds Ethics committee
equipment and report back on
team. Figure 4. An overview of the realist evaluation plan. JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES Specific inclusion crite
did not have any commu
significantly impede compreh
to the extent that they were n equipment and report back on their experiences to the research
team. Specific inclusion criteria for participants were that they
did not have any communication problems that would
significantly impede comprehension or have severe hemiplegia
to the extent that they were not able to get up out of the chair
independently. Recruitment and Participant Involvement All participants were recruited via health services and deemed
to be fit to join the study by the referring physiotherapist. Ethics
approval was obtained through the Leeds Ethics committee
(08/H1306/46), and informed consent was obtained before the
system was deployed to participants’ homes. All participants
had to be able to comprehend written English, not have
significant cognitive impairment, and be clinically stable. The
stroke survivors needed to be willing and able to use the All participants were recruited via health services and deemed
to be fit to join the study by the referring physiotherapist. Ethics
approval was obtained through the Leeds Ethics committee
(08/H1306/46), and informed consent was obtained before the
system was deployed to participants’ homes. All participants
had to be able to comprehend written English, not have
significant cognitive impairment, and be clinically stable. The
stroke survivors needed to be willing and able to use the Participants’ demographic characteristics and baseline clinical
data were recorded at the outset (see Table 1). The stroke
survivors were also interviewed qualitatively before and after
the period of installation about their views and experiences. JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.5
(page number not for citation purposes) http://rehab.jmir.org/2016/1/e1/ XSL•FO
RenderX JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES Mawson et al Table 1. Patient demographics. Walking aid
Able to comprehend
written English
Computer experiencea
Time since
stroke
Side affected
Age of patient/ age of
caregiver
Participant
None (FES)
Yes
++
13 months
R hemi
63/57
17
Frame and tripod
(FES)
Yes
+
18 months
L Hemi
73/73
23
None (FES)
Yes
+++
18 months
R Hemi
45/44
33
None (FES)
Yes
++
15 months
L Hemi
60/60
34
None (FES)
Yes
++
12 months
R Hemi
42/44
35
a+ denotes the amount of computer experience. Table 1. Patient demographics. a+ denotes the amount of computer experience. JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES The treating physiotherapist in partnership with the stroke
survivor personalized the system and the stroke survivor (with
or without their carer) practised using the system under
supervision within the rehabilitation center. The service
participants were then encouraged to continue using the system
for up to 4 weeks independently at home. The participants were
advised to contact a health care professional if any health issues
arose during the deployment period. A researcher was available
by telephone if technical difficulties arose during the 4-week
period. Information collected from the deployed systems were
transferred and stored using a non-identifying format on a server
hosted at one of the partner universities. The security and
privacy of data between the stroke survivor’s devices and the
server were protected using two methods. The first was to keep
the data private by anonymizing all of the data so that sensitive
information was never transmitted across the Internet. The
second was to store the information in a secure manner;
information was stored on a university server that was held in
a secure room under lock and key and behind a firewall. In
addition, the server was also active only during the realist
evaluation and was disconnected from the Internet once the
realist evaluation was completed. Technical support was
available over the telephone and by researcher follow-up visits
where necessary during office hours. JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.6
(page number not for citation purposes) Table 2. Context mechanisms outcome configurations for the PSMrS.
Some potential c
Some plausible mechanisms (why) Some possible outcomes
Some potential contexts (who/in what circum-
stances) Some possible outcomes
Some potential contexts (who/in what circum-
stances) M1: By using the PSMrS, users will gain a sense of
task mastery which might increase their confidence. O1: Increased confidence in the user’s ability
to carry out everyday tasks. Measure: Qualita-
tive data C1: A system that provides rewarding feed-
back as a result of improved symmetry and
heel strikes. O1: Increased confidence in the user’s ability
to carry out everyday tasks. Measure: Qualita-
tive data C1: A system that provides rewarding feed-
back as a result of improved symmetry and
heel strikes. M2: By using the PSMrS, users will be facilitated to
set specific, measurable, attainable, realistic, and time-
specified goals that might promote more responsibility
towards their rehabilitation. C2: A system that is used by a participant
where they continue to desire improvement(s)
and those improvements are achievable. O2: Increased self-efficacy and ownership of
their rehabilitation. Measure: Qualitative data O3: Context-dependent/ place-based and cul-
turally meaningful rehabilitation. Measure:
Qualitative data and quantitative data from the
TELER quiz style indicator. O3: Context-dependent/ place-based and cul-
turally meaningful rehabilitation. Measure:
Qualitative data and quantitative data from the
TELER quiz style indicator. C3, C3a: A system that can be used in the
home and has specific goals and exercises
that can be carried out within the home/do-
mestic environment. M3: By using the PSMrS, users performing selected
exercises in the home and repeating these exercises
might lead to users’ developing knowledge about car-
rying out stroke rehabilitation in the home environ-
ment. O4: Increased users’ agency and their active
roles in self-management. Measure: Online
data sources from insole and qualitative data. M4: By using the PSMrS, users have problem-solving
opportunities that might lead to the successful
achievement of goals and attribution of success to
users’ personal abilities. C4: A system that enables users to set and
achieve personal goals through shared deci-
sion-making between patients and profession-
als. O5: An understanding of symptoms and change
in symptoms throughout the usage of the sys-
tem. Measure: Qualitative data and quantitative
online data sources from insole. C5: A system that translates physiological
data through feedback. M5: The use of the PSMrS will facilitate the translation
of physiological data, which might enable the user to
interpret their symptoms. C6: A system that provides individualized
motivational feedback on the achievement of
walking skill. Table 2. Context mechanisms outcome configurations for the PSMrS.
Some potential c
Some plausible mechanisms (why) M6: The use of the PSMrS might encourage increased
intensity of practice with consequential neuroplastic
changes. O6: Increased functioning and achievement of
improved walking skill. Measure: Online quantitative data sources from insole. Finally, qualitative and quantitative analysis was carried out
across all participant cases to establish whether the theories
underpinning the personalized self-management system had
been supported or refuted [28] and to what extent the
intervention had created change in user behavior. Due to the
extensive amount of information gathered during the evaluation,
this paper reports only the qualitative data with the quantitative
data reported elsewhere [29]. Finally, qualitative and quantitative analysis was carried out
across all participant cases to establish whether the theories
underpinning the personalized self-management system had
been supported or refuted [28] and to what extent the
intervention had created change in user behavior. Due to the
extensive amount of information gathered during the evaluation,
this paper reports only the qualitative data with the quantitative
data reported elsewhere [29]. Observation of Context, Mechanism, and Outcome
Configuration Our goal was to gather both qualitative and quantitative data
before, during, and after participant interaction with the
technology. The quantitative data gathered before, during, and
after the technology deployment enabled us to observe changes
in physical activity, specifically walking ability, and quality and
changes in knowledge levels. To achieve the latter, a measure
called TELER Quiz style outcome indicators was used [24-26]. Quantitative walking data on heel strike, gait speed, and
symmetry was recorded online from the sensors in the intelligent
shoe during the time stroke survivors used the PSMrS. The
amount of walking activity was also measured in order to
provide data to support the proposition around neuroplastic
adaption and intensity of practice. We also applied a measure
of technology usability, the System Usability Scale (SUS) [27]. Data Analysis The focus of the qualitative analysis was based on both the
exploration of the pre-existing context and the development and
refinement of the hypothesized CMOC using thematic analysis
[30-32]. This innovative approach to the analysis draws on Yin
[30], Miles and Huberman [33], and Patton [34] and is
underpinned by the principles of realist evaluation [19]. This approach allowed for themes to emerge from the data and
examines interconnections and relationships between the
mechanisms and contexts in relation to proposed outcomes
[31,32,35]. In order to ensure that the quantitative gait data gathered from
the insole was valid, providing accurate and reliable results,
two approaches were adopted. In the first instance, the hardware
and sensor technology consisted entirely of off-the-shelf
products that were then integrated into the PSMrS in a novel
way. This ensured that the technology complied with European
Union safety, health, and environmental requirements. In
addition, there were assurances that the manufacture has
produced a product that was fit for purpose and had been through
rigorous manufacturing processes such as quality assurance and
testing. Second, a consistent hardware configuration was adopted
in relation to sensor deployment, as any deviation from this
template would have serious implications on accuracy and
repeatability of results. JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.7
(page number not for citation purposes) http://rehab.jmir.org/2016/1/e1/ Conducive Context In order for the mechanisms underpinning the PSMrS to work,
a number of generic contextual conditions had been previously
identified [21,23]. The system had to be reliable, accurate, and
robust; be adapted and personalized to the individual personal,
environmental, and social context of the stroke survivor; be
accessible in the home setting; be person-centered (customized
for the individual) and used independently of the therapist; and
provide the user with adequate resources to enable them to
understand and have knowledge about their stroke and
rehabilitation processes. Five people with stroke were recruited from either Sheffield
Community Intermediate Care Services or the Assessment and
Rehabilitation Centre while they were still receiving
rehabilitation. The engagement of therapists at this service was
obtained through an initial focus group where the technology
was explained and demonstrated together with the requirements
for participant involvement (local agreement for access has
already been obtained). Participants were identified during the
period of community rehabilitation by the therapists, with the
anticipation being that the PSMrS would be integrated into the
standard stroke care pathway prior to discharge from the stroke
service or where they were still engaged in active rehabilitation. Examples of what some of the contexts, mechanisms, and
outcomes (CMO) for the PSMrS are provided in Table 2. This
combination of theory, hypothesis generation, and development
of CMOC was the foundation work for the evaluation; a realist
evaluation demands a synthesis of qualitative and quantitative
methodology. http://rehab.jmir.org/2016/1/e1/ XSL•FO
RenderX JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES Mawson et al Self-Management A number of self-management principles were observed during
testing. These included problem-solving whereby users would
make a conscious effort to change their movements to obtain
higher scores, promoting self-efficacy through mastery,
involving others in the process of rehabilitation to reinforce
behavior change, and utilizing resources (using the system and
its components to improve): “It makes me feel like I’m making
progress. I’m going down that road to full recovery” (Participant
23) and “Oh I’m confident yes, yes! Just little things like in a
morning when I’m at the wash basin in the bathroom I do free
standing now as a matter of course” (Participant 23). All of the users described how being able to make visible the
invisible, observe their improvement, and track progress over
time was of great importance. This would not only indicate that
they are continuing to make improvements but they are also
“returning to normality.” They were therefore using improved
scores as recovery markers: “It makes me feel like I’m making
progress. I’m going down that road to full recovery. I know full
recovery is never going to happen but I just keep saying to J
I’ve passed another milestone” (Participant 23). Two users described how close family members noticed their
improvements, which provided encouragement and reinforced
their efforts to continue striving for improvements. Participant
35 described how she was able to open the door for her
grandchildren when they had come to visit: However, trusting the PSMrS and the scores provided affected
their usage. For example, one of the users suggested that the
system provided unexpected results: “you might not walk
perfectly but the machine says that you’re doing quite well!”
(Participant 17). My nanna look at my nanna!” And it’s what I used
to do whenever they used to come. I used to go to the
door and open the door for them. And I’d done it
again, hadn’t I? And he [son] said it really did them
good to see you do that! [Participant 35] Interestingly, 2 users reported practicing walking around without
the SMART insole in their shoes so that when they used the
insoles, they might get a better score: “I got it down in the low
thirties…so without the sensors on we did an exaggerated
heel–toe, the next time the score had improved a lot” (Participant
23). Technology The limitations of PSMrS and the SMART insole had an impact
on the usage of the system. Users relied on their caregiver to
don the anklet, three of the five experienced Internet connection
difficulties, the system required re-booting due to freezes, and
the on/off switch was fragile and subsequently needed replacing:
“It’s quite fiddly to get the devices around the ankles and the
insoles could do with being stiffer” (Participant 17) and “I
always set off on my walking with my heart in my mouth
thinking ‘is it going to work?’!” (Participant 23). Researchers were interested in the consequences of negative
feedback, that is, how they would respond if they received a
poorer score than previously achieved. However, all of the users
suggested it increased their determination: “It made me want
to do it again, to better it!” (Participant 35). However, a number of negative factors affected the motivation,
such as fear of failure (users would practice without the shoe
to ensure they achieved a better score) and self-awareness of
their limitations (they were aware of how far they could walk,
the risk of falling, environmental obstacles, fatigue, and the
concerns of caregivers/family members). Due to storage and accessibility issues, 3 users suggested that
they would have preferred alternative devices to view their
feedback such as a tablet or smartphone: “that [PSMrS] is a
little bit cumbersome…if that could have been a laptop or an
iPad size where you could put it somewhere. You could hold it
on your knee” (Participant 35). Furthermore, the caregivers also influenced user motivation. Caregivers had safety concerns that the stroke survivor would
push themselves too far in an attempt to achieve greater scores:
“I’m getting more relaxed with it than I was when I thought
b****y hell, what’s she doing!!” (Caregiver 35). What Work Works for Whom, and in What
Circumstances and Ways?
Motivation
Motivation em Motivation emerged as being related to feedback in that the
scores obtained following performance focused their
determination to improve. The users expressed their desire to
strive for better scores following feedback: “I shouldn’t be
satisfied until I’m in the green and that little man pops up”
(Participant 23). Data analysis reveals that in order to achieve desired outcomes
through the use of computer technology, a number of
issues—such as the technology itself, the provision of feedback,
the motivation of the user and what impacts on this, and the
personal and social environment in which the system is
used—can affect the mechanisms underpinning the intervention. The following section will discuss each of these issues in detail. Notably, because they had a score for their performance, the
users were able to involve significant others, which reinforced
behavioral change. This would involve caregivers and family
members expressing their admiration for the improvements
made, which would instill a level of mastery and confidence. Feedback Receiving feedback following performance was of particular
importance to the users. More specifically, the provision of
accurate, reliable quantitative Knowledge of Results (KR)
feedback of goal attainment (ie, 100% heel strikes) affected
users’ motivation to use the system: “Having a numerical result
to what you’re doing helps because it is very easy to see that
you’ve got an improvement” (Participant 23). JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.8
(page number not for citation purposes) Results The next stage of the realist evaluation cycle (see Figure 3)
involves the specification phase where findings are synthesized
and presented as refined CMO configurations to answer the
question, “What works for whom and in what circumstances
and ways?” [19,20]. JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.7
(page number not for citation purposes) XSL•FO
RenderX JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES Mawson et al Self-Management Measure: Online data date
sourced from insole; Qualitative data M4: By using the PSMrS, users have problem-
solving opportunities that might lead to the suc-
cessful achievement of activities/goals and attribu-
tion of success to users’ personal abilities. C4: A system that enables users to set and achieve
personal goals through shared decision-making
between patients and professionals; C4a: A system
that encourages independent use in the home and
to set personal goals. M5: The use of the PSMrS will facilitate the
translation of physiological data, which might
enable users to interpret their symptoms. O5: An understanding of symptoms and
change in symptoms throughout the usage of
the system. Measure: Qualitative data; online
data sources from insole. C5: A system that translates physiological data
through feedback. C6: A system that provides individualized accu-
rate, reliable quantitative motivational feedback
on the achievement of specific tasks. M6: The use of the PSMrS might encourage in-
creased intensity of practice with consequential
neuroplastic changes. O6: Increased functioning and achievement
of life goals. Measure: TELER, online data
sources from insole. self-management aspects of the system. The study revealed that
the system should also encourage independent use and the
setting of personalized goals or activities. The stroke survivors
identified the importance of goals using the words “activities”
and “goals” interchangeably. JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.9
(page number not for citation purposes) http://rehab.jmir.org/2016/1/e1/ Self-Management Occasionally [granddaughter] says to me that I’m
getting like the grandma that I used to be…she tells
me know that I’m getting back to where I was. [Participant 35] http://rehab.jmir.org/2016/1/e1/ JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.8
(page number not for citation purposes) JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.8
(page number not for citation purposes) http://rehab.jmir.org/2016/1/e1/ XSL•FO
RenderX JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES Mawson et al exploring the complex interactions of contexts, mechanisms,
and outcomes. Table 3 sets out the refinement of pre-existing
CMOCs and highlights the changes following the observation
of these CMOCs. Some possible outcomes
Some potential contexts (who/in what circum-
stances) C1: A system that provides rewarding feedback
as a result of improved symmetry and heel strikes. O1: Increased confidence in the user’s ability
to carry out everyday tasks. Measure: Quali-
tative data O1: Increased confidence in the user’s ability
to carry out everyday tasks. Measure: Quali-
tative data O2: Increased self-efficacy and ownership of
their rehabilitation. Measure: qualitative data M2: By using the PSMrS, users will be facilitated
to set specific, measurable, attainable, realistic,
and time-specified goals that might promote more
responsibility towards their rehabilitation. C2: A system that is used by a participant where
they continue to desire improvement(s) and those
improvements are achievable and that provides
accurate, reliable, quantitative KR feedback of
goal attainment. M3: By using the PSMrS, users performing select-
ed exercises in the home and repeating these exer-
cises might lead to users developing knowledge
about the importance of carrying out stroke reha-
bilitation in the home environment for recovery. O3: Context-dependent/place-based and cul-
turally meaningful rehabilitation. Measure:
qualitative data; O3a: An awareness of the
need to carry out rehabilitation C3: A system that can be used in the home and
has specific goals and exercises that can be carried
out within the context of the home/domestic envi-
ronment and provides meaningful feedback fol-
lowing goal-based activity; C3a: A system that
can be used in the home and has specific goals
and exercises that can be carried out within the
context of the home/domestic environment. O4: Increased users’ agency and their active
roles in self-management taking action
(practicing). Measure: Online data date
sourced from insole; Qualitative data O4: Increased users’ agency and their active
roles in self-management taking action
(practicing). Acknowledgments g
The research consortium would like to thank all the stroke survivors and caregivers who gave their time and energy to this study. Their willingness and dedication made the study possible, enhancing our knowledge in this valuable area of work. The research consortium would like to thank all the stroke survivors and caregivers who gave their time and energy to this study. Their willingness and dedication made the study possible, enhancing our knowledge in this valuable area of work. This paper presents independent research by the Engineering and Physical Science Research Council from 2008-2012 and the
National Institute for Health Research Collaboration for Leadership in Applied Health Research and Care Yorkshire and Humber
(NIHR CLAHRC YH). The views and opinions expressed are those of the authors, and not necessarily those of the National
Health Service, the NIHR, or the Department of Health. Principal Findings The PSMrS is a systems change
intervention with complex effects in which contextual factors
such as a network of relationships, as illustrated in this study,
play a significant role in how the intervention is used and how
sets of interdependent factors affect an individual’s decision to
use the system [36]. as the PSMrS could have in changing knowledge and attitude
to lead to behavior change. The PSMrS is a systems change
intervention with complex effects in which contextual factors
such as a network of relationships, as illustrated in this study,
play a significant role in how the intervention is used and how
sets of interdependent factors affect an individual’s decision to
use the system [36]. In its current form, the system and in particular all of its software
components are available to be deployed on a personal computer
and smartphone. Current trends within computing indicate that
the adoption of mobile computing continues to grow and
dominate the market place. Therefore, plans for future work
would focus on porting the current system to mobile-only
platforms such as tablets and mobile phones. There are a number
of advantages to doing this. Usability can be improved as mobile
devices offer more flexibility and can operate in a wide range
of environments and scenarios. Furthermore, practical
considerations relating to the management and operation of any
future randomized controlled trial would be more easily
controlled. Conclusions The research consortium will take this confirmation of theory
and development of new propositions and recommendations
into the development of the next iteration of the system prior
to the implementation of robust population-based evaluation of
a defined technology. This will test the effectiveness of the Conflicts of Interest None declared. References 1. Ones K, Yilmaz E, Cetinkaya B, Caglar N. Quality of life for patients poststroke and the factors affecting it. J Stroke
Cerebrovasc Dis 2005;14(6):261-266. [doi: 10.1016/j.jstrokecerebrovasdis.2005.07.003] [Medline: 17904035] 2. O'Connell B, Hanna B, Penney W, Pearce J, Owen M, Warelow P. Recovery after stroke: a qualitative perspective. J Qual
Clin Pract 2001 Dec;21(4):120-125. [Medline: 11856408] 2. O'Connell B, Hanna B, Penney W, Pearce J, Owen M, Warelow P. Recovery after stroke: a qualitative perspective. J Qual
Clin Pract 2001 Dec;21(4):120-125. [Medline: 11856408] 4. Desrosiers J, Rochette A, Noreau L, Bourbonnais D, Bravo G, Bourget A. Long-term changes in participation after stroke. Top Stroke Rehabil 2006;13(4):86-96. [doi: 10.1310/tsr1304-86] [Medline: 17082173] 4. Desrosiers J, Rochette A, Noreau L, Bourbonnais D, Bravo G, Bourget A. Long-term changes i
Top Stroke Rehabil 2006;13(4):86-96. [doi: 10.1310/tsr1304-86] [Medline: 17082173] 5. Mayo NE, Wood-Dauphinee S, Côté R, Durcan L, Carlton J. Activity, participation, and quality of life 6 months poststroke. Arch Phys Med Rehabil 2002 Aug;83(8):1035-1042. [Medline: 12161823] 5. Mayo NE, Wood-Dauphinee S, Côté R, Durcan L, Carlton J. Activity, participation, and quality of life 6 months poststroke. Arch Phys Med Rehabil 2002 Aug;83(8):1035-1042. [Medline: 12161823] y
g
6. Rochette A, Desrosiers J, Bravo G, St-Cyr-Tribble D, Bourget A. Changes in participation after a mild stroke: quantitative
and qualitative perspectives. Top Stroke Rehabil 2007;14(3):59-68. [doi: 10.1310/tsr1403-59] [Medline: 17577968] 6. Rochette A, Desrosiers J, Bravo G, St-Cyr-Tribble D, Bourget A. Changes in participation after a mild stroke: quantitative
and qualitative perspectives. Top Stroke Rehabil 2007;14(3):59-68. [doi: 10.1310/tsr1403-59] [Medline: 17577968]
7. Strong K, Mathers C, Bonita R. Preventing stroke: saving lives around the world. Lancet Neurol 2007 Feb;6(2):182-187. [doi: 10.1016/S1474-4422(07)70031-5] [Medline: 17239805] 6. Rochette A, Desrosiers J, Bravo G, St-Cyr-Tribble D, Bourget A. Changes in participation after a mild stroke: quantitative
and qualitative perspectives. Top Stroke Rehabil 2007;14(3):59-68. [doi: 10.1310/tsr1403-59] [Medline: 17577968]
7. Strong K, Mathers C, Bonita R. Preventing stroke: saving lives around the world. Lancet Neurol 2007 Feb;6(2):182-187. [doi: 10 1016/S1474 4422(07)70031 5] [Medline: 17239805] 6. Rochette A, Desrosiers J, Bravo G, St-Cyr-Tribble D, Bourget A. Changes in participation after a mild stroke: quantitative
and qualitative perspectives. Top Stroke Rehabil 2007;14(3):59-68. [doi: 10.1310/tsr1403-59] [Medline: 17577968] and qualitative perspectives. Top Stroke Rehabil 2007;14(3):59-68. [doi: 10.1310/tsr1403-59] [Medline: 17577968]
7. Strong K, Mathers C, Bonita R. Preventing stroke: saving lives around the world. Lancet Neurol 2007 Feb;6(2):182-187. [doi: 10.1016/S1474-4422(07)70031-5] [Medline: 17239805] 7. Strong K, Mathers C, Bonita R. Principal Findings This realist evaluation set out to explore the conditions under
which this technology-based rehabilitation solution would most
likely have an impact (outcome) on the motor behavior of people
with stroke, what would work for whom, within a home context,
and in what ways the system would have an impact. The
pre-existing CMOs were based on theories of motor relearning,
neuroplastic adaptation, and behavior change, specifically on
the theories underpinning self-efficacy and the relationship
between changes in self-efficacy and self-managed behaviors. The findings of the study confirmed the original CMOs and
further highlighted two emerging propositions related to the
context of use together with two new outcomes that were
recorded in the qualitative transcripts. The outcomes identified from the data were first related to the
users’ agency and their active role in self-management, where
it emerged that “taking action” independently was an important
outcome. The second related to “knowledge gain” where users
became aware of the need to carry out rehabilitation in order to
achieve their identified goal. This finding links well to the
pre-existing CMO where the need for context-dependant and
culturally meaningful rehabilitation had been identified as an
outcome. We suggest two implications that this study may have for both
clinical practice and research. First the findings suggest any
system that purports to support the self-management of stroke
rehabilitation should give significant consideration to the need
for motivational feedback that provides quantitative, reliable,
accurate, context-specific, and culturally sensitive information
about the achievement of personalized goal-based activities. A
second implication is the role that complex interventions such The first proposition, which is perhaps to be expected, relates
to the need for the system to be reliable and accurate in terms
of providing quantitative feedback to the stroke users. The
results suggest that this feedback should be about the attainment
of goal-based activities with a specific emphasis on “knowledge
of results.” The second proposition to emerge was related to the XSL•FO
RenderX Mawson et al JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES system in the promotion of self-managed rehabilitation and
recovery. as the PSMrS could have in changing knowledge and attitude
to lead to behavior change. http://rehab.jmir.org/2016/1/e1/ JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES Mawson et al 13. Wright P, McCarthy JF. Experience-centered designdesigners, users, and communities in dialogue. New York: Morgan
and Claypool; 2010. 13. Wright P, McCarthy JF. Experience-centered designdesigners, users, and communities in dialogue. New York: Morgan
and Claypool; 2010. yp
14. Carr JH, Shepherd RB. Enhancing physical activity and brain reorganization after stroke. Neurol Res Int 2011;2011:515938
[FREE Full text] [doi: 10.1155/2011/515938] [Medline: 21766024] 14. Carr JH, Shepherd RB. Enhancing physical activity and brain reorganization after stroke. Neurol Res Int 2011;2011:515938
[FREE Full text] [doi: 10.1155/2011/515938] [Medline: 21766024] [
] [
] [
]
15. Kleim JA, Jones TA. Principles of experience-dependent neural plasticity: implications for rehabilitation after brain damage. J Speech Lang Hear Res 2008 Feb;51(1):S225-S239. [doi: 10.1044/1092-4388(2008/018)] [Medline: 18230848] 15. Kleim JA, Jones TA. Principles of experience-dependent neural plasticity: implications for rehabilitation after brain damage. J Speech Lang Hear Res 2008 Feb;51(1):S225-S239. [doi: 10.1044/1092-4388(2008/018)] [Medline: 18230848] 15. Kleim JA, Jones TA. Principles of experience-dependent neural plasticity: implications for rehabilitation after brain damage. J Speech Lang Hear Res 2008 Feb;51(1):S225-S239. [doi: 10.1044/1092-4388(2008/018)] [Medline: 18230848]
16. Krakauer JW. Motor learning: its relevance to stroke recovery and neurorehabilitation. Curr Opin Neurol 2006
F b 19(1) 84 90 [M dli
16415682] 16. Krakauer JW. Motor learning: its relevance to stroke recovery and neurorehabilitation. Curr Opin Neurol 2006
Feb;19(1):84-90. [Medline: 16415682] 16. Krakauer JW. Motor learning: its relevance to stroke recovery and neurorehabilitation. Curr Opin Neurol 2006
Feb;19(1):84-90. [Medline: 16415682] 17. Kreisel SH, Hennerici MG, Bäzner H. Pathophysiology of stroke rehabilitation: the natural course of clinical recovery,
use-dependent plasticity and rehabilitative outcome. Cerebrovasc Dis 2007;23(4):243-255. [doi: 10.1159/000098323]
[Medline: 17192704] 18. Mawson S, Nasr N, Parker J, Zheng H, Davies R, Mountain G. Developing a personalised self-management system for
post stroke rehabilitation; utilising a user-centred design methodology. Disabil Rehabil Assist Technol 2014 Nov;9(6):521-528. [doi: 10.3109/17483107.2013.840863] [Medline: 24131371] 19. Pawson R, Tilley N. Realistic evaluation. London: Sage; 1997. 20. Pawson R. Quality and Quantity, Agency and Structure, Mechanism and Context, Dons and Cons 1. Bulletin de Méthodologie
Sociologique 1995 Jun 01;47(1):5-48. [doi: 10.1177/075910639504700103] 21. Mountain G, Wilson S, Eccleston C, Mawson S, Hammerton J, Ware T, et al. Developing and testing a telerehabilitation
system for people following stroke: issues of usability. J Eng Design 2010 Apr;21(2):223-236. [doi:
10.1080/09544820903333792] 22. Parker J, Mawson S, Mountain G, Nasr N, Davies R, Zheng H. References Preventing stroke: saving lives around the world. Lancet Neurol 2007 Feb;6(2):182-187. [doi: 10.1016/S1474-4422(07)70031-5] [Medline: 17239805] 7. Strong K, Mathers C, Bonita R. Preventing stroke: saving lives around the world. Lancet Neurol 2
[doi: 10.1016/S1474-4422(07)70031-5] [Medline: 17239805] 8. Langhorne P, Bernhardt J, Kwakkel G. Stroke rehabilitation. Lancet 2011 May 14;377(9778):1693-1702. [doi:
10.1016/S0140-6736(11)60325-5] [Medline: 21571152] 8. Langhorne P, Bernhardt J, Kwakkel G. Stroke rehabilitation. Lancet 2011 May 14;377(9778):1693-1702. [doi:
10.1016/S0140-6736(11)60325-5] [Medline: 21571152] 9. Intercollegiate Stroke Working party. National clinical guideline for stroke, 4th edition. London: Royal College of Physicians;
2012. 9. Intercollegiate Stroke Working party. National clinical guideline for stroke, 4th edition. London: Royal College of Physicians;
2012. 10. Department of Health. National Service Framework for Older People. London, UK: Department of Health; 2001. URL:
http://webarchive.nationalarchives.gov.uk/20130107105354/http://www.dh.gov.uk/PublicationsAndStatistics/Publications/
PublicationsPolicyAndGuidance/PublicationsPAmpGBrowsableDocument/fs/
en?CONTENT ID=4096710&MULTIPAGE ID=4901150&chk=9cv7Ff%20 10. Department of Health. National Service Framework for Older People. London, UK: Department of Health; 2001. URL:
http://webarchive.nationalarchives.gov.uk/20130107105354/http://www.dh.gov.uk/PublicationsAndStatistics/Publications/
PublicationsPolicyAndGuidance/PublicationsPAmpGBrowsableDocument/fs/
en?CONTENT_ID=4096710&MULTIPAGE_ID=4901150&chk=9cv7Ff%20 11. Mawson SJ, Mountain GM. The SMART rehabilitation system for stroke self-management: issues and challenges for
evidence-based health technology research. J Phys Ther Educ 2011;25:48. [doi: 10.3109/17483107.2013.840863] 12. Zheng H, Nugent C, McCullagh P, Huang Y, Zhang S, Burns W, et al. Smart self management: assistive technology to
support people with chronic disease. J Telemed Telecare 2010;16(4):224-227. [doi: 10.1258/jtt.2010.004017] [Medline:
20511581] JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.10
(page number not for citation purposes) JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.10
(page number not for citation purposes) http://rehab.jmir.org/2016/1/e1/ XSL•FO
RenderX JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.11
(page number not for citation purposes) JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES The provision of feedback through computer-based technology
to promote self-managed post-stroke rehabilitation in the home. Disabil Rehabil Assist Technol 2014 Nov;9(6):529-538. [doi: 10.3109/17483107.2013.845611] [Medline: 24131369] 23. Parker J, Mawson S, Mountain G, Nasr N, Zheng H. Stroke patients' utilisation of extrinsic feedback from computer-based
technology in the home: a multiple case study realistic evaluation. BMC Med Inform Decis Mak 2014;14:46 [FREE Full
text] [doi: 10.1186/1472-6947-14-46] [Medline: 24903401] 24. Roux A. Teler™: The Concept. Physiotherapy 1993 Nov;79( . Roux A. Teler™: The Concept. Physiotherapy 1993 Nov;79(11):755-758. [doi: 10.1016/S0031-9406( 25. Bartlett YK, Haywood A, Bentley CL, Parker J, Hawley MS, Mountain GA, et al. The SMART personalised self-management
system for congestive heart failure: results of a realist evaluation. BMC Med Inform Decis Mak 2014;14:109 [FREE Full
text] [doi: 10.1186/s12911-014-0109-3] [Medline: 25421307] 26. Le Roux AA. The method of measurement: theory and practice. Sheffield: TELER; 2003. 26. Le Roux AA. The method of measurement: theory and practice. Sheffield: TELER; 2003. ux AA. The method of measurement: theory and prac 27. Brooke J. A “quick and dirty” usability scale. In: Jordan PW, Weerdmeester BA, McClelland A, editors. Usability Evaluation
in Industry. London: Taylor and Francis; 1996. 28. Pawson RD, Wong G, Owen L. Legislating for health: locating the evidence. J Pub Health Policy 2
[doi: 10.1057/jphp.2010.5] 28.
Pawson RD, Wong G, Owe
[doi: 10.1057/jphp.2010.5] [
jp p
]
29. DAVIES R, McCullagh P, Zheng H, Nugent CJ, Mawson S. A self-management System for Rehabilitation of stroke
survivers. In preparation 2015:- (forthcoming)(forthcoming). [
jp p
]
29. DAVIES R, McCullagh P, Zheng H, Nugent CJ, Mawson S. A self-management System for Rehabilitation of stroke
survivers. In preparation 2015:- (forthcoming)(forthcoming). p p
(
g)(
g)
30. Yin RK. Case study research: Design and methods. Thousand Oaks, CA: Sage; 2013. p p
(
g)(
g)
30. Yin RK. Case study research: Design and methods. Thousand Oaks, CA: Sage; 2013. 30. Yin RK. Case study research: Design and methods. Thousand Oaks, CA: Sage; 2013. 31. Pope CMN. Qualitative methods in health research. In: Qualitative Research in Healthcare (3rd ed). Oxford UK: BMJ
Books, Blackwell Publishing Ltd; 2006. 31. Pope CMN. Qualitative methods in health research. In: Qualitative Research in Healthcare (3rd ed). Oxford UK: BMJ
Books, Blackwell Publishing Ltd; 2006. 32. Pope C, Ziebland S, Mays N. Analysing qualitative data. In: Pope C, Mays N, editors. Qualitative R
(3rd ed). Oxford, UK: Blackwell Publishing Ltd; 2006. 33. Miles MB. The qualitative researcher's companion. Thousand Oaks, CA: Sage Publications; 2002. 33. Miles MB. The qualitative researcher's companion. Thousand Oaks, CA: Sage Publications; 20 34. Patton MQ. Utilization-Focused Evaluation. London: Sage Publications, Inc; 2008. 35. Rycroft-Malone J, Wilkinson JE, Burton CR, Andrews G, Ariss S, Baker R, et al. Implementing health research through
academic and clinical partnerships: a realistic evaluation of the Collaborations for Leadership in Applied Health Research
and Care (CLAHRC). Implement Sci 2011;6:74 [FREE Full text] [doi: 10.1186/1748-5908-6-74] [Medline: 21771329]
36. Patton MQ. Developmental Evaluation: Applying Complexity Concepts to Enhance Innovation and Use. New York: The
Guilford Press; 2011. 35. Rycroft-Malone J, Wilkinson JE, Burton CR, Andrews G, Ariss S, Baker R, et al. Implementing health research through
academic and clinical partnerships: a realistic evaluation of the Collaborations for Leadership in Applied Health Research
and Care (CLAHRC). Implement Sci 2011;6:74 [FREE Full text] [doi: 10.1186/1748-5908-6-74] [Medline: 21771329] Abbreviations
CMO: contexts, mechanisms, and outcomes
CMOC: mechanism, context, and outcome configurations
FES: functional electrical stimulation
ICT: information communication technology
KR: knowledge of results
PSMrS: Personalized Self-Management Rehabilitation System
RE: realist evaluation http://rehab.jmir.org/2016/1/e1/ Abbreviations Abbreviations
CMO: contexts, mechanisms, and outcomes
CMOC: mechanism, context, and outcome configurations
FES: functional electrical stimulation
ICT: information communication technology
KR: knowledge of results
PSMrS: Personalized Self-Management Rehabilitation System
RE: realist evaluation JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.11
(page number not for citation purposes) http://rehab.jmir.org/2016/1/e1/ XSL•FO
RenderX XSL•FO
RenderX Mawson et al JMIR Rehabil Assist Technol 2016 | vol. 3 | iss. 1 | e1 | p.12
(page number not for citation purposes) JMIR REHABILITATION AND ASSISTIVE TECHNOLOGIES SUS: System Usability Scale
TELER: system for making and presenting clinical notes on a patient so that they can be used to establish the
effectiveness of the treatment or care SUS: System Usability Scale
TELER: system for making and presenting clinical notes on a patient so that they can be used to establish the
effectiveness of the treatment or care Edited by G Eysenbach; submitted 03.09.15; peer-reviewed by CL Hung; comments to author 07.10.15; revised version received
30.10.15; accepted 01.11.15; published 07.01.16 Please cite as:
Mawson S, Nasr N, Parker J, Davies R, Zheng H, Mountain G
A Personalized Self-Management Rehabilitation System with an Intelligent Shoe for Stroke Survivors: A Realist Evaluation
JMIR Rehabil Assist Technol 2016;3(1):e1
URL: http://rehab.jmir.org/2016/1/e1/
doi:10.2196/rehab.5079
PMID: ©Susan Mawson, Nasrin Nasr, Jack Parker, Richard Davies, Huiri Zheng, Gail Mountain. Originally published in JMIR
Rehabilitation and Assistive Technology (http://rehab.jmir.org), 07.01.2016. 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, first published in JMIR Rehabilitation and Assistive
Technology, is properly cited. The complete bibliographic information, a link to the original publication on http://rehab.jmir.org/,
as well as this copyright and license information must be included. http://rehab.jmir.org/2016/1/e1/ http://rehab.jmir.org/2016/1/e1/ XSL•FO
RenderX
|
https://openalex.org/W4390029495
|
https://www.e3s-conferences.org/articles/e3sconf/pdf/2023/104/e3sconf_9th-iccc_01022.pdf
|
English
| null |
Impacts of seawater level and human activities on Yeh Gangga Beach’s coastal area at Tabanan Town
|
E3S web of conferences
| 2,023
|
cc-by
| 3,190
|
© The Authors, published by EDP Sciences. This is an open access article distributed under the terms of the Creative Commons
Attribution License 4.0 (https://creativecommons.org/licenses/by/4.0/). * Corresponding author: rajendra@unud.ac.id Impacts of seawater level and human activities
on Yeh Gangga Beach’s coastal area at Tabanan
T Anom Rajendra1*, I Wayan Wiryawan1, I Ketut Mudra1 dayana University, Architecture Department, Bukit Jimbaran, Badung, Bali Abstract. The coastal environment of Bali has undergone significant
changes due to rising seawater levels and human activities associated with
tourism. As a result, public beach areas have become narrower, which has
marginalized public interest and religious activities, particularly in coastal
tourist resorts. To address this issue, this research focuses on Yeh Gangga's
coastal area in Tabanan Regency, which is a crucial ritual site for the
Tabanan Town Community, a traditional fisherman's territory, and a
location of conflicts of interest among parties in the use of the beach. Empirical studies in the field, including observation, institutional data, and
theories, were conducted to gather data. From the results of in-depth
interviews conducted by a number of residents, they said that erosion has
been going on for a long time and it is estimated that 20-50 meters of the
coast towards the mainland has become the sea. Hence, the main objective
of this research is to provide factual evidence of the decreasing public
coastal areas as public spaces in Yeh Gangga Beach and to suggest that the
local authorities build an organization body for integrated coastal zone
management. The findings of this research will benefit academic purposes,
urban planners, and local authorities. https://doi.org/10.1051/e3sconf/202346701022 https://doi.org/10.1051/e3sconf/202346701022 E3S Web of Conferences 467, 01022 (2023)
9th ICCC 2023 1 Introduction The impacts of rising sea levels and erosion have already wrought significant damage on the
coastal environment, even in highly visited locations such as Bali Island. It is imperative that
we take steps to address these issues to safeguard these regions and the communities that
depend on them. It has been noted by Ewing that Sea Level Rise (SLR) can lead to erosion
and is caused by extreme temperatures, storms, and global warming, which are all significant
factors in coastal areas [1]. Recent risk studies and climate change adaptation plans have
revealed that the island of Bali has experienced an SLR rate of around 3.5 mm/year to 8.0
mm/year based on historical data, including tidal data in Benoa and altimetry data [2]. This
has hurt the development of coastal areas, causing changes in coastlines due to erosion [3]. p
g
g
In addition to natural factors, human activities such as land clearing and mineral
exploitation on coastal land can also contribute to changes in the coastline and affect its
balance. The coastline is dynamic and can shift according to tidal conditions, making it E3S Web of Conferences 467, 01022 (2023)
9th ICCC 2023 https://doi.org/10.1051/e3sconf/202346701022 crucial for development planning and coastal protection efforts [4]. The Bali coastal area
experiences various geographic processes that contribute to coastal damage through erosion
and accretion, with the vulnerability of the beach itself being a major factor. The interaction
between oceanographic aspects can also cause changes in coastlines [5]. Understanding
changes in coastlines and coastal vulnerability is critical for effective management of Bali's
coastal areas. crucial for development planning and coastal protection efforts [4]. The Bali coastal area
experiences various geographic processes that contribute to coastal damage through erosion
and accretion, with the vulnerability of the beach itself being a major factor. The interaction
between oceanographic aspects can also cause changes in coastlines [5]. Understanding
changes in coastlines and coastal vulnerability is critical for effective management of Bali's
coastal areas. Moreover, the conversion of agricultural land to accommodate the growing population in
Bali has led to the development of built environments and tourist accommodations along the
coast. This has resulted in the shrinking of coastal areas and negative impacts on the
environment and public interests. Unfortunately, land use practices that prioritize short-term
gains without conservation efforts have led to the marginalization of public interests in
coastal areas and the degradation of the environment. 1 Introduction Weak policies and management have
exacerbated these issues, causing losses in the agriculture and fisheries sectors. Research
results have also clarified that the marginalization of public interests in coastal areas and the
degradation of the coastal environment have been commonly caused by weak policies and
management [6], bringing implications for losses in the fisheries and agriculture sectors [7]. To address these problems, Yeh Gangga Beach was chosen as a research location due to
its strategic location for Tabanan community activities, traditional fishing practices, and the
developing tourism industry. Despite severe erosion, the beach now accommodates tourist,
religious, and fishing activities, while public space on the coast has decreased. This has led
to conflicts of interest among parties. To address these issues, this research aims to determine
the extent of erosion and its future impact, as well as the management of coastal areas as
public spaces. 2.2 Sea Level Rise (SLR) & storm surge The rise of sea levels due to global warming plays a significant role in the changes happening
in coastal areas [1]. It is one of the factors accelerating erosion rates, altering coastlines, and
increasing inundation areas along the coast. Marine ecosystems and beaches are also at risk
when sea levels and temperatures exceed the limits of marine biota to adapt [10]. Storm
surges, especially from tropical storms, can cause serious disasters in coastal areas,
particularly in tropical and sub-tropical zones [11]. These surges, caused by wind and
pressure from cyclones, frequently hit coastal waters in the Indian Ocean, including Java,
Bali, and West Nusa Tenggara. They can lead to flooding, relocation of people, and
disruption of tourism and economic activities in the area. A simulation study revealed that
the vulnerability to storm surge events is highest along the south coast of Java, Bali, and West
Nusa Tenggara , where the highest surge was recorded at 19.0 cm [12]. 2 Literature review There are several important concepts from the literature that will guide this research,
including the definitions of coast and beach, sea level rise and surge storm, and coastal area. 2.1 Coast and beach The coast is an interface between land and sea ecosystems that holds immense potential for
natural resources and environmental services [8], [9]. Law No. 27 of 2007 recognizes coastal
areas as transitional zones that are influenced by changes in land and sea. These areas can be
defined as the meeting point of land and sea or the downstream areas with clear boundaries
on the side that borders the sea. Although the terms "coast" and "beach" are often used
interchangeably, they have different meanings. 2.3 The coast/beach erosion Coastal erosion occurs when currents and waves cause the land to move to another location. If a sandy beach is affected, the sand will be transported parallel to the coast or into the deep 2 E3S Web of Conferences 467, 01022 (2023)
9th ICCC 2023 https://doi.org/10.1051/e3sconf/202346701022 sea. Beach erosion occurs when sand is moved due to water and wind factors and also as the
result of water flow breaking and transporting sand over the surface [8]. The erosion process
consists of three parts: detachment, transportation, and sedimentation [13]. The size of the
eroded sand depends on the intensity and type of erosion, as well as the variables that affect
the process. Climate, coastal material, topography, and vegetation cover are the four factors
that determine erosion, and they are used to calculate erosion size with the Universal Soil
Loss Equation (USLE) [14]. 3 Research method Interestingly, only 7.16% of the entire beach
length which is a total of 30.18 km. It falls within the Tabanan Regency (Table 1). 3 Research method This research uses a descriptive quantitative method, in which a selected site was based on
several reasons fulfilling the research objective. The data that has been obtained was analyzed
systematically to generate coastal erosion process data and its impacts. To get a treatment
strategy for coastal erosion. it was carried out through literature studies. The data in this
research includes secondary data and primary data. Data secondary are from the existing,
such as from related research, previous measurements, and observations. These secondary
data were expected to support the research. The secondary data included wind data, tidal data,
and research results which have been done before. Meanwhile, primary data was obtained
through survey activities in the form of observation such as measurement of coastal
morphological data, wind speed and wave, and current coastline data, whilst direct interview
activities were carried out in the field. Yeh Gangga Beach is a picturesque destination located in Sudimara Village, Tabanan
District, Tabanan Regency. Source: Google Map
Figure 1. Map of Research Location
It is approximately 11 km away from the center of Tabanan City, 9 km from the renowned
Tanah Lot Temple, and roughly 31 km from I Gusti Ngurah Rai International Airport (Figure
1). This stunning beach is situated in the southern part of Tabanan Town facing the Indian
Ocean, boasting a coastline that spans 2.16 km. Interestingly, only 7.16% of the entire beach
length which is a total of 30.18 km. It falls within the Tabanan Regency (Table 1). Source: Google Map Figure 1. Map of Research Location It is approximately 11 km away from the center of Tabanan City, 9 km from the renowned
Tanah Lot Temple, and roughly 31 km from I Gusti Ngurah Rai International Airport (Figure
1). This stunning beach is situated in the southern part of Tabanan Town facing the Indian
Ocean, boasting a coastline that spans 2.16 km. Interestingly, only 7.16% of the entire beach
length which is a total of 30.18 km. It falls within the Tabanan Regency (Table 1). It is approximately 11 km away from the center of Tabanan City, 9 km from the renowned
Tanah Lot Temple, and roughly 31 km from I Gusti Ngurah Rai International Airport (Figure
1). This stunning beach is situated in the southern part of Tabanan Town facing the Indian
Ocean, boasting a coastline that spans 2.16 km. 4.1 Result Based on research conducted by PT Parama Kridha Pratama Consultants, erosion has affected
Yeh Gangga Beach over a distance of 1.13 km at a rate of 1.58m/year. Unfortunately, only 3 E3S Web of Conferences 467, 01022 (2023)
9th ICCC 2023 https://doi.org/10.1051/e3sconf/202346701022 60% of this erosion was addressed in 2015. This erosion has resulted in severe environmental
damage, with the sand loss categorized as heavy at 1.58m/year. The prioritized weight for
treatment is between 400 to 499, emphasizing the urgent need for treatment at Yeh Gangga
Beach. 60% of this erosion was addressed in 2015. This erosion has resulted in severe environmental
damage, with the sand loss categorized as heavy at 1.58m/year. The prioritized weight for
treatment is between 400 to 499, emphasizing the urgent need for treatment at Yeh Gangga
Beach. Table 1. List of beach section names according to their village in Tabanan Regency. No
Name of Coast Section
Village
Coastline -
Citra SPOT
(km)
1
Nyanyi and Tanah Lot
Beraban
3.18
2
Kedungu
Belalang
0.99
3
Pangkung Tibah
Pangkung Tibah
2.18
4
Yeh Gangga
Sudimara
2.16
5
Kelating
Kelating
1.39
6
Tibu Biyu
Tibu Biyu
2.36
7
Beraban, Pasut and Abian Kapas
Beraban
1.19
8
Tegal Mengkeb and Klicung
Tegal Mengkeb
2.07
9
Brembeng
Brembeng
0.15
10
Soka and Srijong
Antap
6.70
11
Lalanglinggah, Mekayu and
Balian
Lalang Linggah
4.80
12
Selabih
Selabih
3.01
Tabanan Regency
30.18
Source: Consultan Engnineering of PT. Parama Kridha Pratama. ble 1. List of beach section names according to their village in Tabanan Regency. Since being designated as a special tourist attraction area (Kawasan Daerah Tujuan
Wisata Khusus/KDTWK) under Tabanan Regency Regional Regulation No. 11/2012, Yeh
Gangga Beach has experienced rapid development in its tourism industry. What was once a
location for fishing and rituals has now become a destination for both domestic and foreign
tourists. As the number of visitors to the area has increased, so too has the growth in tourism
facilities, including hotels, villas, restaurants, and recreational activities. This trend began in
2000 and has reached its peak in the last decade (Figure 2). Figure 2. The images of building facilities at Yeh Gangga Beach Figure 2. The images of building facilities at Yeh Gangga Beach 4.2.1 The impact of erosion It was discovered through interviews with residents and the head of Sudimara Village that
the Yeh Gangga coastline has retreated by 20-50 meters. Studies using commercial GIS and 4 https://doi.org/10.1051/e3sconf/202346701022 E3S Web of Conferences 467, 01022 (2023)
9th ICCC 2023 CAD software have also revealed that erosion has affected over 50% of the 2.16 km-long
Yeh Gangga Beach, equating to 1.15 km in total. The average yearly loss of coastal area is
1.58 meters, indicating that the beach will lose approximately 47.4 meters of coastal area
within the next 30 years. This will result in a loss of 48,111 square meters (or 4,811 hectares)
of coastal area, using the length of erosion as 1.15 km. If the estimated price range for the
coastal area is 7 million rupiah/m2, the total loss would amount to a staggering 336,777
billion rupiah. These losses are not just economic, but also social, cultural, and political, as
they result in a loss of open spaces for public use. Furthermore, beaches affected by erosion
will become longer and wider, leading to more severe environmental damage. It is certainly
a sad outcome that will have far-reaching impacts. 4.2.3 The eroded beach handling strategies The issue of erosion and its impact on coastal areas is a pressing concern that requires
immediate action. To effectively resolve this problem, it is important to establish a
management body that is representative of all parties involved in coastal use. This body's
primary objective is to prevent violations of coastal boundaries and preserve the area. Based
on the experience of managing beaches in other parts of Bali, the management body should
consist of four elements: indigenous communities, tourism service entrepreneurs, local
government, and expert groups or academics to ensure democratic decision-making. Since
handling erosion requires a significant amount of funds, cooperation and donations from all
parties are necessary. Furthermore, continuous and sustainable conservation measures must
be implemented to ensure long-term success. Without taking these steps, proper handling of
erosion will be impossible. 4.2.2 The impact of human activities Development in the Yeh Gangga Beach Area was not followed by a strict zoning plan by
considering and implementing the coastal border in accordance with existing regulations. The
weak building permitting process has resulted in the construction of buildings that are not in
accordance with existing regulations, especially the implementation of the coastal border. Based on Presidential Decree No.32 / 1990 and other regulations, it is stated that the coastline
is 100m measured from the highest tide point towards the mainland. This proves how weak
the application of regulations is in granting building permits. Because of the violation of this
boundary, the building directly takes up the beach space in front of it. Loss of beach space is
not only caused by erosion but also by utilization by individuals/groups at the expense of the
public interest. In fact, the beach space that is still in front of it is used for the benefit of the
owner of the building behind it for the sole purpose of commercial interests, ignoring the
public interest. 5 Conclusion Erosion taking place in Yeh Gangga Beach will never stop as long as climate change still
exists on the earth. Climate change will raise the sea water level and then cover the land to
become part of the sea. Without real protection, erosion will become larger and more
widespread, resulting in greater loss of land as coastal space. The existence of fishing
activities, rituals, and recreational activities for the community will be threatened. Whilst,
human activities, especially physical development to support their commercial and tourist
activities, which tend to violate coastal boundaries in regulating the distance from buildings
to the beach, have become another threat to the loss of coastal space. Coastal space is very
crucial in its existence at this time, where its existence in plants will be lost without efforts
and efforts to overcome it. To handle this problem, an integrated management body is needed
which consists of four elements: local indigenous communities, tourism and other
commercial service entrepreneurs, local government, and experts/academics. 5 https://doi.org/10.1051/e3sconf/202346701022 E3S Web of Conferences 467, 01022 (2023)
9th ICCC 2023 The majority of this article derives from historical and empirical studies and observations. We would
like to thank to Tabanan Government and the head of Sudimara Village for supporting additional
documents. Also special thanks to the Department of Architecture, Faculty of Engineering, Udayana
University for their support in encouraging the completion of this article, as well as the Rector of
Udayana University for their support. The majority of this article derives from historical and empirical studies and observations. We would
like to thank to Tabanan Government and the head of Sudimara Village for supporting additional
documents. Also special thanks to the Department of Architecture, Faculty of Engineering, Udayana documents. Also special thanks to the Department of Architecture, Faculty of Engineering, Udayana
University for their support in encouraging the completion of this article, as well as the Rector of
Udayana University for their support. University for their support in encouraging the completion of this article, as well as the Rector of
Udayana University for their support. References 1. L. Ewing, in Handb. Coast. Ocean Eng. (World Scientific, 2010), pp. 997–1021 2. H. Bachtiar, J. Sumber Daya Air 8, 157 (2012) 3. F. M. Fajrin, M. R. Muskananfola, and B. Hendrarto, Manag. Aquat. Resour. J. 5, 43
(2016) 4. N. Anggraini, S. Marpaung, and M. Hartuti, J. Penginderaan Jauh Dan Pengolah. Data
Citra Digit. 14, (2018) 5. S. Sakka, P. Paharuddin, and E. Rupang, Torani J. Fish. Mar. Sci. 24, (2014)
6
J Juhadi J Geogr (2007) 5. S. Sakka, P. Paharuddin, and E. Rupang, Torani J. Fish. Mar. Sci. 24, (2014) 5. S. Sakka, P. Paharuddin, and E. Rupang, Torani J. Fish. Mar. Sci. 24, (2014)
6. J. Juhadi, J. Geogr. (2007) 6. J. Juhadi, J. Geogr. (2007) 7. J. Sihite, Southeast Asia Policy Res. Work. Pap. 91 (2001) 8. J. R. Clark, Ocean Coast. Manag. 37, 191 (1997) 9. O. S. Djunaedi, Bandung: Widya Padjajaran (2011) 10. H. Latief and O. Dominic, Minist. Environ. Indones. (2010) 11. I. P. Samskerta, H. Bachtiar, and F. Riandini, Kolok. Pus. Penelit. Dan Pengemb
Sumber Daya Air 1 (2011) 11. I. P. Samskerta, H. Bachtiar, and F. Riandini, Kolok. Pus. Penelit. Dan Pengemb. Sumber Daya Air 1 (2011) 14. C. Asdak, Hidrologi Dan Pengelolaan Daerah Aliran Sungai (UGM PRESS, 202 Sumber Daya Air 1 (2011) 12. N. S. Ningsih, S. Hadi, A. B. Harto, M. D. Utami, and A. P. Rudiawan, ILMU Kelaut
Indones. J. Mar. Sci. 15, 179 (2010) 12. N. S. Ningsih, S. Hadi, A. B. Harto, M. D. Utami, and A. P. Rudiawan, ILMU Kelaut. Indones. J. Mar. Sci. 15, 179 (2010) 13. M. E. R. Alie, (2015) 14. C. Asdak, Hidrologi Dan Pengelolaan Daerah Aliran Sungai (UGM PRESS, 2023) 14. C. Asdak, Hidrologi Dan Pengelolaan Daerah Aliran Sungai (UGM PRESS, 2023) 6 6
|
https://openalex.org/W4238899189
|
https://peerj.com/articles/4147v0.2/submission
|
English
| null |
Peer Review #1 of "Epigenetic considerations in aquaculture (v0.1)"
| null | 2,017
|
cc-by
| 17,775
|
Mackenzie Gavery 1 , Steven Roberts Corresp. 1 1 School of Aquatic & Fishery Sciences, University of Washington
Corresponding Author: Steven Roberts
Email address: sr320@u.washington.edu Epigenetics has attracted considerable attention with respect to its potential value in many
areas of agricultural production, particularly under conditions where the environment can
be manipulated or natural variation exists. Here we introduce key concepts and definitions
of epigenetic mechanisms, including DNA methylation, histone modifications and non-
coding RNA, review the current understanding of epigenetics in both fish and shellfish, and
propose key areas of aquaculture where epigenetics could be applied. The first key area is
environmental manipulation, where the intention is to induce an ‘epigenetic memory’
either within or between generations to produce a desired phenotype. The second key
area is epigenetic selection, which, alone or combined with genetic selection, may increase
the reliability of producing animals with desired phenotypes. Based on aspects of life
history and husbandry practices in aquaculture species, the application of epigenetic
knowledge could significantly affect the productivity and sustainability of aquaculture
practices. Conversely, clarifying the role of epigenetic mechanisms in aquaculture species
may upend traditional assumptions about selection practices. Ultimately, there are still
many unanswered questions regarding how epigenetic mechanisms might be leveraged in
aquaculture. Manuscript to be reviewed Epigenetic considerations in aquaculture
Mackenzie Gavery, Steven Roberts*
School of Aquatic and Fishery Sciences, University of Washington. Seattle, WA, USA
*Corresponding Author:
Steven B. Roberts
1122 NE Boat St., Seattle, WA, 98122, USA
Email address: sr320@uw.edu
1
2
3
4
5
6
7
8
9
10
Manuscript to be reviewe Manuscript to be reviewed PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Epigenetic considerations in aquaculture
Mackenzie Gavery, Steven Roberts*
School of Aquatic and Fishery Sciences, University of Washington. Seattle, WA, USA
*Corresponding Author:
Steven B. Roberts
1122 NE Boat St., Seattle, WA, 98122, USA
Email address: sr320@uw.edu
1
2
3
4
5
6
7
8
9
10
Manuscript to be review Epigenetic considerations in aquaculture
Mackenzie Gavery, Steven Roberts*
School of Aquatic and Fishery Sciences, University of Washington. Seattle, WA, USA
*Corresponding Author:
Steven B. Roberts
1122 NE Boat St., Seattle, WA, 98122, USA
Email address: sr320@uw.edu
1
2
3
4
5
6
7
8
9
10
Manuscript to be reviewed Epigenetic considerations in aquaculture
Mackenzie Gavery, Steven Roberts*
School of Aquatic and Fishery Sciences, University of Washington. Seattle, WA, USA
*Corresponding Author:
Steven B. Roberts
1122 NE Boat St., Seattle, WA, 98122, USA
Email address: sr320@uw.edu
1
2
3
4
5
6
7
8
9
10
Manuscript to be reviewed Epigenetic considerations in aquaculture
1 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Abstract:
Epigenetics has attracted considerable attention with respect to its potential value in many
areas of agricultural production, particularly under conditions where the environment can
be manipulated or natural variation exists. Here we introduce key concepts and definitions
of epigenetic mechanisms, including DNA methylation, histone modifications and non-
coding RNA, review the current understanding of epigenetics in both fish and shellfish, and
propose key areas of aquaculture where epigenetics could be applied. The first key area is
environmental manipulation, where the intention is to induce an ‘epigenetic memory’ either
within or between generations to produce a desired phenotype. The second key area is
epigenetic selection, which, alone or combined with genetic selection, may increase the
reliability of producing animals with desired phenotypes. Based on aspects of life history
and husbandry practices in aquaculture species, the application of epigenetic knowledge
could significantly affect the productivity and sustainability of aquaculture practices. Conversely, clarifying the role of epigenetic mechanisms in aquaculture species may upend
traditional assumptions about selection practices. Ultimately, there are still many
unanswered questions regarding how epigenetic mechanisms might be leveraged in
aquaculture. 11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27 Abstract:
11 In salmonids, there is some evidence that changes in DNA
methylation are associated with variation in life-history phenotypes including early male
maturation (Morán & Pérez-Figueroa, 2011), smoltification (Morán et al., 2013), anadromy
(Baerwald et al., 2016) and growth potential (Burgerhout et al., 2017). Recent studies in
European sea bass and rainbow trout examined the role of epigenetics in mediating
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
p mechanisms (or ‘marks’), including DNA methylation, histone modifications and non-coding
RNA activity, influence gene expression primarily through the local modification of
chromatin. Unlike DNA, epigenetic marks can be directly influenced by the environment,
and therefore have been shown to be important mediators of phenotypic responses to
environmental signals (Figure 1). For example, in mammals, nutrition (Weaver et al., 2004),
exposure to toxins (Dolinoy et al., 2006), and photoperiod (Azzi et al., 2014) have all been
associated with changes in DNA methylation and concomitant changes in phenotype. DNA
methylation patterns in fish show a similar sensitivity to the environment (Wang et al.,
2009; Strömqvist, Tooke & Brunström, 2010; Campos et al., 2013; Artemov et al., 2017). While many environmentally-induced epigenetic changes are transient, some may persist
over the course of an organism’s lifetime (Weaver et al., 2004; Dolinoy et al., 2006; Heijmans
et al., 2008). Evidence of transgenerationally-inherited epigenetic changes has been
reported in vertebrates (Guerrero-Bosagna et al., 2010; Manikkam et al., 2012; Rodgers et
al., 2015; Knecht et al., 2017), invertebrates (Rechavi et al., 2014; Klosin et al., 2017) and
plants (Hauser et al., 2011). Thus, it is important to understand the nature and function of
these mechanisms and their influence on phenotype in fish and shellfish. 41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56 mechanisms (or ‘marks’), including DNA methylation, histone modifications and non-coding
RNA activity, influence gene expression primarily through the local modification of
chromatin. Unlike DNA, epigenetic marks can be directly influenced by the environment,
and therefore have been shown to be important mediators of phenotypic responses to
environmental signals (Figure 1). Abstract:
11 Abstract:
Epigenetics has attracted considerable attention with respect to its potential value in many
areas of agricultural production, particularly under conditions where the environment can
be manipulated or natural variation exists. Here we introduce key concepts and definitions
of epigenetic mechanisms, including DNA methylation, histone modifications and non-
coding RNA, review the current understanding of epigenetics in both fish and shellfish, and
propose key areas of aquaculture where epigenetics could be applied. The first key area is
environmental manipulation, where the intention is to induce an ‘epigenetic memory’ either
within or between generations to produce a desired phenotype. The second key area is
epigenetic selection, which, alone or combined with genetic selection, may increase the
reliability of producing animals with desired phenotypes. Based on aspects of life history
and husbandry practices in aquaculture species, the application of epigenetic knowledge
could significantly affect the productivity and sustainability of aquaculture practices. Conversely, clarifying the role of epigenetic mechanisms in aquaculture species may upend
traditional assumptions about selection practices. Ultimately, there are still many
unanswered questions regarding how epigenetic mechanisms might be leveraged in
aquaculture. 11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27 Introduction
Maintaining and improving aquaculture production requires an understanding of genetic
and physiological mechanisms that control desired traits. Elucidation of these mechanisms
has led to the development of pioneering biotechnological methods that have important
applications. For example, molecular markers are used in broodstock selection and
transcriptomic studies have been used to improve environmental conditions to decrease
physiological stress in animals. Recently, interest in epigenetics within the agricultural
community has surged as it has become more clear that epigenetic mechanisms can provide
a measurable link between environment and phenotype. Epigenetics refers to processes that result in heritable alterations in gene activity
without manipulating the underlying DNA sequence (Jablonka & Lamb, 2002). Epigenetic
28
29
30
31
32
33
34
35
36
37
38
39
40 Epigenetics refers to processes that result in heritable alterations in gene activity
without manipulating the underlying DNA sequence (Jablonka & Lamb, 2002). Epigenetic
39
40 Epigenetics refers to processes that result in heritable alterations in gene activity
without manipulating the underlying DNA sequence (Jablonka & Lamb, 2002). Abstract:
11 Epigenetic
39
40 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed mechanisms (or ‘marks’), including DNA methylation, histone modifications and non-coding
RNA activity, influence gene expression primarily through the local modification of
chromatin. Unlike DNA, epigenetic marks can be directly influenced by the environment,
and therefore have been shown to be important mediators of phenotypic responses to
environmental signals (Figure 1). For example, in mammals, nutrition (Weaver et al., 2004),
exposure to toxins (Dolinoy et al., 2006), and photoperiod (Azzi et al., 2014) have all been
associated with changes in DNA methylation and concomitant changes in phenotype. DNA
methylation patterns in fish show a similar sensitivity to the environment (Wang et al.,
2009; Strömqvist, Tooke & Brunström, 2010; Campos et al., 2013; Artemov et al., 2017). While many environmentally-induced epigenetic changes are transient, some may persist
over the course of an organism’s lifetime (Weaver et al., 2004; Dolinoy et al., 2006; Heijmans
et al., 2008). Evidence of transgenerationally-inherited epigenetic changes has been
reported in vertebrates (Guerrero-Bosagna et al., 2010; Manikkam et al., 2012; Rodgers et
al., 2015; Knecht et al., 2017), invertebrates (Rechavi et al., 2014; Klosin et al., 2017) and
plants (Hauser et al., 2011). Thus, it is important to understand the nature and function of
these mechanisms and their influence on phenotype in fish and shellfish. Interest in epigenetics has been gaining ground in agricultural science for crops
(Ong-Abdullah et al., 2015; Álvarez-Venegas & De-la-Peña, 2016) and, more recently,
livestock (Goddard & Whitelaw, 2014; González-Recio, Toro & Bach, 2015), but less is
known about epigenetic mechanisms in economically valuable aquaculture species. Since
most aquaculture operations exist in open or natural conditions that are subject to changes
in the environment, it is important to consider the potential role of epigenetics, particularly
now that tools are available to study these important phenomena. Recent studies in species
ranging from salmonids to sea bass to oysters and mussels have provided the first evidence
that epigenetic mechanisms are associated with commercially important traits in
aquaculture species. In sea bass and half-smooth tongue sole, temperature-induced sex-
determination has been associated with changes in DNA methylation (Navarro-Martin et al.,
2011; Shao et al., 2014). PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed phenotypic responses to various aspects of diet (Marandel et al., 2016; Terova et al., 2016;
Panserat et al., 2017). In Pacific oysters, the role of epigenetics in mediating the effects of
temperature on oyster physiology has been investigated (Fellous, Favrel & Riviere, 2015). Recent efforts have also aimed at understanding the role epigenetics may play in other
important phenomena in aquaculture, including sex control via ploidy manipulation
(Covelo-Soto et al., 2015; Jiang et al., 2016; Zhou et al., 2016), the effects of inbreeding
(Venney et al., 2016) and adaptation to captivity (Le Luyer et al., 2017). This review will introduce key concepts and definitions of epigenetic mechanisms,
briefly review the literature as it pertains to the nascent field of epigenetics in aquatic
species and highlight key aspects of aquaculture that could benefit from a deeper
understanding of the role of epigenetics. Several excellent reviews of epigenetics, primarily
DNA methylation, and various aspects of finfish aquaculture (e.g. Li & Leatherland, 2013;
Moghadam, Mørkøre & Robinson, 2015; Labbe et al., 2017) have recently been published,
and these will be highlighted where appropriate. Survey methodology
The authors have been actively involved in epigenetic research over the past decade,
primarily in shellfish, and more recently in finfish (Gavery). As part of this research, we have
performed extensive literature searches and literature reviews in numerous venues
including, but not limited to, university library catalogs, Web of Science, Google Scholar,
Scopus, and general web searches. In addition, we routinely attend local and international
workshops and conferences focused on epigenetics in shellfish and fish, where we interact
with colleagues who are actively engaged in similar research. Platforms such as Twitter
have also been useful for the discovery of new research and associated manuscripts. What is epigenetics? The following section will briefly describe specific epigenetic marks and review where we
stand in terms of understanding (or not understanding) the relationship between
epigenetics, the environment and phenotype in aquaculture species. DNA methylation
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
Manuscript to be reviewed phenotypic responses to various aspects of diet (Marandel et al., 2016; Terova et al., 2016;
Panserat et al., 2017). Abstract:
11 Recent studies in
European sea bass and rainbow trout examined the role of epigenetics in mediating
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewe Manuscript to be reviewed Manuscript to be reviewed In Pacific oysters, the role of epigenetics in mediating the effects of
temperature on oyster physiology has been investigated (Fellous, Favrel & Riviere, 2015). Recent efforts have also aimed at understanding the role epigenetics may play in other
important phenomena in aquaculture, including sex control via ploidy manipulation
(Covelo-Soto et al., 2015; Jiang et al., 2016; Zhou et al., 2016), the effects of inbreeding
(Venney et al., 2016) and adaptation to captivity (Le Luyer et al., 2017). This review will introduce key concepts and definitions of epigenetic mechanisms,
briefly review the literature as it pertains to the nascent field of epigenetics in aquatic
species and highlight key aspects of aquaculture that could benefit from a deeper
understanding of the role of epigenetics. Several excellent reviews of epigenetics, primarily
DNA methylation, and various aspects of finfish aquaculture (e.g. Li & Leatherland, 2013;
Moghadam, Mørkøre & Robinson, 2015; Labbe et al., 2017) have recently been published,
and these will be highlighted where appropriate. 73
74
75
76
77
78
79
80
81
82
83
84
85
86
87 phenotypic responses to various aspects of diet (Marandel et al., 2016; Terova et al., 2016;
Panserat et al., 2017). In Pacific oysters, the role of epigenetics in mediating the effects of
temperature on oyster physiology has been investigated (Fellous, Favrel & Riviere, 2015). Recent efforts have also aimed at understanding the role epigenetics may play in other
important phenomena in aquaculture, including sex control via ploidy manipulation
(Covelo-Soto et al., 2015; Jiang et al., 2016; Zhou et al., 2016), the effects of inbreeding
(Venney et al., 2016) and adaptation to captivity (Le Luyer et al., 2017). 73
74
75
76
77
78
79 Abstract:
11 For example, in mammals, nutrition (Weaver et al., 2004),
exposure to toxins (Dolinoy et al., 2006), and photoperiod (Azzi et al., 2014) have all been
associated with changes in DNA methylation and concomitant changes in phenotype. DNA
methylation patterns in fish show a similar sensitivity to the environment (Wang et al.,
2009; Strömqvist, Tooke & Brunström, 2010; Campos et al., 2013; Artemov et al., 2017). While many environmentally-induced epigenetic changes are transient, some may persist
over the course of an organism’s lifetime (Weaver et al., 2004; Dolinoy et al., 2006; Heijmans
et al., 2008). Evidence of transgenerationally-inherited epigenetic changes has been
reported in vertebrates (Guerrero-Bosagna et al., 2010; Manikkam et al., 2012; Rodgers et
al., 2015; Knecht et al., 2017), invertebrates (Rechavi et al., 2014; Klosin et al., 2017) and
plants (Hauser et al., 2011). Thus, it is important to understand the nature and function of
these mechanisms and their influence on phenotype in fish and shellfish. 41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56 Interest in epigenetics has been gaining ground in agricultural science for crops
(Ong-Abdullah et al., 2015; Álvarez-Venegas & De-la-Peña, 2016) and, more recently,
livestock (Goddard & Whitelaw, 2014; González-Recio, Toro & Bach, 2015), but less is
known about epigenetic mechanisms in economically valuable aquaculture species. Since
most aquaculture operations exist in open or natural conditions that are subject to changes
in the environment, it is important to consider the potential role of epigenetics, particularly
now that tools are available to study these important phenomena. Recent studies in species
ranging from salmonids to sea bass to oysters and mussels have provided the first evidence
that epigenetic mechanisms are associated with commercially important traits in
aquaculture species. In sea bass and half-smooth tongue sole, temperature-induced sex-
determination has been associated with changes in DNA methylation (Navarro-Martin et al.,
2011; Shao et al., 2014). In salmonids, there is some evidence that changes in DNA
methylation are associated with variation in life-history phenotypes including early male
maturation (Morán & Pérez-Figueroa, 2011), smoltification (Morán et al., 2013), anadromy
(Baerwald et al., 2016) and growth potential (Burgerhout et al., 2017). Manuscript to be reviewed Manuscript to be reviewed Manuscript to be reviewed DNA methylation refers to the enzymatic addition of a methyl group to a cytosine residue in
DNA, which occurs almost exclusively at CpG dinucleotides (i.e. a cytosine located 5’ of a
guanine) in animals. The enzymatic machinery supporting DNA methylation includes a
family of DNA methyltransferases (DNMTs), including the maintenance methyltransferase
DNMT1 (responsible for copying pre-existing DNA methylation patterns to the new strand
during mitosis) and the de novo methyltransferases DNMT3A/3B. DNA methylation is
known to be repressive when located in promoters of genes through associations with other
DNA-binding proteins or through the physical blocking of transcription factors (Bell &
Felsenfeld, 2000). However, DNA methylation in gene bodies is associated with high levels of
expression (Jones, 1999). Therefore, although DNA methylation is typically associated with
silencing, its regulatory role is specific to the genomic context. In mammals, DNA
methylation plays important roles in providing genomic stability through the repression of
transposable elements (TEs) (Maloisel & Rossignol, 1998), genomic imprinting (Bell &
Felsenfeld, 2000), and dosage compensation (Csankovszki, Nagy & Jaenisch, 2001). DNA
methylation is also important for cell-type differentiation and embryonic development (Li,
Bestor & Jaenisch, 1992). DNA methylation is the most well-studied epigenetic mechanism,
and most studies have been done in plants and mammals, in which DNA methylation has
been shown to be sensitive to external factors including nutrition (Weaver et al., 2004),
exposure to toxins (Dolinoy et al., 2006), and photoperiod (Azzi et al., 2014). Importantly,
the meiotic transmission of DNA methylation patterns, and thus the opportunity for
transgenerational epigenetic inheritance through DNA methylation, is rare in mammals,
which undergo extensive DNA methylation reprogramming in the early embryo stage
(Daxinger & Whitelaw, 2012). Transgenerational epigenetic inheritance is more common in
plants, which do not exhibit extensive resetting of DNA methylation between generations
(reviewed by Hauser et al., 2011). As discussed below, it is still unclear if and to what extent
DNA methylation resetting occurs in fish and shellfish. Histone variants and post-translational modifications
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131 DNA methylation refers to the enzymatic addition of a methyl group to a cytosine residue in
DNA, which occurs almost exclusively at CpG dinucleotides (i.e. a cytosine located 5’ of a
guanine) in animals. Survey methodology
88 The authors have been actively involved in epigenetic research over the past decade,
primarily in shellfish, and more recently in finfish (Gavery). As part of this research, we have
performed extensive literature searches and literature reviews in numerous venues
including, but not limited to, university library catalogs, Web of Science, Google Scholar,
Scopus, and general web searches. In addition, we routinely attend local and international
workshops and conferences focused on epigenetics in shellfish and fish, where we interact
with colleagues who are actively engaged in similar research. Platforms such as Twitter
have also been useful for the discovery of new research and associated manuscripts. 89
90
91
92
93
94
95
96 The authors have been actively involved in epigenetic research over the past decade,
primarily in shellfish, and more recently in finfish (Gavery). As part of this research, we have
performed extensive literature searches and literature reviews in numerous venues
including, but not limited to, university library catalogs, Web of Science, Google Scholar,
Scopus, and general web searches. In addition, we routinely attend local and international
workshops and conferences focused on epigenetics in shellfish and fish, where we interact
with colleagues who are actively engaged in similar research. Platforms such as Twitter
have also been useful for the discovery of new research and associated manuscripts. 89
90
91
92
93
94
95
96 What is epigenetics? The following section will briefly describe specific epigenetic marks and review where we
stand in terms of understanding (or not understanding) the relationship between
epigenetics, the environment and phenotype in aquaculture species. DNA methylation
97
98
99
100
101
102
103 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Interestingly, it has been
shown in both mammals and zebrafish that certain modified histones are non-randomly
retained during spermatogenesis when most of these proteins are replaced by protamines,
suggesting that these marks may play a role in transferring epigenetic information to the
embryo (Brykczynska et al 2010; Wu Zhang & Cairns 2011)
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167 core histone proteins (H2A, H2B, H3 and H4). Higher-order chromatin structure is
established via the incorporation of linker histones (H1) between nucleosomes. Chromatin
structure can be modified to either enhance or repress transcription through the
incorporation of histone variants and the post-translational modification of histones
(Berger, 2007). These modified chromatin states can be inherited both mitotically and
meiotically, and thus may convey epigenetic information (Henikoff & Smith, 2015). Histone
variants have specialized functions and can be incorporated into nucleosomes in a
replication-independent manner (Henikoff & Smith, 2015). Although histone variants have
been less-studied than post-translational modifications, they can play an important role in
mediating both short- and long-term responses to environmental cues (Talbert & Henikoff,
2014). Both canonical and variant histones can be post-translationally modified, primarily
at their N-terminal tails, which alters the degree of chromatin compaction resulting in either
euchromatin (referring to open chromatin that is accessible to transcription factors, RNA
polymerase II (Pol II) and other DNA-binding proteins that support gene expression) or
heterochromatin (referring to tightly packed DNA associated with transcriptional silencing). These states are dependent on the type (e.g. acetylation, methylation, phosphorylation,
ubiquitylation) and location (e.g. various lysine or arginine residues) of the modification
(see review by Lawrence, Daujat & Schneider, 2016) for a complete list of modifications). These modifications are enabled by various families of enzymes, including histone
acetylases (HATs), histone deacetylases (HDACs), histone methyltransferases (e.g. HMT) and
histone demethylases (e.g. Jumonji and Lys-specific demethylase). Post-translational
modifications are important for the regulation of gene activity, but also play roles in DNA
repair, replication, and cell fate/determination (see reviews by Eberharter & Becker, 2002;
Martin & Zhang, 2005; Lawrence, Daujat & Schneider, 2016). The enzymatic machinery
responsible for these modifications is highly regulated during embryonic development (Lin
& Dent, 2006), and, like DNA methylation, can be altered by various environmental
conditions (Chinnusamy & Zhu, 2009). PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed The enzymatic machinery supporting DNA methylation includes a
family of DNA methyltransferases (DNMTs), including the maintenance methyltransferase
DNMT1 (responsible for copying pre-existing DNA methylation patterns to the new strand
during mitosis) and the de novo methyltransferases DNMT3A/3B. DNA methylation is
known to be repressive when located in promoters of genes through associations with other
DNA-binding proteins or through the physical blocking of transcription factors (Bell &
Felsenfeld, 2000). However, DNA methylation in gene bodies is associated with high levels of
expression (Jones, 1999). Therefore, although DNA methylation is typically associated with
silencing, its regulatory role is specific to the genomic context. In mammals, DNA
methylation plays important roles in providing genomic stability through the repression of
transposable elements (TEs) (Maloisel & Rossignol, 1998), genomic imprinting (Bell &
Felsenfeld, 2000), and dosage compensation (Csankovszki, Nagy & Jaenisch, 2001). DNA
methylation is also important for cell-type differentiation and embryonic development (Li,
Bestor & Jaenisch, 1992). DNA methylation is the most well-studied epigenetic mechanism,
and most studies have been done in plants and mammals, in which DNA methylation has
been shown to be sensitive to external factors including nutrition (Weaver et al., 2004),
exposure to toxins (Dolinoy et al., 2006), and photoperiod (Azzi et al., 2014). Importantly,
the meiotic transmission of DNA methylation patterns, and thus the opportunity for
transgenerational epigenetic inheritance through DNA methylation, is rare in mammals,
which undergo extensive DNA methylation reprogramming in the early embryo stage
(Daxinger & Whitelaw, 2012). Transgenerational epigenetic inheritance is more common in
plants, which do not exhibit extensive resetting of DNA methylation between generations
(reviewed by Hauser et al., 2011). As discussed below, it is still unclear if and to what extent
DNA methylation resetting occurs in fish and shellfish. Histone variants and post-translational modifications
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed 136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167 core histone proteins (H2A, H2B, H3 and H4). Higher-order chromatin structure is
established via the incorporation of linker histones (H1) between nucleosomes. Chromatin
structure can be modified to either enhance or repress transcription through the
incorporation of histone variants and the post-translational modification of histones
(Berger, 2007). These modified chromatin states can be inherited both mitotically and
meiotically, and thus may convey epigenetic information (Henikoff & Smith, 2015). Histone
variants have specialized functions and can be incorporated into nucleosomes in a
replication-independent manner (Henikoff & Smith, 2015). Although histone variants have
been less-studied than post-translational modifications, they can play an important role in
mediating both short- and long-term responses to environmental cues (Talbert & Henikoff,
2014). Both canonical and variant histones can be post-translationally modified, primarily
at their N-terminal tails, which alters the degree of chromatin compaction resulting in either
euchromatin (referring to open chromatin that is accessible to transcription factors, RNA
polymerase II (Pol II) and other DNA-binding proteins that support gene expression) or
heterochromatin (referring to tightly packed DNA associated with transcriptional silencing). These states are dependent on the type (e.g. acetylation, methylation, phosphorylation,
ubiquitylation) and location (e.g. various lysine or arginine residues) of the modification
(see review by Lawrence, Daujat & Schneider, 2016) for a complete list of modifications). These modifications are enabled by various families of enzymes, including histone
acetylases (HATs), histone deacetylases (HDACs), histone methyltransferases (e.g. HMT) and
histone demethylases (e.g. Jumonji and Lys-specific demethylase). Post-translational
modifications are important for the regulation of gene activity, but also play roles in DNA
repair, replication, and cell fate/determination (see reviews by Eberharter & Becker, 2002;
Martin & Zhang, 2005; Lawrence, Daujat & Schneider, 2016). The enzymatic machinery
responsible for these modifications is highly regulated during embryonic development (Lin
& Dent, 2006), and, like DNA methylation, can be altered by various environmental
conditions (Chinnusamy & Zhu, 2009). Less is known about the mechanisms that underlie
the mitotic and meiotic persistence of histone modifications. Manuscript to be reviewed core histone proteins (H2A, H2B, H3 and H4). Higher-order chromatin structure is
established via the incorporation of linker histones (H1) between nucleosomes. Chromatin
structure can be modified to either enhance or repress transcription through the
incorporation of histone variants and the post-translational modification of histones
(Berger, 2007). These modified chromatin states can be inherited both mitotically and
meiotically, and thus may convey epigenetic information (Henikoff & Smith, 2015). Histone
variants have specialized functions and can be incorporated into nucleosomes in a
replication-independent manner (Henikoff & Smith, 2015). Although histone variants have
been less-studied than post-translational modifications, they can play an important role in
mediating both short- and long-term responses to environmental cues (Talbert & Henikoff,
2014). Both canonical and variant histones can be post-translationally modified, primarily
at their N-terminal tails, which alters the degree of chromatin compaction resulting in either
euchromatin (referring to open chromatin that is accessible to transcription factors, RNA
polymerase II (Pol II) and other DNA-binding proteins that support gene expression) or
heterochromatin (referring to tightly packed DNA associated with transcriptional silencing). These states are dependent on the type (e.g. acetylation, methylation, phosphorylation,
ubiquitylation) and location (e.g. various lysine or arginine residues) of the modification
(see review by Lawrence, Daujat & Schneider, 2016) for a complete list of modifications). These modifications are enabled by various families of enzymes, including histone
acetylases (HATs), histone deacetylases (HDACs), histone methyltransferases (e.g. HMT) and
histone demethylases (e.g. Jumonji and Lys-specific demethylase). Post-translational
modifications are important for the regulation of gene activity, but also play roles in DNA
repair, replication, and cell fate/determination (see reviews by Eberharter & Becker, 2002;
Martin & Zhang, 2005; Lawrence, Daujat & Schneider, 2016). The enzymatic machinery
responsible for these modifications is highly regulated during embryonic development (Lin
& Dent, 2006), and, like DNA methylation, can be altered by various environmental
conditions (Chinnusamy & Zhu, 2009). Less is known about the mechanisms that underlie
the mitotic and meiotic persistence of histone modifications. Interestingly, it has been
shown in both mammals and zebrafish that certain modified histones are non-randomly
retained during spermatogenesis when most of these proteins are replaced by protamines,
suggesting that these marks may play a role in transferring epigenetic information to the
embryo (Brykczynska et al., 2010; Wu, Zhang & Cairns, 2011). Manuscript to be reviewed 168 Non-coding RNA
Although a large majority of the genome is transcribed, only a small portion of these
transcripts actually code for protein. The remaining non-coding transcripts, originally
regarded as ‘junk’, are now recognized to play a role in modulating gene expression, and are
categorized broadly as non-coding RNA (ncRNA). There are two major classes of ncRNA:
long ncRNA ( > 200 nt) and small ncRNA (< 200 nt), the latter of which includes micro RNA
(miRNA), short interfering RNA (siRNA), and PIWI-interacting RNA (piRNA). Small ncRNAs
are highly conserved and their major mechanism of action is to inhibit protein synthesis by
blocking or degrading primary transcripts (see review by Castel & Martienssen, 2013). In
contrast, long ncRNAs (lncRNA) are less conserved and have complex mechanisms of action
that may work either in cis or trans (see review by Wang & Chang, 2011). Non-coding RNAs
have important functions in gene expression and have been demonstrated to be important
regulators of genome stability, environmental plasticity and embryonic development
(Mercer, Dinger & Mattick, 2009; Bizuayehu & Babiak, 2014). Generally, ncRNA molecules
are considered to be ‘epigenetic’ in the traditional sense because they interact with other
epigenetic mechanisms such as DNA methylation and histone modifications to silence or
activate various parts of the genome (Peschansky & Wahlestedt, 2014). There is also
evidence that ncRNA, particularly miRNA, plays a role in the transmission of environmental
information from the male parent (via sperm) to offspring in mammals (Gapp et al., 2014;
Rodgers et al., 2015). Evidence of transgenerational inheritance through miRNA has also
been observed in the invertebrate model C. elegans in response to starvation (Rechavi et al.,
2014) and temperature (Klosin et al., 2017) cues. 168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190 Taxa specific Patterns
Epigenetic mechanisms, and particularly DNA methylation, have recently been the
focus of numerous studies in both fish and shellfish. However, most of what we know about
epigenetics in animals comes from studies done in mammals and care should be taken when
generalizing results in mammals to fish and shellfish. Although there are certainly
similarities (e.g. DNA methylation patterns are very similar across all vertebrates), there are
also important differences (e.g. Manuscript to be reviewed Less is known about the mechanisms that underlie
the mitotic and meiotic persistence of histone modifications. Interestingly, it has been
shown in both mammals and zebrafish that certain modified histones are non-randomly
retained during spermatogenesis when most of these proteins are replaced by protamines,
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed invertebrate DNA methylation patterns are very different
191
192
193
194
195
196
197
198 Taxa specific Patterns
Epigenetic mechanisms, and particularly DNA methylation, have recently been the
focus of numerous studies in both fish and shellfish. However, most of what we know about
epigenetics in animals comes from studies done in mammals and care should be taken when
generalizing results in mammals to fish and shellfish. Although there are certainly
similarities (e.g. DNA methylation patterns are very similar across all vertebrates), there are
also important differences (e.g. invertebrate DNA methylation patterns are very different
191
192
193
194
195
196
197
198 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Manuscript to be reviewed from those in vertebrates). This section will focus on foundational information about
epigenetic marks in fish and shellfish, and highlight both significant gaps in our
understanding and differences from well-studied mammalian systems. DNA methylation in fish and shellfish
DNA methylation is the most well-studied epigenetic mark among fish and shellfish. Both
fish and shellfish have genes that encode the basic methylation machinery (e.g. DNMTs and
MBDs) and DNA methylation is present in all species examined to date. However, there are
striking differences in DNA methylation patterns between vertebrates and invertebrates, as
well as significant unknowns in terms of the resetting of DNA methylation in both fish and
shellfish, which will be described below. Considerable work has been done on understanding patterns and functions of DNA
methylation in model fish species such as zebrafish and medaka, and there is also a growing
body of information on DNA methylation in non-model species (e.g. Metzger & Schulte
(2016) reviewed the current state of knowledge of DNA methylation patterns and functions
in marine fish). Generally, DNA methylation patterns are similar across all vertebrates that
exhibit a ‘global’ DNA methylation pattern, which means that most CpGs are methylated
with the exception of regions of DNA with a high CpG content (referred to as CpG islands). However, global DNA methylation levels in fish are higher than those in mammals, though
the significance of this difference remains unclear (Jabbari et al., 1997; Zhang, Hoshida &
Sadler, 2016). The function of DNA methylation also appears to be similar across
vertebrates, with the exception that its role in parental imprinting is likely unique to
mammals (Barlow & Bartolomie, 2014). Manuscript to be reviewed One outstanding question concerns the extent of
DNA methylation resetting in fish. While mammals undergo extensive DNA methylation
reprogramming in the early embryo (Daxinger & Whitelaw, 2012), the extent of DNA
methylation reprogramming in fish is unclear (Jiang et al., 2013; Potok et al., 2013). A recent
study, which is discussed in more detail in the following section, showed clear evidence of
transgenerational inheritance of environmentally-induced DNA methylation patterns in a
fish, suggesting that at least some of the genome escapes putative resetting between
generations (Shao et al., 2014). There is a need for more detailed studies on the extent of
DNA
th l ti
tti g i fi h
ti
l
l i
i
d i
lt
I
dditi
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229 ,
Considerable work has been done on understanding patterns and functions of DNA
methylation in model fish species such as zebrafish and medaka, and there is also a growing
body of information on DNA methylation in non-model species (e.g. Metzger & Schulte
(2016) reviewed the current state of knowledge of DNA methylation patterns and functions
in marine fish). Generally, DNA methylation patterns are similar across all vertebrates that
exhibit a ‘global’ DNA methylation pattern, which means that most CpGs are methylated
with the exception of regions of DNA with a high CpG content (referred to as CpG islands). However, global DNA methylation levels in fish are higher than those in mammals, though
the significance of this difference remains unclear (Jabbari et al., 1997; Zhang, Hoshida &
Sadler, 2016). The function of DNA methylation also appears to be similar across
vertebrates, with the exception that its role in parental imprinting is likely unique to
mammals (Barlow & Bartolomie, 2014). One outstanding question concerns the extent of
DNA methylation resetting in fish. While mammals undergo extensive DNA methylation
reprogramming in the early embryo (Daxinger & Whitelaw, 2012), the extent of DNA
methylation reprogramming in fish is unclear (Jiang et al., 2013; Potok et al., 2013). A recent
study, which is discussed in more detail in the following section, showed clear evidence of
transgenerational inheritance of environmentally-induced DNA methylation patterns in a
fish, suggesting that at least some of the genome escapes putative resetting between
generations (Shao et al., 2014). PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed (2017) showed that parental exposure to an herbicide influences
progeny DNA methylation patterns in oysters. 230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258 p
y
epigenetic changes. Invertebrate DNA methylation patterns are strikingly different from those in
vertebrates. Whereas vertebrates exhibit a global pattern of DNA methylation, invertebrates
show a ‘mosaic’ pattern, with stretches of methylated DNA punctuating regions of
unmethylated DNA (Tweedie et al., 1997; Simmen et al., 1999). We previously examined
DNA methylation throughout the entire genome in the Pacific oyster; 15% of CpGs in
somatic tissue were methylated, whereas 60-70% of CpGs are methylated in mammals
(Gavery & Roberts, 2013). In oysters, as in other invertebrates, the methylated fraction
tends to consist of gene bodies, while other genomic regions exhibit less methylation. Unlike
vertebrate species, transposable elements in oysters and other invertebrate species show
surprisingly little methylation (Simmen et al., 1999; Feng et al., 2010; Zemach et al., 2010). Despite these differences, DNA methylation does appear to be associated with gene
regulation in shellfish. In the Pacific oyster, high levels of methylation in gene bodies are
associated with high levels of expression (Gavery & Roberts, 2013; Olson & Roberts, 2014). Interestingly, genes in oysters with limited methylation show variable exon-specific
expression across tissue types, indicating that hypomethylation allows increased plasticity
(Gavery & Roberts, 2013). DNA methylation patterns in the Pacific oyster are dynamic
across developmental stages, and correlations between DNA methylation and gene
expression patterns suggest that DNA methylation plays a role in gene regulation during
development (Riviere et al., 2017). While more studies are needed to quantify the functional
relationship between DNA methylation and gene expression, there are significant
implications for improving resilience in shellfish — particularly if DNA methylation patterns
are heritable. While few studies have examined the heritability of DNA methylation patterns
in shellfish, a small study that focused on methylation states in parents and larvae found a
significant clustering of methylation patterns within families, indicating that methylation
patterns differ significantly depending on the male parent (Olson & Roberts, 2015). More
recently, Rondon et al. (2017) showed that parental exposure to an herbicide influences
progeny DNA methylation patterns in oysters. Manuscript to be reviewed 231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258 Manuscript to be reviewed There is a need for more detailed studies on the extent of
DNA methylation resetting in fish, particularly in species used in aquaculture. In addition,
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed more studies should examine the potential meiotic inheritance of environmentally-induced
epigenetic changes. 230
231 more studies should examine the potential meiotic inheritance of environmentally-induced
epigenetic changes. Invertebrate DNA methylation patterns are strikingly different from those in
vertebrates. Whereas vertebrates exhibit a global pattern of DNA methylation, invertebrates
show a ‘mosaic’ pattern, with stretches of methylated DNA punctuating regions of
unmethylated DNA (Tweedie et al., 1997; Simmen et al., 1999). We previously examined
DNA methylation throughout the entire genome in the Pacific oyster; 15% of CpGs in
somatic tissue were methylated, whereas 60-70% of CpGs are methylated in mammals
(Gavery & Roberts, 2013). In oysters, as in other invertebrates, the methylated fraction
tends to consist of gene bodies, while other genomic regions exhibit less methylation. Unlike
vertebrate species, transposable elements in oysters and other invertebrate species show
surprisingly little methylation (Simmen et al., 1999; Feng et al., 2010; Zemach et al., 2010). Despite these differences, DNA methylation does appear to be associated with gene
regulation in shellfish. In the Pacific oyster, high levels of methylation in gene bodies are
associated with high levels of expression (Gavery & Roberts, 2013; Olson & Roberts, 2014). Interestingly, genes in oysters with limited methylation show variable exon-specific
expression across tissue types, indicating that hypomethylation allows increased plasticity
(Gavery & Roberts, 2013). DNA methylation patterns in the Pacific oyster are dynamic
across developmental stages, and correlations between DNA methylation and gene
expression patterns suggest that DNA methylation plays a role in gene regulation during
development (Riviere et al., 2017). While more studies are needed to quantify the functional
relationship between DNA methylation and gene expression, there are significant
implications for improving resilience in shellfish — particularly if DNA methylation patterns
are heritable. While few studies have examined the heritability of DNA methylation patterns
in shellfish, a small study that focused on methylation states in parents and larvae found a
significant clustering of methylation patterns within families, indicating that methylation
patterns differ significantly depending on the male parent (Olson & Roberts, 2015). More
recently, Rondon et al. Manuscript to be reviewed Histone variants and post-translational modifications have generally been studied in
model fish species, such as zebrafish. Some histone variants show a conserved function
between lower vertebrates and mammals. For example, histone variant macroH2A has bee
shown to play an important role in development in the zebrafish (Buschbeck et al., 2009). However, while some histone variants are ‘universal’ and can be found in most eukaryotes
(Talbert & Henikoff, 2010), other histone variants appear to be unique to fish (Wu et al.,
2009). Post-translational modifications of histones and their dynamics have also been
studied in zebrafish, and the evidence indicates that modifications are conserved among
vertebrates. The functional analysis of histone acetylation in zebrafish confirms that it play
a role in embryogenesis (Vastenhouw & Schier, 2012) and in tissue regeneration (Stewart,
Hoshida & Sadler, 2009). While studies of histone modification in non-model fish are rare,
recent studies in rainbow trout and European sea bass indicate that diet influences bulk
histone modification levels and can regulate the expression of associated enzymes
(Marandel et al., 2016; Terova et al., 2016; Panserat et al., 2017). With regard to meiotic
inheritance, zebrafish show multivalent modified histone retention in sperm, similar to
mammals (Wu, Zhang & Cairns, 2011). Histone variants have been characterized in various bivalve species (e.g. González-
Romero et al., 2009; González-Romero et al., 2012) and a recent study on the responses of
Eastern oysters to harmful algal blooms reported that the histone variant H2A.X is post-
translationally modified in response to algal toxins (González-Romero et al., 2017). While
post-translational modifications of histones are not well-studied in shellfish, Fellous et al. (2014) identified homologs of Jumonji histone demethylase genes (Jmj) in Pacific oysters
that, as in vertebrates, were regulated during embryonic development. A subsequent study
showed that both bulk histone methylation levels and the expression of histone
demethylases responded to temperature during development, suggesting that histone
modifications play a role in mediating the physiological responses of oysters to temperatur
(Fellous, Favrel & Riviere, 2015). Histones are not replaced by protamines in bivalve sperm as they are in mammals
(Eirin-Lopez & Ausio, 2009). Rather, depending on the species, canonical histones are
replaced by various sperm nuclear basic proteins that can be classified as either protamine
like-type, histone-type or protamine-type (Ausio, 1986; Eirin-Lopez & Ausio, 2009). Histone variants and post-translational modifications in fish and shellfish
259 Histone variants and post-translational modifications in fish and shellfish
259 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Histone variants and post-translational modifications have generally been studied in
model fish species, such as zebrafish. Some histone variants show a conserved function
between lower vertebrates and mammals. For example, histone variant macroH2A has been
shown to play an important role in development in the zebrafish (Buschbeck et al., 2009). However, while some histone variants are ‘universal’ and can be found in most eukaryotes
(Talbert & Henikoff, 2010), other histone variants appear to be unique to fish (Wu et al.,
2009). Post-translational modifications of histones and their dynamics have also been
studied in zebrafish, and the evidence indicates that modifications are conserved among
vertebrates. The functional analysis of histone acetylation in zebrafish confirms that it plays
a role in embryogenesis (Vastenhouw & Schier, 2012) and in tissue regeneration (Stewart,
Hoshida & Sadler, 2009). While studies of histone modification in non-model fish are rare,
recent studies in rainbow trout and European sea bass indicate that diet influences bulk
histone modification levels and can regulate the expression of associated enzymes
(Marandel et al., 2016; Terova et al., 2016; Panserat et al., 2017). With regard to meiotic
inheritance, zebrafish show multivalent modified histone retention in sperm, similar to
mammals (Wu, Zhang & Cairns, 2011). Histone variants have been characterized in various bivalve species (e.g. González-
Romero et al., 2009; González-Romero et al., 2012) and a recent study on the responses of
Eastern oysters to harmful algal blooms reported that the histone variant H2A.X is post-
translationally modified in response to algal toxins (González-Romero et al., 2017). While
post-translational modifications of histones are not well-studied in shellfish, Fellous et al. 260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
Manuscript to be reviewed Furthe
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed studies will be needed to determine the extent to which canonical histones and variants are
retained in bivalve sperm, and this avenue of research could greatly contribute to a greater
understanding of the potential transmission of epigenetic information from parent to
offspring in bivalves. Recent work on the details of experimental approaches and workflows
for the study of chromatin-associated proteins in bivalves (Rivera-Casas et al., 2017) should
facilitate this research. 292
293
294
295
296
297 studies will be needed to determine the extent to which canonical histones and variants are
retained in bivalve sperm, and this avenue of research could greatly contribute to a greater
understanding of the potential transmission of epigenetic information from parent to
offspring in bivalves. Recent work on the details of experimental approaches and workflows
for the study of chromatin-associated proteins in bivalves (Rivera-Casas et al., 2017) should
facilitate this research. 292
293
294
295
296
297 Non-coding RNA in fish and shellfish
Most studies on non-coding RNAs in fish and shellfish, including important
aquaculture species (e.g. Atlantic salmon (Andreassen, Worren & Høyheim, 2013; Bekaert et
al., 2013) and rainbow trout (Juanchich et al., 2016)), have focused on miRNAs. There have
been several studies of miRNAs in a physiological context, including in eggs (e.g. Ma et al.,
2012), immune function (e.g. Andreassen & Høyheim, 2017) and embryo development
(Bizuayehu et al., 2015). There is less information available about other types of small
ncRNA, except in zebrafish where, for example, piRNA has been shown to silence
transposable elements in gametes, and thus functions similarly to that in mammals
(Houwing et al., 2007). Recently, there have been several descriptions of long non-coding
RNAs in salmonids, including associations between lncRNA expression and disease in both
Atlantic salmon and rainbow trout (Boltaña et al., 2016; Paneru et al., 2016; Valenzuela-
Miranda et al., 2016). While there have been few studies on non-coding RNAs in shellfish, generally,
miRNAs and their biogenesis are highly conserved over evolutionary scales (Wheeler et al.,
2009). Indeed, genes for miRNA biogenesis have been detected in available bivalve genomes
(Rosani, Pallavicini & Venier, 2016). With respect to long non-coding RNAs, researchers
have reported an association between lncRNAs and larval development in the Pacific oyster
(Yu, Zhao & Li, 2016). Potential Aquaculture Applications
Environmental manipulation
Given what we know about environmental influences on epigenetic mechanisms in fish and
shellfish and the relationships between these mechanisms and phenotype, a potentially
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321 Non-coding RNA in fish and shellfish
Most studies on non-coding RNAs in fish and shellfish, including important
aquaculture species (e.g. Atlantic salmon (Andreassen, Worren & Høyheim, 2013; Bekaert et
al., 2013) and rainbow trout (Juanchich et al., 2016)), have focused on miRNAs. There have
been several studies of miRNAs in a physiological context, including in eggs (e.g. Ma et al.,
2012), immune function (e.g. Andreassen & Høyheim, 2017) and embryo development
(Bizuayehu et al., 2015). There is less information available about other types of small
ncRNA, except in zebrafish where, for example, piRNA has been shown to silence
transposable elements in gametes, and thus functions similarly to that in mammals
(Houwing et al., 2007). Recently, there have been several descriptions of long non-coding
RNAs in salmonids, including associations between lncRNA expression and disease in both
Atlantic salmon and rainbow trout (Boltaña et al., 2016; Paneru et al., 2016; Valenzuela-
Miranda et al., 2016). 298
299
300
301
302
303
304
305
306
307
308
309
310 Potential Aquaculture Applications
318 Environmental manipulation
Given what we know about environmental influences on epigenetic mechanisms in fish and
shellfish and the relationships between these mechanisms and phenotype, a potentially
319
320
321 Environmental manipulation
Given what we know about environmental influences on epigenetic mechanisms in fish and
shellfish and the relationships between these mechanisms and phenotype, a potentially
319
320
321 Manuscript to be reviewed Manuscript to be reviewed fruitful application of epigenetics to aquaculture could involve environmental manipulation. The possibility of generating environmentally-driven phenotypes mediated through
epigenetic mechanisms should be considered for two stages in the aquaculture life-cycle in
which the animals are particularly sensitive: during larval development and during
broodstock holding/conditioning (Figure 1). The notion of developmental programming suggests that environmental conditions
experienced in early life influence the phenotype later in life, and has gained momentum in
human research (e.g. Gluckman et al., 2008). Thus, developmental programming offers a
memory of the environment that could be beneficial in controlled aquaculture settings. However, in some cases, embryos and juveniles are not raised in the same environmental
conditions as the adults. For example, hatchery-reared salmon or bivalves experience very
different conditions during their larval and adult stages. The identification of sensitive
periods for inducing an environmental memory could offer a “programming window” that
could be leveraged in husbandry practices. Several lines of evidence support the presence of
developmental programming in fish (for an excellent review see Jonsson & Jonsson, 2014). Traits that have been associated with early environmental conditions include metabolism,
growth, sex determination, fecundity, and behavior (Jonsson & Jonsson, 2014). Within-
generation environmental memory has also been described in shellfish. For example, early
exposure of Olympia oyster larvae to ocean acidification has been shown to influence
juvenile traits (Hettinger et al., 2012). 322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341 fruitful application of epigenetics to aquaculture could involve environmental manipulation. The possibility of generating environmentally-driven phenotypes mediated through
epigenetic mechanisms should be considered for two stages in the aquaculture life-cycle in
which the animals are particularly sensitive: during larval development and during
broodstock holding/conditioning (Figure 1). 322
323
324
325
326 fruitful application of epigenetics to aquaculture could involve environmental manipulation. The possibility of generating environmentally-driven phenotypes mediated through
epigenetic mechanisms should be considered for two stages in the aquaculture life-cycle in
which the animals are particularly sensitive: during larval development and during
broodstock holding/conditioning (Figure 1). 322
323
324
325
326 epigenetic mechanisms should be considered for two stages in the aquaculture life-cycle in
which the animals are particularly sensitive: during larval development and during
broodstock holding/conditioning (Figure 1). PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) The notion of developmental programming suggests that environmental conditions
experienced in early life influence the phenotype later in life, and has gained momentum in
human research (e.g. Gluckman et al., 2008). Thus, developmental programming offers a
memory of the environment that could be beneficial in controlled aquaculture settings. However, in some cases, embryos and juveniles are not raised in the same environmental
conditions as the adults. For example, hatchery-reared salmon or bivalves experience very
different conditions during their larval and adult stages. The identification of sensitive
periods for inducing an environmental memory could offer a “programming window” that
could be leveraged in husbandry practices. Several lines of evidence support the presence of
developmental programming in fish (for an excellent review see Jonsson & Jonsson, 2014). Traits that have been associated with early environmental conditions include metabolism,
growth, sex determination, fecundity, and behavior (Jonsson & Jonsson, 2014). Within-
generation environmental memory has also been described in shellfish. For example, early
exposure of Olympia oyster larvae to ocean acidification has been shown to influence
juvenile traits (Hettinger et al., 2012). Two examples of developmental programming in aquaculture, where the epigenetic
mechanisms were described, involve sex determination in fish. In European sea bass
(Dicentrarchus labrax), exposure to high temperature in early development was associated
with a higher proportion of phenotypic males (Navarro-Martin et al., 2009). Navarro-Martin
et al. (2011) found that this early exposure to high temperature was associated with
increased DNA methylation in the promoter of the aromatase gene (cyp19a1a) in adults. Furthermore, they showed that in vitro methylation of the aromatase promoter was
sufficient to suppress transcription of the gene. More recently, the commercially important
half-smooth tongue sole (Cynoglossus semilaevis) was used as a model to investigate the role
of epigenetic regulation in environmental sex determination (Shao et al. 2014). Using
genome-wide DNA methylation profiling, the authors showed that pseudomales (generated
by exposing genetic females to high temperature during a sensitive developmental window)
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353 The notion of developmental programming suggests that environmental conditions
experienced in early life influence the phenotype later in life, and has gained momentum in
human research (e.g. Gluckman et al., 2008). Thus, developmental programming offers a
memory of the environment that could be beneficial in controlled aquaculture settings. Manuscript to be reviewed Manuscript to be reviewed Manuscript to be reviewed exhibit methylation patterns in testes consistent with genetic males, both of which differ
from the ovarian methylome of normal females. Excitingly, it was reported that both the
pseudomale phenotype and the testes-specific methylation patterns are inherited by F1
pseudomale offspring generated by crosses between pseudomales and normal females,
suggesting the transgenerational epigenetic inheritance of environmentally-induced sex
reversal in this species (Shao et al., 2014). The ability to control sex in fish broodstock is
certainly a priority for aquaculture and these studies shed light on the epigenetic
mechanisms that could be leveraged in future work. More studies will be needed to
determine the extent to which the relevant mechanisms are conserved across species that
exhibit environmental sex determination. Nutrition and feeding are important aspects of aquaculture production; and
understanding how early-life nutritional conditions influence key phenotypic traits later in
life is important to consider. In mammals, the nutritional status of the mother can
predispose offspring to adult-onset metabolic disease and mounting evidence suggests that
epigenetic mechanisms are involved (reviewed by Vickers, 2014). In fish, rainbow trout fry
fed a plant-based diet for 3 weeks starting when they were swim-up fry showed higher
growth rates, feed intakes, and feed efficiencies when challenged again with a plant-based
diet after 7 months of grow-out on a fishmeal/fish oil diet (Geurden et al., 2013). Interestingly, in a follow-up study, transcriptomic analyses suggested that epigenetic
mechanisms may be involved in this response (Balasubramanian et al., 2016). In addition, a
study on vitamin supplementation at first feeding in rainbow trout identified changes in
global methylation and histone modification 7 months after the supplementation was
discontinued, despite an apparent lack of phenotypic responses (Panserat et al., 2017). These studies provide the first link between early-environmental exposure and epigenetic
mechanisms in aquaculture species. In addition to developmental programming, broodstock holding/conditioning is also
an important area to consider for the potential transmission of environmentally-induced
epigenetic information between parents and their offspring. This type of non-genetic
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381 exhibit methylation patterns in testes consistent with genetic males, both of which differ
from the ovarian methylome of normal females. Manuscript to be reviewed Excitingly, it was reported that both the
pseudomale phenotype and the testes-specific methylation patterns are inherited by F1
pseudomale offspring generated by crosses between pseudomales and normal females,
suggesting the transgenerational epigenetic inheritance of environmentally-induced sex
reversal in this species (Shao et al., 2014). The ability to control sex in fish broodstock is
certainly a priority for aquaculture and these studies shed light on the epigenetic
mechanisms that could be leveraged in future work. More studies will be needed to
determine the extent to which the relevant mechanisms are conserved across species that
exhibit environmental sex determination. 354
355
356
357
358
359
360
361
362
363 exhibit methylation patterns in testes consistent with genetic males, both of which differ
from the ovarian methylome of normal females. Excitingly, it was reported that both the
pseudomale phenotype and the testes-specific methylation patterns are inherited by F1
pseudomale offspring generated by crosses between pseudomales and normal females,
suggesting the transgenerational epigenetic inheritance of environmentally-induced sex
reversal in this species (Shao et al., 2014). The ability to control sex in fish broodstock is
certainly a priority for aquaculture and these studies shed light on the epigenetic
mechanisms that could be leveraged in future work. More studies will be needed to
determine the extent to which the relevant mechanisms are conserved across species that
exhibit environmental sex determination. 354
355
356
357
358
359
360
361
362
363 exhibit methylation patterns in testes consistent with genetic males, both of which differ
from the ovarian methylome of normal females. Excitingly, it was reported that both the
pseudomale phenotype and the testes-specific methylation patterns are inherited by F1
pseudomale offspring generated by crosses between pseudomales and normal females,
suggesting the transgenerational epigenetic inheritance of environmentally-induced sex
reversal in this species (Shao et al., 2014). The ability to control sex in fish broodstock is
certainly a priority for aquaculture and these studies shed light on the epigenetic
mechanisms that could be leveraged in future work. More studies will be needed to
determine the extent to which the relevant mechanisms are conserved across species that
exhibit environmental sex determination. 354
355
356
357
358
359
360
361
362
363 Nutrition and feeding are important aspects of aquaculture production; and
understanding how early-life nutritional conditions influence key phenotypic traits later in
life is important to consider. 327
328
329
330 j
g
Two examples of developmental programming in aquaculture, where the epigenetic
mechanisms were described, involve sex determination in fish. In European sea bass
(Dicentrarchus labrax), exposure to high temperature in early development was associated
with a higher proportion of phenotypic males (Navarro-Martin et al., 2009). Navarro-Martin
et al. (2011) found that this early exposure to high temperature was associated with
increased DNA methylation in the promoter of the aromatase gene (cyp19a1a) in adults. Furthermore, they showed that in vitro methylation of the aromatase promoter was
sufficient to suppress transcription of the gene. More recently, the commercially important
half-smooth tongue sole (Cynoglossus semilaevis) was used as a model to investigate the role
of epigenetic regulation in environmental sex determination (Shao et al. 2014). Using
genome-wide DNA methylation profiling, the authors showed that pseudomales (generated
by exposing genetic females to high temperature during a sensitive developmental window)
342
343
344
345
346
347
348
349
350
351
352
353 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Manuscript to be reviewed only from the maternal side, but also from the paternal side, which may be more important
than previously thought (Rodgers et al., 2015; reviewed by Soubry et al., 2014). There has
been growing interest in the transgenerational plasticity of fish, particularly as it relates to
predicting responses to climate change (reviewed by Munday, 2014). Similar research
questions are also being addressed in shellfish. Adult Manila clams exposed to low pH
during gonadal maturation have faster-growing offspring compared to controls (Zhao et al.,
2017). In the Sydney rock oyster, larvae produced by parents incubated under low-pH
conditions are larger and develop faster in low-pH conditions and also have higher fitness
as adults (Parker et al., 2012; Parker et al., 2015). In addition to water chemistry, disease is
a significant concern in shellfish aquaculture. There is increasing evidence that prior
exposure to an immune challenge can increase the immune response later in life and that
this environmental memory can be transmitted to offspring. Green et al. (2016)
demonstrated that offspring of Pacific oyster parents treated with poly(I:C) possess
enhanced protection against Ostreid herpesvirus type I infection. Th
h
i
( )
ibl f
idi
hi
f h
i
i
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400 only from the maternal side, but also from the paternal side, which may be more important
than previously thought (Rodgers et al., 2015; reviewed by Soubry et al., 2014). There has
been growing interest in the transgenerational plasticity of fish, particularly as it relates to
predicting responses to climate change (reviewed by Munday, 2014). Similar research
questions are also being addressed in shellfish. Adult Manila clams exposed to low pH
during gonadal maturation have faster-growing offspring compared to controls (Zhao et al.,
2017). In the Sydney rock oyster, larvae produced by parents incubated under low-pH
conditions are larger and develop faster in low-pH conditions and also have higher fitness
as adults (Parker et al., 2012; Parker et al., 2015). In addition to water chemistry, disease is
a significant concern in shellfish aquaculture. There is increasing evidence that prior
exposure to an immune challenge can increase the immune response later in life and that
this environmental memory can be transmitted to offspring. Green et al. (2016)
demonstrated that offspring of Pacific oyster parents treated with poly(I:C) possess
enhanced protection against Ostreid herpesvirus type I infection. Manuscript to be reviewed In mammals, the nutritional status of the mother can
predispose offspring to adult-onset metabolic disease and mounting evidence suggests that
epigenetic mechanisms are involved (reviewed by Vickers, 2014). In fish, rainbow trout fry
fed a plant-based diet for 3 weeks starting when they were swim-up fry showed higher
growth rates, feed intakes, and feed efficiencies when challenged again with a plant-based
diet after 7 months of grow-out on a fishmeal/fish oil diet (Geurden et al., 2013). 364
365
366
367
368
369
370
371 Interestingly, in a follow-up study, transcriptomic analyses suggested that epigenetic
mechanisms may be involved in this response (Balasubramanian et al., 2016). In addition, a
study on vitamin supplementation at first feeding in rainbow trout identified changes in
global methylation and histone modification 7 months after the supplementation was
discontinued, despite an apparent lack of phenotypic responses (Panserat et al., 2017). These studies pro ide the first link bet een earl
en ironmental e posure and epigenetic
372
373
374
375
376
377 In addition to developmental programming, broodstock holding/conditioning is also
an important area to consider for the potential transmission of environmentally-induced
epigenetic information between parents and their offspring. This type of non-genetic
transmission is frequently referred to as ‘transgenerational plasticity’ (Salinas et al., 2013)
and can refer both to maternal provisioning (e.g. bivalve embryos can be influenced by the
type of diet fed to broodstock during conditioning (Utting & Millican, 1997)) and epigenetic
inheritance. Importantly, epigenetic transmission has the potential to be transmitted not
379
380
381
382
383
384
385 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed been considered for finfish aquaculture (see the review by Moghadam, Mørkøre &
Robinson, 2015). Epigenetics could also make genetic selection more challenging. Many organisms
have the potential to generate new genetic variations in response to stressful conditions
through the modulation of epigenetic marks associated with transposable elements (TEs)
(Dowen et al., 2012; Yu et al., 2013; reviewed by Rey et al., 2016). Transposable elements, or
“jumping genes”, are regions of repetitive DNA that can move and amplify their copy
number in the host genome. In the model plant Arabidopsis, the genomic response to
bacterial challenge is a global reduction of DNA methylation and the reactivation of
previously silent TEs associated with defense genes (Yu et al., 2013). It is interesting to
consider that in invertebrates, and specifically in Pacific oysters, TEs are not preferentially
methylated, though this does not preclude silencing via other epigenetic mechanisms
(Gavery & Roberts, 2013; Olson & Roberts, 2015). It has been hypothesized that the lack of
TE silencing by DNA methylation may indicate pressure to generate and maintain genetic
diversity in a species that inhabits heterogeneous environments (Gavery & Roberts, 2014). This means that, in theory, if the culture conditions become stressful, shellfish could
respond by modulating transposable element expression to create new genetic variation
(Rey et al., 2016), thereby having the unintended consequence of “erasing” phenotypic gains
made through selective breeding. Conclusions
Epigenetics has the potential to change the way we think about how a phenotype is
generated and maintained. Through a greater understanding of DNA methylation, histone
modifications and ncRNAs, we can functionally annotate genomes, better predict
phenotypic outcomes of early environmental exposures, and possibly select based on
epigenetic markers. With careful experimental design and special considerations for
epigenetic differences between taxa (see Lea et al., 2016), the aquaculture community is
primed to begin to integrate epigenetics into husbandry practices. The concepts and ideas
of epigenetics provide an attractive lens through which to consider the manipulation of
traits through environmental memory or the selection of beneficial traits based on
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446 been considered for finfish aquaculture (see the review by Moghadam, Mørkøre &
Robinson, 2015). Epigenetics could also make genetic selection more challenging. Manuscript to be reviewed Th
h
i
( )
ibl f
idi
hi
f h
i
i
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400 Epigenetic selection
It is possible that epigenetic markers could be integrated into broodstock selection. The
concept of epigenetic selection has gone from theory to practice in one important
agriculture commodity, oil palms, where it has been shown that it is possible to
epigenetically select for a critical trait: oil content (Ong-Abdullah et al., 2015). While there is
much more we need to learn with regard to desired phenotypes and epialleles, work such as
this demonstrates that it can be useful to consider epigenetics in association studies. Furthermore, Patel et al. (2013) showed in a clinical study that the use of both genetic (SNP)
and epigenetic (DNA methylation) markers in genome-wide association studies improved
associations with a phenotype (i.e. diabetes). The influence of epigenetics, specifically DNA
methylation, on the ability to estimate breeding values for quantitative traits has recently
405
406
407
408
409
410
411
412
413
414
415 Epigenetic selection
It is possible that epigenetic markers could be integrated into broodstock selection. The
concept of epigenetic selection has gone from theory to practice in one important
agriculture commodity, oil palms, where it has been shown that it is possible to
epigenetically select for a critical trait: oil content (Ong-Abdullah et al., 2015). While there is
much more we need to learn with regard to desired phenotypes and epialleles, work such as
this demonstrates that it can be useful to consider epigenetics in association studies. Furthermore, Patel et al. (2013) showed in a clinical study that the use of both genetic (SNP)
and epigenetic (DNA methylation) markers in genome-wide association studies improved
associations with a phenotype (i.e. diabetes). The influence of epigenetics, specifically DNA
methylation, on the ability to estimate breeding values for quantitative traits has recently
405
406
407
408
409
410
411
412
413
414
415 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed epigenetic markers. It is also important to consider that epigenetics may also function to
disrupt predictable, robust phenotypes through the creation of new, unexpected variation. Acknolledgements
The authors would like to thank Guillaume Rivière and the anonymous reviewer for their
helpful and constructive comments that greatly contributed to improving the final
version of the paper. 447
448
449
450
451
452
453 Acknolledgements
The authors would like to thank Guillaume Rivière and the anonymous reviewer for their
helpful and constructive comments that greatly contributed to improving the final
version of the paper. 450
451
452
453 The authors would like to thank Guillaume Rivière and the anonymous reviewer for their
helpful and constructive comments that greatly contributed to improving the final
version of the paper. 451
452
453 Manuscript to be reviewed Many organisms
have the potential to generate new genetic variations in response to stressful conditions
through the modulation of epigenetic marks associated with transposable elements (TEs)
(Dowen et al., 2012; Yu et al., 2013; reviewed by Rey et al., 2016). Transposable elements, or
“jumping genes”, are regions of repetitive DNA that can move and amplify their copy
number in the host genome. In the model plant Arabidopsis, the genomic response to
bacterial challenge is a global reduction of DNA methylation and the reactivation of
previously silent TEs associated with defense genes (Yu et al., 2013). It is interesting to
consider that in invertebrates, and specifically in Pacific oysters, TEs are not preferentially
methylated, though this does not preclude silencing via other epigenetic mechanisms
(Gavery & Roberts, 2013; Olson & Roberts, 2015). It has been hypothesized that the lack of
TE silencing by DNA methylation may indicate pressure to generate and maintain genetic
diversity in a species that inhabits heterogeneous environments (Gavery & Roberts, 2014). This means that, in theory, if the culture conditions become stressful, shellfish could
respond by modulating transposable element expression to create new genetic variation
(Rey et al., 2016), thereby having the unintended consequence of “erasing” phenotypic gains
made through selective breeding. 416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) References
454 Álvarez-Venegas R., De-la-Peña C. 2016. Editorial: Recent Advances of Epigenetics in Crop
Biotechnology. Frontiers in plant science 7:413. 455
456 Álvarez-Venegas R., De-la-Peña C. 2016. Editorial: Recent Advances of Epigenetics in Crop
Biotechnology. Frontiers in plant science 7:413. 455
456 Andreassen R., Worren MM., Høyheim B. 2013. Discovery and characterization of miRNA
genes in atlantic salmon (Salmo salar) by use of a deep sequencing approach. BMC genomics
14:482. 457
458
459 Andreassen R., Worren MM., Høyheim B. 2013. Discovery and characterization of miRNA
genes in atlantic salmon (Salmo salar) by use of a deep sequencing approach. BMC genomics
14:482. 457
458
459 Artemov AV., Mugue NS., Rastorguev SM., Zhenilo S., Mazur AM., Tsygankova SV., Boulygina
ES., Kaplun D., Nedoluzhko AV., Medvedeva YA., Prokhortchouk EB. 2017. Genome-Wide
DNA Methylation Profiling Reveals Epigenetic Adaptation of Stickleback to Marine and
Freshwater Conditions. Molecular biology and evolution 34:2203–2213. 460
461
462
463 Azzi A., Dallmann R., Casserly A., Rehrauer H., Patrignani A., Maier B., Kramer A., Brown SA. 2014. Circadian behavior is light-reprogrammed by plastic DNA methylation. Nature
neuroscience 17:377–382. 464
465
466 Baerwald MR., Meek MH., Stephens MR., Nagarajan RP., Goodbla AM., Tomalty KMH.,
Thorgaard GH., May B., Nichols KM. 2016. Migration-related phenotypic divergence is
associated with epigenetic modifications in rainbow trout. Molecular ecology 25:1785–
1800. 467
468
469
470 Balasubramanian MN., Panserat S., Dupont-Nivet M., Quillet E., Montfort J., Le Cam A.,
Medale F., Kaushik SJ., Geurden I. 2016. Molecular pathways associated with the nutritional
471
472 Balasubramanian MN., Panserat S., Dupont-Nivet M., Quillet E., Montfort J., Le Cam A.,
Medale F., Kaushik SJ., Geurden I. 2016. Molecular pathways associated with the nutritional
471
472 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be review Manuscript to be reviewed Manuscript to be reviewed programming of plant-based diet acceptance in rainbow trout following an early feeding
exposure. BMC genomics 17:449. 473
474 Barlow DP., Bartolomei MS. 2014. Genomic imprinting in mammals. Cold Spring Harbor
perspectives in biology 6. DOI: 10.1101/cshperspect.a018382. 475
476 Bekaert M., Lowe NR., Bishop SC., Bron JE., Taggart JB., Houston RD. 2013. Sequencing and
Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire. PloS one 8:e70136. 477
478
479 Bell AC., Felsenfeld G. 2000. Methylation of a CTCF-dependent boundary controls imprinted
expression of the Igf2 gene. Nature 405:482–485. 480
481 Bell JT., Pai AA., Pickrell JK., Gaffney DJ., Pique-Regi R., Degner JF., Gilad Y., Pritchard JK. 2011. DNA methylation patterns associate with genetic and gene expression variation in HapMap
cell lines. Genome biology 12:R10. 482
483
484 Berger SL. 2007. The complex language of chromatin regulation during transcription. Nature 447:407–412. 485
486 Bizuayehu TT., Babiak I. 2014. MicroRNA in teleost fish. Genome biology and evolution
6:1911–1937. 487
488 Bizuayehu TT., Johansen SD., Puvanendran V., Toften H., Babiak I. 2015. Temperature during
early development has long-term effects on microRNA expression in Atlantic cod. BMC
genomics 16:305. 489
490
491 Bizuayehu TT., Johansen SD., Puvanendran V., Toften H., Babiak I. 2015. Temperature during
early development has long-term effects on microRNA expression in Atlantic cod. BMC
genomics 16:305. 489
490
491 Boltaña S., Valenzuela-Miranda D., Aguilar A., Mackenzie S., Gallardo-Escárate C. 2016. Long
noncoding RNAs (lncRNAs) dynamics evidence immunomodulation during ISAV-Infected
Atlantic salmon (Salmo salar). Scientific reports 6:22698. 492
493
494 Boltaña S., Valenzuela-Miranda D., Aguilar A., Mackenzie S., Gallardo-Escárate C. 2016. Long
noncoding RNAs (lncRNAs) dynamics evidence immunomodulation during ISAV-Infected
Atlantic salmon (Salmo salar). Scientific reports 6:22698. 492
493
494 Brykczynska U., Hisano M., Erkek S., Ramos L., Oakeley EJ., Roloff TC., Beisel C., Schübeler D.,
Stadler MB., Peters AHFM. 2010. Repressive and active histone methylation mark distinct
promoters in human and mouse spermatozoa. Nature structural & molecular biology
17:679–687. 495
496
497
498 Brykczynska U., Hisano M., Erkek S., Ramos L., Oakeley EJ., Roloff TC., Beisel C., Schübeler D.,
Stadler MB., Peters AHFM. 2010. Repressive and active histone methylation mark distinct
promoters in human and mouse spermatozoa. Nature structural & molecular biology
17:679–687. 495
496
497
498 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Manuscript to be reviewed Dowen RH., Pelizzola M., Schmitz RJ., Lister R., Dowen JM., Nery JR., Dixon JE., Ecker JR. 2012. 525 Dowen RH., Pelizzola M., Schmitz RJ., Lister R., Dowen JM., Nery JR., Dixon JE., Ecker JR. 2012. Widespread dynamic DNA methylation in response to biotic stress. Proceedings of the
National Academy of Sciences of the United States of America 109:E2183–91. 525
526
527 Dowen RH., Pelizzola M., Schmitz RJ., Lister R., Dowen JM., Nery JR., Dixon JE., Ecker JR. 2012. Widespread dynamic DNA methylation in response to biotic stress. Proceedings of the
National Academy of Sciences of the United States of America 109:E2183–91. 525
526
527 Eberharter A., Becker PB. 2002. Histone acetylation: a switch between repressive and
permissive chromatin. Second in review series on chromatin dynamics. EMBO reports
3:224–229. 528
529
530 Eirín-López JM., Ausió J. 2009. Origin and evolution of chromosomal sperm proteins. BioEssays: news and reviews in molecular, cellular and developmental biology 31:1062–1070. 531
532 Eirín-López JM., Ausió J. 2009. Origin and evolution of chromosomal sp
531 Fellous A., Favrel P., Guo X., Riviere G. 2014. The Jumonji gene family in Crassostrea gigas
suggests evolutionary conservation of Jmj-C histone demethylases orthologues in the oyster
gametogenesis and development. Gene 538:164–175. 533
534
535 suggests evolutionary conservation of Jmj-C histone demethylases orthologues in the oyster
gametogenesis and development. Gene 538:164–175. 534
535 Fellous A., Favrel P., Riviere G. 2015. Temperature influences histone methylation and mRNA
expression of the Jmj-C histone-demethylase orthologues during the early development of
the oyster Crassostrea gigas. Marine genomics 19:23–30. 536
537
538 Feng S., Cokus SJ., Zhang X., Chen P-Y., Bostick M., Goll MG., Hetzel J., Jain J., Strauss SH.,
Halpern ME., Ukomadu C., Sadler KC., Pradhan S., Pellegrini M., Jacobsen SE. 2010. Conservation and divergence of methylation patterning in plants and animals. Proceedings
of the National Academy of Sciences of the United States of America 107:8689–8694. 539
540
541
542 Frehlick LJ., Eirín-López JM., Prado A., Su HWH., Kasinsky HE., Ausió J. 2006. Sperm nuclear
basic proteins of two closely related species of Scorpaeniform fish (Sebastes maliger,
Sebastolobus sp.) with different sexual reproduction and the evolution of fish protamines. Journal of experimental zoology. Part A, Comparative experimental biology 305:277–287. 543
544
545
546 Gapp K., Jawaid A., Sarkies P., Bohacek J., Pelczar P., Prados J., Farinelli L., Miska E., Mansuy
IM. 2014. Manuscript to be reviewed Burgerhout E., Mommens M., Johnsen H., Aunsmo A., Santi N., Andersen Ø. 2017. Genetic
background and embryonic temperature affect DNA methylation and expression of
myogenin and muscle development in Atlantic salmon (Salmo salar). PloS one 12:e0179918. 499
500
501 Burgerhout E., Mommens M., Johnsen H., Aunsmo A., Santi N., Andersen Ø. 2017. Genetic
background and embryonic temperature affect DNA methylation and expression of
myogenin and muscle development in Atlantic salmon (Salmo salar). PloS one 12:e0179918. 499
500
501 Buschbeck M., Uribesalgo I., Wibowo I., Rué P., Martin D., Gutierrez A., Morey L., Guigó R.,
López-Schier H., Di Croce L. 2009. The histone variant macroH2A is an epigenetic regulator
of key developmental genes. Nature structural & molecular biology 16:1074–1079. 502
503
504 Buschbeck M., Uribesalgo I., Wibowo I., Rué P., Martin D., Gutierrez A., Morey L., Guigó R.,
López-Schier H., Di Croce L. 2009. The histone variant macroH2A is an epigenetic regulator
of key developmental genes. Nature structural & molecular biology 16:1074–1079. 502
503
504 Campos C., Valente LMP., Conceição LEC., Engrola S., Fernandes JMO. 2013. Temperature
affects methylation of the myogenin putative promoter, its expression and muscle cellularity
in Senegalese sole larvae. Epigenetics: official journal of the DNA Methylation Society 8:389–
397. 505
506
507
508 Castel SE., Martienssen RA. 2013. RNA interference in the nucleus: roles for small RNAs in
transcription, epigenetics and beyond. Nature reviews. Genetics 14:100–112. 509
510 Cheung P., Allis CD., Sassone-Corsi P. 2000. Signaling to chromatin through histone
modifications. Cell 103:263–271. 511
512 Chinnusamy V., Zhu J-K. 2009. Epigenetic regulation of stress responses in plants. Current
opinion in plant biology 12:133–139. 513
514 Covelo-Soto L., Leunda PM., Pérez-Figueroa A., Morán P. 2015. Genome-wide methylation
study of diploid and triploid brown trout (Salmo trutta L.). Animal genetics 46:280–288. 515
516 ,
,
g
,
y
study of diploid and triploid brown trout (Salmo trutta L.). Animal genetics 46:280–288. 516 histone hypoacetylation in maintaining X chromosome inactivation. The Journal of cell
biology 153:773–784. 518
519 Daxinger L., Whitelaw E. 2012. Understanding transgenerational epigenetic inheritance via
the gametes in mammals. Nature reviews genetics 13:153–162. 520
521 Dolinoy DC., Weidman JR., Waterland RA., Jirtle RL. 2006. Maternal genistein alters coat
color and protects Avy mouse offspring from obesity by modifying the fetal epigenome. Environmental health perspectives 114:567–572. 522
523
524 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Manuscript to be reviewed Implication of sperm RNAs in transgenerational inheritance of the effects of early
trauma in mice. Nature neuroscience 17:667–669. 547
548
549 Gapp K., Jawaid A., Sarkies P., Bohacek J., Pelczar P., Prados J., Farinelli L., Miska E., Mansuy
IM. 2014. Implication of sperm RNAs in transgenerational inheritance of the effects of early
trauma in mice. Nature neuroscience 17:667–669. 547
548
549 Gavery MR., Roberts SB. 2013. Predominant intragenic methylation is associated with gene
expression characteristics in a bivalve mollusc. PeerJ 1:e215. 550
551 Gavery MR., Roberts SB. 2013. Predominant intragenic methylation is associated with gene
expression characteristics in a bivalve mollusc. PeerJ 1:e215. 550
551 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Gavery MR., Roberts SB. 2014. A context dependent role for DNA methylation in bivalves. Briefings in functional genomics 13:217–222. 552
553 Gavery MR., Roberts SB. 2014. A context dependent role for DNA methylation in bivalves. B i fi
i f
i
l
i
13 217 222
552
553 Gavery MR., Roberts SB. 2014. A context dependent role for DNA methylation in bivalves. Briefings in functional genomics 13:217–222. 552
553 Geurden I., Borchert P., Balasubramanian MN., Schrama JW., Dupont-Nivet M., Quillet E.,
Kaushik SJ., Panserat S., Médale F. 2013. The Positive Impact of the Early-Feeding of a Plant-
Based Diet on Its Future Acceptance and Utilisation in Rainbow Trout. PloS one 8:e83162. 554
555
556 Gluckman PD., Hanson MA., Cooper C., Thornburg KL. 2008. Effect of in utero and early-life
conditions on adult health and disease. The New England journal of medicine 359:61–73. 557
558 Goddard ME., Whitelaw E. 2014. The use of epigenetic phenomena for the improvement of
sheep and cattle. Frontiers in genetics 5:247. 559
560 González-Recio O., Toro MA., Bach A. 2015. Past, present, and future of epigenetics applied
to livestock breeding. Frontiers in genetics 6:305. 561
562 González-Romero R., Ausió J., Méndez J., Eirín-López JM. 2009. Histone genes of the razor
clam Solen marginatus unveil new aspects of linker histone evolution in protostomes. Genome 52:597–607. 563
564
565 González-Romero R., Rivera-Casas C., Frehlick LJ., Méndez J., Ausió J., Eirín-López JM. 2012. Histone H2A (H2A.X and H2A.Z) variants in molluscs: molecular characterization and
potential implications for chromatin dynamics. PloS one 7:e30006. 566
567
568 Gonzalez-Romero R., Suarez-Ulloa V., Rodriguez-Casariego J., Garcia-Souto D., Diaz G., Smith
A., Pasantes JJ., Rand G., Eirin-Lopez JM. 2017. Effects of Florida Red Tides on histone variant
expression and DNA methylation in the Eastern oyster Crassostrea virginica. Aquatic
toxicology 186:196–204. 569
570
571
572 Green TJ., Helbig K., Speck P., Raftos DA. 2016. Primed for success: Oyster parents treated
with poly(I:C) produce offspring with enhanced protection against Ostreid herpesvirus type
I infection. Molecular immunology 78:113–120. 573
574
575 Guerrero-Bosagna C., Settles M., Lucker B., Skinner MK. 2010. Epigenetic transgenerational
actions of vinclozolin on promoter regions of the sperm epigenome. PloS one 5. DOI:
10.1371/journal.pone.0013100. 576
577
578 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Manuscript to be reviewed Jonsson B. , Jonsson N. 2014. Early environment influences later performance in fishes. Journal of fish biology. 85: 151-188. 604
605 Jonsson B. , Jonsson N. 2014. Early environment influences later performance in fishes. 604 Jonsson B. , Jonsson N. 2014. Early environment influences later performance in fishes. Journal of fish biology. 85: 151-188. 604
605 Journal of fish biology. 85: 151-188. 605 Juanchich A., Bardou P., Rué O., Gabillard J-C., Gaspin C., Bobe J., Guiguen Y. 2016. 606 Characterization of an extensive rainbow trout miRNA transcriptome by next generation
sequencing. BMC genomics 17:164. 607
608 Klosin A., Casas E., Hidalgo-Carcedo C., Vavouri T., Lehner B. 2017. Transgenerational
transmission of environmental information in C. elegans. Science 356:320–323. 609
610 Knecht AL., Truong L., Marvel SW., Reif DM., Garcia A., Lu C., Simonich MT., Teeguarden JG.,
611 Knecht AL., Truong L., Marvel SW., Reif DM., Garcia A., Lu C., Simonich MT., Teeguarden JG.,
Tanguay RL. 2017. Transgenerational inheritance of neurobehavioral and physiological
611
612 Knecht AL., Truong L., Marvel SW., Reif DM., Garcia A., Lu C., Simonich MT., Teeguarden JG.,
Tanguay RL. 2017. Transgenerational inheritance of neurobehavioral and physiological
deficits from developmental exposure to benzo[a]pyrene in zebrafish. Toxicology and
applied pharmacology 329:148–157. 611
612
613
614 Tanguay RL. 2017. Transgenerational inheritance of neurobehavioral and physiological
deficits from developmental exposure to benzo[a]pyrene in zebrafish. Toxicology and
612
613 g
y
g
p y
g
deficits from developmental exposure to benzo[a]pyrene in zebrafish. Toxicology and
applied pharmacology 329:148–157. 613
614 Labbé C., Robles V., Herraez MP. 2017. Epigenetics in fish gametes and early embryo. Aquaculture 472:93–106. 615
616 Lawrence M., Daujat S., Schneider R. 2016. Lateral Thinking: How Histone Modifications
Regulate Gene Expression. Trends in genetics: TIG 32:42–56. 617
618 Le Luyer J., Laporte M., Beacham TD., Kaukinen KH., Withler RE., Leong JS., Rondeau EB.,
Koop BF., Bernatchez L. 2017. Parallel epigenetic modifications induced by hatchery rearing
in a Pacific Salmon. bioRxiv:148577. DOI: 10.1101/148577. 619
620
621 Le Luyer J., Laporte M., Beacham TD., Kaukinen KH., Withler RE., Leong JS., Rondeau EB.,
Koop BF., Bernatchez L. 2017. Parallel epigenetic modifications induced by hatchery rearing
in a Pacific Salmon. bioRxiv:148577. DOI: 10.1101/148577. 619
620
621 Lea A., Vilgalys T., Durst P., Tung J. 2017. Maximizing ecological and evolutionary insight
from bisulfite sequencing data sets. Nature ecology and evolution 1:1074
622
623 Lea A., Vilgalys T., Durst P., Tung J. 2017. Manuscript to be reviewed Hauser M-T., Aufsatz W., Jonak C., Luschnig C. 2011. Transgenerational epigenetic
inheritance in plants. Biochimica et biophysica acta 1809:459–468. 579
580 Heijmans BT., Tobi EW., Stein AD., Putter H., Blauw GJ., Susser ES., Slagboom PE., Lumey LH. 2008. Persistent epigenetic differences associated with prenatal exposure to famine in
humans. Proceedings of the National Academy of Sciences of the United States of America
105:17046–17049. 581
582
583
584 Henikoff S., Smith MM. 2015. Histone variants and epigenetics. Cold Spring Harbor
perspectives in biology 7:a019364. 585
586 Hettinger A., Sanford E., Hill TM., Russell AD., Sato KNS., Hoey J., Forsch M., Page HN., Gaylord
B. 2012. Persistent carry-over effects of planktonic exposure to ocean acidification in the
Olympia oyster. Ecology 93:2758–2768. 587
588
589 Houwing S., Kamminga LM., Berezikov E., Cronembold D., Girard A., van den Elst H., Filippov
DV., Blaser H., Raz E., Moens CB., Plasterk RHA., Hannon GJ., Draper BW., Ketting RF. 2007. A
role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell 129:69–82. 590
591
592
593 Jabbari K., Cacciò S., Païs de Barros JP., Desgrès J., Bernardi G. 1997. Evolutionary changes in
CpG and methylation levels in the genome of vertebrates. Gene 205:109–118. 594
595 Jablonka E., Lamb MJ. 2002. The changing concept of epigenetics. Annals of the New York
Academy of Sciences 981:82–96. 596
597 Jenuwein T., Allis CD. 2001. Translating the histone code. Science 293:1074–1080. 598 Jiang Q., Li Q., Yu H., Kong L-F. 2013. Genetic and epigenetic variation in mass selection
populations of Pacific oyster Crassostrea gigas. Genes & genomics 35:641–647. 599
600 Jiang Q., Li Q., Yu H., Kong L. 2016. Inheritance and Variation of Genomic D
01 Jiang Q., Li Q., Yu H., Kong L. 2016. Inheritance and Variation of Genomic DNA Methylation in
Diploid and Triploid Pacific Oyster (Crassostrea gigas). Marine biotechnology 18:124–132. 601
602 J
g Q ,
Q ,
,
g
y
Diploid and Triploid Pacific Oyster (Crassostrea gigas). Marine biotechnology 18:124–132. 602 Jones PA. 1999. The DNA methylation paradox. Trends in genetics: TIG 15:34–37. 603 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Maximizing ecological and evolutionary insight
from bisulfite sequencing data sets. Nature ecology and evolution 1:1074
622
623 Li E., Bestor TH., Jaenisch R. 1992. Targeted mutation of the DNA methyltransferase gene
results in embryonic lethality. Cell 69:915–926. 624
625 Li M., Leatherland JF. 2013. The implications for aquaculture practice of epigenomic
programming of components of the endocrine system of teleostean embryos: lessons
learned from mammalian studies. Fish and fisheries 14:528–553. 626
627
628 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Manuscript to be reviewed Navarro-Martín L., Blázquez M., Viñas J., Joly S., Piferrer F. 2009. Balancing the effects of
rearing at low temperature during early development on sex ratios, growth and maturation
in the European sea bass (Dicentrarchus labrax).: Limitations and opportunities for the
production of highly female-biased stocks. Aquaculture 296:347–358. 655
656
657
658 Navarro-Martín L., Viñas J., Ribas L., Díaz N., Gutiérrez A., Di Croce L., Piferrer F. 2011. DNA
Methylation of the Gonadal Aromatase (cyp19a) Promoter Is Involved in Temperature-
Dependent Sex Ratio Shifts in the European Sea Bass. PLoS genetics 7:e1002447. 659
660
661 Navarro-Martín L., Viñas J., Ribas L., Díaz N., Gutiérrez A., Di Croce L., Piferrer F. 2011. DNA
Methylation of the Gonadal Aromatase (cyp19a) Promoter Is Involved in Temperature-
Dependent Sex Ratio Shifts in the European Sea Bass. PLoS genetics 7:e1002447. 659
660
661 Olson CE., Roberts SB. 2014. Genome-wide profiling of DNA methylation and gene
expression in Crassostrea gigas male gametes. Frontiers in physiology 5:224. 662
663 Olson CE., Roberts SB. 2014. Genome-wide profiling of DNA methylation and gene
expression in Crassostrea gigas male gametes. Frontiers in physiology 5:224. 662
663 Olson CE., Roberts SB. 2015. Indication of family-specific DNA methylation patterns in
developing oysters. bioRxiv:012831. DOI: 10.1101/012831. 664
665 Olson CE., Roberts SB. 2015. Indication of family-specific DNA methylation patterns in
developing oysters. bioRxiv:012831. DOI: 10.1101/012831. 664
665 Ong-Abdullah M., Ordway JM., Jiang N., Ooi S-E., Kok S-Y., Sarpan N., Azimi N., Hashim AT.,
Ishak Z., Rosli SK., Malike FA., Bakar NAA., Marjuni M., Abdullah N., Yaakub Z., Amiruddin
MD., Nookiah R., Singh R., Low E-TL., Chan K-L., Azizi N., Smith SW., Bacher B., Budiman MA.,
Van Brunt A., Wischmeyer C., Beil M., Hogan M., Lakey N., Lim C-C., Arulandoo X., Wong C-K.,
Choo C-N., Wong W-C., Kwan Y-Y., Sharifah Shahrul Rabiah., Sambanthamurthi R.,
Martienssen RA. 2015. Loss of Karma transposon methylation underlies the mantled
somaclonal variant of oil palm. Nature 525:533–537. 666
667
668
669
670
671
672 Paneru B., Al-Tobasei R., Palti Y., Wiens GD., Salem M. 2016. Differential expression of long
non-coding RNAs in three genetic lines of rainbow trout in response to infection with
Flavobacterium psychrophilum. Scientific reports 6:36032. 673
674
675 Paneru B., Al-Tobasei R., Palti Y., Wiens GD., Salem M. 2016. Differential expression of long
non-coding RNAs in three genetic lines of rainbow trout in response to infection with
Flavobacterium psychrophilum. Scientific reports 6:36032. Manuscript to be reviewed Lin W., Dent S.Y. 2006. Functions of histone-modifying enzymes in development. Current
opinion in genetics and development 16:137–142. 629
630 Ma H., Hostuttler M., Wei H., Rexroad CE 3rd., Yao J. 2012. Characterization of the rainbow
trout egg microRNA transcriptome. PloS one 7:e39649. 631
632 Maloisel L., Rossignol JL. 1998. Suppression of crossing-over by DNA methylation in
Ascobolus. Genes & development 12:1381–1389. 633
634 Manikkam M., Guerrero-Bosagna C., Tracey R., Haque MM., Skinner MK. 2012. 635 Manikkam M., Guerrero-Bosagna C., Tracey R., Haque MM., Skinner MK. 2012. Transgenerational Actions of Environmental Compounds on Reproductive Disease and
Identification of Epigenetic Biomarkers of Ancestral Exposures PloS one 7:e31901
635
636
637 Manikkam M., Guerrero Bosagna C., Tracey R., Haque MM., Skinner MK. 2012. Transgenerational Actions of Environmental Compounds on Reproductive Disease and
Identification of Epigenetic Biomarkers of Ancestral Exposures. PloS one 7:e31901. 635
636
637 Transgenerational Actions of Environmental Compounds on Reproduct
636 Marandel L., Lepais O., Arbenoits E., Véron V., Dias K., Zion M., Panserat S. 2016. Remodelling
of the hepatic epigenetic landscape of glucose-intolerant rainbow trout (Oncorhynchus
mykiss) by nutritional status and dietary carbohydrates. Scientific reports 6:32187. 638
639
640 Martin C., Zhang Y. 2005. The diverse functions of histone lysine methylation. Nature
reviews. Molecular cell biology 6:838–849. 641
642 Mercer TR., Dinger ME., Mattick JS. 2009. Long non-coding RNAs: insights into functions. Nature reviews. Genetics 10:155–159. 643
644 Metzger DCH., Schulte PM. 2016. Epigenomics in marine fishes. Marine genomics 30:43–54. 645 Moghadam H., Mørkøre T., Robinson N. 2015. Epigenetics—Potential for Programming Fish
for Aquaculture? Journal of marine science and engineering 3:175–192. 646
647 Morán P., Marco-Rius F., Megías M., Covelo-Soto L., Pérez-Figueroa A. 2013. Environmental
induced methylation changes associated with seawater adaptation in brown trout. Aquaculture 392-395. DOI: 10.1016/j.aquaculture.2013.02.006. 648
649
650 Morán P., Pérez-Figueroa A. 2011. Methylation changes associated with early maturation
stages in the Atlantic salmon. BMC genetics 12:86. 651
652 Munday PL. 2014. Transgenerational acclimation of fishes to climate change and ocean
acidification. F1000prime reports 6:99. 653
654 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Manuscript to be reviewed Parker LM., Ross PM., O’Connor WA., Borysko L., Raftos DA., Pörtner H-O. 2012. Adult
exposure influences offspring response to ocean acidification in oysters. Global change
biology 18:82–92. 683
684
685 Patel CJ., Chen R., Kodama K., Ioannidis JPA., Butte AJ. 2013. Systematic identification of
interaction effects between genome- and environment-wide associations in type 2 diabetes
mellitus. Human genetics 132:495–508. 686
687
688 Peschansky VJ., Wahlestedt C. 2014. Non-coding RNAs as direct and indirect modulators of
epigenetic regulation. Epigenetics: official journal of the DNA Methylation Society 9:3–12. 689
690 Potok ME., Nix DA., Parnell TJ., Cairns BR. 2013. Reprogramming the maternal zebrafish
genome after fertilization to match the paternal methylation pattern. Cell 153:759–772. 691
692 Rechavi O., Houri-Ze’evi L., Anava S., Goh WSS., Kerk SY., Hannon GJ., Hobert O. 2014. 693 Starvation-induced transgenerational inheritance of small RNAs in C. elegans. Cell 158:277–
287. 694
695 Rey O., Danchin E., Mirouze M., Loot C., Blanchet S. 2016. Adaptation to Global Change: A
Transposable Element–Epigenetics Perspective. Trends in ecology & evolution 31:514–526. 696
697 Rivera-Casas C., Gonzalez-Romero R., Garduño RA., Cheema MS., Ausio J., Eirin-Lopez JM. 2017. Molecular and Biochemical Methods Useful for the Epigenetic Characterization of
Chromatin-Associated Proteins in Bivalve Molluscs. Frontiers in physiology 8:490. 698
699
700 Rivera-Casas C., Gonzalez-Romero R., Garduño RA., Cheema MS., Ausio J., Eirin-Lopez JM. 2017. Molecular and Biochemical Methods Useful for the Epigenetic Characterization of
Chromatin-Associated Proteins in Bivalve Molluscs. Frontiers in physiology 8:490. 698
699
700 2017. Molecular and Biochemical Methods Useful for the Epigenetic Characterization of
Chromatin-Associated Proteins in Bivalve Molluscs. Frontiers in physiology 8:490. 699
700 Riviere G., He Y., Tecchio S., Crowell E., Gras M., Sourdaine P., Guo X., Favrel P. 2017. Dynamics
of DNA methylomes underlie oyster development. PLoS genetics 13:e1006807. 701
702 Riviere G., He Y., Tecchio S., Crowell E., Gras M., Sourdaine P., Guo X., Favrel P. 2017. Dynamics
of DNA methylomes underlie oyster development. PLoS genetics 13:e1006807. 701
702 Riviere G., He Y., Tecchio S., Crowell E., Gras M., Sourdaine P., Guo X., Favrel P. 2017. Dynamics
of DNA methylomes underlie oyster development. PLoS genetics 13:e1006807. 701
702 Rodgers AB., Morgan CP., Leu NA., Bale TL. 2015. Transgenerational epigenetic
programming via sperm microRNA recapitulates effects of paternal stress. Proceedings of
the National Academy of Sciences 112:13699–13704. 703
704
705 Rodgers AB., Morgan CP., Leu NA., Bale TL. 2015. Manuscript to be reviewed 673
674
675 Panserat S., Marandel L., Geurden I., Veron V., Dias K., Plagnes-Juan E., Pegourié G., Arbenoits
E., Santigosa E., Weber G., Verlhac Trichet V. 2017. Muscle catabolic capacities and global
hepatic epigenome are modified in juvenile rainbow trout fed different vitamin levels at first
feeding. Aquaculture 468, Part 1:515–523. 676
677
678
679 Panserat S., Marandel L., Geurden I., Veron V., Dias K., Plagnes-Juan E., Pegourié G., Arbenoits
E., Santigosa E., Weber G., Verlhac Trichet V. 2017. Muscle catabolic capacities and global
hepatic epigenome are modified in juvenile rainbow trout fed different vitamin levels at first
feeding. Aquaculture 468, Part 1:515–523. 676
677
678
679 Parker LM., O’Connor WA., Raftos DA., Pörtner H-O., Ross PM. 2015. Persistence of Positive
Carryover Effects in the Oyster, Saccostrea glomerata, following Transgenerational Exposure
to Ocean Acidification. PloS one 10:e0132276. 680
681
682 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Transgenerational epigenetic
programming via sperm microRNA recapitulates effects of paternal stress. Proceedings of
the National Academy of Sciences 112:13699–13704. 703
704
705 Rondon R., Grunau C., Fallet M., Charlemagne N., Sussarellu R., Chaparro C., Montagnani C.,
Mitta G., Bachère E., Akcha F., Cosseau C. 2017. Effects of a parental exposure to diuron on
Pacific oyster spat methylome. DOI: 10.1093/eep/dvx004. 706
707
708 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Manuscript to be reviewed Rosani U., Pallavicini A., Venier P. 2016. The miRNA biogenesis in marine bivalves. PeerJ
4:e1763. 709
710 Salinas S., Brown SC., Mangel M., Munch SB. 2013. Non-genetic inheritance and changing
environments. Non-Genetic Inheritance 1. DOI: 10.2478/ngi-2013-0005. 711
712 Sellos D. 1985. The histones isolated from the sperm of the oyster Crassostrea gigas. Cell
differentiation 17:183–192. 713
714 Shao C., Li Q., Chen S., Zhang P., Lian J., Hu Q., Sun B., Jin L., Liu S., Wang Z., Zhao H., Jin Z.,
Liang Z., Li Y., Zheng Q., Zhang Y., Wang J., Zhang G. 2014. Epigenetic modification and
inheritance in sexual reversal of fish. Genome research 24:604–615. 715
716
717 Simmen MW., Leitgeb S., Charlton J., Jones SJ., Harris BR., Clark VH., Bird A. 1999. 718 Nonmethylated transposable elements and methylated genes in a chordate genome. Science
283:1164–1167. 719
720 Soubry A., Hoyo C., Jirtle RL., Murphy SK. 2014. A paternal environmental legacy: evidence
for epigenetic inheritance through the male germ line. BioEssays: news and reviews in
molecular, cellular and developmental biology 36:359–371. 721
722
723 Stewart S., Tsun Z-Y., Izpisua Belmonte JC. 2009. A histone demethylase is necessary for
regeneration in zebrafish. Proceedings of the National Academy of Sciences of the United
States of America 106:19889–19894. 724
725
726 Strömqvist M., Tooke N., Brunström B. 2010. DNA methylation levels in the 5’ flanking
region of the vitellogenin I gene in liver and brain of adult zebrafish (Danio rerio)--sex and
tissue differences and effects of 17alpha-ethinylestradiol exposure. Aquatic toxicology
98:275–281. 727
728
729
730 Talbert PB., Henikoff S. 2010. Histone variants--ancient wrap artists of the epigenome. Nature reviews. Molecular cell biology 11:264–275. 731
732 Talbert PB., Henikoff S. 2014. Environmental responses mediated by histone variants. Trends in cell biology 24:642–650. 733
734 Talbert PB., Henikoff S. 2014. Environmental responses mediated by histone variants. Trends in cell biology 24:642 650
733
734 Talbert PB., Henikoff S. 2014. Environmental responses mediated by histone variants. Trends in cell biology 24:642–650. 733
734 ,
p
y
Trends in cell biology 24:642–650. 734 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Terova G., Díaz N., Rimoldi S., Ceccotti C., Gliozheni E., Piferrer F. 2016. Effects of Sodium
Butyrate Treatment on Histone Modifications and the Expression of Genes Related to
Epigenetic Regulatory Mechanisms and Immune Response in European Sea Bass
(Dicentrarchus Labrax) Fed a Plant-Based Diet. PloS one 11:e0160332. 735
736
737
738 Terova G., Díaz N., Rimoldi S., Ceccotti C., Gliozheni E., Piferrer F. 2016. Effects of Sodium
735 Terova G., Díaz N., Rimoldi S., Ceccotti C., Gliozheni E., Piferrer F. 2016. Effects of Sodium
Butyrate Treatment on Histone Modifications and the Expression of Genes Related to
Epigenetic Regulatory Mechanisms and Immune Response in European Sea Bass
(Dicentrarchus Labrax) Fed a Plant-Based Diet. PloS one 11:e0160332. 735
736
737
738 Terova G., Díaz N., Rimoldi S., Ceccotti C., Gliozheni E., Piferrer F. 2016. Effects of Sodium
Butyrate Treatment on Histone Modifications and the Expression of Genes Related to
Epigenetic Regulatory Mechanisms and Immune Response in European Sea Bass
(Di
h
L b
) F d
Pl
B
d Di
Pl S
11 0160332
735
736
737
738 Butyrate Treatment on Histone Modifications and the Expression of Genes Related to
736 (Dicentrarchus Labrax) Fed a Plant-Based Diet. PloS one 11:e0160332. 738 Tweedie S., Charlton J., Clark V., Bird A. 1997. Methylation of genomes and genes at the
invertebrate-vertebrate boundary. Molecular and cellular biology 17:1469–1475. 739
740 Tweedie S., Charlton J., Clark V., Bird A. 1997. Methylation of genomes and genes at the
invertebrate-vertebrate boundary. Molecular and cellular biology 17:1469–1475. 739
740 Utting SD., Millican PF. 1997. Techniques for the hatchery conditioning of bivalve
broodstocks and the subsequent effect on egg quality and larval viability. Aquaculture
741
742 Utting SD., Millican PF. 1997. Techniques for the hatchery conditioning of bivalve
broodstocks and the subsequent effect on egg quality and larval viability. Aquaculture
155:45–54
741
742
743 Utting SD., Millican PF. 1997. Techniques for the hatchery conditioning
741 broodstocks and the subsequent effect on egg quality and larval viability. Aquaculture
155:45–54. 742
743 Valenzuela-Miranda D., Gallardo-Escárate C. 2016. Novel insights into the response of
Atlantic salmon (Salmo salar) to Piscirickettsia salmonis: Interplay of coding genes and
lncRNAs during bacterial infection. Fish & shellfish immunology 59:427–438. 744
745
746 Atlantic salmon (Salmo salar) to Piscirickettsia salmonis: Interplay of coding genes and
lncRNAs during bacterial infection. Fish & shellfish immunology 59:427–438. Manuscript to be reviewed 745
746 t a t c sa
o (Sa
o sa a ) to
sc
c etts a sa
o
s:
te p ay o cod
g ge es a d
lncRNAs during bacterial infection. Fish & shellfish immunology 59:427–438. 5
746 Vastenhouw NL., Schier AF. 2012. Bivalent histone modifications in early embryogenesis. Current opinion in cell biology 24:374–386. 747
748 Venney CJ., Johansson ML., Heath DD. 2016. Inbreeding effects on gene-specific DNA
methylation among tissues of Chinook salmon. Molecular ecology 25:4521–4533. 749
750 Wang KC., Chang HY. 2011. Molecular mechanisms of long noncoding RNAs. Mol Cell. 43(6):
904–914. 751
752 Wang Y., Wang C., Zhang J., Chen Y., Zuo Z. 2009. DNA hypomethylation induced by
tributyltin, triphenyltin, and a mixture of these in Sebastiscus marmoratus liver. Aquatic
toxicology 95:93–98. 753
754
755 Weaver ICG., Cervoni N., Champagne FA., D’Alessio AC., Sharma S., Seckl JR., Dymov S., Szyf
M., Meaney MJ. 2004. Epigenetic programming by maternal behavior. Nature neuroscience
7:847–854. 756
757
758 Wheeler BM., Heimberg AM., Moy VN., Sperling EA., Holstein TW., Heber S., Peterson KJ. 2009. The deep evolution of metazoan microRNAs. Evolution & development 11:50–68. 759
760 Wheeler BM., Heimberg AM., Moy VN., Sperling EA., Holstein TW., Heber S., Peterson KJ. 2009. The deep evolution of metazoan microRNAs. Evolution & development 11:50–68. 759
760 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Manuscript to be reviewed Manuscript to be reviewed Wu N., Yue H-M., Chen B., Gui J-F. 2009. Histone H2A has a novel variant in fish oocytes. 761 Biology of reproduction 81:275–283. 762 Wu S-F., Zhang H., Cairns BR. 2011. Genes for embryo development are packaged in blocks
of multivalent chromatin in zebrafish sperm. Genome research 21:578–589. 763
764 Yu A., Lepère G., Jay F., Wang J., Bapaume L., Wang Y., Abraham A-L., Penterman J., Fischer
RL., Voinnet O., Navarro L. 2013. Dynamics and biological relevance of DNA demethylation
in Arabidopsis antibacterial defense. Proceedings of the National Academy of Sciences of the
United States of America 110:2389–2394. 765
766
767
768 Yu H., Zhao X., Li Q. 2016. Genome-wide identification and characterization of long
769 intergenic noncoding RNAs and their potential association with larval development in the
Pacific oyster. Scientific reports 6:20796. 770
771 intergenic noncoding RNAs and their potential association with larval development in the
Pacific oyster. Scientific reports 6:20796. 770
771 Zemach A., McDaniel IE., Silva P., Zilberman D. 2010. Genome-wide evolutionary analysis of
eukaryotic DNA methylation. Science 328:916–919. 772
773 Zemach A., McDaniel IE., Silva P., Zilberman D. 2010. Genome-wide evolutionary analysis of
eukaryotic DNA methylation. Science 328:916–919. 772
773 Zhang C., Hoshida Y., Sadler KC. 2016. Comparative Epigenomic Profiling of the DNA
Methylome in Mouse and Zebrafish Uncovers High Interspecies Divergence. Frontiers in
genetics 7:110. 774
775
776 Zhao L., Schöne BR., Mertz-Kraus R., Yang F. 2017. Sodium provides unique insights into
transgenerational effects of ocean acidification on bivalve shell formation. The Science of the
total environment 577:360–366. 777
778
779 Zhou H., Ma T-Y., Zhang R., Xu Q-Z., Shen F., Qin Y-J., Xu W., Wang Y., Li Y-J. 2016. Analysis of
Different Ploidy and Parent-Offspring Genomic DNA Methylation in the Loach Misgurnus
anguillicaudatus. International journal of molecular sciences 17. DOI:
10.3390/ijms17081299. 780
781
782
783 Zhou H., Ma T-Y., Zhang R., Xu Q-Z., Shen F., Qin Y-J., Xu W., Wang Y., Li Y-J. 2016. Analysis of
Different Ploidy and Parent-Offspring Genomic DNA Methylation in the Loach Misgurnus
anguillicaudatus. International journal of molecular sciences 17. DOI:
10.3390/ijms17081299. 780
781
782
783 785 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Manuscript to be reviewed Manuscript to be reviewed Manuscript to be reviewed Figure 1. Schematic diagram of the aquaculture life-cycle highlighting key areas
lhere epigenetics could be applied to improve productivity and efficiency: Epigenetic
selection (red text) could be used, alone or in combination with genetic selection, to identify
individuals with desired traits. Environmental manipulation (blue text) refers to generating
environmentally-driven phenotypes mediated through epigenetic mechanisms. Two life
stages which may be particularly sensitive to generating within- or between-generation
‘epigenetic memories’ are larvae and broodstock, respectively. 786
787
788
789
790
791
792 Figure 1. Schematic diagram of the aquaculture life-cycle highlighting key areas
lhere epigenetics could be applied to improve productivity and efficiency: Epigenetic
selection (red text) could be used, alone or in combination with genetic selection, to identify
individuals with desired traits. Environmental manipulation (blue text) refers to generating
environmentally-driven phenotypes mediated through epigenetic mechanisms. Two life
stages which may be particularly sensitive to generating within- or between-generation
‘epigenetic memories’ are larvae and broodstock, respectively. 786
787
788
789
790
791
792 PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017) Figure 1 Schematic diagram of the aquaculture life-cycle highlighting key areas where
epigenetics could be applied to improve productivity and efficiency Epigenetic selection (red text) could be used, alone or in combination with genetic selection,
to identify individuals with desired traits. Environmental manipulation (blue text) refers to
generating environmentally-driven phenotypes mediated through epigenetic mechanisms. Two life stages which may be particularly sensitive to generating within- or between-
generation ‘epigenetic memories’ are larvae and broodstock, respectively. PeerJ reviewing PDF | (2017:08:20067:1:0:NEW 13 Nov 2017)
|
https://openalex.org/W4287219364
|
https://www.research-collection.ethz.ch/bitstream/20.500.11850/563579/3/fphar-13-916641.pdf
|
English
| null |
Buddhist-like opposite diminishing and non-judging during ketamine infusion are associated with antidepressant response: an open-label personalized-dosing study
|
Frontiers in pharmacology
| 2,022
|
cc-by
| 11,197
|
ETH Library Author(s): ( )
Stocker, Kurt; Hartmann, Matthias; Reissmann, Steffen; Kist, Andreas; Liechti, Matthias E. Rights / license: Originally published in:
Frontiers in Pharmacology 13, https://doi.org/10.3389/fphar.2022.916641 This page was generated automatically upon download from the ETH Zurich Research Collection. For more information, please consult the Terms of use. TYPE Original Research
PUBLISHED 25 July 2022
DOI 10.3389/fphar.2022.916641 TYPE Original Research
PUBLISHED 25 July 2022
DOI 10.3389/fphar.2022.916641 Buddhist-like opposite
diminishing and non-judging
during ketamine infusion are
associated with antidepressant
response: an open-label
personalized-dosing study OPEN ACCESS
EDITED BY
Candace R. Lewis,
Arizona State University, United States
REVIEWED BY
Kai Zhang,
Anhui Medical University, China
Lijia Chang,
Chiba University, Japan
*CORRESPONDENCE
Kurt Stocker,
kurt.stocker@usb.ch
SPECIALTY SECTION
This article was submitted to
Neuropharmacology,
a section of the journal
Frontiers in Pharmacology
RECEIVED 09 April 2022
ACCEPTED 30 June 2022
PUBLISHED 25 July 2022 OPEN ACCESS
EDITED BY
Candace R. Lewis,
Arizona State University, United States
REVIEWED BY
Kai Zhang,
Anhui Medical University, China
Lijia Chang,
Chiba University, Japan Kurt Stocker 1,2,3,4*, Matthias Hartmann4, Steffen Reissmann3,
Andreas Kist 5 and Matthias E. Liechti1 1Psychopharmacology Research, Division of Clinical Pharmacology and Toxicology, Department of
Clinical Research, University Hospital Basel and University of Basel, Basel, Switzerland, 2Chair of
Cognitive Science, Department of Humanities, Social and Political Sciences, ETH Swiss Federal
Institute of Technology Zurich, Zurich, Switzerland, 3Department of Psychology, University of Zurich,
Zurich, Switzerland, 4Faculty of Psychology, UniDistance Suisse, Brig, Switzerland, 5Medical Office for
Anesthesiology Zelenka and Colleagues, Villingen-Schwenningen, Germany CITATION
Stocker K, Hartmann M, Reissmann S,
Kist A and Liechti ME (2022), Buddhist-
like opposite diminishing and non-
judging during ketamine infusion are
associated with antidepressant
response: an open-label personalized-
dosing study. Background: Cognition that is not dominated by thinking in terms of opposites
(opposite diminishing) or by making judgments (non-judging) can be found
both in Buddhist/mindfulness contexts and in mental states that are fostered by
dissociative
psychedelics
(N-methyl-D-aspartate
antagonists)
such
as
ketamine. Especially for
the Buddhist/mindfulness case,
both
opposite
diminishing and non-judging have been proposed to relate to mental well-
being. Whether ketamine-occasioned opposite diminishing and/or non-
judging relate to increased mental well-being in the form of antidepressant
response is unknown, and was investigated in the present study. Front. Pharmacol. 13:916641. doi: 10.3389/fphar.2022.916641 Front. Pharmacol. 13:916641. doi: 10.3389/fphar.2022.916641 Introduction judging” (e.g., Kabat-Zinn, 2003, p. 150)—stance toward one’s
current mental life or one’s current life in general. Descriptions of mental realms where one’s cognition is not
dominated
by thinking
in
terms
of
opposites
(opposite
diminishing) and where one’s cognition is not dominated by
making judgments (non-judging) can be found both in relation
to Buddhist meditation and its modern secularized mindfulness
forms and in relation to mental states that are occasioned by
dissociative
psychedelics
(N-methyl-D-aspartate,
NMDA,
antagonists)
such
as
ketamine. Additionally,
opposite
diminishing
and
non-judging
have
also
been
(mostly
theoretically) proposed to be associated with increased mental
well-being, especially in the Buddhist/mindfulness-meditation
case (Kabat-Zinn, 2003; Kornfield, 2008). Although in Buddhist/
mindfulness-meditation opposite diminishing, non-judging, and
mental well-being are usually characterized to be able to occur in
close relation to one another (e.g., Kornfield, 2008, pp. 376–381),
it is not known for dissociative psychedelics whether these three
characteristics can also occur in relation to one another. This
study sets out to investigate these issues with regard to the
NMDA receptor antagonist ketamine. This study is to our
knowledge the first investigating whether a) the occurrence of
opposite diminishing, non-judging, and well-being (measured
here as a decrease in depression) can occur in interrelated ways
within the ketamine experience, and b) if they do, whether the
occurrence of opposite diminishing and/or non-judging can
predict
antidepressant
response
in
ketamine-treated
individuals suffering from depression. In the remainder of this
introduction,
we
first
lay
out
the
relevant
background
information that is needed to understand our experimental
hypotheses,
before
then
presenting
the
experimental
hypotheses and how we investigated them. The non-judging aspect in relation to being mindful is well
known and is also covered in most mindfulness questionnaires
(Buchheld et al., 2001; Baer et al., 2004, 2006; Bishop et al., 2004;
Walach et al., 2006; Feldman et al., 2007; Cardaciotto et al., 2008;
Chadwick et al., 2008). However, Buddhist and mindfulness
scholars sometimes describe non-judgment to be related to a
mental realm where one seems to be no longer thinking about
things in terms of opposites. This relationship has not been
investigated by the modern mindfulness research community. For exemplification, consider the following passage of Jon Kabat
Zinn the founder of the mindfulness-based-stress-reduction
program: So, when we speak of mindfulness as being non-judgmental
awareness, it doesn’t mean that there won’t be judgements. COPYRIGHT
© 2022 St COPYRIGHT
© 2022 Stocker, Hartmann, Reissmann,
Kist and Liechti. 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. Methods: In this open-label outpatient study, the dose level and frequency for
the ketamine infusions were adjusted individually in close consultation with the
patients suffering from depression with the overall goal to maximize
antidepressant benefits—a novel dose regimen that we term personalized
antidepressant dosing. In general, treatment started with an initial series of
ketamine infusions with a dosage of 0.5 mg/kg body weight and was then
adjusted (usually increased). A possible relationship between ketamine-induced
antidepressant benefits and retrospectively reported peri-infusion experiences
of opposite diminishing and non-judging was assessed based on a total of
45 ketamine-infusion treatment sessions from 11 different patients suffering
from depression. Opposite diminishing and non-judging were measured with
the two items from the Altered States of Consciousness Inventory (ASCI) that
measure these concepts. Depression was measured with the Beck Depression
Inventory (BDI-II). Results: Peri-infusion experiences of both opposite diminishing and non-
judging were associated with antidepressant responses confirming our
hypothesis. Furthermore, opposite diminishing and non-judging were closely 01 Frontiers in Pharmacology Frontiers in Pharmacology frontiersin.org Stocker et al. 10.3389/fphar.2022.916641 10.3389/fphar.2022.916641 related
to
one
another
while
relating
to
antidepressant
response
in
distinguishable ways. Conclusion: Future controlled randomized trials with dissociative and other
psychedelics and with a larger number of participants are needed to establish
the possible link of psychedelically induced opposite diminishing and non-
judging with an antidepressant response more firmly. Stocker et al. Introduction It
means that you will be aware of how judgmental we actually
are, and then “not judge” the judging, and when we relate to it
in that kind of a way, then we begin to see that our judging is
very often “black and white.” It’s either this or that, good or
bad, like—dislike, want—don’t want. And we get imprisoned
by that kind of view . . . being non-judgmental . . . means that
we will cultivate discernment. This is the capacity to see
what’s actually unfolding, but not to judge it, but to recognize
it, and to understand it, in relationship to our experience . . . In over days, weeks, months, and years, we can begin to
actually find a way to navigate through are judging, in such a
way that it no longer dominates our lives in quite the same
way, and we recognize when it comes up, that it’s actually in
some sense “toxic,” and the more we challenge it, and the
more we rest in discernment and in pure awareness, the more
we can live life authentically in the present moment, without
getting caught by our own “habits of mind”—“unhealthy” if
you will, “habits of mind” (Kabat-Zinn (n.d.) in Spiritual
Mind, 2022, 0:48). While the term “mindfulness” is defined differently in
Buddhist and modern research-community contexts (Dahl
et al., 2015; Brandmeyer et al., 2019), in the research
community, it “often refers to a self-regulated attentional
stance oriented toward the present-moment experience that is
characterized by curiosity, openness, and acceptance” (Dahl
et
al.,
2015,
p. 516),
which
includes
“a
non-evaluative
awareness of one’s thoughts, emotions, and other experiences
in the moment” (Lebois et al., 2015, p. 506). Thus, mindfulness
involves an accepting, non-evaluative—often also termed a “non- In
this
passage,
Kabat-Zinn
clearly
associates
being
judgmental with thinking in opposites, as he says that judging
“very often” involves thinking about things in terms of “black and
white.” This also implies that being non-judgmental relates to
thinking less (or perhaps at times not at all) in terms of opposites Frontiers in Pharmacology 02 frontiersin.org 10.3389/fphar.2022.916641 Stocker et al. (implies that non-judging relates to opposite diminishing). Kabat-Zinn’s description is also in line with how many non-
judging questions are phrased in mindfulness questionnaires. Introduction To
give one example, four out of the 11 questions that make up the
factor “non-judging of experience” in the five facets mindfulness
questionnaire are phrased in terms of opposite pairs—e.g., “I
make judgments about whether my thoughts are good or bad”
(Baer et al., 2006, p. 35). It is important to note, however, that
while it is true that opposite diminishing (thinking less in terms
of opposites) is often associated with non-judging by mindfulness
scholars and in mindfulness research, this usually only happens
implicitly (by often using opposite examples when describing
non-judging, but by not making the opposite topic explicit). To
our knowledge, opposite diminishing as such is not much of a
topic in modern mindfulness research, and thus opposite
diminishing in itself does also not feature as an explicitly
worked out theme in any of the currently used mindfulness
questionnaires (eight questionnaires) known to us (Buchheld
et al., 2001; Brown and Ryan, 2003; Baer et al., 2004, 2006; Bishop
et al., 2004; Walach et al., 2006; Feldman et al., 2007; Cardaciotto
et al., 2008; Chadwick et al., 2008). judgmental (as such a state can be discovered by “let [ting] things
take their natural course”), and, on the other hand, also with
mental well-being. Indeed, he associates opposite diminishing
and mental well-being rather explicitly, when he states above that
the “middle way is found between all opposites. Rest in the
middle and find well-being wherever you are.” The
overall
theoretical
view
that
emerges
from
the
observations/descriptions above is that a mental realm that is
characterized by opposite diminishing should also be associated
with non-judging as well as with mental well-being. Our
proposed theoretical model for this view is schematically
depicted in Figure 1. Above Kornfield (and Kabat-Zinn, but more implicitly so)
has described opposite diminishing, non-judging, and increased
mental well-being as mental aspects that can be achieved through
meditation. Interestingly, some first observations suggest that
these three mental aspects can also be evoked and investigated by
dissociative psychedelics. The main receptor interaction of dissociative psychedelics
such as ketamine and nitrous oxide involves NMDA receptor
antagonism (Harrison and Simmonds, 1985; Kalmoe et al., 2020;
Krediet et al., 2020). While the group of compounds including
ketamine and nitrous oxide is often termed “dissociative
anesthetics,” this group is increasingly also (including this
paper) alternatively termed “dissociative psychedelics” (cf. Introduction Block et al., 1990; Sanz et al., 2018; Krediet et al., 2020)—in
order to highlight that the acute experiences of these compounds
often do not only include dissociative aspects (such as an out-of-
body experience), but also psychedelic aspects other than
dissociation such as mystical-type feelings of oneness, visions,
and clarity of thought (Studerus et al., 2010). Additionally, these
compounds might also be able to occasion opposite diminishing,
non-judging, and increased mental well-being. Unlike in mindfulness psychometrics, the Buddhist scholar
Jack Kornfield—a meditation teacher and Buddhist psychologist,
who trained as a Buddhist monk and also holds a Ph.D. in clinical
psychology—does make opposite diminishing a most central part
of a mental realm that can be fostered by Buddhist meditation
practice: BUDDHIST PSYCHOLOGY . . . shows us the paradox of the
universe, within and beyond the opposites. It teaches us to
be in the world but not of the world. This realization is called
the middle way . . . The middle way describes the middle
ground between attachment and aversion, between being and
non-being, between form and emptiness, between free will
and determinism. The more we delve into the middle way the
more deeply we come to rest between the play of opposites
. . . To discover the middle way, he [Ajahn Chah, Kornfield’s
then meditation master] went on, “Try to be mindful, and let
things take their natural course” . . . The Perfect Wisdom
Text describes it [the middle way] as “realization of suchness
beyond attainment of good or bad” . . . Here is a . . . principle
of Buddhist psychology: . . .The middle way is found between
all opposites. Rest in the middle and find well-being wherever
you are (2008, pp. 367–369; caps and italics his). First, a link between dissociative psychedelics and an acute
experience of opposite diminishing has already been described in
1882 by one of the founding fathers of modern psychology,
William James. Of course in James’ days, terms like “dissociative
anesthetics” or “dissociative psychedelics” were not born yet to
refer to such experiences; rather he referred to the nitrous-oxide-
occasioned experience as the “the anaesthetic revelation” (James,
1902, p. 389), taking over the term from Blood (1874). He
described his self-experiment with nitrous oxide as follows. 1
The original item used in Studerus et al. (2010) is in German and reads
“Gegensätze und Widersprüche schienen sich aufzulösen” (cf. Dittrich
et al., 2006) which the authors—using the English translation in relation
to Dittrich et al. (2010)—translate as: “Conflicts and contradictions
seemed to dissolve.” However, a more accurate English translation
of the German word “Gegensätze” than “conflicts” is clearly “opposites”
(for “conflicts” there is the German word “Konflikte”). That is why we
have rendered the translation of the item used in German in the above
text accordingly Introduction Whatever the idea of representation occurred to the mind
was seized by the same logical forceps, and served to illustrate
the same truth; and that truth was that every opposition,
among whatsoever things, vanishes in a higher unity in which
it is based; that all contradictions, so-called, are of a common
kind; that unbroken continuity is of the essence of being . . . It
is impossible to convey an idea of the torrential character of
the identification of opposites as it streams through the mind
in this experience. I have sheet after sheet of phrases dictated
or written during the intoxication, which to the sober reader Thus, Kornfield characterizes the aspired Buddhist mental
realm (often termed the middle way) as a mental realm in which
one does not think of things in terms of opposites, but rather of a
mental realm that is “between” or “beyond . . . opposites” such as
“good or bad.” Furthermore, he associates such a mental
condition
in
which
thinking
about
things
in
terms
of
opposites diminishes (a state in which we “we come to rest
between the play of opposites”) with, one the hand, being non- Frontiers in Pharmacology 03 frontiersin.org Stocker et al. 10.3389/fphar.2022.916641 FIGURE 1
Opposite diminishing is proposed to be a mental realm where one is neither mentally drawn to thinking in terms of one opposite pole of pair of
opposites (such as “this is good”, “I like this,” etc.) nor is mentally drawn to thinking in terms of the other opposite pole of the same pair of opposites
(such as “this is bad”, “I don’t like this,” etc.). Rather it is a mental realm in which one is located exterior (“between”, “beyond”) to either side of the
opposite poles. Such a mental state is proposed to be associated with non-judging, and both of these mental conditions (opposite diminishing
and non-judging) are proposed to be associated with mental well-being. FIGURE 1
Opposite diminishing is proposed to be a mental realm where one is neither mentally drawn to thinking in terms of one opposite pole of pair of
opposites (such as “this is good”, “I like this,” etc.) nor is mentally drawn to thinking in terms of the other opposite pole of the same pair of opposites
(such as “this is bad”, “I don’t like this,” etc.). Introduction Rather it is a mental realm in which one is located exterior (“between”, “beyond”) to either side of the
opposite poles. Such a mental state is proposed to be associated with non-judging, and both of these mental conditions (opposite diminishing
and non-judging) are proposed to be associated with mental well-being. evidence for this is found for ketamine. In relation to
ketamine (in healthy participants), a subscale termed
“experience
of
unity”—from
a
new
factor
analysis
(Studerus et al., 2010) of the Five-Dimensional Altered
States of Consciousness Rating Scale (5D-ASC) (Dittrich,
1998; Dittrich et al., 2006, 2010)—showed somewhat higher
(not statistically compared) response for ketamine than for
the 5-hydroxytryptamine-2A (5-HT2A) receptor agonist
(classic-psychedelic)
psilocybin
and
the
serotonin/
dopamine/oxytocin
releaser
(entactogen/empathogen)
3,4-methylenedioxymethamphetamine
(MDMA). The
subscale experience of unity contains the item “Opposites
and contradictions seemed to dissolve”1 and therefore asks
quite clearly about the occurrence of opposite diminishing. However, since the other items of the subscale experience of
unity are not about opposite diminishing perception, the
relation of ketamine to opposite diminishing as such cannot
be discerned from the findings of this study. seem meaningless drivel, but which at the moment of
transcribing were fused in the fire of infinite rationality. God and devil, good and evil, life and death, I and thou,
sober and drunk, matter and form, black and white, quality
and quantity, shiver of ecstasy and shudder of horror,
vomiting and swallowing, inspiration and expiration, fate
and reason, great and small, extent and intent, joke and
earnest, tragic and comic, and fifty other contrasts figure in
these pages in the same monotonous way. The mind saw how
each term belonged to its contrast through a knife-edge
moment
of transition which it effected, and which,
perennial and eternal, was the nunc stans of life (1882,
pp. 206–207). At least in this self-experiment case study, the NMDA
receptor
antagonist
nitrous
oxide
evoked
an
opposite
diminishing of a very strong kind—not only did opposites
seem to “vanish,” they also “vanish [ed] in a higher unity” of
“unbroken continuity.” James’ initiative to undertake a nitrous-
oxide self-experiment was inspired by the reports of Benjamin
Blood
(1874)
about
his
decade-long
nitrous-oxide
self-
experiments whose subjective experiences can—according to
the writer Lachman (2003)—also be interpreted as opposite
diminishing: Second, the NMDA receptor antagonist ketamine can
induce a post-acute experience of non-judging/acceptance as
illustrated by this qualitative report of an individual
suffering
from
depression. Introduction This open-minded “I accepted that all of the stuff that
happened, happened” clearly seems to resemble Buddhist or
mindfulness characterizations of non-judging/acceptance as
described above. However, the quoted example was not
analyzed in terms of non-judging by the investigators, but in
relation to the more abstract notion of “change in their [patients
suffering from depression receiving ketamine treatment] feelings
around problems in life” (p. 954). Other articles known to us also
mention enhanced non-judging/acceptance capacities in relation
to ketamine-assisted psychotherapy only in passing (Dore et al.,
2019, p. 192; Halstead et al., 2021, p. 320). phenomenology in domains other than opposite-diminishing/
non-judging; for instance, both are known to be involved in
dissolving the sense of self (e.g., Studerus et al., 2010; Millière
et al., 2018). However, while we expect opposite diminishing and
non-judging to closely relate to one another (when one occurs,
the other is often likely to occur as well), and while we expect that
they both relate to antidepressant response, they should still
relate to antidepressant response in somewhat distinguishable
ways, since, after all, opposite diminishing and non-judging are
two semantically different concepts. Third, there is clear evidence that ketamine can increase well-
being. Ketamine produces a rapid antidepressant response in
individuals suffering from depression in many studies (e.g.,
Zarate et al., 2006; Murrough et al., 2013), and the same has
been shown for nitrous oxide in a first proof-of-concept study
(Nagele et al., 2015; Kalmoe et al., 2020). Given what has been said above, opposite diminishing can be
characterized as cognition that is not dominated by thinking in
terms of opposites. It is a mental realm in which one is located
exterior (“between”, “beyond”) to either side of the opposite poles
(cf. Figure 1). As such, opposite-diminishing is more of a
perceptual
concept—while
in
opposite-diminishing
one
perceives things without applying an opposite-thinking frame
to them, the concept says nothing about one’s attitude toward
whatever is perceived in opposite-diminishing ways. In contrast,
also given what has been said above, non-judging can be
characterized as cognition that is not dominated by making
judgments (which also often involves refraining from applying
an opposite-thinking frame on the cognition in question), but
non-judging can additionally also be characterized as accepting
whatever it is that one perceives in non-judging terms. Introduction As such,
non-judging is also an attitudinal concept; although in non-
judging (as in opposite-diminishing) one perceives things
without applying an opposite-thinking frame on the cognition
in question, the concept also reflects one’s attitude toward
whatever is perceived in non-judging ways—this attitude
being an accepting stance toward the cognition is in question. While opposite diminishing, non-judging, and mental
well-being are usually characterized as being interrelated to
one another in the Buddhist/mindfulness case (cf. above), it is
not known whether these three characteristics can also occur
in interrelated ways with dissociative psychedelics such as
ketamine and nitrous oxide. When it comes to dissociative
psychedelics and opposite diminishing/non-judging/well-
being all we have at hand are some isolated observations/
findings for each of these three characteristics as they have
been illustrated above. The present study thus sets out to
address the question whether the three aspects of opposite
diminishing, non-judging, and mental well-being all occur in
the ketamine experience, and if they do, how they relate to one
another. The two main hypotheses of the current study are 1) both a
ketamine-peri-infusion experience of opposite diminishing as
well as a peri-infusion experience of non-judging are associated
with increased well-being—measured as an antidepressant
response (e.g., Wersebe et al., 2018)—and 2) the experiences
of opposite diminishing and non-judging relate to antidepressant
benefits in comparable/related, yet still distinct ways. We addressed the questions of our hypotheses in an open-
label, prospective, and non-interventional study. To an existing
ketamine treatment regimen of an ambulatory anesthesiological
day clinic for patients suffering from depression, we added a new
enhanced scale to measure altered states of consciousness
(ASCs)—the Altered State of Consciousness Inventory (ASCI)
(Reissmann et al., 2022)—and the Beck Depression Inventory II
(BDI-II) (Beck et al., 2009). Regarding the dosing regimen, the
dose level and frequency for the ketamine infusion were adjusted
individually in close consultation with the patient with the overall
goal to maximize antidepressant benefit—a novel dose regimen
that we term personalized antidepressant dosing [for more Hypothesis 1 is based on a Buddhist/mindfulness analogy. Kornfield for instance writes of the “joyful experience of moving
. . . out of duality” (2008, p. 369). And associating Buddhist non-
judging with well-being he writes: “It’s our task to learn from the
world as it is. For the awakening of the heart, conditions are
always good enough” (p. 369). Furthermore, Brown et al. Introduction Treated
with
ketamine
therapy,
she
reported
the
effects
thereof
in
the
following way: Second, the NMDA receptor antagonist ketamine can
induce a post-acute experience of non-judging/acceptance as
illustrated by this qualitative report of an individual
suffering
from
depression. Treated
with
ketamine
therapy,
she
reported
the
effects
thereof
in
the
following way: I felt like I was able to deal with the issues in a self-nurturing
way. Just that I accepted that all of the stuff that happened, Blood’s anesthetic revelation . . . is rife with contradictory
statements that in any normal discourse would cancel each
other out. In Blood’s vision, however, they act as a kind of
propositional ladder, reaching to a higher, encompassing, all-
inclusive reconciliation (2003, p. 17). Other than these self-experiments of Blood (1874) and
James (1882), we are not aware of much other literature that
also investigated whether NMDA receptor antagonists such
as ketamine or nitrous oxide would occasion the subjective
experience of opposite diminishing. However, some more Frontiers in Pharmacology 04 frontiersin.org 10.3389/fphar.2022.916641 Stocker et al. psychometrics suggest (either explicitly or implicitly) that
judging often seems to involve thinking in terms of one of
two poles of a given opposite pair (e.g., “this is good” vs. “this
is bad”). Thus, it is suggested that thinking in terms of opposites
and judging—as well as their counterparts opposite diminishing
and non-judging—are closely related to one another. In analogy,
we suspect that such a close interrelation of opposite diminishing
and non-judging also occurs in the ketamine experience because
there is evidence of overlap between ketamine-induced and
meditation-induced
altered-states-of-consciousness
phenomenology in domains other than opposite-diminishing/
non-judging; for instance, both are known to be involved in
dissolving the sense of self (e.g., Studerus et al., 2010; Millière
et al., 2018). However, while we expect opposite diminishing and
non-judging to closely relate to one another (when one occurs,
the other is often likely to occur as well), and while we expect that
they both relate to antidepressant response, they should still
relate to antidepressant response in somewhat distinguishable
ways, since, after all, opposite diminishing and non-judging are
two semantically different concepts. happened and it’s not the end of the world, don’t need to hate
myself over things that I haven’t done right (Sumner et al.,
2021, p. 954). Introduction (2015)
have found an association between an increase in mindfulness
non-judging and a decrease in depressive symptoms and anxiety. Hypothesis 2 is also based on a Buddhist/mindfulness
analogy. As shown above, Buddhist or mindfulness scholars
like
Kornfield
and
Kabat-Zinn
as
well
as
mindfulness Frontiers in Pharmacology 05 frontiersin.org 10.3389/fphar.2022.916641 Stocker et al. TABLE 1 Mean BDI-II and opposite-dissolving and non-judging values for all patients. TABLE 1 Mean BDI-II and opposite-dissolving and non-judging values for all patients. Patient
Age
Gender
NSessions
Dosea
(mg/kg)
BDI-II
Pre
BDI-II
Post
Opposite-dissolving
Non-Judging
M [Min, Max, Opt.]
M [Min, Max]
M [Min, Max]
M [Min, Max]
M [Min, Max]
1
39
m
8
2.0 [1.2, 3.1, 3.1]
26.3 [18, 38]
16.0 [7, 23]
3.3 [2, 5]
7.5 [2, 22]
2
62
m
11
0.6 [0.5, 0.9, 0.8]
19.1 [11, 31]
15.4 [4, 37]
14.7 [0, 69]
25.9 [0, 97]
3
69
m
1
0.5 [0.5, 0.5, 0.5]
20.0 [20, 20]
18.0 [18, 18]
6.0 [6, 6]
15.0 [15, 15]
4
31
m
6
0.7 [0.5, 0.8, 0.8]
18.3 [9, 23]
8.0 [1, 16]
38.2 [11, 55]
50.3 [0, 84]
5
27
f
3
0.7 [0.5, 1.0, 1.0]
41.7 [33, 48]
39.7 [32, 46]
3.0 [0, 9]
32.7 [0, 98]
6
22
m
5
n.a. 17.6 [13, 26]
3.0 [0, 9]
92.6 [81, 100]
61.6 [0, 81]
7
65
m
2
0.5 [0.5, 0.6, 0.6]
34.0 [31, 37]
21.0 [13, 29]
31.5 [9, 54]
21.5 [7, 36]
8
30
m
3
0.5 [0.5, 0.5, 0.5]
34.7 [24, 45]
16.0 [7, 23]
41.0 [39, 44]
64.7 [13, 95]
9
54
m
1
0.7 [0.7, 0.7, 0.7]
23.0 [23, 23]
8.0 [8, 8]
63.0 [63, 63]
82.0 [82, 82]
10
70
f
2
n.a. 15.5 [15, 16]
9.0 [8, 10]
35.5 [33, 38]
43.5 [9, 78]
11
66
f
3
n.a. 42.0 [38, 44]
23.3 [16, 36]
0.0 [0, 0]
31.0 [4, 68]
The theoretical score range for the BDI-II, is 0–63 and for the opposite-dissolving/non-judging 0–100. NSessions is the number of sessions per patient, or respectively the number of data
points for each patient that was analyzed. Opt. = optimal dose for each patient (dose used after initial adjustment). Except for one patient, the optimal dose corresponded to the highest dose
applied (Max.). The n.a. values are due to missing weight information of three patients. 2
In the original German version these two items were, respectively:
“Gegensätze und Widersprüche schienen sich aufzulösen” and “Ich
konnte mein Leben so akzeptieren, wie es ist, ohne den Drang zu
haben, es bewerten zu müssen.” Introduction Asking retrospectively—shortly after
the
altered
state
of
consciousness
(ASC)—about
the
experiences during the ASC is a standard procedure that
applies to most ASC questionnaires. While
the
ASCI
was
administered
retrospectively—i.e.,
shortly
after
the
infusion—the
questionnaire still asks about the subjective experiences
during the infusion (“Please rate the extent to which the
following statements [. . .] apply to your experience during
the ketamine infusion”). Asking retrospectively—shortly after
the
altered
state
of
consciousness
(ASC)—about
the
experiences during the ASC is a standard procedure that
applies to most ASC questionnaires. The ASCI is a partially new questionnaire that consists of two
parts. First, it consists of a validated 11-subscales factor analysis
(Studerus et al., 2010) of the 5-Dimensional Altered States of
Consciousness Rating Scale (5D-ASC) (Dittrich, 1998; Dittrich
et al., 2006, 2010): the 5D-ASC/11. Second, in addition to the 5D-
ASC/11, the ASCI contains also new self-generated items whose
factor structure has not been investigated yet. However, it is
important to highlight that in this given study the factor structure
of the ASCI plays no role. We simply selected the two individual
items from the ASCI that most closely matched opposite
diminishing and non-judging, irrespective of their factor or
potential factor structure. If our initial exploration of this
topic confirms our hypotheses, then it might be worthwhile to
develop more items for both opposite diminishing and non-
judging so that they can then also be analyzed on the factor level. Introduction aThe exact dose value for each session, in case that this is not already visible in Table 1, is: Patient 1: 1.2, 1.2, 1.4, 1.7, 2.0, 2.3, 2.5, 3.1. Patient 2: 0.5, 0.5, 0.5, 0.6. 0.5. 0.5, 0.5, 0.5, 0.8, 0.9, 0.9. Patient 4: 0.5, 0.6, 0.6, 0.7, 0.7, 0.8. Patient 5: 0.5, 0.7, 1.0. Patient 8: 0.5, 0.5, 0.6. The theoretical score range for the BDI-II, is 0–63 and for the opposite-dissolving/non-judging 0–100. NSessions is the number of sessions per patient, or respectively the number of data
points for each patient that was analyzed. Opt. = optimal dose for each patient (dose used after initial adjustment). Except for one patient, the optimal dose corresponded to the highest dose
applied (Max.). The n.a. values are due to missing weight information of three patients. aThe exact dose value for each session, in case that this is not already visible in Table 1, is: Patient 1: 1.2, 1.2, 1.4, 1.7, 2.0, 2.3, 2.5, 3.1. Patient 2: 0.5, 0.5, 0.5, 0.6. 0.5. 0.5, 0.5, 0.5, 0.8, 0.9, 0.9. Patient 4: 0.5, 0.6, 0.6, 0.7, 0.7, 0.8. Patient 5: 0.5, 0.7, 1.0. Patient 8: 0.5, 0.5, 0.6. For possible development of a non-judging ASC factor in the
future,
ASC
psychometrics
could
draw
inspiration
from
mindfulness
psychometrics,
where
non-judging
and/or
acceptance has already been developed into a factor in various
ways (Baer et al., 2004, 2006; Cardaciotto et al., 2008). For possible development of a non-judging ASC factor in the
future,
ASC
psychometrics
could
draw
inspiration
from
mindfulness
psychometrics,
where
non-judging
and/or
acceptance has already been developed into a factor in various
ways (Baer et al., 2004, 2006; Cardaciotto et al., 2008). general aspects on personalized dosing with psychedelics see
Liechti and Holze (2021)]. Regarding the measurement of
opposite diminishing and non-judging, answers to the two
questionnaire items of the ASCI for these concepts were
analyzed to see if they relate to the BDI-II scores in the
predicted ways. These two ASCI items were “Opposites and
contradictions seemed to dissolve” for opposite diminishing, and
“I was able to accept my life as it is, without the urge to evaluate
it” for non-judging.2 y
While
the
ASCI
was
administered
retrospectively—i.e.,
shortly
after
the
infusion—the
questionnaire still asks about the subjective experiences
during the infusion (“Please rate the extent to which the
following statements [. . .] apply to your experience during
the ketamine infusion”). Participants Patients suffering from depression who underwent ketamine-
infusion therapy at the anesthesiological day clinic Dres. Gugath,
Kist, and Schmitz-Buchholz (later Zelenka and colleagues) in
Villingen-Schwenningen (Germany), were asked if they would be
willing to participate in the current study. The decision of the
patients to additionally participate in this study or not did not
influence the medical treatment. All participants provided written
informed consent after the study procedures were fully explained. The inclusion criteria for the study were 1) a minimum age of
18 years, 2) suffering from depression, and 3) meeting the health Frontiers in Pharmacology 06 frontiersin.org 10.3389/fphar.2022.916641 Stocker et al. requirements
for
ketamine
administration. These
health
requirements were determined independently of the study, when
suitability for ketamine treatment was medically assessed, and
mainly included as exclusion criteria acute suicidality, any disease
involving the need to avoid excessive increases in blood pressure
and/or heart rate, as well as substance use disorders. The present
study
was
authorized
by
the
ethics
committee
of
the
Landesärztekammer
Baden-Württemberg
(Germany). Patients
had the possibility to withdraw from the study at any time
without giving reasons and without any influence on their
medical treatment. The administering physicians were trained
anesthesiologists, and consistent medical care was ensured. Włodarczyk et al., 2021). After these initial (up to three) infusions
of 0.5 mg/kg, each patient’s individual response in terms of
tolerability
and
change
in
depressive
symptomatology
determined the dose level and frequency of the subsequent
infusions. The main criterion for determining the optimal
personalized dose was the patients’ subjective feedback on
whether they felt that the infusion was sufficient to have had
an antidepressant effect. This criterion usually resulted in
increasing the initial doses. Generally, doses were adjusted in one of two basic ways in the
dosing regimen of this clinic: 1) in most cases doses were adjusted
for the next session based on the patient’s feedback from the
previous session, or, 2) less often, doses were also adjusted during
the 40-min sessions without altering the runtime. Eleven
patients
(3
females,
8
males)
suffering
from
depression with recurrent major depressive episodes and no
resounding
therapeutic
success
before
they
started
the
ketamine treatment were included in the study. Their mean
age was 48.6 years (ranging from 22 to 70 years; see Table 1
for a summary of demographic information). Participants These patients were
diagnosed with depression on average 17.6 years before the start
of the ketamine treatment (ranging from 3 to 49; one missing
information). Ten out of the 11 patients received at least two
previous treatments other than ketamine, whereby only two of
those reported reduced depressive symptoms due to these
previous treatments. Dose adaptions for the next session based on the patient’s
feedback from the previous session. This dose-adaption approach
involved talking to the patient shortly after an infusion, and if he/
she felt that the acute effect was not sufficient during the infusion,
then over the next sessions the dosage was successively increased
until a result was achieved that was perceived by the patient as
both pleasant and effective in terms of antidepression. Once this
result was achieved, then the dose was usually maintained for any
further treatments. Dose adaptions during the sessions. This dose-adaption
approach involved adjusting the dose during the 40-min
ketamine infusion and was used less frequently than adjusting
the dosage before the next session. This approach more often
involved patients experienced with ketamine infusions who came
back regularly for treatment for a longer period of time. At least
every 10 min during the infusion (cf. below), the treating
physician asked the patient if he/she is doing well, and if he/
she thinks that the dose is sufficient. If the impression of the
patient was that the antidepressant response was not sufficient,
then the dose could also be increased during the infusion. In very
rare instances, the dose was also decreased during a ketamine
infusion. In these rare cases, this was mainly due to either a
psychological effect that is too negative (e.g., frightening
hallucinations) or as a physical effect that is considered too
negative (e.g., hypertension). Furthermore, some of the patients had other psychiatric
diagnoses in addition to suffering from a depressive disorder
(e.g., anxiety disorder, post-traumatic stress disorder), but for
all patients, the main reason to undergo ketamine treatment
was their suffering from depression. Nine out of the
11
patients
(one
missing
information)
underwent
psychotherapeutic
treatment,
and
seven
(one
missing
information) received medical treatment during the time of
the ketamine treatment. Motivated by the lack of therapeutic
response to previous pharmacological and psychotherapeutic
treatments, patients reached out to the day clinic on their own
behalf and were not referred by a psychiatrist or other health
professional to the ketamine therapy. Analysis As shown in Figure 2, there were some sessions in which
patients did not report to experience opposite-diminishing (n =
11) or non-judging (n = 7) mental realms. In order to show that
the results reported above were not biased by these zero values,
we repeated the analysis without these datapoints. The results
confirmed significant associations with depression-reduction
effects for both opposite diminishing, estimate = 0.50, SEM =
0.13, t = 3.99, p < 0.001, R2
marginal = 32.5%, and non-judging,
estimate = 0.31, SEM = 0.12, t = 2.53, p = 0.020, R2marginal
= 15.1%. Data from a total of 49 ketamine-treatment sessions were
collected. Data from four of these sessions were not included in
the analysis because the BDI-II scores prior to the sessions were
below the cut-off value of 9 for minimal depression (Wintjen and
Petermann, 2010). Thus, a possible relationship between
ketamine-induced
antidepressant
benefits
and
opposite
diminishing and/or non-judging was assessed based on a total
of 45 ketamine treatment sessions from 11 different patients. To
account for the nested data structure (45 sessions from
11 patients), a linear mixed-effect model was computed with
the patient as a random intercept effect. Since there were only
one-to-three values for most of the patients, the data was not
sufficiently informative to also add a random slope per
participant (singular fit issue). Two separate models were
computed with either opposite diminishing or non-judging as
fixed
effect
predictors. The
dependent
variable
was
the
improvement in the BDI-II score after the treatment in % to
the pre-treatment BDI-II assessment (baseline). Thus, positive
values indicate reduced BDI-II scores, and we consequently
expected positive estimates of the fixed effects. The mixed-
effect models were computed using the lme4 package in R
(Bates et al., 2014). Unstandardized estimates are reported,
and p-values were calculated using Satterthwaite degrees of
freedom. We also report the explained variance (R2). These
values correspond to marginal pseudo-R2 (i.e., the explained
variance based on the fixed effects in the mixed models), as
derived from the jtools-package following the procedure
described by Nakagawa and Schielzeth (2013). When the model with opposite diminishing as a predictor
was compared to a model that includes both opposite
diminishing and non-judging as predictors, the explained
variance in depression-reduction effects did not change (from
39.1% to 39.3% (ΔR = 0.2, χ2 (1) = 0.77, p = 0.380)). 3
As there is no instrument available that measures changes in depressive
symptoms within such a short time interval as they can be induced by
ketamine, we changed the acquisition period from 2 weeks to 1 h. Physiological monitoring For dosing, a personalized regimen was applied. Specifically,
the dose level and frequency for the ketamine infusion were
adjusted individually in close consultation with the patient with
the overall goal to maximize antidepressant benefits and
tolerability
of
the
infusion
(personalized
antidepressant
dosing). Treatment started with an initial ketamine infusion
(Ketamine Inresa) with a dose of 0.5 mg/kg body weight and
a runtime of 40 min to evaluate the patient’s initial response to
the treatment—this dosage is an internationally used standard
that has been proven to be safe and has often shown
antidepressant response (Berman et al., 2000; Zarate et al.,
2006; Murrough et al., 2013; Xu et al., 2016; Niciu et al., 2018; During the ketamine infusion, the patient’s vital signs
were monitored by continuous electrocardiogram (ECG)
monitoring,
pulse
oximetry,
and
blood
pressure
measurement, complemented with regular checks (at least
every 10 min) by the treating physician and/or medical staff
of the day clinic. After the infusion, the patient remained in
the treatment room or in the waiting area of the day clinic as a
precaution. The length of this stay was based on the patient’s
tolerance of the infusion and on his/her physical and mental
response to the ketamine. Frontiers in Pharmacology 07 frontiersin.org Stocker et al. 10.3389/fphar.2022.916641 Questionnaires When averaged across the 45 sessions, BDI-II scores before
ketamine infusion were 24.8 (SD = 10.1), and 15.2 (SD = 11.0)
after the infusion. Thus, ketamine infusion led to an average
decrease in BDI-II scores of 9.6 (38.7%). Averaged scores for
opposite diminishing were 27.0 (SD = 31.9) and 34.8 (SD = 34.9)
for non-judging. Mean values per patient are summarized in
Table 1. There was a significant correlation between opposite
diminishing and non-judging, rSpearman = 0.61, p < 0.001. In each session, patients completed the BDI-II3 before the
ketamine infusion (as well as additional questionnaires that were
not part of the present study). No later than 40–60 min after the
end of the infusion, all mind-altering effects of the ketamine were
expected to have subsided (Włodarczyk et al., 2021). Within this
post-infusion
time
window
and
after
inspection
by
the
experienced professional, the ASCI (Reissmann et al., under
review)
was
administered,
followed
by
the
second
administration of the BDI-II. In the context of this study,
only the opposite-diminishing and non-judging items of the
ASCI were analyzed (cf. Introduction). Linear
mixed-effects
analyses
revealed
significant
depression-reduction effects both for opposite diminishing,
estimate = 0.64, SEM = 0.13, t = 4.89, p < 0.001, R2
marginal =
39.1%, and for non-judging, estimate = 0.37, SEM = 0.12, t = 2.94,
p = 0.005, R2
marginal = 15.8%, as illustrated in Figure 2. Linear
mixed-effects
analyses
revealed
significant
depression-reduction effects both for opposite diminishing,
estimate = 0.64, SEM = 0.13, t = 4.89, p < 0.001, R2
marginal =
39.1%, and for non-judging, estimate = 0.37, SEM = 0.12, t = 2.94,
p = 0.005, R2
marginal = 15.8%, as illustrated in Figure 2. Analysis Thus, non-
judging did not explain additional variance when opposite
diminishing was already used as a predictor. In contrast,
when
the
model
with
non-judging
as
a
predictor
was
compared to a model that included both opposite diminishing
and non-judging as predictors, the explained variance in the
change in BDI-II increased markedly from 15.8% to 39.3%
(ΔR2 = 23.5, χ2 (1) = 10.22, p = 0.001). Accounting for the distressing experience. In order to account
for possible distressing ketamine-induced ASCs, we created an
additional variable that we termed “distressing experience.” As
mentioned in the Introduction section, the ASCI also contains all
items of the eleven validated subscales from the 5D/ASC-11
(Studerus et al., 2010). Two of these eleven subscales cover
distressing ASC experiences: the subscales anxiety (6 items)
and impaired control and cognition (7 items). Anxiety contains
items like “I was afraid that the state I was in would last forever”
or “I felt threatened.” Impaired control and cognition contains
items like “I felt isolated from everything and everyone” or “I had
the feeling that I no longer had a will of my own.” Distressing
experience had a mean of 19.1 (SD = 17.8). Distressing
experience was neither associated with antidepressant effects
(spearman rho = -0.03, p = 0.843) nor with non-judging
(rSpearman = 0.10, p = 0.509). However, distressing experience
was positively associated with opposite-diminishing (rSpearman = Frontiers in Pharmacology 08 frontiersin.org 10.3389/fphar.2022.916641 Stocker et al. FIGURE 2
Positive values indicate a reduction in BDI-II score (in % to baseline) following ketamine infusion. Reduction in BDI-II was associated with
opposite-dissolving (A) and non-judging (B). FIGURE 2
Positive values indicate a reduction in BDI-II score (in % to baseline) following ketamine infusion. Reduction in BDI-II was associated with
opposite-dissolving (A) and non-judging (B). support that opposite diminishing and non-judging increase
mental well-being in the ketamine experience—as Buddhist/
mindfulness scholars propose it for the Buddhist/mindful
experience (see Introduction). Why do opposite-diminishing
and non-judging seem closely related to one another? To our
knowledge, this question has not been addressed much in
modern
research. However,
according
to
Buddhist
or
mindfulness
scholars
like
Kornfield
and
Kabat-Zinn
(cf. Introduction), judging often seems to involve thinking in
terms of one of two poles of a given opposite pair (e.g., “this
is good,” “this is bad”). Analysis So, if judging and thinking in terms of
opposites might be so closely related to one another, then one
could speculate that if thinking in opposites starts to decrease in
the Buddhist/mindfulness or the ketamine experience, then
judging should correspondingly also decrease. This is supported
by our finding that non-judging does not explain further variance
in a reduction in depression scores when opposite diminishing is
already a predictor. This suggests that the antidepressant effect of
non-judging is already covered by opposite diminishing, whereas
non-judging alone does not necessarily cover the antidepressant
effect of opposite diminishing. Future research is needed to better
understand these interactive processes. 0.30, p = 0.047). When distressing experience was entered as
control variable into the linear mixed effect models, there was still
a significant positive association between antidepressant effects
and opposite diminishing, estimate = 0.72, SEM = 0.12, t = 6.08,
p < 0.001, R2
marginal = 46.8%, as well as for non-judging,
estimate = 0.34, SEM = 0.13, t = 2.71, p = 0.010, R2
marginal =
15.3%. From this additional analysis, we can conclude that
distressing ASCs did not play a critical role in the outcome of
this study. It should also be noted that distressing psychedelic
experiences are not necessarily negative experiences per se (see
Discussion). Frontiers in Pharmacology Discussion Our results showed (supporting hypothesis 1) that both the
experience of opposite diminishing as well as a mental state of
non-judging during the ketamine infusion was significantly
associated with reductions in depression scores in individuals
suffering from depression. Our finding also showed (supporting
hypothesis 2) that opposite-dissolving and non-judging were
associated with one another, but that they still did not predict
antidepressant response in the same way, especially since non-
judging did not explain further variance in a reduction in
depression scores when opposite diminishing was already a
predictor. Overall, our findings thus give some first empirical Like the NMDA receptor antagonists ketamine and nitrous
oxide (Zarate et al., 2006; Murrough et al., 2013; Nagele et al.,
2015),
5-HT2A
receptor
agonists
(classic
or
serotonergic
psychedelics) have also shown rapid antidepressant responses Frontiers in Pharmacology 09 frontiersin.org 10.3389/fphar.2022.916641 Stocker et al. phase quickly subsided for all participants who experienced it, and
consistently led to significant moments of acceptance, surrender,
and new understandings (pp. 497–498). phase quickly subsided for all participants who experienced it, and
consistently led to significant moments of acceptance, surrender,
and new understandings (pp. 497–498). in patients with depression (Carhart-Harris et al., 2016; Griffiths
et al., 2016). Furthermore, several studies documented increased
non-judging (measured with mindfulness questionnaires) after
administration of the serotonergic psychedelics ayahuasca and 5-
methoxy-N,N-dimethyltryptamine (Soler et al., 2016, 2018;
Sampedro et al., 2017; Uthaug et al., 2018, 2019, 2020; van
Oorsouw et al., 2021) (5-MeO-DMT)—see also Watts et al. (2017) for a comparable result in relation to serotonergic
psychedelic psilocybin. However, unlike in the current study,
non-judging in these studies was not measured in relation to the
acute psychedelic phase, but rather for the post-acute phase
(“after-glow,” for example, up to 24 h after substance intake)
and/or as a follow-up (up to 2 months after substance intake). While the results in these studies are somewhat mixed overall, in
most of these studies the classic psychedelics have shown
significant increases in non-judging both for the post-acute
phase and for the follow-up (including the 2-months follow-
up). The finding of our study suggests that it might also be
worthwhile for future studies with classic psychedelics to not only
measure non-judging for time periods after substance intake, but
also for the acute phase. Discussion Conversely, the post-substance findings
of these classic-psychedelic studies suggest that non-judging
should also be investigated for the post-acute phase and as a
follow-up for dissociative psychedelics, which is something that
has not been done in the current study nor in any other
dissociative-psychedelic study that we are aware of. Also, since
we found a strong correlation between opposite diminishing and
anti-depression in the current study, future studies on classic
psychedelics and non-judging could consider broadening their
conceptual scope to not only investigate the clinical potential of
psychedelically-fostered non-judging (and other mindfulness
aspects), but also the clinical potential of psychedelically-
fostered opposite diminishing. Opposite diminishing may be a
mediator of the therapeutic effects of psychedelics. Additionally,
therapeutic responses to psychedelics may be consolidated by
non-pharmacological
interventions
enabling
opposite
diminishing such as meditation practices. Richards (2015) who has worked in psychedelic-assisted
psychotherapy (with classic psychedelics) for decades sums up
his experiences with distressing psychedelic experiences as follows: [Classic-psychedelic substances] can also trigger personal
psychological experiences, such as regression to childhood
traumas or confrontation with unresolved grief, fear, anger,
or guilt. Such experiences ... may well have potentially
significant value in accelerating psychotherapy and personal
growth ... Further, especially if one is unprepared and seeks to
control or escape from emerging inner experiences, the flow of
unique mental adventures facilitated by psychedelic substances
can culminate in episodes of panic, paranoia, confusion, and
somatic distress (2015, p. 16) Whether any of these distressing facets of classic-psychedelically
evoked ASCs have also been at work in our dissociative-psychedelic
study cannot be determined from our data and has to be left to
future investigation. However, we may note that in our study a
ketamine-occasioned ASC experience that correlated highly with
antidepression—opposite-diminishing—also correlated with ASC
distressing experience. Thus, it remains at least a possibility that
the distressing experience of our patients reflected more of a
constructive type of distressing ASC experience (e.g., necessary
confrontational predecessor to a positive experience). Clearly, this
merits further research. As mentioned in the Introduction section, to our knowledge,
mindfulness psychometrics does not capture opposite diminishing,
and does not directly investigate whether the tendency to think in one
pole of given opposite pair is reduced in the mindful trait or state of
mind. Discussion Given that mindfulness non-judging has been shown to be
related to a decrease in depressive symptoms and anxiety (Brown
et al., 2015), and given that in our study we did not only find a
correlation to antidepressant response in relation to non-judging, but
also to opposite-diminishing, we think it would be worthwhile for
mindfulness research to start to investigate whether it might be
advantageous
to
integrate
opposite
diminishing
into
the
mindfulness psychometric research canon. After all, according to
the Buddhist psychologist Jack Kornfield (cf. Introduction), a mental
realm in which “we come to rest between the play of opposites” (2008,
p. 368) lies at the very heart of the Buddhist middle way. Furthermore, it is also worthy of note that opposite-
diminishing
was
positively
associated
with
distressing
experience. At first sight, this might seem in contradiction
with the part of our hypothesis that opposite diminishing is
associated with well-being. However, although not studied in
enough detail yet, there have been some first observations in
relation to classic psychedelics (especially in some qualitative
studies) that a distressing/confrontational ASC experience might
sometimes be a necessary predecessor of a positive ASC
experience. In
relation
to
classic-psychedelic
(psilocybin) induced ASCs in psychedelic-assisted treatment of
cancer-related distress (Swift et al., 2017) for instance write: Conflict of interest ML is a consultant for Mind Medicine Inc. The remaining 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. Data availability statement balanced number of participants are needed to establish our findings
more firmly. This article also shares the common problem with all other
next-generation rapid-acting antidepressant studies, which is the lack of
a valid assessment tool that captures short-term (within hours) changes
in depressive symptomatology. The raw data supporting the conclusion of this article will be
made available by the authors, without undue reservation. In addition, while dosage amount was varied in the dosage
regimen of the clinic where the study was conducted, the
international standard time of 40 min running time was never
varied in our study. We are not aware of any depression ketamine
studythat systematically hasvaried ketamine’srunningtime. Thus,this
study shares this limitation—not to have explored different running
times to perhaps maximize ketamine’s antidepressant potential—with
other ketamine studies with individuals suffering from depression. Limitations The major limitations of this study were the lack of a control group
allowing blinding, a small number of participants (n = 11, respectively
45 sessions), and an unbalanced male/female ratio (9 males, 3 females). Therefore, future controlled randomized trials with a larger and more The immersive quality of the experience was felt as overwhelming,
challenging, or fearful for many ... of the participants, particularly
in the early stages of the session ... The intensity of this initial Frontiers in Pharmacology 10 frontiersin.org Stocker et al. 10.3389/fphar.2022.916641 Acknowledgments The authors thank Doris Teufel-Schöpflin and Heike Stenske for
accompanying the patients and for their large contribution to data
collection. We also thank Dr. Michael Gugath und Dr. Marek
Zelenka for contributions to the clinical infrastructure that made
this study possible. Additionally, we thank Dr. Daniel Schmitz-
Buchholz for his help in the initial set up of this study. Finally, it is also important to keep in mind that our analysis is of
correlational nature. One cannot conclude that ketamine-induced
opposite diminishing and non-judging caused antidepressant effects. Rather, these specific experiences might also be indicators of how
well ketamine generally worked on a physiological level (e.g., the
strength of NDMA receptor antagonism) in a given session. However, speaking against such a physiological interpretation is
our finding that the associations between opposite diminishing/non-
judging hold true even when controlling for other ketamine-induced
ASC experiences (distressing ASC effects). This suggests that there is
at least a specific relationship between opposite diminishing/non-
judging and antidepressant effects. Funding ML received funding for the present study by the Swiss
National Science Foundation (grant no. 32003B_185111). Author contributions KS conceived the study. MH performed the statistical analysis
and wrote the statistics section. AK was the treating physician. KS
drafted the first version of the manuscript. ML provided critical
revisions for the manuscript. SR also contributed to revisions. All
authors provided final inputs for the manuscript. Furthermore, it should also be kept in mind that our study exclusion
criteria did not include other psychiatric disorders (e.g., anxiety disorders
or post-traumatic stress disorders). Thus, while the current study can
provide some first evidence that ketamine-induced opposite diminishing
and non-judging are related to antidepressant response, we did not
measure whether ketamine-induced opposite diminishing and non-
judging might also be related to improvement in anxiety or PTSD
symptoms. Potential clinical benefits of ketamine-induced opposite
diminishing and non-judging other than improvements of depressive
symptoms is a topic that warrants future study. Ethics statement The studies involving human participants were reviewed and
approved by the Ethics Committee of the Landesärztekammer
Baden-Württemberg
(Germany). The
patients/participants
provided their written informed consent to participate in this study. Another limitation in relation to the dose regimen is that it is
likely that an optimal dose—the dose that was usually kept constant
after adjusting the dose according to the subjective feedback of the
patient in the first initial sessions—has a stronger effect on ASC
experiences (such as opposite diminishing and non-judging) and
consequently on depression reduction than a suboptimal dose. However, for the present study, there were not enough data to
systematically assess the potential effect of optimal dose. References R). J. Psychopathol. Behav. Assess. 29, 177–190. doi:10.1007/s10862-006-
9035-8 Baer, R. A., Smith, G. T., and Allen, K. B. (2004). Assessment of mindfulness by
self-report: the Kentucky inventory of mindfulness skills. Assessment 11, 191–206. doi:10.1177/1073191104268029 Baer, R. A., Smith, G. T., and Allen, K. B. (2004). Assessment of mindfulness by
self-report: the Kentucky inventory of mindfulness skills. Assessment 11, 191–206. doi:10.1177/1073191104268029 Griffiths, R. R., Johnson, M. W., Carducci, M. A., Umbricht, A., Richards, W. A.,
Richards, B. D., et al. (2016). Psilocybin produces substantial and sustained
decreases in depression and anxiety in patients with life-threatening cancer: a
randomized double-blind trial. J. Psychopharmacol. (Oxf.) 30, 1181–1197. doi:10. 1177/0269881116675513 Baer, R. A., Smith, G. T., Hopkins, J., Krietemeyer, J., and Toney, L. (2006). Using
self-report assessment methods to explore facets of mindfulness. Assessment 13,
27–45. doi:10.1177/1073191105283504 Bates, D., Mächler, M., Bolker, B., and Walker, S. (2014). Fitting linear mixed-
effects models using lme4. J. Stat. Softw. 67, 5823. ArXiv Prepr. ArXiv14065823
1406. doi:10.18637/jss.v067.i01 Halstead, M., Reed, S., Krause, R., and Williams, M. T. (2021). Ketamine-assisted
psychotherapy for PTSD related to racial discrimination. Clin. Case Stud. 20,
310–330. doi:10.1177/1534650121990894 Beck, A. T., Steer, R.-A., and Brown, G. K. (2009). Beck-Depressions-Inventar
(BDI–II, dt. Version: M. Hautzinger, F. Keller & C. Kühner, 2. Aufl.). Frankfurt:
Pearson Assessment. Harrison, N. L., and Simmonds, M. A. (1985). Quantitative studies on some
antagonists of N-methyl D-aspartate in slices of rat cerebral cortex. Br. J. Pharmacol. 84, 381–391. doi:10.1111/j.1476-5381.1985.tb12922.x Berman, R. M., Cappiello, A., Anand, A., Oren, D. A., Heninger, G. R., Charney,
D. S., et al. (2000). Antidepressant effects of ketamine in depressed patients. Biol. Psychiatry 47, 351–354. doi:10.1016/s0006-3223(99)00230-9 James, W. (1882). On some Hegelisms. Mind 7, 186–208. James, W. (1902). The varieties of religious experience: a study in human nature. New York: Longmans. Bishop, S. R., Lau, M., Shapiro, S., Carlson, L., Anderson, N. D., Carmody, J., et al. (2004). Mindfulness: a proposed operational definition. Clin. Psychol. Sci. Pract. 11,
230–241. doi:10.1093/clipsy.bph077 Kabat-Zinn, J. (2003). Mindfulness-based interventions in context: past, present,
and future. Clin. Psychol. Sci. Pract. 10, 144–156. doi:10.1093/clipsy/bpg016 Block, R. I., Ghoneim, M. M., Kumar, V., and Pathak, D. (1990). Psychedelic
effects of a subanesthetic concentration of nitrous oxide. Anesth. Prog. 37, 271–276. Kalmoe, M. C., Janski, A. M., Zorumski, C. F., Nagele, P., Palanca, B. J., Conway,
C. R., et al. (2020). References Ketamine and nitrous oxide: the evolution of NMDA receptor
antagonists as antidepressant agents. J. Neurol. Sci. 412, 116778. doi:10.1016/j.jns. 2020.116778 Blood, B. P. (1874). The anaesthetic revelation and the gist of philosophy. Miami
FL: HardPress Kinde Edition. Kornfield, J. (2008). The wise heart: Buddhist psychology for the West. New York:
Bandam. Brandmeyer, T., Delorme, A., and Wahbeh, H. (2019). The neuroscience of
meditation: classification, phenomenology, correlates, and mechanisms. Prog. Brain
Res. 244, 1–29. doi:10.1016/bs.pbr.2018.10.020 Krediet, E., Bostoen, T., Breeksema, J., van Schagen, A., Passie, T., Vermetten, E.,
et al. (2020). Reviewing the potential of psychedelics for the treatment of PTSD. Int. J. Neuropsychopharmacol. 23, 385–400. doi:10.1093/ijnp/pyaa018 Brown, D. B., Bravo, A. J., Roos, C. R., and Pearson, M. R. (2015). Five facets of
mindfulness and psychological health: evaluating a psychological model of the
mechanisms of mindfulness. Mindfulness 6, 1021–1032. doi:10.1007/s12671-014-
0349-4 Lachman, G. (2003). A secret history of consciousness. Great Barrington MA:
Lindisfarne Books. Brown, K. W., and Ryan, R. M. (2003). The benefits of being present: mindfulness
and its role in psychological well-being. J. Pers. Soc. Psychol. 84, 822–848. doi:10. 1037/0022-3514.84.4.822 Lebois, L. A., Papies, E. K., Gopinath, K., Cabanban, R., Quigley, K. S.,
Krishnamurthy, V., et al. (2015). A shift in perspective: decentering through
mindful attention to imagined stressful events. Neuropsychologia 75, 505–524. doi:10.1016/j.neuropsychologia.2015.05.030 Buchheld, N., Grossman, P., and Walach, H. (2001). Measuring mindfulness in
insight
meditation
(vipassana)
and
meditation-based
psychotherapy:
the
development of the Freiburg Mindfulness Inventory (FMI). J. Medit. Medit. Res. 1, 11–34. Liechti, M. E., and Holze, F. (2021). Dosing psychedelics and MDMA. Curr. Topics Behav. Neurosci. doi:10.1007/7854_2021_270 Millière, R., Carhart-Harris, R. L., Roseman, L., Trautwein, F.-M., and Berkovich-
Ohana, A. (2018). Psychedelics, meditation, and self-consciousness. Front. Psychol. 9, 1475. doi:10.3389/fpsyg.2018.01475 Cardaciotto, L., Herbert, J. D., Forman, E. M., Moitra, E., and Farrow, V. (2008). The assessment of present-moment awareness and acceptance: the
Philadelphia
Mindfulness
Scale. Assessment
15,
204–223. doi:10.1177/
1073191107311467 Murrough, J. W., Perez, A. M., Pillemer, S., Stern, J., Parides, M. K., aan het Rot,
M., et al. (2013). Rapid and longer-term antidepressant effects of repeated ketamine
infusions in treatment-resistant major depression. Biol. Psychiatry 74, 250–256. doi:10.1016/j.biopsych.2012.06.022 Carhart-Harris, R. L., Bolstridge, M., Rucker, J., Day, C. M., Erritzoe, D., Kaelen,
M., et al. (2016). (2016). Psilocybin with psychological support for treatment-
resistant depression:
an open-label feasibility study. Lancet Psychiatry 3,
619–627.doi:10.1016/S2215-0366(16)30065-7 Nagele, P., Duma, A., Kopec, M., Gebara, M. Publisher’s note Both descriptions of Buddhist and mindfulness scholars and
the results of our present ketamine study suggest that mental
states including opposite diminishing may be linked to increased
mental well-being. Further studies are needed to clarify the
mediating role of opposite diminishing in the benefits of
psychedelic-assisted therapy. Allclaimsexpressedinthisarticlearesolelythoseoftheauthorsand
do not necessarily represent those of their affiliated organizations, or
those of the publisher, the editors, and the reviewers. Any product that
may be evaluated in this article, or claim that may be made by
its manufacturer, is not guaranteed or endorsed by the publisher. Frontiers in Pharmacology 11 frontiersin.org Stocker et al. 10.3389/fphar.2022.916641 References A., Parsoei, A., Walker, M., et al. (2015). Nitrous oxide for treatment-resistant major depression: a proof-of-concept
trial. Biol. Psychiatry 78, 10–18. doi:10.1016/j.biopsych.2014.11.016 Chadwick, P., Hember, M., Symes, J., Peters, E., Kuipers, E., and Dagnan, D. (2008). Responding mindfully to unpleasant thoughts and images: reliability and
validity of the Southampton Mindfulness Questionnaire (SMQ). Br. J. Clin. Psychol. 47, 451–455. doi:10.1348/014466508X314891 Nakagawa, S., and Schielzeth, H. (2013). A general and simple method for
obtaining R2 from generalized linear mixed-effects models. Methods Ecol. Evol. 4, 133–142. doi:10.1111/j.2041-210x.2012.00261.x Dahl, C. J., Lutz, A., and Davidson, R. J. (2015). Reconstructing and
deconstructing the self: cognitive mechanisms in meditation practice. Trends
Cogn. Sci. 19, 515–523. doi:10.1016/j.tics.2015.07.001 Niciu, M. J., Shovestul, B. J., Jaso, B. A., Farmer, C., Luckenbaugh, D. A., Brutsche,
N. E., et al. (2018). Features of dissociation differentially predict antidepressant
response to ketamine in treatment-resistant depression. J. Affect. Disord. 232,
310–315. doi:10.1016/j.jad.2018.02.049 Dittrich, A., Lamparter, D., and Maurer, M. (2006). 5D-ABZ: Fragebogen zur
Erfassung Aussergewöhnlicher Bewusstseinszustände: eine kurze Einführung. Zurich:
PSIN Plus. Reissmann, S., Hartmann, M., Kist, A., Liechti, M. E., and Stocker, K. (2022). Assessing ketamine’s acute psychoactive properties with an enhanced scale for altered
states of consciousness: a repeated-infusions study in a depressed patient [Manuscript
submitted for publication]. Zurich, Switzerland: Department of Psychology,
University of Zurich. Dittrich, A., Lamparter, D., and Maurer, M. (2010). 5D-ASC: Questionnaire for
the assessment of altered states of consciousness. a short introduction. Zurich: PSIN
Plus. Dittrich, A. (1998). The standardized psychometric assessment of altered states of
consciousness (ASCs) in humans. Pharmacopsychiatry 31, 80–84. doi:10.1055/s-
2007-979351 Richards, W. A. (2015). Sacred knowledge: psychedelics and religious experience. New York: Columbia University Press. Sampedro, F., de la Fuente Revenga, M., Valle, M., Roberto, N., Domínguez-
Clavé, E., Elices, M., et al. (2017). Assessing the psychedelic “after-glow” in
ayahuasca users: post-acute neurometabolic and functional connectivity changes
are associated with enhanced mindfulness capacities. Int. J. Neuropsychopharmacol. 20, 698–711. doi:10.1093/ijnp/pyx036 Dore, J., Turnipseed, B., Dwyer, S., Turnipseed, A., Andries, J., Ascani, G., et al. (2019). Ketamine assisted psychotherapy (KAP): patient demographics, clinical
data and outcomes in three large practices administering ketamine with
psychotherapy. J. Psychoact. Drugs 51, 189–198. doi:10.1080/02791072.2019. 1587556 Sanz, C., Zamberlan, F., Erowid, E., Erowid, F., and Tagliazucchi, E. (2018). The
experience elicited by hallucinogens presents the highest similarity to dreaming
within a large database of psychoactive substance reports. Front. Neurosci. 12, 7. References doi:10.3389/fnins.2018.00007 Feldman, G., Hayes, A., Kumar, S., Greeson, J., and Laurenceau, J.-P. (2007). Mindfulness and emotion regulation: the development and initial validation of
the
Cognitive
and
Affective
Mindfulness
Scale-Revised
(CAMS- Frontiers in Pharmacology 12 frontiersin.org Stocker et al. Stocker et al. 10.3389/fphar.2022.916641 affect
and
cognitive
thinking
style
and
their
association
with
ego
dissolution. Psychopharmacol. (Berl.) 235, 2979–2989. doi:10.1007/s00213-
018-4988-3 Soler, J., Elices, M., Dominguez-Clavé, E., Pascual, J. C., Feilding, A., Navarro-Gil,
M., et al. (2018). Four weekly ayahuasca sessions lead to increases in “acceptance”
capacities: A comparison study with a standard 8-week mindfulness training
program. Front. Pharmacol. 9, 224. doi:10.3389/fphar.2018.00224 van Oorsouw, K. I., Uthaug, M. V., Mason, N. L., Broers, N. J., and Ramaekers,
J. G. (2021). Sub-acute and long-term effects of ayahuasca on mental health and
well-being in healthy ceremony attendants: a replication study. J. Psychedelic Stud. 5, 103–113. doi:10.1556/2054.2021.00174 Soler, J., Elices, M., Franquesa, A., Barker, S., Friedlander, P., Feilding, A., et al. (2016). Exploring the therapeutic potential of ayahuasca: acute intake increases mindfulness-
related capacities. Psychopharmacol. (Berl.) 233, 823–829. doi:10.1007/s00213-015-4162-0 Walach, H., Buchheld, N., Buttenmüller, V., Kleinknecht, N., and Schmidt, S. (2006). Measuring mindfulness—the Freiburg Mindfulness Inventory (FMI). Pers. Individ. Dif. 40, 1543–1555. doi:10.1016/j.paid.2005.11.025 Spiritual
Mind
(2022). Non-judgement Jon
Kabat-Zinn. Non-judgmental
awareness - habits of mind [video]. YouTube. Available at: https://www.youtube. com/watch?v=oKE8IiK3O1U. Watts, R., Day, C., Krzanowski, J., Nutt, D., and Carhart-Harris, R. (2017). Patients’ accounts of increased “connectedness” and “acceptance” after psilocybin
for treatment-resistant depression. J. Humanist. Psychol. 57, 520–564. doi:10.1177/
0022167817709585 Studerus, E., Gamma, A., and Vollenweider, F. X. (2010). Psychometric
evaluation of the altered states of consciousness rating scale (OAV). PloS One 5,
e12412. doi:10.1371/journal.pone.0012412 Sumner, R. L., Chacko, E., McMillan, R., Spriggs, M. J., Anderson, C., Chen, J.,
et al. (2021). A qualitative and quantitative account of patient’s experiences of
ketamine and its antidepressant properties. J. Psychopharmacol. (Oxf.) 35, 946–961. doi:10.1177/0269881121998321 Wersebe, H., Lieb, R., Meyer, A. H., Miche, M., Mikoteit, T., Imboden, C., et al. (2018). Well-being in major depression and social phobia with and without
comorbidity. Int. J. Clin. Health Psychol. 18, 201–208. doi:10.1016/j.ijchp.2018. 06.004 Swift, T. C., Belser, A. B., Agin-Liebes, G., Devenot, N., Terrana, S., Friedman, H. L., et al. (2017). Cancer at the dinner table: experiences of psilocybin-assisted
psychotherapy for the treatment of cancer-related distress. J. Humanist. Psychol. 57,
488–519. doi:10.1177/0022167817715966 Wintjen, L., and Petermann, F. (2010). Beck-Depressions-Inventar Revision
(BDI–II). Z. fur Psychiatr. Psychol. Psychother. 58, 243–245. Uthaug, M. V., van Oorsouw, K., Kuypers, K. P. C., van Boxtel, M., Broers, N.
J., Mason, N. L., et al. (2018). Sub-acute and long-term effects of ayahuasca on References doi:10.1024/1661-
4747/a000033 Uthaug, M. V., Lancelotta, R., Szabo, A., Davis, A. K., Riba, J., Ramaekers, J. G., et al. (2020). Prospective examination of synthetic 5-methoxy-N, N-dimethyltryptamine
inhalation: effects on salivary IL-6, cortisol levels, affect, and non-judgment. Psychopharmacol. (Berl.) 237, 773–785. doi:10.1007/s00213-019-05414-w Włodarczyk, A., Cubała, W. J., Gałuszko-Węgielnik, M., and Szarmach, J. (2021). Dissociative
symptoms
with
intravenous
ketamine
in
treatment-resistant
depression exploratory observational study. Med. Baltim. 100, e26769. doi:10. 1097/MD.0000000000026769 Uthaug, M. V., Lancelotta, R., van Oorsouw, K., Kuypers, K. P. C., Mason, N., Rak,
J., et al. (2019). A single inhalation of vapor from dried toad secretion containing 5-
methoxy-N,N-dimethyltryptamine (5-MeO-DMT) in a naturalistic setting is
related to sustained enhancement of satisfaction with life, mindfulness-related
capacities, and a decrement of psychopathological symptoms. Psychopharmacol. (Berl.) 236, 2653–2666. doi:10.1007/s00213-019-05236-w Xu, Y., Hackett, M., Carter, G., Loo, C., Gálvez, V., Glozier, N., et al. (2016). Effects of low-dose and very low-dose ketamine among patients with major
depression:
a
systematic
review
and
meta-analysis. Int. J. Neuropsychopharmacol. 19, pyv124. doi:10.1093/ijnp/pyv124 Zarate, C. A., Singh, J. B., Carlson, P. J., Brutsche, N. E., Ameli, R., Luckenbaugh,
D. A., et al. (2006). A randomized trial of an N-methyl-D-aspartate antagonist in
treatment-resistant major depression. Arch. Gen. Psychiatry 63, 856–864. doi:10. 1001/archpsyc.63.8.856 Uthaug, M. V., van Oorsouw, K., Kuypers, K. P. C., van Boxtel, M., Broers, N. J., Mason, N. L., et al. (2018). Sub-acute and long-term effects of ayahuasca on 13 Frontiers in Pharmacology 13 frontiersin.org
|
https://openalex.org/W2969903489
|
https://research.monash.edu/files/288276942/283276144_oa.pdf
|
English
| null |
Inhibition of amyloid beta toxicity in zebrafish with a chaperone-gold nanoparticle dual strategy
|
Nature communications
| 2,019
|
cc-by
| 19,417
|
ARTICLE Inhibition of amyloid beta toxicity in zebrafish with
a chaperone-gold nanoparticle dual strategy Ibrahim Javed
1,2, Guotao Peng
2, Yanting Xing3, Tianyu Yu2, Mei Zhao2, Aleksandr Kakinen1, Ava Faridi1,
Clare L. Parish4, Feng Ding
3, Thomas P. Davis
1,5, Pu Chun Ke
1 & Sijie Lin
2 Alzheimer’s disease (AD) is the most prevalent form of neurodegenerative disorders, yet no
major breakthroughs have been made in AD human trials and the disease remains a para-
mount challenge and a stigma in medicine. Here we eliminate the toxicity of amyloid beta
(Aβ) in a facile, high-throughput zebrafish (Danio rerio) model using casein coated-gold
nanoparticles (βCas AuNPs). βCas AuNPs in systemic circulation translocate across the
blood brain barrier of zebrafish larvae and sequester intracerebral Aβ42 and its elicited
toxicity in a nonspecific, chaperone-like manner. This is evidenced by behavioral pathology,
reactive oxygen species and neuronal dysfunction biomarkers assays, complemented by brain
histology and inductively coupled plasma-mass spectroscopy. We further demonstrate the
capacity of βCas AuNPs in recovering the mobility and cognitive function of adult zebrafish
exposed to Aβ. This potent, safe-to-use, and easy-to-apply nanomedicine may find broad use
for eradicating toxic amyloid proteins implicated in a range of human diseases. 1 ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal
Parade, Parkville, VIC 3052, Australia. 2 College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute,
Shanghai East Hospital, Shanghai Institute of Pollution Control and Ecological Security, Key Laboratory of Yangtze River Water Environment, Tongji
University, 1239 Siping Road, Shanghai 200092, China. 3 Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA. 4 The Florey
Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, VIC 3052, Australia. 5 Australian Institute for
Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia. Correspondence and requests for materials should be
addressed to F.D. (email: fding@clemson.edu) or to T.P.D. (email: thomas.p.davis@monash.edu) or to P.C.K. (email: pu-chun.ke@monash.edu)
or to S.L. (email: lin.sijie@tongji.edu.cn) 1 NATURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 T T
he aggregation of proteins into amyloid fibrils and plaques,
under abnormal physiological conditions, is a phenom-
enon common to a range of human amyloid diseases
including amyloid beta (Aβ) for Alzheimer’s disease (AD),
α-synuclein for Parkinson’s disease (PD), and human islet amy-
loid polypeptide for type 2 diabetes (T2D)1. Results and discussion g
Among the common strategies against amyloidosis, peptides,
small molecules, monoclonal antibodies and, more recently,
engineered nanoparticles, have shown various degrees of promise
as inhibitors20–27. For in vivo applications, these inhibitors are
designed to satisfy—partially or fully—the following criteria:
minimal toxicity, good circulation/repeated dosing, good trans-
location efficacy across the blood brain barrier (BBB), as well as
capabilities in targeting and further eliminating toxic oligomers,
protofibrils, and fibrils of amyloid proteins. β casein (βCas), a
whey protein, along with αs1 casein, possesses a chaperone-like
activity, similarly to small heat-shock proteins and extracellular
clusterin. This activity of the caseins arises from the following: (1)
a lack of tertiary structure and solvent-exposed hydrophobicity
with well separated hydrophilic regions, (2) existence as hetero-
geneous oligomers, (3) dynamics and malleable protein regions,
and
(4)
ability
to
bind
with
a
wide
range
of
partially
folded proteins preventing their aggregation28. One factor that
attributes to these properties is the presence of a high percentage
of proline residues, i.e., 18% in the case of βCas, and no disulfide
bonds that provide them with an open and flexible conforma-
tion29. The chaperone-like behavior of βCas and αs1 caseins
shields the amyloidogenic regions and naturally prevents the
amyloidosis of αs2 and κ-casein in mammary glands or milk while
inhibiting the amyloidosis of insulin and Aβ40 in vitro30–32. Structurally, monomeric caseins are mostly disordered, but tend
to form micelles mediated by hydrophobic and electrostatic
interactions28. In vitro interaction of βCas AuNPs and Aβ. Aβ was fibrillized
in vitro from random coils to β-sheet rich amyloid fibrils within
48 h at 37 °C. A thioflavin T (ThT) assay was used to study the
fibrillization kinetics (Fig. 1a), while transmission electron
microscopy (TEM) (Fig. 1b) and circular dichroism (CD) spec-
troscopy were employed to investigate fibril formation and sec-
ondary structural transitions of Aβ (Fig. 1c, d). βCas AuNPs
(Fig. 1e) often clustered together after binding with Aβ (Fig. 1f)
and prevented β-sheet formation of the peptide (Fig. 1a). The
presence of Aβ coronae on βCas AuNPs was evident from TEM
imaging (Fig. 1f inset). The secondary structure of βCas AuNPs
was predominantly random coils that transitioned into α helices
in Aβ-βCas AuNPs complex (Fig. 1g, d). βCas formed micelles of
~100 nm in size in the aqueous medium (Fig. 1h). Results and discussion Scheme of study. Different fractions of caseins, e.g., αs1 and β,
have a known potential for surface-assisted sequestration and
colloidal inhibition of Aβ40 and insulin amyloid formation31,32. Herein, βCas with an intrinsic chaperone-like activity33 was
coated on AuNPs by NaBH4-assisted reduction of Au. Synthesis
of the βCas AuNPs was optimized at room temperature to obtain
~5 nm in size for efficient BBB translocation while preserving the
random coil structure of βCas that is required for its chaperone
activity30. βCas AuNPs were then characterized for their inhibi-
tory activity against Aβ42 (abbreviated as Aβ from hereon)
fibrillization in vitro. For in vivo translation, an Aβ toxicity model
was developed in zebrafish larvae by cerebroventricular injection
of Aβ. The biodistribution and translocation of βCas AuNPs
across the larval zebrafish BBB were then determined after
introducing the nanoparticles into the bloodstream via intra-
cardiac injection. Finally, Aβ and βCas AuNPs were co-
administered via cerebroventricular and intracardiac injections
into zebrafish larvae, and alleviations of Aβ-induced behavioral
symptoms were quantified. In addition, Aβ-induced behavioral
pathology and cognitive dysfunction in adult zebrafish were
rescued by βCas AuNPs, further implicating the chaperone
potential of βCas AuNPs against Aβ toxicity in vivo. p
β
AD is a primary form chronic neurodegenerative disorder and
a major cause of dementia, impairing 46 million people world-
wide5. The pathological origin of AD is highly debatable, but is
believed to be associated with a range of health, genetics, envir-
onmental and lifestyle factors, as well as inflammation6–9. The
etiology of AD includes a number of events that precede Aβ
plaque formation, such as autophagy or endosomal dysfunc-
tion10,
endoplasmic
reticulum
stress11,
oxidative
stress
or
hypoxia, vasculature and mitochondrial dysfunction12, and prior
history of bacterial infections13. Aβ42 is one of the two most
abundant peptide species derived from amyloid precursor protein
(APP) through proteolysis and, alongside tau, is strongly asso-
ciated with the pathology of AD14. Despite much research over
the past decades devoted to understanding the origin, diagnosis
and prevention of AD, there is a glaring lack of success against Aβ
amyloidosis marked by recent withdrawals of clinical trials with
Eli Lilly, Pfizer, and Biogen15–17. This indicates failures in current
anti-amyloid therapeutic approaches, compounded by a lack of
suitable in vivo models for high throughput screening18,19, fur-
ther justifying the urgency for developing alternative strategies
against AD. Inhibition of amyloid beta toxicity in zebrafish with
a chaperone-gold nanoparticle dual strategy The amyloid
hypothesis regards oligomers as the most toxic species2, where
protofibrils or oligomers of amyloid proteins are proposed to
induce local inflammation, failed autophagy, and membrane
perturbation that are responsible for the further loss of neuronal
or pancreatic β-cells mass3,4. essential role of the AuNPs in delivering the protein. This
demonstrates the inhibition potential of a chaperone protein
integrated with a biocompatible nanomaterial against Alzhei-
mer’s-like symptoms. The established zebrafish model also opens
the door to economically viable, high-throughput in vivo
screening of emerging nanomedicines targeting a wide range of
amyloid diseases. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 Source data are provided as a Source Data file CD (mdeg)
c
g
j
–9
–7
–5
–3
–1
1
3
190
210
230
βCas AuNPs
βCas AuNPs + Aβ
–7
–5
–3
–1
1
3
190
210
230
Aβ
Aβ amyloid
–7
–5
–3
–1
1
3
190
210
230
βCas
βCas + Aβ
Wavelength (nm) e
0
5
10
15
20
0
12
24
36
48
ThT fluorescence
Time (h)
Aβ
Aβ + βCas AuNPs
Aβ + βCas
a f
100 nm
b 0
50
100
βCas + Aβ
βCas
βCas AuNPs
+ Aβ
βCas AuNPs
Aβ aymloid
Aβ
Content (%)
α Helices
β Sheets
Turns
Random coils
*
*
**
*
**
*
**
d b d c a f f g e f
5 nm e
h
Time (h) Random coils h j i i h Content (%) Wavelength (nm) n l 0
3
6
9
12
15
1
10
100
1000
10,000
Intensity (%)
Hydrodynamic diameter (nm)
βCas AuNPs
βCas AuNPs + Aβ
βCas
βCas + Aβ
Aβ 0 h
Aβ 48 h
k n
000
10,000
r (nm)
s AuNPs + Aβ
s + Aβ
8 h
0
50
100
150
200
250
1
10
100
1000
Aβ bound (μM)
Aβ added (μM)
βCas AuNPs + Aβm
βCas AuNPs + Aβo
βCas + Aβm
βCas + Aβo
l
**
**
m m k n m Fig. 1 In vitro inhibitory interactions between βCas AuNPs and βCas with Aβ. a ThT assay of Aβ alone (50 µM) and in the presence of βCas AuNPs
(equivalent to 6.25 µM of βCas) and βCas (6.25 µM) (n = 4). βCas AuNPs completely inhibited while βCas decreased (p < 0.005) the lag time and plateau
ThT fluorescence of Aβ fibrillization. b TEM image of fibrillized Aβ. c CD spectra of Aβ (100 µM) before and after fibrillization indicate conformation change
from random coils (198 nm peak) to β-sheets (220 nm peak). d Secondary structure of Aβ (100 µM) fibrillized with and without βCas AuNPs or βCas
(n = 4). TEM images of βCas AuNPs before (e) and after incubation with Aβ (f; inset shows Aβ corona on a βCas AuNP). g CD spectra of βCas AuNPs
before and after incubation with Aβ. TEM images of βCas before (h) and after (i) incubation with Aβ. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 e
f
h
i
CD (mdeg)
c
g
j
n
5 nm
100 nm
0
5
10
15
20
0
12
24
36
48
ThT fluorescence
Time (h)
Aβ
Aβ + βCas AuNPs
Aβ + βCas
a
b
–9
–7
–5
–3
–1
1
3
190
210
230
βCas AuNPs
βCas AuNPs + Aβ
–7
–5
–3
–1
1
3
190
210
230
Aβ
Aβ amyloid
–7
–5
–3
–1
1
3
190
210
230
βCas
βCas + Aβ
Wavelength (nm)
0
3
6
9
12
15
1
10
100
1000
10,000
Intensity (%)
Hydrodynamic diameter (nm)
βCas AuNPs
βCas AuNPs + Aβ
βCas
βCas + Aβ
Aβ 0 h
Aβ 48 h
k
0
50
100
150
200
250
1
10
100
1000
Aβ bound (μM)
Aβ added (μM)
βCas AuNPs + Aβm
βCas AuNPs + Aβo
βCas + Aβm
βCas + Aβo
l
**
**
0
50
100
βCas + Aβ
βCas
βCas AuNPs
+ Aβ
βCas AuNPs
Aβ aymloid
Aβ
Content (%)
α Helices
β Sheets
Turns
Random coils
*
*
**
*
**
*
**
d
m
Fig. 1 In vitro inhibitory interactions between βCas AuNPs and βCas with Aβ. a ThT assay of Aβ alone (50 µM) and in the presence of βCas AuNPs
(equivalent to 6.25 µM of βCas) and βCas (6.25 µM) (n = 4). βCas AuNPs completely inhibited while βCas decreased (p < 0.005) the lag time and plateau
ThT fluorescence of Aβ fibrillization. b TEM image of fibrillized Aβ. c CD spectra of Aβ (100 µM) before and after fibrillization indicate conformation change
from random coils (198 nm peak) to β-sheets (220 nm peak). d Secondary structure of Aβ (100 µM) fibrillized with and without βCas AuNPs or βCas
(n = 4). TEM images of βCas AuNPs before (e) and after incubation with Aβ (f; inset shows Aβ corona on a βCas AuNP). g CD spectra of βCas AuNPs
before and after incubation with Aβ. TEM images of βCas before (h) and after (i) incubation with Aβ. j Appearance of a negative peak at 218 nm in CD
spectra of βCas + Aβ indicates limited Aβ fibrillization into β-sheets. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 j Appearance of a negative peak at 218 nm in CD
spectra of βCas + Aβ indicates limited Aβ fibrillization into β-sheets. After binding with Aβ, the α-helix contents of βCas AuNPs were decreased
significantly (p < 0.05) from 56 to 21%; while in the case of βCas, α-helices decreased from 41 to 22% (p < 0.005) and β-sheets increased from 24 to 38%
(p < 0.05). k Hydrodynamic radius of Aβ before and after fibrillization in the presence and absence of βCas AuNPs or βCas. l Quantification of binding
capacity of βCas AuNPs or βCas with Aβm or Aβo (n = 4). βCas AuNPs (6.25 µM βCas equivalent) were able to bind up to 152.3 ± 13.4 and 190.7 ± 10.9 µM
of Aβm and Aβo. βCas (6.25 µM) was only able to adsorb 62.4 ± 3.4 and 26.4 ± 4.6 µM of Aβm and Aβo, indicating a significant (p < 0.005) increase in Aβ
binding capacity of βCas in the form of βCas AuNPs. m, n Enhanced binding of Aβm and Aβo with βCas promoted by the AuNP substrate. Scale bars in
TEM images is 100 nm, while F inset is 5 nm. Error bars represent the standard deviation. Source data are provided as a Source Data file 0.3 and 0.06 mM for βCas AuNPs and βCas, respectively, sug-
gesting binding saturations (Supplementary Fig. 1E). The differ-
ential binding of βCas and βCas AuNPs with Aβm/o is illustrated
in Fig. 1m, n. of amyloid proteins14, interactions of βCas AuNPs with Aβ
monomers (Aβm) and Aβ oligomers (Aβo) were also examined. The in vitro binding between Aβo/m and βCas or βCas AuNPs
was further quantified by a bicinchoninic acid assay (BCA) and
thermogravimetric analysis (TGA). βCas or βCas AuNPs were
incubated with different concentrations of Aβm or Aβo for 48 h
and centrifuged to remove free Aβ. The centrifuged pellets con-
taining Aβm or Aβo bound to βCas or βCas AuNPs were sub-
jected to analysis (Supplementary Fig. 1D). The maximum
binding capacity between Aβ and βCas (6.25 µM) was quantified
to be 62 and 26 µM for Aβm and Aβo, respectively (Fig. 1l). However, when βCas AuNPs (containing 6.25 µM βCas) were
exposed to Aβ, the maximum binding capacity was increased to
152 and 190 µM for Aβm and Aβo, respectively. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 After binding with Aβ, the α-helix contents of βCas AuNPs were decreased
significantly (p < 0.05) from 56 to 21%; while in the case of βCas, α-helices decreased from 41 to 22% (p < 0.005) and β-sheets increased from 24 to 38%
(p < 0.05). k Hydrodynamic radius of Aβ before and after fibrillization in the presence and absence of βCas AuNPs or βCas. l Quantification of binding
capacity of βCas AuNPs or βCas with Aβm or Aβo (n = 4). βCas AuNPs (6.25 µM βCas equivalent) were able to bind up to 152.3 ± 13.4 and 190.7 ± 10.9 µM
of Aβm and Aβo. βCas (6.25 µM) was only able to adsorb 62.4 ± 3.4 and 26.4 ± 4.6 µM of Aβm and Aβo, indicating a significant (p < 0.005) increase in Aβ
binding capacity of βCas in the form of βCas AuNPs. m, n Enhanced binding of Aβm and Aβo with βCas promoted by the AuNP substrate. Scale bars in
TEM images is 100 nm, while F inset is 5 nm. Error bars represent the standard deviation. Results and discussion Upon incu-
bation with Aβ, βCas (in the absence of the AuNPs) induced an
early onset of fibrillization as revealed by the ThT assay (Fig. 1a),
which can be attributed to the fast nucleation of Aβ promoted by
βCas micelles in vicinity34. However, Aβ fibrillization was not
inhibited and random aggregates of the peptide were observed
under TEM (Fig. 1i). CD spectroscopy indicated that the α-helix
rich structure of βCas was converted to β-sheets in βCas + Aβ
aggregates due to Aβ fibrillization (Fig. 1j, d). The hydrodynamic
diameters of βCas AuNPs and βCas were increased from 7.5 ± 2.6
and 156.3 ± 34.4 nm to 39.3 ± 5.4 and 496.1 ± 114 nm (n = 3),
respectively (Fig. 1k and Supplementary Table 1). The zeta
potential of βCas AuNPs was markedly elevated from −11.7 ± 1.8
to −33.7 ± 2.1 mV (n = 3), indicating adsorption of anionic Aβ
onto the surfaces of βCas AuNPs (Supplementary Table 1). Clusterization of βCas AuNPs was confirmed by hyperspectral
imaging (HSI), where the surface plasmon resonance (SPR) of
βCas AuNPs was red shifted from 490 ± 21 to 601 ± 24 nm (n =
3) upon aggregation and light illumination (Supplementary
Fig. 1A–C). As oligomers/protofibrils are the main toxic species Here, we devise a facile method of coating βCas onto gold
nanoparticles (AuNPs). We systemically deliver the βCas AuNPs
via intracardial administration to mitigate the toxicity of Aβ42
induced in the brain of zebrafish larvae and adults (Danio rerio). βCas AuNPs sequester toxic Aβ42 in the brain of zebrafish larvae
and adults through a nonspecific, chaperone-like manner. No
such mitigation is obtained with caseins alone, indicating the TURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications 2 NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 Although we did not perform simula-
tions for the binding of Aβ with βCas AuNP, due to the prohi-
bitively large system, we expected similar trends of secondary
structure changes as observed in the experiments (Fig. 1d). Representative structures of the binding complexes obtained from
the simulations (Supplementary Fig. 4A) suggest that βCas could
bind Aβ and form either β sheets or helices (Supplementary
Fig. 4B), which in turn inhibited Aβ aggregation by sequestering
Aβ in solution or capping Aβ fibrils from elongation. Moreover,
simulations of βCas with a preformed cross-β Aβ oligomer formation on the nanoparticles (Supplementary Fig. 2C). Further-
more, CD results indicated similar secondary structural distribu-
tions of Aβo and Aβo-βCas AuNPs complex. Thus, the α helices
in Aβo-βCas AuNPs complex can be attributed to the Aβo corona
on βCas AuNPs (Supplementary Fig. 2D, E). Incubation of βCas
AuNPs with Aβm did not present any difference in the secondary
structure of βCas AuNPs. That, together with the UV-SPR,
fluorescence and TEM results, confirmed the high affinity of βCas
AuNPs for Aβo. formation on the nanoparticles (Supplementary Fig. 2C). Further-
more, CD results indicated similar secondary structural distribu-
tions of Aβo and Aβo-βCas AuNPs complex. Thus, the α helices
in Aβo-βCas AuNPs complex can be attributed to the Aβo corona
on βCas AuNPs (Supplementary Fig. 2D, E). Incubation of βCas
AuNPs with Aβm did not present any difference in the secondary
structure of βCas AuNPs. That, together with the UV-SPR,
fluorescence and TEM results, confirmed the high affinity of βCas
AuNPs for Aβo. DMD simulations of βCas binding with AuNP and Aβ
monomer/oligomer. To gain a molecular insight into the
adsorption of βCas onto an AuNP surface (i.e., the formation of a
βCas AuNP “corona”) and the inhibition mechanism of βCas
AuNPs against Aβ aggregation, discrete molecular dynamics
(DMD) simulations—an accurate and rapid molecular dynamics
algorithm widely used to study the structure and dynamics of
large molecular systems35,36—were performed (Fig. 2). The
binding of a βCas monomer with an AuNP (4 nm in diameter),
an Aβ monomer and an Aβ oligomer were examined (Supple-
mentary Methods), and the control simulations included an
isolated βCas, an Aβ monomer, and an Aβ oligomer. We first
computed secondary structure contents from equilibrium simu-
lations (e.g., radius of gyration in Supplementary Fig. 3A and
number of hydrogen bond in Supplementary Fig. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 5A indicated
simulations reaching steady states) and used them to estimate the
expected CD spectra for different molecular systems (Fig. 2b). The predicted CD spectra agreed well with the experimental
results (Fig. 1c, g, j, d) in terms of secondary structural changes. As expected, βCas was intrinsically disordered with unstructured
coils as the dominant secondary structure. Upon binding the Aβ monomer
Binding probability
0
Residue index of β-casein
25
50
75
100
125
150
175
200
225
0.2
0.4
0.1
0.3
Aβ oligomer
0.2
0.4
0.1
0.3
0
0.4
0.8
0.2
0.6
AuNP
0
190
200
210
220
230
240
Wavelength (nm)
–2
–1
0
CD a.u. Aβm
βCas
βCas + Aβm
βCas + AuNP
Aβm
βCas
βCas + Aβm
βCas + AuNP
Helix
Sheet
Turn
Coil
0
100
Content (%)
a
b
c
1.2
1.0
Fig. 2 DMD simulations of βCas binding with AuNP, Aβ monomer, and oligomer. a Binding probabilities of βCas with an AuNP, an Aβ monomer and an Aβ
oligomer, where high-binding is defined as residues with binding probabilities above one standard deviation from the average (dash lines). βCas high-
binding residue regions with AuNP and with Aβ monomer/oligomer are highlighted with bars (inset). b Predicted CD spectra of secondary structure
contents (inset) derived from simulations. c Predicted βCas-AuNP corona structures comprised of three βCas proteins on an AuNP surface (right) and
corresponding molecular surfaces of the proteins (left) are shown to highlight their binding with an Aβ monomer, where each βCas residue was colored
from purple (low) to red (high) according to its binding probability with Aβ monomer as in panel A middle. Source data are provided as a Source Data file
4
NATURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications Aβ monomer
Binding probability
0
Residue index of β-casein
25
50
75
100
125
150
175
200
225
0.2
0.4
0.1
0.3
Aβ oligomer
0.2
0.4
0.1
0.3
0
0.4
0.8
0.2
0.6
AuNP
0
a
1.2
1.0 a 190
200
210
220
230
240
Wavelength (nm)
–2
–1
0
CD a.u. Aβm
βCas
βCas + Aβm
βCas + AuNP
Aβm
βCas
βCas + Aβm
βCas + AuNP
Helix
Sheet
Turn
Coil
0
100
Content (%)
b b c c c Fig. 2 DMD simulations of βCas binding with AuNP, Aβ monomer, and oligomer. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 Similar results
were obtained with TGA, where no difference in the TGA curve
was observed when the concentration of Aβ was increased beyond g
The high affinity of βCas AuNPs for Aβo can be attributed to
the ability of βCas to bind with misfolded/molten globules of
proteins28. To further investigate the differential binding of βCas
AuNPs with Aβo and Aβm, we incubated βCas AuNPs with
preformed Aβo and Aβm for 3 h and separated them from
unbound Aβo/m via centrifugal washing. The UV-SPR spectra of
βCas AuNPs were significantly suppressed upon incubation with
Aβo as compared to Aβm (Supplementary Fig. 2A). Similarly, the
fluorescence of neutral red-conjugated AuNPs (NR-βCas AuNPs)
was suppressed when incubated with Aβo (Supplementary
Fig. 2B). This indicates increased adsorption of Aβo than Aβm
by βCas AuNPs, as further confirmed by TEM imaging of corona TURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications 3 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 AuNP, βCas exhibited increased coil and decreased helix and
sheet contents both in silico (Fig. 2b inset) and in vitro (Fig. 1g, j,
d). Analysis identified several specific binding sites of βCas for the
AuNP, such as residues His65, Phe67, Lys122, Met124, and
His159 (the upper panel in Fig. 2a). Based on clustering analysis
of the structural ensemble from multiple independent DMD
simulations (Supplementary Methods), representative binding
structures of βCas monomers with the AuNP were obtained
(Supplementary Fig. 3B), where individual βCas partially covered
the AuNP. To form a monolayer protein corona, at least three
βCas molecules were required to fully coat the AuNP surface
(Fig. 2c, estimated by covering the NP surface with randomly
selected centroid structures from top ten clusters shown in Sup-
plementary Fig. 3B). When βCas bound to an Aβ monomer, the
overall contents of ordered helices and sheets increased while
coils decreased (Fig. 2b), in agreement with the experiments
(Fig. 1c, j, d). Residues in βCas that had strong binding with the
Aβ monomer did not overlap with those preferred to bind the
AuNP (Fig. 2a). This result suggests that βCas AuNP could still
bind to Aβ monomers, as illustrated by the βCas-AuNP complex
where Aβ-binding residues were exposed (Fig. 2c, with the pro-
tein surface color-coded according to their binding probabilities
with the Aβ monomer). NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 Whole-mount imaging was performed under the
RFP channel of a fluorescence microscope at 0.5, 6, and 12 h after
injection in order to trace the biodistribution of NR-βCas AuNPs
in different regions of the larvae (Fig. 4b). No fluorescence was
observed from the dorsal or lateral view of the larvae in the
control (Supplementary Fig. 9). The zebrafish BBB is a double-
layered membrane separating cerebral blood vessels from brain
tissues. Alongside tight junctions, zebrafish BBB expresses
occluding, claudins and p-glycoproteins and thus possesses a
selectivity against xenobiotics42,43. In the present study, upon
intracardiac injection of NR-βCas AuNPs into larvae, bright red
fluorescence was observed from the brain after 0.5 h, indicating
translocation of βCas AuNPs across the BBB (Fig. 4c). At 6 h after
injection, the fluorescence from the cerebral region was decreased
while it was recorded in the liver. However, the fluorescence was
diminished from the liver at 12 h. βCas AuNPs were detectable by
HSI and the SPR signals of the AuNPs were recorded from the
brain sections of the larvae, prepared 0.5 h post injection of βCas
AuNPs (Fig. 4d). However, no AuNPs or SPR were detected from
the brain of untreated control. Finally, inductively coupled
plasma mass spectroscopy (ICP-MS) was performed to further
quantify the presence of AuNPs in the brain. The larvae treated
with intracardiac injection of βCas AuNPs were euthanized at 0.5,
0.6, and 12 h and their heads were homogenized and quantified
for Au in the brain and trunks. The concentration of Au was the
highest in the brain at 0.5 h while decreased to the lowest level at
12 h (Fig. 4e). A correlation of AuNPs injected in the heart and
delivered across the brain is shown in Fig. 4f. Injection of 1.5, 3,
and 6 ng Au equivalent AuNPs via the heart delivered around
0.15, 0.45, and 0.5 ng of AuNPs to the brain, indicating that
injection of >3 ng of AuNPs did not increase the delivery of
AuNPs to the cerebral region. TEM images of microtome slices of
the zebrafish larval brain also showed the presence of βCas
AuNPs in the intracellular space (Supplementary Fig. 10). Development of Aβ toxicity model in zebrafish larvae. Zebra-
fish larvae express human orthologues of Aβ, APP, and γ-
secretase components (PSENEN37, NCTN38, APH1b37) 24 h after
hatching39. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 Gene knockout or chemical inhibitors may create an
imbalance among these protein components to result in neuro-
logical and behavioral abnormalities40,41. Here, an Aβ toxicity
model was developed using zebrafish larvae (5 days old) by
injecting Aβ into the cerebroventricular space (Fig. 3a and Sup-
plementary Fig. 7). In vivo oligomerization of Aβ into toxic oli-
gomeric species induced pathological features in zebrafish larvae
after 5 days of Aβ treatment (Fig. 3b). Different concentrations of
Aβ were injected into the larvae and no lethality was observed
even with the highest concentration of Aβ, at 1200 fM per larva. However, reduced locomotion of the larvae was notable in a
concentration dependent manner, with nonresponsive mobility
and a loss of balance at higher Aβ concentrations (≥75 fM)
(Fig. 3c). The nonresponsiveness of the larvae was recorded
using tapping as a stimulus and loss of balance was observed as a
tilt of the larvae from the normal horizontal axis to the imbal-
anced vertical axis (Supplementary Videos 1–3). The larvae
injected with 10, 50, and 100 fM Aβ were characterized on an
automated zebrafish behavior analysis system, to quantify total
distance traveled and frequency of movement during the 1 h
recording period. Observations were made on the third (Sup-
plementary Fig. 8A) and fifth (Fig. 3d) day post treatment with
Aβ. Significant reductions in both total distance traveled and
frequency of movements were noted, in a concentration-
dependent manner on the fifth day, in Aβ-treated larvae com-
pared to untreated control. To visualize the presence of Aβ fibrils
in the brain of the larvae, Congo red dye was injected in the
cerebroventricular space of zebrafish larvae (Fig. 3e) on the third
(Supplementary Fig. 8B) and fifth day post injection of Aβ
(Fig. 3f). Significantly increased fluorescence was observed
from the brain of the Aβ-injected larvae on the fifth day post
injection. By comparison, Congo red dye was injected in
untreated control and no fluorescence was observed (Fig. 3g). Aβ
amyloid formation in the brain of zebrafish larvae was further
confirmed
by
matrix
assisted
laser
desorption/ionization
(MALDI) analysis. Five days post injection with Aβ, the larvae
heads
were
excised
after
euthanization,
homogenized
in
phosphate-buffered saline (PBS) buffer and analyzed by MALDI. A peak corresponding to the molecular weight of Aβ was
observed at 4538.1 mz−1 (Fig. 3h). Aβ treated larvae were further
fixed, cryo-sectioned and stained with Congo red. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 a Binding probabilities of βCas with an AuNP, an Aβ monomer and an Aβ
oligomer, where high-binding is defined as residues with binding probabilities above one standard deviation from the average (dash lines). βCas high-
binding residue regions with AuNP and with Aβ monomer/oligomer are highlighted with bars (inset). b Predicted CD spectra of secondary structure
contents (inset) derived from simulations. c Predicted βCas-AuNP corona structures comprised of three βCas proteins on an AuNP surface (right) and
corresponding molecular surfaces of the proteins (left) are shown to highlight their binding with an Aβ monomer, where each βCas residue was colored
from purple (low) to red (high) according to its binding probability with Aβ monomer as in panel A middle. Source data are provided as a Source Data file
4
NATURE COMMUNICATIONS | (2019)10 3780 | htt
//d i
/10 1038/ 41467 019 11762 0 |
t
/
t
i
ti NATURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications 4 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 of a microscope (Fig. 3i). No red fluorescence was observed in
untreated control (Fig. 3j). indicate that the βCas-AuNP complex could bind Aβ oligomer
(Fig. 2a) and the strong binding between βCas and Aβ oligomer
(Supplementary Fig. 5D) inhibited further growth of the initial
oligomer (i.e., inset of Supplementary Fig. 5E) into an extended β-
sheet structure via conformational rearrangements. Taken toge-
ther, our simulations were not only consistent with the ensemble
measurements in vitro, but also uncovered the molecular
mechanism for the formation of the βCas AuNP complex and
their inhibition of Aβ aggregation via either sequestering of Aβ
monomers or capping of Aβ fibril elongation. In addition, the
binding of Aβ with a bare AuNP is presented in Supplementary
Fig. 6. Approximating the binding affinity and energy differences
between the complex (βCas + AuNP, Aβ + AuNP) and indivi-
dual components (βCas, Aβ) from DMD simulations (Fig. 2 and
Supplementary Fig. 6) revealed that the binding of βCas with the
AuNP was significantly stronger than the binding of Aβ with the
AuNP
(ΔΔG ~ −194 kcal mol−1)
(Supplementary
Table
2). Hence, replacement of βCas corona with Aβ was energetically
unfavorable. Biodistribution of βCas AuNPs in zebrafish larvae. The bio-
distribution of βCas AuNPs was characterized by conjugating the
AuNPs with NR dye and injecting the AuNPs via the intracardiac
route (Fig. 4a). NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 c Disruptive locomotive behavior was recorded in terms of percentage of larvae who failed to respond upon tapping (blue bars) and unable to maintain
horizontal swimming position (orange bars) (n = 10). d The behavior of the larvae was further recorded on an automated zebrafish behavior monitoring
system for 1 h at 5 days post Aβ treatment (n = 10). Total distance traveled along with movement frequency was significantly decreased compared to
untreated control (p < 0.005). Representative trajectories of 100 fM Aβ treated and untreated larvae inside a single well of a 96-well plate, during 1 h of
observation. e Five days after Aβ (100 fM) treatment, larvae were further treated with Congo red (100 fM) via cerebroventricular injection. Whole mount
larvae were imaged under the RFP channel 6 h after Aβ treatment. f Significant fluorescence was retained in the cereberal region of larvae on the fifth day
post Aβ treatment. g Congo red injected in untreated larva was not retained in the cerebral region. h MALDI detection of Aβ in the brain of zebrafish larvae,
5 days post Aβ injection (n = 10, Mean ± SD). Five days after cerebroventricular injection of Aβ, the heads of zebrafish larvae were excised after
euthanization. The heads were homogenized in Holtfreter’s buffer and subjected to MALDI-TOF/TOF analysis. Peak corresponding to Aβ molecular weight
was observed at 4538.1 mz−1. Untreated larvae and matrix alone were used as controls. i Congo red-stained thin section (sagittal) of Aβ treated larvae
brain tissue. Bright red spots were observed in the cerebral region of larvae, corresponding to the Aβ amyloid or plaque formation. j In thin sections of the
brain tissue of untreated larvae (negative control), no red spots were observed. Scale bars in all images are 200 µM, while in i and j inset are 20 µM. Error
bars represent the standard deviation. Source data are provided as a Source Data file addition, citrate-capped AuNPs failed to rescue the larvae from
Aβ toxicity, implicating that βCas, but not AuNPs was mainly
responsible for toxicity mitigation (Fig. 5a). symptoms. However, treatment with βCas AuNPs 12 h after Aβ
injection did not rescue the larvae from Aβ toxicity, indicating the
neurotoxicity of Aβ had been initiated. This observation corre-
lates with the nucleation and oligomerization of Aβ into toxic
species around 12 h, as indicated by the ThT kinetic assay
(Fig. 1a). NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 i Congo red-stained thin section (sagittal) of Aβ treated larvae
Bright red spots were observed in the cerebral region of larvae corresponding to the Aβ amyloid or plaque formation j In thin sections of the a
Aβ microinjection in
zebrafish larvae 5 days
Aβ fibrillization
b b a d
5 days
Aβ fibrillization
b
jection in
larvae
10 fM
50 fM
100 fM
0
12
24
0
12
24
0
20
40
60
Aβ
Control
Distance (cm)
Time (min)
Movement frequency (turns per min)
0
20
40
Untreated
Distance travelled
Movement frequency
Trajectories
per h
Trajectories
**
** c
0
25
50
75
100
Control
0.07
0.15
0.29
0.58
1.17
2.34
4.68
9.37
18.75
37.5
75
150
300
600
1200
Impaired locomotor
response (%)
Aβ concentration (fM per larva)
Immobility
Imbalance d d
10 fM
50 fM
100 fM
Aβ
Control
Distance (cm)
0
20
40
Untreated
Distance travelled
** c 0
12
24
0
12
24
0
20
40
60
Time (min)
Movement frequency (turns per min)
Movement frequency
Trajectories
per h
Trajectories
** Trajectories Distance travelled Bright field
RFP
f
Bright field
Congo red
e
h
i
j
response (%)
0
1
2
3
1000
2000
3000
4000
5000
Intensity (a.u.) × 104
m z–1
0
200
400
600
800
4000
6000
8000
10,000 12,000
Intensity (a.u.)
m z–1
Aβ-treated larvae
Untreated larvae
Blank
4538.1
4538.1 Bright field
RFP
f
Bright field
RFP
g
Bright field
RFP
i
j
5000
,000
Aβ-treated larvae
Untreated larvae
Blank
4538.1 Bright field
RFP
f
Bright field
go red
i
j
response (%)
2000
3000
4000
5000
m z–1
0
200
400
600
800
4000
6000
8000
10,000 12,000
Intensity (a.u.)
m z–1
Aβ-treated larvae
Untreated larvae
Blank
4538.1
4538.1 Bright field
RFP
f
Bright field
i
j
000
5000
00 12,000
Aβ-treated larvae
Untreated larvae
Blank
4538.1 Bright field
RFP
g
RFP Congo red
e Bright field
g
RFP f g e h
0
1
2
3
1000
2000
3000
4000
5000
Intensity (a.u.) × 104
m z–1
0
200
400
600
800
4000
6000
8000
10,000 12,000
Intensity (a.u.)
m z–1
Aβ-treated larvae
Untreated larvae
Blank
4538.1
4538.1 i Bright field
i
j h RFP RFP RFP j Fig. 3 Aβ toxicity in zebrafish (Danio rerio) larvae. a Five-day-old zebrafish larvae were treated with Aβ and developed pathological symptoms (b). NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 d
c
Bright field
RFP
f
Bright field
RFP
g
Bright field
RFP
5 days
Aβ fibrillization
Congo red
b
a
e
h
i
j
0
25
50
75
100
Control
0.07
0.15
0.29
0.58
1.17
2.34
4.68
9.37
18.75
37.5
75
150
300
600
1200
Impaired locomotor
response (%)
Aβ concentration (fM per larva)
Immobility
Imbalance
Aβ microinjection in
zebrafish larvae
10 fM
50 fM
100 fM
0
12
24
0
12
24
0
20
40
60
Aβ
Control
Distance (cm)
Time (min)
Movement frequency (turns per min)
0
20
40
Untreated
Distance travelled
Movement frequency
Trajectories
per h
Trajectories
**
**
0
1
2
3
1000
2000
3000
4000
5000
Intensity (a.u.) × 104
m z–1
0
200
400
600
800
4000
6000
8000
10,000 12,000
Intensity (a.u.)
m z–1
Aβ-treated larvae
Untreated larvae
Blank
4538.1
4538.1
oxicity in zebrafish (Danio rerio) larvae. a Five-day-old zebrafish larvae were treated with Aβ and developed pathological symptoms (b). e locomotive behavior was recorded in terms of percentage of larvae who failed to respond upon tapping (blue bars) and unable to maintain
wimming position (orange bars) (n = 10). d The behavior of the larvae was further recorded on an automated zebrafish behavior monitoring
1 h at 5 days post Aβ treatment (n = 10). Total distance traveled along with movement frequency was significantly decreased compared to
ontrol (p < 0.005). Representative trajectories of 100 fM Aβ treated and untreated larvae inside a single well of a 96-well plate, during 1 h o
. e Five days after Aβ (100 fM) treatment, larvae were further treated with Congo red (100 fM) via cerebroventricular injection. Whole moun
imaged under the RFP channel 6 h after Aβ treatment. f Significant fluorescence was retained in the cereberal region of larvae on the fifth day
atment. g Congo red injected in untreated larva was not retained in the cerebral region. h MALDI detection of Aβ in the brain of zebrafish larvae
t Aβ injection (n = 10, Mean ± SD). Five days after cerebroventricular injection of Aβ, the heads of zebrafish larvae were excised after
on. The heads were homogenized in Holtfreter’s buffer and subjected to MALDI-TOF/TOF analysis. Peak corresponding to Aβ molecular weigh
ed at 4538.1 mz−1. Untreated larvae and matrix alone were used as controls. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 Aβ plaques
were observed using the red fluorescence protein (RFP) channel p
pp
y
g
Apart from the brain, 5 nm βCas AuNPs (conjugated with NR
dye) also distributed to the fins and were imaged while circulating
inside the microvasculature of zebrafish larvae (Supplementary
Fig. 11). In contrast to βCas AuNPs, NR-conjugated βCas
micelles (4.5 ng) were not able to translocate across the BBB and,
instead, accumulated in the liver 6 and 12 h post injection
(Supplementary Fig. 12) due to their larger sizes. Mitigation of Aβ toxicity and pathological symptoms. Mitiga-
tion of Aβ toxicity was first assessed in vitro with SH-SY5Y
neuronal cells. βCas AuNPs were able to sequester Aβ toxicity
against SH-SY5Y cells in the viability assay (Supplementary
Fig. 13A). Helium ion microscopy (HIM) revealed morphological
damage induced by Aβ to the SH-SY5Y cells and their recovery
by βCas AuNPs (Supplementary Fig. 13B, C). For in vivo, Aβ
toxicity was induced in the zebrafish larvae by cerebroventricular
injection of Aβ and was relieved by intracardiac injection of βCas
AuNPs. Specifically, βCas AuNPs were administered at different
time intervals post Aβ injection and the exposed larvae were
studied for their behaviors 3 (Supplementary Fig. 14) and 5 days
(Fig. 5a) post Aβ injection. βCas AuNPs completely relieved the
symptoms when treated within 2 h of Aβ injection, as indicated
by the total distance traveled, movement frequency and trajec-
tories during 1 h of observation. Administration of βCas AuNPs,
6 h after Aβ treatment, partially alleviated the behavioral TURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications 5 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 ARTICLE Brightfield
RFP
Brightfield
RFP
Brightfield
RFP
0.5 h
6 h
12 h
a
d
Dorsal
Lateral
βCas AuNPs
in larvae
0
0.2
0.4
0.6
1.5
3
6
Au-delivered per brain (ng)
Au-injected per
larva (ng)
0
0.4
0.8
0.5
6
12
Au per brain (ng)
Time (h)
f
e
βCas AuNPs-
treated larvae
Untreated control
βCas AuNPs
Darkfield
HSI
SAM
HSI + SAM
Rule
SPR
NR
fluorescence
6 h
12 h
c
0.5 h
b
0
500
1000
1500
2000
400
500
600
700
800
Wavelength (nm)
0
500
1000
1500
2000
400
500
600
700
800
Intensity (a.u.)
Wavelength (nm)
0
500
1000
1500
2000
400
500
600
700
800
Intensity (a.u.)
Wavelength (nm)
Intensity (a.u.)
Fig. 4 In vivo biodistribution of βCas AuNPs in zebrafish larvae. a βCas AuNPs were conjugated with neutral red and injected to zebrafish larvae (5 day old)
via the intracardiac route in a dose equivalent to 3 ng Au per 4.5 ng βCas. b Labeled βCas AuNPs were traced for in vivo distribution at 0.5, 6, and 12 h in
dorsal and lateral positions (c). Bright fluorescence was observed from the brain 0.5 h after AuNP administration. However, fluorescence was eliminated
from the cerebral region in 6 h, while it took 12 h to eliminate from the body (scale bars: 200 µM). d Tissue microtome of zebrafish brain was subjected to
HSI imaging. Spectral angular mapping (SAM) images were built from HSI by scanning against the βCas AuNPs spectral library. SAM and Rule images
colored the pixels as red and black, respectively, that have matching spectra of βCas AuNPs. Zebrafish larvae with βCas AuNPs in the brain presented black
spots in Rule images and red pixels in SAM images. SPR spectra with peak ~530 nm were observed in the brain of βCas AuNPs treated larvae. No such
spectra were recorded for control larva (scale bars: darkfield 200 µM; HSI, SAM, HSI + SAM, Rule: 10 µM; inset scale bar: 2 µM; scale bar for βCas AuNPs:
10 µM, inset scale bar: 0.5 µM). e ICP MS analysis, where the AuNP concentration was the highest in the larval brain at 0.5 h, i.e., equivalent to 0.6 ± 0.1 ng
of Au, and dropped to 0.05 ± 0.01 and 0.02 ± 0.008 ng at 6 and 12 h, respectively (n = 10). f Dose–response relationship between the amount of AuNPs
injected vs. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 the amount of AuNPs delivered across the brain (n = 10). Significantly (p < 0.05) increased amount of Au was delivered when intracardiac dose
of AuNPs was increased from 1.5 to 3 ng equivalent. However, increasing the dose from 3 to 6 ng did not improve AuNP delivery across the BBB, indicating
a dose saturation. Error bars represent the standard deviation. Source data are provided as a Source Data file
NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0
ARTICLE Brightfield
RFP
Brightfield
RFP
Brightfield
RFP
0.5 h
6 h
12 h
a
d
Dorsal
Lateral
βCas AuNPs
in larvae
βCas AuNPs-
treated larvae
Untreated control
βCas AuNPs
Darkfield
HSI
SAM
HSI + SAM
Rule
SPR
NR
fluorescence
6 h
12 h
c
0.5 h
b
0
500
1000
1500
2000
400
500
600
700
800
Wavelength (nm)
0
500
1000
1500
2000
400
500
600
700
800
Intensity (a.u.)
Wavelength (nm)
0
500
1000
1500
2000
400
500
600
700
800
Intensity (a.u.)
Wavelength (nm)
Intensity (a.u.) a
NR
fluorescence 0.5 h
b b a 6 h 12 h 12 h 6 h c d 0
0.2
0.4
0.6
1.5
3
6
Au-delivered per brain (ng)
Au-injected per
larva (ng)
0
0.4
0.8
0.5
6
12
Au per brain (ng)
Time (h)
f
e
g
( 0
0.2
0.4
0.6
1.5
3
6
Au-delivered per brain (ng)
Au-injected per
larva (ng)
f f Fig. 4 In vivo biodistribution of βCas AuNPs in zebrafish larvae. a βCas AuNPs were conjugated with neutral red and injected to zebrafish larvae (5 day old)
via the intracardiac route in a dose equivalent to 3 ng Au per 4.5 ng βCas. b Labeled βCas AuNPs were traced for in vivo distribution at 0.5, 6, and 12 h in
dorsal and lateral positions (c). Bright fluorescence was observed from the brain 0.5 h after AuNP administration. However, fluorescence was eliminated
from the cerebral region in 6 h, while it took 12 h to eliminate from the body (scale bars: 200 µM). d Tissue microtome of zebrafish brain was subjected to
HSI imaging. Spectral angular mapping (SAM) images were built from HSI by scanning against the βCas AuNPs spectral library. SAM and Rule images
colored the pixels as red and black, respectively, that have matching spectra of βCas AuNPs. Zebrafish larvae with βCas AuNPs in the brain presented black
spots in Rule images and red pixels in SAM images. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 In contrast, βCas micelles failed to rescue the larvae
from Aβ toxicity even injected 2 h after Aβ administration. βCas
AuNPs and βCas as controls did not induce any behavioral
abnormalities in zebrafish larvae (Supplementary Fig. 15). In p
y
g
g
Microtome slices of the brain tissues of zebrafish larvae, treated
with Aβ and βCas AuNPs, were prepared on the fifth day post Aβ
treatment and stained with Congo red. No amyloid plaque
formation was observed (Fig. 5b), indicating elimination of Aβ
species by βCas AuNPs. Immunohistochemistry (IHC) (Fig. 5c)
and polarized light microscopy (Fig. 5d) further confirmed NATURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications 6 NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 NATURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 The biomarkers were first
evaluated on the fifth day post Aβ (6 fM per larva) treatment. AChE levels in the Alzheimer’s affected brain are known to be
decreased45, however, here no significant differences in the AChE
activity (0.10 ± 0.02 a.u. per brain) or GLT level (17.9 ± 1.2 nm
per brain) were observed compared to untreated control (0.09 ±
0.01 a.u. for AchE and 19.7 ± 1.2 nm for GLT per brain) with 6 fM
Aβ. As severe cases of Alzheimer’s presence increased levels of
AchE46, the biomarker assay was performed with 600 fM Aβ and
the AChE levels were found to increase twofold compared to the
control, i.e., 0.22 ± 0.01 a.u. AChE per brain (Fig. 6a). AChE levels
were close to the control in the larvae treated with βCas AuNPs
(3 ng Au equivalent) + Aβ (600 fM). βCas AuNPs and βCas, as
controls, did not elicit any impact on the AChE levels. Similar
results were observed for GLT, where βCas AuNPs reduced the
GLT level from 29.2 ± 5.08 to 18.1 ± 3.07 nm per brain (Fig. 6b). According to the literature, the Aβ42 concentration in the
gray and white matter of the brain of AD patients is 1.3 and
0.25 nm mg−1, respectively47. Tg2576 mice models of AD present ~1600–1700 fM mg−1 of Aβ42 after developing the disease
symptoms48. However, the wet weight of whole zebrafish larva
is ~1 mg and its brain is 4–5 times smaller than its body weight49. Considering this physiological relevance of the body weight, Aβ42
was injected in zebrafish larvae over a concentration range of
0.07–1200 fM per larva and based on locomotor response (Fig. 3c)
100 fM was selected for further experiments. However, 100 fM of
Aβ concentration did not produce any difference in neurotrans-
mitter levels that are usually disturbed in severe cases of AD46. Therefore, Aβ of 600 fM was used to observe any possible
fluctuations in neurotransmitters. ROS generation was quantified by a direct measurement of
dichlorofluorescin diacetate (DCF) fluorescence from the larval
brain (Fig. 6c, d). It has been shown in literature that oligomeric
amyloid proteins directly interacted with cell membranes to
induce cytotoxicity by membrane disruption and subsequent ROS
generation14. Aβo were injected in the cerebroventricular space
and their associated toxicity was determined by ROS generation,
in comparison with the positive control of H2O2. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 Aβ
Aβ+
βCas AuNPs
after 2 h
Aβ+
βCas AuNPs
after 6 h
Aβ +
βCas AuNPs
after 12 h
Aβ +
βCas AuNPs
after 24 h
10 fM
50 fM
100 fM
0
8
16
24
0
8
16
24
0
8
16
24
0
8
16
24
Time (min)
10 fM
50 fM
100 fM
10 fM
50 fM
100 fM
10 fM
50 fM
100 fM
10 fM
50 fM
100 fM
10 fM
50 fM
100 fM
0
8
16
24
Aβ +
βCas
after 2 h
0
8
16
24
Aβ concentration
Movement frequency (turns per min)
Trajectories
per h
0
20
40
Untreated
Untreated
control
0
8
16
24
0
20
40
60
Distance travelled
Movement frequency
Trajectories
0
8
16
24
0
8
16
24
10 fM
50 fM
100 fM
Cit
AuNPs
Cit AuNPs
alone
Cit AuNPs
+ Aβ
Brightfield
RFP
Inset
Aβ
Aβ +
βCas AuNPs
Buffer
control
a
b
c
Brightfield
GFP
DAPI
Merged
Distance (cm)
Aβ
Aβ +
βCas AuNPs
Buffer
control
Fig. 5 Mitigation of Aβ toxicity in zebrafish larvae with βCas AuNPs. a Aβ peptide was injected into the cerebroventricular space at 10, 50, and 100 fM
concentrations (n = 20, mean ± SD). Zebrafish larvae were monitored on an automated behavior monitoring system at fifth day post Aβ treatment and
parameters of total distance traveled, movement frequency and trajectory path were observed for 1 h. Significant (p < 0.005) difference in the behavior of
the larvae was observed on the fifth day post treatment. βCas AuNPs injected, via the intracardiac route 2 and 6 h after the Aβ treatment, rescued the
larvae from Aβ toxicity and from developing Alzheimer’s-like symptoms. Representative trajectories of the larvae are displayed in the far-right column. Treating the larvae with βCas AuNPs, 12 and 24 h post Aβ treatment, failed to protect the larvae from developing Aβ toxicity. b Zebrafish larvae, treated
with βCas AuNPs 2 h after Aβ treatment were fixed, sliced and stained with Congo red to image any Aβ fibrils that could have formed. Tissue slices of the
brain section did not present any red fluorescence, indicating no Aβ fibril formation in βCas AuNPs treated larvae (scale bars: 200 µM; inset scale bar:
20 µM). NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 SPR spectra with peak ~530 nm were observed in the brain of βCas AuNPs treated larvae. No such
spectra were recorded for control larva (scale bars: darkfield 200 µM; HSI, SAM, HSI + SAM, Rule: 10 µM; inset scale bar: 2 µM; scale bar for βCas AuNPs:
10 µM, inset scale bar: 0.5 µM). e ICP MS analysis, where the AuNP concentration was the highest in the larval brain at 0.5 h, i.e., equivalent to 0.6 ± 0.1 ng
of Au, and dropped to 0.05 ± 0.01 and 0.02 ± 0.008 ng at 6 and 12 h, respectively (n = 10). f Dose–response relationship between the amount of AuNPs
injected vs. the amount of AuNPs delivered across the brain (n = 10). Significantly (p < 0.05) increased amount of Au was delivered when intracardiac dose
of AuNPs was increased from 1.5 to 3 ng equivalent. However, increasing the dose from 3 to 6 ng did not improve AuNP delivery across the BBB, indicating
a dose saturation. Error bars represent the standard deviation. Source data are provided as a Source Data file deposition of Aβ amyloids in the brain tissues of zebrafish larvae,
but not in βCas AuNPs-treated or untreated control larvae. The
positive controls of fibrillized Aβ analyzed by IHC and polarized
light microscopy were shown in Supplementary Fig. 16. were quantified and loss of synaptophysin was imaged (Fig. 6), to
vindicate the potency of βCas AuNPs against the toxicity of Aβ. Zebrafish are reported to possess cholinergic, glutamatergic and
GABAergic neurotransmission that change in response to
neurological dysfunction44. The acetylcholine esterase (AchE)
and glutamate (GLT) levels were therefore assayed in Aβ and In addition to the behavioral symptoms, the neurotransmitters
associated with Aβ toxicity and reactive oxygen species (ROS) TURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications 7 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 Furthermore, immunohistochemistry (IHC) (c) and polarized light microscopy (apple green birefringence of amyloid) (d) revealed deposition of
aggregated Aβ in the larval brain while no Aβ deposition was observed in βCas AuNPs or buffer treated larvae (Scale bars: IHC, 30 µM; polarized light
microscopy, 50 µM). Error bars represent the standard deviation. Source data are provided as a Source Data file 0
8
16
24
0
8
16
24
0
8
16
24
0
8
16
24
Time (min)
0
8
16
24
0
8
16
24
Movement frequency (turns per min)
Trajectories
per h
0
8
16
24
0
20
40
60
Movement frequency
Trajectories
0
8
16
24
0
8
16
24 Aβ
Aβ+
βCas AuNPs
after 2 h
Aβ+
βCas AuNPs
after 6 h
Aβ +
βCas AuNPs
after 12 h
Aβ +
βCas AuNPs
after 24 h
10 fM
50 fM
100 fM
10 fM
50 fM
100 fM
10 fM
50 fM
100 fM
10 fM
50 fM
100 fM
10 fM
50 fM
100 fM
10 fM
50 fM
100 fM
Aβ +
βCas
after 2 h
Aβ concentration
0
20
40
Untreated
Untreated
control
Distance travelled
10 fM
50 fM
100 fM
Cit
AuNPs
Cit AuNPs
alone
Cit AuNPs
+ Aβ
a
Distance (cm) Brightfield
RFP
Inset
Aβ
Aβ +
βCas AuNPs
Buffer
control
b
c
Brightfield
GFP
DAPI
Merged
Aβ
Aβ +
βCas AuNPs
Buffer
control b a c Movement frequency (turns per min) Buffer
control Fig. 5 Mitigation of Aβ toxicity in zebrafish larvae with βCas AuNPs. a Aβ peptide was injected into the cerebroventricular space at 10, 50, and 100 fM
concentrations (n = 20, mean ± SD). Zebrafish larvae were monitored on an automated behavior monitoring system at fifth day post Aβ treatment and
parameters of total distance traveled, movement frequency and trajectory path were observed for 1 h. Significant (p < 0.005) difference in the behavior of
the larvae was observed on the fifth day post treatment. βCas AuNPs injected, via the intracardiac route 2 and 6 h after the Aβ treatment, rescued the
larvae from Aβ toxicity and from developing Alzheimer’s-like symptoms. Representative trajectories of the larvae are displayed in the far-right column. Treating the larvae with βCas AuNPs, 12 and 24 h post Aβ treatment, failed to protect the larvae from developing Aβ toxicity. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 b Zebrafish larvae, treated
with βCas AuNPs 2 h after Aβ treatment were fixed, sliced and stained with Congo red to image any Aβ fibrils that could have formed. Tissue slices of the
brain section did not present any red fluorescence, indicating no Aβ fibril formation in βCas AuNPs treated larvae (scale bars: 200 µM; inset scale bar:
20 µM). Furthermore, immunohistochemistry (IHC) (c) and polarized light microscopy (apple green birefringence of amyloid) (d) revealed deposition of
aggregated Aβ in the larval brain while no Aβ deposition was observed in βCas AuNPs or buffer treated larvae (Scale bars: IHC, 30 µM; polarized light
microscopy, 50 µM). Error bars represent the standard deviation. Source data are provided as a Source Data file Aβ + βCas AuNPs treated larvae. The heads were separated from
the euthanized larvae, homogenized and used for the assays to
minimize interference from the trunks. The biomarkers were first
evaluated on the fifth day post Aβ (6 fM per larva) treatment. AChE levels in the Alzheimer’s affected brain are known to be
decreased45, however, here no significant differences in the AChE
activity (0.10 ± 0.02 a.u. per brain) or GLT level (17.9 ± 1.2 nm
per brain) were observed compared to untreated control (0.09 ±
0.01 a.u. for AchE and 19.7 ± 1.2 nm for GLT per brain) with 6 fM
Aβ. As severe cases of Alzheimer’s presence increased levels of
AchE46, the biomarker assay was performed with 600 fM Aβ and
the AChE levels were found to increase twofold compared to the
control, i.e., 0.22 ± 0.01 a.u. AChE per brain (Fig. 6a). AChE levels
were close to the control in the larvae treated with βCas AuNPs
(3 ng Au equivalent) + Aβ (600 fM). βCas AuNPs and βCas, as
controls, did not elicit any impact on the AChE levels. Similar
results were observed for GLT, where βCas AuNPs reduced the
GLT level from 29.2 ± 5.08 to 18.1 ± 3.07 nm per brain (Fig. 6b). According to the literature, the Aβ42 concentration in the
gray and white matter of the brain of AD patients is 1.3 and
0.25 nm mg−1, respectively47. Tg2576 mice models of AD present Aβ + βCas AuNPs treated larvae. The heads were separated from
the euthanized larvae, homogenized and used for the assays to
minimize interference from the trunks. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 41 ± 7.9 and 42.9 ± 8.7, respectively. However, upon
treated larvae presented a significant loss of synapto
0
10
20
30
40
Glutamate level
per brain (nM)
0.05
0.1
0.15
0.2
0.25
AchE activity
per brain (a.u.)
a
b
**
**
*
p > 0.05
p > 0.05
**
**
*
p > 0.05
p > 0.05
d
c
H2O2
Aβ
Aβ +
βCas AuNPs
Untreated
control
Aβ
Aβ +
βCas AuNPs
Untreated
control
DAPI
GFP
Merged
e
0
30
60
DCF fluorescence
(a.u.)
**
**
p > 0.05
Aβ (600 fM)
H2O2
Aβ
Aβ + βCas AuNPs
CDF control
Aβ (6 fM)
Aβ + βCas AuNPs
Aβ + βCas
βCas
βCas AuNPs
Control
Aβ (600 fM)
Aβ (6 fM)
Aβ + βCas AuNPs
Aβ + βCas
βCas
βCas AuNPs
Control
ransmitters and reactive oxygen species (ROS) in the brain of Aβ treated larvae. The biomarkers were measured 5 days post Aβ
ular injection of Aβ peptide at 6 fM per larvae did not significantly (p > 0.05) influence the AchE (a) and GLT (b) levels in zebrafish
, increasing the Aβ dose to 600 fM significantly increased (p < 0.05) AchE and GLT levels. βCas AuNPs (3 ng Au per 4.5 ng βCa
reatment, significantly (p < 0.005) reduced the AchE and GLT levels on the 5th day post Aβ (600 fM) treatment. βCas micelle
βCas in 3 ng βCas AuNPs), in comparison, failed to improve (p > 0.05) the biomarker levels. c ROS generation was significantly
ated (600 fM) larvae. ROS generation was supressed in βCas AuNPs treated larvae and close to control (n = 10). d Representativ
ae expressing DCF/ROS fluorescence when treated with H2O2, Aβ, Aβ + βCas AuNPs, and Aβ + βCas. e Larvae’s brain sections w
hysin. Aβ-treated larvae presented loss of synaptophysin indicating neurodegeneration. Scale bars in all images are 200 µM. Err
standard deviation. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 Source data are provided as a Source Data file 0
10
20
30
40
Glutamate level
per brain (nM)
b
**
**
*
p > 0.05
p > 0.05
d
H2O2
Aβ
Aβ +
βCas AuNPs
Untreated
control
Aβ (600 fM)
Aβ (6 fM)
Aβ + βCas AuNPs
Aβ + βCas
βCas
βCas AuNPs
Control b a d
H2O2
Aβ
Aβ +
βCas AuNPs
Untreated
control
Aβ + d c
0
30
60
DCF fluorescence
(a.u.)
**
**
p > 0.05
H2O2
Aβ
Aβ + βCas AuNPs
CDF control d c Untreated
control Aβ
Aβ +
βCas AuNPs
Untreated
control
DAPI
GFP
Merged
e e Fig. 6 Neurotransmitters and reactive oxygen species (ROS) in the brain of Aβ treated larvae. The biomarkers were measured 5 days post Aβ treatment. Cerebrovascular injection of Aβ peptide at 6 fM per larvae did not significantly (p > 0.05) influence the AchE (a) and GLT (b) levels in zebrafish larvae (n =
10). However, increasing the Aβ dose to 600 fM significantly increased (p < 0.05) AchE and GLT levels. βCas AuNPs (3 ng Au per 4.5 ng βCas), injected
2 h post Aβ treatment, significantly (p < 0.005) reduced the AchE and GLT levels on the 5th day post Aβ (600 fM) treatment. βCas micelles (dose
equivalent to βCas in 3 ng βCas AuNPs), in comparison, failed to improve (p > 0.05) the biomarker levels. c ROS generation was significantly (p < 0.005)
high in Aβ treated (600 fM) larvae. ROS generation was supressed in βCas AuNPs treated larvae and close to control (n = 10). d Representative images of
zebrafish larvae expressing DCF/ROS fluorescence when treated with H2O2, Aβ, Aβ + βCas AuNPs, and Aβ + βCas. e Larvae’s brain sections were stained
for synaptophysin. Aβ-treated larvae presented loss of synaptophysin indicating neurodegeneration. Scale bars in all images are 200 µM. Error bars
represent the standard deviation. Source data are provided as a Source Data file larvae were 41 ± 7.9 and 42.9 ± 8.7, respectively. However, upon
treatment with βCas AuNPs, the CT fluorescence was reduced to
14.5 ± 5.4, comparable to DCF as negative control (8 ± 3.4). Synaptophysin-based neurodegeneration, an indicator for neuro-
nal synapsis, was also imaged via immunostaining (Fig. 6e). Aβ larvae were 41 ± 7.9 and 42.9 ± 8.7, respectively. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 The samples
were mixed with DCF prior to microinjection in larvae. The
corrected total (CT) fluorescence from H2O2 and Aβ treated NATURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications 8 NATURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 This remarkable capacity of eliminating toxic
Aβo and rescuing the animal from AD-like symptoms was
evidenced by in vitro assays of ThT, CD, and TEM, in silico 0
10
20
30
40
50
0
100
200
300
400
500
600
Movement frequency
(turns per min)
Distance travelled (cm)
Distance
Movement frequency
0
10
20
30
40
50
0
100
200
300
400
500
600
Movement frequency
(turns per min)
Distance travelled (cm)
Distance
Movement frequency
p > 0.05
0
10
20
30
0
100
200
300
400
Movement frequency
(turns per min)
Distance travelled (cm)
Distance
Movement frequency
Trajectories per min
Aβ
Aβ +
βCas AuNPs
Aβ
Aβ + βCas AuNPs
βCas AuNPs
Buffer
Untreated
Aβ
Before training
Aβ + βCas AuNPs
βCas AuNPs
Buffer
Untreated
βCas AuNPs
Buffer control
Untreated
Arena 1 Arena 2
Trajectories per min
Aβ
Aβ +
βCas AuNPs
βCas AuNPs
Buffer control
Untreated
Before training
**
p > 0.05
a
b
c
c
p > 0.05
**
**
e
f
Arena 1
Arena 2
Aβ
Aβ +
βCas AuNPs
Untreated
Merged
DAPI
GFP
Aβ
Before training
Aβ + βCas AuNPs
βCas AuNPs
Buffer
Untreated
Fig. 7 Mitigation of Aβ toxicity and Alzheimer’s-like symptoms in adult zebrafish with βCas AuNPs. a Adult zebrafish (10 months old) were microinject
(cerebroventricular) with Aβ (1 µL, 50 µM) and observed for behavioral pathologies at 2 weeks post injection (n = 4, SD ± mean). To study the mitigati
with βCas AuNPs, βCas AuNPs were microinjected (retro-orbital, 1 µL, 0.5 mM) 2 h prior to Aβ treatment. Aβ induced significant reduction in total distan
traveled and movement frequency in adult zebrafish while βCas AuNPs were able to rescue the symptoms. Movement trajectories are presented in
(b). Observations were made for 1 min, three times at a 2 h interval for each fish (n = 3). c IHC was performed on adult zebrafish brain sections to ima
the Aβ deposition. The first column represents the right cerebral brain of adult zebrafish in the GFP channel (Scale bars: 200 µM). DAPI, GFP, and merg
images at higher magnifications revealed Aβ plaque deposition in Aβ treated but not in Aβ + βCas AuNPs, or untreated control (Scale bars: 20 µM). Furthermore, cognitive behavior of adult zebrafish was analyzed. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 and
nano-chaperone
activity
of
βCas
AuNPs. These
advantages can be employed to screen or study the efficacy,
pharmacokinetics
and
pharmacology
of
anti-Alzheimer’s
drugs,
specifically
nano-chaperone
based
therapeutic
modalities. However, despite possessing a vertebrate nervous
system, zebrafish larvae still develop cognitive and learning
functions. Therefore, the behavioral pathology observed in this
study may not be clinically equivalent to Alzheimer’s symptoms. To study the Aβ toxicity and chaperone activity of βCas AuNPs,
adult zebrafish was employed to offer a more advanced in vivo
model with a cognitive capacity50. Microinjection of Aβ (1 µL,
50 µM) in adult zebrafish produced behavioral toxicity (Fig. 7a, b),
Aβ aggregation in brain (Fig. 7c) and clinically relevant
Alzheimer’s-like symptoms (Fig. 7d–f). Retro-orbital microinjec-
tion (1 µL, 0.5 mM) of βCas AuNPs, 2 h post Aβ treatment,
rescued the adult zebrafish from developing the cognitive
dysfunction. and
nano-chaperone
activity
of
βCas
AuNPs. These
advantages can be employed to screen or study the efficacy,
pharmacokinetics
and
pharmacology
of
anti-Alzheimer’s
drugs,
specifically
nano-chaperone
based
therapeutic
modalities. However, despite possessing a vertebrate nervous
system, zebrafish larvae still develop cognitive and learning
functions. Therefore, the behavioral pathology observed in this
study may not be clinically equivalent to Alzheimer’s symptoms. To study the Aβ toxicity and chaperone activity of βCas AuNPs,
adult zebrafish was employed to offer a more advanced in vivo
model with a cognitive capacity50. Microinjection of Aβ (1 µL,
50 µM) in adult zebrafish produced behavioral toxicity (Fig. 7a, b),
Aβ aggregation in brain (Fig. 7c) and clinically relevant
Alzheimer’s-like symptoms (Fig. 7d–f). Retro-orbital microinjec-
tion (1 µL, 0.5 mM) of βCas AuNPs, 2 h post Aβ treatment,
rescued the adult zebrafish from developing the cognitive
dysfunction. Expression of human orthologues of Aβ-associated neuronal
machinery at 24 h post fertilization suggests suitability of
zebrafish for AD modeling39,51. Macro-organization of the brain
and cellular morphology of zebrafish are parallel to vertebrates
and have led to studies of neurobehavioral pharmacology and
stress-induced behavior52. In addition, exogenous microinjection
or genetic overexpression of Tau in zebrafish has resulted in
intracellular tangle formation and abnormalities in the animal’s
development and swimming behaviors53,54. These, together with
our observations,
support Aβ toxicity induction
and AD
modeling in zebrafish, especially within the context of cerebral
deposition of Aβ and their associated behavioral pathology. β
gy
Intracardiac injection of βCas AuNPs mitigated the toxicity of
cerebroventricularly injected Aβ42 in a new, high-throughput
zebrafish model. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 f Zebrafish were trained to avoid swimming into the right half (Arena 2) of the swimmi
tank (1 L) that was labeled red and attached with a source of electric shock (9 V) (Supplementary Fig. 17). After training, the electric source was remov
and the cognitive memory of the fish to remain in arena 1 and to avoid arena 2 was assessed for a period of 2 min (n = 3, three times for each fish at a 2
interval). The movement trajectories of the fish in arena 1 vs. arena 2 are presented in panel F. Comparative analysis of distance traveled and moveme
frequency of the fish in arena 1 (d) vs. arena 2 (e) revealed cognitive dysfunction of Aβ-treated fish that were unable to avoid arena 2. However, βC
AuNPs treated, buffer control and untreated control fish were able to avoid swimming into arena 2. Error bars represent the standard deviation. Source da
are provided as a Source Data file p > 0.05
0
10
20
30
0
100
200
300
400
Movement frequency
(turns per min)
Distance travelled (cm)
Aβ
s AuNPs
s AuNPs
Buffer
ntreated
**
p > 0.05
a Trajectories per min
Aβ
Aβ +
βCas AuNPs
βCas AuNPs
Buffer control
Untreated
b b a c p > 0.05
0
10
20
30
0
100
200
300
400
Movement frequency
(turns per min)
Distance travelled (cm)
Distance
Movement frequency
Aβ
Aβ + βCas AuNPs
βCas AuNPs
Buffer
Untreated
**
p > 0.05
a c
Aβ
Aβ +
βCas AuNPs
Untreated
Merged
DAPI
GFP Arena 1 Arena 2
Trajectories per min
Aβ
Aβ +
βCas AuNPs
βCas AuNPs
Buffer control
Untreated
Before training
c 0
10
20
30
40
50
0
100
200
300
400
500
600
Movement frequency
(turns per min)
Distance travelled (cm)
Distance
Movement frequency
0
10
20
30
40
50
0
100
200
300
400
500
600
Movement frequency
(turns per min)
Distance travelled (cm)
Distance
Movement frequency
Aβ
Before training
Aβ + βCas AuNPs
βCas AuNPs
Buffer
Untreated
p > 0.05
**
**
e
f
Arena 1
Arena 2
Aβ
Before training
Aβ + βCas AuNPs
βCas AuNPs
Buffer
Untreated c Fig. 7 Mitigation of Aβ toxicity and Alzheimer’s-like symptoms in adult zebrafish with βCas AuNPs. NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 However, upon
treatment with βCas AuNPs, the CT fluorescence was reduced to
14.5 ± 5.4, comparable to DCF as negative control (8 ± 3.4). Synaptophysin-based neurodegeneration, an indicator for neuro-
nal synapsis, was also imaged via immunostaining (Fig. 6e). Aβ treated larvae presented a significant loss of synaptophysin as
compared to Aβ + βCas AuNPs or untreated control larvae. In this study, zebrafish larvae is developed and used as
a simple, in vivo visual model to study Aβ fibrillization, toxicity,
behavioral pathology, neurodegeneration, and biodistribution treated larvae presented a significant loss of synaptophysin as
compared to Aβ + βCas AuNPs or untreated control larvae. p
β
β
In this study, zebrafish larvae is developed and used as
a simple, in vivo visual model to study Aβ fibrillization, toxicity,
behavioral pathology, neurodegeneration, and biodistribution 9 ARTICLE Methods
A i
l h Animal husbandry and ethics statement. The AB wild-type zebrafish (Danio
rerio) was maintained in a fish breeding circulatory system (Haisheng, Shanghai,
China) at 28 ± 0.5 °C with a 14 h light: 10 h dark cycle. The embryos were produced
by adult spawning. For spawning, two pairs of male and female were placed in tank
with shallow water. The male and female were separated by a removable partition
and kept overnight. The spawning was triggered by removing the partition with
first light in the morning and embryos were collected 2 h later, washed with 0.5
ppm methylene blue and placed in petri dish with Holtfreter’s buffer. The healthy
embryos at the same developmental stage were selected and developed to 5-day-old
larvae for further measurement. All the experiments were performed with larvae in
Holtfreter’s buffer55. Tricaine (0.4% in Holtfreter’s buffer) was used for anesthesia. When required, larvae were euthanized by placing in 0.01% tricaine in Holtfreter’s
buffer for 10 min that was pre-chilled at 4 °C. The excision of head from the trunk
was performed under an optical stereomicroscope with a sharp surgical blade. All
zebrafish experiments were performed in accordance to the ethical guidelines of
Tongji University and the protocols were approved by the Animal Center of Tongji
University (Protocol #TJLAC-019-113). All in vitro and other experiments were
performed in compliance with the relevant ethics, laws, and institutional guidelines
of Monash University Occupational Health & Safety. To assess binding affinity, βCas AuNPs or NR-βCas AuNPs (12.5 µM βCas
equivalent) were incubated with preformed Aβo or Aβm (100 µM) for 3 h at 37 °C
and unbound Aβm/o was removed via centrifugal washing thrice (25,000 × g for
10 min at 4 °C). CD and TEM were performed as described above in the respective
sections. UV-SPR for βCas AuNPs and fluorescence spectra (NR-βCas AuNPs,
excitation at 470 nm) were recorded with a microplate reader. Synthesis of βCas AuNPs. HAuCl4 (1 mM, PBS pH 6) was heated at 40 °C and
while stirring at 1000 rpm, added with an equal volume of βCas in PBS (pH 6) at
the concentration of 1 mg mL−1. The heating continued for 10 min and 100 µL of
0.5 mM NaBH4 was added dropwise to the reaction mixture. The solution turned
wine red indicating the formation of βCas AuNPs. Heating was stopped after 2 h
while the reaction was kept on stirring for overnight. ARTICLE ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 examination of Aβ-βCas AuNP binding, ex vivo assays of
microtome, HSI, ICP-MS, and MALDI analyses of Aβ impaired
zebrafish brain, in vivo assays of ROS, behavior and neurological
dysfunction biomarkers of zebrafish larvae, and cognition of adult
zebrafish. The binding between Aβ and βCas was mediated by
nonspecific interactions via the residues of the whey protein that
were free from engagement with the AuNP surface. Adsorption of
βCas onto an AuNP surface enabled trafficking of βCas across the
zebrafish larvae BBB where βCas was then capable of efficiently
binding Aβ for elimination. Furthermore, βCas AuNPs induced
no harmful effects on the development of healthy zebrafish,
owing to the biocompatibility of both the chaperone-like protein
and the AuNPs. As this nano-formulation meets all key criteria
for a potent in vivo amyloidosis inhibitor, it holds the promise to
be further developed into safe-to-use, preventative nanomedicines
against the pathologies of AD and other debilitating human
amyloid diseases. Although zebrafish lack advanced cognitive
capacity as possessed by rodents, they can serve as a robust,
economic, and high-throughput alternative to complement
neurological
mouse
models
that
are
no
longer
deemed
sufficient19. was recorded with excitation at 445 nm and emission at 488 nm, at 30 min intervals
for 48 h. was recorded with excitation at 445 nm and emission at 488 nm, at 30 min intervals
for 48 h. was recorded with excitation at 445 nm and emission at 488 nm, at 30 min intervals
for 48 h. Transmission electron microscopy. Aβ was mixed with βCas or βCas AuNPs in
the same ratio as for the ThT assay and incubated for 48 h. After incubation, a drop
of each sample was placed on a glow discharged, carbon coated copper grid
and blotted after 1 min The sample-coated grid was negatively stained with 1%
uranyl acetate that was blotted after 30 s. The grid was dried in vacuum and
visualized with a Technei F20 transmission electron microscope operated at a
voltage of 200 kV. CD spectroscopy, hydrodynamic size, and zeta potential. The secondary
structural contents of βCas, βCas AuNPs, Aβm, Aβo, Aβ fibrillized w/o βCas or
βCas AuNPs were determined by CD spectroscopy. In all, 200 µL of the sample was
pipetted into a CD cuvette and the concentration of Aβ was 100 µM while βCas and
βCas AuNPs were 12.5 µM βCas equivalent in all CD measurements. Methods
A i
l h βCas AuNPs were purified by
centrifugal filtration with 100 kDa spin filters. AuNPs were washed 3× with
deionized water, transferred to PBS (pH 7.4) and stored at 4 °C for further
experimentation. After purification, the βCas concentration in βCas AuNPs was
determined by the BCA method56. Citrate-capped AuNPs (Cit AuNPs) were
synthesized via a reported method57. Briefly, a solution of HAuCl4 (10 mL, 1 mM)
was brought to boiling at 120 °C and then 1 mL (10 mM) trisodium citrate was
added dropwise. The solution turned to wine red, indicating the formation of Cit
AuNPs. The solution was brought to room temperature, purified via centrifugal
washing with deionized water and stored in dark for further use. Cellular toxicity. SH-SY5Y (ATCC® CRL-2266™) human bone marrow neuro-
blastoma cells were cultured in Dulbecco's Modified Eagle Medium: Nutrient
Mixture F-12 (DMEM/F12) with 10% fetal bovine serum (FBS). A 96-well plate
(Costar black/clear bottom) was coated with 70 µL of poly-L-lysine (Sigma, 0.01%)
and incubated at 37 °C for 30 min. After removing poly-L-lysine, the wells were
washed by PBS thrice. Cells (~50,000 cells per well per 200 µL medium) were added
to the wells and incubated at 37 °C with 5% CO2 for 24 h to reach ~70–80% of
confluency. The cell culture medium was then refreshed with 1 µM propidium (PI)
dye in DMEM/F12 with 10% FBS and incubated for another 30 min Aβ was freshly
dissolved in 0.005% NH4OH buffer, in the presence or absence of βCas AuNPs and
added to the wells with final concentration of 20 and 50 µM for Aβ and βCas
AuNPs, respectively. Cellular toxicity was recorded by Operetta (PerkinElmer,
20× PlanApo microscope objective, numerical aperture: 0.7) in a live cell chamber
(37 °C, 5% CO2) after 15 h of treatment. The percentage of dead cells (PI-positive)
to total cell count was determined by a built-in bright-field mapping function of
Harmony High-Content Imaging and Analysis software (PerkinElmer). The
measurement was performed in triplicate and conducted at five reads per well. Untreated cells were recorded as control. Neutral red (NR) dye was conjugated to βCas and βCas AuNPs for tracing their
biodistributions in zebrafish larvae. The dye was conjugated via 1-ethyl-3-(3-
dimethylaminopropyl)carbodiimide (EDC) coupling. Briefly, 2 mL of 6.25 µM of
βCas or equivalent concentration of βCas AuNPs was stirred overnight with 18 µM
of EDC, 23 µM of N-hydroxysuccinimide (NHS), and 14 µM of the NR dye. ARTICLE The incu-
bation time was 48 h at 37 °C and the incubation medium was deionized water. CD
spectra were recorded from 190 to 240 nm with a 1 nm step size. The acquired data
were presented in the unit of millidegrees (mdeg). Percentage secondary structure
contents were determined by analyzing the CD data via Dichroweb with Contin/
reference set 458. The hydrodynamic diameter and zeta potential of the AuNPs
were measured with dynamic light scattering under ambient conditions (Malvern
Instruments). The concentrations and incubation conditions were the same as for
the CD experiments. Binding capacity (BCA, TGA, TEM, CD, UV-SPR, and fluorescence micro-
scopy). The binding capacity between Aβ and βCas or βCas AuNPs was deter-
mined via a BCA assay56 and TGA. Briefly, 6.25 µM of βCas or equivalent βCas
AuNPs were incubated with varying concentrations of Aβm (monomers) or Aβo
(oligomers) ranging from 2 to 1137 µM. Incubation time was 48 h at 37 °C in
deionized water. HFIP-treated Aβ was considered as Aβm while Aβm incubated in
water for 12 h at 4 °C was considered as Aβo. After incubation, the samples were
centrifuged at 17,300 × g for 30 min and the pellets were redispersed in 10 µL of
deionized water and subjected to BCA protein content quantification. The BCA
binding efficacy was presented in terms of the amount of Aβ bound to βCas or
βCas AuNPs. For TGA analysis, the pellet dispersed in 10 µL water was placed as a
drop on a platinum pan. The samples were held at 80 °C for 30 min and then
scanned from 80 to 800 °C at a scanning rate of 10 °C min−1 under a constant flow
of nitrogen of 1 mg mL−1. For Aβm and Aβo, 10 µL of 1 mg mL−1 of the peptide
was placed on a TGA pan and scanned under the same conditions. Methods
A i
l h The
NR-conjugated βCas or βCas AuNPs were purified via centrifugal filtration,
transferred to PBS (pH 7.4) and stored for in vivo assays. Helium ion microscopy. SH-SY5Y neuronal cells were incubated with Aβ in the
presence or absence of βCas AuNPs as described for the cellular toxicity assay. The
incubation was performed for 2 h at 37 °C and then stabilized by 2.5% paraf-
ormaldehyde. The samples were incubated at 4 °C overnight. The paraformalde-
hyde/medium was replaced with gradient concentrations of ethanol in the five steps
of 20%, 40%, 60%, 80%, and 95%, respectively, with ~2 h of rest time at each
gradient. In all, 30 µL suspension of cells was air-dried on a carbon tape and the
morphologies of the cells were visualized by HIM (Orion NanoFab, Zeiss, USA). Untreated cells were used as control. ThT kinetic assay. Aβ was treated with hexafluoro-2-propanol (HFIP) to break-
down pre-existing small aggregates. Specifically, 0.5 mg of Aβ (Anaspec Inc.,
purity ≥95%) was dissolved in 500 µL of HFIP, incubated for 3 h, aliquoted to
different concentrations and dried to evaporate the HFIP. The dried Aβ was dis-
solved in 0.01% NH4OH for dissolution purpose and left in the open for 20 min to
evaporate NH4OH, leaving behind the aqueous solution of Aβ that was used for
further experiments. For the thioflavin T (ThT) assay, a 50 µL aqueous solution of
50 µM Aβ and 100 µM of ThT were incubated with or without βCas (6.25 µM) or
equivalent concentration of βCas AuNPs in a 96-well plate. The ThT fluorescence ThT kinetic assay. Aβ was treated with hexafluoro-2-propanol (HFIP) to break-
down pre-existing small aggregates. Specifically, 0.5 mg of Aβ (Anaspec Inc.,
purity ≥95%) was dissolved in 500 µL of HFIP, incubated for 3 h, aliquoted to
different concentrations and dried to evaporate the HFIP. The dried Aβ was dis-
solved in 0.01% NH4OH for dissolution purpose and left in the open for 20 min to
evaporate NH4OH, leaving behind the aqueous solution of Aβ that was used for
further experiments. For the thioflavin T (ThT) assay, a 50 µL aqueous solution of
50 µM Aβ and 100 µM of ThT were incubated with or without βCas (6.25 µM) or
equivalent concentration of βCas AuNPs in a 96-well plate. The ThT fluorescence Microinjection of Aβ, βCas, βCas AuNPs, and Cit AuNPs in zebrafish larvae. NATURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 a Adult zebrafish (10 months old) were microinjected
(cerebroventricular) with Aβ (1 µL, 50 µM) and observed for behavioral pathologies at 2 weeks post injection (n = 4, SD ± mean). To study the mitigation
with βCas AuNPs, βCas AuNPs were microinjected (retro-orbital, 1 µL, 0.5 mM) 2 h prior to Aβ treatment. Aβ induced significant reduction in total distance
traveled and movement frequency in adult zebrafish while βCas AuNPs were able to rescue the symptoms. Movement trajectories are presented in
(b). Observations were made for 1 min, three times at a 2 h interval for each fish (n = 3). c IHC was performed on adult zebrafish brain sections to image
the Aβ deposition. The first column represents the right cerebral brain of adult zebrafish in the GFP channel (Scale bars: 200 µM). DAPI, GFP, and merged
images at higher magnifications revealed Aβ plaque deposition in Aβ treated but not in Aβ + βCas AuNPs, or untreated control (Scale bars: 20 µM). Furthermore, cognitive behavior of adult zebrafish was analyzed. f Zebrafish were trained to avoid swimming into the right half (Arena 2) of the swimming
tank (1 L) that was labeled red and attached with a source of electric shock (9 V) (Supplementary Fig. 17). After training, the electric source was removed
and the cognitive memory of the fish to remain in arena 1 and to avoid arena 2 was assessed for a period of 2 min (n = 3, three times for each fish at a 2 h
interval). The movement trajectories of the fish in arena 1 vs. arena 2 are presented in panel F. Comparative analysis of distance traveled and movement
frequency of the fish in arena 1 (d) vs. arena 2 (e) revealed cognitive dysfunction of Aβ-treated fish that were unable to avoid arena 2. However, βCas
AuNPs treated, buffer control and untreated control fish were able to avoid swimming into arena 2. Error bars represent the standard deviation. Source data
are provided as a Source Data file NATURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications 10 ARTICLE The dried sample was processed same as for larva tissue
sections for immunostaining and polarized light microscopy and used as control. Polarized light microscopy was performed on the Congo red-stained larvae
tissue sections. The slides were imaged for birefringence under an Abrio
polarization microscope. A drop (50 μL, 20 μM) of fibrillized Aβ was placed and
dried on a glass slide. The dried sample was processed same as for larva tissue
sections for immunostaining and polarized light microscopy and used as control. Darkfield HSI. Zebrafish larvae at 0.5 h post treatment with intracardiac micro-
injection of βCas AuNP (3 ng Au per 4.5 ng βCas equivalent) were euthanized and
fixed in 2.5% paraformaldehyde for 12 h and then sliced to thin sections, dehy-
drated and mounted on glass slides with the same procedure as described for
fluorescence microscopy. HSI was performed with a CytoViva darkfield micro-
scope equipped with a pixelFly CCD camera. ENVI 4.8 software was used to
capture and process the images and to acquire AuNPs spectra. The darkfield
images were captured and then scanned for HSI for βCas AuNPs treated larvae,
untreated control larvae and βCas AuNPs alone. βCas AuNPs alone as control were
used to acquire the spectral library of AuNPs by selecting ~1500 pixels with region
of interest function of ENVI 4.8. Spectral libraries obtained from βCas AuNPs and
a mean spectral signature was generated. The mean spectral signature of βCas
AuNPs was used to filter against the selected pixels (~1000) from βCas AuNPs
treated and untreated control larval images to generate spectral angular mapping
images. Rule images were obtained by matching the pixel spectra from βCas
AuNPs against βCas AuNPs or untreated larval images. Rule images darkened the
pixels with matching spectra of βCas AuNPs. All images were normalized against
lamp spectra. For HSI imaging of βCas AuNPs and βCas AuNPs incubated with
Aβ, the AuNPs were incubated with Aβ at the same ratio as for ThT for 48 h. A
drop of each sample was placed on a glass slide covered with a slip. Darkfield
images and SPR spectra of the AuNPs were obtained by scanning ~1500 pixels for
each sample. Zebrafish larvae behavioral pathology. Larval response to tapping stimuli in a
96-well plate was observed. The 96-well plate was tapped gently at the rate of 1
per sec and the larvae unable to move after five consecutive stimuli were counted as
nonresponsive. ARTICLE Slide mounted
slices were dewaxed by treating with (1) xylene for 2 h, (2) absolute ethanol for
15 min, and (3) 75% ethanol for 5 min and then rinsed with deionized water. The
slices were treated with 0.5% Congo red stain in 50% ethanol for 20 min, rinsed
with water, differentiated with 1% NaOH solution in 50% ethanol (5–10 dips) and
again rinsed with water. The slices were then dehydrated with 95% ethanol (3 min)
and 2 dips in 100% ethanol (each 3 min) and cleared with 2 dips in xylene (each
3 min). The samples were finally sealed with neutral gum and imaged with an
optical microscope. Matrix-assisted laser desorption ionization-time of flight mass spectrometry
(MALDI TOF MS). Saturated solution of sinapinic acid (SA) was prepared in
ethanol and 1 µL of the sample was dried on a ground steel MALDI plate. Another
saturated solution of SA was prepared in acetonitrile and trifluoroacetic acid (30:70,
v/v) and mixed with the zebrafish larvae head homogenate at a 1:1 ratio. In all,
0.5 µL of this mixture was applied to previously dried SA layer. The dried layer was
analyzed by a Bruker ultraflextreme MALDI-TOF/TOF in the linear positive mode. The instrument was calibrated using protein calibration standards I and II. A total
of 8000 shots were gathered across the sample spots using Flexcontrol software
(3.4) in the range of 1–20 kDa. The acquired spectra were processed by baseline
subtraction and peak picking using Flexanalysis software (3.4). p
p
For IHC, 5 μM thick sections of zebrafish larvae were mounted on glass slides as
for Congo red staining. The dried sections were washed in PBS (pH 7.4) and
TritonX-100 (0.05% in PBS) for 5 min each. A drop (50 μL, 2 μg mL−1) of primary
antibody (Anti-amyloid β42, mouse monoclonal, Anaspec, AS-55922) was placed
on each section on the glass slides and incubated at 4 °C overnight. Primary
antibodies were washed away from the sections by dipping in PBS and TritonX-100
(0.05% in PBS) for 5 min. Sections were incubated with a drop (50 μL, 2 μg mL−1)
of secondary antibody (Goat anti-mouse HiLyteTM Fluor 488—labeled, Anaspec,
AS-61057-05-H488) for 6 h at room temperature. The secondary antibodies were
washed away by dipping the slides in TritonX-100 (0.05% in PBS) for 5 min. ARTICLE Furthermore, the larvae losing their horizontal swimming position
at higher doses of Aβ were also counted and the percentage of the larvae losing
response to stimuli and their swimming position was calculated. The swimming
behavior of zebrafish larvae was observed with an automated zebrafish behavior
recording system ZebraBox (Viewpoint) and characterized in terms of total dis-
tance traveled by the larvae in a 96-well plate and range of the movement that was
>90°, clockwise or counter clockwise, were counted. Representative trajectories of
the movement were also recorded by built-in sensors. The observation period was
1 h. The number of larvae in each group was 20 and 3 groups were used for each
sample. The larvae treated with βCas or βCas AuNPs, 2 h after Aβ treatment, were
monitored for behavioral pathology with the same method. TEM imaging of brain tissues. For TEM analysis of tissues, zebrafish larvae were
injected with 3 ng Au per 4.5 ng βCas equivalent βCas AuNPs via intracardiac
microinjection as described above, euthanized and fixed in 2.5% glutaraldehyde
0.5 h post treatment. The larvae were treated with 1% osmium tetroxide for 4 h
(4 °C) and then washed three times with 0.1 M PBS buffer (pH 7.4), 15 min each. The larvae were then treated with 1% citrate in 0.1 M PBS buffer (pH 7.4, 20 °C) for
2 h and again washed three times with 0.1 M PBS (pH 7.4), at 15 min each. After
that the larvae were dehydrated by treating with 50, 60, 70, 80, 90, and 100%
ethanol, at 15 min each. Following that the larvae were treated with acetone: 812
embedding agent (1:1) and then with 812 embedding agent, both for overnight and
then baked at 60 °C for 4 h for polymerization of embedding resin. The larvae were
finally sliced into ultra-thing sections of 60–80 nm with Diatome ultra 45°. The
sections were double stained with 2% solutions of uranyl acetate and lead citrate,
15 min each, dried overnight and then imaged with a transmission electron
microscope (Technei G2 20 TWIN) operated at 80 kV. Fluorescence imaging, IHC, and polarized light microscopy. Whole mount
larval imaging was performed under the brightfield (BF) and RFP channels of a
stereomicroscope (Olympus MVX10). ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 secondary antibodies (50 μL, 2 μg mL−1 of Goat Anti-Rabbit IgG H&L, Alexa
Fluor® 488, abcam, Cat# ab150081). 100 µM. Dilutions of 0.07–1200 fM of Aβ per 5 nL were made in PBS and injected
(5 nL injection volume) into the cerebroventricular space of 5 days old zebrafish
larvae. PBS alone was used as negative control. For microinjection, zebrafish larvae
were anesthetized by adding 2 drops of 0.4% tricaine in petri dish and waited until
the larvae stopped moving in response to tapping on the table. The larvae were
positioned on a 1% agarose gel plate and microinjected with Aβ peptide. Micro-
injections were performed with a fine calibrated needle of a pneumatic micro-
injection system (PV830 Pneumatic Picopump, WPI) operated under 20 psi of
injection pressure. The tip of the glass capillary needle was inserted in the ven-
tricular space, across the dorsal soft skin tissue. The tip was ensured not to
penetrate more than 0.1–0.3 mm across the center meeting point of left and right
telencephalon (Supplementary Video 4). βCas and βCas AuNPs were administered
under similar conditions via intracardiac microinjection (Supplementary Video 5). The original as-synthesized βCas AuNPs solution contained 1 and 1.5 ng of Au and
βCas per 5 nL. The original βCas AuNPs solution was concentrated 3× and
redispersed in PBS. A 5 nL of this solution was microinjected into zebrafish
larvae via the intracardiac route and each 5 nL contained 3 ng of Au per 4.5 ng
(37.5 µM mL−1) of βCas in the form of βCas AuNPs. βCas solution of equivalent
concentration was prepared in PBS for microinjection. For dose dependent delivery
of βCas AuNPs in cerebral tissues, the original βCas AuNPs solution was con-
centrated to 1.5, 3, and 6×, and dispersed in PBS prior to intracardiac micro-
injection to zebrafish larvae. Cit AuNPs were concentrated to equal concentration
as βCas AuNPs and microinjected into the larvae with the same protocol. secondary antibodies (50 μL, 2 μg mL−1 of Goat Anti-Rabbit IgG H&L, Alexa
Fluor® 488, abcam, Cat# ab150081). Polarized light microscopy was performed on the Congo red-stained larvae
tissue sections. The slides were imaged for birefringence under an Abrio
polarization microscope. A drop (50 μL, 20 μM) of fibrillized Aβ was placed and
dried on a glass slide. ARTICLE The larvae
were placed in Holtfreter’s buffer for 6 h to allow staining of the amyloids. The
larvae were anesthetized immediately prior to imaging with 0.4% tricaine, and
positioned in dorsal or lateral view in a drop of 1% low-melting agarose gel. The
cerebral region, fin and mid-vascular region of the larvae were imaged with the
same method. The biodistribution of NR-conjugated βCas or βCas AuNPs was
imaged by following the same method 0.5, 6, and 12 h post-βCas or βCas AuNPs
treatment via intracardiac microinjection. The microinjection volume was 5 nL
with a dose of 4.5 ng for βCas (37.5 µM) or βCas AuNPs equivalent to 4.5 ng βCas. Inductively coupled plasma-mass spectrometry. Delivery of βCas AuNPs across
the larvae’s brain was quantified with ICP-MS analysis. Zebrafish larvae were
microinjected with 1.3, 3, and 6 ng Au equivalent βCas AuNPs via the intracardiac
route with the same method as described above. The larvae were euthanized 0.5, 6,
and 12 h post microinjection and their heads were excised and homogenized in
PBS (pH 7.4) in a Teflon-glass homogenizer (70 Hz for 1 min). Brain or trunk
homogenate was made up to 1 mL with PBS (pH 7.4), added with 9 mL of 68%
HNO3 and digested by stepwise heating at 100, 150, 170, and 190 °C for 30, 30, 30,
and 90 min, respectively. The dried and digested layer was dissolved in 1 mL of 4%
HNO3 and analyzed with ICP-MS (Agilent 7700) for quantification of Au. The
instrument was operated under 0.75 MPa Ar pressure and a standard calibration
was made with Au spiked PBS samples, digested in the same way as the larval
samples. Untreated larvae and PBS alone were used as negative controls. The
number of larvae in each group was 20 and 3 groups per sample were used for
analysis. g
β
µ
β
q
g β
For Congo red staining of the sliced sections of the zebrafish larvae, Aβ
(100 fM) treated larvae were first fixed in 2.5% paraformaldehyde for 12 h at 4 °C. Microtome slices of zebrafish larvae were prepared by embedding the larvae into
paraffin. The paraffin-embedded larvae were cut into thin slices of 5 µM via
microtome and slices were placed in a hot water bath (40 °C) for removal of any
wrinkles. The slices were then mounted on glass slides and dried. Methods
A i
l h HFIP-treated Aβ (10 µg) was dissolved in PBS (pH 7.4) to make a stock solution of Microinjection of Aβ, βCas, βCas AuNPs, and Cit AuNPs in zebrafish larvae. HFIP-treated Aβ (10 µg) was dissolved in PBS (pH 7.4) to make a stock solution of 11 ARTICLE For imaging of Aβ in the cerebral region, the
Aβ treated larvae (100 fM, cerebroventricular microinjection) was microinjected
with 100 fM of Congo red on the third and fifth day post Aβ treatment. The larvae
were placed in Holtfreter’s buffer for 6 h to allow staining of the amyloids. The
larvae were anesthetized immediately prior to imaging with 0.4% tricaine, and
positioned in dorsal or lateral view in a drop of 1% low-melting agarose gel. The
cerebral region, fin and mid-vascular region of the larvae were imaged with the
same method. The biodistribution of NR-conjugated βCas or βCas AuNPs was
imaged by following the same method 0.5, 6, and 12 h post-βCas or βCas AuNPs
treatment via intracardiac microinjection. The microinjection volume was 5 nL
with a dose of 4.5 ng for βCas (37.5 µM) or βCas AuNPs equivalent to 4.5 ng βCas. For Congo red staining of the sliced sections of the zebrafish larvae, Aβ
(100 fM) treated larvae were first fixed in 2.5% paraformaldehyde for 12 h at 4 °C. Microtome slices of zebrafish larvae were prepared by embedding the larvae into
paraffin. The paraffin-embedded larvae were cut into thin slices of 5 µM via
microtome and slices were placed in a hot water bath (40 °C) for removal of any
wrinkles. The slices were then mounted on glass slides and dried. Slide mounted
slices were dewaxed by treating with (1) xylene for 2 h, (2) absolute ethanol for
15 min, and (3) 75% ethanol for 5 min and then rinsed with deionized water. The
slices were treated with 0.5% Congo red stain in 50% ethanol for 20 min, rinsed
with water, differentiated with 1% NaOH solution in 50% ethanol (5–10 dips) and
again rinsed with water. The slices were then dehydrated with 95% ethanol (3 min)
and 2 dips in 100% ethanol (each 3 min) and cleared with 2 dips in xylene (each
3 min). The samples were finally sealed with neutral gum and imaged with an
optical microscope. Fluorescence imaging, IHC, and polarized light microscopy. Whole mount
larval imaging was performed under the brightfield (BF) and RFP channels of a
stereomicroscope (Olympus MVX10). For imaging of Aβ in the cerebral region, the
Aβ treated larvae (100 fM, cerebroventricular microinjection) was microinjected
with 100 fM of Congo red on the third and fifth day post Aβ treatment. References Natl Acad. Sci. USA
113, E1316–E1325 (2016). Behavioral pathology and cognitive function test of adult zebrafish. The adult
zebrafish microinjected with the above described samples were monitored on a
daily basis for any apparent change to their swimming activity. The swimming
activity of the fish started to change 1-week post treatment and became sig-
nificantly apparent at 2 weeks post treatment. The behavioral pathology of the fish
was recorded with ZebraBox (Viewpoint), using a 1 L fish tank, and characterized
for total distance traveled and movement frequency. The recording was performed
for 1 min, 3 times for each fish at a 2-h interval. 9. What Causes Alzheimer's Disease? https://www.nia.nih.gov/health/what-
causes-alzheimers-disease (2017). 10. Peric, A. & Annaert, W. Early etiology of Alzheimer’s disease: tipping the
balance toward autophagy or endosomal dysfunction? Acta Neuropathol. 129,
363–381 (2015). 11. Gerakis, Y. & Hetz, C. Emerging roles of ER stress in the etiology and
pathogenesis of Alzheimer's disease. FEBS J. 285, 995–1011 (2018). Cognitive function test was performed by hypothetically dividing the 1 L fish
tank into two halves, i.e., arenas 1 and 2 (Supplementary Fig. 17). A red colored
paper was attached to the bottom of the tank to associate a color with arena 2. Fish
were allowed to freely swim in the whole tank for 30 min and then trained for
20 min to avoid swimming into arena 2 by using an electric shock punishment. Whenever the fish swam into the red arena 2, it was punished by dipping the
electrodes of 9 V in electric potential. After 20 min of training, the electric source
was removed and the cognitive ability of the fish to avoid arena 2, while swimming
in arena 1 was recorded for 2 min The comparative distance traveled and
movement frequency of the fish in arena 1 vs. 2 were recorded simultaneously. The
recordings were made 3 times for each fish (n = 3) at 2 h intervals. The results were
analyzed via EthnoVision X1. The analysis parameters were as follows; animal:
adult zebrafish, arena: open field square template (divided into two-halves for the
cognitive function test), tracking feature: central point, sample rate: 5 per second,
detection setting level: sensitive enough to track the fish in the whole tank,
threshold for movement frequency: 50° turn (clockwise or counter clockwise) and
minimum 0.5 cm of travel. 12. Selfridge, J. E., Lezi, E., Lu, J. & Swerdlow, R. H. References Microinjection in adult zebrafish. Adult zebrafish at the age of 10 mth were used
for the cognition experiment. The fish was maintained, before and during the
experiment, as described in the “Animal husbandry and ethics statement” section. For microinjection, adult fish were anesthetized with ice chilled tricaine (0.01% in
Holtfreter’s buffer for 20 s). Cerebroventricular microinjection of Aβ (1 µL, 50 µM)
was performed via 1 µL Hamilton glass syringes. Aβ peptide was injected in
between the right and left telencephalon and the needles did not penetrate more
than 1 mm (Supplementary Video 6). The fish were held in place via a forcep. The
syringes were washed with 70% ethanol and 1× PBS twice, in between the injec-
tions. For the group with Aβ with βCas AuNPs, βCas AuNPs were injected 2 h
prior to the injection of Aβ. βCas AuNPs (1 µL, 0.5 mM, 20 psi injection pressure)
were slowly introduced into the systemic circulation of the fish via retro-orbital
microinjection (7 o'clock position), using a sharp glass capillary needle (Supple-
mentary Video 7). The fish was placed back into the tank for recovery. The adult
zebrafish were grouped (n = 3) and injected with Aβ, Aβ with βCas AuNPs, βCas
AuNPs alone and PBS. Buffer injected and untreated fish were considered as
controls. 1. Knowles, T. P., Vendruscolo, M. & Dobson, C. M. The amyloid state and its
association with protein misfolding diseases. Nat. Rev. Mol. Cell Biol. 15, 384
(2014). 2. Hardy, J. A. & Higgins, G. A. Alzheimer’s disease: the amyloid cascade
hypothesis. Science 256, 184–186 (1992). 3. Sakono, M. & Zako, T. Amyloid oligomers: formation and toxicity of Aβ
oligomers. FEBS J. 277, 1348–1358 (2010). 4. Benilova, I., Karran, E. & De Strooper, B. The toxic Aβ oligomer and
Alzheimer's disease: an emperor in need of clothes. Nat. Neurosci. 15, 349–357
(2012). 5. Cummings, J. et al. Drug development in Alzheimer’s disease: the path to
2025. Alzheimers Res. Ther. 8, 39 (2016). 6. Javed, I. et al. Probing the aggregation and immune response of human islet
amyloid polypeptides with ligand-stabilized gold nanoparticles. ACS Appl. Mater. Interfaces 11, 10462–10471 (2019). f
7. Rogers, J., Strohmeyer, R., Kovelowski, C. & Li, R. Microglia and inflammatory
mechanisms in the clearance of amyloid β peptide. Glia 40, 260–269 (2002). 8. Marsh, S. E. et al. The adaptive immune system restrains Alzheimer’s disease
pathogenesis by modulating microglial function. Proc. ARTICLE Slides
were dried, mounted with a cover slip using a drop of 50% glycerol and imaged
under a fluorescence microscope (Nikon Ti-Eclipse). The larvae’s brain sections
were immunostained for synaptophysin with the same method using primary
(50 μL, 2 μg mL−1 of anti-Synaptophysin antibody, abcam, Cat# ab32594) and Biomarkers and ROS assay. Acetylcholine esterase (AchE) and glutamate (GLT)
levels were measured as biomarkers for neurodegeneration. Briefly, zebrafish larvae
treated with Aβ, Aβ + βCas, and Aβ + βCas AuNPs were euthanized and their
heads were excised from the trunks. The heads were homogenized in PBS (pH 7.4) 12 NATURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 Received: 10 December 2018 Accepted: 4 August 2019 Received: 10 December 2018 Accepted: 4 August 2019 References Role of mitochondrial
homeostasis and dynamics in Alzheimer's disease. Neurobiol. Dis. 51, 3–12
(2013). 13. Itzhaki, R. F. et al. Microbes and Alzheimer’s disease. J. Alzheimers Dis. 51,
979–984 (2016). 14. Ke, P. C. et al. Implications of peptide assemblies in amyloid diseases. Chem. Soc. Rev. 46, 6492–6531 (2017). 15. Steenhuysen, J. Biogen Scraps Two Alzheimer Drug Trials, Wipes $18 Billion
from Market Value. https://www.reuters.com/article/us-biogen-alzheimers/
biogen-scraps-two-alzheimer-drug-trials-wipes-18-billion-from-market-
value-idUSKCN1R213G (2019). 16. Doody, R. S. et al. Phase 3 trials of solanezumab for mild-to-moderate
Alzheimer's disease. N. Engl. J. Med. 370, 311–321 (2014). 17. Salloway, S. et al. Two phase 3 trials of bapineuzumab in mild-to-moderate
Alzheimer's disease. N. Engl. J. Med. 370, 322–333 (2014). 18. The Lancet. Alzheimer’s disease: expedition into the unknown. Lancet 388,
2713 (2016). IHC was performed on adult zebrafish brain sections. Adult zebrafish at 2 weeks
post Aβ or Aβ + βCas AuNPs treatment were euthanized by placing the animals in
ice chilled tricaine (1% in Holtfreter’s buffer for 1 min). The heads were separated
from the bodies, at pectoral fin, with a sharp scalpel and fixed in 2.5%
paraformaldehyde overnight. The heads were treated with 20% sucrose overnight,
fixed in Tissue Trek OCT mounting medium at −20 °C and sectioned into 20 µM
thick sections via cryostat. The sections were mounted on gelatinized glass slides,
immunostained for Aβ as described above in the “Fluorescence imaging, IHC, and
polarized light microscopy” section and imaged via a fluorescence microscope. IHC was performed on adult zebrafish brain sections. Adult zebrafish at 2 weeks
post Aβ or Aβ + βCas AuNPs treatment were euthanized by placing the animals in
ice chilled tricaine (1% in Holtfreter’s buffer for 1 min). The heads were separated
from the bodies, at pectoral fin, with a sharp scalpel and fixed in 2.5% 19. Reardon, S. Frustrated Alzheimer’s researchers seek better lab mice. Nature
563, 611–612 (2018). paraformaldehyde overnight. The heads were treated with 20% sucrose overnight,
fixed in Tissue Trek OCT mounting medium at −20 °C and sectioned into 20 µM
thick sections via cryostat. The sections were mounted on gelatinized glass slides,
immunostained for Aβ as described above in the “Fluorescence imaging, IHC, and
polarized light microscopy” section and imaged via a fluorescence microscope. 20. Ke, P. C. et al. Mitigation of amyloidosis with nanomaterials. Adv. Mater. 1901690 (2019) h
//d i
/10 1002/ d
201901690 20. Ke, P. C. et al. Data availability and AchE and GLT levels were estimated using assay kits according to reported
literature59,60. and AchE and GLT levels were estimated using assay kits according to reported
literature59,60. Data supporting the findings of this paper are available from the corresponding authors
upon reasonable request. Reporting summary of this article is available as Supplementary
Information file. The raw data underlying the respective main text (Figs. 1–7) and
Supplementary figures (Supplementary Figs. 1, 2, 8, 13, 14 and 15) are provided as Source
Data File. For ROS assay, Aβ (100 fM) were injected to the cerebroventricular space of
zebrafish larvae and 2',7'-DCF (5 nL of 2 µM) was injected 5 days post Aβ
treatment. The whole mount larvae were imaged under the green fluorescence
protein channel of an optical microscope 1 h after DCF treatment. For βCas
AuNPs, the nanoparticles were injected 2 h post Aβ treatment followed by the same
procedure. H2O2 (5 nL of 0.1%) was used as positive control and injected 3 h prior
to DCF microinjection in positive control larvae. DCF fluorescence was quantified
by excising the head from the trunk of euthanized larvae, homogenizing in PBS
buffer (50 µL, pH 7.4) and reading the DCF fluorescence with a microplate reader
with excitation/emission at 495 nm/529 nm. NATURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications Competing interests: The authors declare no competing interests. y
g
45. García-Ayllón, M.-S. et al. Altered levels of acetylcholinesterase in Alzheimer
plasma. PLoS ONE 5, e8701 (2010). Reprints and permission information is available online at http://npg.nature.com/
reprintsandpermissions/ Reprints and permission information is available online at http://npg.nature.com/
reprintsandpermissions/ 46. Sáez‐Valero, J., Sberna, G., McLean, C. A. & Small, D. H. Molecular isoform
distribution and glycosylation of acetylcholinesterase are altered in brain and
cerebrospinal fluid of patients with Alzheimer’s disease. J. Neurochem. 72,
1600–1608 (1999). Peer review information: Nature Communications would like to thank Morgan
Newman, George Perry, and other, anonymous, reviewers for their contributions to the
peer review of this work. Peer review reports are available. Peer review information: Nature Communications would like to thank Morgan
Newman, George Perry, and other, anonymous, reviewers for their contributions to the
peer review of this work. Peer review reports are available. 47. Roher, A. E. et al. Amyloid beta peptides in human plasma and tissues and
their significance for Alzheimer's disease. Alzheimer's Dement. 5, 18–29
(2009). 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. 48. Pacheco-Quinto, J. et al. Hyperhomocysteinemic Alzheimer’s mouse model of
amyloidosis shows increased brain amyloid β peptide levels. Neurobiol. Dis. 22, 651–656 (2006). 49. Avella, M. A. et al. Lactobacillus rhamnosus accelerates zebrafish backbone
calcification and gonadal differentiation through effects on the GnRH and IGF
systems. PloS ONE 7, e45572 (2012). 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 license, and indicate if changes were made. The images or other third party
material in this article are included in the article’s Creative Commons license, unless
indicated otherwise in a credit line to the material. If material is not included in the
article’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. To view a copy of this license, visit http://creativecommons.org/
licenses/by/4.0/. 50. Lau, B. Y., Mathur, P., Gould, G. G. & Guo, S. ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11762-0 28. Thorn, D. C., Ecroyd, H. & Carver, J. A. The two-faced nature of milk casein
proteins: amyloid fibril formation and chaperone-like activity. Aust. J. Dairy
Technol. 64, 34 (2009). 55. Lin, S. et al. High content screening in zebrafish speeds up hazard ranking of
transition metal oxide nanoparticles. ACS Nano 5, 7284–7295 (2011). 56. Smith, P. E. et al. Measurement of protein using bicinchoninic acid. Anal. Biochem. 150, 76–85 (1985). 29. Guha, S., Manna, T. K., Das, K. P. & Bhattacharyya, B. Chaperone-like activity
of tubulin. J. Biol. Chem. 273, 30077–30080 (1998). 57. Javed, I. et al. Lecithin-gold hybrid nanocarriers as efficient and pH selective
vehicles for oral delivery of diacerein—in-vitro and in-vivo study. Colloids
Surf. B 141, 1–9 (2016). 30. Thorn, D. C. et al. Amyloid fibril formation by bovine milk κ-casein and its
inhibition by the molecular chaperones αS-and β-casein. Biochemistry 44,
17027–17036 (2005). 58. Whitmore, L. & Wallace, B. A. Protein secondary structure analyses from
circular dichroism spectroscopy: methods and reference databases. Biopolymers: Original Research on. Biomolecules 89, 392–400 (2008). 31. Librizzi, F., Carrotta, R., Spigolon, D., Bulone, D. & San Biagio, P. L. α-Casein
inhibits insulin amyloid formation by preventing the onset of secondary
nucleation processes. J. Phys. Chem. Lett. 5, 3043–3048 (2014). y
y
g
nucleation processes. J. Phys. Chem. Lett. 5, 3043–3048 (2014 59. Pan, Y., Chatterjee, D. & Gerlai, R. Strain dependent gene expression and
neurochemical levels in the brain of zebrafish: focus on a few alcohol related
targets. Physiol. Behav. 107, 773–780 (2012). 32. Carrotta, R. et al. Inhibiting effect of αs1-casein on Aβ1–40 fibrillogenesis. Biochim. Biophys. Acta 1820, 124–132 (2012). p y
33. Zhang, X. et al. Chaperone-like activity of β-casein. Int. J. Biochem. Cell Biol. 37, 1232–1240 (2005). 60. Richetti, S. K. et al. Acetylcholinesterase activity and antioxidant capacity of
zebrafish brain is altered by heavy metal exposure. Neurotoxicology 32,
116–122 (2011). 34. Gladytz, A., Abel, B. & Risselada, H. J. Gold‐induced fibril growth: the
mechanism of surface‐facilitated amyloid aggregation. Angew. Chem. Int. Ed. 55, 11242–11246 (2016). Acknowledgements 35. Proctor, E. A. & Dokholyan, N. V. Applications of discrete molecular
dynamics in biology and medicine Curr Opin Struc Biol 37 9 13 (2016) 35. Proctor, E. A. & Dokholyan, N. V. Applications of discrete molecular
dynamics in biology and medicine. Curr. Opin. Struc. Biol. 37, 9–13 (2016). This work was supported by ARC Project No. CE140100036 (Davis), the NSFC grant
#21607115 and #21777116 (Lin), NSF CAREER CBET-1553945 (Ding), and NIH MIRA
R35GM119691 (Ding). Javed acknowledges the support of Monash International Post-
graduate Research Scholarship (MIPRS) and Australian Government Research Training
Program Scholarship. TEM imaging was performed at Bio21 Advanced Microscopy
Facility, University of Melbourne and polarized light microscopy was performed at
Monash Micro Imaging, Monash University. Javed and Lin thank Shanghai Science and
Technology Commission “Belt and Road” initiative program, Grant no. 17230743000. The authors acknowledge the support from Profs. Ting Xu and Daqiang Yin on the
Zebrabox instrument. y
gy
p
36. Javed, I. et al. Cofibrillization of pathogenic and functional amyloid proteins
with gold nanoparticles against amyloidogenesis. Biomacromolecules 18,
4316–4322 (2017). 37. Francis, R. et al. aph-1 and pen-2 are required for Notch pathway signaling, γ-
secretase cleavage of βAPP, and presenilin protein accumulation. Dev. Cell 3,
85–97 (2002). 38. Team, M. G. C. P. Generation and initial analysis of more than 15,000 full-
length human and mouse cDNA sequences. Proc. Natl Acad. Sci. USA 99,
16899–16903 (2002). 39. Newman, M., Ebrahimie, E. & Lardelli, M. Using the zebrafish model for
Alzheimer’s disease research. Front. Genet. 5, 189 (2014). Author contributions 40. Geling, A., Steiner, H., Willem, M., Bally‐Cuif, L. & Haass, C. A γ‐secretase
inhibitor blocks Notch signaling in vivo and causes a severe neurogenic
phenotype in zebrafish. EMBO Rep. 3, 688–694 (2002). P.C.K., I.J., S.L. and T.P.D. designed the project. I.J. and P.C.K. wrote the paper. I.J. performed AuNP synthesis, TEM, CD, UV-SPR, fluorescence characterizations, larval,
and adult zebrafish behavioral and cognitive assays, histology, and polarized light
microscopy. I.J., M.Z. and T.Y. performed in vivo microinjection. I.J. and G.P. performed
ICP-MS analysis. Y.X. and F.D. conducted DMD simulations. A.F. performed cell via-
bility assay and HIM imaging. C.L.P. and A.K. provided inputs to the discussion of the
paper. All authors agreed on the presentation of the paper. 41. Joshi, P., Liang, J. O., DiMonte, K., Sullivan, J. & Pimplikar, S. W. Amyloid
precursor protein is required for convergent-extension movements during
Zebrafish development. Dev. Biol. 335, 1–11 (2009). 42. Xie, J., Farage, E., Sugimoto, M. & Anand-Apte, B. A novel transgenic
zebrafish model for blood-brain and blood-retinal barrier development. BMC
Dev. Biol. 10, 76 (2010). Supplementary Information accompanies this paper at https://doi.org/10.1038/s41467-
019-11762-0. (
)
44. Santana, S., Rico, E. P. & Burgos, J. S. Can zebrafish be used as animal model
to study Alzheimer's disease? Am. J. Neurodegener. Dis. 1, 32 (2012). Competing interests: The authors declare no competing interests. Additional information 43. Fleming, A., Diekmann, H. & Goldsmith, P. Functional characterisation of the
maturation of the blood-brain barrier in larval zebrafish. PloS ONE 8, e77548
(2013). Supplementary Information accompanies this paper at https://doi.org/10.1038/s41467-
019-11762-0. Supplementary Information accompanies this paper at https://doi.org/10.1038/s41467-
019-11762-0. References Mitigation of amyloidosis with nanomateria
1901690 (2019). https://doi.org/10.1002/adma.201901690. g
21. Luo, Q. et al. A self-destructive nanosweeper that captures and clears amyloid
β-peptides. Nat. Commun. 9, 1802 (2018). 22. Lansbury, P. T. & Lashuel, H. A. A century-old debate on protein aggregation
and neurodegeneration enters the clinic. Nature 443, 774 (2006). g
23. Kim, D. et al. Graphene quantum dots prevent α-synucleinopathy in
Parkinson’s disease Nat Nanotech 13 812 (2018) 23. Kim, D. et al. Graphene quantum dots prevent α-sy 23. Kim, D. et al. Graphene quantum dots prevent α-syn
Parkinson’s disease. Nat. Nanotech. 13, 812 (2018). Parkinson’s disease. Nat. Nanotech. 13, 812 (2018). Statistical analysis. All the experiments in the manuscript were repeated three
times, unless specified, and data was presented as mean ± SD. For the zebrafish
experiments, 20 larvae per group and 3 group per sample were used to minimize
experimental error. The significance of results was determined by one-way
ANOVA followed by Turkey’s test and p values less than 0.05 were considered
significant (presented with * in figures) while p values less than 0.005 were con-
sidered as highly significant (presented with ** in figures). 24. Javed, I. et al. In vivo mitigation of amyloidogenesis through
functional–pathogenic double-protein coronae. Nano Lett. 18, 5797–5804
(2018). 25. Gao, N. et al. Transition-metal-substituted polyoxometalate derivatives as
functional anti-amyloid agents for Alzheimer’s disease. Nat. Commun. 5, 3422
(2014). 26. Faridi, A. et al. Mitigating human IAPP amyloidogenesis in vivo with chiral
silica nanoribbons. Small 14, 1802825 (2018). Reporting summary. Further information on research design is available in
the Nature Research Reporting Summary linked to this article. 27. Bieschke, J. et al. Small-molecule conversion of toxic oligomers to nontoxic β-
sheet–rich amyloid fibrils. Nat. Chem. Biol. 8, 93 (2012). 13 COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunications Competing interests: The authors declare no competing interests. Identification of a brain center
whose activity discriminates a choice behavior in zebrafish. Proc. Natl Acad. Sci. USA 108, 2581–2586 (2011). 51. Howe, K. et al. The zebrafish reference genome sequence and its relationship
to the human genome. Nature 496, 498 (2013). 52. Mathuru, A. S. & Jesuthasan, S. The medial habenula as a regulator of anxiety
in adult zebrafish. Front. Neural Circuits 7, 99 (2013). 53. Tomasiewicz, H. G., Flaherty, D. B., Soria, J. & Wood, J. G. Transgenic
zebrafish model of neurodegeneration. J. Neurosci. Res. 70, 734–745 (2002). 54. Van Bebber, F., Paquet, D., Hruscha, A., Schmid, B. & Haass, C. Methylene
blue fails to inhibit Tau and polyglutamine protein dependent toxicity in
zebrafish. Neurobiol. Dis. 39, 265–271 (2010). 14 NATURE COMMUNICATIONS | (2019) 10:3780 | https://doi.org/10.1038/s41467-019-11762-0 | www.nature.com/naturecommunicatio
|
https://openalex.org/W3107868738
|
https://www.researchsquare.com/article/rs-15025/v1.pdf?c=1631845459000
|
English
| null |
Clinical outcomes and prognostic factors in bloodstream infections due to extended-spectrum β-lactamase-producing Enterobacteriaceae among patients with malignancy: a meta-analysis
|
Annals of clinical microbiology and antimicrobials
| 2,020
|
cc-by
| 7,610
|
Clinical outcomes and prognostic factors in
bloodstream infections due to extended-spectrum
β-lactamase-producing Enterobacteriaceae among
patients with malignancy: a meta-analysis Ai-Min Jiang
Xi'an Jiaotong University Medical College First Affiliated Hospital Department of Medical Oncology
Na Liu
Xi'an Jiaotong University Medical College First Affiliated Hospital Department of Medical Oncology
Rui Zhao
Huazhong University of Science and Technology
Hao-Ran Zheng
Xi'an Jiaotong University Medical College First Affiliated Hospital Department of Medical Oncology
Xue Chen
Xi'an Jiaotong University Medical College First Affiliated Hospital Department of Medical Oncology
Chao-Xin Fan
Xi'an Jiaotong University Medical College First Affiliated Hospital Department of Medical Oncology
Rui Zhang
Xi'an Jiaotong University Medical College First Affiliated Hospital Department of Medical Oncology
Xiao-Qiang Zheng
Xi'an Jiaotong University Medical College First Affiliated Hospital Department of Medical Oncology
Xiao Fu
Xi'an Jiaotong University Medical College First Affiliated Hospital Department of Medical Oncology
Yu Yao
Xi'an Jiaotong University Medical College First Affiliated Hospital Department of Medical Oncology
Tao Tian
(
tiantao0607@163.com
) Version of Record: A version of this preprint was published on November 23rd, 2020. See the published
version at https://doi.org/10.1186/s12941-020-00395-7. License:
This work is licensed under a Creative Commons Attribution 4.0 International
License.
Read Full License Research Page 1/18
Keywords: Bloodstream infection, Extended-spectrum β-lactamase, ESBL-PE, Malignancy, Mortality, Meta-
analysis
Posted Date: February 25th, 2020
DOI: https://doi.org/10.21203/rs.2.24466/v1 Keywords: Bloodstream infection, Extended-spectrum β-lactamase, ESBL-PE, Malignancy, Mortality, Meta-
analysis Keywords: Bloodstream infection, Extended-spectrum β-lactamase, ESBL-PE, Malignancy, Mortality, Meta-
analysis DOI: https://doi.org/10.21203/rs.2.24466/v1 Page 1/18 License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full License Version of Record: A version of this preprint was published on November 23rd, 2020. See the published
version at https://doi.org/10.1186/s12941-020-00395-7. Page 2/18 Abstract Background The colonization of Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-
PE) in bloodstream infections (BSIs) has been increased dramatically worldwide, and it was associated
with worse clinical outcomes in patients with malignancy. We performed the meta-analysis to investigate
the prognosis and risk factors in BSIs caused by ESBL-PE in oncological patients. Methods PubMed and EMBASE were searched for related studies. All-cause mortality was considered as
the primary outcome. Subgroup analyses, meta-regression analyses, and sensitivity analysis were used to
investigate heterogeneity and reliability in results. Results 6729 patients from 25 studies were eligible. Six studies enrolled oncological patients with BSIs
caused by ESBL-PE only, while 19 studies both enrolled ESBL-PE and non-ESBL-PE infections. The results
showed that BSIs caused by ESBL-PE in patients with malignancy was associated with higher mortality
than non-ESBL-PE infections (RR = 2.21, 95% CI: 1.60–3.06, P < 0.001), with a significant between-study
heterogeneity (I2 = 78.3%, P < 0.001). Subgroup analyses showed that children (RR = 2.80, 95% CI: 2.29–
3.43, P < 0.001) and hematological malignancy (RR =3.20, 95% CI: 2.54–4.03, P < 0.001) were associated
with a higher mortality. Severe sepsis/ septic shock, pneumonia, and ICU admission were the most
common predictors of mortality. Conclusions Our study identified that BSIs caused by ESBL-PE in patients with malignancy was
associated with worse clinical outcomes compared with non-ESBL-PE infections. Furthermore, children
and hematological malignancy were associated with higher mortality. Severe sepsis/ septic shock,
pneumonia, and ICU admission were the most common predictors of mortality. Study selection Inclusion criteria were as follows: (1) BSIs caused by ESBL-PE in patients with malignancy; (2) total
number of BSIs cases and ESBL-PE caused BSIs were reported; (3) the mortality of BSIs due to ESBL-PE
was reported; (4) performed univariate and multivariate analysis to identify the risk factors of mortality;
(5) studies included only patients with ESBL-PE infections, or a subset of BSI caused by ESBL-PE in
patients with malignancies, but provided specific data on outcomes. Literature that satisfied the following
criteria were excluded: (1) letters, case reports, editorials, expert opinion or reviews without original data;
(2) overlapping or duplicate data; (3) incomplete data about outcomes; (4) articles were not described in
the English language; (5) the sample size of BSIs caused by ESBL-PE in oncological patients less than 10;
(6) studies only focusing on risk factors for ESBL-PE infections. Search strategy Our meta-analysis was based on the Preferred Reporting Items for Systematic Reviews and Meta-
Analyses (PRISMA) guidelines. (9) We conducted an overall literature retrieval for PubMed and EMBASE
published up to 10 December 2019. Studies using the following terms for selection: “(ESBL OR (extended-
spectrum beta-lactamase) OR (extended-spectrum β-lactamase)) AND (tumor OR neoplasia OR
malignancy OR cancer OR carcinoma OR sarcoma OR leukemia OR leukaemia OR lymphoma OR
hematolog* OR haematolog* OR oncolog*)”. We manually screened other relevant studies and reference
lists. The search was performed independently by two investigators (AM Jiang and N Liu). Background In recent years, the incidence of bloodstream infections (BSIs) caused by Extended-spectrum β-
lactamase-producing Enterobacteriaceae (ESBL-PE) has been increasing over time all over the world.(1)
There is a growing body of evidence showed that BSIs caused by ESBL-PE are more worrisome in clinical
practice since Extended-spectrum β-lactamases (ESBLs) mediates resistance to a wide variety of
antibiotics, including third-generation cephalosporins, aminoglycosides, and quinolones, and most
empirical antimicrobial regimens can not cover these pathogens.(2, 3) Therefore, the antimicrobial
therapeutic regimens are often limited in these infections.(1) Patients with malignancy are more vulnerable to developing severe infection, including those caused by
ESBL-PE since they are more likely to be immunocompromised due to chemotherapy, radiotherapy,
surgery, invasive procedures, malnutrition, and malignancy itself. (4, 5) As a result, these infections have
become significant therapeutic challenges for clinicians due to delayed initiation of chemotherapy,
reduced standard dosage, prolonged hospitalization, increased financial burden on healthcare, and raised
severe morbidity and mortality.(3, 6) Therefore, rapid initiation of appropriate antibiotic therapy is pivotal Page 3/18 Page 3/18 for oncological patients with BSIs caused by ESBL-PE,(4) while inappropriate empirical antibiotic
treatment is associated with worse outcomes and survival.(3) Previous meta-analyses have investigated the prevalence of BSIs caused by ESBL-PE in patients with
malignancy. (7, 8) However, there was no further analysis of clinical outcomes and risk factors in these
populations. Therefore, we conducted this study to assess the prognosis and risk factors of BSIs due to
ESBL-PE in patients with malignancy and provide updated evidence via meta-analysis. Study characteristics and quality assessment Our literature search identified 1245 studies. After excluding repeated records and the initial screening
based on titles and abstracts, 25 articles were eligible in this study. Of these, six studies enrolled
oncological patients with BSIs caused by ESBL-PE only, while 19 studies both enrolled ESBL-PE and non-
ESBL-PE infections. Of the 25 studies, there were eight prospective cohort studies, 14 retrospective cohort
studies, and three case-control studies. All included studies were published between 2009 and 2019, and
there were six studies published in 2019, accounting for 24%. There were 15 studies conducted in Asia,
seven studies conducted in Europe, and three studies were conducted in North America. The detailed flow
chart of the study selection process was described in Figure 1. Table 1 summarized the characteristics of
25 selected studies. NOS scores for all studies were more than 6 points, and 21 studies included in this
article were high-quality studies. Table S1 presented the results of the quality assessment. Statistical analysis The RRs and 95% CIs for mortality were calculated to assess the outcomes of BSIs caused by ESBL-PE in
oncological patients. All results were depicted as forest plots. Heterogeneity was assessed using
Cochran’s Q test and the I2 statistic test. When the heterogeneity was statistically significant (P < 0.05 and
I2 > 50%), a random-effects model was applied to obtain the pooled RRs; otherwise, a fixed-effects model
was performed. Subgroup analyses and meta-regression analyses were conducted to explore the sources
of heterogeneity. We also performed a sensitivity analysis to evaluate the quality and stability of results
by omitting one study in each turn. Begg’s test and Egger’s test were used to assess the publication bias. Statistical tests were two-tailed at the significance level of P < 0.05. All analyses were used with STATA
V.14.0 (Stata Corporation, College Station, TX). Definitions and study outcomes Neutropenia was defined as an absolute neutrophil count of <500 neutrophils/mm3. (11) Initial antibiotics treatment was considered inappropriate once the antibiotics could not suppress the
activity of the isolated pathogens according to the results of antimicrobial susceptibility tests during the
first 24 h after the blood culture was obtained. (11) The all-cause mortality at the end of the study and the predictors in BSIs due to ESBL-PE in patients with
malignancy were the primary outcomes in the study. (12) Data extraction and quality assessment Two investigators (AM Jiang and N Liu) independently extracted the data using a standardized approach. Any disagreement in the study selection and data extraction phases was resolved through discussion
with the third investigator (R Zhao). The following data information was retrieved from each article: first
author’s name, year of publication, country, study population, infection type of BSIs, the total number of
screened subjects, the total number of ESBL-PE caused BSIs, the total number of BSIs caused death and
ESBL-PE BSIs caused death, and ESBL detection method. The data was extracted from texts or tables in
articles. Newcastle Ottawa Quality Assessment Scale (NOS) was used in our research to assess the Page 4/18 Page 4/18 quality of selected studies (10). The scale included three aspects: selection, comparability, and outcome. Studies that scored more than six were considered of high quality. Mortality Page 5/18 In all the studies, the time of death records was not similar. The majority of studies used 30-day mortality
to evaluate the clinical outcomes of BSIs caused by ESBL-PE in patients with malignancy, (13-29) only
one study did not report a particular time of death. (30) The mortality varied from 10.7% to 31.0% in
studies only enrolled oncological patients with ESBL-PE infections. However, the mortality of BSIs varied
from 4.8% to 51% in studies both enrolled ESBL-PE and non-ESBL-PE infections, respectively. We finally
included 19 studies that enrolled both ESBL-PE and non-ESBL-PE infected oncological patients into
analyses to estimate the mortality of BSIs caused by ESBL-PE in patients with malignancy. The results
showed that in patients with malignancy, ESBL-PE infections was associated with a higher mortality risk
from BSIs than non-ESBL-PE infections (RR = 2.21, 95 % CI: 1.60–3.06, P < 0.001) (Figure 2), with a
significant between-study heterogeneity (I2 = 78.3%, P < 0.001). Subgroup analyses and meta-regression analyses Subgroup analyses in all selected studies were conducted by study design, region, study population,
malignancy type, FN, ESBL detection methods, and NOS score. Most of the subgroups (study design,
region, study population, malignancy type, and ESBL detection methods) were consistent with the overall
trend and showed statistically significant increases, except for the subgroup without FN, and the
subgroup with NOS score < 6. The subgroup analyses suggested that study region was identified as
potential sources of the heterogeneity (test for subgroup difference: P =0.014), and the RR of mortality in
studies from Asia (RR = 1.49, 95 % CI: 1.22–1.82) was lower compared with Europe and North America,
with no evidence of heterogeneity (I2 = 27.3%, P = 0.177). The detailed information was in Table 2 and
Figure S1. Sensitivity analysis and publication bias We then carried out the sensitivity analysis by omitting each study in turn. As summarized in Figure S2,
the pooled RRs and 95% CIs of mortality ranged from 2.03 (1.53-2.68) to 2.36 (1.72-3.25). The results of
the sensitivity analysis show that our results are stable and reliable since there were no individual studies
influenced the overall results. Begg’s test and Egger’s test showed no evidence of publication bias (P =
0.944 for Begg’s test; P = 0.538 for Egger’s test, respectively) (Figure S3). Discussion Over the past ten years, the colonization and prevalence of ESBL-PE infections have continued to
increase rapidly all over the world,(36) and these infections generally associated with worse clinical
outcomes, prolonged hospitalization, extra healthcare burden, and delayed initiation of treatment for
malignancy.(3) Patients with malignancy are more easily to developing BSIs caused by ESBL-PE since
oncological patients are easily immunocompromised due to a series of mechanisms as mentioned
before.(5) Therefore, timely and appropriate empirical antimicrobial therapeutic regimen is pivotal for
patients with malignancy who developed BSIs caused by ESBL-PE. (5) In this meta-analysis, we included 19 studies that both enrolled oncological patients with ESBL-PE and
non-ESBL-PE infections, and the results showed that the mortality in BSIs caused by ESBL-PE among
patients with malignancy was higher compared with non-ESBL-PE infections (RR = 2.21, 95 % CI: 1.60–
3.06, P < 0.001). Consistent with our findings, Trecarichi EM et al. reported that ESBL-PE caused BSIs in
patients with malignancy was associated with high mortality compared with non-ESBL-PE infections.(13,
14, 16) This result suggests that we should think highly of BSIs caused by ESBL-PE in patients with
malignancy during hospitalization, and the rapid initiation of antibiotics treatment should be considered
as early as possible once it was recognized. The results of the subgroup analyses showed that the mortality of ESBL-PE BSIs varies from different
regions. We found that the mortality in North America and Europe was higher than in Asia. It could be
explained by the fact that the majority of studies were conducted in Asia, and the study region was
confirmed as a source of heterogeneity after further meta-regression analyses. Alevizakos M et al. reported that ESBL-PE are the causative agents of approximately 10.0% BSIs among patients with
malignancy in Southeast Asia, and it has been associated with increased mortality in these subjects
compared with Europe and Amecira.(37) Therefore, more studies on other continents will need to be
included in the future so as to draw more reliable conclusions. We also found that children and
hematological malignancy were also associated with worse prognosis in BSIs caused by ESBL-PE. Predictors of mortality in BSIs caused by ESBL-PE among patients with malignancy We then summarized the risk factors for BSIs caused by ESBL-PE in patients with malignancy. It showed
that the most commonly studied risk factors for BSIs caused by ESBL-PE in patients with malignancy
were age, gender, ESBL production, neutropenia, inadequate initial antimicrobial treatment, ICU
admission, intra-abdominal infection, pneumonia, Pitt bacteremia score, severe sepsis/ septic shock,
solid tumor, and concurrent corticosteroid therapy. However, metastasis and mechanical ventilation were
the least studied variables. We also found that the most common independent risk factors of mortality
were severe sepsis/ septic shock, pneumonia, ICU admission, and neutropenia. At the same time,
indwelling urinary catheter,(23) pneumonia,(31) Pitt bacteremia score,(32) and severe sepsis/ septic
shock(31) were the most common independent risk factors of mortality in studies that only enrolled Page 6/18 Page 6/18 patients with BSIs caused by ESBL-PE. In studies that both included ESBL-PE and non-ESBL-PE
infections, severe sepsis/ septic shock, (14, 16, 18, 19, 22, 24, 28, 33) ICU admission, (14, 19, 27, 33, 34)
neutropenia, (13, 14, 24, 35) and pneumonia (14, 16, 21, 28) were the most commonly investigated
independent risk factors, respectively. Interestingly, there were only three studies (13, 14, 16) identified
that ESBL production was associated with unfavorable outcomes in these patients. The detailed
information was in Table 3. Discussion It
probably due to the fact that the included children population were mainly diagnosed with hematological
malignancy, which were more vulnerable to develop immunosuppression, prolonged neutropenia, and
septic shock.(38, 39) Interestingly, FN was not associated with higher mortality in oncological patients
with BSIs caused by ESBL-PE, which could be attributed to there are only three studies included patients
with FN, while some studies enrolled a subset of FN patients, but the data were not accessible to
analysis.(13, 14, 16, 21, 24, 25, 30, 34, 40) Among these studies, Kang CI et al. reported that FN/ Page 7/18 Page 7/18 neutropenia was not the risk factor for mortality in BSIs caused by ESBL-PE among patients with
malignancy.(14, 16, 21, 24) Hence, the accuracy of the conclusion needs to be further confirmed. The
combined RR of sensitivity analysis further confirmed the stability of the results. Besides, the meta-
regression analyses also suggested that the study region might be the source of heterogeneity in this
meta-analysis, despite other relevant factors such as age, comorbidities, and antimicrobial treatment
regimens cannot be analyzed due to lack of relevant data. However, Begg’s test and Egger’s test showed
there was no evidence of publication bias in our study. In our study, approximately 72.0% of studies analyzed the relationship between age and mortality of BSIs
caused by ESBL-PE in patients with malignancy. However, there were no studies that identified age as
independent predictors. Furthermore, more than 50.0% of studies concluded that severe sepsis/ septic
shock, pneumonia, and ICU admission were the most common independent risk factors in mortality. Besides, fewer studies confirmed that neutropenia was more common in patients who died. According to
a study conducted by Vardakas KZ et al., they reported that underlying diseases and severity scores were
the most commonly identified prognostic factors of mortality in patients with infections due to multi-drug
resistant Gram-negative bacteria (MDRGNB).(12) Similar to the previous study,(12) we also found that
severe sepsis/ septic shock was the most common risk factor in mortality. However, only fewer studies
concluded that the Pitt bacteremia score and Charlson Index Score (CCI) were more common in patients
who died. An interesting finding of our study is that only three studies confirmed ESBL production was an
independent risk factor in mortality. Rottier WC et al. Discussion reported that ESBL production was associated with
higher mortality compared with bacteremia with non-ESBL-PE.(41) This could be due to the small sample
size of some studies we included in this study. Therefore, more prospective multicenter studies and
clinical trials were urgently needed in the future to provide sufficient evidence. In our study, approximately 72.0% of studies analyzed the relationship between age and mortality of BSIs
caused by ESBL-PE in patients with malignancy. However, there were no studies that identified age as
independent predictors. Furthermore, more than 50.0% of studies concluded that severe sepsis/ septic
shock, pneumonia, and ICU admission were the most common independent risk factors in mortality. To our knowledge, this is the first study that evaluated the clinical outcomes and risk factors in BSIs
caused by ESBL-PE among patients with malignancy using Meta-analysis. However, our study has
several limitations. First, all of the included articles were observational studies and published in English. Besides, high-estimated heterogeneity was observed, which is probably related to different design, study
region, and study population. Moreover, some studies included oncological patients with FN, but the data
were not available for subgroup analysis. Therefore, the clinical outcomes of BSIs caused by ESBL-PE in
these patients should be further validated since these patients are more vulnerable to severe infections. To sum up, clinical conclusions need to be comprehensive assessment in combination with other
indicators, and more sample sizes and studies need to be added to verify our results. Abbreviations ESBL-PE: extended-spectrum β-lactamase-producing Enterobacteriaceae; BSI: bloodstream infection; SC:
single-center; MC: multicenter; NR: not reported; FN: febrile neutropenia; RR: relative risk; CI: confidence
interval; NOS, Newcastle-Ottawa scale; CCI: Charlson Index Score; ICU: intensive care unit. Consent for publication Not applicable. Author Contributions T.T. and Y.Y. conceived the study. A.M.J., N.L., and R.Z. performed the search, extracted the data and
performed the analyses. H.R.Z., X.C., C.X.F, and R.Z. participated in the study design and helped with the
data analyses. X.Q.Z. and X.F. participated in the study design and manuscript revision. All authors
interpreted the data, and A.M.J. and N.L. wrote the paper. All authors read and approved the final
manuscript. Ethics approval and consent to participate Not applicable. Acknowledgments Not applicable. Availability of data and material Data sharing is not applicable to this article as no datasets were generated or analyzed during the current
study. Funding This research did not receive any specific grant from funding agencies in the public, commercial, or not-
for-profit sectors. Declarations Page 8/18 Page 8/18 Competing interests The authors declare that they have no competing interests. References 1. Alevizakos M, Gaitanidis A, Andreatos N, Arunachalam K, Flokas ME, Mylonakis E. Bloodstream
infections due to extended-spectrum beta-lactamase-producing Enterobacteriaceae among patients
with malignancy: a systematic review and meta-analysis. Int J Antimicrob Agents. 2017;50(5):657-
63. 1. Alevizakos M, Gaitanidis A, Andreatos N, Arunachalam K, Flokas ME, Mylonakis E. Bloodstream
infections due to extended-spectrum beta-lactamase-producing Enterobacteriaceae among patients
with malignancy: a systematic review and meta-analysis. Int J Antimicrob Agents. 2017;50(5):657-
63. 2. Paterson DL, Bonomo RA. Extended-spectrum beta-lactamases: a clinical update. Clin Microbiol Rev. 2005;18(4):657-86. 2. Paterson DL, Bonomo RA. Extended-spectrum beta-lactamases: a clinical update. Clin Microbiol Rev. 2005;18(4):657-86. 2. Paterson DL, Bonomo RA. Extended-spectrum beta-lactamases: a clinical update. Clin Microbiol Rev. 2005;18(4):657-86. 3. Biehl LM, Schmidt-Hieber M, Liss B, Cornely OA, Vehreschild MJ. Colonization and infection with
extended spectrum beta-lactamase producing Enterobacteriaceae in high-risk patients - Review of the 3. Biehl LM, Schmidt-Hieber M, Liss B, Cornely OA, Vehreschild MJ. Colonization and infection with
extended spectrum beta-lactamase producing Enterobacteriaceae in high-risk patients - Review of the Page 9/18 Page 9/18 Page 9/18 literature from a clinical perspective. Crit Rev Microbiol. 2016;42(1):1-16. 4. Alevizakos M, Karanika S, Detsis M, Mylonakis E. Colonisation with extended-spectrum beta-
lactamase-producing Enterobacteriaceae and risk for infection among patients with solid or
haematological malignancy: a systematic review and meta-analysis. Int J Antimicrob Agents. 2016;48(6):647-54. 5. Gudiol C, Aguado JM, Carratala J. Bloodstream infections in patients with solid tumors. Virulence. 2016;7(3):298-308. 5. Gudiol C, Aguado JM, Carratala J. Bloodstream infections in patients with solid tumors. Virulence. 2016;7(3):298-308. 6. Ndir A, Diop A, Ka R, Faye PM, Dia-Badiane NM, Ndoye B, et al. Infections caused by extended-
spectrum beta-lactamases producing Enterobacteriaceae: clinical and economic impact in patients
hospitalized in 2 teaching hospitals in Dakar, Senegal. Antimicrob Resist Infect Control. 2016;5:13. 6. Ndir A, Diop A, Ka R, Faye PM, Dia-Badiane NM, Ndoye B, et al. Infections caused by extended-
spectrum beta-lactamases producing Enterobacteriaceae: clinical and economic impact in patients
hospitalized in 2 teaching hospitals in Dakar, Senegal. Antimicrob Resist Infect Control. 2016;5:13. 7. Alevizakos M, Karanika S, Detsis M, Mylonakis E. Colonisation with extended-spectrum β-lactamase-
producing Enterobacteriaceae and risk for infection among patients with solid or haematological
malignancy: a systematic review and meta-analysis. International journal of antimicrobial agents. 2016;48(6):647-54. 8. Alevizakos M, Gaitanidis A, Andreatos N, Arunachalam K, Flokas ME, Mylonakis E. Bloodstream
infections due to extended-spectrum β-lactamase-producing Enterobacteriaceae among patients with
malignancy: a systematic review and meta-analysis. References International journal of antimicrobial agents. 2017;50(5):657-63. 9. Liberati A, Altman DG, Tetzlaff J, Mulrow C, Gotzsche PC, Ioannidis JP, et al. The PRISMA statement
for reporting systematic reviews and meta-analyses of studies that evaluate healthcare interventions:
explanation and elaboration. BMJ (Clinical research ed). 2009;339:b2700. 9. Liberati A, Altman DG, Tetzlaff J, Mulrow C, Gotzsche PC, Ioannidis JP, et al. The PRISMA statement
for reporting systematic reviews and meta-analyses of studies that evaluate healthcare interventions:
explanation and elaboration. BMJ (Clinical research ed). 2009;339:b2700. 10. Stang A. Critical evaluation of the Newcastle-Ottawa scale for the assessment of the quality of
nonrandomized studies in meta-analyses. European journal of epidemiology. 2010;25(9):603-5. 10. Stang A. Critical evaluation of the Newcastle-Ottawa scale for the assessment of the quality of
nonrandomized studies in meta-analyses. European journal of epidemiology. 2010;25(9):603-5. 11. Ha YE, Kang CI, Cha MK, Park SY, Wi YM, Chung DR, et al. Epidemiology and clinical outcomes of
bloodstream infections caused by extended-spectrum beta-lactamase-producing Escherichia coli in
patients with cancer. Int J Antimicrob Agents. 2013;42(5):403-9. 11. Ha YE, Kang CI, Cha MK, Park SY, Wi YM, Chung DR, et al. Epidemiology and clinical outcomes of
bloodstream infections caused by extended-spectrum beta-lactamase-producing Escherichia coli in
patients with cancer. Int J Antimicrob Agents. 2013;42(5):403-9. 12. Vardakas KZ, Rafailidis PI, Konstantelias AA, Falagas ME. Predictors of mortality in patients with
infections due to multi-drug resistant Gram negative bacteria: the study, the patient, the bug or the
drug? J Infect. 2013;66(5):401-14. 12. Vardakas KZ, Rafailidis PI, Konstantelias AA, Falagas ME. Predictors of mortality in patients with
infections due to multi-drug resistant Gram negative bacteria: the study, the patient, the bug or the
drug? J Infect. 2013;66(5):401-14. 13. Trecarichi EM, Tumbarello M, Spanu T, Caira M, Fianchi L, Chiusolo P, et al. Incidence and clinical
impact of extended-spectrum-β-lactamase (ESBL) production and fluoroquinolone resistance in
bloodstream infections caused by Escherichia coli in patients with hematological malignancies. Journal of Infection. 2009;58(4):299-307. 13. Trecarichi EM, Tumbarello M, Spanu T, Caira M, Fianchi L, Chiusolo P, et al. Incidence and clinical
impact of extended-spectrum-β-lactamase (ESBL) production and fluoroquinolone resistance in
bloodstream infections caused by Escherichia coli in patients with hematological malignancies. Journal of Infection. 2009;58(4):299-307. 14. Kang CI, Chung DR, Ko KS, Peck KR, Song JH. Risk factors for infection and treatment outcome of
extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae
bacteremia in patients with hematologic malignancy. Annals of hematology. 2012;91(1):115-21. 14. References Kang CI, Chung DR, Ko KS, Peck KR, Song JH. Risk factors for infection and treatment outcome of
extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae
bacteremia in patients with hematologic malignancy. Annals of hematology. 2012;91(1):115-21. 15. Wu UI, Chen WC, Yang CS, Wang JL, Hu FC, Chang SC, et al. Ertapenem in the treatment of
bacteremia caused by extended-spectrum beta-lactamase-producing Escherichia coli: a propensity 15. Wu UI, Chen WC, Yang CS, Wang JL, Hu FC, Chang SC, et al. Ertapenem in the treatment of
bacteremia caused by extended-spectrum beta-lactamase-producing Escherichia coli: a propensity Page 10/18 Page 10/18 score analysis. International journal of infectious diseases : IJID : official publication of the
International Society for Infectious Diseases. 2012;16(1):e47-52. score analysis. International journal of infectious diseases : IJID : official publication of the
International Society for Infectious Diseases. 2012;16(1):e47-52. 16. Ha YE, Kang CI, Cha MK, Park SY, Wi YM, Chung DR, et al. Epidemiology and clinical outcomes of
bloodstream infections caused by extended-spectrum β-lactamase-producing Escherichia coli in
patients with cancer. International journal of antimicrobial agents. 2013;42(5):403-9. 16. Ha YE, Kang CI, Cha MK, Park SY, Wi YM, Chung DR, et al. Epidemiology and clinical outcomes of
bloodstream infections caused by extended-spectrum β-lactamase-producing Escherichia coli in
patients with cancer. International journal of antimicrobial agents. 2013;42(5):403-9. 17. Kang CI, Wi YM, Ko KS, Chung DR, Peck KR, Lee NY, et al. Outcomes and risk factors for mortality in
community-onset bacteremia caused by extended-spectrum beta-lactamase-producing Escherichia
coli, with a special emphasis on antimicrobial therapy. Scandinavian journal of infectious diseases
2013;45(7):519-25. 18. Kim SH, Kwon JC, Choi SM, Lee DG, Park SH, Choi JH, et al. Escherichia coli and Klebsiella
pneumoniae bacteremia in patients with neutropenic fever: factors associated with extended-
spectrum beta-lactamase production and its impact on outcome. Annals of hematology. 2013;92(4):533-41. 19. Bodro M, Gudiol C, Garcia-Vidal C, Tubau F, Contra A, Boix L, et al. Epidemiology, antibiotic therapy
and outcomes of bacteremia caused by drug-resistant ESKAPE pathogens in cancer patients. Supportive care in cancer : official journal of the Multinational Association of Supportive Care in
Cancer. 2014;22(3):603-10. 19. Bodro M, Gudiol C, Garcia-Vidal C, Tubau F, Contra A, Boix L, et al. Epidemiology, antibiotic therapy
and outcomes of bacteremia caused by drug-resistant ESKAPE pathogens in cancer patients. Supportive care in cancer : official journal of the Multinational Association of Supportive Care in
Cancer. 2014;22(3):603-10. 20. References Han SB, Jung SW, Bae EY, Lee JW, Lee DG, Chung NG, et al. Extended-spectrum beta-lactamase-
producing Escherichia coli and Klebsiella pneumoniae bacteremia in febrile neutropenic children. Microbial drug resistance (Larchmont, NY). 2015;21(2):244-51. 20. Han SB, Jung SW, Bae EY, Lee JW, Lee DG, Chung NG, et al. Extended-spectrum beta-lactamase-
producing Escherichia coli and Klebsiella pneumoniae bacteremia in febrile neutropenic children. Microbial drug resistance (Larchmont, NY). 2015;21(2):244-51. 21. Cattaneo C, Zappasodi P, Mancini V, Annaloro C, Pavesi F, Skert C, et al. Emerging resistant bacteria
strains in bloodstream infections of acute leukaemia patients: results of a prospective study by the
Rete Ematologica Lombarda (Rel). Annals of hematology. 2016;95(12):1955-63. 21. Cattaneo C, Zappasodi P, Mancini V, Annaloro C, Pavesi F, Skert C, et al. Emerging resistant bacteria
strains in bloodstream infections of acute leukaemia patients: results of a prospective study by the
Rete Ematologica Lombarda (Rel). Annals of hematology. 2016;95(12):1955-63. 22. Ma J, Li N, Liu Y, Wang C, Liu X, Chen S, et al. Antimicrobial resistance patterns, clinical features, and
risk factors for septic shock and death of nosocomial e coli bacteremia in adult patients with
hematological disease. Medicine (United States). 2017;96(21). 23. Cattaneo C, Di Blasi R, Skert C, Candoni A, Martino B, Di Renzo N, et al. Bloodstream infections in
haematological cancer patients colonized by multidrug-resistant bacteria. Annals of hematology. 2018;97(9):1717-26. 23. Cattaneo C, Di Blasi R, Skert C, Candoni A, Martino B, Di Renzo N, et al. Bloodstream infections in
haematological cancer patients colonized by multidrug-resistant bacteria. Annals of hematology. 2018;97(9):1717-26. 24. Çeken S, İskender G, Gedik H, Duygu F, Mert D, Kaya AH, et al. Risk factors for bloodstream infections
due to extended-spectrum β-lactamase producing enterobacteriaceae in cancer patients. Journal of
Infection in Developing Countries. 2018;12(4):265-72. 24. Çeken S, İskender G, Gedik H, Duygu F, Mert D, Kaya AH, et al. Risk factors for bloodstream infections
due to extended-spectrum β-lactamase producing enterobacteriaceae in cancer patients. Journal of
Infection in Developing Countries. 2018;12(4):265-72. 25. Islas-Muñoz B, Volkow-Fernández P, Ibanes-Gutiérrez C, Villamar-Ramírez A, Vilar-Compte D, Cornejo-
Juárez P. Bloodstream infections in cancer patients. Risk factors associated with mortality. International Journal of Infectious Diseases. 2018;71:59-64. 25. Islas-Muñoz B, Volkow-Fernández P, Ibanes-Gutiérrez C, Villamar-Ramírez A, Vilar-Compte D, Cornejo-
Juárez P. Bloodstream infections in cancer patients. Risk factors associated with mortality. International Journal of Infectious Diseases. 2018;71:59-64. 26. Isendahl J, Giske CG, Tegmark Wisell K, Ternhag A, Nauclér P. References Risk factors for community-onset
bloodstream infection with extended-spectrum β-lactamase-producing Enterobacteriaceae: national
population-based case–control study. Clinical Microbiology and Infection. 2019;25(11):1408-14. 26. Isendahl J, Giske CG, Tegmark Wisell K, Ternhag A, Nauclér P. Risk factors for community-onset
bloodstream infection with extended-spectrum β-lactamase-producing Enterobacteriaceae: national
population-based case–control study. Clinical Microbiology and Infection. 2019;25(11):1408-14. Page 11/18 Page 11/18 27. Gudiol C, Calatayud L, Garcia-Vidal C, Lora-Tamayo J, Cisnal M, Duarte R, et al. Bacteraemia due to
extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) in cancer patients: clinical
features, risk factors, molecular epidemiology and outcome. The Journal of antimicrobial
chemotherapy. 2010;65(2):333-41. 28. Kim SJ, Park KH, Chung JW, Sung H, Choi SH, Choi SH. Prevalence and impact of extended-spectrum
β-lactamase production on clinical outcomes in cancer patients with enterobacter species
bacteremia. Korean Journal of Internal Medicine. 2014;29(5):637-46. 28. Kim SJ, Park KH, Chung JW, Sung H, Choi SH, Choi SH. Prevalence and impact of extended-spectrum
β-lactamase production on clinical outcomes in cancer patients with enterobacter species
bacteremia. Korean Journal of Internal Medicine. 2014;29(5):637-46. 29. Gudiol C, Royo-Cebrecos C, Abdala E, Akova M, Alvarez R, Maestro-de la Calle G, et al. Efficacy of
beta-Lactam/beta-Lactamase Inhibitor Combinations for the Treatment of Bloodstream Infection
Due to Extended-Spectrum-beta-Lactamase-Producing Enterobacteriaceae in Hematological Patients
with Neutropenia. Antimicrobial agents and chemotherapy. 2017;61(8). 30. Namikawa H, Yamada K, Yamairi K, Shibata W, Fujimoto H, Takizawa E, et al. Mortality caused by
extended-spectrum beta-lactamase-producing Enterobacteriaceae bacteremia; a case control study:
alert to Enterobacteriaceae strains with high minimum inhibitory concentrations of
piperacillin/tazobactam. Diagnostic microbiology and infectious disease. 2019;94(3):287-92. 31. Wang SS, Lee NY, Hsueh PR, Huang WH, Tsui KC, Lee HC, et al. Clinical manifestations and
prognostic factors in cancer patients with bacteremia due to extended-spectrum β-lactamase-
producing Escherichia coli or Klebsiella pneumoniae. Journal of Microbiology, Immunology and
Infection. 2011;44(4):282-8. 32. Benanti GE, Brown ART, Shigle TL, Tarrand JJ, Bhatti MM, McDaneld PM, et al. Carbapenem versus
Cefepime or Piperacillin-Tazobactam for Empiric Treatment of Bacteremia Due to Extended-
Spectrum-beta-Lactamase-Producing Escherichia coli in Patients with Hematologic Malignancy. Antimicrobial agents and chemotherapy. 2019;63(2). 33. Zhang Q, Gao HY, Li D, Li Z, Qi SS, Zheng S, et al. Clinical outcome of Escherichia coli bloodstream
infection in cancer patients with/without biofilm formation: a single-center retrospective study. Infection and drug resistance. 2019;12:359-71. 33. Zhang Q, Gao HY, Li D, Li Z, Qi SS, Zheng S, et al. References Clinical outcome of Escherichia coli bloodstream
infection in cancer patients with/without biofilm formation: a single-center retrospective study. Infection and drug resistance. 2019;12:359-71. 34. Metan G, Demiraslan H, Kaynar LG, Zararsiz G, Alp E, Eser B. Factors influencing the early mortality in
haematological malignancy patients with nosocomial Gram negative bacilli bacteraemia: a
retrospective analysis of 154 cases. The Brazilian journal of infectious diseases : an official
publication of the Brazilian Society of Infectious Diseases. 2013;17(2):143-9. 34. Metan G, Demiraslan H, Kaynar LG, Zararsiz G, Alp E, Eser B. Factors influencing the early mortality in
haematological malignancy patients with nosocomial Gram negative bacilli bacteraemia: a
retrospective analysis of 154 cases. The Brazilian journal of infectious diseases : an official
publication of the Brazilian Society of Infectious Diseases. 2013;17(2):143-9. 35. Kim YJ, Jung SM, Kang J, Ryoo SM, Sohn CH, Seo DW, et al. Risk factors for extended-spectrum beta-
lactamase-producing Enterobacteriaceae infection causing septic shock in cancer patients with
chemotherapy-induced febrile neutropenia. Internal and emergency medicine. 2019;14(3):433-40. 35. Kim YJ, Jung SM, Kang J, Ryoo SM, Sohn CH, Seo DW, et al. Risk factors for extended-spectrum beta-
lactamase-producing Enterobacteriaceae infection causing septic shock in cancer patients with
chemotherapy-induced febrile neutropenia. Internal and emergency medicine. 2019;14(3):433-40. 36. Pitout JDD, Laupland KB. Extended-spectrum β-lactamase-producing Enterobacteriaceae: an
emerging public-health concern. The Lancet Infectious Diseases. 2008;8(3):159-66. 36. Pitout JDD, Laupland KB. Extended-spectrum β-lactamase-producing Enterobacteriaceae: an
emerging public-health concern. The Lancet Infectious Diseases. 2008;8(3):159-66. 37. Alevizakos M, Mylonakis E. Colonization and infection with extended-spectrum beta-lactamase
producing Enterobacteriaceae in patients with malignancy. Expert Rev Anti Infect Ther. 2017;15(7):653-61. Page 12/18 Page 12/18 38. Schelenz S, Nwaka D, Hunter PR. Longitudinal surveillance of bacteraemia in haematology and
oncology patients at a UK cancer centre and the impact of ciprofloxacin use on antimicrobial
resistance. J Antimicrob Chemother. 2013;68(6):1431-8. 39. Satlin MJ, Cohen N, Ma KC, Gedrimaite Z, Soave R, Askin G, et al. Bacteremia due to carbapenem-
resistant Enterobacteriaceae in neutropenic patients with hematologic malignancies. J Infect. 2016;73(4):336-45. 40. Cornejo-Juarez P, Perez-Jimenez C, Silva-Sanchez J, Velazquez-Acosta C, Gonzalez-Lara F, Reyna-
Flores F, et al. Molecular analysis and risk factors for Escherichia coli producing extended-spectrum
beta-lactamase bloodstream infection in hematological malignancies. PloS one. 2012;7(4):e35780. 41. Rottier WC, Ammerlaan HS, Bonten MJ. Effects of confounders and intermediates on the association
of bacteraemia caused by extended-spectrum beta-lactamase-producing Enterobacteriaceae and
patient outcome: a meta-analysis. J Antimicrob Chemother. 2012;67(6):1311-20. 42. Table 1 coli
350
95
(27.1%)
52
21
(22.1%)
Disk
diffusion
Kim
SH
SC
2013
Korea
Adults
with
E
coli
and
96
23
8
4
MicroScan ESBL-PE only
Wang
SS
(31)
MC
retrospective
cohort
2011
Taiwan,
China
Wu UI (15)
SC
prospective
cohort
2012
Taiwan,
China
Kang
CI
(17)
MC
retrospective
cohort
2013
Korea
Gudiol
C
(29)
MC
retrospective
cohort
2017
Spain
Cattaneo
C (23)
MC
prospective
cohort
2018
Germany
Benanti
GE (32)
SC
retrospective
cohort
2019
USA
ESBL-PE and non-ESBL-PE
Trecarichi
EM (13)
SC
retrospective
cohort
2009
Italy
Gudiol
C
(27)
SC
prospective
cohort
2010
Spain
Cornejo-
Juarez
P
(40)
Case-control
study
2012
Mexico
Kang
CI
(14)
MC
retrospective
cohort
2012
Korea
Ha
YE
(16)
SC
retrospective
cohort
2013
Korea
Kim
SH
(18)
SC
retrospective
cohort
2013
Korea
Metan
G
(34)
SC
retrospective
cohort
2013
Turkey
Bodro
M
SC
2014
Spain ESBL-PE only
Wang
SS
(31)
MC
retrospective
cohort
2011
Taiwan,
China
Adults with solid
or hematological
malignancy
E. coli
and
Klebsiella
351
113
(32.2%)
35
35
(31.0%)
MicroScan
Wu UI (15)
SC
prospective
cohort
2012
Taiwan,
China
Adults with solid
or hematological
malignancy
E. coli
97
39
(40.2%)
10
10
(25.6%)
Disk
diffusion
Kang
CI
(17)
MC
retrospective
cohort
2013
Korea
Adults with solid
malignancy
E. coli
92
36
(39.1%)
6
6
(16.7%)
Microdilution
or
disk diffusion
Gudiol
C
(29)
MC
retrospective
cohort
2017
Spain
Adults
with
acute leukemia
and neutropenia
E. coli,
Klebsiella, and
Enterobacter
cloacae
NR
425
65
65
(15.3%)
Disk
diffusion
Cattaneo
C (23)
MC
prospective
cohort
2018
Germany
Adults
with
hematological
malignancy
E. coli,
Klebsiella, and
other
Enterobacter
spp
137
61
(44.5%)
10
10
(16.4%)
Microdilution
Benanti
GE (32)
SC
retrospective
cohort
2019
USA
Adults
with
hematological
malignancy
E. coli
NR
103
11
11
(10.7%)
NR
ESBL-PE and non-ESBL-PE
Trecarichi
EM (13)
SC
retrospective
cohort
2009
Italy
Adults
and
children
with
hematological
malignancy
E. coli
107
26
(24.3%)
13
11
(42.3%)
Disk
diffusion
Gudiol
C
(27)
SC
prospective
cohort
2010
Spain
Adults
and
children
with
solid
or
hematological
malignancy
E. coli
531
17
(3.2%)
29
6
(35.3%)
MicroScan
Cornejo-
Juarez
P
(40)
Case-control
study
2012
Mexico
Adults
and
children
with
hematological
malignancy
E. coli
670
100
(14.9%)
102
51
(51%)
MicroScan
Kang
CI
(14)
MC
retrospective
cohort
2012
Korea
Adults
with
hematological
malignancy
E. References Ben-Chetrit E, Eldaim MA, Bar-Meir M, Dodin M, Katz DE. Associated factors and clinical outcomes of
bloodstream infection due to extended-spectrum β-lactamase-producing Escherichia coli and
Klebsiella pneumoniae during febrile neutropenia. International journal of antimicrobial agents. 2019;53(4):423-8. Tables Page 13/18 Table 1 Characteristics of the studies and their populations included in the review. Characteristics of the studies and their populations included in the review. First
author
Design
Year
Country
Population
Infection
type - bacteria
No. of
screened
No. of
ESBL-
PE
BSIs
(%)
No. of
BSIs
caused
death
No. of
ESBL-
PE
BSIs
caused
death
(%)
ESBL
detection
method
ESBL-PE only
Wang
SS
(31)
MC
retrospective
cohort
2011
Taiwan,
China
Adults with solid
or hematological
malignancy
E. coli
and
Klebsiella
351
113
(32.2%)
35
35
(31.0%)
MicroScan
Wu UI (15)
SC
prospective
cohort
2012
Taiwan,
China
Adults with solid
or hematological
malignancy
E. coli
97
39
(40.2%)
10
10
(25.6%)
Disk
diffusion
Kang
CI
(17)
MC
retrospective
cohort
2013
Korea
Adults with solid
malignancy
E. coli
92
36
(39.1%)
6
6
(16.7%)
Microdilution
or
disk diffusion
Gudiol
C
(29)
MC
retrospective
cohort
2017
Spain
Adults
with
acute leukemia
and neutropenia
E. coli,
Klebsiella, and
Enterobacter
cloacae
NR
425
65
65
(15.3%)
Disk
diffusion
Cattaneo
C (23)
MC
prospective
cohort
2018
Germany
Adults
with
hematological
malignancy
E. coli,
Klebsiella, and
other
Enterobacter
spp
137
61
(44.5%)
10
10
(16.4%)
Microdilution
Benanti
GE (32)
SC
retrospective
cohort
2019
USA
Adults
with
hematological
malignancy
E. coli
NR
103
11
11
(10.7%)
NR
ESBL-PE and non-ESBL-PE
Trecarichi
EM (13)
SC
retrospective
cohort
2009
Italy
Adults
and
children
with
hematological
malignancy
E. coli
107
26
(24.3%)
13
11
(42.3%)
Disk
diffusion
Gudiol
C
(27)
SC
prospective
cohort
2010
Spain
Adults
and
children
with
solid
or
hematological
malignancy
E. coli
531
17
(3.2%)
29
6
(35.3%)
MicroScan
Cornejo-
Juarez
P
(40)
Case-control
study
2012
Mexico
Adults
and
children
with
hematological
malignancy
E. coli
670
100
(14.9%)
102
51
(51%)
MicroScan
Kang
CI
(14)
MC
retrospective
cohort
2012
Korea
Adults
with
hematological
malignancy
E. coli
and
Klebsiella
142
29
(20.4%)
29
13
(44.8%)
Microdilution
or
disk diffusion
Ha
YE
(16)
SC
retrospective
cohort
2013
Korea
Adults with solid
or hematological
malignancy
E. Table 1 coli
and
Klebsiella
142
29
(20.4%)
29
13
(44.8%)
Microdilution
or
disk diffusion
Ha
YE
(16)
SC
retrospective
cohort
2013
Korea
Adults with solid
or hematological
malignancy
E. coli
350
95
(27.1%)
52
21
(22.1%)
Disk
diffusion
Kim
SH
(18)
SC
retrospective
cohort
2013
Korea
Adults
with
hematological
malignancy and
FN
E. coli
and
Klebsiella
96
23
(24.0%)
8
4
(17.4%)
MicroScan
Metan
G
(34)
SC
retrospective
cohort
2013
Turkey
Adults
and
children
with
hematological
malignancy
E. coli,
Klebsiella, and
Enterobacter
cloacae
154
40
(26.0%)
30
5
(12.5%)
NR
Bodro
M
SC
2014
Spain
Adults with solid
Klebsiella and
392
19
18
4
Disk or hematological
malignancy
other
Enterobacter
spp
(4.8%)
(21.1%)
diffusion
Adults
and
children
with
solid
or
hematological
malignancy
Enterobacter
spp
203
31
(15.3%)
34
6
(19.4%)
Disk
diffusion
Children
with
solid
or
hematological
malignancy and
FN
E. coli
and
Klebsiella
59
21
(35.6%)
3
1
(4.8%)
VITEK®2
automat
system
Adults
with
acute
leukaemia
Enterobacter
spp
433
36
(8.3%)
37
5
(13.9%)
Microdil
or
disk diffu
Adults
with
hematological
malignancy
E. coli
168
97
(57.7%)
21
15
(15.5%)
Disk
diffusion
Adults with solid
or hematological
malignancy
E. coli
and
Klebsiella
122
70
(57.4%)
31
23
(32.9%)
VITEK®2
automat
system
Adults with solid
or hematological
malignancy
E. coli,
Klebsiella, and
Enterobacter
spp
496
123
(24.8%)
89
37
(30.1%)
Disk
diffusion
Adults with solid
or hematological
malignancy
E. coli
and
Klebsiella
88
26
(19.5%)
17
6
(7.5%)
NR
Adults
and
children
with
solid
or
hematological
malignancy
E. coli
and
Klebsiella
945
238
(25.2%)
107
45
(18.9%)
NR
Adults with solid
or hematological
malignancy and
FN
E. coli
and
Klebsiella
179
23
(12.8%)
51
8
(34.8%)
MicroSc
Adults with solid
or hematological
malignancy
E. coli,
Klebsiella, and
Enterobacter
spp
65
42
(64.6%)
13
9
(21.4%)
NR
Adults with solid
or hematological
malignancy
E. coli
324
160
(49.3%)
71
39
(24.4%)
VITEK®2
automat
system
-lactamase-producing Enterobacteriaceae; BSI, bloodstream infection; SC, single-center;
openia tive
or hematological
malignancy
other
Enterobacter
spp
(4.8%)
(21.1%)
tive
2014
Korea
Adults
and
children
with
solid
or
hematological
malignancy
Enterobacter
spp
203
31
(15.3%)
34
6
(19.4%)
ctive
2015
Korea
Children
with
solid
or
hematological
malignancy and
FN
E. coli
and
Klebsiella
59
21
(35.6%)
3
1
(4.8%)
tive
2016
Italy
Adults
with
acute
leukaemia
Enterobacter
spp
433
36
(8.3%)
37
5
(13.9%)
ctive
2017
China
Adults
with
hematological
malignancy
E. Table 1 coli
168
97
(57.7%)
21
15
(15.5%)
ctive
2018
Turkey
Adults with solid
or hematological
malignancy
E. coli
and
Klebsiella
122
70
(57.4%)
31
23
(32.9%)
tive
2018
Mexico
Adults with solid
or hematological
malignancy
E. coli,
Klebsiella, and
Enterobacter
spp
496
123
(24.8%)
89
37
(30.1%)
ctive
2019
Israel
Adults with solid
or hematological
malignancy
E. coli
and
Klebsiella
88
26
(19.5%)
17
6
(7.5%)
ntrol
2019
Sweden
Adults
and
children
with
solid
or
hematological
malignancy
E. coli
and
Klebsiella
945
238
(25.2%)
107
45
(18.9%)
tive
2019
Korea
Adults with solid
or hematological
malignancy and
FN
E. coli
and
Klebsiella
179
23
(12.8%)
51
8
(34.8%)
ntrol
2019
Japan
Adults with solid
or hematological
malignancy
E. coli,
Klebsiella, and
Enterobacter
spp
65
42
(64.6%)
13
9
(21.4%)
ctive
2019
China
Adults with solid
or hematological
malignancy
E. coli
324
160
(49.3%)
71
39
(24.4%)
PE, extended-spectrum β-lactamase-producing Enterobacteriaceae; BSI, bloodstream infection; SC, sing (19)
prospective
cohort
Kim
SJ
(28)
SC
prospective
cohort
2014
Korea
Han
SB
(20)
SC
retrospective
cohort
2015
Korea
Cattaneo
C (21)
MC
prospective
cohort
2016
Italy
Ma J (22)
SC
retrospective
cohort
2017
China
Çeken
S
(24)
SC
retrospective
cohort
2018
Turkey
Islas-
Muñoz
B
(25)
SC
prospective
cohort
2018
Mexico
Ben-
Chetrit E
(42)
SC
retrospective
cohort
2019
Israel
Isendahl J
(26)
Case-control
study
2019
Sweden
Kim
YJ
(35)
SC
prospective
cohort
2019
Korea
Namikawa
H (30)
Case-control
study
2019
Japan
Zhang
Q
(33)
SC
retrospective
cohort
2019
China
Abbreviations: ESBL-PE, extended-spectrum β
multicenter; NR, not reported; FN, febrile neut (19) Page 15/18 Page 15/18 Page 15/18 Page 15/18 2 oup analysis for meta-analysis of mortality. reviations: ESBL-PE, extended-spectrum β-lactamase-producing Enterobacteriaceae; CCI, Charlson Index Score; ICU, intensive care unit;
efers to the variables for which data were reported in the individual studies. r heterogeneity within each subgroup. r heterogeneity within each subgroup. r heterogeneity between subgroups with meta-regression analyses. Figures Figures Figures Page 17/18
Figure 1
Flow chart of the eligible studies for meta-analysis. Table 1 p
y
y
y
bles
No
RR (95% CI)
I2
Pa
Pb
n
Retrospective cohort
10
1.72(1.38-2.14)
62.2%
0.005
0.395
Prospective cohort
6
2.02(1.57-2.60)
75.7%
0.001
Case-control study
3
3.11(2.47-3.92)
90.2%
<0.001
n
Europe
5
2.79(2.10-3.69)
78.2%
0.001
0.014
Asia
12
1.49(1.22-1.82)
27.3%
0.177
North America
2
3.47(2.73-4.41)
93.5%
<0.001
ation
Adults and children
7
2.80(2.29-3.43)
88.3%
<0.001
0.303
Adults
12
1.80(1.50-2.15)
28.4%
0.167
nancy type
Hematological
7
3.20(2.54-4.03)
83.0%
<0.001
0.355
Solid or hematological
12
1.81(1.54-2.14)
60.9%
0.003
Yes
3
1.48(0.87-2.53)
0.0%
0.418
0.530
No
16
2.21(1.92-2.54)
80.8%
<0.001
detection methods
Disk diffusion
6
2.21(1.72-2.83)
64.6%
0.015
0.554
MicroScan
4
3.99(3.10-5.15)
85.9%
<0.001
<6
2
0.76(0.39-1.49)
16.5%
0.274
0.065
≥6
17
2.30(2.00-2.64)
77.3%
<0.001
viations: RR, relative risk; CI, confidence interval; FN, febrile neutropenia; ESBL, extended-spectrum β-lactamase; NOS, Newcastle-
a scale le 3 most commonly studied characteristics as predictors of mortality in the reviewed studiesa. k factor
ESBL-PE only studies
n/N (%)
ESBL-PE vs
non- ESBL-PE
studies
n/N (%)
Total
n/N (%)
Identified as independent
predictor for mortality
5/6 (83.3)
13/19 (68.4)
18/25 (72.0)
0+0
der
4/6 (66.7)
11/19 (57.9)
15/25 (60.0)
0+1(22)
1/6 (16.7)
4/19 (21.1)
5/25 (20.0)
0+2(16, 42)
L production
1/6 (16.7)
12/19 (63.2)
13/25 (52.0)
0+3(13, 14, 16)
tropenia
2/6 (33.3)
11/19 (57.9)
13/25 (52.0)
0+4(13, 14, 24, 35)
dequate initial antimicrobial treatment
3/6 (50.0)
13/19 (68.4)
16/25 (64.0)
0+3(13, 19, 25)
admission
2/6 (33.3)
6/19 (31.6)
8/25 (32.0)
0+5(14, 19, 27, 33, 34)
munosuppressant use
0
3/19 (15.8)
3/25 (12.0)
0+1(14)
welling urinary catheter
2/6 (33.3)
1/19 (5.3)
3/25 (12.0)
1(23)+1(14)
cting organism, Klebsiella pneumoniae
0
5/19 (26.3)
5/25 (20.0)
0+1(18)
a-abdominal infection
4/6 (66.7)
3/19 (15.8)
7/25 (28.0)
0+1(28)
hanical ventilation
0
2/19 (10.5)
2/25 (8.0)
0+1(16)
astasis
0
1/19 (5.3)
1/25 (4.0)
0+1(33)
an failure
1/6 (16.7)
2/19 (10.5)
3/25 (12.0)
0+1(33)
umonia
1/6 (16.7)
5/19 (26.3)
6/25 (24.0)
1(31)+4(14, 16, 21, 28)
bacteremia score
4/6 (66.7)
4/19 (21.1)
8/25 (32.0)
1(32)+2(14, 42)
ere sepsis/ septic shock
3/6 (50.0)
11/19 (57.9)
14/25 (56.0)
1(31)+8(14, 16, 18, 19, 22, 24, 28, 33)
d tumor
3/6 (50.0)
8/19 (42.1)
11/25 (44.0)
0+1(27)
ultaneous corticosteroid therapy
0
8/19 (42.1)
8/25 (32.0)
0+2(19, 27)
reviations: ESBL-PE, extended-spectrum β-lactamase-producing Enterobacteriaceae; CCI, Charlson Index Score; ICU, intensive care unit; most commonly studied characteristics as predictors of mortality in the reviewed studiesa. Page 16/18 Figure 2 Forest plots of mortality in BSIs due to ESBL-PE among patients with malignancy. RR, relative risk; CI,
confidence interval; BSIs, bloodstream infections; Weights are from random-effects analysis. The size of
the squares is analogous to the study's weight. Diamonds represent the pooled RRs and their confidence
interval. Figure 1 Flow chart of the eligible studies for meta-analysis. Page 17/18 Page 17/18 Additionalfile1.pdf Supplementary Files This is a list of supplementary files associated with this preprint. Click to download. Page 18/18
|
https://openalex.org/W2908998255
|
https://europepmc.org/articles/pmc6359204?pdf=render
|
English
| null |
A Handy Flexible Micro-Thermocouple Using Low-Melting-Point Metal Alloys
|
Sensors
| 2,019
|
cc-by
| 8,364
|
Received: 5 December 2018; Accepted: 10 January 2019; Published: 14 January 2019 Abstract: A handy, flexible micro-thermocouple using low-melting-point metal alloys is proposed in
this paper. The thermocouple has the advantages of simple fabrication and convenient integration. Bismuth/gallium-based mixed alloys are used as thermocouple materials. To precisely inject the metal
alloys to the location of the sensing area, a micro-polydimethylsiloxane post is designed within the
sensing area to prevent outflow of the metal alloy to another thermocouple pole during the metal-alloy
injection. Experimental results showed that the Seebeck coefficient of this thermocouple reached
−10.54 µV/K, which was much higher than the previously reported 0.1 µV/K. The thermocouple was
also be bent at 90◦more than 200 times without any damage when the mass ratio of the bismuth-based
alloy was <60% in the metal-alloy mixture. This technology mitigated the difficulty of depositing
traditional thin–film thermocouples on soft substrates. Therefore, the thermocouple demonstrated its
potential for use in microfluidic chips, which are usually flexible devices. Keywords: micro-thermocouple; flexible sensor; low-melting-point alloys; liquid metal Sensors 2019, 19, 314; doi:10.3390/s19020314 sensors sensors sensors A Handy Flexible Micro-Thermocouple Using
Low-Melting-Point Metal Alloys Qifu Wang 1,2
, Meng Gao 1
, Lunjia Zhang 1,2, Zhongshan Deng 1,2 and Lin Gui 1,2,*
1
CAS Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of
Sciences, Beijing 100190, China; wangqifu16@mails.ucas.ac.cn (Q.W.); mgao@mail.ipc.ac.cn (M.G.);
zhanglunjia14@mails.ucas.ac.cn (L.Z.); zsdeng@mail.ipc.ac.cn (Z.D.)
2
School of Future Technology, University of Chinese Academy of Sciences, Beijing 100149, China
*
Correspondence: lingui@mail.ipc.ac.cn; Tel.: +86-10-8254-3483 Qifu Wang 1,2
, Meng Gao 1
, Lunjia Zhang 1,2, Zhongshan Deng 1,2 and Lin Gui 1,2,*
1
CAS Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of
Sciences, Beijing 100190, China; wangqifu16@mails.ucas.ac.cn (Q.W.); mgao@mail.ipc.ac.cn (M.G.);
zhanglunjia14@mails.ucas.ac.cn (L.Z.); zsdeng@mail.ipc.ac.cn (Z.D.)
2
School of Future Technology, University of Chinese Academy of Sciences, Beijing 100149, China
*
Correspondence: lingui@mail.ipc.ac.cn; Tel.: +86-10-8254-3483 Qifu Wang 1,2
, Meng Gao 1
, Lunjia Zhang 1,2, Zhongshan Deng 1,2 and Lin Gui 1,2,*
1
CAS Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of
Sciences, Beijing 100190, China; wangqifu16@mails.ucas.ac.cn (Q.W.); mgao@mail.ipc.ac.cn (M.G.);
zhanglunjia14@mails.ucas.ac.cn (L.Z.); zsdeng@mail.ipc.ac.cn (Z.D.)
2
School of Future Technology, University of Chinese Academy of Sciences, Beijing 100149, China
*
Correspondence: lingui@mail.ipc.ac.cn; Tel.: +86-10-8254-3483 1. Introduction Temperature is one of the most important physical signals in many microfluidic applications. For example, the rate of temperature change in the sub-microliter-scale polymerase chain reaction
(PCR) directly affects the efficiency of DNA extraction and separation [1,2]. Temperature gradient can
help to separate ionic species in a microchannel or a capillary device [3]. Variations in temperature in a
microreactor illustrate the process of chemical reaction [4]. A single cell may have a gene mutation
because of a temperature change [5]. Thermocouples [6,7], thermal resistance sensors [8], and optical methods [9,10] are traditionally
usually used to measure microfluidic temperature. Optical systems can measure the entire microfluidic
channel when thermo-photosensitive reagents are dispersed throughout the sample fluid. However,
these sensitive reagents contaminate the sample fluid. Solid-metal thin films are widely used to fabricate thermocouples or thermal-resistance sensors
by deposition or sputtering [11]. These thin-film sensors have high resolution and quick response
because of their small size (usually nanometer-level thickness). However, thin-film sensors have some
limitations. For example, the process of deposition or sputtering solid metal onto a rigid substrate is
complicated, expensive, and time-consuming. Solid-metal thin films also usually have a coefficient of
thermal expansion (CTE) different from that of the substrate. Consequently, thin-film sensors have
been easily damaged when temperatures rise [8]. Moreover, they have been proven unsuitable for some
microfluidic systems requiring flexibility and deformation. With the development of microfluidics,
a demand has emerged to develop a flexible temperature microsensor with simple fabrication. Sensors 2019, 19, 314; doi:10.3390/s19020314 www.mdpi.com/journal/sensors 2 of 11 Sensors 2019, 19, 314 Low-melting-point metals or alloys (gallium, gallium-based alloys, and bismuth-based alloys)
have been used in microfluidic systems. An important merit of these metals or alloys is that they
remain liquid around room temperature. They can be easily injected into microchannels to fabricate
microdevices using a handy syringe [12]. In particular, these microdevices can work well even if they
are heated, bended, or twisted [13]. In 2007, for the first time, Siegel et al. [14] proposed a method of
fabricating metallic microstructures in microchannels by injecting liquid solder at 180 ◦C. Recently,
a room-temperature, gallium-based-alloy liquid metal was used to fabricate many devices in microscale
channels, such as an electroosmotic flow pump [15], sensors [16,17], antennas [18], and electrodes [19]. Dickey et al. [12] used liquid metal to fabricate a stable microstructure in a microchannel in 2008. Gao et al. 1. Introduction [20] proposed a liquid-metal resistance temperature detector to measure the microscale
temperature from 20 ◦C to 70 ◦C. They also demonstrated a fast-thermal response microfluidic system
using liquid metal in 2016 [21]. However, the shape of the liquid–metal microchannel has an important
impact on the thermal resistance of the sensor. The resistance of the liquid-metal microstructure
changes largely when the sensor is bent or twisted [16]. Conversely, thermocouples do not have this
shortcoming because the Seebeck coefficient of their material is irrelevant to their shape and size. However, the Seebeck coefficient of thermocouples fabricated using room-temperature
gallium-based-alloy liquid metal is very small (0.1 µV/K) and cannot be measured easily using
normal equipment [20,22]. Bismuth has a much higher Seebeck coefficient (−75.4 µV/K) than
indium (6.9 µV/K), tin (4.2 µV/K), and gallium (0.1 µV/K) with a platinum electrode as the
connection wire [20,23]. Thus, in the present work, we present a bismuth-based alloy combined
with a room-temperature gallium-based-alloy liquid metal to fabricate a flexible thermocouple with a
high Seebeck coefficient. 2.1. Preparation of Metal Alloys Room temperature liquid-metal eutectic gallium–indium–tin alloy (EGaInSn; 68.5% Ga 21.5%
In, 13% Sn by weight; 11 ◦C melting point) was used to fabricate one pole of the thermocouple. Two
low-melting-point Bi-based metal–alloy mixtures, namely, EBiIn–EGaInSn and EBiInSn–EGaInSn,
were used to fabricate the other pole of the thermocouple. EBiIn–EGaInSn is a mixture of
eutectic bismuth–indium (EBiIn; 67% Bi 33% In by weight; 109 ◦C melting point) and eutectic
gallium–indium–tin (EGaInSn; 68.5% Ga 21.5% In 13% Sn by weight; 11 ◦C melting point). EBiInSn–EGaInSn is a mixture of eutectic bismuth–indium–tin (EBiInSn; 32.5% Bi 51% In 15.5%
Sn by weight; 60 ◦C melting point) and eutectic gallium–indium–tin (EGaInSn; 68.5% Ga 21.5% In 13%
Sn by weight; 11 ◦C melting point). To prepare these two mixtures, a fixed mass of solid EBiIn or a fixed mass of EBiInSn was initially
placed on a thermostatic plate at 125 ◦C. When the solid EBiIn or EBiInSn melted, a fixed mass of
EGiInSn was added into EBiIn or EBiInSn. After stirring the mixture with a glass rod for 3 min,
an EBiIn–EGaInSn mixture was obtained. Six mixtures of EBiIn–EGaInSn or EBiInSn–EGaInSn (40%,
50%, 60%, 70%, 80%, and 90% mass ratio of EBiIn or EBiInSn in total mixture) were prepared to
determine the optimal mixture for fabricating the thermocouples. 2.2. Chip Design and Fabrication (c) Local map of the thermocouple chip showing that one pole
of the thermocouple channel was filled with the mixture and another pole was filled with EGaInSn. (d) Sketch of bending test. (e) Sketch of temperature-measurement test. A 20 μm-thick
polydimethylsiloxane (PDMS) membrane was placed between the thermocouple and the microheater
Figure 1. (a) Schematic of the ohm-shape micro-thermocouple; one pole of the channel was filled
with EGaInSn, and the other pole of the thermocouple was filled with low-melting-point Bi-based
metal–alloy mixture. (b) Zoom in of schematic (a), wherein EGaInSn and the mixture converged
at the middle of the channel (sensing area). (c) Local map of the thermocouple chip showing
that one pole of the thermocouple channel was filled with the mixture and another pole was
filled with EGaInSn. (d) Sketch of bending test. (e) Sketch of temperature-measurement test. A 20 µm-thick polydimethylsiloxane (PDMS) membrane was placed between the thermocouple and
the microheater chip. chip. 3. Results and Discussion
Low-melting-point Bi-based alloys as the material of thermocouples have higher Seebeck
coefficient than room-temperature Ga-based alloys. However, Bi-based alloys are easily damaged
after filling and solidifying into microchannels because of their brittleness [19]. To prevent this
problem, mixtures with Bi-based alloy and EGaInSn were proposed in this work. Figure 2 shows the images of six EBiIn–EGaInSn alloys and six EBiInSn–EGaInSn alloys with
different mass ratios of Bi-based alloy in mixtures. As shown in Figure 2ai,bi, the mixture with 40%
A challenge for injecting these two different metal alloys into the microchannel to fabricate
thermocouples was that both metal alloys had to flow smoothly in the microchannel and accurately
stop at the sensing area. When injecting one of these two metal alloys into its thermocouple pole,
overflowing to another thermocouple pole was easy, leading to thermocouple fabrication failure. To prevent this problem, we designed a micro-PDMS post within the sensing area to increase the
flow resistance of metal alloy and serve as a control point for the injection of metal alloy. As shown
in Figure 1b, the micro-PDMS post (50 µm long and 30 µm wide) was fabricated at the intersection
of these two thermocouple poles to ensure that the EGaInSn and the Bi-based metal–alloy mixture
converged well at the micro-PDMS post. To vent the air from the microchannel when injecting metal
alloys, a 30 µm-wide small microchannel was fabricated near the sensing area (Figure 1b). 2.2. Chip Design and Fabrication Figure 1a shows the microfluidic chip embedded with a handy, flexible micro-thermocouple
using low-melting-point metal alloys. This microfluidic chip consisted of a polydimethylsiloxane
(PDMS) slab (1 mm thick) and a PDMS membrane (50 µm thick). The PDMS slab had an ohm-shape
microchannel (5 cm long, 100 µm wide, and 50 µm high) for the thermocouple. Two identical injection
holes were designed 2.5 mm away from the microchannel. One pole of the thermocouple microchannel
was filled with EGaInSn, and the other was filled with the Bi-based metal–alloy mixture. The PDMS
gap between these two thermocouple poles was 100 µm. 3 of 11
en the Sensors 2019, 19, 314
placed over the
th
l (a)
(b)
(c)
(d)
(e)
Figure 1. (a) Schematic of the ohm-shape micro-thermocouple; one pole of the channel was filled with
EGaInSn, and the other pole of the thermocouple was filled with low-melting-point Bi-based metal–
alloy mixture. (b) Zoom in of schematic (a), wherein EGaInSn and the mixture converged at the
middle of the channel (sensing area). (c) Local map of the thermocouple chip showing that one pole
of the thermocouple channel was filled with the mixture and another pole was filled with EGaInSn. (d) Sketch of bending test. (e) Sketch of temperature-measurement test. A 20 μm-thick
polydimethylsiloxane (PDMS) membrane was placed between the thermocouple and the microheater
Figure 1. (a) Schematic of the ohm-shape micro-thermocouple; one pole of the channel was filled
with EGaInSn, and the other pole of the thermocouple was filled with low-melting-point Bi-based
metal–alloy mixture. (b) Zoom in of schematic (a), wherein EGaInSn and the mixture converged
at the middle of the channel (sensing area). (c) Local map of the thermocouple chip showing
that one pole of the thermocouple channel was filled with the mixture and another pole was
filled with EGaInSn. (d) Sketch of bending test. (e) Sketch of temperature-measurement test. A 20 µm-thick polydimethylsiloxane (PDMS) membrane was placed between the thermocouple and
the microheater chip. (a)
(b)
( (b) (c) (a) (a) (b) (c) (d) (e) (d) (e) Figure 1. (a) Schematic of the ohm-shape micro-thermocouple; one pole of the channel was filled with
EGaInSn, and the other pole of the thermocouple was filled with low-melting-point Bi-based metal–
alloy mixture. (b) Zoom in of schematic (a), wherein EGaInSn and the mixture converged at the
middle of the channel (sensing area). 2.2. Chip Design and Fabrication All chips for thermocouples were fabricated by standard soft-lithography. SU-8 2050 (MicroChem
Corp., Worcester, MA, USA) was used to fabricate 50 µm-high microchannel patterns for thermocouple
poles on a 4-in silicon wafer. Liquid PDMS (PDMS monomer and a curing agent at a 10:1 ratio by
weight, Dow Corning Corp., Wiesbaden, Germany) was directly poured onto the pattern to fabricate
the PDMS slab containing thermocouple poles. Then, the PDMS slab was peeled off from the wafer
after being cured at 60 ◦C for 2.5 h. To obtain the PDMS membrane (50 µm thick), liquid PDMS was
spin-coated on a silicon wafer (speed, 1500 rpm; spin time, 30 s) and then baked at 75 ◦C for 30 min. The PDMS slab and the PDMS membrane were irreversibly bonded together using oxygen plasma
treatment (plasma cleaner, YZD08-2C, Tangshan Yanzhao Technology, Tangshan, China). Sensors 2019, 19, 314 4 of 11 The EGaInSn and the Bi-based metal–alloy mixture were injected into the microchannels using a
syringe. The mixture was initially melted on a thermostatic plate at 125 ◦C, and then filled into the pole
of the microchannel from the injection hole using an electrical heating syringe (110 ◦C). By adjusting
the injection pressure and time, the mixture flowed smoothly into the microchannel and stopped when
it came into contact with the micro-PDMS post. After cooling this mixture to room temperature in the
microchannel, the EGaInSn was then injected into different pole of the microchannel than the injection
hole. To keep full contact with the mixture around the micro-PDMS post, EGaInSn was pumped into
the microchannel for a much longer injection time until it overflowed from the small microchannel near
the sensing area (Figure 1c). Finally, copper-leading wires (200 µm diameter) were inserted into the
two injection holes, which were sealed with a package adhesive sealant (705 RTV Transparent Silicone
Rubber). The outflow reservoir of the small microchannel was also sealed using this adhesive sealant. 2.5. Calibration To calibrate the fabricated thermocouples, the sensing area of each thermocouple was placed
onto a thermostatic plate, and the other part of the thermocouple with copper-leading wires was
fully immersed in an ice–water mixture. Standard K-type thermocouples were used to measure the
temperature of the thermostatic plate and the ice–water mixture. The thermoelectric potential was
monitored with an Agilent 34970A (Keysight Technologies, Santa Rosa, CA, USA). During calibration,
the temperature of the thermostatic plate increased by 5 ◦C after each test and was maintained for
3 min. The data acquisition frequency was 2 Hz. 2.3. DSC Measurement To understand the physical properties of the low-melting-point Bi-based metal–alloy mixture,
differential scanning calorimetry (DSC) was performed. The rates of temperature-up and
temperature-down were 10 ◦C/min. 2.7. Temperature Measurement of Microheater To test the performance of the thermocouple in a microscale temperature measurement,
a microfluidic chip with an EGaInSn liquid-metal microheater was fabricated. As shown in Figure 1e,
the channel width of the heating area in the microheater was 100 µm and the channel width of the
extended section was 200 µm. The resistance of the microheater was 3.6 Ω. The thermocouple was
placed over the microheater. A 20 µm-thick PDMS membrane was placed between the thermocouple
and the microheater (Figure 1e). A DC power supply (DH1720A, DaHua Power, resolution 15 mA)
was used to apply heating voltages to the microheater. 2.6. Bending Test To test the bending performance of these thermocouples, they were suspended on a flat panel. The thermocouples were bent 200 times at 90◦bending angle (Figure 1d). 2.4. Electron Microscope Observation To analyze the morphology features of these metal–alloy mixtures, these materials were observed
in the electron microscope. The shape, size, and stoichiometry of the materials were obtained. 3. Results and Discussion Low-melting-point Bi-based alloys as the material of thermocouples have higher Seebeck
coefficient than room-temperature Ga-based alloys. However, Bi-based alloys are easily damaged after
filling and solidifying into microchannels because of their brittleness [19]. To prevent this problem,
mixtures with Bi-based alloy and EGaInSn were proposed in this work. 5 of 11 Sensors 2019, 19, 314 Figure 2 shows the images of six EBiIn–EGaInSn alloys and six EBiInSn–EGaInSn alloys with
different mass ratios of Bi-based alloy in mixtures. As shown in Figure 2ai,bi, the mixture with 40%
Bi-based alloy and 60% EGalnSn was liquid, with some solid particles, at room temperature. When
the mass ratio of Bi-based alloy reached 60%, the mixture remained sticky but still was not fully
solidified (Figure 2a(iii),b(iii)). When the mass ratio of the Bi-based alloy was close to or more than
70%, the mixture became a powdery solid after cooling (Figure 2a(iv–vi),b(iv–vi)). The mixture with
less than 40% mass ratio of Bi-based alloy was not considered because it did not have sufficient solid
particles filled in the microchannel, which led to the easy movement of solid particles within the liquid
metal. As a result, the mixture easily back-flowed from the channel when EGaInSn was injected from
the other pole of the channel. The 100% mass ratio of Bi-based alloy was also not considered because
of its brittleness. nsors 2019, 19, x FOR PEER REVIEW
5 of 10
i-based alloy and 60% EGalnSn was liquid, with some solid particles, at room temperature. When
he mass ratio of Bi-based alloy reached 60%, the mixture remained sticky but still was not fully
olidified (Figure 2aiii,2biii). When the mass ratio of the Bi-based alloy was close to or more than 70%,
he mixture became a powdery solid after cooling (Figure 2aiv–vi,biv–vi). The mixture with less than
0% mass ratio of Bi-based alloy was not considered because it did not have sufficient solid particles
lled in the microchannel, which led to the easy movement of solid particles within the liquid metal. s a result, the mixture easily back-flowed from the channel when EGaInSn was injected from the
ther pole of the channel. The 100% mass ratio of Bi-based alloy was also not considered because of
s brittleness. (a)
(b)
Figure 2. (a) Image of different mass ratios of EBiInSn in mixture. (b) Image of different mass ratios
of EBiIn in mixture. 3. Results and Discussion With increased mass ratio of bismuth-based alloy, the mixture changes from a
liquid to a powdery solid. Scale bars: 1 mm (the experimental mixing videos (S1 and S2) are included
in the Supplementary Materials). Figure 2. (a) Image of different mass ratios of EBiInSn in mixture. (b) Image of different mass ratios of
EBiIn in mixture. With increased mass ratio of bismuth-based alloy, the mixture changes from a liquid
to a powdery solid. Scale bars: 1 mm (the experimental mixing videos (S1 and S2) are included in the
Supplementary Materials). (a) (a) (a) (b) gure 2. (a) Image of different mass ratios of EBiInSn in mixture. (b) Image of different mass ratios
EBiIn in mixture. With increased mass ratio of bismuth-based alloy, the mixture changes from a
uid to a powdery solid. Scale bars: 1 mm (the experimental mixing videos (S1 and S2) are included
the Supplementary Materials). Figure 2. (a) Image of different mass ratios of EBiInSn in mixture. (b) Image of different mass ratios of
EBiIn in mixture. With increased mass ratio of bismuth-based alloy, the mixture changes from a liquid
to a powdery solid. Scale bars: 1 mm (the experimental mixing videos (S1 and S2) are included in the
Supplementary Materials). As shown in Figure 3, all the mixtures were scanned in the scanning electron microscope (SEM). igure 3a,b show the SEM images for the textures of different ratio of bismuth/gallium-based alloy
mixtures. In order to reveal the distribution of metal elements, all of these textures were examined
hrough energy dispersive spectrum and Figure 3c shows the results from the alloy mixture with 80%
i-based alloy. Comparing Figure 3cii,cv or 3cvii,cx, it is found that the distribution of Ga and Bi is
ot uniform, and they seem to “repel” each other, which indicates that Ga and Bi do not mix in
microscale. Figure 3ciii or Figure 3d shows the distribution map of In in 80% EBiInSn. As shown in
igure 3d, the red dashes and yellow dashes represent the area of Bi and Ga, respectively. It can be
een that the distribution of In in the red (Bi) area was much heavier than that in the yellow (Ga) area,
which means that the In in the Bi-based alloy did not diffuse into Ga-based alloy. 3. Results and Discussion On the contrary, as
hown in Figure 3civ,3cix, Sn distributed almost uniformly throughout the whole area, except in the
mpty space SEM cannot detect. What should be pointed out is that, in Figure 3cix, the Sn was
upposed to be absent in the Bi area because EBiIn did not contain any Sn before the mixing. The Sn
was still quite uniformly distributed in the whole area, both in Ga–area and Bi–area, which means
he Sn entered EBiIn very easily during the mixing. In summary, the Ga-based alloy and Bi-based
loy are thoroughly intermingled with each other and filled the entire space (SEM images for the
mixture with other ratios can be found in the Supplementary Materials). As shown in Figure 3, all the mixtures were scanned in the scanning electron microscope (SEM). Figure 3a,b show the SEM images for the textures of different ratio of bismuth/gallium-based alloy
mixtures. In order to reveal the distribution of metal elements, all of these textures were examined
through energy dispersive spectrum and Figure 3c shows the results from the alloy mixture with 80%
Bi-based alloy. Comparing Figure 3cii,cv or Figure 3c(vii,cx), it is found that the distribution of Ga and
Bi is not uniform, and they seem to “repel” each other, which indicates that Ga and Bi do not mix in
microscale. Figure 3c(iii) or Figure 3d shows the distribution map of In in 80% EBiInSn. As shown
in Figure 3d, the red dashes and yellow dashes represent the area of Bi and Ga, respectively. It can
be seen that the distribution of In in the red (Bi) area was much heavier than that in the yellow (Ga)
area, which means that the In in the Bi-based alloy did not diffuse into Ga-based alloy. On the contrary,
as shown in Figure 3c(iv,cix), Sn distributed almost uniformly throughout the whole area, except in
the empty space SEM cannot detect. What should be pointed out is that, in Figure 3c(ix), the Sn was
supposed to be absent in the Bi area because EBiIn did not contain any Sn before the mixing. The Sn
was still quite uniformly distributed in the whole area, both in Ga–area and Bi–area, which means the
Sn entered EBiIn very easily during the mixing. 3. Results and Discussion In summary, the Ga-based alloy and Bi-based alloy are
thoroughly intermingled with each other and filled the entire space (SEM images for the mixture with
other ratios can be found in the Supplementary Materials). 6 of 11
6 of 10 Sensors 2019, 19, 314
Sensors 2019, 19, x FO (a)
(b)
(c)
(d)
Figure 3. (a) SEM graphics of EBiInSn-based alloy mixtures. (b) SEM graphics of EBiIn-based alloy
mixtures. (c) Energy spectrum diagram of 80% Bi-based alloy mixtures. The element gallium and
bismuth were intermingled with each other, filling the entire space. (d) Distribution map of
In in 80% EBiInSn. The area in red dashes and the yellow dashes represent the area of Bi
and Ga respectively
Figure 3. (a) SEM graphics of EBiInSn-based alloy mixtures. (b) SEM graphics of EBiIn-based alloy
mixtures. (c) Energy spectrum diagram of 80% Bi-based alloy mixtures. The element gallium and
bismuth were intermingled with each other, filling the entire space. (d) Distribution map of In in 80%
EBiInSn. The area in red dashes and the yellow dashes represent the area of Bi and Ga, respectively. (a) (a) (c) (c) (c) (c)
(d) (d) Figure 3. (a) SEM graphics of EBiInSn-based alloy mixtures. (b) SEM graphics of EBiIn-based alloy
mixtures. (c) Energy spectrum diagram of 80% Bi-based alloy mixtures. The element gallium and
bismuth were intermingled with each other, filling the entire space. (d) Distribution map of
In in 80% EBiInSn. The area in red dashes and the yellow dashes represent the area of Bi
Figure 3. (a) SEM graphics of EBiInSn-based alloy mixtures. (b) SEM graphics of EBiIn-based alloy
mixtures. (c) Energy spectrum diagram of 80% Bi-based alloy mixtures. The element gallium and
bismuth were intermingled with each other, filling the entire space. (d) Distribution map of In in 80%
EBiInSn. The area in red dashes and the yellow dashes represent the area of Bi and Ga, respectively. and Ga, respectively. To identify the specific ingredients of the mixtures, we performed DSC tests on all mixtures. Figure 4a shows the DSC phase diagrams of the Bi-based alloy mixture with 50% mass ratio of
EBiInSn. Four peaks indicate that the mixture comprised two metal alloys with different melting
points. The first and fourth peaks represented the melting endothermic process and the solidification
exothermic process of one metal alloy in the mixture, respectively. 3. Results and Discussion Figure 4a clearly shows that the
melting point was 11.06 °C and the solidification temperature was –42.61 °C. This melting point was
equal to the melting point of EGaInSn. Thus, the liquid portion of the mixture was EGaInSn at room
temperature. Similarly, the melting and freezing points of the second metal were 42.00 and 32.72 °C. The melting point of this metal was lower than that of EBiInSn (60 °C). This metal may be a new
metal–alloy mixture of EBiInSn and EGaInSn. The formation of this new metal can be explained from
To identify the specific ingredients of the mixtures, we performed DSC tests on all mixtures. Figure 4a shows the DSC phase diagrams of the Bi-based alloy mixture with 50% mass ratio of
EBiInSn. Four peaks indicate that the mixture comprised two metal alloys with different melting
points. The first and fourth peaks represented the melting endothermic process and the solidification
exothermic process of one metal alloy in the mixture, respectively. Figure 4a clearly shows that the
melting point was 11.06 ◦C and the solidification temperature was –42.61 ◦C. This melting point was
equal to the melting point of EGaInSn. Thus, the liquid portion of the mixture was EGaInSn at room
temperature. Similarly, the melting and freezing points of the second metal were 42.00 and 32.72 ◦C. The melting point of this metal was lower than that of EBiInSn (60 ◦C). This metal may be a new
metal–alloy mixture of EBiInSn and EGaInSn. The formation of this new metal can be explained
from the energy spectrum. As mentioned above, in the energy spectrum analysis, during the mixing, 7 of 11
on was Sensors 2019, 19, 314
ge e ate t is
ew
As shown in Sn transferred between Ga-based alloy and Bi-based alloy easily. The Sn transfer phenomena may
generate this new alloy. Supplementary Materials) with the increment of the portion of Bi-based alloy, the peak of EGaInSn
decreased and the new metal alloy increased. It can also be seen that the liquid portion of the mixture
decreased and the solid portion increased with the mass ratio increment of Bi-based alloy p
y
(a)
(b)
Figure 4. (a) Differential scanning calorimetry (DSC) phase diagram of mixture with 50% mass ratio
of EBiInSn. (b) DSC phase diagram of mixture with 50% mass ratio of EBiIn. Figure 4. 3. Results and Discussion (a) Differential scanning calorimetry (DSC) phase diagram of mixture with 50% mass ratio of
EBiInSn. (b) DSC phase diagram of mixture with 50% mass ratio of EBiIn. (a) (b) (b) (a) Figure 4. (a) Differential scanning calorimetry (DSC) phase diagram of mixture with 50% mass ratio
of EBiInSn. (b) DSC phase diagram of mixture with 50% mass ratio of EBiIn. Figure 4. (a) Differential scanning calorimetry (DSC) phase diagram of mixture with 50% mass ratio of
EBiInSn. (b) DSC phase diagram of mixture with 50% mass ratio of EBiIn. Figure 5a,b show the thermoelectric potential of the thermocouples with different mass ratios of
Bi-based alloy at different temperatures. The thermoelectric potential of the thermocouple increased
with increased mass ratio of Bi-based alloy at a fixed temperature. With further increased
temperature of the thermocouple, the increase rate of the thermoelectric potential at a fixed
temperature decreased abruptly. This fixed temperature was higher than the melting point of the
As shown in Figure 4b, the liquid portion of the mixture was EGaInSn, and the solid portion was
the new alloy. Comparing the other phase diagrams with different mass ratio of Bi-based alloy (see
Supplementary Materials) with the increment of the portion of Bi-based alloy, the peak of EGaInSn
decreased and the new metal alloy increased. It can also be seen that the liquid portion of the mixture
decreased and the solid portion increased with the mass ratio increment of Bi-based alloy. p
p y
p
g
g p
mixture. The thermoelectric potential almost linearly increased with increased temperature before
the mixture melted. Thus, the thermocouple measured microfluidic temperature below the melting
point of the mixture. Moreover, when the temperature was higher than the melting point of mixture, the
thermoelectric potential did not change any further. Although the mixture at the hot end completely
melted, an incomplete solidified mixture remined at the cold end. The maximum temperature of this
part of the mixture was close to the melting temperature. Thus, this part of the unsolidified mixture
Figure 5a,b show the thermoelectric potential of the thermocouples with different mass ratios of
Bi-based alloy at different temperatures. The thermoelectric potential of the thermocouple increased
with increased mass ratio of Bi-based alloy at a fixed temperature. With further increased temperature
of the thermocouple, the increase rate of the thermoelectric potential at a fixed temperature decreased
abruptly. 3. Results and Discussion This fixed temperature was higher than the melting point of the mixture. The thermoelectric
potential almost linearly increased with increased temperature before the mixture melted. Thus,
the thermocouple measured microfluidic temperature below the melting point of the mixture. p
g
p
,
p
was responsible for maintaining the thermoelectric constant. The Seebeck coefficient is an important factor in evaluating the performance of thermocouples. The thermoelectric potential of the thermocouple is related to the material properties and the
structure of the thermocouple, according to the theoretical formula of a thermocouple as follows:
(
)
(
)
E
T T
T
T
(1)
Moreover, when the temperature was higher than the melting point of mixture, the thermoelectric
potential did not change any further. Although the mixture at the hot end completely melted,
an incomplete solidified mixture remined at the cold end. The maximum temperature of this part
of the mixture was close to the melting temperature. Thus, this part of the unsolidified mixture was
responsible for maintaining the thermoelectric constant. (
)
0
( ,
)
AB
AB
h
c
E
T T
T
T
α
=
⋅
−
,
(1)
where
AB
E
is the thermoelectric power of the thermocouple,
AB
α
is the Seebeck coefficient of
th
l
i
t
i l
d T
d T
th
t
t
t th
h t
d
ld j
ti
The Seebeck coefficient is an important factor in evaluating the performance of thermocouples. The thermoelectric potential of the thermocouple is related to the material properties and the structure
of the thermocouple, according to the theoretical formula of a thermocouple as follows: S
(1) beck coefficient of the thermocouple from Equation (1). oeffi ie t of the EBiI
EGaI S
the
o ou le a d the EBiI S
EAB(T, T0) = αAB · (Th −Tc),
(1) g
p
EGaInSn thermocouple. A higher mass ratio of bismuth meant a higher Seebeck coefficient. The
Seebeck coefficient of EBiIn–EGaInSn was also higher than that of EBiInSn–EGaInSn. Among all of
these thermocouples, the highest and lowest Seebeck coefficients were −0.55 and −10.54 μV/K,
where EAB is the thermoelectric power of the thermocouple, αAB is the Seebeck coefficient of
thermocouple wire material, and Th and Tc are the temperature at the hot and cold junctions,
respectively. We obtained the Seebeck coefficient of the thermocouple from Equation (1). 3. Results and Discussion p
g
μ
respectively, which were much greater than the previously reported 0.1 μV/K [20]. However, a high
ratio of Bi-based alloy in mixture corresponded to a high Seebeck coefficient of the thermocouples,
but they became easily damaged when bent. Figure 5d shows the results of the bending test of these
thermocouples. Thermocouples with 40%, 50%, and 60% mass ratios of the Bi-based alloy in mixture
still worked well after being bent 200 times continuously. Thermocouples with 70%, 80%, and 90%
Figure 5c shows the Seebeck coefficients of the EBiIn–EGaInSn thermocouple and the
EBiInSn–EGaInSn thermocouple. A higher mass ratio of bismuth meant a higher Seebeck coefficient. The Seebeck coefficient of EBiIn–EGaInSn was also higher than that of EBiInSn–EGaInSn. Among all
of these thermocouples, the highest and lowest Seebeck coefficients were −0.55 and −10.54 µV/K,
respectively, which were much greater than the previously reported 0.1 µV/K [20]. However, a high
ratio of Bi-based alloy in mixture corresponded to a high Seebeck coefficient of the thermocouples,
but they became easily damaged when bent. Figure 5d shows the results of the bending test of these 8 of 11
he first
ending Sensors 2019, 19, 314
mass ratio of the
be di
te t The thermocouples. Thermocouples with 40%, 50%, and 60% mass ratios of the Bi-based alloy in mixture
still worked well after being bent 200 times continuously. Thermocouples with 70%, 80%, and 90%
mass ratio of the EBiIn in the mixture did not present flexibility and were damaged during the first
bending test. Thermocouples with 70% and 80% mass ratios of EBiInSn were damaged after bending
tests were done, five and two times, respectively. The thermocouple with 90% mass ratio of EBiInSn
was also damaged after the first bending test. The decrease in mass ratio of the Bi-based alloy in the
mixture improved the flexibility of the thermocouples. In other words, because of the presence of the
room–temperature liquid–metal EGaInSn in the mixture, the thermocouple eliminated the brittleness
of bismuth and was thus flexible and bendable. In microfluidic systems, when a thermal microchip
requires thermocouples with high flexibility, the mass ratio of Bi-based alloy in the mixture for the
thermocouple can be suggested to be <60%. After the bending test, the undamaged thermocouple was
tested again. Compared to its state before bending, the thermocouple’s Seebeck coefficient was nearly
equal (see Supplementary Materials). tests were done, five and two times, respectively. 3. Results and Discussion The thermocouple with 90% mass ratio of EBiInSn
was also damaged after the first bending test. The decrease in mass ratio of the Bi-based alloy in the
mixture improved the flexibility of the thermocouples. In other words, because of the presence of the
room–temperature liquid–metal EGaInSn in the mixture, the thermocouple eliminated the brittleness
of bismuth and was thus flexible and bendable. In microfluidic systems, when a thermal microchip
requires thermocouples with high flexibility, the mass ratio of Bi-based alloy in the mixture for the
thermocouple can be suggested to be <60%. After the bending test, the undamaged thermocouple
was tested again. Compared to its state before bending, the thermocouple’s Seebeck coefficient was
nearly equal (see Supplementary Material). In addition, to test the stability of these thermocouples, each thermocouple was tested for three
heating and cooling cycles. The results showed that the Seebeck coefficients of these thermocouples
were basically unchanged in the effective temperature range (see Supplementary Materials). It is
noteworthy that the alloy mixture was definitely not as stable as pure solid material, however, we
still suggest that, for high accuracy, a calibration be required before using these “soft” thermocouples. (a)
(b)
(c)
(d)
Figure 5. (a) Calibration curve of thermocouples with different ratios of EBiInSn. (b) Calibration curve
of thermocouples with different ratios of EBiIn. (c) Seebeck coefficients of thermocouples calculated
by the data of the calibration curve. (d) Results of bending test of thermocouples with different ratios
of Bi-based alloy (the experimental bending test videos (S3 and S4) are included in the Supplementary
Figure 5. (a) Calibration curve of thermocouples with different ratios of EBiInSn. (b) Calibration curve
of thermocouples with different ratios of EBiIn. (c) Seebeck coefficients of thermocouples calculated by
the data of the calibration curve. (d) Results of bending test of thermocouples with different ratios of
Bi-based alloy (the experimental bending test videos (S3 and S4) are included in the Supplementary
Materials). (a) (b) (b) (a) (d) (c) (c) (d) Figure 5. (a) Calibration curve of thermocouples with different ratios of EBiInSn. (b) Calibration curve
of thermocouples with different ratios of EBiIn. (c) Seebeck coefficients of thermocouples calculated
by the data of the calibration curve. (d) Results of bending test of thermocouples with different ratios
of Bi-based alloy (the experimental bending test videos (S3 and S4) are included in the Supplementary
Figure 5. (a) Calibration curve of thermocouples with different ratios of EBiInSn. 4. Conclusions
4. Conclusions A low-melting-point Bi-based alloy micro-thermocouple was proposed and fabricated using fast
microfluidic injection method for the first time. This technology mitigated the difficulty of depositing
traditional thin-film thermocouples on soft substrates. By mixing a proper amount of EGaInSn alloy
into the Bi-based alloy, the thermocouple can present good flexibility and deformability. Moreover,
the results of the SEM illustrated that the Ga-based alloy and Bi-based alloy were thoroughly
intermingled with each other and filled the entire channel. The thermocouple had a significant
thermoelectric potential that reached –10.54 μV/K, much larger than the previously reported 0.1μV/K. After three repeated heating/cooling processes, these thermocouples still maintained good linearity. A low-melting-point Bi-based alloy micro-thermocouple was proposed and fabricated using fast
microfluidic injection method for the first time. This technology mitigated the difficulty of depositing
traditional thin-film thermocouples on soft substrates. By mixing a proper amount of EGaInSn alloy
into the Bi-based alloy, the thermocouple can present good flexibility and deformability. Moreover, the
results of the SEM illustrated that the Ga-based alloy and Bi-based alloy were thoroughly intermingled
with each other and filled the entire channel. The thermocouple had a significant thermoelectric
potential that reached –10.54 µV/K, much larger than the previously reported 0.1µV/K. After three
repeated heating/cooling processes, these thermocouples still maintained good linearity. A e
ee epea e
ea i g/coo i g p ocesses,
ese
e
ocoup es s i
ai
ai e
goo
i ea i y
This kind of thermocouple could easily be integrated into microfluidic systems, if the structures
of both thermocouple and microfluidic system are simultaneously designed and fabricated in just
one step of soft lithography. Thus, this thermocouple proved its potential for use in many thermal
microfluidic applications (which is also our future work), such as PCR chip, on-chip cell culture, etc. In addition, it was found that the distribution of each of the four elements—Ga, Bi, In, and Sn—was
quite different. Particularly, Sn was almost uniformly distributed in the whole space, while others
were not. Based on this knowledge, it was speculated that Sn had a greater influence on the
uniformity and stability of the mixtures. Thus, another future work might be analyzing the
relationship between the Sn and the thermoelectric effect of the mixtures. 3. Results and Discussion (b) Calibration curve
of thermocouples with different ratios of EBiIn. (c) Seebeck coefficients of thermocouples calculated by
the data of the calibration curve. (d) Results of bending test of thermocouples with different ratios of
Bi-based alloy (the experimental bending test videos (S3 and S4) are included in the Supplementary
Materials). Materials). The thermocouple with 40% mass ratio of EBiIn was chosen to measure the temperature of
EGaInSn microheater. Using the calibration curve (Figure 5a), the voltage signal collected by the
liquid-metal thermocouple was converted into a temperature signal. The test was performed at 25
°C. Figure 6 shows the experimental results of temperature measurement for the liquid-metal
In addition, to test the stability of these thermocouples, each thermocouple was tested for three
heating and cooling cycles. The results showed that the Seebeck coefficients of these thermocouples
were basically unchanged in the effective temperature range (see Supplementary Materials). It is
noteworthy that the alloy mixture was definitely not as stable as pure solid material, however, we still
suggest that, for high accuracy, a calibration be required before using these “soft” thermocouples. Materials). The thermocouple with 40% mass ratio of EBiIn was chosen to measure the temperature of
EGaInSn microheater. Using the calibration curve (Figure 5a), the voltage signal collected by the
liquid-metal thermocouple was converted into a temperature signal. The test was performed at 25
°C. Figure 6 shows the experimental results of temperature measurement for the liquid-metal
In addition, to test the stability of these thermocouples, each thermocouple was tested for three
heating and cooling cycles. The results showed that the Seebeck coefficients of these thermocouples
were basically unchanged in the effective temperature range (see Supplementary Materials). It is
noteworthy that the alloy mixture was definitely not as stable as pure solid material, however, we still
suggest that, for high accuracy, a calibration be required before using these “soft” thermocouples. C. Figure 6 shows the experimental results of temperature measurement for the liquid metal
microheater. With increased voltage by 0.5 V per test, the thermocouple monitored the temperature
The thermocouple with 40% mass ratio of EBiIn was chosen to measure the temperature of
EGaInSn microheater. Using the calibration curve (Figure 5a), the voltage signal collected by the 9 of 11 Sensors 2019, 19, 314 liquid-metal thermocouple was converted into a temperature signal. The test was performed at 25 ◦C. 3. Results and Discussion Figure 6 shows the experimental results of temperature measurement for the liquid-metal microheater. With increased voltage by 0.5 V per test, the thermocouple monitored the temperature change over
time. When the voltage reached 0.65 V, the temperature of the microheater was 83 ◦C. These findings
indicated that this thermocouple worked well below 83 ◦C. Sensors 2019, 19, x FOR PEER REVIEW
9 of 10
change over time. When the voltage reached 0.65 V, the temperature of the microheater was 83 °C. These findings indicated that this thermocouple worked well below 83 °C. Figure 6. Experimental results of the performance test of thermocouple. The thermocouple with 40%
ratio of EBiIn was used to monitor the temperature change of GaInSn microheater. Figure 6. Experimental results of the performance test of thermocouple. The thermocouple with 40%
ratio of EBiIn was used to monitor the temperature change of GaInSn microheater. l
i Figure 6. Experimental results of the performance test of thermocouple. The thermocouple with 40%
ratio of EBiIn was used to monitor the temperature change of GaInSn microheater. Figure 6. Experimental results of the performance test of thermocouple. The thermocouple with 40%
ratio of EBiIn was used to monitor the temperature change of GaInSn microheater. 31427801) and Chip Sensor Project of State Grid Corpor
Conflicts of Interest: There are no conflicts to declare. and Lin Gui wrote the paper.
Funding: This work is financially supported by the National Natural Science Foundation of China (Grant No.
Funding: This work is financially supported by the National Natural Science Foundation of China (Grant No.
31427801) and Chip Sensor Project of State Grid Corporation of China. Author Contributions: Qifu Wang, Lunjia Zhang, and Lin Gui conceived and designed the experiments; Qifu
Wang produced the sensor system and performed the experiments; Qifu Wang, Meng Gao, Zhongshan Deng
Author Contributions: Q.W., L.Z., and L.G. conceived and designed the experiments; Q.W. produced the sensor
system and performed the experiments; Q.W., M.G., Z.D. and L.G. wrote the paper. References 1. Farrar, J.S.; Wittwer, C.T. Extreme pcr: Efficient and specific DNA amplification in 15–60 seconds. Clin. Chem. 2015, 61, 145–153. [CrossRef] [PubMed] 1. Farrar, J.S.; Wittwer, C.T. Extreme pcr: Efficient and specific DNA amplification in 15–60 seconds. Clin. Chem. 2015, 61, 145–153. [CrossRef] [PubMed] 2. Ouyang, Y.; Duarte, G.R.; Poe, B.L.; Riehl, P.S.; dos Santos, F.M.; Martin-Didonet, C.C.; Carrilho, E.;
Landers, J.P. A disposable laser print-cut-laminate polyester microchip for multiplexed pcr via
infra-red-mediated thermal control. Anal. Chim. Acta 2015, 901, 59–67. [CrossRef] 3. Ross, D.; Locascio, L.E. Microfluidic Temperature Gradient Focusing. Anal. Chem. 2002, 74, 2556–2564. [CrossRef] [PubMed] 4. Hergt, R.; Dutz, S.; Muller, R.; Zeisberger, M. Magnetic particle hyperthermia: Nanoparticle magnetism and
materials development for cancer therapy. J. Phys. Condens. Matter 2006, 18, S2919–S2934. [CrossRef] 5. Sposito, A.; Hoang, V.; DeVoe, D.L. Rapid real-time pcr and high resolution melt analysis in a self-filling
thermoplastic chip. Lab Chip 2016, 16, 3524–3531. [CrossRef] [PubMed] 6. Ranaweera, M.; Kim, J.-S. Cell integrated multi-junction thermocouple array for solid oxide fuel cell
temperature sensing: N + 1 architecture. J. Power Sources 2016, 315, 70–78. [CrossRef] 7. Yamaguchi, T.; Shibata, M.; Kumagai, S.; Sasaki, M. Thermocouples fabricated on trench sidewall in
microfluidic channel bonded with film cover. Jpn. J. Appl. Phys. 2015, 54, 030219. [CrossRef] 8. Kim, M.; Choi, W.; Lim, H.; Yang, S. Integrated microfluidic-based sensor module for real-time measurement
of temperature, conductivity, and salinity to monitor reverse osmosis. Desalination 2013, 317, 166–174. [CrossRef] 9. Fan, Y.; Dong, D.; Li, Q.; Si, H.; Pei, H.; Li, L.; Tang, B. Fluorescent analysis of bioactive molecules in single
cells based on microfluidic chips. Lab Chip 2018, 18, 1151–1173. [CrossRef] 10. Glawdel, T.; Almutairi, Z.; Wang, S.; Ren, C. Photobleaching absorbed rhodamine b to improve temperature
measurements in PDMS microchannels. Lab Chip 2009, 9, 171–174. [CrossRef] 11. Matsuki, K.; Narumi, R.; Azuma, T.; Yoshinaka, K.; Sasaki, A.; Okita, K.; Takagi, S.; Matsumoto, Y. Temperature distributions measurement of high intensity focused ultrasound using a thin-film thermocouple
array and estimation of thermal error caused by viscous heating. In Proceedings of the 2013 35th Annual
International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Osaka, Japan,
3–7 July 2013; pp. 3722–3725. [CrossRef] 12. Dickey, M.D.; Chiechi, R.C.; Larsen, R.J.; Weiss, E.A.; Weitz, D.A.; Whitesides, G.M. Eutectic gallium-indium
(egain): A liquid metal alloy for the formation of stable structures in microchannels at room temperature. Adv. Funct. Mater. 4. Conclusions
4. Conclusions This kind of thermocouple could easily be integrated into microfluidic systems, if the structures
of both thermocouple and microfluidic system are simultaneously designed and fabricated in just
one step of soft lithography. Thus, this thermocouple proved its potential for use in many thermal
microfluidic applications (which is also our future work), such as PCR chip, on-chip cell culture, etc. In addition, it was found that the distribution of each of the four elements—Ga, Bi, In, and Sn—was
quite different. Particularly, Sn was almost uniformly distributed in the whole space, while others
were not. Based on this knowledge, it was speculated that Sn had a greater influence on the uniformity
and stability of the mixtures. Thus, another future work might be analyzing the relationship between
the Sn and the thermoelectric effect of the mixtures. Supplementary Materials: Supplemental Video S1: EBiInSn is mixed with EGaInSn. Supplemental Video S2:
EBiIn is mixed with EGaInSn. Supplemental Video S3: EBiInSn mixture bending test. Supplemental Video S4:
EBiIn mixture bending test. Supplementary document: Auxiliary experimental data. Supplementary Materials: The following are available online at http://www.mdpi.com/1424-8220/19/2/314/s1,
Supplemental Video S1: EBiInSn is mixed with EGaInSn. Supplemental Video S2: EBiIn is mixed with EGaInSn. Supplemental Video S3: EBiInSn mixture bending test. Supplemental Video S4: EBiIn mixture bending test. Supplementary document: Auxiliary experimental data. Author Contributions: Qifu Wang, Lunjia Zhang, and Lin Gui conceived and designed the experiments; Qifu
Wang produced the sensor system and performed the experiments; Qifu Wang, Meng Gao, Zhongshan Deng
Author Contributions: Q.W., L.Z., and L.G. conceived and designed the experiments; Q.W. produced the sensor
system and performed the experiments; Q.W., M.G., Z.D. and L.G. wrote the paper. and Lin Gui wrote the paper. Funding: This work is financially supported by the National Natural Science Foundation of China (Grant No. Funding: This work is financially supported by the National Natural Science Foundation of China (Grant No. 31427801) and Chip Sensor Project of State Grid Corporation of China. 31427801) and Chip Sensor Project of State Grid Corpo
Conflicts of Interest: There are no conflicts to declare. 10 of 11 10 of 11 Sensors 2019, 19, 314 22.
Bradley, C.C. The experimental determination of the thermoelectric power in liquid metals and alloys.
Philos. Mag. 1962, 7, 1337–1347. [CrossRef] g
23.
Qi, G.; Zhou, S.; Wang, Z. Handbook of Science; Shanxi Renmin Publishing House: Xi’an, China, 1983; Volume
4. (In Chinese) © 2019 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 (http://creativecommons.org/licenses/by/4.0/). References 2008, 18, 1097–1104. [CrossRef] 13. Yang, J.; Zhou, T.; Zhang, L.; Zhu, D.; Handschuh-Wang, S.; Liu, Z.; Kong, T.; Liu, Y.; Zhang, J.;
Zhou, X. Defect-free, high resolution patterning of liquid metals using reversibly sealed, reusable
polydimethylsiloxane microchannels for flexible electronic applications. J. Mater. Chem. C 2017, 5, 6790–6797. [CrossRef] 14. Siegel, A.C.; Bruzewicz, D.A.; Weibel, D.B.; Whitesides, G.M. Microsolidics: Fabrication of three-dimensional
metallic microstructures in poly(dimethylsiloxane). Adv. Mater. 2007, 19, 727–733. [CrossRef] 15. Gao, M.; Gui, L. A handy liquid metal based electroosmotic flow pump. Lab Chip 2014, 14, 1866–1872. [CrossRef] [PubMed] 16. Jung, T.; Yang, S. Highly stable liquid metal-based pressure sensor integrated with a microfluidic channel. Sensors 2015, 15, 11823–11835. [CrossRef] [PubMed] 17. Yong-Lae, P.; Bor-Rong, C.; Wood, R.J. Design and fabrication of soft artificial skin using embedded
microchannels and liquid conductors. IEEE Sens. J. 2012, 12, 2711–2718. [CrossRef] 18. Wang, M.; Trlica, C.; Khan, M.R.; Dickey, M.D.; Adams, J.J. A reconfigurable liquid metal antenna driven by
electrochemically controlled capillarity. J. Appl. Phys. 2015, 117, 194901. [CrossRef]
19
Cheng S ; Wu Z Microfluidic electronics Lab Chip 2012 12 2782–2791 [CrossRef] y
p
y
pp
y
19. Cheng, S.; Wu, Z. Microfluidic electronics. Lab Chip 2012, 12, 2782–2791. [CrossRef] Li, H.; Yang, Y.; Liu, J. Printable tiny thermocouple by liquid metal gallium and its matching metal
Appl. Phys. Lett. 2012, 101, 073511. [CrossRef] 21. Gao, M.; Gui, L. Development of a fast thermal response microfluidic system using liquid metal. J. Micromech. Microeng. 2016, 26, 075005. [CrossRef] 11 of 11 Sensors 2019, 19, 314 22. Bradley, C.C. The experimental determination of the thermoelectric power in liquid metals and alloys. Philos. Mag. 1962, 7, 1337–1347. [CrossRef]
23. Qi, G.; Zhou, S.; Wang, Z. Handbook of Science; Shanxi Renmin Publishing House: Xi’an, China, 1983; Volume 22. Bradley, C.C. The experimental determination of the thermoelectric power in liquid metals and alloys. Philos. Mag. 1962, 7, 1337–1347. [CrossRef] © 2019 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 (http://creativecommons.org/licenses/by/4.0/).
|
https://openalex.org/W4286559880
|
https://www.researchsquare.com/article/rs-1880802/latest.pdf
|
English
| null |
Key factors in the internationalization process of born global Romanian software companies: an exploratory study
|
Research Square (Research Square)
| 2,022
|
cc-by
| 14,255
|
Key factors in the internationalization process of
born global Romanian software companies: an
exploratory study Anca Butnariu
(
anca.butnariu@tuiasi.ro
) (
@
)
University ”Gheorghe Asachi” Iasi
https://orcid.org/0000-0002-9738-3030 Florin Alexandru Luca
https://orcid.org/0000-0002-0691-4191 Abstract The general objective of this study is to bring several insights into the enablers of the internationalization
process of Romanian software technology companies, in the framework of recent research that
challenged the traditional theories on internationalization. Due to Romanian software companies’
increasing levels of international direct investments and the strategic importance of this sector, our aim
was to uncover the most relevant features that several born global firms in this industry possess. More
explicitely, our goal is to elucidate the factors and distinctive conditions that trigger the occurrence and
further development of Born Globals, in comparison with the companies that do not show the fast
internationalization tendency from their inception or soon after. Our qualitative empirical research, based
on four case studies, argues that strategic flexibility, innovation capability and entrepreneurial ability
allowed sees in IT Romanian industry to rapidly internationalise in unknown markets and become
international successful players. This confirms existing theoretical frameworks that recognised
knowledge-intensity, capacity of networking and client orientation as important internationalization
explaining mechanisms. Drawing on theories of internationalization as RBV, KBV, DCV, international
entrepreneurship, we argue that SMEs in IT industry are characterized by a mix of the features mentioned
by these frameworks. Our results determine that BGs are more entrepreneurial, have more innovation
capabilities, learning capability, are more customer-oriented and are part of collaborative networks, have
flexible strategies than other companies. The prior international experience or market knowledge of the
founders was not found to be one of the triggers that led to the rapid international success of romnaina
IT companies. Keywords: License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full License License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Page 1/32 Page 1/32 1. Introduction At the beginning of the 1990s, the extant gradualist internalization models became unable to
comprehensively explain the evolution of some SMEs that have been internationalizing more rapidly than
those models predicted (Oviatt & McDougall, 2005). Researchers outlined that some SMEs, especially
form knowledge-intensive industries, tend to skip some phases in their internalizations process,
experiencing an accelerated international evolution (Kalinic&Forza, 2012). These companies are termed
in the literature International New Ventures (INV), NTBF (New Technology Based Firms), Born Global (BG)
firms, global start-ups (Kalinic&Forza, 2012; Cahen, Miranda Oliveira&mendes Borini, 2017). Born Globals are defined as companies that began their international expansion since their inception or
shortly after, managing to achieve an important level of internationalization within a relatively short time
span (e.g. several years). They often have scant or no experience on external markets, with high physical
and psychic distance (Cahen, Miranda Oliveira&Mendes Borini, 2017). In the literature it cannot be found a unique set of criteria to define a Born Global firm. Cahen, Miranda
Oliveira&Mendes Borini (2017) made a literature synthesis on this topic, founding that the most referred
criteria to identify such a company are the age (companies founded after 1990), the emergence of Page 2/32 Page 2/32 external activities after the inception (ranging from 2 to 15 years), the proportion of income obtained from
external operations (varying from 5–75%) and the number of markets they are active on. external activities after the inception (ranging from 2 to 15 years), the proportion of income obtained from
external operations (varying from 5–75%) and the number of markets they are active on. In spite of the rich literature on this theme, there are authors that deem that a capacious elucidation and
detailed models of this type of companies’ occurence are still incomplete (Knight and Cavusgil, 1996),
emphasizing the need for both theoretical developments and new empirical confirmation efforts. In our study we aim at analyzing the characteristics and expected triggers of these characteristics which
differentiate born globals/NTBFs from companies that seem to follow traditional gradualist models. We
investigated the reasons for some firms become international in a short time span after their foundation
and which factors are relevant for grasping their behavior The characteristics are proposed based on a
synthesis of different scientific approaches that study the internalization process of SMEs. 1. Introduction Intangible
assets and value creation sources are considered the enablers of a rapid internationalization by Resource
Based View (RBV)(Peng, 2001) and Dynamic Capabilities View (DCV) (Zahra, Sapienza, & Davidsson,
2006); the existence of international business networks is highlighted by Network Approach (Oviatt &
McDougall, 2005), and the role of previous international experience and of good market knowledge are
emphasized by Organizational learning approach (Oviatt & McDougall, 2005). The Romanian IT industry has reached a value of over 5 billion Euros yearly, with a number of active
firms of about 15000, among which there are extremely dynamic start ups that are making their way in
the international business arena. Within the last 20 years, an important number of Romanian small-medium enterprises (SMEs) have
increased their international undertaking by creating subsidiaries in remote countries (from a
geographical and cultural point of view) despite their limited business experience and limited resources. Our study focuses on these fast growing, highly innovative born global Romanian Software companies,
with the aim to explain the mechanisms behind their rapid internationalization in unknown markets
process and to characterize and describe the peculiar features of this process for Romanian IT
companies. We also aim at increasing research interest on this topic and to further the existing
knowledge on internationalization process of born globals from eastern and central Europe, since this
field for this region was the subject of very scarce research until now. Uncovering key factors for the antecedents and specific conditions that positively influence the
emergence and further development on international markets of IT Romanian companies will help us
examine the validity of existing born global internationalization theories. Our article has the following structure: first, the main theories on the rapid internationalization found in
the literature are presented and a parallel is made between them. In the second section, we present the
theoretical context and the research method. Owing to the aim of the research, i.e. putting together the
qualitative information about internationalization strategies of the Romanian born global firms, we
employed a qualitative multiple case study analysis. Page 3/32 Page 3/32 The third section presents four case studies of Romanian based software products providers, therefore
establishing the existence of concepts from these theories, but also focusing on software special
features of the internationalization process. The case companies were selected according to criteria
established in the literature for the born globals. 1. Introduction We are using the comparison method to confront the features of some case companies with a number of
factors associated in the literature with the born globals. The following section present the analysis of the
results and the discussion on the validity of our conclusions. The last section concludes by presenting
the limitations and implications of the study. The empirical evidence implies that strategic flexibility and
proactivity, as well as knowledge-intensity (in contrast to international network and international
experience) and a client oriented approach are the major success triggers of the internationalization
process. The specific route followed by the NTBFs is described and explained by analyzing four case firms,
confirming or contradicting the leading literature. Our results indicate that BGs are more entrepreneurial,
have more innovation capabilities, learning capability, are more customer-oriented and are part of
collaborative networks, have flexible strategies than other companies. Our results have academic
(contributing to the advance of the research in the field of born global), managerial and policy-making
implications (for the public policies that influence the born global firms’ evolution). The academic contributions of our work can be analyzed on three levels. First, it investigates the
phenomenon of early internationalization in a country from Central and Eastern Europe, region for which
there are few studies in this field. Second, the phenomenon of born globals is examined through the lens
of existing recognized and accepted theories by delivering empirical-based explanations of the
mechanism behind the pace and success of internationalization. Third, it is highlighted the importance of
innovation capability and of organizational culture as trigger factors for early internationalization,
proposing an exploratory framework of the key organizational capabilities that favor this evolution. 2. Theoretical Background The evolution of a SME operating exclusively on its domestic market to an international company has
been the topic of several theoretic developments. The traditional theories (also called stage models), such
as the Uppsala model, define the internationalization process as being gradual, conditioned by increasing
experiential knowledge of firms. These models have been challenged, as the accelerated
internationalization process of BGs could not be properly explained by these traditional theories,
considered to be deterministic (not allowing companies to make strategic choices) (Andersson S., Wictor,
2003). As a consequence, scholars began to examine their evolution through the lenses of other
important theoretical frameworks: the Resource-based theory, the Capability View, the Organizational
Learning Theory, the Innovation Theory and the International Entrepreneurship Perspective (Tabares,
Alvarez&Urbano, 2015). Page 4/32 The Resource-Based View suggests that the superior international performance is the result of the
existence and effective utilization of resources. This theory argues that firms that possess high
quality resources, the capability to combine effectively these resources and to generate a new value
are prone to achieve long-term success on the international market. This theory states that the
resources have to fulfill the next conditions: (1) valuable, (2) rare, (3) imperfectly imitable, and (4)
non-substitutable (Barney, 1991). In the business environment, there are scarce physical (tangible)
resources that fulfill simultaneously all of these conditions (Bouncken R., Schuessler F. & Kraus S.,
2015). The intangible resources or the abstract assets have a higher likelihood to fit in these
conditions because of their intrinsic complex nature, and because they are the result of accumulation
processes preventing their imitation or substitution on short and medium term (Losada Otalora &
Casanova, 2012). Tabares, Alvarez & Urbano (2015) present several types of intangible assets on the basis an extensive
literature review. The intangible assets can be of human nature (such as the employees' skills and
mindset for settling problems or for innovating, the experience, expertise and the know-how of human
resources, the organizational capability of effectively exploit the human resources), technological and
organizational resources (firm culture, organizational behavior and values, organizational structure and
procedures, learning facilities, research and development procedures, product innovation, legal protection
by copyrights and trademarks) and relational resources (the ability to establish relationships with internal
and external stakeholders). 2. Theoretical Background Studies on early internationalization deal with identifying a company’s internal factors, thus RBV being
capable of explaining the international entrepreneurship phenomenon and the emergence of international
SMEs by answering a key question: in what manner have succeeded young and small business with
limited resources to expand their international operations without passing through the gradual steps
described by the traditional internationalization models? The literature on BGs characterizes them as SMEs with restricted financial, material and human resources
that have a successful international activity thanks to their intangible resources and some organizational
capabilities such as: a differentiation product strategy, an international entrepreneurial and marketing
orientation, leadership in technology, and intensive international network relationships (Rialp et al., 2005). In the last part of the decade 1990–2000, the resource-based theory was extended by important
researchers to a level that allowed the development of other theoretical approaches founded on this
theory, the most meaningful being the knowledge-based view (Grant, 1996) and the dynamic capabilities
view (Teece, Pisano & Shuen, 1997). The Knowledge-Based View studies the emergence of knowledge within the organizations. The Knowledge-Based View studies the emergence of knowledge within the organizations. The Knowledge-Based View studies the emergence of knowledge within the organizations. Knowledge is considered by several authors as a key resource, the most important resource that can
contribute to new value creation and competitive advantage. This theory considers the individual as
the center of the learning process. Knowledge is considered by several authors as a key resource, the most important resource that can
contribute to new value creation and competitive advantage. This theory considers the individual as
the center of the learning process. Page 5/32 Knowledge is analyzed from two points of view: formal knowledge (included in documents or other
informational products) and tacit knowledge (informal routines). The latter can be only learned
individually, is subjective, depending on personal experiences, expectations and abilities (Nonaka, 1994). In the case of BGs, the international business experience or the international network of individuals and
companies that the manager or the founder possesses is considered to be the essential element of the
successful internationalization. These resources offer access to business opportunities and to foreign
markets by providing the acquirement of resources and knowledge (Bouncken, Schuessler& Kraus, 2015). The individual knowledge acquired by individuals through cooperation with external partners is
transferred to the entire company. 2. Theoretical Background Knowledge is a resource that could be also developed by innovation
investments, (implying high costs and risks), thus knowledge becoming an asset that is difficult to
replicate and that brings competitive advantage for the company. Knowledge must be legally protected
against imitation. Liebeskind (1996) illustrates this by discussing the example of a manufacturing
process which is difficult to copy, contrasting with a physical asset or product that is relatively easy to
disassemble and replicate (Bouncken, Schuessler & Kraus, 2015). In the case of BGs, knowledge is not
obtained through incremental learning processes, as the traditional internationalization approach
considers, but trough a rapid access and assimilation of knowledge, often based on aggressive
acquisitions (Ayden et al., 2020). A company that became familiar with operating in its domestic market and established routines will learn
to operate and accumulate knowledge about foreign markets in a more difficult manner, because it will
more slowly identify international opportunities and get over its habitual practices in the domestic market
(Rialp & Rialp, 2007). RBV led to the emergence of another theory during the 1990s, which is used to explain the evolution
of BGs, the Dynamic Capability View (Teece, Pisano & Shuen, 1997). This theory explains that the
differences between firms in terms of their competitive advantage and performance are due to their
capabilities to combine, reconfigure and renew their valuable, rare, non-imitable and non-
substitutable resources (Schilke, Hu & Helfat, 2018). These capabilities, different from the
operational capabilities, are called “dynamic” and are defined as a firm’s ability to “integrate, build,
and reconfigure internal and external competences to address rapidly changing environments”
(Teece, Pisano &Shuen, 1997). Capabilities are defined as the company’s capacities to coordinate
and dispose of its resources, resulted by combining varied intellectual capital assets that include
intricate interplays between individuals, groups and organizational procedures. The capabilities are
also firm-specific, non-transferable abilities that allow a company to increase the productivity of its
other resources, to promptly readjust to modifications in their business environment (Ayden et al.,
2020) and to internalize knowledge about the external markets. (Jantunen et al., 2008). The Dynamic-Strategy View of the Firm premises that optimum dynamic strategies empower a faster and
more effective resource deployment, increased learning, higher performance and decreased waste; and
thus leading to augmented internationalization and faster development. Dynamic capabilities i.e. 2. Theoretical Background the Page 6/32 Page 6/32 firm’s abilities to integrate, build, and reconfigure internal and external competencies to address rapidly
changing environments increase the likelihood of dynamic strategies adoption. Dynamic capabilities thus
picture an organization’s ability to achieve new and innovative forms of competitive advantage, which
further enable firms to become effective dynamic strategies (Teece, Pisano & Shuen 1997) of their own,
and even enhance the activities of their partners in mutual value chains and alliances. The Network-Based View of the firm posits that an extensive network of companies may enable
access to a bundle of international resources and markets for reciprocal use and benefit of network
members. NBV emphasizes on the durability of firm-specific resources and capabilities obtained by
synergy of the network members, capabilities that bring permanent competitive advantage (Sliwinski,
2012). This theory considers that business networks play a key role in the internationalization process of a firm,
being a trigger for the market selection, and for the strategic entry mode (Reuwer, Jansen& Brinkkemper,
2013). These networks are collective actors that foster rapid internationalization, through the experience,
knowledge and resources provided by external partners (Mitgwe, 2006). Existing business relationships favor the identification and exploitation of opportunities. Knowledge and
learning processes are developed by interacting with business partners, not only in the first
internationalization steps but also in the further development of international operations (Stoian et al.,
2016). Existing business relationships favor the identification and exploitation of opportunities. Knowledge and
learning processes are developed by interacting with business partners, not only in the first
internationalization steps but also in the further development of international operations (Stoian et al.,
2016). The network theory is also asset-based, as knowledge built by interaction with foreign partners is a
valuable asset. According to international entrepreneurship theory, the entrepreneurial behavior of individuals and
firms plays the key role in the evolution of BGs. Zahra and George (2002) define international
entrepreneurship as the process of identifying and exploiting opportunities in the international
market in a creative way, succeeding to create value and competitive advantage. The role of
entrepreneurs is fundamental in this process. Smaller companies are more flexible and more inclined
to take risks that they succeed to manage more effectively (Reuwer, Jansen& Brinkkemper, 2013). Oviatt and McDougall (2005) found that the evolution of many companies in several industries confirm
this theory. 2. Theoretical Background Entrepreneurs that possess relational resources (knowledge, experience, entrepreneurial skills)
are considered to be the trigger of the internationalization process, identifying business opportunities and
creating durable competitive advantage. The resources provided by these are individual, thus difficult to
imitate. Zahra and George (2002) also emphasized that an entrepreneur of a born global has a high
propensity towards risk taking, is the possessor of a social capital and has an international experience. According to the previous comprehensive review, we can conclude that there is no unity of opinions on
the factors that explain the phenomenon of early and accelerated internationalization, but some factors
are recurrent in the literature as principal triggers of this process. Page 7/32 Page 7/32 Since earlier studies have tackled a wide number of internal and external triggers of the occurrence of
born globals, we conducted an inclusive literature review with the aim to select the motivators that could
be applicable in the Romanian context. The long list of motivators can be divided in several categories:
the characteristics of entrepreneur/manager, firm internal resources and capabilities, external factors as
industry structure and attributes and country characteristics (Butnariu and Luca, 2021). We have chosen to analyze the internal factors (resources, capabilities, strategic orientation) of a
company related to early internationalization, as the literature on the role of entrepreneurs’ characteristics
is rich, so their positive influence on a company’s early and accelerated internationalization is already
demonstrated. We will detail each factor. Small and young companies, although endowed with fewer resources, can outrun their competitors on
foreign markets by managing to obtain unique capabilities to operate internationally (Ferreira Ribeiro et
al., 2014). Knight and Cavusgil (2004) and Knight and Kim (2009) also found that the ability of small young
companies to be competitive on international markets is due to some specific skills and resources, over
against multinational corporations that benefit from substantial financial and tangible resources and
usually follow traditional internalization strategies. Unique technologies in combination with high innovation capability were deemed to characterize such
companies (Knight and Cavusgil, 2004; Cavusgil and Knight, 2015). They emphasized the strongly
innovative nature of BGs as the key factor in developing the dynamic capabilities needed to obtain an
early superior performance in external markets. 2. Theoretical Background Other authors emphasize the role of other intangible assets such as intellectual capital assets, human
resources, structural and relational capital and their compounding in generating essential organizationa
capabilities that are difficult to imitate, at least on short term, capabilities leading to early access on
international markets (Tabares, Alvarez&Urbano, 2015), despite the scant financial, human and other
tangible resources that the majority of new businesses possess. The leveraging of human capital on
individual and firm level, of structural capital by investing in innovative technological processes and
creating strong organizational culture and of relational capital by creating strong network with
stakeholders will lead to the creation of unique capabilities and products (Tabares, Alvarez & Urbano,
2015). Knight and Cavusgil (2004) found that BGs base their competitive advantage on human resources, and
thus tacit knowledge. Page 8/32
Stoian et al. (2016), analyzing the internalization of SMEs from eastern and central European counties,
also emphasized that small companies from transitional economies are often less resource endowed
than similar companies from well established market economies. Thus, these companies found their Page 8/32 competitive advantage on their learning capability instead of detaining more resources than their
competitors. New production processes can be considered intangible services or assets. Uniqueness is based on
knowledge capability and on a capability to learn that differs substantially from that of traditional firms. Traditional businesses internationalize because they search for exploitation of their assets such as
knowledge which they have developed on domestic markets, while BGs internationalize because they
want to gain new knowledge assets (Gabrielsson et al., 2008). The lack of experience in their home markets could be also an advantage as there are no established
routines that impede a domestic company to adapt to new remote markets (Fereira Ribeiro et al., 2014). Rialp & Rialp (2007) found that intangible resources as human capital and the organizational flexibility
have o greater influence on internationalization process. In young companies, with little experience on
internal markets, there are no domestic routines and procedures that complicate the adaptation of large
companies to external environments, thus it could be easier for the former to enter international markets. Eriksson et al. (1997) found that knowledge about the internalization process is not market related (as it
is assumed in traditional internalization models) but it is a firm-specific knowledge and it is related to
every market a firm would endorse to extend its operations. 2. Theoretical Background Martin and Salomon (2003) stated that the
more implicit is a technology or the knowledge of a firm, the more it will enable a firm to obtain the
knowledge on foreign markets. Innovative companies seek location advantages of specific countries that
can provide complementary resources or assets (strategic advantages). The flexibility of new ventures
will make them able to move to the most strategic locations. Their conclusion is that companies that see
the opportunity to strategically create knowledge by locating near customers or partners will
internationalize. For BGs, the main resource that contributes to attaining competitive advantage is the human resource
and consequently, tacit knowledge. BGs develop dynamic capabilities necessary for reaching their goals
in the process of internationally expanding their businesses (Knight & Cavusgil, 2004). These capabilities
comprise the skills to adapt to new business environment conditions and to renew competencies (Teece,
Pisano, & Shuen, 1997). The lack of tangible resources financial, human resources, tangible resources as facilities, equipment,
goods that Born Globals possess (compared to multinational companies) is compensated by a high
degree of product knowledge and expertise, necessitating continuous innovation (Knight and Cavusgil,
2004; Cavusgil and Knight, 2015). The competitive advantages emerge from the unique, innovative
products. The capability to constantly innovate allows NTBFs to internationalize rapidly and to outrun
their competition. Rialp et al. (2005) emphasized the role market and product knowledge has. Rialp et al. (2005) emphasized the role market and product knowledge has Page 9/32 Page 9/32 The products that have a potential to be marketed globally must be positioned with distinct
differentiation strategy. Such products envelop unique technologies, a distinctive superior design or
unique services, etc. (Gabrielsson et al., 2008) Born Globals are companies that focus on niche markets, which represent convenient segments that are
better served by new and small firms than by larger companies that are not efficient enough on them. The
ability of small companies to adapt and customize their products to fulfill the new requirements of niche
clients is higher. Niche markets are usually not attractive for large companies because demand is too
small or specific (Cahen, de Miranda Oliveira& Mendes Borini, 2017). Cahen, de Miranda Oliveira& Mendes Borini (2017) mention another unique intangible asset, the brand
awareness, which is likely to substantially contribute to the successful internalization process. Stoian et al. (2016) found that networks play a key role in the development of international activity of a
SME. For the creation of new knowledge, it is necessary that companies dynamically interact with
business partners. Learning occur in these business networks, thus companies being able to see the
opportunities and make successful decisions regarding market selection and degree of involvement. Monferrer, Blesa & Ripollés (2015), reviewing the literature, found that the importance of networks
stretches from the point of firm’s creation to the process of its consolidation. The relations developed help
the firm to gather diverse information and to identify and to exploit the market opportunities and to find
the required resources for this goal. Oviat and McDougal (2005) also found that rapid internalization is based on two key factors, knowledge
and international networking. The higher the market knowledge is (owing to the founder’s international
experience or to the network), the higher is the probability to develop a learning capability to further in
gathering new international knowledge. Johanson and Vahlne (2009) also argue that the major obstacle
in developing international activity is the lack of membership in an international network. The strategic orientation of a company, to meet international clients demands and a good knowledge of
market is also found to be related to early expansion of activity (Knight and Kim, 2009), Gabrielsson et al. (2008) emphasize the effectiveness or the speed of internalization process that a BG
must achieve. Rialp et al. (2005) emphasized the role market and product knowledge has. Successful BGs must exhibit a rapid growth and a high performance on global markets,
not only an early start on international markets. BGs have a global vision from the beginning, high
commitment and strategic capability. Kalinic and Forza (2012) analyzed the role strategic flexibility plays in the fast development of
international activity of a SME. The flexibility of some SMEs is one of the essential strategic success
factors needed to successfully internationalize that they poses compared to MNCs. Flexibility allow
companies to rapidly change strategies and goals, to use development strategies and increase the level
of commitment by founding subsidiaries or on the contrary, to withdraw from certain markets or ventures
in response to turbulent business environments. Page 10/32 Monferer, Blesa & Ripoles (2015) emphasized the role market orientation has on the providing of
information and knowledge firms require to successfully evolve in disruptive markets and on the
embedding of this knowledge in the company. Fernhaber, McDougall and Oviart (2007), based on an extensive literature review, concluded that
innovative firms relied on close contacts with customers and organizations within their industries in order
to develop technologies, by contrast with conventional firms that purchase or acquire existing
technologies. The international market orientation is mentioned by Persinger, Civi & Walsh Vostine (2007) as a key
factor that firms that became BGs possess. Dib, da Rocha & da Silva (2010) also confirmed that software
companies with high international marketing abilities, which are customer oriented and offer customized
products are more prone to become BGs. Knight and Kim (2009) emphasized the role international marketing skills have on the internationalization
process and defined them as the capability of a company to create added value for international clients
by integrating the marketing activities, by using market segmentation and by differentiating their
products in order to meet the preferences of international clients. Etemad (2019) also found that BGs are more innovative than other companies, are more aware of the
international opportunities and the related risks, are more proactive in responding to latent needs of
customers, are agile and resilient owing to their organizational and strategic flexibility, are very sensitive
to market dynamics, are more prone to join or establish collaborative international networks, and have a
high learning capacity. Rialp et al. (2005) emphasized the role market and product knowledge has. Based on the previous review, we propose several features of the born globals that are the outcome of the
scientific approaches on the internationalization process and that are divided into attributes of BGs that
are expected triggers for the early and accelerated internationalization in unknown markets. The
characteristics and attributes of BGs presented in Table 1. By referencing these characteristics and
attributes, we envisage the understanding of which features can be found in the BGs in Romania. Page 11/32 Page 11/32 Table 1
Expected characteristics of born globals
Dimension
Characteristics
Expected triggers
Organizational
resources and
capabilities
Strategic orientation
Entrepreneurship
orientation
International market
knowledge
Intangible assets
Value creation sources
Networking
Strategic proactivity and
flexibility
Marketing orientation
and relationship with
clients
High risk acceptance, being innovative and
opportunity seeking
High level of market knowledge (based on
learning capability)
Unique intangible assets(based usually on
knowledge management processes)
Differentiated products, technological
innovativeness, leadership in quality
Being part of international networks of suppliers,
experts, distributors and so on
High proactivity and flexibility to adapt to
changing business environments
Small customer groups, strong marketing
orientation and close relationships with
customers Table 1
Expected characteristics of born globals
aracteristics
Expected triggers 3. Methodology In this section, we present the results of our research, based on four cases analysis. The first step
consists of a brief description of each case, followed by their cross-comparison, in a pattern-matching
approach. Thus the different factors described in our theoretical framework that comprises a literature
synthesis are overlapped with the empirical findings, with the aim to uncover in what extent these firm
cases match the predicted pattern of internationalization. Researchers did not come to a consensus regarding the appropriate measure of the internationalization
degree, in the attempt to rigorously define a born global. Following the approach of Zahra, Matherne &
Carleton (2003) that consider international strategies as value creating, we use the percent of foreign
sales in total sales as a measure of the degree of internationalization for technology BGs. Another
criterion is the speed of internationalization, measured as the time span between the inception date of a
new venture in Romania and the date of its first product launching in a foreign market. In addition to being an IT Romanian company, in the category of SMEs, potential case firms had to fulfill
the following requirements: the internationalization process should have begun within a time span of
maximum 15 years from the inception of the company and the weight of the current external turnover in
the total turnover should exceed the value of 25%. The analyzed data was gathered from secondary sources: company sites, databases, news articles,
interviews with the founders and annual reports. Page 12/32 We used for each case a pattern-matching technique to overlap the empirically established pattern with
the theoretical one. We employed as well a cross-synthesis technique, treating every case as a separate
study, finding both similarities and differences. Then we assembled them for general findings across the
cases. We employed the case study method because it is the most appropriate method in the exploratory studies
to answer the questions”how” and “why” about a set of events over which we didn’t have control. The
companies were codified in order to ensure confidentiality. Firm A – provider of digital products and businesses Company A is an international technology and innovation company that creates and invests in digital
products and businesses for global start-ups and organizations. It uses technologies as experience
design, rapid prototyping and emerging technologies as AI to create innovative products and services that
help big organizations to take the steps towards the hyper-scalable digital economy of the 21 century. The company was founded in 2007 by two business partners and has reached in 2020 a number of 200
employees, from which 150 programmers and a turnover of 11 million Euros. The company has today
subsidiaries on 3 continents and builds digital products and services that use emergent technology for
some of the biggest global brands. In 2013 it began the international extension of its business, starting the collaboration with the first clients
in US. In 2016 it purchased an experience design start up in US, which became the company’s American
office. In the same year, the founder of that start-up joined the management of the company as managing
partner and innovation manager, and then as chief executive officer. In 2016 the company opened its first
office in Sidney, where it started the development of innovation projects with global brands. In 2019, the
company founded its first subsidiaries, in US and Australia. Company A has entered in several tops of European companies with the fastest ascension, having an
average growth rate of 38.3%, a turnover of 4.2 million Euros and 143 employees in 2015, such as
Financial Times top Inc.Magazine, Deloitte. The company activates in the segment of technology innovation, more precisely in services of
consultancy in digital transformation and innovation, where it has not identified direct Romanian
competitors and in the segment of technology outsourcing where it has numerous local competitors. The company differentiates its offer by designing innovative products, being one of the few companies in
Eastern Europe that approach innovation projects, for example augmented reality for a luxury home
electronic products manufacturer in Australia. Other examples of the innovative digital products that the
company offers are: mobile applications, applications for the medical field, and virtual mirrors for malls. Page 13/32 Page 13/32 Another differentiating point for company A is the speed with which it can develop a product or a service. Firm A – provider of digital products and businesses The company obtains a prototype developed from an idea in two days, an a validated product from a
prototype in 10 weeks, while most companies need 12 to 18 months to develop a prototype from an idea. The company is capable to obtain such performances by developing and using its own innovation
framework, which brings innovation in the operational process combining the rapid prototyping
technique, the Agile and skunkworks methodologies and emerging technologies as AI and machine
learning. The company builds and scales digital businesses for its clients, centering on rapid development of
digital solutions – in which it includes strategy, product design, behavioral psychology, growth marketing
and experience design. The business technology innovation activities bring 38% of the total external turnover, and 31% of total
number of employees work in technology innovation area, while 57% work in technology outsourcing,
31% in technology innovation and 12% in administrative area. In 2017, within the pale of technology innovation segment, the company scored 2 new income categories: In 2017, within the pale of technology innovation segment, the company scored 2 new income categories:
income from consultancy services and incomes from maintenance services, which represents together
3.59% of the income from technology innovation. income from consultancy services and incomes from maintenance services, which represents together
3.59% of the income from technology innovation. income from consultancy services and incomes from maintenance services, which represents together
3.59% of the income from technology innovation. A part of the revenues obtained from the innovation technology segment are represented by the incomes
from the R&D activity, that reached in 2016 a value of 800000 euros, meaning 54% of the total revenues
from technology innovation. A part of the revenues obtained from the innovation technology segment are represented by the incomes
from the R&D activity, that reached in 2016 a value of 800000 euros, meaning 54% of the total revenues
from technology innovation. Company B- developer of custom digital products and services The company develops custom software for its clients, big companies or start-ups, building dedicated
teams for companies in a variety of industries, as financial sector, health, commerce, communications
industry. Company B is one of the biggest providers of software services in the region, repeatedly included in
several tops of technology companies with fastest growing rate and of companies that provide business
excellence. Company B began its activity with 60 employees in 2003, now having over 800 software engineers. Company B began its activity with 60 employees in 2003, now having over 800 software engineers. In 2005 it started its first collaborations with external clients and in 2019 it opened its first office in the
US. Today, the commercial projects in the US represent 45% of the total number of commercial contracts. The company has a portfolio of over two hundred client companies. In 2005 it started its first collaborations with external clients and in 2019 it opened its first office in the
US. Today, the commercial projects in the US represent 45% of the total number of commercial contracts. The company has a portfolio of over two hundred client companies. Page 14/32
The company acts as an integrant part of the technical ecosystem of clients, following an adaptive
collaboration model. It facilitates the achievement of competitive advantages for its clients by using
dedicated software development teams, capability to scale and high software engineering expertise. The company has expertise in industries like healthcare, financial services, automotive and covers the end-to-
end software lifecycle development, delivering innovation, scalability, quality and speed. In the last 5 years, the company invested in 15 tech start-ups over 4 million dollars, the majority of them
being located in the US, but also in 2 Romanian start-ups, offering them not only financial capital, but
also the option of product and business development or becoming partners with experts in different areas
that want to involve in the business. D – developer of software in outsourcing system and of digital products Company D is a software developer with expertise in automotive industry, IoT, travel & hospitality, life
sciences, enterprise solutions. The three business lines of the company – software development in
outsourcing system, software solutions for internal market and retailing of navigation systems placed the
company in the top five of technology companies with the fastest growth pace in Eastern and Central
Europe. The company was mentioned four years consecutively in the Deloitte Technology FAST 50 CET
Report, and received many awards and nominalizations in numerous European events. Today the company has over 800 employees and has offices in 7 countries and 25% of the total income,
estimated at about 30 million Euros, is generated by the external subsidiaries It was founded in 1998 and it began its activity with 10 employees that developed products in
outsourcing system for important companies in Western Union and the US. The experience gained in the
collaboration with global players was used to develop its first own products in 2003, a series of software
solutions for Romanian market: a solution for sales forces automation, systems for automotive fleet
localization and monitoring and tourism agencies applications. The number of national clients that use
these solutions is over 400. In 2006, company D has diversified its activities by initiating a new business
line, becoming national distributor of complete GPS navigation systems and of GPS smart phones. In
2008 the company launched the first Romanian brand of navigation systems. Today, the company sells 3
models of navigation systems and a netbook. The products in fleet management area are already stable
in the top of providers in Eastern and South-Eastern Europe. In 2011 the company extended its activity on international markets, opening subsidiaries in four
countries. In 2011 the company extended its activity on international markets, opening subsidiaries in four
t i Beginning with 2013, the company has begun its process of integrating several local players as well, in
order to develop the product and service lines it provides, and also to diversify the industries it activates
in. In 2014 the company decided to set up a new division, beside the four existing ones, with resources
dedicated for R&D of new ideas and technologies. The Innovative projects division is a lab dedicated to
R&D of projects for the private and public sector. In 2018 the company absorbed a local company that produces software solutions for HR and
remuneration management. C – provider of business informatics systems Company C is one of the most important regional providers of business informatics systems ((ERP, HCM,
CRM, DM and BI) and one of the top global players on the financial and leasing applications market. The
company has now over 700 employees and projects in 46 countries, on four continents. Company C
develops o suite of business software solutions –that includes ERP systems, remuneration and HR
management solutions, solutions for the banking and financial companies, solutions for medical activity
management and eBusiness applications. The applications suite is complemented by services of HR
management outsourcing. Also the company implements the CRM informatic system for its clients. Company C was founded in Bucharest by six software experts in 1994, two years later beginning to
develop software for external clients. In 2001 the development of its first ERP system began, system that
was launched internationally in 2004 and became the most important software products for retail and
distribution companies in Romania. The division of HR solutions launched the first product of Self
Service HR in Romania. 2002 is the third year with a consecutive growth of over 50% in turnover. In 2006
the company entered the leasing and financial informatics products market, and in 2008 it approached a
new market niche, multimedia and infotainment systems for automotive industry. In 2010 the mobile devices division is founded, division that developed over 10 applications, among
which the first business intelligence application available on mobile devices in the world and the first
service of credit risk appraisal. Beginning with this year, the company opened subsidiaries in five
countries. 2012 was the fourth year in which the company occupied the first place in the ERP Romanian providers
and was the market leader for software systems for services, retail and distribution companies. In the
same year it launched three new products in the ERP suite and it developed and implemented CRM
platforms for multinational companies, also providing solutions and services for project management. he international activity of the company outspread on 35 countries in 2014. n 2019, the income from external markets reached 35% of the total income. In 2019, the income from external markets reached 35% of the total income. In 2018 the company bought and integrated a group of companies specialized in outsourcing, technology
and business management. Page 15/32 Page 15/32 D – developer of software in outsourcing system and of digital products It also purchased a Hungarian company with the purpose to become one of
the biggest players on the car monitoring services market in central and south-eastern Europe and also a
company in Belgium, whose products and services are complementary with the company’s own products,
in the areas of fleet management, automation process, but also on educational software area. 3.2. Cross-case analysis 3.2. Cross-case analysis 3.2. Cross-case analysis Page 16/32 Page 16/32 In this section the cases are cross-compared, the characteristics of every company being also compared
with the conceptual framework depicted in the literature. This way, we can identify the expected triggers
that drive the Romanian software companies to internationalize at a rapid pace. In this section the cases are cross-compared, the characteristics of every company being also compared
with the conceptual framework depicted in the literature. This way, we can identify the expected triggers
that drive the Romanian software companies to internationalize at a rapid pace. Organizational resources and capabilities Entrepreneurship orientation This characteristic seems to be common to all the four analyzed companies. The founders of company A
seized the opportunities the fundamental technologic evolution would offer and the fact that a new era
for businesses would begin. The future evolutions meant user experience that could allow the company
to build extraordinary successful MVPs (Minimum Viable Products). “Businesses outside technology
seem unsuccessful to me, because somebody else will use technology in the same business idea and will
scale them exponentially”, says one of the founders and managers of company A. The founders of the
company invested in innovation area, the company passing in a short span of time from offering
software outsourcing services to develop software using clients’ specifications and then to writing its
own specifications and building its own innovative IT products for some of the biggest brands in the
world, for example developing an augmented reality product for a luxury domestic appliances company. “The difference is the courage to involve in the most complex projects and bring 10 times a benefit to the
clients through software applications” – is another idea expressed by the managers. The growth of the company was accelerated, the challenge being a more structured and prudent
expansion of the business, as founders declare. Another challenge was to create and build a consistent
and coherent company culture. International market knowledge The previous international market knowledge is a characteristic only for company B, whose founder had
a previous significant international experience in IT industry, which allowed him to acquire many useful
abilities. The entrepreneur decided to capitalize this experience by opening his first business. For company A, international market knowledge was acquired from the beginning of its activity by
attracting experts that form a Board of Advisors with international experience, especially founders of
technology start-ups. Company C gained market experience by working with important international
clients. Company D uses the strategy of audacious acquisitions in order to gain external market
knowledge. But the common characteristic of all four companies is all the founders had a global vision from the start,
the companies starting to work with international clients from the beginning, even if the knowledge of
international markets was scarce. D – developer of software in outsourcing system and of digital products Company B is also characterized by a high entrepreneurship orientation, beginning its activity by being a
code developer company, then seizing the opportunity of becoming a provider of complete IT services
range, integrating business analysis, architectures, complex applications and project management
practices for healthcare, financial services and automotive companies. Company B also established an investment division that has the goal to support start-up companies to
reach their business objectives, creating joint ventures. In the last five years, company B invested capital
in 13 tech start-ups, the majority of them in US, but also in 2 Romanian start-ups, the last major
investments being companies that offer financial software and tele-medical services. This investment
division offers not only financial capital for the start-ups, but also the support for product and business
development or the opportunity of becoming partners with experts in diverse areas that are willing to start
a business. The product investment manager of company says “we searched for solutions whose clients
we may become ourselves”. P
17/32
Company C also exhibits an entrepreneurial behavior and a high risk taking attitude, entering new market
niches, diversifying its product lines and launching some innovative products. The company began its
activity by offering software services for other companies, in several years managing to launch on the
international market its first own product, an ERP solution. Company C also seized the opportunity to Page 17/32 launch the first business intelligence applications for mobile devices in the world and also some local
premieres, such as a service of credit risk assessment. launch the first business intelligence applications for mobile devices in the world and also some local
premieres, such as a service of credit risk assessment. Company D has implemented the strategy of growing by acquiring new companies, the audacious
acquisitions diversifying constantly the range of products it offers. The economic and medical crisis in
2020 was seen as an opportunity to develop a new telemetric platform for car fleet management, in order
to enhance the services it offers. The company realized quickly that the clients’ needs are changing, in
unpredictable environments, so it enhanced the flexibility of the instruments it provides to customers,
including in the telematics platform a mobile application that clients can use. Intangible assets The main asset that brings company A competitive advantage is the innovation capacity. There are very
few companies in Eastern Europe that approach innovation projects. The innovation process in the
operational field, that combines the technique of rapid prototyping, the principles of design thinking, the
Agile and Skunkworks methodologies and emerging technologies as AI and Machine learning contributes
to the development of revolutionary products and services that are subsequently implemented, as for
example a solution for augmented reality for a luxury home electronic products company in Australia. Company A has an R&D division, whose activity brought in the last 4 years between 14 and 54% of the
revenues obtained by company A from the innovation technology segment The innovation capability lead to the creation of a technology platform that covers 70% of the digital
products and services development effort, facilitating the building of infrastructure and the generic
functionalities and assuring the development of a technical MVP for clients in only 10 weeks. Another intangible asset is the organizational culture, which is centered on people. The company is very
careful with their development needs, taking constant efforts to reduce the risk of losing employees that Page 18/32 Page 18/32 have specific skills and key roles. “Comfort and death are good friends” is an idea included in the set of
cultural instruments used by the company, which encourages employees to outgrow themselves and not
to become auto-sufficient. The company implements a retention plan that contains actions like the annual salary renegotiation,
performance bonuses, continuous evaluation processes, trainings for professional development (e-
learning platform subscriptions, library), but also the possibility to allocate shares by the programs of
stock option. The development of team’s competencies is assured by the company’s own e-learning platform –
BottomUp Skills, by which the employees but also the technology and business community are provided
with the advanced courses on innovation technologies and digital tools that help them to create digital
products and experiences with impact and value for users – design thinking, rapid prototyping, business
innovation etc. The classes are available in podcast and masterclass format. An important intangible asset of company B is the know-how on the model of team extending, acquired
after years of calibrating it. Also the communication skills and cultural affinity enable the company to
bring real value for customers. Intangible assets The company constantly invests in enhancing employees’ skills and competencies by using an organized
centralized system for knowledge sharing, coaching, training, and internal communication, built on the
Atlassian collaboration tools. All employees have unlimited access to a technical knowledge base that is
constantly extended through members’ contributions. The common practices used to enhance project or product teams’ competencies are informal learning
sessions and presentations across projects. Many software developers of company B are involved in
company-wide communities, where monthly meetings are held in order to share knowledge about
technology and software practices. The company also has an internal network of coaches, which has the
role to promptly transfer knowledge across all departments of the organization. Company C has a high innovation capacity, making investments in the adoption of new technologies, in
the enhancement or re-writing of new technologies of over 10 million euros in the last 3 years. The budget
for investments in technology, products and innovation is 5 million euros. The company uses internship programs in order to attract young employees but is open to attract
experienced employees also. In order to enhance the employees experience the environment is collaborative, the teams are aligned to
the same vision, objectives and strategies. The values of the company are translated in actual behaviors
that inspire the employees, imbuing them the sense of pride for contributing to the creation of some of
the most successful products in the world, for example in the credit and leasing area, and the redefinition
of performances assessment system. The goal is that employees find their intrinsic motivation to Page 19/32 Page 19/32 Page 19/32 contribute to daily activity and to encourage them to enhance their abilities, investing in their training. In
2019 the company had a generous budget for external training. contribute to daily activity and to encourage them to enhance their abilities, investing in their training. In
2019 the company had a generous budget for external training. Company D also possesses a high innovative capability and has a division called Innovative projects that
is a lab dedicated to project R&D activity. The ability to encourage innovative projects within the company
is based on the long term perspective the founder of the company had even from the beginning of the
activity in 1998 about the importance of durable innovation development, of generating and collecting
new software solutions ideas and transforming them in prototypes and products. Value creation sources Company A provides business consultancy and digital strategy for its clients, and also technological
implementation of the strategies. The company practically builds digital businesses, focusing on a rapid
development of digital solutions, in which it includes strategic, product design, behavioral psychology,
growth marketing and experience design for the client. Thus company A addresses the whole value chain
of the client companies, beginning with the identification of the business problem, offering business
consultancy, creating strategies for the client and then translating these strategies in digital products and
services that are implemented in the client companies. This approach is unique, no other competitors
succeeding to offer such comprehensive services. The company also offers stable and safe MVP (minimum viable products) for the clients in only 10
weeks, owing to its own library of reusable technological components, tested and enhanced for 10 years
of technology and digital products development. The company’s platform exponentially reduces the
period of time necessary for the development of digital products, covering a variety of necessities in
development – from infrastructure, UI/UX, mobile – iOS and Android to front-end and back-end web. Company B covers the end-to-end software lifecycle development, delivering its clients innovative
products, scalability, quality and speed, having expertise in healthcare, financial services, automotive. The
whole span of a software product is covered, from need assessment, UI/UX, application development,
testing and quality ensuring to maintenance or project management The company is not only providing software customized products for the client companies, but is also
provides support that enables decision making and change management for its clients. These services
smooth the running of operational processes across the client companies and ensure the objectives they
settled are met. Company B treats every client with most care, configurating dedicated software
development teams that work exclusively on client’s projects. Such teams can extend the client
company’s in-house software development capacity or add specific knowledge to its team, working
together closely with its developers and testers. The teams that will work with a specific client are also selected by taking into account the cultural
matching, the members’ desire and interest to work on a particular project, and not only their technical
skills and relevant experience. Thus it is assured an effective knowledge transfer through workshops and Page 20/32 Page 20/32 intense collaboration. Knowledge transfer is ensures also workshops and intense collaboration, either on
company’s premises or at the client’s site. intense collaboration. Value creation sources Knowledge transfer is ensures also workshops and intense collaboration, either on
company’s premises or at the client’s site. Company C sells digital products for companies that have a high impact on their businesses, such as the
reduction of costs, the reduction of time necessary for repetitive tasks. The main product is a software
solution for ERP, which includes segments for accountability, sales and for financial flow management. The clients manage to reduce their costs and obtain important increase in their productivity, some of
them declaring that the ERP solution has helped them to make progress every month and that without the
positive impact of this digital product, their business would close. Company D offers solutions for business optimization, car fleet management and HR management. The
solution for business optimization is created for the necessities of implementation of internal processes
for small or medium companies and represents an alternative to CRM solutions (a plurality of
instruments for organizing intra and inter departmental interactions, as well as interactions with
prospects, clients, providers and other companies) at a much lower cost. The solution helps company D’s
customers to improve their relations with their own clients. The product of company D is not only a
software product, but a tool useful for business strategy, flexible and easy to implement, on a growing
market of companies that begin to use CRM solutions in order to enhance their relations and interactions
with existing or potential clients and UCMS solutions (instruments to measure a team’s performance)
because they need to manage their remote teams. In the middle of 2008 crisis, another product of company D, a solution for car fleet monitoring became
market leader, because offered the companies a solution to optimize their costs and to increase their
human resources efficiency. The product brought a reduction of car fleet expenses with 30%. The software solutions for HR management are characterized by a very good customer experience and
an agile reaction in the implementation process. They offer a very good customer experience, an agile
reaction in the process of implementation for the final customer and are consolidated by the newest
technologies. The company also offers advanced client services and frequently re-designs all its digital solutions so
they form an integrated system of digitalization, optimization and flexibility. Strategic orientation Networking Networking All of the examined companies are part of business networks that allowed them to access new technical
and business knowledge. For example, company A experienced a boom of its activity beginning with
2012, after it reached the US market Silicon Valley and started collaborations in Silicon Valley. The
company integrated an American start up of experience design and storytelling, whose founder joined the
management of the company as managing partner and innovation manager and then became CEO. The
experience and business network of the new manager helped the company establish a subsidiary in Page 21/32 Australia and develop its business globally. Company A also attracted several entrepreneurs and experts
from American IT industry as advisors. Australia and develop its business globally. Company A also attracted several entrepreneurs and experts
from American IT industry as advisors. Company B established strategic partnerships with leading companies in complementary sectors,
ensuring that their clients receive the best services for their digital challenges and complex needs. Through industry affiliations, it keeps up to date with the dynamic landscape in every ecosystem, from
healthcare to fintech and automotive, continuously aligning the services of custom software development
with the latest innovations and trends. Also, the company’s business model itself is to develop nearshore dedicated partnerships, building teams
for the long term needs of its customers. Every customer benefits from team extensions, the success of
this tactic laying in the collaborations the company has built. The networking ability has allowed company B to also engage in partnerships that led to the creation of
new companies. The knowledge capital of the founders is transferred to the new companies, the most
recent start-ups that company B has created together with its business partners as joint ventures
activating in the tele-medical services and in financial services. The start-ups are provided with support
for product or business development and with the opportunity to meet different experts in its business
network. Company C also exhibited networking abilities since the beginning of its activity, becoming a founding
member of the romanian association of software and services industry in 1998. It also established
partnerships with a world leader in business intelligence technologies, with the main European talent
management provider and with a leading company in HR services in order to enhance its products’
features and to find new international clients. Company D has chosen to develop its activity by using the acquisition strategy. Networking It strengthened and
diversified its offer for its clients, absorbing companies in several countries. This way, the product line
company D provides has enriched with HR management software solutions, fleet management, CRM,
automation of processes for companies in FMCG industry, warehouse management systems, distribution
management. Strategic proactivity and flexibility All of the examined companies have proven to employ flexible strategies and to have a proactive
business approach. Company A exhibits a high strategic flexibility, passing through three profound changes of its business –
which the founders call “re-inventions”, from outsourcing software to innovation activities (design and
building of digital products and services that use emergent technologies, including artificial intelligence). The founders of the company started with a low budget and had to be inventive in order to identify
financing sources. The beginnings of the company, which were “a little bit forced” (as one of the founders Page 22/32 says) - meaning the growth was too fast, gave it resistance and attention to details, making it extremely
resilient. The economical crisis is seen by the managers of the company as bringing opportunities to sign
new contracts, starting new digital projects for several clients in the financial area. Company B is one of the most dynamic software developers in south and Eastern Europe. It changed its
leadership structure, including new functionalities in the areas of project management, processes and
quality. The company passed through accelerated evolutions, calling for a need of business processes
optimization. For this task, company B, as well as the other companies in the selected group, is using the
strategy of recruiting international experts, whose knowledge can help the organization develop
successfully abroad. The proactivity of company B is illustrated by an investment division, which has the
goal to identify the opportunities for new investments in potentially successful start-ups. Company C’ business extending to an international level was not based on a clear stated strategy,
according to its founder. The company flexibly adapted its activity to the requests of multinational
companies, former clients, which wanted company C to become the provider of software systems for
other subsidiaries. The structure of the company was modified and the internal processes were adapted
to the continuous growth of its business. Company D’s founder deems a crisis is testing a company’s adaptability capacity and forces it to get out
of its comfort area and to find new business solutions. In the context of the pandemic 2020 crisis, many
customers of company D reacted rapidly and well when they had to let their employees to work from
home, but they also faced the challenge to manage remote teams and remote prepare time sheets. Strategic proactivity and flexibility Company D adapted a HR management product for the new needs of its customers, seeing the crisis as
an opportunity and benefiting from it. It also saw the opportunity to develop a new telematics platform,
with the purpose to enhance the services it provides to customers, with a mobile application, available on
app stores, included. The recent crisis taught the company a lesson about unpredictability, highlighting the level of
adaptability, from all points of view: internal and external communication, re-organization and re-
dimension of operations, keeping the balance even in rough conditions. With seven national offices and
six international subsidiaries and over 950 employees, company D succeeded a successful re-thinking of
its internal systems, business strategies and work methods. Marketing orientation and relationship with clients Our clients
become dependent on our products, they use them several years”, declares the founder of the company. Company D is constantly improving the products and services it offers to its customers, complying with
the always changing needs of its customers, because it realized that they need flexibility, in unpredictable
environments. Company D implements as flexibly as possible the instruments needed by the customers,
an example being the adaptation of a HR management product for the new clients’ needs of remote team
management and of remote time sheet preparing. Marketing orientation and relationship with clients All of the four analyzed companies exhibit a client-oriented culture and excellent customer care services. The culture of company A is built on the idea of customer care. All the employees are encouraged to
thoroughly analyze the needs of the clients and to find the sources of value creation for every client, by
maintaining a close relationship with every client. The managers encourage the employees, even the
programmers, to dialogue with the clients, to thoroughly understand the business they are working for,
before they are starting their activity and to offer advices where needed. Page 23/32 Page 23/32 Company B is also characterized by strong customer care competencies. “We have learnt that any
technological intervention implies more profound changes in the client organization”, declares one of the
managers. In the light of this understanding, company B’s employees practice a consultative approach,
facilitating the navigation of every step in the development and acquisition of a new software project. The dedication of the teams that develop “carefully crafted custom software” for established companies,
startups, software houses and solution providers is acknowledged by its former clients. Company B’s
teams are self managed, can add new members as needed, are flexible, and ensure knowledge transfer to
client teams through workshops and intense collaboration, establishing together a remote process and
communication, thus operating as integrant part in clients’ technical ecosystem, on a model of adaptive
collaboration, ensuring that the distributed team works seamlessly. The excellent communication process
with the clients led to an increasing market share in the US. Although the company had a 15 years experience in international market and a commercial portfolio
generated in a proportion of 45% by American clients, it decided in 2019 to enhance its services for
customers and in order to put this into practice, it established an office in US where a multi-disciplinary
team, composed by software architects, business and sales consultants will ensure a close relationship
with the prospects and clients in the region. The purpose is to deepen its understanding of local market
specific needs. In order to acquire marketing and customer care competencies, company C’s founder recruited an
international sales manager with a high expertise in this area. The integrated business solutions are sold
in the entire Europe, the company having excellent relations with its customers. “We sell trust. 4. Discussion Our case studies enabled us to identify the triggers of the early and fast internationalization of BGs. In all
the cases an important trigger was the global vision of the founders, which insisted on developing a
global business from the beginning. This vision does not always derive from the background of the
entrepreneurs. Previous international market knowledge is not a common feature of the studied
companies. The only exception is company B’s founder that had an international experience in IT industry
and decided to capitalize the acquired abilities in founding its own business. The other founders’
international experience was limited, the common thing being their international view from the beginning. In order to gain international experience, company A attracted international experts in a board of advisors
since the beginning of its activity and company D used a strategy of acquisitions to develop its external Page 24/32 Page 24/32 market knowledge. These results contrast with the findings of Andersson and Wictor (2003), that
emphasize the role of previous international experience of the managers and entrepreneurs that founded
the born-globals but confirm the findings of Rialp et al. (2005). Our findings also confirm the hypothesis of Gabrielson et al. (2008) that the early commitment to
international activities is generated by the global vision of the entrepreneur and not by experiential
knowledge. The cooperation with foreign partners began immediately, because the SMEs had business
contacts that provided them rapid subsequent global growth. Examples are the contracts company A
signed with Adobe and Microsoft, for testing software services (one of the founders of company A was a
former Adobe employee), company C that began its activity as distributor for Microsoft and for a
reputable company that sells project portfolio management solutions, two years later beginning to
develop software for external clients. Entrepreneurship orientation seems to be particularly relevant for the evolution of BGs. The risks a BG is
willing to take on are much bigger than the risk a traditional exporting SME faces. All of the founders of
the studied companies invested all profits at the beginning of their endeavor, taking a double risk, a risk of
new products that are launched on new markets, in the conditions of limited financial resources. The value fast internationalizing Romanian IT companies provides for their customers derives from the
highly innovative capacity these companies hold. 4. Discussion For example, company A has an R&D division, whose
activity brought in the last 4 years between 14 and 54% of the revenues obtained by company A from the
innovation technology segment, company A being one of the few companies in eastern Europe that are
able to approach such innovative projects. Company C also invests high amounts in the adoption of new
technologies, in the enhancement or re-writing new technologies. The budget for investments in
technology, products and innovation is 5 million Euros. Company D has a special lab dedicated to R&D
projects. The ability to encourage innovative projects and to develop the R&D capacity of these companies is
based on the long term view their founders had from the beginning of the activity about the importance
of sustained innovation development. The main sources of value creation for customers derive from
innovation and technology intensive processes and from unique, highly differentiated products. These
findings confirm Rialp et al.2005. Another capability these companies share is the capacity to enhance their teams’ competencies. For
example, company A has developed its own e-learning platform, by which the employees are provided
with advanced courses on innovation technologies and digital tools. Company B also uses a comprehensive centralized system of knowledge sharing that provides
employees with coaching, training and internal communication services. The company also employs
informal learning sessions and presentations for a product or a project’s team and even for all employees,
with information that cross several projects. Page 25/32 Page 25/32 Page 25/32 Many software developers from companies A and B are engaged in technology or business based
communities, sharing technology, software and business practices topics. In company B, additionally, an
internal network of coaches is set up to ensure the knowledge transfer throughout the organization. Company C created a collaborative work environment, creating a culture of pride that motivates
employees to find their intrinsic motivation to enhance their abilities, complementary with a generous
budget for external training. Managers of these companies develop knowledge that is a unique and
difficult to imitate resource by embedding into the companies’ culture values and routines that help
employees to enhance their competences. This confirms the findings of Knight and Cavusgil (2004). These intangible assets allow BGs to provide their clients high value added products that enable their
clients to gain important competitive advantages or to substantially improve their productivity or cost
structure. 4. Discussion For Page 26/32 Page 26/32 Page 26/32 example, company A passed through three profound changes, beginning its activity with outsourcing
software, then it focused on project development for its customers, today its activity residing mainly in
innovation activities (design and building of digital products and services that use emergent
technologies, including artificial intelligence. example, company A passed through three profound changes, beginning its activity with outsourcing
software, then it focused on project development for its customers, today its activity residing mainly in
innovation activities (design and building of digital products and services that use emergent
technologies, including artificial intelligence. All companies changed their leadership structure in short periods of time, including new functionalities in
areas as project management, operations, quality, sales, and recruiting international experts whose
knowledge helped the rapid and successful international growth. The structure of the companies and the internal processes were rapidly modified and adapted to the
continuous international growth and recently to the new pandemic crisis. All of the companies
successfully modified their internal and external communications, re-organized and re-dimensioned their
operations, re-thought their internal systems, work methods (for example they passed to remote work)
and business strategies. These findings are in line with those of Kalinic and Forza (2012) that emphasize the flexibility, the quick
reaction to feedback from external conditions by changing their goals and the risk taking behavior of
BGs. 4. Discussion Some clients describe those products as “vital” for their business. The international success of these companies is also supported by their networking capability. The
international networks have been rapidly developed, as in the case of companies A and D that became
members of new business networks by using acquisition strategies. This allowed them to acquire
experience, technical abilities, and access to new markets. Company B even based their business model
on the networking ability, the strategic partnerships allowing them to ensure complex teams to address
the needs of their clients. Company B also engaged in long term partnerships by creating several new
start-up joint ventures together with its business partners. We can establish that wider and stronger
networking orientation and capabilities of BGs decision makers allow them to exploit of opportunities
that other companies leave out. This confirms the findings of Rialp et al (2005) and of Knight and
Cavusgil (1996). All of the studied companies exhibit a high customer orientation. The close relationships with the clients
allowed them to find sources of value creation for every client. Even the employees that usually do not
interact directly with the clients, as programmers, are encouraged to dialogue with them and to offer
advices where needed. The strong customer care competencies embed a consultative approach and
excellent customer services before, during and after the digital products are developed and implemented
for the customers. Some of the former clients became even business partners of these companies. Although had a 15 years experience on American market, company B decided to open an office in US to
ensure a closer relationship with the prospects and clients in the region and to deepen its understanding
of the market specific needs. The customer orientation of the BGs is also found to be a source of value
creation process by Tabares, Alvares and Urbano (2015). All of the four companies exhibit a profound
knowledge of customers, capability to adapt and develop customized, high quality products for clients
and a skillful usage of marketing tactics to target foreign clients, conclusion that is in line with those of
Knight and Cavusgil (2004), but contrast the findings of Rialp et al. (2005). All of the four studied companies also show a high adaptability to the business environment and a
strategic flexibility that allowed them to modify their business models when the opportunity occurred. 5. Conclusion Our study investigated the explanatory mechanisms that stand behind the rapid internationalization of
some small and medium companies in unknown markets. The study is based on an extensive review of existing theories on the rapid internationalization of small
and medium enterprises, called born globals. We selected the most important characteristics of such
companies, organized on two dimensions: Organizational resources and capabilities and Strategic
orientation and then put them against the characteristics of several Romanian companies. The study is exploratory but does provide some insights into the internationalization process of
Romanian software companies. Our sources of information were secondary data about four
representative IT Romanian companies. Nonetheless, our study provides insights into the factors that
distinguish companies with a high speed of internationalization from other companies and highlights
several interesting areas for further study. Our results have academic (contributing to the deepening of scientific knowledge in the field of born
global), managerial and policy-making implications (for the public policies that influence the born global
firms’ evolution). From an academic point of view, our findings are in line with the existing literature on the theme of born
globals companies, with one exception: the prior international market knowledge that the entrepreneur
possesses is scarce, but his global perspective exists from the beginning. Page 27/32 We also established that the high growth rate of the turnover form external clients is influenced by the
innovation capability (that leads to product/services development) and by the organizational learning
capability. All of the studied companies invested high amounts in developing their innovation capacity
and their employees’ knowledge and competencies. These intangible assets enable born globals to offer
their clients products with high value added, having unique features, adaptable or customized and
excellent services. The networking capability is involved in Romanian software companies’ high speed rate of
internationalization process. Firms internationalize mainly to be close to their strategic clients or to gain
higher market shares by absorbing foreign companies. We also found that these companies exhibit a
high strategic flexibility and proactivity, being able to quickly extend their business on new the markets,
offering new products and services, seizing new opportunities, the strategy of audacious acquiring of
foreign companies being very common among these companies. They also exhibit a deep understanding
of every client’s needs, the relational approach of marketing activity being common to all of the studied
companies. 5. Conclusion For managers and entrepreneurs, the implications of our study are that the enhancement of the
networking capability, of the marketing and client orientation and of the innovation capability are vital in
order to achieve quick results that sustain the business and lead it to becoming a successful international
player. For policy makers, our empirical research implications are that their efforts should be oriented towards
encouraging international network and partnership formation and also investments in innovation of the
companies. A good example would be to decrease the level of income tax from R&D activities of the
companies and also to provide grants for these activities and support for the participation of small
companies in international events. Due to the qualitative nature of our research, we admit that the case study method does not allow a
generalization of our findings to other contexts, but it helps reaching the goal of exploring the
phenomenon of born global Romanian companies, which has never been investigated in the literature
prior to our research. Future research might employ a quantitative method to confirm our findings and to
further investigate the role of external factors in the rapid internationalization path some companies
follow. Our results could also be of interest for researchers that want to explore the evolution of born
globals in other eastern and central Europe countries, in order to broaden these findings to wider groups
of companies and to compare the empirical results with existing research on this topic. Andersson S., Wictor I. (2003). Innovative Internationalisation in New Firms: Born Globals – the Swedish
Case. Journal of Internationational Entrepreneurship, 1, pp. 249-276. References Andersson S., Wictor I. (2003). Innovative Internationalisation in New Firms: Born Globals – the Swedish
Case. Journal of Internationational Entrepreneurship, 1, pp. 249-276. Page 28/32 Ayden Y., Tatoglu E., Glaister K.W., Demirbag M. (2021). Exploring the internationalization strategies of
Turkish multinationals: A multi-perspective analysis. Journal of International Management, Volume 27,
Issue 3,100783, ISSN 1075-4253. Ayden Y., Tatoglu E., Glaister K.W., Demirbag M. (2021). Exploring the internationalization strategies of
Turkish multinationals: A multi-perspective analysis. Journal of International Management, Volume 27,
Issue 3,100783, ISSN 1075-4253. Barney, J. B. (1991). Firm resources and sustained competitive advantage, Journal of Management, 17,
99–120. Barney, J. B. (1991). Firm resources and sustained competitive advantage, Journal of Management, 17,
99–120. Bouncken R., Schuessler F., Kraus S. (2015), The Theoretical Embedding Of Born Globals: Challenging
Existing Internationalization Theories, International Business & Economics Research Journal, Volume 14,
Number 1. Butnariu A., Luca F.A. (2021). Triggers of Born Global Companies, Network Intelligence Studies, volume IX,
issue 18, 161-169. Cahen R.F., de Miranda Oliveira M., Mendes Borini F. (2017), The internationalisation of new technology-
based firms from emerging markets, Int. J. Technology Management, Vol. 74, Nos. 1/2/3/4. Cavusgil, S., Knight, G. (2015). The born global firm: An entrepreneurial and capabilities perspective on
early and rapid internationalization. Journal of International Business Studies, 46, 3–16. Dib, L.A., da Rocha, A. & da Silva, J.F. (2010). The internationalization process of Brazilian software firms
and the born global phenomenon: Examining firm, network, and entrepreneur variables, Journal of
International Entrepreneurship, 8, 233–253. Eriksson, K., Johanson, J., Majkga˚rd, A., Sharma, D.D. (1997). Experiential knowledge and cost in the
internationalization process. Journal of International Business Studies, 28, 337 – 360. Etemad H. (2019), Revisiting interactions of entrepreneurial, marketing, and other orientations with
internationalization strategies, Journal of International Entrepreneurship, 17, 1–18. Ferreira Ribeiro F., De Miranda Jr. M., Borini F.M., Bernardes R. (2014), Accelerated Internationalization in
Emerging Markets: Empirical Evidence from Brazilian Technology-Based Firms, Journal of Technology
Management & Innovation, Volume 9, Issue 1. Fernhaber, S. A., McDougall, P. P., Oviart, B. M. (2007), Exploring the Role of Industry Structure in New
Venture Internationalization, Scholarship and Professional Work - Business. 91.https://digitalcommons.butler.edu/cob_papers/91 Gabrielsson M., Kirpalani M., Dimitratos P., Solberg C.A., Zucchella A. (2008). Born globals: Propositions
to help advance the theory, International Business Review 17, 385–401. Garvey, D., Brennan, L. (2006). The Internationalisation of Indigenous Irish Software Technology
Companies: An Exploratory Study, Irish Journal of Management, 26, 2. References Page 29/32 Grant R.M. (1996). Toward a knowledge-based theory of the firm, Strategic Management Journal, Vol. 17,
109-122. Jantunen A., Nummela N., Puumalainen K., Saarenketo K. (2008). Strategic orientations of born globals—
Do they really matter?, Journal of World Business,Vol. 43 (2), 158-170. Johanson J., Vahlne JE. (2009). The Uppsala internationalization
process model revisited: From liability of foreignness to liability of
outsidership, Journal of International Business Studies, 40, 1411–
1431. Kalinic I., Forza C. (2012). Rapid internationalization of traditional SMEs: Between gradualist models and
born globals, International Business Review, 21, 694-707. Kennedy A., Keeney K. (2009). Strategic partnerships and the internationalization process of software
sees, Serv ice Business, 3(3), 259–273. Knight, G., Cavusgil, S. T. (1996). The Born Global Firm: A Challenge to Traditional Internationalization
Theory, in Advances in International Marketing, Vol. 8, Cavusgil, S., Madsen, T., (eds.), Greenwich, CT: JAI
Press, pp. 11-26. Knight, G., Cavusgil, S. (2004). Innovation, organizational capabilities, and the born-global firm. Journal of
International Business Studies, 35, 124–141. Knight, G., Kim, D. (2009). International business competence and the contemporary firm. Journal of
International Business Studies, 40, 255–273. Liebeskind, JP. (1996). Knowledge, Strategy, and the Theory of the Firm, Strategic Management Journal,
Vol. 17, Special Issue: Knowledge and the Firm, pp. 93-107 Losada Otalora M., Casanova L. (2012). Resources and Internalisation Strategies: The Case of Latin
American Multinationals, Insead Faculty & Research Working Paper. Martin X., Salomon R. (2003). Tacitness, Learning, and International Expansion: A Study of Foreign Direct
Investment in a Knowledge-Intensive Industry, Organization Science, Vol. 14, No. 3, 297–311. Monferrer D., Blesa A., Ripollés M. (2015). Born globals trough knowledge-based dynamic capabilities and
network market orientation, Business Research Quarterly, 18, 18-36. Mitgwe, B. (2006). Theoretical Milestones in International Business: The Journey to International
Entrepreneurship Theory. Journal of International Entrepreneurship, 4, 5-25. Page 30/32 Nonaka I., (1994), A Dynamic Theory of Organizational Knowledge Creation, Organisation Science, Vol. 5,
No. 1. Oviatt, B., McDougall, P.(2005). The internationalization of entrepreneurship. Journal of International
Business Studies, 36, 2–8. Peng M. (2001), The resource-based view and international business, Journal of Management,Volume 27,
Issue 6, pp. 803-829,ISSN 0149-2063,https://doi.org/10.1016/S0149-2063(01)00124-6. Persinger E., Civi E., Walsh Vostine S. (2007). The Born Global Entrepreneur In Emerging Economies,
International Business & Economics Research Journal, Volume 6, Number 3. Reuwer T., Jansen S., Brinkkemper S. (2013). References Key Factors in the Internationalization Process of SMEs
Exporting Business Software as a Service, International Journal of Business Information Systems 2013,
12, 140–162. Rialp A., Rialp J., Urbano D., Vaillant Y. (2005). The Born-Global Phenomenon: A Comparative Case Study
Research, Journal of International Entrepreneurship, 3, 133–171. Rialp A., & Rialp J. (2007). Faster and More Successful Exporters: An Exploratory Study of Born Global
Firms from the Resource-Based View, Journal of Euromarketing, 16:1-2, 71-86. Śliwiński R. (2012). Internationalization strategies of Polish fast growing enterprises, Poznan University
of Economics Review, Volume 12 Number 1. Schilke O., Hu S., Helfat C. (2018). Quo vadis, dynamic capabilities? A content-analytic review of the
current state of knowledge and recommendations for future research, Academy of Management Annals,
12(1), 390–439. Stoian M.C., Rialp A., Rialp J., Jarvis R. (2016), Internationalisation of Central and Eastern European small
firms, Journal of Small Business and Enterprise Development, 23 (1), 105 – 121. Tabares A., Alvarez C., Urbano D. (2015). Born Globals From the Resource-Based Theory: a Case Study in
Colombia, Journal of Technology Management & Innovation, 10(2). Teece D.J., Pisano G., Shuen A. (1997). Dynamic Capabilities and Strategic Management. Strategic Management Journal, Vol. 18(7), 509–533. Zahra S., Matherne B., Carleton J. (2003). Technological Resorce Leveraging and the Internationalisation
of New Ventures , Journal of International Entrepreneurship, 1, 163-186. Zahra S., George G. (2002). The Net-Enabled Business Innovation Cycle and the Evolution of Dynamic
Capabilities. Information Systems Research 13 (2), 147-150. Page 31/32 Zahra S.A., Sapienza H., Davidsson P. (2006). Entrepreneurship and Dynamic Capabilities: A Review,
Model and Research Agenda, Journal of Management Studies 43:4 Zahra S.A., Sapienza H., Davidsson P. (2006). Entrepreneurship and Dynamic Capabilities: A Review,
Model and Research Agenda, Journal of Management Studies 43:4 Zahra S.A., Sapienza H., Davidsson P. (2006). Entrepreneurship and Dynamic Capabilities: A Review,
Model and Research Agenda, Journal of Management Studies 43:4 Zahra S.A., Sapienza H., Davidsson P. (2006). Entrepreneurship and Dynamic Capabilities: A Review,
Model and Research Agenda, Journal of Management Studies 43:4 Declarations The authors did not receive support from any organization for the submitted work. All authors certify that
they have no affiliations with or involvement in any organization or entity with any financial interest in the
subject matter or materials discussed in this manuscript. Page 32/32
|
https://openalex.org/W4382137956
|
https://link.springer.com/content/pdf/10.1007/s11081-023-09813-z.pdf
|
English
| null |
Trajectory optimization for arbitrary layered geometries in wire-arc additive manufacturing
|
Optimization and engineering
| 2,023
|
cc-by
| 12,032
|
Optimization and Engineering (2024) 25:529–553
https://doi.org/10.1007/s11081-023-09813-z Optimization and Engineering (2024) 25:529–553
https://doi.org/10.1007/s11081-023-09813-z RESEARCH ARTICLE Abstract In wire-arc additive manufacturing, a wire is molten by an electrical or laser arc
and deposited droplet-by-droplet to construct the desired workpiece, given as a set
of two-dimensional layers. The weld source can move freely over a substrate plate,
processing each layer, but there is also the possibility of moving without welding. A
primary reason for stress inside the material is the large thermal gradient caused by
the weld source, resulting in lower product quality. Thus, it is desirable to control the
temperature of the workpiece during the process. One way of its optimization is the
trajectory of the weld source. We consider the problem of finding a trajectory of the
moving weld source for a single layer of an arbitrary workpiece that maximizes the
quality of the part and derive a novel mixed-integer PDE-constrained model, including
the calculation of a detailed temperature distribution measuring the overall quality. The resulting optimization problem is linearized and solved using the state-of-the-art
numerical solver IBM CPLEX. Its performance is examined by several computational
studies. Keywords Mixed-integer programming · Wire are additive manufacturing ·
Trajectory planning · Partial differential equations · Finite element method · Heat
conduction Trajectory optimization for arbitrary layered geometries
in wire-arc additive manufacturing Johannes Schmidt1 · Armin Fügenschuh1 Received: 6 February 2023 / Revised: 16 June 2023 / Accepted: 16 June 2023 /
Published online: 26 June 2023
© The Author(s) 2023 B Johannes Schmidt
johannes.schmidt@b-tu.de 1
Brandenburg University of Technology Cottbus-Senftenberg, Platz der Deutschen Einheit 1, 03046
Cottbus, Germany 1 Introduction In the class of direct energy deposition additive manufacturing processes, wire-arc
additive manufacturing (WAAM) evolved into a promising alternative to common 1
Brandenburg University of Technology Cottbus-Senftenberg, Platz der Deutschen Einheit 1, 03046
Cottbus, Germany 123 530 J. Schmidt, A. Fügenschuh manufacturing processes like forging due to its large deposit rate, nearly limitless
build size, and commonly available hardware (Williams et al. 2016). A wire is molten
by an electrical or laser arc weld source and deposited in droplets onto a clamped
substrate plate. The weld source can move freely around the workspace, building the
desired workpiece layer by layer. If necessary, it can also move without welding,
called transiting, but the required switch-off and switch-on of the weld source can
produce condensation, reducing the quality of the workpiece. Next to this, the large
temperature of the weld source has a significant effect on it. On the one hand, if the
temperature of the already printed material is too high, it remelts when the next layer
is processed, leading to deformations. On the other hand, high thermal gradients cause
stress inside the workpiece, which results in strain or even cracks. Thus, controlling
the temperature during the manufacturing process is crucial to achieving high-quality
products. p
The tool path planning problem for the considered process asks for a trajectory of
the weld source such that material is deposited at all relevant places and the finished
workpiece has the highest possible quality. Due to the high complexity of a whole
workpiece consisting of many layers, we assume a single two-dimensional layer. We
consider the tool path planning problem for the considered case as a split delivery
vehicle routing problem (SDVRP), introduced by Dror and Trudeau (1990). Therein,
a given fleet of vehicles must serve a set of customers, but every customer can be visited
multiple times, delivering only a fraction of his demand. A survey about this problem
class with theoretical properties and different solution methods is given by Archetti and
Speranza(2008).Nexttothetrajectoryoftheweldsource,theheattransmittancewithin
the workpiece affects its temperature distribution. Thus, the heat equation (Fourier
1878) with suitable boundary conditions to describe radiation to the environment
is incorporated, yielding a mixed-integer problem with partial differential equations
(PDE) constraints (MIPDECO). The solution of MIPDECO problems is challenging due to the combination of
discrete decision variables with complex numerical discretization schemes. Several
approaches were discussed in the literature. Hahn et al. 123 1 Introduction (2022) use partial outer con-
vexification to transform the discrete variables of a MIPDECO problem into binary
variables and afterward solve its canonical continuous relaxation. The solution of
the original problem with discrete variables can then be reconstructed by applying
appropriate rounding algorithms. Furthermore, they show the convergence of their
improved rounding techniques. Gnegel et al. (2021) presented a solution framework
using a mixed-integer linear program (MILP), where the linear system, resulting from
the discretization of the PDE, is solved for the basis of the control space in a prepro-
cessing step. The effect of the PDE is then incorporated into the objective function. Vogt et al. (2022) formulate a MIPDECO problem for electromagnetic cloaking and
describe a heuristic trust-region approach to solve it incorporating also uncertainty. Considering WAAM, the research interest for the process parameters and the con-
nected trajectory planning problem was constantly growing during the last years, as
shown in the recent survey of Treutler and Wesling (2021). It gives a detailed overview
of active research groups and the state-of-the-art for different materials and modeling
approaches with the respective results. Due to the recency of this survey, we only
mention some other recently published literature. Ferreira and Scotti (2021) proposed Trajectory optimization for arbitrary layered geometries… 531 a modeling approach called pixels, where a bulky layer is represented by a grid of
nodes and every node must be visited once. The resulting traveling salesman problem
(TSP) is solved heuristically using a randomized greedy adaptive search to find a most
continuous trajectory of minimal length, but temperature aspects are neglected in this
procedure. For the case of multidirectional WAAM, Schmitz et al. (2021) presented
a trajectory planning procedure incorporating the weld robot kinematic. The possible
rotation of the workpiece during the process in their framework makes the trajectory
planning more difficult since the slicing can be performed in an arbitrary direction. Thus, existing methods cannot be used efficiently. Zhang et al. (2020) generated for a
bulky example geometry several trajectories by combining the zigzag and the contour-
offset strategy to examine the influence of the weld trajectory on the residual stress for
building a single layer while maintaining shape outline accuracy. Their study shows
that with the combination of two common strategies, the residual stress can already
be reduced. 1 Introduction We contribute to the state-of-the-art by formulating the trajectory planning problem
for a single two-dimensional layer consisting of thin-walled parts and bulky regions as
a MIPDECO problem. In the literature, geometries including only one of both types
were studied (Diourté et al. 2021; Ferreira and Scotti 2021; Ma et al. 2019; Michel
et al. 2019). For its solution, we follow the approach from Gnegel et al. (2021),
transform the problem into a MILP by applying linear discretization schemes to the
PDE constraints and show its applicability to the numerical solver IBM CPLEX in
several computational experiments. This paper is structured as follows. In Sect. 2, the heat conduction model is stated
and its linearization is derived. The whole optimization model, consisting of path
generation and temperature calculation, is then described in Sect. 3, next to possi-
ble objective functions. In Sect. 4, the performance of the model and its details are
examined in several numerical experiments before we conclude and give directions
for future work in Sect. 5. 2 Heat conduction model To manufacture a three-dimensional workpiece, it is sliced horizontally to obtain
the single layers. The following procedure must be carried out for each of them,
but for more clarity, we consider a single two-dimensional layer with domain ⊆
R2 throughout this article and omit an additional index referring to its horizontal
layer slice. Defining a temperature function θ : × [0, T ] →R over for a given
time interval [0, T ], the two-dimensional heat conduction problem for one layer is
formulated by ∂θ
∂t (x, y, t) = α
∂2θ
(∂x)2 (x, y, t) + ∂2θ
(∂y)2 (x, y, t)
+ q(x, y, t) ∀(x, y) ∈,
t ∈(0, T ] ,
(1a)
∂θ
∂⃗n (x, y, t) = κa
ϕadd −θ(x, y, t)
∀(x, y) ∈∂,
t ∈[0, T ] ,
(1b) ∂θ
∂t (x, y, t) = α
∂2θ
(∂x)2 (x, y, t) + ∂2θ
(∂y)2 (x, y, t)
+ q(x, y, t) ∀(x, y) ∈,
t ∈(0, T ] ,
(1a) (1a) ∂θ
∂⃗n (x, y, t) = κa
ϕadd −θ(x, y, t)
∀(x, y) ∈∂,
t ∈[0, T ] ,
(1b) (1b) 123 532 J. Schmidt, A. Fügenschuh ) = θinit(x, y) ∀(x, y) ∈,
(1c) θ(x, y, 0) = θinit(x, y) ∀(x, y) ∈, θ(x, y, 0) = θinit(x, y) ∀(x, y) ∈, (1c) with thermal diffusivity α ∈R+, artificial cooling factor κa ∈(0, 1] and heat source
q(x, y, t) : × [0, T ] →R+. Note that (1) neglects heat exchange by radiation
within the layer. with thermal diffusivity α ∈R+, artificial cooling factor κa ∈(0, 1] and heat source
q(x, y, t) : × [0, T ] →R+. Note that (1) neglects heat exchange by radiation
within the layer. A general description of the heat exchange at the boundary ∂ ⊆ is taken
from Hahn and Özisik (2012), maintaining energy conservation and incorporating
convection and radiation. 2 Heat conduction model It is given by ∂θ
∂⃗n (x, y, t) = −h
λ
θ(x, y, t) −θamb(x, y, t)
−εσ
λ
θ(x, y, t)4 −θamb(x, y, t)4
∀(x, y) ∈∂, ∀t ∈[0, T ] ,
(2) (2) with thermal conductivity λ ∈R+, heat transfer coefficient h ∈R+, total emissivit
ε ∈R+, Stefan–Boltzmann constant σ, and ambient temperature θamb : ×[0, T ] → with thermal conductivity λ ∈R+, heat transfer coefficient h ∈R+, total emissivity
ε ∈R+, Stefan–Boltzmann constant σ, and ambient temperature θamb : ×[0, T ] →
R+. To obtain a linear approximation scheme after discretization, the Rosseland
approximation from Bähr et al. (2021) is applied to the non-linear radiation term
in (2), resulting in the Robin boundary condition (1b) with cooling factor κa ∈[0, 1]
and additive constant ϕadd ∈R+. Let ∂ ⊂R2 be a Lipschitz boundary and the heat source function q
∈
L2 ( × [0, T ]). Using domain decomposition (Quarteroni and Valli 1999), the given
layer is split up into two different parts. On the one hand, there are thin-walled struc-
tures, which are an arrangement of single weld beads connected only at their end
points. On the other hand, there are bulky regions, where an area must be filled with
material. While the former ones are processed by tracking them and only the order of
the segments remains to be determined, for the latter ones there is no information about
the trajectory available. Every part of the layer can be assigned to exactly one of these
two cases, thin-walled or bulky. Thus, this approach yields a domain decomposition
of containing subdomains with non-overlapping interior. Let 1 ⊆ denote the
subdomain including all thin-walled structures, 2 ⊆, the subdomain containing
all bulky regions, = 1 ∩2 their common interface, and ⃗n ∈R2 the outward
normal vector. An example of this decomposition can be found in Fig. 1. 2 Heat conduction model p
p
g
Then, the heat conduction problem (1) is transformed to Then, the heat conduction problem (1) is transformed to ∂θi
∂t (x, y, t) = α
∂2θi
(∂x)2 (x, y, t) + ∂2θi
(∂y)2 (x, y, t)
+ q(x, y, t)
∀(x, y) ∈i,
i ∈{1, 2},
t ∈(0, T ] ,
(3a)
∂θi
∂⃗n (x, y, t) = κa
ϕadd −θi(x, y, t)
∀(x, y) ∈∂ ∩∂i, i ∈{1, 2}, t ∈[0, T ] ,
(3b) (3a) ∀(x, y) ∈i,
i ∈{1, 2},
t ∈(0, T ] ,
(3a)
∂θi
∂⃗n (x, y, t) = κa
ϕadd −θi(x, y, t)
∀(x, y) ∈∂ ∩∂i, i ∈{1, 2}, t ∈[0, T ] , ∂θi
∂⃗n (x, y, t) = κa
ϕadd −θi(x, y, t)
∀(x, y) ∈∂ ∩∂i, i ∈{1, 2}, t ∈[0, T ] , ∂n
(3b) (3b) θi(x, y, 0) = θinit(x, y) ∀(x, y) ∈i,
i ∈{1, 2},
(3c)
θ1(x, y, t) = θ2(x, y, t) ∀(x, y) ∈,
t ∈[0, T ] ,
(3d) θi(x, y, 0) = θinit(x, y) ∀(x, y) ∈i,
i ∈{1, 2},
(3c)
θ1(x, y, t) = θ2(x, y, t) ∀(x, y) ∈,
t ∈[0, T ] ,
(3d)
∂θ1 (x y t) = ∂θ2 (x y t) ∀(x y) ∈∂
t ∈[0 T ]
(3e) θ1(x, y, t) = θ2(x, y, t) ∀(x, y) ∈,
t ∈[0, T ] ,
(3d)
∂θ1
∂⃗n (x, y, t) = ∂θ2
∂⃗n (x, y, t) ∀(x, y) ∈∂,
t ∈[0, T ] . (3e) ∂θ1
∂⃗n (x, y, t) = ∂θ2
∂⃗n (x, y, t) ∀(x, y) ∈∂,
t ∈[0, T ] . (3e) ∂θ1
∂⃗n (x, y, t) = ∂θ2
∂⃗n (x, y, t) ∀(x, y) ∈∂,
t ∈[0, T ] . (3e) 123 Trajectory optimization for arbitrary layered geometries… 533 Fig. 1 Domain decomposition of
an example geometry. The
thin-walled structures are
collected in 1 (red), while
2 (blue) contains the bulky part Fig. 1 Domain decomposition of
an example geometry. The
thin-walled structures are
collected in 1 (red), while
2 (blue) contains the bulky part The heat Eq. (3a) and the Robin boundary (3b) are now applied to the respective
domains. In (3c), the given initial temperature distribution θinit(x, y) : →R+ is
applied. 2 Heat conduction model To enable the connection between the heat conduction problems on every sub-
domain, the transmission conditions (3d), (3e) are applied, guaranteeing the equality
of the solutions and energy conservation at the common interface. The heat Eq. (3a) and the Robin boundary (3b) are now applied to the respective
domains. In (3c), the given initial temperature distribution θinit(x, y) : →R+ is
applied. To enable the connection between the heat conduction problems on every sub-
domain, the transmission conditions (3d), (3e) are applied, guaranteeing the equality
of the solutions and energy conservation at the common interface. To discretize (3), different methods are applied to the two subdomains. Concerning
2, we use the known velocity of the weld source while processing vw ∈R+ and
a chosen time step length t ∈R+ to cover it by a grid of squares with equal side
length h = min{bw, vwt}, where bw ∈R+ is the width of one weld bead. Then,
each square is identified by a node i placed at its center (xi, yi) ∈R2 and collected in
the set V p. Let A = (ai, j) ∈V p × V p denote the adjacency matrix of all areas with
ai, j = 1 if and only if, the squares related to the nodes i, j ∈V p have a common
side. Furthermore, ∂V p ⊂V p describes the set of nodes i ∈V p whose related squares
belong to ∂ ∩∂1. Using linear triangle elements, we apply a triangulation E to
the node set V p and set up a finite element method to approximate the solution of (3)
on 2 with nodes i ∈V p, elements e ∈E, and boundary ∂V p. The general triangle
element is represented by its three corner points P1, P2, P3 ∈R2 with coordinates
(xi, yi), i = 1, 2, 3, oriented counterclockwise. It is displayed in Fig. 2. Let ψe : V p →{1, 2, 3} denote the function assigning the global nodes to the
corner points of the triangle element e ∈E. According to the derivation by Taler and
Ocło´n (2014), the solution of the finite element method for the problem (3a), (3b),
(3c) with backward difference time scheme is given by (M + t K)⃗θt+1 = t(⃗qt+1 ⃗f H + ϕadd ⃗f R) + M ⃗θt. (4) 123 12 3 534 J. Schmidt, A. Fügenschuh Fig. 2 The general triangle
element Fig. 2 Heat conduction model It is computed by K e = α
4A K H,e + κa
cϱ
(h,p)∈∂
lh,pK R,e
h,p ,
(7) (7) 123 123 Trajectory optimization for arbitrary layered geometries… Trajectory optimization for arbitrary layered geometries… 535 K H,e =
⎛
⎜⎜⎝
k H,e
11
k H,e
12
k H,e
13
k H,e
12
k H,e
22
k H,e
23
k H,e
13
k H,e
23
k H,e
33
⎞
⎟⎟⎠,
(8)
k H,e
11
= (y2 −y3)2 + (x3 −x2)2 ,
k H,e
12
= (y2 −y3) (y3 −y1) + (x3 −x2) (x1 −x3) ,
k H,e
13
= (y2 −y3) (y1 −y2) + (x3 −x2) (x2 −x1) ,
k H,e
22
= (y3 −y1)2 + (x1 −x3)2 ,
k H,e
23
= (y3 −y1) (y1 −y2) + (x1 −x3) (x2 −x1) ,
k H,e
33
= (y1 −y2)2 + (x2 −x1)2 ,
⎧
⎪⎪⎪⎪⎪⎪⎪
1
3, i = j = ψe(h)
1
3
i = j = ψe(p) K H,e =
⎛
⎜⎜⎝
k H,e
11
k H,e
12
k H,e
13
k H,e
12
k H,e
22
k H,e
23
k H,e
13
k H,e
23
k H,e
33
⎞
⎟⎟⎠,
k H,e
11
= (y2 −y3)2 + (x3 −x2)2 ,
k H,e
12
= (y2 −y3) (y3 −y1) + (x3 −x2) (x1 −x3) ,
k H,e
13
= (y2 −y3) (y1 −y2) + (x3 −x2) (x2 −x1) ,
k H,e
22
= (y3 −y1)2 + (x1 −x3)2 ,
k H,e
23
= (y3 −y1) (y1 −y2) + (x1 −x3) (x2 −x1) ,
k H,e
33
= (y1 −y2)2 + (x2 −x1)2 , K H,e =
⎛
⎜⎜⎝
k H,e
11
k H,e
12
k H,e
13
k H,e
12
k H,e
22
k H,e
23
k H,e
13
k H,e
23
k H,e
33
⎞
⎟⎟⎠,
(8)
H
2
2 (8) (8) k H,e
23
= (y3 −y1) (y1 −y2) + (x1 −x3) (x2 −x1) , K R,e
h,p = (k R,e
h,p)i, j =
⎧
⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎨
⎪⎪⎪⎪⎪⎪⎪⎪⎪⎪⎩
1
3, i = j = ψe(h)
1
3, i = j = ψe(p)
1
6, i = ψe(h),
j = ψe(p)
1
6,
j = ψe(h),
i = ψe(p)
0,
else
. (9) (9) The element load vectors ⃗f H,e ∈R3 and ⃗f R,e ∈R3 represent the effect of the
heat source within the heat Eq. 2 Heat conduction model 2 The general triangle
element Fig. 2 The general triangle
element Therein, the mass matrix M ∈R|V p|×|V p|, the stiffness matrix K ∈R|V p|×|V p|, load
vectors ⃗f H ∈R|V p| and ⃗f R ∈R|V p|, the nodal temperature vector ⃗θ ∈R|V p|, and
the heat input vector ⃗q ∈R|V p| are required and must be calculated. Therein, the mass matrix M ∈R|V p|×|V p|, the stiffness matrix K ∈R|V p|×|V p|, load
vectors ⃗f H ∈R|V p| and ⃗f R ∈R|V p|, the nodal temperature vector ⃗θ ∈R|V p|, and
the heat input vector ⃗q ∈R|V p| are required and must be calculated. The three linear basis functions for the corner points of the general triangle are
defined by ϕ1(x, y) = 1
2A (x2y3 −x3y2 + (y2 −y3) x + (x3 −x2) y) ,
(5a)
ϕ2(x, y) = 1
2A (x3y1 −x1y3 + (y3 −y1) x + (x1 −x3) y) ,
(5b)
ϕ3(x, y) = 1
2A (x1y2 −x2y1 + (y1 −y2) x + (x2 −x1) y) ,
(5c) (5a) (5b) (5c) where A denotes the area of the triangle. Using these functions, the element mass
matrix Me ∈R3×3 and the element stiffness matrix K e ∈R3×3 can be computed. The former one is constant for every triangle element and given by Me = Ae
⎛
⎜⎜⎝
1
6
1
12
1
12
1
12
1
6
1
12
1
12
1
12
1
6
⎞
⎟⎟⎠,
(6) (6) with Ae ∈R+ the area of triangle element e ∈E, c ∈R+ the specific heat capacity of
the material, and ρ ∈R+ its density. The latter one is the sum of matrices K H,e ∈R3×3
and K R,e
h,p ∈R3×3, representing the influence of the heat Eq. (3a) and the Robin
boundary condition (3b), respectively. It is computed by with Ae ∈R+ the area of triangle element e ∈E, c ∈R+ the specific heat capacity of
the material, and ρ ∈R+ its density. The latter one is the sum of matrices K H,e ∈R3×3
and K R,e
h,p ∈R3×3, representing the influence of the heat Eq. (3a) and the Robin
boundary condition (3b), respectively. 2 Heat conduction model (3a) and of the ambient temperature within the Robin
boundary condition (3b), respectively. Assuming a constant heat input q ∈R over the
area related to one node, they are calculated by ⃗f H,e = Ae
⎛
⎝
1
31
31
3
⎞
⎠,
(10)
⃗f R,e = κa
(h,p)∈∂
lh,p ⃗f R,e
h,p ,
(11)
⃗f R,e
h,p =
f R,e
h,p
i =
⎧
⎪⎨
⎪⎩
1
2, i = ψe(h)
1
2, i = ψe(p)
0,
else
. (12) (10) (11) ⃗f R,e
h,p =
f R,e
h,p
i =
⎧
⎪⎨
⎪⎩
1
2, i = ψe(h)
1
2, i = ψe(p)
0,
else
. (12) (12) Summing the local matrices K e, Me, and vectors f H,e, f R,e up for all elements e ∈E,
the global matrices K, M and vectors f H, f R are obtained (Taler and Ocło´n 2014). Concerning 1, we define a node at every intersection point between two thin-
walled segments and collect them in the set Ve. Let Vc ⊆V p denote the set containing
all nodes at the interface, then every thin-walled welding segment is described as 3 536 J. Schmidt, A. Fügenschuh an element of the set We ⊆Ve × (Ve ∪Vc). Thus, the subdomain 1 is again
decomposed into smaller subdomains, one for each (i, j) ∈We. On every segment, a
one-dimensional heat equation must be solved, while the new transmission conditions
between adjacent segments must be incorporated. Similar to Bähr et al. (2021), we add Ni, j ∈N equidistantly distributed discretiza-
tion points to every segment (i, j) ∈We of lengthli, j, yielding xi, j =
li, j
Ni, j+1. Every
discretization point is identified with its position k ∈{0, 1, . . . , Ni, j + 1} within the
segment, starting with 0 at i ∈Ve and ending with Ni, j + 1 at j ∈Ve. Furthermore,
let Li, j = {1, . . . , Ni, j} denote the set of the interior discretization points for every
segment (i, j) ∈We. The interior discretization points of all segments are stored in
the set Vint and let V = Ve ∪V p ∪Vint denote the set of all nodes within the layer. The function ξ : We × {0, 1, . . . 2 Heat conduction model , Ni, j + 1} →V is used to map the local labels at
every segment to the global node labels for the layer. Applying finite differences of
the backward time centered space (BTCS) scheme gives θk,t−1 = −˜αi, jθk−1,t + (1 + 2˜αi, j)θk,t −˜αi, jθk+1,t −tqk,t
∀(i, j) ∈We,
k ∈Li, j,
t ∈T ,
(13)
θ0,t = θi,t
∀(i, j) ∈We,
t ∈T0,
(14)
θNi, j+1,t = θ j,t
∀(i, j) ∈We,
t ∈T0,
(15) (15) with transformed diffusivity ˜αi, j =
αt
(xi, j)2 , discretized heat source qk,t, representing
the function value of q(x, y, t) at the position of interior point k ∈Li, j at time step
t ∈T . with transformed diffusivity ˜αi, j =
αt
(xi, j)2 , discretized heat source qk,t, representing
the function value of q(x, y, t) at the position of interior point k ∈Li, j at time step
t ∈T . By applying the global node set V, the transmissions conditions (3d) and (3e) are
guaranteed implicitly since it holds Vc ⊆V p and the normal vector ⃗n is defined to
point outside of the respective domain. 3 Mixed-integer optimization model In this section, we derive a MIPDECO formulation for the trajectory planning problem
of the weld source of the general form max
T
0
f (t, θ(x, t)) dt,
(16a)
s.t. ∂tθ(x, t) = α∇θ(x, t) + q(x, w, t) ∀x ∈, t ∈[0, T ] ,
(16b)
∂nθ(x, t) = κa
θ(x, t) −ϕadd
∀x ∈∂, t ∈[0, T ] ,
(16c) max
T
0
f (t, θ(x, t)) dt,
(16a)
s.t. ∂tθ(x, t) = α∇θ(x, t) + q(x, w, t) ∀x ∈, t ∈[0, T ] ,
(16b)
∂nθ(x, t) = κa
θ(x, t) −ϕadd
∀x ∈∂, t ∈[0, T ] ,
(16c)
θ(x, 0) = θinit(x) ∀x ∈,
(16d)
Aw ≤b,
(16e)
w ∈{0, 1}|M|,
(16f) max
T
0
f (t, θ(x, t)) dt,
(16a)
s.t. ∂tθ(x, t) = α∇θ(x, t) + q(x, w, t) ∀x ∈, t ∈[0, T ] ,
(16b)
∂nθ(x, t) = κa
θ(x, t) −ϕadd
∀x ∈∂, t ∈[0, T ] ,
(16c)
θ(x, 0) = θinit(x) ∀x ∈,
(16d)
Aw ≤b,
(16e)
w ∈{0, 1}|M|,
(16f) s.t. ∂tθ(x, t) = α∇θ(x, t) + q(x, w, t) ∀x ∈, t ∈[0, T ] ,
(16b)
∂nθ(x, t) = κa
θ(x, t) −ϕadd
∀x ∈∂, t ∈[0, T ] ,
(16c) θ(x, 0) = θinit(x) ∀x ∈,
(16d) w ∈{0, 1}|M|,
(16f) w ∈{0, 1}|M|,
(16f) 123 123 Trajectory optimization for arbitrary layered geometries… 537 Fig. 3 Top view on an example geometry (left) and the associated graph G (right). The boundaries of the
pixels covering the bulky part are displayed in gray. Every node of the global node set V is represented by
a circle which is not filled for the decision nodes in the set V Fig. 3 Top view on an example geometry (left) and the associated graph G (right). The boundaries of the
pixels covering the bulky part are displayed in gray. Every node of the global node set V is represented by
a circle which is not filled for the decision nodes in the set V and discretize and linearize it to achieve a MILP formulation. The objective func-
tion (16a) measures the quality of the workpiece incorporating the time t and the
temperature distribution θ(x, t). 3 Mixed-integer optimization model In the constraints, two parts, one for the tempera-
ture calculation (16b)–(16d) and another for the trajectory generation (16e), (16f),
are coupled by the binary variables w using the weld source term q(x, w, t). These
binary variables describe the trajectory of the weld source in a time expanded
graph. In the following, let δ( j) : Ve →N denote the function assigning the
node degree to every node j ∈Ve regarding the set of welding segments We and
Vodd = { j ∈Ve | δ( j) = 2k −1 ∧k ∈N} the set of nodes in 1 with odd node
degree. Since the resulting trajectory should be most continuous, transition moves
should be avoided if possible. Thus, we allow them only between nodes i, j ∈Vodd. Otherwise, one can find a feasible trajectory requiring fewer transition moves. and discretize and linearize it to achieve a MILP formulation. The objective func-
tion (16a) measures the quality of the workpiece incorporating the time t and the
temperature distribution θ(x, t). In the constraints, two parts, one for the tempera-
ture calculation (16b)–(16d) and another for the trajectory generation (16e), (16f),
are coupled by the binary variables w using the weld source term q(x, w, t). These
binary variables describe the trajectory of the weld source in a time expanded
graph. In the following, let δ( j) : Ve →N denote the function assigning the
node degree to every node j ∈Ve regarding the set of welding segments We and
Vodd = { j ∈Ve | δ( j) = 2k −1 ∧k ∈N} the set of nodes in 1 with odd node
degree. Since the resulting trajectory should be most continuous, transition moves
should be avoided if possible. Thus, we allow them only between nodes i, j ∈Vodd. Otherwise, one can find a feasible trajectory requiring fewer transition moves. Since every node j ∈Ve with δ( j) = 2 has only one neighbor in either direction,
the further trajectory is determined when arriving at this point. If there is no edge
(i, k) ∈We connecting its neighbors i, k ∈Ve ∪Vc, the node j can be removed from
the set Ve and seen as an additional interior node. Therefore, the edges (i, j), ( j, k) ∈
We are replaced by the new edge (i, k) with Li,k = {1, . . . 3 Mixed-integer optimization model , Ni, j + N j,k + 1}, where
node i is at position 0, j is the interior node at position Ni, j + 1, and k has the last
position Ni, j + N j,k + 2. By applying this transformation, the set of nodes, where a
decision regarding the progression of the trajectory is possible, is given by V = V p ∪
j ∈Ve | δ( j) ≥3 ∨
δ( j) = 2 ∧(i, j), ( j, k), (i, k) ∈We
. V = V p ∪
j ∈Ve | δ( j) ≥3 ∨
δ( j) = 2 ∧(i, j), ( j, k), (i, k) ∈We
. (17) (17) The set of feasible connections between the nodes in V p can be obtained from the
adjacency matrix A and is given by A = {(i, j) ∈V p × V p | ai, j = 1}. Thus, the
considered layer is represented by the graph G = (V, We ∪A) as displayed in Fig. 3. The set of feasible connections between the nodes in V p can be obtained from the
adjacency matrix A and is given by A = {(i, j) ∈V p × V p | ai, j = 1}. Thus, the
considered layer is represented by the graph G = (V, We ∪A) as displayed in Fig. 3. 123 538 J. Schmidt, A. Fügenschuh To obtain the number of discrete time steps to process the complete layer, the time
for welding and the time for transition moves must be taken into account. Since the
length of each welding segment (i, j) ∈We is known, the number of time steps to
weld all segments of one layer is given by T e =
(i, j)∈We τ w
i, j with τ w
i, j =
li, j
vwt . Due to the applied space discretization of the areas, the weld source requires one
time step to reach the next node i ∈V p. Thus, there are T p = |V p| −1 time steps
necessary to manufacture all bulky parts and it holds τ w
i, j = 1 for all (i, j) ∈A. 3 Mixed-integer optimization model Although in practical applications the velocity vm of the weld source while moving
without welding is much greater than vw, already for medium-scaled workpieces the
required time for necessary transition moves must be taken into account. Since their
duration depends on the chosen trajectory, the processing time to finish one layer is
unknown a priori. Nevertheless, an upper bound can be obtained since the number
of necessary transition moves ω ∈N ∪{0} should be minimal. Assuming that the
weld source uses the euclidean distance di, j to travel between nodes i, j ∈Vodd, the
number of time steps for this action is computed by τ m
i, j =
di, j
vmt . Thus, the number
of necessary time steps to process the whole layer is bounded from above by T max =
T e + T p + ω maxi, j∈Vodd τ m
i, j and the discrete time horizon is T0 = {0, 1, . . . , T max}. As abbreviations we use in the following T = T0\{0}, T −= T \{T max}. Furthermore,
let denote T w = {0, . . . , T e + T p −1 + ω mini, j∈Vodd τ m
i, j} the number of time steps
before the whole layer can be processed. All used sets, intervals, parameters, and
variables of the resulting MILP are listed in Tables 1, 2and 3. 3.1 Path generation According to the space discretization of 2 in Sect. 2, it is necessary to visit every
node in V p \Vc once to fill its related square with the material. For all nodes j ∈Vc in
the common interface, there are at most
δ( j)
2
+1 visits due to their adjacent welding
segments. These are processed by tracking them once. Thus, also all interior nodes
Vint are visited exactly once and for all nodes j ∈Ve the number of visits is
δ( j)
2
. Let ν( j) : V →N denote the function assigning the maximum number of visits to
every node by ν( j) =
⎧
⎪⎪⎪⎪⎪⎨
⎪⎪⎪⎪⎪⎩
δ( j)
2
+ 1 , j ∈Vc,
δ( j)
2
, j ∈Ve,
1
, else. (18) (18) The problem of finding a feasible trajectory for a given layer can be formulated as
an SDVRP on the graph G with one (artificial) depot and ω identical vehicles with
unbounded capacity in the following way. By setting the delivered demand per visit to
one and the total demand of node j ∈V to ν( j), we ensure that the whole layer is pro-
cessed.Everyvehicletourrepresentsacontinuouspartoftheweldingtrajectoryandthe
edges from the endpoint of one tour to the depot and from the depot to the starting point 123 Trajectory optimization for arbitrary layered geometries… 539 Table 1 Overview of the sets and intervals used in the trajectory planning problem
Symbol
Index
Definition
Li, j = {1, . . . , Ni, j}
k
Set of interior discretization points of welding segment
(i, j)
Pk =
rk−1,rk
Distance from the weld source where the proportion of
the temperature gain κw
k applies
T = {1, . . . , T max}
t
Set of discrete time steps
T0 = {0, . . . , T max}
t
Set of time steps including zero
T −= {1, . . . 3.1 Path generation , T max −1}
t
Set of discrete time steps excluding the last one
T w ⊆T
t
Minimal set of discrete time steps to process the whole
layer
U∗
(i, ti, j, t j)
Set of time-expanded transition moves
V
j
Set of decision nodes
V = V ∪Vint
j
Set of all nodes
Vc
j
Set of nodes in the bulky region which have at least one
neighbor in the thin-walled parts
Ve
j
Set of nodes in the thin-walled parts
Vint
j
Set of nodes within all welding segments
Vodd
j
Set of nodes with odd node degree
V p
j
Set of nodes in the bulky region
We
(i, j)
Set of welding segments in the thin-walled parts
W∗
(i, ti, j, t j)
Set of time-expanded welding segments in either
direction Table 1 Overview of the sets and intervals used in the trajectory planning problem of the next tour are summarized into a transition move. By this approach, the depot can
be neglected in the model. To eliminate subtours, we apply a time-expanded formula-
tion. Every segment can be welded in either direction and to incorporate the welding
time τ w
i, j, we introduce the sets W
e = {(i, j) ∈V × V | (i, j) ∈We ∨( j, i) ∈We}
and W∗=
(i, ti, j, t j) ∈V × T0 × V × T | (i, j) ∈W
e ∪A ∧t j = ti + τ w
i, j
,(19) respectively. For the transition moves, let U =
(i, j) ∈Vodd × Vodd | i ̸= j
denote
the set of all possible transition moves and respectively. For the transition moves, let U =
(i, j) ∈Vodd × Vodd | i ̸= j
denote
the set of all possible transition moves and U∗=
(i, ti, j, t j) ∈V × T × V × T −| (i, j) ∈U ∧t j = ti + τ m
i, j
(20) (20) be its extension, incorporating the time to move. be its extension, incorporating the time to move. 3.1 Path generation To compute the trajectory of the weld source, binary variables wi,ti, j,t j ,
(i, ti, j, t j) ∈W∗, indicating whether segment (i, j) ∈W is welded from time
step ti ∈T0 to time step t j ∈T , and ui,ti, j,t j , (i, ti, j, t j) ∈U∗, indicating whether
the weld source transits from i ∈Vodd to j ∈Vodd from time step ti ∈T to time step J. Schmidt, A. Fügenschuh 540 Table 2 Overview of the parameters used in the trajectory planning problem
Symbol
Domain
Definition
f H
j
R
j-th element of the load vector of the heat
source in the heat equation obtained by
FEM
f R
j
R
j-th element of the load vector of the
ambient temperature in the boundary
condition obtained by FEM
K w
N
Number of radii for the discretization of the
weld area
ki, j
R
(i, j)-th element of the stiffness matrix
obtained by FEM
mi, j
R
(i, j)-th element of the mass matrix obtained
by FEM
˜αi, j
R+
Transformed thermal diffusivity of welding
segment (i, j)
t
R+
Length of one time step
ν( j)
N
Maximum number of visits at node j
κa
[0, 1]
Cooling factor in the linear approximation of
the radiation
κw
k
(0, 1]
Proportion of the temperature gain of the
weld source applied for radius k
θinit
j
R+
Initial temperature of node j
θtar
j,t
R+
Target temperature of node j at time step t
θtar,+
j,t
R+
Upper bound of the target temperature
interval of node j at time step t
θtar,−
j,t
R+
Lower bound of the target temperature
interval of node j at time step t
ϕadd
R+
Additive constant in the linear
approximation of the radiation
ϕmax
R+
Temperature gain at the center of the weld
source
ξ(i, j, k)
N
Global node number of the k-th interior node
of welding segment (i, j) ∈T , are introduced. In the following, the abbreviation t j ∈T , are introduced. 3.1 Path generation In the following, the abbreviation w j,t =
⎧
⎪⎪⎪⎨
⎪⎪⎪⎩
k,tk:( j,0,k,tk)∈W∗w j,0,k,tk,
j ∈V, t = 0,
i,ti:(i,ti, j,t)∈W∗wi,ti, j,t +
i,ti:(i,ti, j,t)∈U∗ui,ti, j,t,
j ∈V, t ∈T ,
(i,ti,k,tk)∈W∗
ξ(i,k,h)= j
t=ti+h
wi,ti,k,tk +
(k,tk,i,ti)∈W∗
ξ(i,k,h)= j
t=ti−h
wk,tk,i,ti ,
j ∈Vint, t ∈T0
(21) w j,t =
⎧
⎪⎪⎪⎨
⎪⎪⎪⎩
k,tk:( j,0,k,tk)∈W∗w j,0,k,tk,
j ∈V, t = 0,
i,ti:(i,ti, j,t)∈W∗wi,ti, j,t +
i,ti:(i,ti, j,t)∈U∗ui,ti, j,t,
j ∈V, t ∈T ,
(i,ti,k,tk)∈W∗
ξ(i,k,h)= j
t=ti+h
wi,ti,k,tk +
(k,tk,i,ti)∈W∗
ξ(i,k,h)= j
t=ti−h
wk,tk,i,ti ,
j ∈Vint, t ∈T0
(21) (21) 123 Trajectory optimization for arbitrary layered geometries… 541 Table 3 Overview of the variables used in the trajectory planning problem
Symbol
Domain
Definition
q j,t
R+
Variable indicating the temperature gain
from the weld source of node j at time step
t
u−
j
{0, 1}
Binary variable indicating whether the
trajectory starts at node j
u+
j,t
{0, 1}
Binary variable indicating whether the
trajectory ends at node j at time step t
ui,ti , j,t j
{0, 1}
Binary variable indicating whether a
transition move between nodes i and j
from time step ti to t j is performed
w j,t
{0, 1}
Abbreviation (21) indicating whether the
weld source is positioned above node j at
time step t
wi,ti , j,t j
{0, 1}
Binary variable indicating whether the
welding segment between nodes i and j is
welded from time step ti to t j
zmax
R+
Variable indicating the last processing time
step
θ j,t
R+
Variable indicating the temperature of node
j at time step t
ϑ+
i, j,t
R+
Variable indicating the positive proportion of
the absolute temperature difference
between nodes i and j at time step t
ϑ−
i, j,t
R+
Variable indicating the negative proportion
of the absolute temperature difference
between nodes i and j at time step t
ϑ+
j,t
R+
Variable indicating the positive proportion of
the absolute temperature difference
between node j and its target temperature
at time step t
ϑ−
j,t
R+
Variable indicating the negative proportion
of the absolute temperature difference
between node j and its target temperature
at time step t is used describing at which node j ∈V the weld source is positioned at time step
t ∈T0. j∈V p∪Ve
u−
j = 1, 3.1 Path generation Fügenschuh k,tk:( j,0,k,tk)∈W∗
w j,0,k,tk = u−
j
∀j ∈V,
(22b)
j∈V
t∈T \T w
u+
j,t = 1,
(22c)
w j,t =
k,tk:( j,t,k,tk)∈W∗
w j,t,k,tk +
k,tk:( j,t,k,tk)∈U∗
u j,t,k,tk
∀j ∈V, t ∈T w, (22d)
w j,t =
k,tk:( j,t,k,tk)∈W∗
w j,t,k,tk
+
k,tk:( j,t,k,tk)∈U∗
u j,t,k,tk + u+
j,t
∀j ∈V, t ∈T \ T w,
(22e)
(i,ti, j,t j)∈U∗
ui,ti, j,t j = ω,
(22f)
t∈T0
w j,t = ν( j) ∀j ∈V \ Vc,
(22g)
t∈T0
w j,t ≥ν( j) −1 ∀j ∈Vc,
(22h)
t∈T0
w j,t ≤ν( j) ∀j ∈Vc,
(22i) k,tk:( j,0,k,tk)∈W∗
w j,0,k,tk = u−
j
∀j ∈V,
(22b)
j∈V
t∈T \T w
u+
j,t = 1,
(22c) k,tk:( j,0,k,tk)∈W∗
w j,0,k,tk = u−
j
∀j ∈V,
(22b)
j∈V
t∈T \T w
u+
j,t = 1,
(22c)
w j,t =
k,tk:( j,t,k,tk)∈W∗
w j,t,k,tk +
k,tk:( j,t,k,tk)∈U∗
u j,t,k,tk
∀j ∈V, t ∈T w, (22d)
w j,t =
k,tk:( j,t,k,tk)∈W∗
w j,t,k,tk
+
k,tk:( j,t,k,tk)∈U∗
u j,t,k,tk + u+
j,t
∀j ∈V, t ∈T \ T w,
(22e)
(i,ti, j,t j)∈U∗
ui,ti, j,t j = ω,
(22f)
t∈T0
w j,t = ν( j) ∀j ∈V \ Vc,
(22g)
t∈T0
w j,t ≥ν( j) −1 ∀j ∈Vc,
(22h)
t∈T0
w j,t ≤ν( j) ∀j ∈Vc,
(22i) j∈V
t∈T \T w
u+
j,t = 1, (22c) w j,t =
k,tk:( j,t,k,tk)∈W∗
w j,t,k,tk +
k,tk:( j,t,k,tk)∈U∗
u j,t,k,tk
∀j ∈V, t ∈T w j,t,k,tk +
k,tk:( j,t,k,tk)∈U∗
u j,t,k,tk + u+
j,t
∀j ∈V, t ∈T \ T w,
(22e)
(i,ti, j,t j)∈U∗
ui,ti, j,t j = ω,
(22f)
t∈T0
w j,t = ν( j) ∀j ∈V \ Vc,
(22g)
t∈T0
w j,t ≥ν( j) −1 ∀j ∈Vc,
(22h)
t∈T0
w j,t ≤ν( j) ∀j ∈Vc,
(22i) (i,ti, j,t j)∈U∗
ui,ti, j,t j = ω,
t∈T0
w j,t = ν( j) ∀j ∈V \ Vc,
t∈T0
w j,t ≥ν( j) −1 ∀j ∈Vc,
t∈T0
w j,t ≤ν( j) ∀j ∈Vc, 0
ti,t j:(i,ti, j,t j)∈W∗
wi,ti, j,t j +
t j,ti:( j,t j,i,ti)∈W∗
w j,t j,i,ti
= 1 ∀(i, j) ∈We : τ w
i, j = 1. (22j) ti,t j:(i,ti, j,t j)∈W∗
wi,ti, j,t j +
t j,ti:( j,t j,i,ti)∈W∗
w j,t j,i,ti
= 1 ∀(i, j) ∈We : τ w
i, j = 1. (22j) (22j) Constraints (22a)–(22c) specify the start and end point of the trajectory. 3.1 Path generation Further binary variables u−
j ∈{0, 1} and u+
j,t ∈{0, 1}, indicating whether the
trajectory starts at node j ∈V p ∪Ve or ends in this node at time step t ∈T \ T w,
respectively, are required to determine the start and the end of the trajectory correctly. Note that the latter ones are defined for a set of time steps since the discrete time
horizon can contain more time steps than the process requires to finish. Thus, the
problem of finding a feasible welding trajectory for a single layer is given by j∈V p∪Ve
u−
j = 1, (22a) 12 3 542 J. Schmidt, A. constraint (22j) can be extended to ti,t j:(i,ti, j,t j)∈W∗
wi,ti, j,t j +
t j,ti:( j,t j,i,ti)∈W∗
w j,t j,i,ti = 1 ∀(i, j) ∈We. (24) All welding segments not included in (22j) contain at least one interior node and (24)
is implied by (22g) for i ∈Vint. 3.1 Path generation Its continuity
is ensured by (22d) and (22e). The number of transition moves is limited by (22f) and
the correct number of visits is guaranteed by (22g) for all nodes in V \ Vc. Due to the
geometry of the layer, it can be possible that a node j ∈Vc of the common interface
is visited only
δ( j)
2
times if all other nodes in V p can be reached without visiting
node j. Thus, the number of visits can vary by one and (22h), (22i) are required to
incorporate this case into the model. Furthermore, we formulate two cutting planes to accelerate the solution process. At first, every feasible trajectory holds i,ti:(i,ti, j,t)∈U∗
ui,ti, j,t +
k,tk:( j,t,k,tk)∈U∗
u j,t,k,tk ≤1 ∀j ∈Vodd, t ∈T −. (23) i,ti:(i,ti, j,t)∈U∗
ui,ti, j,t +
k,tk:( j,t,k,tk)∈U∗
u j,t,k,tk ≤1 ∀j ∈Vodd, t ∈T −. (23) (23) Otherwise, both transition moves can be merged into a single one, leading to a solution
with ω −1 transition moves. This contradicts the definition of ω to be minimal. Also 123 Trajectory optimization for arbitrary layered geometries… 543 constraint (22j) can be extended to constraint (22j) can be extended to 2j) can be extended to 3.2 Temperature calculation Following the assumption of uniform heat input from Sect. 2, we adapt the piece-wise
constant, circular approximation of the Goldak heat source used by Bähr et al. (2021)
and assume that it is constant over the area related to any node in V. By this approach,
each node gets heated proportionally to its distance to the center of the weld source. Due to the used space discretization in Sect. 2, the weld source is centered above one
node i ∈V at the end of every time step. Thus, the required distances to all other
nodes j ∈V are given by the euclidean distances di, j. For a set of K w radii rw
k ,
k = 1, . . . , K w, we define factors κw
k , k = 1, . . . , K w and intervals Pk = (rk−1,rk
,
k = 2, . . . , K w. They describe the proportion of the temperature gain ϕmax at the
center of the weld source. Setting rw
1 = 0, κw
1 = 1 and P1 = {0}, the temperature
gain q j,t of every node j ∈V at time step t ∈T0 is calculated by q j,t = ϕmax
K w
k=1
i∈V
di, j∈Pk
κw
k w j,t
∀j ∈V,
∀t ∈T0,
(25) (25) where w j,t is again from (21). where w j,t is again from (21). The temperature of every node j ∈V at time step t ∈T0 is stored at the variable
θ j,t ∈R+ and the initial temperature distribution is given by θinit
j
∈R. Using the
results of Sect. 3.2 Temperature calculation 2, the temperature distribution within the workpiece is computed by θ j,0 = θinit
j
+
ϕmax −θinit
j
ϕmax
q j,0
∀j ∈V
(26)
h∈V p
(m j,h + tk j,h)θh,t =
h∈V p
m j,hθh,t−1 + t
q j,t f H
j + ϕadd f R
j
∀j ∈V p, t ∈T ,
(27) (26) h∈V p (27) ∀j ∈V p, t ∈T ,
(27) ∀j ∈V p, t ∈T , θξ(i, j,k),t−1 = −˜αi, jθξ(i, j,k−1),t + (1 + 2˜αi, j)θξ(i, j,k),t
−˜αi, jθξ(i, j,k+1),t −tqξ(i, j,k),t
∀(i, j) ∈We, k ∈Li, j, t ∈T ,
(2
θ j,t = (1 −κa)θ j,t−1 + tq j,t + κaϕadd
∀j ∈Ve, t ∈T
(2 θξ(i, j,k),t−1 = −˜αi, jθξ(i, j,k−1),t + (1 + 2˜αi, j)θξ(i, j,k),t
−˜αi, jθξ(i, j,k+1),t −tqξ(i, j,k),t
∀(i, j) ∈We, k ∈Li, j, t ∈T , (28) θ j,t = (1 −κa)θ j,t−1 + tq j,t + κaϕadd
∀j ∈Ve, t ∈T . (29) 123 123 544 J. Schmidt, A. Fügenschuh Since the welding head is already centered above a node at the beginning and the
welding process starts at t = 0, the position-dependent temperature gain q j,t, scaled
to yield the welding temperature, must be incorporated into the initial temperature dis-
tribution in (26). The approximated solutions of the heat equation for the subdomains
1 and 2 are calculated in (27)–(29). 3.3 Objective function In additive manufacturing, there are different objectives possible to choose the best
welding trajectory from a feasible set. Here we discuss the criteria used by Jiang and
Ma (2020): material/time savings, part quality, and material properties. Material/time savings Since we consider only a single layer without support structures
and allow no cooling breaks, the necessary material is constant and the processing time
d
d
l l
th
f
d t
iti
Th bi
i bl
+
d In additive manufacturing, there are different objectives possible to choose the best
welding trajectory from a feasible set. Here we discuss the criteria used by Jiang and
Ma (2020): material/time savings, part quality, and material properties. Material/time savings Since we consider only a single layer without support structures
and allow no cooling breaks, the necessary material is constant and the processing time
depends solely on the performed transition moves. The binary variables u+
j,t are used
to minimize the processing time of the considered layer by min
⎛
⎜⎝max
j∈V
t∈T \T w
tu+
j,t
⎞
⎟⎠. (30) (30) To linearize (30), a new variable zmax ∈R+ is defined with To linearize (30), a new variable zmax ∈R+ is defined with tu+
j,t ≤zmax
∀j ∈V, t ∈T \ T w. (31) (31) The objective function is then rewritten as The objective function is then rewritten as min
zmax. (32) (32) Part quality To compare different trajectories in terms of the quality of their resulting
workpiece, one must first define measurable criteria for the quality. In this work, we
consider the objective of minimizing thermal stress to measure quality since strain
within the material causes warping or can lead to cracks. In the work of Bähr et al. (2021), thermal gradients are identified as a source of thermal stress, leading to the
objective function min
t∈T0
(i, j)∈W
|θi,t −θ j,t|. (33) (33) Duetothenonlinearityoftheabsolutevaluefunction,objective (33)mustbelinearized. Therefore, non-negative auxiliary variables ϑ+
i, j,t ∈R+ and ϑ−
i, j,t ∈R+ for every
segment (i, j) ∈W and time step t ∈T0 are introduced, representing the positive and
negative portion of the absolute value function. They are calculated by Duetothenonlinearityoftheabsolutevaluefunction,objective (33)mustbelinearized. Therefore, non-negative auxiliary variables ϑ+
i, j,t ∈R+ and ϑ−
i, j,t ∈R+ for every
segment (i, j) ∈W and time step t ∈T0 are introduced, representing the positive and
negative portion of the absolute value function. leading to the linear objective function leading to the linear objective function min
t∈T0
(i, j)∈W
ϑ+
i, j,t + ϑ−
i, j,t. (35) (35) Material Properties Depending on cooling time and temperature, metal develops dif-
ferent material properties. Thus, it can be desirable to ensure a certain temperature at
some segments or even the whole workpiece to achieve characteristics supporting the
functional aspects of the finished product. A possible approach is the minimization of
the absolute deviation between the temperature of a node j ∈V at time step t ∈T0
and a given target temperature θtar
j,t ∈R+, leading to the objective function min
t∈T0
j∈V
|θ j,t −θtar
j,t |. (36) (36) The objective (36) also must be linearized. Defining again non-negative auxiliary
variables ϑ+
j,t ∈R+ and ϑ−
j,t ∈R+, representing the positive and negative portion of
the deviation, gives the objective function The objective (36) also must be linearized. Defining again non-negative auxiliary
variables ϑ+
j,t ∈R+ and ϑ−
j,t ∈R+, representing the positive and negative portion of
the deviation, gives the objective function min
t∈T0
j∈V
ϑ+
j,t + ϑ−
j,t,
(37) (37) with the additional constraint ϑ+
j,t −ϑ−
j,t = θ j,t −θtar
j,t
∀j ∈V,
t ∈T0. (38) (38) If a segment or larger parts of the workpiece should have the same temperature, then
the parameter θtar
j,t is set to the same value for the subset of nodes describing this
segment or part. For practical applications, this approach may be too strict since often it is sufficient
to maintain certain temperature intervals to achieve a special property. To relax the
last approach to minimize the distance of the temperature θ j,t of node j ∈V at time
step t ∈T0 to a desired temperature interval
θtar,−
j,t
, θtar,+
j,t
, objective (37) is used
and only constraint (38) is replaced by θ j,t + ϑ−
j,t ≥θtar,−
j,t
∀j ∈V,
t ∈T0,
(39)
θ j,t −ϑ+
j,t ≤θtar,+
j,t
∀j ∈V,
t ∈T0,
(40) (39) (40) where ϑ−
j,t and ϑ+
j,t now represent the deviation of the temperature to the left and the
right interval endpoint, respectively. The appearance of the absolute value function in (33) and (36) has a significant
impact on the applicable solution methods. On the one hand, it rules out the compu-
tation of the PDE system in a preprocessing step from Gnegel et al. 3.3 Objective function They are calculated by ϑ+
i, j,t −ϑ−
i, j,t = θi,t −θ j,t
∀(i, j) ∈W,
t ∈T0,
(34) (34) 123 Trajectory optimization for arbitrary layered geometries… 545 leading to the linear objective function (2021) since it
cannot be predetermined if the temperature gain in a node is beneficial to the objective 12 3 546 J. Schmidt, A. Fügenschuh Table 4 Interval lengths and
factors of the piece-constant
approximated heat distribution
of the weld source Fronius TPS/i
500 from Bähr et al. (2021)
k
1
2
3
4
5
Interval
Pk
[0, 0]
(0, 1]
(1, 2]
(2, 3]
(3, 5]
Factor
κw
k
1
0.96
0.7
0.37
0.1 function value. On the other hand, in an optimal solution of its linear programming
(LP) relaxation, the temperature gain of the weld source is spread over all nodes. Espe-
cially for the objective function (33), this leads to many very small positive fractional
values for the variables wi,ti, j,t j and ui,ti, j,t j and an objective function value close to
zero. Regarding the objective function (36), the LP relaxation yields slightly better
variable values due to the given target temperature instead of a second variable in the
absolute value function. This problem is also mentioned by Beisegel et al. (2021). For the procedure of Hahn et al. (2022), the solution values of the variables wi,ti, j,t j
and ui,ti, j,t j are required as input for the rounding algorithms, making the rounding
decisions difficult. Table 4 Interval lengths and
factors of the piece-constant
approximated heat distribution
of the weld source Fronius TPS/i
500 from Bähr et al. (2021) 4 Computational results To achieve realistic results, the weld source and material parameters are chosen follow-
ing practically used values. The time step length is set to t = 0.5 s and the transiting
velocity is given by vm = 30 mm s−1. For the weld source, we assume a Fronius
TPS/i 500 welding device similar to Bähr et al. (2021), also following the piece-wise
constant discretization therein. Thus, the weld source velocity while welding is set to
vw = 6.67 mm s−1 and the parameters for its discretized heat distribution are given
in Table 4using K w = 5 intervals. As welding material, steel is considered with a thermal diffusivity of α =
3.774 mm2 s−1. The temperature-related parameters are artificial and must be esti-
mated. They are chosen according to the estimation results from Beisegel et al. (2021)
yielding ϕmax = 1569 K, κa = 0.1741, and ϕadd = 709.56 K. The necessary number of transition moves ω depends on the geometry of the layer
and can, in general, not be read off the instance directly but obtained in a preprocessing
step. Therefore, we solve the MILP consisting of the path generation constraints (22)–
(24) with the objective (24) with the objective min
(i,ti, j,t j)∈U∗
ui,ti, j,t j ,
(41) (41) minimizing the number of transition moves. In the case of a layer consisting only
thin-walled structures, it holds ω = ⌈|Vodd|
2
⌉−1 since every feasible trajectory is an
Eulerian path (Bähr et al. 2021). For the computational experiments, the model consisting of constraints (22a)–(22i),
(23)–(29), and (38) is considered with the objective function (37). The target tempera-
ture is set to θtar
i,t = 973.15 K for all nodes i ∈V and time steps t ∈T0, while the initial 123 Trajectory optimization for arbitrary layered geometries… 547 Fig. 4 Computation time concerning the number of nodes increasing in steps of five Fig. 4 Computation time concerning the number of nodes increasing in steps of five Fig. 4 Computation time concerning the number of nodes increasing in steps of five temperature is set to θinit
i
= 709.56 K. All instances were solved using IBM ILOG
CPLEX 20.1.0.0 (International Business Machines Corporation 2021) on a Mac Pro
with an Intel Xeon W running 32 threads parallel at 3.2 GHz clock speed and 768 GB
RAM. 4 Computational results For all computations, a time limit of 10,800s was set and a branching priority
by increasing cost per coefficient count was enabled. 4.1 CPU time sensitivity analysis In the first set of experiments, the effect of various input parameters is studied con-
cerning the runtime behavior of the solver. This gives insights to which complexity
and size an instance can be solved within the given time limit. Number of Nodes Varying the node number from 35 to 70 in steps of five nodes, 41
instances with ω = 1 were randomly generated for each value. The computation of
all 328 instances required 1,455,812s and the CPU time for each run is given in Fig. 4
, together with three common mean values. For all instances with 35 nodes, the optimal solution is obtained in less than 1800s
and the average solution time increases with every additional node. Furthermore, there
is a large spread of the solution time within the instances with equal node numbers. Already for 45 nodes, one instance is not solved to global optimality, while for the
largest instances with 70 nodes, there are some whose proven optimal trajectory is
found in less than 5400s. Number of transition moves Now the number of necessary transition moves ω is
varied between zero and three, while the number of nodes is kept at 50. Again, 41
instances were generated for each value and the computation of all of them finished
after 1,134,978s. The detailed solution times of the 164 instances are displayed in
Fig. 5, together with three common mean values. It shows that the number of necessary transition moves has a great impact on the
computation time. In the absence of transition moves, the global optimal solution is 12 3 548 J. Schmidt, A. Fügenschuh Fig. 5 Computation time concerning the number of necessary transition moves Fig. 5 Computation time concerning the number of necessary transition moves computed very fast (less than 1000s), but, already in the presence of a single one,
there is a large spread of the solution times from 222s to the time limit of 10,800s
and a resulting gap of 19.9%. For more than a single transition move, only one of
the respective 82 instances was solved within the given time limit. This behavior
is a consequence of the massive increase of possible trajectories in the presence of
transition moves since for every node in Vodd there is now the possibility of moving
at certain time steps also to more distant parts of the geometry instead of only visiting
its neighbors. 4.3 LP relaxation In this experiment, we study the effect of the objective functions (33) and (36) to the LP
relaxation of the model using the respective objective with the necessary constraints. Therefore, relaxed binary variables with a value smaller than 10−3 are neglected to
achieve clear results. For the computations, the instance from Sect. 4.2 is taken again. Detailed information about the the solutions can be found in the Tables 5and 6. For both objective functions, the solution of the LP relaxation yields a similar
distribution of the relaxed variables on the interval [0, 1]. Regarding the absolute
difference between adjacent nodes (33), 97.8% of them have a value smaller than 0.1
and only three of them are greater than 0.5. Considering the absolute deviation from
a target temperature (36), 91.2% of the variables are smaller than 0.1 and only five
are greater than 0.5. Interestingly, the variables ui,ti, j,t j for the transition moves are
all smaller than 0.1 in both cases, yielding no information about preferable transition
moves. As expected, the number of variables with a value greater or equal to 10−3
is smaller for the objective function (36) since the given target temperature requires
more heating of the node to reduce the absolute deviation. 4.2 Detailed temperature progression In this experiment, the focus is on the temperature progression within the workpiece. We consider an instance with 50 nodes and ω = 2. Its solution took 9233s. The optimal
trajectory and the temperature progression of two selected nodes are displayed in
Fig. 6. The red circled node is within the thin-walled part of the instance. Its initial tempera-
ture is higher than the given value due to its proximity to the starting node. Furthermore,
it is the first node visited by the weld source, yielding a large increase in its temper-
ature. Every trespassing of it generates a peak in the node’s temperature progression,
followed by a cooling phase. Therein, the radiation in the environment is the primary
source of the heat loss. For the blue node located in the bulky part of the instance, the effect of the heat
conduction is better visible. Its initial temperature equals the prescribed value. Due
to the heating of the nodes on the left of the bulky part, its temperature increases due
to the heat conduction. At the fourteenth welding move (at time step 28), there is a
significant temperature gain caused by its proximity to the weld source, followed by
a cooling phase, where heat radiation and heat conduction nearly balance each other. Trajectory optimization for arbitrary layered geometries… 549 Fig. 6 Optimal trajectory of the considered instance (left) with the chosen welding order and the temperature
progression of two selected nodes (right), marked by a red and blue circle, respectively. The bulky part
is represented with all possible connections by thin grey lines. Transition moves are displayed by dashed
arrows and the starting node is highlighted by a red square Fig. 6 Optimal trajectory of the considered instance (left) with the chosen welding order and the temperature
progression of two selected nodes (right), marked by a red and blue circle, respectively. The bulky part
is represented with all possible connections by thin grey lines. Transition moves are displayed by dashed
arrows and the starting node is highlighted by a red square At the trespassing of the weld source in the 29th weld move (at time step 56), there is
again a large increase in the temperature. 5 Conclusions and future work In this work, we presented a MIPDECO model to optimize the trajectory of the weld
source in WAAM for a single layer of arbitrary geometry. Its formulation as a MILP 123 123 550 J. Schmidt, A. Conflict of interest The authors declare that there is no conflict of interest. Conflict of interest The authors declare that there is no conflict of interest. OpenAccess ThisarticleislicensedunderaCreativeCommonsAttribution4.0InternationalLicense,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/. 5 Conclusions and future work Schmidt, A. Fügenschuh was introduced and a detailed heat conduction model, including also heat radiation
into the environment, was incorporated by applying finite element and finite difference
methods. For different optimization goals, we presented possible objective functions
and proved the applicability of our approach using the state-of-the-art numerical solver
CPLEX in several experiments. The effect of the number of considered nodes and
the number of necessary transition moves were extensively studied, revealing that
especially the latter has a great impact on the model complexity and the computation
time. Furthermore, a detailed discussion of the temperature progression highlighting
the considered aspects of heat transmittance was given for an example instance. In our future work, we will accelerate the solution process to allow the computation
of large-size workpieces and compare the computed temperature distribution to the
one measured during the manufacturing process. Therefore, it is also necessary to
extend the model into three dimensions to calculate several connected layers at once
and incorporate the choice of different trajectories per layer. Otherwise, there will be
joints reducing the quality of the finished workpiece. In future experiments, we will
also study the effect of the ratio |1|
|2| to the computation time. Funding Open Access funding enabled and organized by Projekt DEAL. 5 Conclusions and future work Fügenschuh Table 5 Number of relaxed binary variables greater or equal than 10−3 and their minimum and maximum values for the objective function (33)
Variable
Index set
Total number
Number (optimal solution)
≥10−3
Minimum
Maximum
wi,ti , j,t j
W∗
5580
34
1345
0.001
0.773
ui,ti , j,t j
U∗
9644
2
108
0.001
0.069
u−
j
V
24
1
6
0.079
0.208
u+
j,t
V × T w
72
1
3
0.055
0.805 Table 5 Number of relaxed binary variables greater or equal than 10−3 and their minimum and maximum values for the objective function (33)
Variable
Index set
Total number
Number (optimal solution)
≥10−3
Minimum
Maximum
wi,ti , j,t j
W∗
5580
34
1345
0.001
0.773
ui,ti , j,t j
U∗
9644
2
108
0.001
0.069
u−
j
V
24
1
6
0.079
0.208
u+
j,t
V × T w
72
1
3
0.055
0.805 123 Trajectory optimization for arbitrary layered geometries… 551 layered geometries…
Table 6 Number of relaxed binary variables greater or equal than 10−3 and their minimum and maximum values for the objective function (36)
Variable
Index set
Total number
Number (optimal solution)
≥10−3
Minimum
Maximum
wi,ti , j,t j
W∗
5580
34
755
0.001
0.840
ui,ti , j,t j
U∗
9644
2
70
0.002
0.078
u−
j
V
24
1
5
0.130
0.403
u+
j,t
V × T w
72
1
2
0.160
0.840 Table 6 Number of relaxed binary variables greater or equal than 10−3 and their minimum and maximum values for the objective function (36)
Variable
Index set
Total number
Number (optimal solution)
≥10−3
Minimum
Maximum
wi,ti , j,t j
W∗
5580
34
755
0.001
0.840
ui,ti , j,t j
U∗
9644
2
70
0.002
0.078
u−
j
V
24
1
5
0.130
0.403
u+
j,t
V × T w
72
1
2
0.160
0.840 Table 6 Number of relaxed binary variables greater or equal than 10−3 and their minimum and maximum values for the objective function (36)
Variable
Index set
Total number
Number (optimal solution)
≥10−3
Minimum
Maximum
wi,ti , j,t j
W∗
5580
34
755
0.001
0.840
ui,ti , j,t j
U∗
9644
2
70
0.002
0.078
u−
j
V
24
1
5
0.130
0.403
u+
j,t
V × T w
72
1
2
0.160
0.840
1 3 Table 6 Number of relaxed binary variables greater or equal than 10−3 and their minimum and maximum values for the objective function (36)
Variable
Index set
Total number
Number (optimal solution)
≥10−3
Minimum
Maximum
wi,ti , j,t j
W∗
5580
34
755
0.001
0.840
ui,ti , j,t j
U∗
9644
2
70
0.002
0.078
u−
j
V
24
1
5
0.130
0.403
u+
j,t
V × T w
72
1
2
0.160
0.840 Table 6 Number of relaxed binary variables greater or equal than 10−3 and their minimum and maximum values for the objective function (36)
Variable
Index set
Total number
Number (optimal solution)
≥10−3
Minimum
Maximum
wi,ti , j,t j
W∗
5580
34
755
0.001
0.840
ui,ti , j,t j
U∗
9644
2
70
0.002
0.078
u−
j
V
24
1
5
0.130
0.403
u+
j,t
V × T w
72
1
2
0.160
0.840 123 12 552 J. Funding Open Access funding enabled and organized by Projekt DEAL. References Archetti C, Speranza MG (2008) The split delivery vehicle routing problem: a survey. In: The vehicle
routing problem: latest advances and new challenges. Springer, pp 103–122 Bähr M, Buhl J, Radow G, Schmidt J, Bambach M, Breuß M, Fügenschuh A (2021) Stable honeycomb
structures and temperature based trajectory optimization for wire-arc additive manufacturing. Optim
Eng 22(2):913–974 Beisegel J, Buhl J, Israr R, Schmidt J, Bambach M, Fügenschuh A (2021) Mixed-integer programming for
additive manufacturing. Cottbus Math 1–32 Diourté A, Bugarin F, Bordreuil C, Segonds S (2021) Continuous three-dimensional path planning (CTPP
for complex thin parts with wire arc additive manufacturing. Addit Manuf 37:101622 Dror M, Trudeau P (1990) Split delivery routing. Naval Res Logist (NRL) 37(3):383–402 Ferreira RP, Scotti A (2021) The concept of a novel path planning strategy for wire-arc additive
manufacturing of bulky parts: pixel. Metals 11(3):498 Fourier JBJ (1878) The analytical theory of heat. The University Press Fourier JBJ (1878) The analytical theory of heat. The University Press Gnegel F, Fügenschuh A, Hagel M, Leyffer S, Stiemer M (2021) A solution fr
constrained mixed-integer problems. Math Program 188(2):695–728 Hahn DW, Özisik MN (2012) Heat conduction. Wiley 123 123 Trajectory optimization for arbitrary layered geometries… 553 Hahn M, Kirches C, Manns P, Sager S, Zeile C (2022) Decomposition and approximation for PDE-
constrained mixed-integer optimal control. In: Non-smooth and complementarity-based distributed
parameter systems. Springer, pp 283–305 International Business Machines Corporation (2021) IBM ILOG CPLEX optimizer reference manual. https://www.ibm.com/docs/en/icos/20.1.0 Jiang J, Ma Y (2020) Path planning strategies to optimize accuracy, quality,
additive manufacturing: a review. Micromachines 11(7):633 Jiang J, Ma Y (2020) Path planning strategies to optimize accuracy, quality, build time and material use in
additive manufacturing: a review. Micromachines 11(7):633 Ma G, Zhao G, Li Z, Xiao W (2019) A path planning method for robotic wire and arc additive manufacturing
of thin-walled structures with varying thickness. In: IOP conference series: materials science and
engineering, vol 470. IOP Publishing, p 012018 Michel F, Lockett H, Ding J, Martina F, Marinelli G, Williams S (2019) A modular path planning solution
for wire+ arc additive manufacturing. Robot Comput Integr Manuf 60:1–11 Quarteroni A, Valli A (1999) Domain decomposition methods for partial differential equations. Oxford
University Press Schmitz M, Wiartalla J, Gelfgren M, Mann S, Corves B, Hüsing M (2021) A robot-centered path-
planning algorithm for multidirectional additive manufacturing for WAAM processes and pure object
manipulation. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps
and institutional affiliations. References Appl Sci 11(13):5759 Taler J, Ocło´n P (2014) Finite element method in steady-state and transient heat conduction. Encycl Therm
Stress 4:1604–1633 Treutler K, Wesling V (2021) The current state of research of wire arc additive manufacturing (WAAM): a
review. Appl Sci 11(18):8619 Vogt RH, Leyffer S, Munson TS (2022) A mixed-integer PDE-constrained optimization formulation f
electromagnetic cloaking. SISC 44(1):B29–B50 Williams SW, Martina F, Addison AC, Ding J, Pardal G, Colegrove P (2016) Wire+ arc additive
manufacturing. Mater Sci Technol 32(7):641–647 Zhang C, Shen C, Hua X, Li F, Zhang Y, Zhu Y (2020) Influence of wire-arc additive manufacturing path
planning strategy on the residual stress status in one single buildup layer. Int J Adv Manuf Technol
111(3):797–806 Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps
and institutional affiliations. 123
|
https://openalex.org/W2146567731
|
https://hal.inria.fr/hal-01055675/file/Paper_7_-_FREUNDT.pdf
|
English
| null |
Modular and Generic Control Software System for Scalable Automation
|
IFIP advances in information and communication technology
| 2,010
|
cc-by
| 3,854
|
To cite this version: Christian Brecher, Martin Freundt, Daniel Schöllhorn. Modular and Generic Control Software System
for Scalable Automation. 5th IFIP WG 5.5 International Precision Assembly Seminar (IPAS), Feb
2010, Chamonix, France. pp.263-270, 10.1007/978-3-642-11598-1_31. hal-01055675 Distributed under a Creative Commons Attribution 4.0 International License Modular and Generic Control Software System for
Scalable Automation
Christian Brecher, Martin Freundt, Daniel Schöllhorn
Fraunhofer Institute for Production Technology, Steinbachstrasse 17,
52074 Aachen, Germany, Tel.: +46(0)241-8904-253, Fax.: +49(0)241-8904-6253,
E-mail: martin.freundt@ipt.fraunhofer.de Abstract. The development of automated production systems is subdivided in
two mayor tasks. One is the development of the processes needed to meet the
requirements for the product, the other is the setup of a control system enabling
the hardware to perform these processes. Typically the larger amount of the
available resources is needed for the setup of hardware and implementation of
the required control mechanism, leaving only limited resources for the process
development. Especially for small scale and prototype production with a high
rate of changes, this is why fully automated solutions don't pay off and manual
or partial manually assembly is preferred [1]. This paper introduces an approach
how to separate the implementation effort of the hardware specific tasks from
the process definition, allowing a fast and easy setup for new automation
systems, due to simultaneous development and a high rate of reuse of previous
solutions. Keywords: software, framework, control system, one piece flow, assembly HAL Id: hal-01055675
https://inria.hal.science/hal-01055675v1
Submitted on 13 Aug 2014 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 Introduction For most R&D orientated Enterprises as well as high tech production sites the
implementation of automated processes is dominated by fast changing equipment and
complex production or test setups. To be able to cover various automation tasks, a
wide range of equipment (e.g. Sensors, Robots, Actuators) has to be integrated within
the assembly system [2]. In order to make different types of hardware work together,
engineering the control software usually takes most of the time. Even when
components have been used in automated setups before, the interfaces have to be
adapted to each other and the particular process requirements. As a result, a lot of
work is required to integrate the same hardware again and again just because the setup
of the hardware configuration has changed. Even the control programs for the realization of the processes are developed
specific to the particular application without the option to efficiently prepare for a
future reuse of software code due to the interdependences of process and hardware. According to the experience with hardware setup and process development the effort
needed for automation was about 70 % of the overall time leaving only 30% of the
resources for the actual task, the process engineering. To be able to focus on the process engineering it is necessary to decouple hardware
setup and process development, at least in regard to the software programming. A 2 2 Modular and Generic Control Software System for Scalable Automation new approach within software for the automation of processes is required. This
software system must enable a full reuse of previously developed solutions of
hardware specific code as well as code describing the process flow. Once developed
and implemented, a process like gripping a part in a special way or moving a robot
towards a position and orientation, should be a procedure that does not require
additional programming when used in another context. The same applies for the code
providing hardware specific functions, like taking care about signal generation,
positioning processes and communication with controllers. The aim is to program the hardware typical functions within “hardware specific”
and “process specific” code separated from each other. Thereby the point of view has
to be changed form the conventional thinking “what the robot has to do in order to
make the process happening” towards focusing on “what has to happen with the parts
in order to assemble them”. Introduction Thereby, it doesn’t matter which kind of hardware
configuration will be used to implement the process description. In addition, the
software has to be extendable to allow a fast and easy integration of new components. Based on this vision, a software system was designed and realized, achieving the
separation of process related and hardware related code elements. Therefore the
control system has to be grouped in different divisions representing characteristic
aspects of the overall system: -
Hardware representation: Encapsulating all properties and functions of the
available hardware, including data communication and control of hardware
internal functions -
Process representation: All process specific elements have to be
encapsulated within a code division, so that reuse is independent form the
hardware components which are utilized for execution. -
Basic system functionality: The interaction between the hardware specific
code elements and the process specific code has to be organized by a
component. This component has to ensure that the process description will be
put into action as adequate hardware is available. -
Basic system functionality: The interaction between the hardware specific
code elements and the process specific code has to be organized by a
component. This component has to ensure that the process description will be
put into action as adequate hardware is available. Main condition is, that these software divisions are independent from each other
although they need to interact in order to perform the designated tasks. The key
benefit of this approach is the complete separation of the hardware control
programming effort from the process description programming effort. In doing so, it
is possible to setup and configure the processes without the need of knowledge about
the hardware of the system that performs the later actions. Furthermore, the hardware
control can be configured without the knowledge of the processes allowing a
separated development process. programming effort from the process description programming effort. In doing so, it
is possible to setup and configure the processes without the need of knowledge about
the hardware of the system that performs the later actions. Furthermore, the hardware
control can be configured without the knowledge of the processes allowing a
separated development process. This is a key feature for a fast and efficient process development as existing
solutions like gripping a component or aligning a component based on a reference
signal can be reused without code implementation. Application Scenario AutoMiPro To realize the development and implementation of a software system with the
abilities and specification described above an adequate application scenario is Christian Brecher, Martin Freundt, Daniel Schöllhorn 3 required. Inside the AutoMiPro research project at the Fraunhofer IPT, logistics in
terms of the design of hard- and software solutions for a changeable production
respectively a one piece material flow within automated precision and micro assembly
processes was developed. A demonstrator was rigged at the Fraunhofer IPT,
consisting of four main components shown in figure 1. The skills of component
processing are demonstrated within a diode laser assembly process containing various
micro optical components. Therefore, hardware is needed capable of handling parts
with different shapes, materials and handling requirements. As micro mechanical and
optical parts of diode laser systems differ in their parameters due to the production
process, flexibility is required. In order to increase efficiency by minimizing the use
of sensor systems, every part must be treated as a unique entity with its corresponding
data sheet characterizing the part. Thus it is possible to allow for handling and
positioning of each part based on its real properties within a distanced process. In
addition, information generated during the production process can directly be stored
part specific, enabling a full traceability of each production step. The assembly
process of a diode laser system itself is very complex. Alignment of at least one, Fig. 1. Demonstrator setup of the AutoMiPro Project – Application: diode laser assembly
1. 2. 3. 4. 1. 2. 3. 4. Flexible assembly station (1)
Three reference stations (2)
Transport system (3)
Storing device (4)
Assembly cell Storing cell Gripper exchange
Reference station Component carrier Transport Assembly cell Storing cell Gripper exchange Fig. 1. Demonstrator setup of the AutoMiPro Project – Application: diode laser assembly often more degrees of freedom is required for most of the optical parts. The
alignment starts to get more complex as different alignment movements within the
multiple degrees of freedom affect each other. By using the unique data for every part
it gets possible to apply adjustment processes on different parts or at least part
variations without change effort, once part properties are used to parameterize the
alignment processes. In order to allow for a company-overreaching production it gets even more
important to separate the process description for hardware and form part specific
properties and functions. Application Scenario AutoMiPro As the production chain overreaches different hardware
equipment and technology, a hardware independent description of the processing is
required. This hardware independent process information is linked to parts itself, the
same way the properties of the part are stored. The part so called “carries its own
assembly description” through the production process. Assuming that all hardware
control systems are capable of using this information, the necessary activation of
hardware can be generated automatically inside the software. In this case no Modular and Generic Control Software System for Scalable Automation 4 and Generic Control Software System for Scalable Autom additional input to the system is needed, realizing a clear separation between the
hardware control issues and the product, respectively the process leading to the
product. Design of the Software System To implement a software system that completely separates the programming of the
hardware control form the specification of the process information two different types
of software fields are needed. One for the hardware and its capabilities and one for the
process information describing parts and procedures. The framework organisation
element has to be capable to separate and organize the interaction between the
hardware and the process description. In addition it must allow for flexible, fast and
easy reconfiguration of the current hardware setup. Those three components,
represent all aspects of a fully functional assembly system. (ref. figure 1). Fig. 2. Software components required to represent all aspects of an automated process flow
including hardware control
Hardware
representation
Process
representation
Framework
organization
- Robots
- Gripper
- Sensors
- Movement
- Adjustment
- Gripping
- Configuration
- Module
Communication
Software configuration
representing the
real world Fig. 2. Software components required to represent all aspects of an automated process flow
including hardware control To equip an organisation component with an appropriate logic, allowing to
organize module interaction, causes additional effort for configuration. It also
handicaps the goal of being universally usable and scalable as configuration specific,
application related code is required [3]. Due to a required reduction of complexity it is
essential, that the organisation component do not have to be aware of the specific
system constellation in order to avoid the described effort for an omniscient
organisation component. Hardware representing Modules The main goal regarding efficiency within the setup of an automated device is
reusability of known and already realized functions, like accessing hardware via
external interfaces or using positioning strategies for a robot system. Further, being
able to apply changes within a running system without retesting and modifying
further system programming is important to extent and optimizes functionalities. 5 Christian Brecher, Martin Freundt, Daniel Schöllhorn Conventional control systems, often decentralized on robot controllers are highly
integrated due to the limited abilities of the programming language or fundamental
execution of NC-Code. All hardware components therefore have to be controlled by
one device allowing for accessing all data and being able to integrate flexibility. In
order to be able to use knowledge and skills of e.g. computer science personal, a PC
platform and a common high level language like C#, capable to realize object
orientated software has to be utilized. The object orientated programming allows for separation of properties and
functionalities into separate software objects, each representing the smallest entity of
a hardware component. A device with an integrated pneumatic actuator for example
would be separated into the device specific part and the pneumatic actuator. This
actuator itself is connected to a standard component, a pneumatic valve, which is
already available and completely represented within the software framework. Thereby
the functions for switching valves and accounting for actor properties, already is
included within the software and can be reused. In order to minimize the effort of extending the system with additional objects the
method of inheritance of software objects is used. Inside the developed software
structure every part of the real world is represented by a single software object,
containing all information and providing all functions of its real-world counterpart. By strictly separating and isolating functions and properties into software objects,
it gets possible to modify and even replace whole elements with no or at least minimal
effort. Communication between these objects is realized by primitive commands
respectively messages. Therefore each object is programmed to be capable to process
certain messages and commands. In order to avoid the implementation and configuration of an omniscient
organisation component, the software objects, representing hardware components, are
organized within a hierarchical, tree like structure. This structure between the
software objects has to be defined at system start up based on the relations of the real
system configuration. Hardware representing Modules The system automatically keeps it up to date during automated
processing. With this approach production hardware as well as product parts can be
described the same way. Figure 3 illustrates how a gripper carries a part, in this case a
Fast-Axis-Collimation lens. The gripper is subordinated underneath the bottom side
of the gripper interface, which is connected to the upper interface side. The upper
interface is linked to the robot taking care about its positioning. All information concerning the position and orientation of components is defined
relative to the superior component. This allows for a fully automated update of the
data, allowing automated configuration modifications like gripper exchange or the
gripping and releasing of parts. Therefore the part is always dedicated to the
component defining its position within the real setup. If it is placed within a fixture,
its position is defined relative to the fixture. In case a robot respectively a gripper
handles it, it is dedicated relative to the gripper, which defines its current position. In
order to extract the information about position and orientation of a component, the
part can be “asked” for its position. Once this request is started, internal functions all
objects provide, causes the calculation of the absolute position based on all relative
data independent to the current configuration of the system. In order to ensure proper precision of the virtual model, certain process steps can
be used to update the relative position of a component. A fully traceable production Modular and Generic Control Software System for Scalable Automation 6 can be realized linking all historical data and part information within the data set for
the assembled product. Even relevant process data can be collected within processing
and assigned to the processed components for full traceability within conventional
production as well as for process ramp up or process development. Fig. 3. Example for the representation of real world elements within the software system
Hardware Part
Assembly Part
Hardware Link Fig. 3. Example for the representation of real world elements within the software system In addition, the modular concept of the software control guarantees an easy
exchange or modification of hardware components or process logics. If for example a
new gripping device is added, only the gripper software object needs to be exchanged. Therefore, an existing gripper class definition can be derivated to a new gripper
subclass or only be parameterized without adding further functions. Hardware representing Modules All other
participating modules, controlling the other hardware and processes, stay as they are,
with the ability to use the new gripper right away. Thus a toolbox of different
software modules is created. The operator is allowed to simply select and connect the
required modules and configure the hardware setup as needed. Process Representing Control Modules The second software element addresses the way process information is described. Due to the modular and flexible setup of the assembly, the description of the
processes has to be hardware independent. This is crucial for parallel development of
hardware and process as well it is a basic condition for reusability of developed
process steps. Therefore, all process descriptions are defined parameterized. Parameters can be software objects representing hardware components like grippers
or representations of objects being processed as well as simple parameters. All
absolute values, in particular position and orientation values, required for the
execution of handling processes are thereby defined based on the component data,
calculated on the fly once the process description is executed. This ensures that
current configurations and positions of robots or other variegating properties are
included once a command or process description is executed. Christian Brecher, Martin Freundt, Daniel Schöllhorn 7 On behalf of a deterministic process development, detailed process descriptions
can be used for defining the processing based on elementary commands, like “move
left 2 mm”, with no margin for variances. Due to changeability demands and the need
for simplification of the process development, more abstract commands like “position
part A next to part B with an offset of 2 mm” can be executed and realized. For more
complex logics, as alignment processes, a process command object is available
allowing for encapsulation of process logic by the generation of command primitives,
executable by the software framework. Process Example – Diode Laser Assembly Process To adjust a micro optical lens in front of the diode laser source, multiple different
procedures have to be executed. As described, the information specifying these
procedures are stored as a list of components dedicated to the part information of a so
called master part, describing only the “what is to do” but not the “how to do it”. This
includes command primitives and complex process descriptions like adjustment and
alignment functions e.g. for the fully automated active alignment of a Fast-Axis-
Collimation lens. As the assembly process is started, for example the FAC lens is
asked to move itself towards the diode laser in, in order to get it into adjustment
position as shown in figure 5. For this operation it is completely regardless where the
part is located or how it will be transported. The part, supposed to move itself just Fig. 4. Fully automated FAC alignment at the Fraunhofer IPT using hardware independent
process descriptions and process independent hardware programming
beam guidance for
vision system
analyses
detected image
Intensity measurement Fig. 4. Fully automated FAC alignment at the Fraunhofer IPT using hardware independent
process descriptions and process independent hardware programming creates a new command to provoke its transport to the target position, as it is not
capable to move itself. This command is always addressed to the superior software
object until a software object is identified, accepting the command for execution (ref. Figure 3). In case of the linking of a positioning task, each rejection of the command
causes a modification in order to accomplish the initial positioning request. As the
part wants to be moved and is not capable to move, it asks the gripper, currently
defining its position to move. The gripper, itself not capable to move, recalculates the
moving request in a way that it wishes to get moved by its superior object so that the
FAC lens will be moved the way wanted to, initially. By this, a command is
transferred through the hierarchical system, although no component is aware of the creates a new command to provoke its transport to the target position, as it is not
capable to move itself. This command is always addressed to the superior software
object until a software object is identified, accepting the command for execution (ref. Figure 3). Summary and Outlook The presented software framework is currently in implementation. Defining
hardware-independent positioning processes and executing theses on different
hardware configurations is already put into application. Further expansion of the
system by integration of additional devices is ongoing. As the designed system
provides a solid base for complex automation tasks, additional research will be
conducted within the field of the design of more complex process objects in order to
allow for automated rigging and adaptive or self learning processes. Acknowledgements The authors thank the German Federal Ministry of Education and Research
(BMBF) within the project »AutoMiPro«, part of the Framework Concept »Research
for Tomorrow’s Production« (02PB3140) managed by the Project Management
Agency Forschungszentrum Karlsruhe, Production and Manufacturing Technologies
Division (PTKA-PFT). Process Example – Diode Laser Assembly Process In case of the linking of a positioning task, each rejection of the command
causes a modification in order to accomplish the initial positioning request. As the
part wants to be moved and is not capable to move, it asks the gripper, currently
defining its position to move. The gripper, itself not capable to move, recalculates the
moving request in a way that it wishes to get moved by its superior object so that the
FAC lens will be moved the way wanted to, initially. By this, a command is
transferred through the hierarchical system, although no component is aware of the 8 Modular and Generic Control Software System for Scalable Automation 8 overall structure, until a software object accepts execution of the current command. By this means, boundary conditions like acceptable gripping methods or gripping
force limitations can be accounted for in an unknown environment of hardware
components. This enabled for parallelisation of development and extendibility of
already producing systems but also cause only partial predictable process realisation. Although it is possible to assign commands to be executed by predefined hardware
components, using their unique object ID, instead of using hardware independent
commands. This option keeps the concept scalable for development and introduction
within industrial applications; even some of the advantages of the concept thereby get
reduced. Similar to parts provoking their own processing by creating command
primitives, process objects itself can create requests to get for example information
out of a vision system as it is required for the handling and alignment of a FAC lens
as shown in figure 4. References 1. J. Hesselbach et al.: mikroPRO – Untersuchung zum internationalen Stand der
Mikroproduktionstechnik. Essen: Vulkan-Verlag, 2002 1. J. Hesselbach et al.: mikroPRO – Untersuchung zum internationalen Stand der
Mikroproduktionstechnik. Essen: Vulkan-Verlag, 2002 p
g
2. Robot Visions to 2020 and beyond – The Strategic Research Agenda for robotics
in Europe, 2009 2. Robot Visions to 2020 and beyond – The Strategic Research Agenda for robotics
in Europe, 2009 3. J. Bara, L. Cararinha-Maos: Coalitions of manufacturing components for shop
floor agility. International journal of networking and virtual organisations IJNVO
2003 ISBN 1470-9503
|
https://openalex.org/W3047077548
|
https://ieeexplore.ieee.org/ielx7/6287639/8948470/09159568.pdf
|
English
| null |
Optimization of the ISP Parameters of a Camera Through Differential Evolution
|
IEEE access
| 2,020
|
cc-by
| 11,880
|
Received July 26, 2020, accepted August 2, 2020, date of publication August 5, 2020, date of current version August 17, 2020. Received July 26, 2020, accepted August 2, 2020, date of publication August 5, 2020, date of current version August 17, 2020 Digital Object Identifier 10.1109/ACCESS.2020.3014558 LUIS V. HEVIA1, MIGUEL A. PATRICIO
2, (Member, IEEE), JOSÉ M. MOLINA2, (Member, IEEE),
AND ANTONIO BERLANGA2, (Member, IEEE)
1BQ Engineering Team, 28232 Las Rozas-Madrid, Spain (
)
1BQ Engineering Team, 28232 Las Rozas-Madrid, Spain
2Applied Artificial Intelligence Group, Universidad Carlos III de Madrid, 28270 Colmenarejo, Spain
Corresponding author: Miguel A. Patricio (mpatrici@inf.uc3m.es) (
)
1BQ Engineering Team, 28232 Las Rozas-Madrid, Spain
2Applied Artificial Intelligence Group, Universidad Carlos III de Madrid, 28270 Colmenarejo, Spain
Corresponding author: Miguel A. Patricio (mpatrici@inf.uc3m.es) This work was supported in part by the Private Research Project of the Company BQ, and in part by the Public Research Projects of the
Spanish Ministry of Economy and Competitiveness (MINECO) under Grant TEC2017-88048-C2-2-R, Grant RTC-2016-5595-2,
Grant RTC-2016-5191-8, and Grant RTC-2016-5059-8. ABSTRACT Within the design and development of a smartphone, an important phase arises regarding time,
which is related to the tuning of the ISP (image signal processor) of the camera. The ISP is an element that
allows the adjustment of the images captured by a sensor in order to achieve the best image quality. The ISP
implements different image improvement algorithms such as white balancing, denoising, and demosaicing
as well as other image enhancement algorithms. The purpose of the ISP tuning process is to configure the
parameters of these algorithms so that the processed images are of the highest quality. This task is carried out
by the camera tuning engineer, who iteratively adjusts the ISP parameters through trial and error procedures
until the desired quality is achieved. The complete adjustment process can be extended to several weeks
and even months. The authors present a novel solution based on differential evolution, which allows a
first-adjusted approximation of the ISP in a few hours. This work presents an architecture based on an
optimization through a differential evolution algorithm with which different ISP tuning tests are carried
out, and the good results in quality and time are verified. INDEX TERMS Differential evolution, ISP tuning, smartphone desig INDEX TERMS Differential evolution, ISP tuning, smartphone design. is work is licensed under a Creative Commons Attribution 4.0 License. For more information, see https://creativecommons.org/licenses/by/4.0/ I. INTRODUCTION Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE libraries for the camera. It is an iterative process between
these professionals that usually starts by defining an appropri-
ate scenario for the tuning and analysis, such as a test chart to
obtain distinctively objective values by metrics or a still-life
image to acquire a desirably pleasing feeling for most people. Then, the professionals start to tune the values by starting
with the factory values or those from previous models, such
that the libraries have to be compiled and loaded onto the
device. Subsequently, the scenario is photographed by the
programmers with all the different libraries that they prepared
under different values of lighting to check the response of the
camera. After all of the needed images are taken, the analysts
give feedback and the corrections that they see fit. The whole
process continues until there is a consensus, which, as we
previously mentioned, can take weeks or months. our work in that they automatically search the ISP parameters
that allow the capture of the images with the best quality. Bioinspired techniques that use a metaphor of natural
evolution have proven to be very useful in addressing opti-
mization problems. All of these approaches are based on
the application of two operators, selection and search, which
allow exploring and exploiting the information in the search
space [17]. The recombination and mutation operators are
used as search operators, and for the selection operator,
the well-known biological natural selection metaphor is
applied to make it more likely to survive the most adapted
solutions; i.e., the solutions that best solve the problem will
transmit their achievement to the next generation. Computational evolution techniques have been used to
solve problems in different areas. Within the area of computer
vision, different works make use of these techniques. In [18],
different works can be found that are related to the appli-
cation of evolutionary algorithms (EAs) in computer vision
problems, such as the accurate modeling of image features,
an intelligent approach for three-dimensional reconstruction,
or multiobjective sensor planning for accurate reconstruc-
tion. The main techniques, referred to as EAs, are genetic
algorithms, genetic programming and evolution strategies. I. INTRODUCTION Differential evolution (DE) proposed by Storn and Price [19],
[20] has emerged as an EA technique with the objective
of improving the efficiency of the rest of the techniques in
the search for the global optimum with the least number of
parameters possible. Only 3 parameters need to be specified:
the size of the population, the crossover rate (these parameters
are in common with the rest of the EA techniques) and a
parameter specific to the DE technique called the scale factor. The differential feature of DE versus other EA techniques
is found in the self-referential mutation property. That is,
the scale factor allows an automatic and gradual adaptation
on all the parameters of the solution vector proportional to
the dispersion of each one [21], [22]. Some research papers have been published in the field
of ISP tuning. The work that can approximate the problem
posed in our proposal is that of Nishimura et al. [13]. An ISP
has a pipeline architecture composed of different dedicated
hardware blocks that execute a given reconstruction algo-
rithm. The algorithm used by Nishimura et al. is a nonlinear
optimization algorithm based on Nelder-Mead Simplex [14]
and Subplex. Unlike the work presented in this article, in [13],
it focuses on the optimization of a limited set of parameters
(3 or 4 per block), while the number of parameters sought by
our work is much higher, as we will see in the experimentation
section. The search for an optimal result in a multidimen-
sional search space is a problem of great complexity. As we
will see later, the process of evaluating a possible solution
requires more time than other problems, so it is necessary
to arrive at a good solution with the minimum number of
evaluations. Another work related to the ISP tuning process,
in this case focused on advanced driver assistance systems
(ADAS), is the study carried out by Yahiaoui et al. [15] from
Valeo. In their experimental work, the authors demonstrate
the difference of tuning the ISP for a commercial camera
that seeks the image quality with respect to the subjective
appearance of the human eye, compared to the tuning of an
ISP whose system aims to improve the image processing
algorithms. The work shows how the accuracy of people
detection can be improved by tuning the ISP sharpening
parameters. I. INTRODUCTION the ISP (image signal processor) [12]. This chip performs
the job of interpreting the photons that reach the sensor and
processes the colors, but it can also perform other functions,
such as noise reduction, edge enhancement, dynamic range
processing and other types of adjustments and filters. This
chip can greatly change the perception of an image with-
out the user having to do anything, but its adjustment is
a factory-based implementation or it is upgradable by the
seller. It is key that this chip is well tuned so the camera can
take good quality images from the start. However, since it is
able to do so many things, the combination of parameters
and settings can become unmanageable, taking weeks and
even months of work by the company employees to find
the best values for each new product. Therefore, the ISP
tuning process is one of the bottlenecks in the transition of
a smartphone from the factory to the market. Smartphones have become something beyond devices with a
simple communication function. These devices are made up
of a set of sensors that allow the creation of the most inno-
vative applications [1]–[5]. Undisputedly, the most important
sensor is the camera [6]–[9]. Mobile manufacturing compa-
nies always seek to improve the photographic quality of their
cameras at all levels [10]. This rationale has been carried
out to such an extent that now, the sights of many of these
companies have been set on artificial intelligence to achieve
this goal. This improvement can be achieved in different
ways, for example, through photographic filters that are most
sought after by users, such as portrait mode, where Google
has stood out with its Pixel 2, which contains an excellent
portrait mode owing to the help of neural networks [11]. Nevertheless, filters are not the only way to improve photo-
graphic quality; the other important part of image quality is its
processing. For this task, there is a chip in the camera called The main problem with the parameter tuning of the ISP
is that, in many cases, it completely involves manual labor
performed by different professionals to accomplish it, from
photograph experts who analyze the quality and feel of
the camera to the programmers who prepare and build the The associate editor coordinating the review of this manuscript and
approving it for publication was Gustavo Olague
. 143479 L. V. II. IMAGE QUALITY II. IMAGE QUALITY Image quality is defined as a set of factors that reflect the level
of accuracy of the system to capture, process, store, com-
press, transmit and display the signals that form an image. Another definition would be the ‘‘weighted combination of
the visually significant attributes of an image’’ [25]. The key
difference is that the second definition places more emphasis
on evaluation through the perception of attributes that make
an image attractive to a human being. Some characteristic
attributes and elements that define image quality are the
following: Although several of these attributes are quantifiable, not all
follow standardized measures, since several are subjective to
the observer. I. INTRODUCTION A revealing aspect of their work is that they
indicate that the tuning process improves the performance
of the computer vision algorithms, but they do not provide
an automatic solution to find the best parameters of the ISP,
as we will demonstrate in our work. Also in the field of ADAS
is the work of Mody et al. [16] from Texas Instruments. In this
case, the ISP tuning process is carried out by establishing
some predetermined ISP parameters (there are four in this
case: noise Filter, sharpness, defect correction and contrast)
depending on the conditions of the scenes being displayed. Depending on the combined conditions of analog gain, expo-
sure time and color temperature, the parameters (initially
preset) to be used by the ISP are determined. Although their
work is an adaptive tuning according to the conditions of the
capture of the images, the authors depart from the purpose of Of course, similar to all EA techniques, the approach has
the limitations expressed in the NFL (no free lunch) theorem,
and it has been described that DE has a great capacity to
efficiently explore the search space and find the region in
which the global optimum exists, but it is more inefficient in
exploiting solutions to refine the result [23]. For this reason,
DE will be applied in this work to find the region containing
the best solution that human operators will subsequently
refine manually. This article presents a solution to the ISP tuning process
problem, where the validation of a possible configuration is
costly in time, so the priority is to obtain an acceptable solu-
tion in a few iterations of search and with a limited population
in size, rather than finding the best solution. The fine-tuning
process can be carried out manually by a camera tuning engi-
neer and without having to involve numerous trial and error
tests, which, in practice, are usually very time-consuming
tasks (several weeks and even months). In this way, the whole
process (Figure 1) is based on a first phase where several
hundred images are analyzed automatically, finding the most 143480 143480 VOLUME 8, 2020 VOLUME 8, 2020 L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE FIGURE 1. Complete process for ISP tuning. values by reducing the amount of variation, leading to a
loss of quality incurred by both extremes. A. RESOLUTION AND MODULATION TRANSFER FUNCTION Before tackling the oversharpening of edges and the modula-
tion transfer function (MTF), we must explain the concept
of resolution. The resolution is the amount of detail cap-
tured in the image (as opposed to the sharpness, which is
the amount of detail perceived), measured by the accuracy
of capturing the smallest details possible. The resolution is
usually measured by observing the number of discernible
lines in a vertical section (lines per millimeter, ln/mm) from
a photograph to a test chart (see Figure 2). • Sharpness: Determines the amount of detail that an
image transmits. It is perceived through the definition
of the edges of the image. You can increase the percep-
tion of sharpness through edge enhancement, but if it
becomes excessive, it becomes an embossed envelope
of edges and you begin to see halos. • Noise: Random variation of the density of the image,
visible as a film granulate or as variations of pixels in
digital images. One problem with this is that the ability to discern lines also
depends on the ability of the observer. In this way, the MTF
can be used to determine the resolution. The idea of this is that
the MTF allows us to calculate the contrast, which describes
the detail in the lines. The MTF equation (Equation (2))
is derived from the sinusoidal pattern of the contrast C(f )
(Equation (1)) at a spatial frequency f (the spatial frequency
is the distance of the elements of a pattern [26]), where: • Dynamic Range: The range of light levels that a camera
can capture. This relates to the smallest and the largest
amount of light level that can processed. In case there
is information that cannot be processed because it is
outside of that range, it is depicted as noise. • Tone Reproduction: It is the relation between the lumi-
nosity of the scene and the brightness reproduced in
the image. This tries to represent light in a scene by
balancing the brightness and intensity of colors in the
elements of the image. C(f ) = Vmax −Vmin
Vmax + Vmin
(1) (1) for luminance (intensity) V MTF(f ) = 100% × C(f )
C(0)
(2) (2) • Contrast: It is the slope of the curve of the tonal repro-
duction. High contrast means less intermediate values
between tones, whereas a low contrast increases those normalizes MTF 100% at low spatial frequencies. I. INTRODUCTION values by reducing the amount of variation, leading to a
loss of quality incurred by both extremes. • Color Accuracy: Is the measure of color changes, satu-
ration and effectiveness of white balance. • Distortion: It is an aberration that causes straight lines to
curve in the image. • Vignette: It is the gradient of light at the edges of an
image, caused by the difference in light received at
the different points of the lens (being convex normally,
the center of the lens receives more light, especially in
wide-angle cameras). • Exposure: The amount of light per unit area received in
the sensor, determined by the shooting speed, the aper-
ture of the lens and the light of the scene. FIGURE 1. Complete process for ISP tuning. • Chromatic Aberration: It is an aberration produced by
the lens that causes the convergence of colors in the same
point, rendering the inability to focus them correctly. promising region quickly. In a second stage, the engineer
with a few tens of images performs the fine-tuning. In the
first section of the paper, we will describe the parameters
related to the quality of the image that will help us understand
the quality objectives that we want to obtain. Then, the DE
algorithm that is developed for optimizing the ISP parameters
is described. Finally, the results obtained in different experi-
ments will be presented. • Lens Flare: It is a phenomenon in which a ray of light
is dispersed and captured in the lens, causing brightness
and reflections between the lens and the elements of the
camera, generating noise, loss of detail and color in the
image. • Artifacts: Different software processes can cause distor-
tions in the image due to the compression and transmis-
sion of the image, causing loss of detail through halos or
noise. FIGURE 2. Imatest SFRPlus test chart [24]. FIGURE 2. Imatest SFRPlus test chart [24]. FIGURE 4. Gray patches from Imatest ISO-12233 extract [24]. Obviously, the spatial frequency is related to the under-
standing that, in a low-frequency space, the lines to be eval-
uated are smaller, so the closer it is to 0, the less contrast
there is, and therefore, fewer lines can be identified. The best
case is when the MTF is equal to 50%, which indicates that
it is visible, and below 20% −10% is the case when it is
considered indistinguishable. FIGURE 3. Slanted edges from Imatest ISO-12233 extract [24]. FIGURE 3. Slanted edges from Imatest ISO-12233 extract [24]. By the standard established by the CPIQ (1858-2016 -
IEEE Standard for Camera Phone Image Quality Standard),
resolution is no longer measured with the bar system, but
rather with slanted edges and the MTF, and the slanted edges
can be seen in Fig. 3. This is because of the advantages it
offers; it does not depend on the distance with the chart, it has
reduced space so it can fit on different charts, and there is no
need of manual counting of the visible lines; thus, it is capable
of being automated. FIGURE 4. Gray patches from Imatest ISO-12233 extract [24]. way, the visual SNR is calculated with a series of complex
formulas specified in the IEEE CPIQ P1858 of 2017 [25],
where there are different calculations that include the effects
of the human vision system. A. RESOLUTION AND MODULATION TRANSFER FUNCTION normalizes MTF 100% at low spatial frequencies. 143481 143481 143481 VOLUME 8, 2020 L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE where: • nPH is the number of vertical pixels. • d is the viewing distance. • PF is the height of the image in cm. III. DIFFERENTIAL EVOLUTION Differential evolution (DE) is a stochastic search algorithm,
which belongs to the set of evolutionary algorithms, based on
recombination, evaluation and selection of individuals. It was
designed with the aim of optimizing continuous nonlinear
and nondifferential functions [19], [20], [28]. In our work,
DE was chosen over other evolutionary algorithms since DE
does not need large populations or many generations to reach
a solution. This aspect is important due to the time factor
when carrying out the experiments since the process of taking
photographs can take many generations and individuals and
takes a long time. The strategy of the algorithm is that,
for each individual, a random selection of a set of different
parents is made, and a random recombination between them
forms a new individual, which in turn receives a random set
of mutations. The new individual is evaluated, and the best is
selected between the new and the old. FIGURE 5. Imatest ISO-12233 test chart for SFRPlus analysis [24]. The regions of interest that are chosen from this chart are
the sides of the gray squares by measuring the sharpness of
the edges and taking the average of each region. The SQF
values are intended to be proportionally linear to perception,
with an SQF difference of 5 being the perceptible amount of
sharpness change. This means that a viewer may not notice
the difference in sharpness between an image with an SQF
of 88 and an SQF of 90 but will notice the difference in
images between 88 and 93. This brings us to the values of
the acutance (see Table 1) Algorithm 1 Differential Evolution
Data: Population Size (N), Problem Size (X), Mutation
Factor (F), Recombination Factor (Cr)
Result: Best solution (xBest)
Population ←Initialize_Population (N);
Evaluate_Population (Population);
XBest ←Get_Best (Population);
while ! Stop_Criteria do
New_Population ←0 ;
for i < N do
vi ←New_Individual (xi, N, F, Cr) ;
if xi ≤vi then
New_Population ←vi;
else
New_Population ←xi;
end
end
Population ←New_Population ;
Evaluate_Population (Population);
XBest ←Get_Best (Population);
end
return SBest is initially calculated in Imatest as cycles/pixel, so that:
f (cycles/degree) = πnPHdf (cycles/pixel)
180PF
(4) is initially calculated in Imatest as cycles/pixel, so that: FIGURE 5. Imatest ISO-12233 test chart for SFRPlus analysis [24]. (4) where: TABLE 1. Acutance values. Algorithm 1 Differential Evolution
Data: Population Size (N), Problem Size (X), Mutation
Factor (F), Recombination Factor (Cr)
Result: Best solution (xBest)
Population ←Initialize_Population (N);
Evaluate_Population (Population);
XBest ←Get_Best (Population);
while ! Stop_Criteria do
New_Population ←0 ;
for i < N do
vi ←New_Individual (xi, N, F, Cr) ;
if xi ≤vi then
New_Population ←vi;
else
New_Population ←xi;
end
end
Population ←New_Population ;
Evaluate_Population (Population);
XBest ←Get_Best (Population);
end
return SBest Algorithm 1 Differential Evolution Algorithm 1 Differential Evolution Algorithm 1 Differential Evolution B. SIGNAL-TO-NOISE RATIO AND VISUAL NOISE The SQF (subjective quality factor), is a measure of the per-
ceived sharpness of an image through a function that consid-
ers the height of the image and the distance of visualization of
it. It tries to describe the subjective perception of a spectator. Noise is a very important factor when determining the quality
of an image, given that noise is the amount of random signal
variations for each pixel. It is usually measured by means
of the SNR function, the signal-to-noise ratio, where the
amount of noise is expressed through the standard deviation
of pixels measured in decibels (dB). However, we are going
to focus on the measure of the visual SNR, or visual noise,
consisting of the amount of noise that can be perceived by a
human. This measure is calculated through a series of patches
in the range of grays in the test chart (Fig. 4), taking the
measurements from three points of view, where each one
is specified through its height and viewing distance. In this The SQF of an image is measured by analyzing a pho-
tograph taken on a test chart; specifically for this project,
the ISO-12233 for SFRPlus has been used in this work (see
Figure 5). For the analysis, a series of regions of inter-
est (ROIs) distributed by the image are determined, where the
SQF values are calculated and distributed in three regions that
are weighted according to their distance to the center of the
image, with the center being the most significant region [25]. 143482 VOLUME 8, 2020 VOLUME 8, 2020 L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE is initially calculated in Imatest as cycles/pixel, so that:
f (cycles/degree) = πnPHdf (cycles/pixel)
180PF
(4) is initially calculated in Imatest as cycles/pixel, so that:
f (cycles/degree) = πnPHdf (cycles/pixel)
180PF
(4) The ideal values of acutance are from 94−100, as indicated
in the table (see Table 1), but an image with much noise or
sharpening can surpass the 100 score despite not having an
adequate quality. The reason is that the calculus of the SQF
(Equation (3)) takes the MTF value into account. This means
that since the approach can find regions filled with high con-
trast frequencies due to the noise, it obfuscates the measure,
making it believe that the image is properly sharpened. Next,
its value calculation is expressed [27]: SQF = K
Z 0
∞
CSF(f ) · MTF(f ) · d(lnf )
= K
Z 0
∞
CSF(f ) · MTF(f )
f
· df
(3) (3) Evaluate_Population (Population); where: • CSF is the contrast sensitivity function of humans; CSF
(f) is close to 0 for f > 60 cycles/degree end end return SBest L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE Algorithm 2 New_Individual
Data: Individual (xi), Population Size (N), Mutation
Factor (F), Recombination Factor (Cr)
Result: New Individual (vi)
do
p1 ←Random_Individual (Population) ;
until xi ̸= p1;
do
p2 ←Random_Individual (Population) ;
until xi ̸= p2 and p1 ̸= p2;
do
p3 ←Random_Individual (Population) ;
until xi ̸= p3 and p1 ̸= p3 and p2 ̸= p3;
for j in xi do
if random() < Cr then
vi,j ←(p1,j + F × (p2,j −p3,j) );
else
vi,j ←xi,j ;
end
end
return vi Algorithm 2 New_Individual
Data: Individual (xi), Population Size (N), Mutation
Factor (F), Recombination Factor (Cr)
Result: New Individual (vi)
do • Population Size: The number of individuals with whom
the algorithm will work. DE does not need a large num-
ber of individuals to reach a solution, but if it is too small,
it is likely to stagnate or take a long time to converge;
however, its appropriate size depends on the size of the
problem. p1 ←Random_Individual (Population) ;
until xi ̸= p1;
do • Problem Size: It is the space in which the problem is
found. It is the number and type of variables with their
ranges of possible values. p2 ←Random_Individual (Population) ;
until xi ̸= p2 and p1 ̸= p2;
do p2 ←Random_Individual (Population) ;
until xi ̸= p2 and p1 ̸= p2;
do • Mutation Factor: It is a factor normally between [0, 2]
that controls the amplification of the difference between
two of the parents to generate new parameters during the
creation of a new individual in a generation. p3 ←Random_Individual (Population) ;
until xi ̸= p3 and p1 ̸= p3 and p2 ̸= p3;
for j in xi do p3 ←Random_Individual (Population) ;
until xi ̸= p3 and p1 ̸= p3 and p2 ̸= p3;
for j in xi do • Recombination Factor: It is a factor between [0, 1] that
controls the probability that the donor’s new value will
be applied to the new individual. 3) After the reboot, we take a photograph with the library. vi,j ←p1,j−F × (p2,j −p3,j)
(5) (5) 4) Then, we repeat the load, reboot and take the photo-
graph for each of the libraries. In this way, the new values are dependent on the par-
ents, but by mutating, they can empower the individual
regardless of their quality. 5) Once we have all the images, we analyze each of them
with Imatest to obtain the quality metrics and store the
results. It should be noted that the algorithm always approaches a
better solution, never a worse one. It may happen that, if there
is little diversity among the population, it will stagnate and
not progress for many generations since it will have reached
a point where it can only advance through random enhance-
ments of the mutation. Normally, at this point where the entire
population has little difference with the best individual, it is
considered that it has converged to that solution. 6) We compare the quality of the new individuals with
their correspondent of the previous generation and keep
the best. Since we store the results of previous individ-
uals, we do not need to analyze old photographs again,
just compare the stored values. In terms of time, there are great variations in the amount
of time taken by each step, where the fastest is to generate all
the libraries for the generation, which takes up to 4 seconds;
then, taking a photograph takes approximately 5 to 15 sec-
onds each; finally, the slowest step involves analyzing the
photographs, and this has usually taken up to 30 seconds if random() < Cr then
vi,j ←(p1,j + F × (p2,j −p3,j) );
else
vi,j ←xi,j ;
end In Algorithm 1, we can also find the use of the following
characteristic functions: In Algorithm 1, we can also find the use of the following
characteristic functions: • Initialize_Population: This involves generating a new
population randomly with a number of individuals equal
to the population size. • Evaluate_Population: To evaluate each individual of the
population, it is necessary to have an objective value
that is taken from some type of criterion pertaining to
the problem (the value of some function through the
parameters, for example), which allows us to calculate
the error of each individual regarding the target value. of the smartphones with which we work (Snapdragon 660). This ISP has been designed to support quality photography
through noise reduction, low-light algorithms, and computa-
tional camera innovations. The ISP has a set of parameters
that must be specified for each model of the mobile device
to be manufactured. Therefore, our goal is to find those
ISP parameters that obtain an improved image quality for a
particular model of the smartphone. • Get_Best: It is about obtaining the individual that best
meets the assessment. Depending on how the value of
the evaluation is interpreted, minimization or maximiza-
tion is performed. • New_Individual(vi,j):
For
a
better
understanding,
the pseudocode is shown in Algorithm 2. First, different
random individuals are selected from each other and
from the original individual, called parents (p1, p2, p3). Once the three parents are obtained, the values (j) of the
original individual (xi) are modified, with a probability
determined by the recombination factor (Cr), through
the following function (see Equation (5)): • New_Individual(vi,j):
For
a
better
understanding,
the pseudocode is shown in Algorithm 2. First, different
random individuals are selected from each other and
from the original individual, called parents (p1, p2, p3). Once the three parents are obtained, the values (j) of the
original individual (xi) are modified, with a probability
determined by the recombination factor (Cr), through
the following function (see Equation (5)): We will now describe the process of obtaining the ideal
parameters: 1) Starting with the algorithm, once we have the param-
eter of the ISP for each individual, we generate and
compile the libraries for the camera. 2) Then, the library is loaded onto the camera, and the
phone is rebooted to catch it. return SBest f
f
y
g
• MTF (f) is the modulation transfer function. • MTF (f) is the modulation transfer function. (f)
• K =
100%
R
CSF(f )d(lnf )) =
100%
R CSF(f )
f
df is the normalization
constant: SQF is equal to MTF (f) with a constant value
of 1. In Algorithm 1, a scheme of the general pseudocode of the
differential evolution is shown, where the inputs, the output
and the basic operation are described. The entries are com-
posed of the following: To calculate the CSF (f), it is necessary to present the
spatial frequency (f) in cycles / degree (Equation (4)), which 143483 VOLUME 8, 2020 A. ISP PARAMETERS AND RESTRICTIONS Since the ISP contains many modules for the image process-
ing, each of them dedicated to a different aspect of image
quality, we have focused on those related to the processes of
sharpening and noise reduction to reduce the size of the prob-
lem so that it can be better addressed. The optimization could
be done with other parameters of the ISP; these two have been
chosen because they are two that are mostly contradictorily
processed. For contrast enhancement, contrast effects are
usually accentuated so that some amount of noise is always
generated collaterally, while blur reduction techniques are
usually used to increase the homogeneity of pixels, which
results in a loss of detail at the edges. However, this process
could be repeated with other parameters. The ISP library parameters that we are going to optimize
belong to the ISO 800 section, whose restrictions are the
following: • Denoise Scale Y: It is a vector of 4 decimal values
between [1, 10]. It serves to reduce the noise of the lumi-
nance channel. Each value affects a different frequency,
and the higher it is, the greater the effect. The default values of the ISP library are depicted
in Table 2: A picture taken with these default parameters is shown
in Figure 7. At first glance, you can see that this picture is
quite clear and has little noise. However, when a 100% zoom
is made, as seen in Figure 8, there is a certain amount of
oversharpening of edges, perceived with a slight halo, but
indeed with very little noise, just a slight chroma noise in the
dark square. • Denoise Scale Chroma: It is a vector of 4 decimal values
between [1, 20]. It is used to reduce chroma channel
noise. Each value affects a different frequency, and the
higher it is, the greater the effect. • Denoise Edge Softness Y: It is a vector of 4 decimal
values between [1, 15]. It serves to soften the edges and
reduce the noise of the luminance channel even more. Each value affects a different frequency, and the higher
it is, the greater the effect. TABLE 2. Default values of the ISP library. Each of the elements of this optimization process will be
described in more detail in the following sections. IV. PROBLEM STATEMENT In the case of our experimentation, we are going to work with
the ISP Qualcomm Spectra 160, which includes the processor VOLUME 8, 2020 L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE Each value affects a different frequency, and the higher
it is, the greater the effect. each. The time taken for the overall process would be approx-
imately 10 to 15 minutes per generation, always considering
that if there are more individuals, the time for each generation
is increased since there are more photographs to take and
analyze, as these are the largest bottlenecks. The outline of
the described process is shown in Figure 6. • Denoise Weight Y: It is a vector of 4 decimal values
between [0, 1]. It serves to eliminate details of the lumi-
nance channel and reduce the noise even more. The
lower the value is, the more effect that is applied. • Lut 1: It is a vector of 24 decimal values between
[0, 7.95]. It is used to indicate the intensity of the hori-
zontal edge enhancement with a noise threshold. It gen-
erates an upward curve to reduce small amounts of noise
at the edges. FIGURE 6. Scheme of the optimization process. Although they have not been included, there are a number
of general guidelines that are usually met, including that the
parameters that affect chroma should have values with very
little difference between one or the other or that the Lut should
form an ascending curve, but we have decided not include
them as restrictions to check if they are really necessary or
not to obtain good results. FIGURE 6. Scheme of the optimization process. C. DIFFERENTIAL EVOLUTION FIGURE 7. Photograph of ISO-12233 with default values [24]. FIGURE 7. Photograph of ISO-12233 with default values [24]. The algorithm shown in section III (Algorithm 1 and 2) is
a version with a slight modification of the standard algo-
rithm with a binomial version of Crossover. In the standard
algorithm, when a new individual (solution) is created, it is
evaluated to see if it is better than the previous solution. In our problem, to reduce the time between generations,
it is first instantiated and compiled all libraries of the new
individuals. Then, after all are created, it is evaluated and
compared each new individual with its previous iteration and
then decide which is the best. This small adjustment saved
us a considerable amount of time since the libraries could
be compiled all at once and the images could be analyzed as
batches. FIGURE 8. Zoom of Figure 7. In order to fine-tune the parameters of the algorithm,
the population size and the number of generations, some
measurements of the behaviour of the algorithm were made
by modifying the population size. The Ackley function was
used [29], a non-convex, scalable function with many local
minima with a global optimum value at 0. We estimate that the parameter search performed to have
an approximation to the optimal region in Ackley’s function
could be suitable for the ISP parameter adjustment problem. We made 100 runs of the modified DE algorithm (DEm)
and the standard DE algorithm (DEs) with populations of 5,
10, 15, 20, 25, 30 and 40 individuals for 100 generations. Figures 9, 10, and 11 show the boxplot of the best individ-
uals for Ackley’s function with 5, 10 and 44 dimensions,
respectively. This last value matches the dimensionality of
the ISP setting. It can be seen that for low dimensions both
DEm and DEs have a similar behavior. It agrees, as expected,
with the worst result for the population of 5 individuals. For
dimension 44, it can be seen that DEm improves the DEs
by approximating the region in which the global optimum
is found. Specifically, the best result is produced from a
population of 15 individuals. In the tests carried out in the
experimental section, populations of 15 and 30 individuals
are selected. These results validate the modification of DE
and justify the population size. FIGURE 8. Zoom of Figure 7. output formats. B. IMATEST MASTER Imatest Master is an image quality analysis program that is
part of Imatest. With this program, we will be able to analyze
the test chart that has already been shown in Figure 3 and
take out the necessary values for the evaluation in different • Denoise Edge Softness Chroma Y: It is a vector of
4 decimal values between [1, 25]. It serves to soften
the edges and reduce chroma channel noise even more. VOLUME 8, 2020 L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE FIGURE 7. Photograph of ISO-12233 with default values [24]. FIGURE 8. Zoom of Figure 7. output formats. The program allows us to generate diagrams,
Excel tables and JSON files with the results, but for greater
convenience and speed, we will only take into account the
results stored in the JSON files, and we will not generate any
of the other files during the process to obtain a solution, only FIGURE 7. Photograph of ISO-12233 with default values [24]. • SQF: It is a vector of 36 values, where each value
corresponds to a different distance. We are interested in
a viewing distance of 30 centimeters, and we will choose
the value 11 of the vector. FIGURE 7. Photograph of ISO-12233 with default values [24]. • OversharpeningPCT: It is a vector with the percentages
of oversharpened edges in each region of interest of the
test chart. We will take the average among all and try to
take it to the point that interests us. • SNR Visual Noise: It is a vector that contains the amount
of noise measured in the gray range patch in the center
of the test chart. We take the average of the centrals
since those of the extremes correspond to the blacks and
whites and can generate problems when calculating the
average. • SNR Visual Noise: It is a vector that contains the amount
of noise measured in the gray range patch in the center
of the test chart. We take the average of the centrals
since those of the extremes correspond to the blacks and
whites and can generate problems when calculating the
average. C. DIFFERENTIAL EVOLUTION The program allows us to generate diagrams,
Excel tables and JSON files with the results, but for greater
convenience and speed, we will only take into account the
results stored in the JSON files, and we will not generate any
of the other files during the process to obtain a solution, only
as part of the validation of results. It should be noted that
Imatest Master is a program primarily designed for manual
analysis and therefore has a graphic interface designed for it. However, Imatest Master contains a dynamic library called
Imatest Push Interface, which allows the user to make use of
Imatest through C ++ so that even though the user interface
can continue to be run, the user can send them to analyze
images automatically. The Imatest application returns a set of parameters that
measure the quality of an image. Of all the measures provided
by JSON, we will focus on three indexes: For the search of the parameters that satisfy the quality con-
ditions of an image, we will use the evolutionary differential 143486 VOLUME 8, 2020 VOLUME 8, 2020 L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE FIGURE 9. Modified vs standard DE performance in Ackley (dim. 5). with these parameters will be taken and their quality will
be assessed using the Imatest application. The fitness func-
tion of each of the individuals is described as the deviation
of the values obtained in Imatest from the target values. For instance, the deviation value of the SQF image quality
attribute (DevSQF) is calculated by applying Equation (6). DevSQF =
1 −
SQFtarget −SQFobtained
SQFtarget
× 100
(6) (6) where SQFtarget is the ideal value to be obtained and
SQFobtained is the value obtained by a given individual. Sim-
ilarly, we will obtain the values for DevOV y DevVN, or any
other image quality attribute to be optimized. FIGURE 9. Modified vs standard DE performance in Ackley (dim. 5). Once we have obtained these deviations, the fitness func-
tion is in the form of the linear regression function of Equa-
tion (7). FIGURE 10. Modified vs standard DE performance in Ackley (dim. 10). (7) fitness = DevSQF × P1 + DevOV × P2 + DevVN × P3
(7) where P1, P2 and P3 are weighting values. C. DIFFERENTIAL EVOLUTION During the
research, those values were determined by the head engineers
from BQ based on the results, so it was an iterative process. In the end, those parameters mark the relevance of the dif-
ferent quality measures, so, for example, if what you want is
to value more the sharpness over the visual noise, you would
increase the SQF percentage (P1) on the final measure. The
values P1, P2 and P3 are established by the team of expert
engineers, thanks to their experience. These values can be
used by them when tuning the ISP of other camera models. FIGURE 10. Modified vs standard DE performance in Ackley (dim. 10). In addition, to penalize and further restrict certain val-
ues, we place them in a minimum range to calculate their
deviation: FIGURE 11. Modified vs standard DE performance in Ackley (dim. 44). • The SQF must be less than 120 to be taken into account;
otherwise, its deviation will be worth 0. • The oversharpening of edges must be less than 100 to be
taken into account; otherwise, its deviation will be worth
0. • The visual noise must be less than 50 to be taken into
account; otherwise, its deviation will be 0. The evaluation cycle will be carried out according to the
scheme in Fig. 6 until the stop condition is met. In our case,
the stop condition is a specific number of generations. Finally, the quality of solutions should be the final point
of the optimization procedures, and in this case, we have
an evaluation of experts: engineers who optimize the param-
eters for each type of terminal. The solution is that the
algorithm finds the starting point for these engineers, and
the validation of these solutions is given by the subjective
opinions of the experts. If solutions generate a probabilistic
distribution defined by the average and deviation, it is not
so representative here because the problem is not to find the
‘‘optimal solution’’; rather, the problem is only to find the
start region that is near the optimal solution and thus begin
the engineering work. FIGURE 11. Modified vs standard DE performance in Ackley (dim. 44). algorithm described in Algorithm 1. At the beginning of
the search, we have a set of individuals, which describe
certain values for the ISP parameters. Initially, they will
take a random value. C. DIFFERENTIAL EVOLUTION The objective is to find the set of ISP
parameters that allow obtaining an image whose quality met-
rics (SQF, OversharpeningPCT (OV) and SNR Visual Noise
(VN)) approach initially defined target values. Photographs 143487 VOLUME 8, 2020 VOLUME 8, 2020 L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE FIGURE 13. Evolution of the best final individual of Test1. V. DISCUSSION OF RESULTS
A. TESTS PERFORMED The tests have been carried out in a dark room, where the
only illumination came from the two focuses centered and
oriented at 30◦with respect to the test chart. The photographs
were taken at 45 cm to focus only the 4:3 section of the test
chart to facilitate the analysis with Imatest. In the following
paragraphs, we will discuss the tests performed, where the
objective values of the tests were changed, in a search for
better results. In these tests, a recombination factor of 0.7 and
a mutation factor of 0.5 were established. This decision
was made in order to generate individuals with exaggerated
modifications, and since there are many parameters, when
reaching an advanced point in the generations, the modifi-
cations should not be so radical due to the sensitivity of the
modifications. FIGURE 13. Evolution of the best final individual of Test1. In Fig. 13, we can see the evolution of the best final individ-
ual throughout the generations. This individual has not been
the best in all generations, but it allows us to obtain an idea
of how an individual progresses. In this case, we can verify
that there was very sharp progress from generation 8, where
the oversharpening dropped enough to allow the value of the
SQF to exceed the threshold and be considered mainly in the
function. We can also verify that there are slight alterations
regarding what values are enhanced in each generation. For
instance, in generation 38, it can be seen that part of the
visual noise is exchanged for better edge sharpening, but only
because the sum of both provided a better score. Likewise,
we can see that the criterion that does not reach the objective
value is the visual noise, which indicates that the objective
value is not entirely attainable or compatible with the rest
of the criteria. This observation is confirmed when looking
carefully at the values of visual noise of the other individuals
that do not reach the target. B. TEST1 This test was performed with a population of 15 individuals,
with the following targets: • SQF: 100 • Oversharpening of edges: 5 • Visual noise: 35 In addition, the objective function was weighted as: • The deviation of SQF by 20% of the score • The deviation of the oversharpening of edges by 35% • The deviation of visual noise by 45% These weights were chosen after realizing that the sharp
edge envelope greatly influenced the SQF, and the visual
noise ended up being set aside in a more homogeneous distri-
bution. This test has required 1, 290 photographs, which took
an approximate total time of 15 hours. In Fig. 12, the evolution of the generations through the
average of the scores of the individuals and the best individual
is depicted. In Table 3 and 4, the quality values achieved by the best
individual and their ISP parameters are depicted. Photograph of the best individual of Test1. FIGURE 14. Photograph of the best individual of Test1. FIGURE 16. Evolution of the best individual of Test2. FIGURE 14. Photograph of the best individual of Test1. fairly high sense of sharpness, with very little noise, which
corresponds to the results in the evaluation criteria. FIGURE 16. Evolution of the best individual of Test2. TABLE 3. TEST 1. Quality values obtained of the best individual of Test1. FIGURE 12. Evolution of the generations of Test1. TABLE 3. TEST 1. Quality values obtained of the best individual of Test1. Comparing the values of these parameters with the default
values (Table 2), we can observe that there is a greater inten-
sity in the majority of noise reduction parameters and that,
in addition, it does not follow the same type of distribution
where the majority of values of the same vector are the same,
although there is a certain tendency for them to be close to
each other. In the Lut, we have that the function described is
quite abrupt but moderately increasing. As we will see, this
property translates to a certain amount of the sharp envelope. In Fig. 14, which corresponds to the photograph taken with
this library, it can be verified that it actually provides a FIGURE 12. Evolution of the generations of Test1. We can verify that the algorithm begins to converge
approximately from generation 55 and finishes doing so at
approximately generation 80. 143488 143488 VOLUME 8, 2020 VOLUME 8, 2020 L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE TABLE 4. TEST 1. ISP parameters of the best individual of Test1. FIGURE 14. Photograph of the best individual of Test1. FIGURE 15. Evolution of the generations of Test2. TABLE 4. TEST 1. ISP parameters of the best individual of Test1. ABLE 4. TEST 1. ISP parameters of the best individual of Test1. TABLE 4. TEST 1. ISP parameters of the best individual of Test1. FIGURE 15. Evolution of the generations of Test2. This test is subject to the same conditions as in Test1,
except that there are 30 individuals, so we can see that,
being a larger population, it has taken less time to converge;
however, in turn, it can also be seen that the progress of the
average is softer. It can be seen that it begins to converge from
generation 27 and that from 35 there is very little variation. In generation 45, the average value is 87.73, while the best
value is 91.74. Compared with the previous test, we can see
that the value of the best individual is very similar, while the
value of the average is slightly lower because there is more
variety. FIGURE 14. C. TEST2 In Fig. 16, the evolution that the best final individual
has followed throughout the generations can be observed. This individual has not been the best in all generations,
but it allows us to obtain an idea of how an individual
progresses. In this case, we can verify that there was very
sharp progress from generation 12, where the oversharpen-
ing dropped enough to allow the SQF value to exceed the
threshold and be considered in the function, in the same
way as the best individual of Test1. We can observe that,
in this case, generation 27 was reached, and part of the value
of the oversharpening was lost in exchange for achieving a
better noise reduction, but in generation 28, both values were This test was performed with a population of 30 individuals,
with the following targets: • SQF: 100 • Oversharpening of edges: 5 • Visual noise: 35 • Visual noise: 35
In addition, the objective function was weighted as: In addition, the objective function was weighted as: • The deviation of SQF by 20% of the score • The deviation of the oversharpening of edges by 35% • The deviation of visual noise by 45% In Fig. 15, the evolution of the best individual and the
average of individuals in each generation is shown. 143489 VOLUME 8, 2020 L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE FIGURE 17. Photograph of the best individual of Test2. recovered to the maximum reached. Again in this test, it can
be seen that the objective value that is not reached is that
of noise reduction, so it confirms that it is not an adequate
objective value. In Table 5 and 6, the quality values achieved by the best
individual and their ISP parameters are depicted. TABLE 5. TEST2. Quality values obtained of the best individual of Test2. TABLE 5. TEST2. Quality values obtained of the best individual of Test2. TABLE 5. TEST2. Quality values obtained of the best individual of Test2. FIGURE 17. Photograph of the best individual of Test2. TABLE 6. TEST2. ISP parameters of the best individual of Test2. TABLE 6. TEST2. ISP parameters of the best individual of Test2. TABLE 6. TEST2. ISP parameters of the best individual of Test2. TABLE 6. TEST2. ISP parameters of the best individual of Test2. C. TEST2 needed is significantly less, which leads us to observe that
the evolution of individuals is much faster because there is a
greater diversity of parameters to work with. D. TEST3 This test was performed with a population of 30 individuals,
with the following targets: • SQF: 100 • Oversharpening of edges: 2 • Visual noise: 25 • MTF: 0.3 In addition, the objective function was weighted as: In addition, the objective function was weighted as: • The deviation of SQF by 20% of the score • The deviation of the oversharpening of edges by 30% • The deviation of visual noise by 30% • The deviation of MTF by 20% In this experiment, we decided to introduce one more image
quality attribute (MTF). We wanted to check the behavior of
the optimization when introducing MTF, so we redefined the
initial fitness function of (7) by the following function: Comparing the ISP parameters of the best individual with
the default values (Table 2) and the values of Test2 (Table 6),
we can see that again there is a greater intensity in the
majority of noise reduction parameters and that, in addition,
it follows the same type of distribution as the default values. However, again there is a tendency to have values that are
close to each other, although in very different ways than in
Test1. In the Lut, we have that the function described is quite
abrupt, reaching many peaks. This translates, as we will see
in photography, to a special type of edge sharpening with
many artifacts and a very increased halo. In Fig. 17, which
corresponds to the photograph taken with the parameters of
the best individual of Test2, it can be verified that, as indicated
by the SQF, it gives a feeling of high sharpness. fitness = DevSQF × 0.2 + DevOV × 0.3
+DevVN × 0.3 + DevMTF × 0.2
(8) (8) In Fig. 18, the evolution of the best individual and the
average of individuals in each generation is shown. yp
However, again there is a tendency to have values that are
close to each other, although in very different ways than in
Test1. In the Lut, we have that the function described is quite
abrupt, reaching many peaks. This translates, as we will see
in photography, to a special type of edge sharpening with
many artifacts and a very increased halo. In Fig. D. TEST3 17, which
corresponds to the photograph taken with the parameters of
the best individual of Test2, it can be verified that, as indicated
by the SQF, it gives a feeling of high sharpness. In Fig. 18, the rapid convergence of the population in the
generation from generation 17 is shown. This is the case of the
fastest evolution that we have obtained in the tests performed. It can also be observed that, as in Test2, the population growth
is smoother due to the number of individuals. In generation
20, the value of the average population is 92.61, while the
best individual has a value of 96.13. This test has required 1, 380 photographs, which took an
approximate total time of 16 hours. This result implies that
in 16 hours, the same result has been achieved as that in Test1,
which required 15 hours; however, the amount of generations Fig 19 shows the process that the best final individual has
followed throughout the generations. This individual has not
been the best in all generations, but it allows us to obtain an
idea of how an individual progresses. In this case, we can 143490 143490 VOLUME 8, 2020 L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE FIGURE 18. Evolution of the generations of Test3. FIGURE 19. Evolution of the best individual of Test3. FIGURE 18. Evolution of the generations of Test3. FIGURE 19. Evolution of the best individual of Test3. TABLE 8. TEST3. ISP parameters of the best individual of Test3. we can see that, in this case, the intensity of the noise reduc-
tion parameters is lower and somewhat less homogeneous. In Lut, we have that the function it describes remains quite
abrupt, reaching many initial and final peaks. This result
translates, as we will see again in photography, to a spe-
cial type of edge sharpening with many artifacts and a very
enlarged halo, which partly gives some diffuse sensations
at various edges On the other hand it is verified that the FIGURE 18. Evolution of the generations of Test3. TABLE 8. TEST3. ISP parameters of the best individual of Test3. TABLE 8. TEST3. ISP parameters of the best individual of Test3. FIGURE 18. Evolution of the generations of Test3. FIGURE 18. Evolution of the generations of Test3. FIGURE 19. Evolution of the best individual of Test3. REFERENCES [1] H. S. Hawley and E. Robert McClain, ‘‘Visualizing sound directivity via
smartphone sensors,’’ Phys. Teacher, vol. 56, no. 2, pp. 72–74, 2018. [2] N. Chandra, R. S. Chin, E. Cardova, M. D. Pratiwi, and Nadia, ‘‘Imple-
mentation of gyroscope sensor to presentation application on Android
smartphone,’’ in Proc. Indonesian Assoc. for Pattern Recognit. Int. Conf. (INAPR), Sep. 2018, pp. 197–201. [3] L. Wang, T. Gu, A. X. Liu, H. Yao, X. Tao, and J. Lu, ‘‘Assessing user
mental workload for smartphone applications with built-in sensors,’’ IEEE
Pervas. Comput., vol. 18, no. 1, pp. 59–70, Jan. 2019. [4] M. M. Hassan, M. Z. Uddin, A. Mohamed, and A. Almogren, ‘‘A robust
human activity recognition system using smartphone sensors and deep
learning,’’ Future Gener. Comput. Syst., vol. 81, pp. 307–313, Apr. 2018. This article has addressed the challenge of adjusting many
more ISP parameters than has ever been accomplished in
previous work, as described in the introduction. Further-
more, as indicated in the state-of-the-art literature, this chal-
lenge remains an open problem in the engineering field. The described work shows that optimal ISP tuning allows
for performance improvements in computer vision algo-
rithms [15] and adaptability to different image acquisition
conditions [16]. In [15], the authors propose automatic ISP
tuning as a challenge for the future. [5] Y. Chen and C. Shen, ‘‘Performance analysis of smartphone-sensor behav-
ior for human activity recognition,’’ IEEE Access, vol. 5, pp. 3095–3110,
2017. [6] T. Leeuw and E. Boss, ‘‘The HydroColor app: Above water measurements
of remote sensing reflectance and turbidity using a smartphone camera,’’
Sensors, vol. 18, no. 1, p. 256, Jan. 2018. [7] R. Shea, D. Fu, A. Sun, C. Cai, X. Ma, X. Fan, W. Gong, and A. Liu,
‘‘Location-based augmented reality with pervasive smartphone sensors:
Inside and beyond pokemon go,’’ IEEE Access, 2017. [8] B. P. Yan, C. K. Chan, C. K. Li, O. T. To, W. H. Lai, G. Tse, Y. C. Poh, and
M.-Z. Poh, ‘‘Resting and postexercise heart rate detection from fingertip
and facial photoplethysmography using a smartphone camera: A validation
study,’’ JMIR mHealth uHealth, vol. 5, no. 3, p. e33, Mar. 2017. Future work includes improving the process in a way
that reduces the time spent on each generation. The execu-
tion time of a generation is approximately 10-20 minutes. In future work, we envision parallelizing the implementation,
which would considerably reduce the time of the generations. D. TEST3 we can see that, in this case, the intensity of the noise reduc-
tion parameters is lower and somewhat less homogeneous. In Lut, we have that the function it describes remains quite
abrupt, reaching many initial and final peaks. This result
translates, as we will see again in photography, to a spe-
cial type of edge sharpening with many artifacts and a very
enlarged halo, which partly gives some diffuse sensations
at various edges. On the other hand, it is verified that the
introduction of a new image quality attribute (MTF) does not
affect the optimization process. In Fig. 20, which corresponds
to the photograph taken with this library, it can be seen that it
gives a high sharpness sensation. FIGURE 19. Evolution of the best individual of Test3. FIGURE 19. Evolution of the best individual of Test3. verify that the evolution was alternating between yielding to
being oversharpened by visual noise and vice versa until find-
ing a balance of the two. This outcome may be because, in the
objective function, both parameters are equally weighted. In turn, we see that MTF does not vary much over the gener-
ations, but we can see a certain relationship with visual noise
since they tend to vary at the same time. In this test, it can
be seen that, despite the fact that the objective values are not
reached at 100%, in this case, the value of the visual noise
and the oversharpening is quite high compared to the previous
results. FIGURE 20. Photograph of the best individual of Test2. In Table 7 and 8, the quality values achieved by the best
individual and their ISP parameters are depicted. TABLE 7. TEST3. Quality values obtained by the best individual of Test3. TABLE 7. TEST3. Quality values obtained by the best individual of Test3. TABLE 7. TEST3. Quality values obtained by the best individual of Test3. FIGURE 20. Photograph of the best individual of Test2. This test has required 630 photographs, which took an
approximate total time of 8 hours. This result implies that Comparing the values of the best individual with the
default values (Table 2) and the values of Test3 (Table 8), VOLUME 8, 2020 L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE region. From this region, they would perform the fine tuning. D. TEST3 Anyway, the multi-objective version of the problem will be
considered for an extension of the project. in 8 hours, a similar result has been achieved compared with
those of previous tests; however, the number of generations
required is significantly less than those of previous tests,
indicating that we have found a better distribution of weights
and evaluation criteria. As has been proven in the work, the optimization process
has a high computing cost because it is necessary to modify,
compile and load the library with the parameters of each indi-
vidual. A possible improvement of the optimization process
would be the application of surrogate models [31]. We can say
that, during the optimization process, the only information we
have about the objective function comes from the evaluation
of each individual. Once the individual is evaluated, certain
information is lost. A surrogate model aims to establish a
correspondence between individuals and their evaluation in
order to establish a meta-model that learns this correspon-
dence. Once this correspondence is modelled, it could be used
to estimate the evaluation of new individuals. The application
of surrogate models can be a good approximation for future
work related to ISP tuning, as it would probably accelerate
the process. VI. CONCLUSION In this article, the authors present a solution to the problem
of the ISP tuning process. This process is usually performed
manually by the camera tuning engineer through a trial and
error process until finding the parameters that satisfy the
image quality conditions. It is a very important and very
complex process due to the large number of variables to
take into account, which is why it is the best reason to use
optimization algorithms to solve it. One of most substantial
problems in this case is the quality criteria since photography
has a great subjective factor. Not everyone likes the same
intensity of color or definition of edges; however, there are
certain quality standards that can be followed and formulas
that allow us to evaluate many of them. As a solution to this problem, we present a differential evo-
lution algorithm that allows obtaining a first approximation
of the ISP parameters. This evolutionary paradigm has been
selected because it needs very few adjustment parameters
and can find an acceptable solution with a small number of
iterations due to its good exploration capacity [30]. Once the
exploration task has been carried out, it will be the experts
who will carry out the exploitation manually. The camera
tuning engineer can easily perform fine-tuning to determine
the final configuration, guided by his or her experience. REFERENCES Another option, proposed by one reviewer, would be to sim-
ulate the software in such a way that we would avoid the time
dedicated to the configuration/boot/shooting of the image. The idea would be to take an image, store it in raw mode
and apply the differential evolution method with the simu-
lator. In this sense, we would need to have an ISP software
simulator that, at present, does not exist. [9] M. S. Hossain and G. Muhammad, ‘‘An emotion recognition system for
mobile applications,’’ IEEE Access, vol. 7, pp. 2281–2287, 2017. [10] W. Hauser, B. Neveu, J. B. Jourdain, C. Viard, and A. Guichard, ‘‘Image
quality benchmark of computational Bokeh,’’ Electron. Imag., vol. 18,
no. 21, pp. 340–341, 2018. [11] A. Ignatov, R. Timofte, W. Chou, K. Wang, M. Wu, T. Hartley, and
A. V. Gool, ‘‘AI benchmark: Running deep neural networks on Android
smartphones,’’ in Proc. Eur. Conf. Comput. Vis., 2019, pp. 1–4. [12] L.-L. Chen, R.-P. Han, and Y.-X. Bao, ‘‘Brief analysis of image signal
processing for smart phone,’’ in Proc. Int. Conf. Comput., Mechatronics
Electron. Eng., 2016, pp. 1–7. [13] J. Nishimura, T. Gerasimow, R. Sushma, A. Sutic, C.-T. Wu, and
G. Michael, ‘‘Automatic ISP image quality tuning using nonlinear opti-
mization,’’ in Proc. 25th IEEE Int. Conf. Image Process. (ICIP), Oct. 2018,
pp. 2471–2475. At the beginning of the project, it was thought to model the
problem as a multi-objective problem. However, due to prac-
ticality issues, the expert engineers of Bq company wanted to
have a control of the weight of each target to find a candidate [14] J. A. Nelder and R. Mead, ‘‘A simplex method for function minimization,’’
Comput. J., vol. 7, no. 4, pp. 308–313, Jan. 1965. [15] L. Yahiaoui, J. Horgan, B. Deegan, S. Yogamani, C. Hughes, and P. Denny,
‘‘Overview and empirical analysis of ISP parameter tuning for visual
perception in autonomous driving,’’ J. Imag. vol. 5, no. 10, p. 78, 2019. 143492 VOLUME 8, 2020 L. V. Hevia et al.: Optimization of the ISP Parameters of a Camera Through DE [16] M. Mody, S. Dabral, M. Magla, H. Sanghvi, N. Nandan, K. Chitnis,
B. Jadhav, R. S. Allu, and G. Hua, ‘‘High quality image processing system
for ADAS,’’ in Proc. IEEE Int. Conf. Electron., Comput. Commun. Technol. (CONECCT), Jul. 2019, pp. 1–4. MIGUEL A. PATRICIO (Member, IEEE) received
the B.Sc. and M.Sc. REFERENCES degrees in computer science
and the Ph.D. degree in artificial intelligence from
the Universidad Politécnica de Madrid, in 1991,
1995, and 2002, respectively. He is currently an
Associate Professor with the Escuela Politécnica
Superior, Universidad Carlos III de Madrid. He is
a coauthor of over 100 books, book chapters,
journal articles, and technical reports; published
by organizations, including Elsevier, IEEE, ACM,
AAAI, Springer Verlag, and Kluwer; and most of these present practical and
theoretical achievements of data analysis, computer vision, and distributed
systems. [17] M. Crepinsek, S. H. Liu, and M. Mernik, ‘‘Exploration and exploitation
in evolutionary algorithms: A survey,’’ ACM Comput. Surv., vol. 45, no. 3,
pp. 1–33, 2013. [18] G. Olague, ‘‘Evolutionary computer vision: The 1st footprints,’’ in Natural
Computing Series. Berlin, Germany: Springer, 2016. [19] R. Storn and K. Price, ‘‘Differential evolution—A simple and effi-
cient adaptive scheme for global optimization over continuous spaces,’’
J. Global Optim., vol. 11, no. 4, pp. 341–359, 1995. [20] R. Storn and K. Price, ‘‘Differential Evolution - A Simple and Efficient
Heuristic for Global Optimization over Continuous Spaces,’’ J. Global
Optim., 1997. [21] S. Das, S. S. Mullick, and P. N. Suganthan, ‘‘Recent advances in differential
evolution – an updated survey,’’ Swarm Evol. Comput., vol. 27, pp. 1–30,
Apr. 2016. [22] F. Neri and V. Tirronen, ‘‘Recent advances in differential evolution:
A survey and experimental analysis,’’ Artif. Intell. Rev., vol. 33, nos. 1–2,
pp. 61–106, Feb. 2010. [23] S. Das, A. Abraham, U. K. Chakraborty, and A. Konar, ‘‘Differential
evolution using a neighborhood-based mutation operator,’’ IEEE Trans. Evol. Comput., vol. 13, no. 3, pp. 526–553, Jun. 2009. p
,
,
, pp
,
[24] Automated Image Quality Analysis, Imatest, Boulder, CO, USA, 2020. tomated Image Quality Analysis, Imatest, Boulder, CO, USA, 202 [24] Automated Image Quality Analysis, Imatest, Boulder, CO [25] IEEE Standard for Camera Phone Image Quality, Standard 1858-2016,
2017. JOSÉ M. MOLINA (Member, IEEE) received the
Ph.D. degree in telecommunications engineering
from the Universidad Politécnica de Madrid. He is
currently a Full Professor of computer science
with the Carlos III University of Madrid. He also
coordinates the Applied Artificial Intelligence
Group. His research interests include applying
soft-computing techniques to radar data process-
ing, air traffic management, e-commerce, and
ambient intelligence. [26] D. Glenn Boreman, ‘‘Modulation transfer function in optical and
electro-optical systems,’’ Tech. Rep., 2010. [Online]. Available: https://
doi.org/10.1117/3.419857 [27] E. M. Granger and K. N. REFERENCES Cupery, ‘‘An optical merit function (SQF),
which correlates with subjective image judgments,’’ Photograph. Sci. Eng.,
vol. 16, pp. 221–230, 1972. [28] J. Brownlee,
‘‘Clever
algorithms:
Nature-inspired
programming
recipes,’’ Tech. Rep., 2011. [Online]. Available: https://www.amazon.es/
dp/1446785068?tag=amz-mkt-chr-es-21&ascsubtag=1ba00-01000-
org00-mac00-other-nomod-es000-pcomp-feature-scomp-wm-5&ref=aa_
scomp_sosp1 [29] D. H. Ackley, A Connectionist Mach. for Genetic Hillclimbing. Dordrecht,
The Netherlands: Kluwer, 1987. [30] A. W. Mohamed, ‘‘Differential evolution (DE): A short review,’’ Robot. Autom. Eng. J., vol. 2, no. 1, pp. 18–24, Jan. 2017. [31] A. Diaz-Manriquez, G. Toscano-Pulido, and W. Gomez-Flores, ‘‘On the
selection of surrogate models in evolutionary optimization algorithms,’’ in
Proc. IEEE Congr. Evol. Comput. (CEC), Jun. 2011, pp. 2155–2162. ANTONIO
BERLANGA
(Member,
IEEE)
received
the
degree
in
physics
from
the
Autonomous University of Madrid, Spain, in 1995,
and the Ph.D. degree in computer engineering
from the Carlos III University of Madrid, in 2000. He has been an Associate Professor with the Com-
puter Science Department, Universidad Carlos
III de Madrid, since 2000. His research interests
include evolutionary computation, multiobjective
evolutionary algorithms, machine learning, and
data mining. ANTONIO
BERLANGA
(Member,
IEEE)
received
the
degree
in
physics
from
the
Autonomous University of Madrid, Spain, in 1995,
and the Ph.D. degree in computer engineering
from the Carlos III University of Madrid, in 2000. He has been an Associate Professor with the Com-
puter Science Department, Universidad Carlos
III de Madrid, since 2000. His research interests
include evolutionary computation, multiobjective
evolutionary algorithms, machine learning, and
data mining. LUIS V. HEVIA received the degree in computer
science from Carlos III University, in 2018. He is
currently a DevOps Engineer with the MasMovil
Group, Business Intelligence Department. His
research interests include the applications of arti-
ficial intelligence in automation and optimization
of processes. LUIS V. HEVIA received the degree in computer
science from Carlos III University, in 2018. He is
currently a DevOps Engineer with the MasMovil
Group, Business Intelligence Department. His
research interests include the applications of arti-
ficial intelligence in automation and optimization
of processes. 143493 VOLUME 8, 2020
|
https://openalex.org/W2619065465
|
https://revistia.com/index.php/ejmn/article/view/5018/4871
|
English
| null |
Qualitative Data Regarding the Macrophytic Communities Structure in the Wave Breaking Zone at the Romanian Black Sea Littoral
|
European journal of interdisciplinary studies
| 2,016
|
cc-by
| 7,107
|
Abstract At the Romanian seaside the development of macro-algae mass is reported mainly in summer and is registered
especially by the group green macro-algae; thus the largest deposits occur ashore after periods of storm especially,
but especially after bottom movement, when a large area of shallow coastline is "shaved" of vegetal carpet. Most
macrophyte algae from the Romanian littoral are seasonal species; typical for low temperatures are species of red
algae: Bangia, Porphyra and Ectocarpus; species Dasya, Chondria are typical for the summer temperatures and others
are frequently met especially in spring – fall; in addition to these, a number of species belonging to the group of green
algae. Enteromorpha, Cladophora, are present in all associations succeeding in the year. Keywords: Black Sea Romanian littoral, macroalgal species, hard substratum Gabriela–Mihaela Paraschiv 3“Ovidius” University of Constanta, Natural and Agriculture Sciences Faculty, Constanta Romania Constanta Romania European Journal of European Journal of July - December 2019
Volume 2, Issue 2 ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online) Medicine and Natural Sciences Qualitative Data Regarding the Macrophytic Communities Structure in
the Wave Breaking Zone at the Romanian Black Sea Littoral Emin Cadar Emin Cadar
U.M.F. “Carol Davila”, Faculty of Pharmacy, Bucharest, Romania U.M.F. “Carol Davila”, Faculty of Pharmacy, Bucharest, Romania Qualitative Data Regarding the Macrophytic Communities Structure in
the Wave Breaking Zone at the Romanian Black Sea Littoral Ticuta Negreanu-Pirjol
“Ovidius” University of Constanta, Faculty of Pharmacy, Constanta, Romania Introduction The frequency of episodes with macroalgal deposits is higher in the southern sector (and over longer periods of time), a
fact explained by the very presence of submerse limestone platforms (Fig. 1). The frequency of episodes with macroalgal deposits is higher in the southern sector (and over longer periods of time), a
fact explained by the very presence of submerse limestone platforms (Fig. 1). Fig. 1. The South Romanian littoral of the B Sea
The macrophytobenthos is made up of macroscopic algae (green, brown and red) and phanerogams. It is spread over the
north-western continental platform of the Black Sea basin (in littoral zones of low depth) and it can sometimes form important
deposits at the shore, especially in the pre-vernal or vernal season or after storms. The 1980s represent a period of increased eutrophication and pollution, which generated important modifications in the
qualitative structure of macrophytobenthos. The effects of these modifications are still felt today [4], [19], 86 macroalgal
species were cited in the 1970s-1980s [1], 69 species were cited in the 1980s-1990s and only 55 species after 1990 [20],
[21]. This decrease in the number of species (apart from the pollution phenomenon) was attributed to climate changes –
Cape Singol/Constanta
Influence
area of
Danube
water
Vama Veche
N
S
Vama Veche
Costineşti
Vadu-Mamaia Costineşti Fig. 1. The South Romanian littoral of the B Sea The macrophytobenthos is made up of macroscopic algae (green, brown and red) and phanerogams. It is spread over the
north-western continental platform of the Black Sea basin (in littoral zones of low depth) and it can sometimes form important
deposits at the shore, especially in the pre-vernal or vernal season or after storms. The macrophytobenthos is made up of macroscopic algae (green, brown and red) and phanerogams. It is spread over the
north-western continental platform of the Black Sea basin (in littoral zones of low depth) and it can sometimes form important
deposits at the shore, especially in the pre-vernal or vernal season or after storms. The 1980s represent a period of increased eutrophication and pollution, which generated important modifications in the
qualitative structure of macrophytobenthos. The effects of these modifications are still felt today [4], [19], 86 macroalgal
species were cited in the 1970s-1980s [1], 69 species were cited in the 1980s-1990s and only 55 species after 1990 [20],
[21]. Introduction The Romanian littoral of the Black Sea has a length of 245 km (6 % of the total length of the Black Sea shore, Fig. 1),
between the flowing mouth of the Chilia Branch, to the border with Ukraine in the north and with Bulgaria in the south. The Romanian coastal area is divided into two geographical and geomorphic units [3], [13]. The Romanian coastal area is divided into two geographical and geomorphic units [3], [13]. The northern unit (N) occupies 2/3 of the total littoral length and stretches between Musura Bay, at the flowing mouth of the
Chilia Branch and Cape Singol, including the shore of the Danube Delta Biosphere Reservation (Fig. 1). The area is
characterized by sandy beaches with low altitudes and reduced submarine slopes. The beaches are generally wide and
made up of sediments which include a large variety of fine sand, silt and sludge fractions, 75% of this area displaying a
relatively high degree of sediment compaction. It is characterized by the presence of narrow beaches interrupted by limestone platforms that extend into water, and high
seawalls (Fig. 1). The superficial sediments include a large variety of mollusk shells and gravel, these beaches being made
up of coarse sand with medium granulometry. 31 ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online)
European Journal of
Medicine and Natural Sciences
July - December 2019
Volume 2, Issue 2 ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online) ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online) European Journal of Medicine and Natural Sciences Between the two big geomorphic units of the Romanian littoral, the continental platform extends more to the north (Danube
Delta). The terrigenous runoff transported by the Danube causes the sedimentary substrate to be dominated by clay and
silt, not favorable for the attachment of macrophytobenthos [2], [3], [7], [8], [9]. Despite this fact, the protection jetties for
the harbor and beaches, but most especially the presence of the deep mussel infralittoral biocoenosis (Mytilus
galloprovincialis Lamarck, 1819) and its extension (relatively large, from St. George Branch to Vadu and Constanta)
determine the development of a harder substrate (shell layer) which permits the installation and development of
macrophytobenthos [20], [21], [22], [23], [24], [25 - 28]. This explains the occasional presence of algal deposits at the shore,
especially after storms. Brown algae – PHEOPHYTA Brown algae prefer cold marine waters, developing exuberantly at greater depths than green algae. Representatives from
three classes are found at the Romanian littoral: Isogeneratae (with two species of Ectocarpus and one species of
Scytosiphon), Heterogenerateae (Punctaria) and Cyclosporeae (with the most representative species at the Romanian
littoral from this group, Cystosera barbata (Good et Wood Ag.) The representatives of the first two classes register reduced biomasses compared to the representatives of green algae,
especially in spring and autumn. In the Black Sea, Cystoseira barbata forms a perennial association fixed to the hard
substrate, especially in the southern sector of the Romanian littoral. If in the past in was one of the most important
associations, covering the infralittoral zone between Agigea-Vama Veche, it is currently much reduced (due to the frost
periods in 1975 but also to pollution, increased water turbidity and substrate clogging). The biomass of this alga in deposits
at the seashore is relatively reduced, but its importance is given by the fact that its relatively rigid thallus constitutes a
substrate for a rich fauna and for epiphytic algae. Introduction This decrease in the number of species (apart from the pollution phenomenon) was attributed to climate changes – The 1980s represent a period of increased eutrophication and pollution, which generated important modifications in the
qualitative structure of macrophytobenthos. The effects of these modifications are still felt today [4], [19], 86 macroalgal
species were cited in the 1970s-1980s [1], 69 species were cited in the 1980s-1990s and only 55 species after 1990 [20],
[21]. This decrease in the number of species (apart from the pollution phenomenon) was attributed to climate changes – 32 ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online) European Journal of Medicine and Natural Sciences frost at the Romanian littoral (for unprecedented long periods of time) on the one hand and to the deposits of clay sediments
on limestone platforms (fraction mobilized and brought to the sea mass as a result of hydrotechnical constructions in the
Harbors of Cape Midia and Agigea South) on the other hand. The sedimentation of clay fractions on the limestone substrate
did not permit the attachment of plantules to the substrate [18], [19]. The taxonomic structure of macroalgal communities at the Romanian littoral The qualitative analysis of the marine macroalgal communities consists of the elaboration of lists of species, as well as a
comparative analysis of communities from different littoral sectors. A previous documentation must be done because there
are species with development phase in the prevernal – cold season (February-March), this being the period when they can
be encountered at the shore [1], [3], [4], [5], [17], [18]. Green algae – CHLOROPHYTA Distributed over the entire length of the Romanian sector, from south of the Danube flowing mouths to the southern
extremity of the littoral (Vama Veche). They are more developed in the Cape Singol-Constanta to Vama Veche sector. The
mass development of the macroalgal carpet in this sector is explained by the very presence of limestone platforms which
cover almost entirely the shallow waters and which represent the ideal substrate for their attachment. The group includes representatives of Clorophyceae, three orders: Ulvales, Cladophorales and Bryopsidales (Table1); the
vegetative apparatus is diverse: lamellate, filamentous, tubular or cladomial [1], [6], [18], [19], [20], [21] (Table.2). Red algae - RHODOPHYTA The representatives of this group make up the phytobenthos in the deep zone of the infralittoral. The algal deposits register an increased biomass compared to brown algae, but reduced in comparison to green algae. Two
classes have representatives in the Black Sea: - Bangiophyceae (with Porphyra leucosticta Thur and Bangia fuscopurpurea Lyngb. Both are cold water species and grow
at the end of winter till March without developing significant biomasses, compared to green algae); - Bangiophyceae (with Porphyra leucosticta Thur and Bangia fuscopurpurea Lyngb. Both are cold water species and grow
at the end of winter till March without developing significant biomasses, compared to green algae); - Florideophyceae – with the perennial species, Hildenbrandtia rubra Menegh., (distributed in the shallow zone, attached
to rocks or to mollusk shells). The species Corallina officinalis L. (pharmaceutical importance – vermifuge) develops in the
shallow infralittoral - permanently covered by water - and shelters a characteristic fauna. It rarely occurs in shore algal
deposits. Four species of the genus Phyllophora form “Zernov’s field” in the north-western basin of the Black Sea. It registers
maximum development at depths of 20-25 m and attaches to sandy substrate with sludgedy matrix. This field suffered a
significant reduction but clusters that form associations specific to the invertebrate fauna can still be encountered. The
biomass is reduced in the shore deposits. There are four representatives of Ceramiaceae: Callithamnion corymbosum
Lyngb. and three species of the genus Ceramium (these develop significant biomasses in the shallow zone – depths - Florideophyceae – with the perennial species, Hildenbrandtia rubra Menegh., (distributed in the shallow zone, attached
to rocks or to mollusk shells). The species Corallina officinalis L. (pharmaceutical importance – vermifuge) develops in the
shallow infralittoral - permanently covered by water - and shelters a characteristic fauna. It rarely occurs in shore algal
deposits. Four species of the genus Phyllophora form “Zernov’s field” in the north-western basin of the Black Sea. It registers
maximum development at depths of 20-25 m and attaches to sandy substrate with sludgedy matrix. This field suffered a
significant reduction but clusters that form associations specific to the invertebrate fauna can still be encountered. The
biomass is reduced in the shore deposits. There are four representatives of Ceramiaceae: Callithamnion corymbosum
Lyngb. Red algae - RHODOPHYTA and three species of the genus Ceramium (these develop significant biomasses in the shallow zone – depths 33 European Journal of European Journal of Medicine and Natural Sciences Medicine and Natural Sciences between 1.5 to 4-5 m, (Fig. 2), in the prevernal and vernal season. One species from Rhodomelaceae – Polysiphonia
denudata Grev. encountered in the warm season but without significant biomasses [4], [5], [17], [18]. between 1.5 to 4-5 m, (Fig. 2), in the prevernal and vernal season. One species from Rhodomelaceae – Polysiphonia
denudata Grev. encountered in the warm season but without significant biomasses [4], [5], [17], [18]. between 1.5 to 4-5 m, (Fig. 2), in the prevernal and vernal season. One species from Rhodomelaceae – Polysiphonia
denudata Grev. encountered in the warm season but without significant biomasses [4], [5], [17], [18]. Table 1. Representatives of Clorophyceae encountered at the Romanian littoral of the Black Sea (according to Sava
2006 [18], [25 - 28], photo: Sava, Paraschiv)
Species of Ulvales that develop appreciable biomass especially in the prevernal, vernal ant autumnal season
Order
Family
Species
Photo
Observations
Ulvales
Ulvaceae
Ulva rigida Ag. Maximum development in winter-spring,
attached to rocks, at low depths;
frequent in areas with high
concentrations of nutrients, together
with sp. Entromorpha. They are the first
species of macroalgae that colonize the
substrate. Enteromorpha
intestinalis (L) Link. All the species of
the genus
Enteromorpha
display wide
ecological
valences being
cosmopolite. Develops
appreciable
biomasses
especially in
prevernal and
vernal seasons,
forming a
compact vegetal
carpet on the
surface of rock
platforms. It
dominates in a
proportion of 80%
the algal deposits
at the sea shore. eurybiont
E. compressa (L)
Grev. It develops well in
waters rich in
organic
compounds of
sulfur and
nitrogen. E. linza (L) Ag. eurybiont
E. flexuosa (Wulf) Ag. Important for the
antibacterial
activity
Mycobacterium
tuberculosis and
possible bio-
indicator for
waters
contaminated
with heavy metals
E prolifera (O.Müll) J. Ag. eurybiont
Ulotrichaceae
Ulothrix implexa
(Kütz.) Kütz. Develops especially in the cold period
of the year, in spring and autumn on
hard substrate and epiphyte on the
thallus of other macroalgae. g
[ ], [ ], [
], [
]
Table 1. Red algae - RHODOPHYTA Abundant in the warm season, in shallow waters;
it is considered valuable as food in the extreme
east. Bryopsidales
Bryopsidaceae
Bryopsis plumosa (Huds.) Ag. It develops well in the warm period of the year, in
eutrophicated waters – even polluted
B. hypnoides Lamor
Fig. 2. Algal deposit at the sea shore made up of species from the genus Ceramium and depigmented green algae
in advanced decomposition state (Eforie Sud, Photo: Paraschiv)
Materials and Methods
Collection and processing of samples of macrophytic algae
1. Qualitative analysis
It involves the collection of samples from different places along the transect line without applying the sampling method (Fig. 3). The result of this type of analysis is represented by the list of species. Medicine and Natural Sciences ISSN 2601-6400 (Online)
Medicine and Natural Sciences
Volume 2, Issue 2
Table 2. Species of Cladophorales that develop appreciable biomass in the prevernal, vernal and autumnal season
[25 - 28]
Order
Family
Species
Observations
Cladophorales
Acrosiphonaceae
Urospora penicilliformis (Roth.) Aresh. Cold water species
considered arctic relic. It grows in midlittoral
waters, attached to
rocks but can also
reach greater depths. It lacks in the
Mediterranean. Filamentous thallus,
non-ramified that can
reach 30 cm in length
Cladophoraceae
Cladophora vagabunda (L) Hoek. Very abundant at our littoral; a good indicator for
highly eutrophicated waters; wide ecological
valences
C. sericea (Huds) Kütz. C. laetevirens (Dillw.) Kütz. C. albida (Huds) Kütz. C. dalmatica Kütz. Chaetomorpha aerea (Dillw.) Kütz. Abundant in the warm season, in shallow waters;
it is considered valuable as food in the extreme
east. Bryopsidales
Bryopsidaceae
Bryopsis plumosa (Huds.) Ag. It develops well in the warm period of the year, in
eutrophicated waters – even polluted
B. hypnoides Lamor
Fig. 2. Algal deposit at the sea shore made up of species from the genus Ceramium and depigmented green algae
in advanced decomposition state (Eforie Sud, Photo: Paraschiv)
Materials and Methods Table 2. Species of Cladophorales that develop appreciable biomass in the prevernal, vernal and autumnal season
[25 - 28]
Order
Family
Species
Observations
Cladophorales
Acrosiphonaceae
Urospora penicilliformis (Roth.) Aresh. Cold water species
considered arctic relic. It grows in midlittoral
waters, attached to
rocks but can also
reach greater depths. It lacks in the
Mediterranean. Filamentous thallus,
non-ramified that can
reach 30 cm in length
Cladophoraceae
Cladophora vagabunda (L) Hoek. Very abundant at our littoral; a good indicator for
highly eutrophicated waters; wide ecological
valences
C. sericea (Huds) Kütz. C. Red algae - RHODOPHYTA Representatives of Clorophyceae encountered at the Romanian littoral of the Black Sea (according to Sava
2006 [18], [25 - 28], photo: Sava, Paraschiv)
Species of Ulvales that develop appreciable biomass especially in the prevernal, vernal ant autumnal season
Order
Family
Species
Photo
Observations
Ulvales
Ulvaceae
Ulva rigida Ag. Maximum development in winter-spring,
attached to rocks, at low depths;
frequent in areas with high
concentrations of nutrients, together
with sp. Entromorpha. They are the first
species of macroalgae that colonize the
substrate. Enteromorpha
intestinalis (L) Link. All the species of
the genus
Enteromorpha
display wide
ecological
valences being
cosmopolite. Develops
appreciable
biomasses
especially in
prevernal and
vernal seasons,
forming a
compact vegetal
carpet on the
surface of rock
platforms. It
dominates in a
proportion of 80%
the algal deposits
at the sea shore. eurybiont
E. compressa (L)
Grev. It develops well in
waters rich in
organic
compounds of
sulfur and
nitrogen. E. linza (L) Ag. eurybiont
E. flexuosa (Wulf) Ag. Important for the
antibacterial
activity
Mycobacterium
tuberculosis and
possible bio-
indicator for
waters
contaminated
with heavy metals
E prolifera (O.Müll) J. Ag. eurybiont
Ulotrichaceae
Ulothrix implexa
(Kütz.) Kütz. Develops especially in the cold period
of the year, in spring and autumn on
hard substrate and epiphyte on the
thallus of other macroalgae. Table 1. Representatives of Clorophyceae encountered at the Romanian littoral of the Black Sea (according to Sava,
2006 [18], [25 - 28], photo: Sava, Paraschiv) Develops especially in the cold period
of the year, in spring and autumn on
hard substrate and epiphyte on the
thallus of other macroalgae. 34 European Journal of European Journal of ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online)
European Journal of
Medicine and Natural Sciences
July - December 2019
Volume 2, Issue 2
Table 2. Species of Cladophorales that develop appreciable biomass in the prevernal, vernal and autumnal season
[25 - 28]
Order
Family
Species
Observations
Cladophorales
Acrosiphonaceae
Urospora penicilliformis (Roth.) Aresh. Cold water species
considered arctic relic. It grows in midlittoral
waters, attached to
rocks but can also
reach greater depths. It lacks in the
Mediterranean. Filamentous thallus,
non-ramified that can
reach 30 cm in length
Cladophoraceae
Cladophora vagabunda (L) Hoek. Very abundant at our littoral; a good indicator for
highly eutrophicated waters; wide ecological
valences
C. sericea (Huds) Kütz. C. laetevirens (Dillw.) Kütz. C. albida (Huds) Kütz. C. dalmatica Kütz. Chaetomorpha aerea (Dillw.) Kütz. Red algae - RHODOPHYTA laetevirens (Dillw.) Kütz. C. albida (Huds) Kütz. C. dalmatica Kütz. Chaetomorpha aerea (Dillw.) Kütz. Abundant in the warm season, in shallow waters;
it is considered valuable as food in the extreme
east. Bryopsidales
Bryopsidaceae
Bryopsis plumosa (Huds.) Ag. It develops well in the warm period of the year, in
eutrophicated waters – even polluted
B. hypnoides Lamor Fig. 2. Algal deposit at the sea shore made up of species from the genus Ceramium and depigmented green algae
in advanced decomposition state (Eforie Sud, Photo: Paraschiv) Fig. 2. Algal deposit at the sea shore made up of species from the genus Ceramium and depigmented green algae Fig. 2. Algal deposit at the sea shore made up of species from the genus Ceramium and depigmented green algae
in advanced decomposition state (Eforie Sud, Photo: Paraschiv) Sample collection for qualitative determinations Observations and collection of algae for qualitative determination was made monthly, especially after storm periods, to
identify the dominant perennial and seasonal species, and to capture the different stages of the development cycle. Fresh
algal samples were taken in the laboratory, washed of the associated fauna and sorted in the main groups; the sampling is
done so that the estimation of the abundance can be done (after density and biomass); for this purpose, a classical
procedure was pursued, but unanimously supported by specialists in the world community, that of sampling the "square
sample". Samples are obtained by integral collecting of plant biomass by scraping the substrate corresponding to a square sample;
for each sample at least one replicate was taken; samples are stored in the chest freezer and will be processed in the
laboratory. Photographs in the field, before taking samples, will complete the picture of the structure of macro-algal
associations from the southern part of the Romanian coast. In this case, the study objective was to establish a list of species in a given region. The study of biodiversity is complex and
long, its purpose being more than just the publication of lists of species valid at one moment, but also the appreciation of
the way in which these lists change in time and space, as well as the reasons for these changes, which can be due to
natural variability or the impact of biotic and abiotic factors. In order to obtain this kind of long-term results and for their comparison in time and space, it is necessary to standardize
them and maintain them at the same level of precision in sample collection, as well as their processing and analysis. These
objectives are difficult to reach for practical reasons, especially in the case of macrophytes. Algae collection for qualitative determinations takes place monthly or at least once every other month in order to detect not
only the perennial but also the seasonal species, as well as for the determination of stages in the development cycle. Also,
it is recommended to collect whole samples, both with the fixing portions (rhizoids, disks or cramps) and the apical parts of
the thallus, all structures being necessary for the correct identification of species. Algal samples are brought fresh to the laboratory, washed from the associated fauna and sorted on main groups. 2. Quantitative analysis This type of analysis involves the collection of biological samples usable for an estimation of abundance (according to
density and biomass) [8]. For this purpose, a classical method is used as it is unanimously accepted by specialists and
known as the sampling by means of the “sample square.” Materials and Methods Collection and processing of samples of macrophytic algae 1. Qualitative analysis It involves the collection of samples from different places along the transect line without applying the sampling method (Fig. 3). The result of this type of analysis is represented by the list of species. It involves the collection of samples from different places along the transect line without applying the sampling method (Fig. 3). The result of this type of analysis is represented by the list of species. 3). The result of this type of analysis is represented by the list of species. 35 ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online)
European Journal of
Medicine and Natural Sciences
July - December 2019
Volume 2, Issue 2 ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online) Medicine and Natural Sciences Sample collection for qualitative determinations The fresh
material is determined macroscopically and microscopically, using field guides or specialized papers: Ulvales (Chlorophyta)
from URSS Seas (Vinogradova, 1974); A critical survey of European Taxa in Ulvales (Bliding, 1963); Revision of European
species of Cladophora (van Hoek, 1963); Sur le Ceramium de la Mer Noire (Celan şi Şerbănescu, 1959); Algology Book
vol II, vol III (1977, 1979); Wold Life Diversity–Ilustrated Book of Romanian Flora and Fauna, vol I –Marine Environmental
(1995); Guides des algues des mers d’Europe (Bouduresque, 1992). Sample collection for quantitative determinations The quantitative estimations are important for the understanding of the structure and functioning of a population, for the
analysis of the biochemical compounds, as well as for the estimation of current deposits, especially in the case of species
valuable from the economical point of view. The quantitative collection of macrophytic algae is realized using the square method, by means of frames of proper sizes,
which are established according to the characteristics of the respective population, as well as to the type of substrate. In concrete conditions regarding the type of macrophytic algal vegetation at our littoral, as well as the substrate it prefers,
wooden frames (10/10 cm) are used for quantitative collection (Fig. 3). All the algae from this surface are collected, each sample being introduced into a plastic bag and labeled with the date,
place and depth of collection. Three replicates are usually collected from each depth. All the algae from this surface are collected, each sample being introduced into a plastic bag and labeled with the date,
place and depth of collection. Three replicates are usually collected from each depth. The fresh samples brought to the laboratory are washed from the associated fauna, sorted on main groups (green, red and
brown algae). Then, the species are separated in each group after their prior identification. The fresh samples brought to the laboratory are washed from the associated fauna, sorted on main groups (green, red and
brown algae). Then, the species are separated in each group after their prior identification. In order to obtain the dry biomass values, the samples are dried at 1050C in the drying oven for 24 hours. The biomass is
calculated for each species and the final value is represented by the average of each species collected in the three samples
from each depth, then multiplied by 100 and expressed in g*m-2. In order to obtain the dry biomass values, the samples are dried at 1050C in the drying oven for 24 hours. The biomass is
calculated for each species and the final value is represented by the average of each species collected in the three samples
from each depth, then multiplied by 100 and expressed in g*m-2. The value of abundance according to the dry biomass (e.g. Substrate In the distribution of flora and algal vegetation, the nature and aspect of the substrate are very important. Apart from the
rocky substrate (Fig. 3.b), limestone platforms, protection jetties), two other factors are also important: the substrate
represented by mollusk shells and the thallus of certain algae, for fauna. Materials and equipment Simple and accessible equipment is needed for the collection of samples: knife, plastic bags, cloth sacks, plastic dishes,
tracing paper, pencil, refrigerating box. The samples are obtained by the total collection/scraping from the substrate of a
vegetal biomass corresponding to a sample. At least one replicate will be taken for each collection. The samples are kept
in the refrigerating box and processed in the laboratory. Sample collection for quantitative determinations for Cladophora vagabunda), collected from a depth of 1 m: A1
– value of dry biomass from the first replicate; A 2 – value of dry biomass from the second replicate; A 3 – value of dry biomass
from the third replicate; B g/m2 (Cladophora biomass at 1 m) = (A1 + A2 + A3) x 100 At the end of sample processing and identification of species, the individuals in each species are counted and thus we
obtain the abundance on sample surface. The arithmetic mean is realized depending on replicates and its value is
extrapolated to square meter (surface unit) and represents abundance according to density (expressed in number of
individuals per species*m-2). Establishing transects (Fig. 3.a). nsects that conform to certain conditions must be chosen in order to collect samples of macrophytic algae •
To be accessible in different climatic conditions,
•
To be easy to locate but to maintain the collection conditions,
•
To tolerate repeated collections (samples), at different distances from the shoreline. •
To be accessible in different climatic conditions, •
To be easy to locate but to maintain the collection conditions, •
To tolerate repeated collections (samples), at different distances from the shoreline. 36 ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online)
European Journal of
Medicine and Natural Sciences
July - December 2019
Volume 2, Issue 2 ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online) European Journal of Medicine and Natural Sciences Results and Discussions Macrophytes recorded mass development during periods of optimal thermal and nutrients regime, as follows: species of
clorophyte group (Table 3): Urospora penicilliformis, red algae species, Bangia fuscopurpurea, Porphyra leucosticta,
Ectocarpus siliculosus are frequently met in February and May, while species Dasya, Chondria appear during summer;
cosmopolite species belonging to genus Enteromorpha (E. intestinalis, E. compressa, E. linza, E. flexuosa, E. prolifera)
Ulva rigida, Ceramium (C. elegans, C. diaphanum) are present in all the associations follow one another during the year. Perennial algae: Cystoseira barbata and Cy. bosphorica from the shallow rocky littoral areas and Phyllophora nervosa, Ph. brodiaei from greater depths of circa littoral, but until 50 m (almost 50 years ago a wide field of about 11000 km2, in the NW 37 37 ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online) European Journal of Medicine and Natural Sciences part of the sea was described as a true red “plain” formed by species of genus Phyllophora – with a biomass over 5,6 million
tone; this representing one of the basic biological characteristics of the Black Sea [17]. part of the sea was described as a true red “plain” formed by species of genus Phyllophora – with a biomass over 5,6 million
tone; this representing one of the basic biological characteristics of the Black Sea [17]. Observations and studies that we have done over several years enabled us to identify the two summer periods in which
large amounts of macro-algae are detached from the substrate and bonded to the shore (especially in the group of green
algae-Chlorophyta), in June – August . In addition to natural factors such as prolonged periods of freezing from the Romanian seaside in the years `70 -`80, the
emergence of high intensity storms, the anthropogenic factors have had an important contribution; studies in recent years
have shown a significant decrease in the number of species of algae covering the shallow littoral south of Constanta (Table
4, [18]), and this was made on behalf of human impact stemming mainly from the work of the Port of Constanta South
Agigea (large amounts of fine clay sediments reached the water through port works and hydro technical works, determining
decrease of transparency and change of shallow bottom waters because the sediments that were deposited on hard
substrate created a mobile substrate and prevented macro-algae deposition). substrate created a mobile substrate and prevented macro-algae deposition). Results and Discussions CYCLOSPOREAE - PHAEOPHYTA
14
Fucales
Cystoseira barbata (Good et Wood) Ag. FLORIDEOPHYCEAE-RHODOPHYTA
15
Ceramiales
Callithamnion corymbosum (Smith.) Lyngb. 16
Ceramium rubrum (Huds) Ag. 17
Ceramium elegans (Roth.) Ducl. Table 3. The most abundant algae species identified in algae agglomerations on the sho
(after Sava, [18], [25 - 28])
Nr. crt. Taxonomic group
Species
CHLOROPHYCEAE
1
Ulvales
Ulva rigida (lactuca) (L.)
2
Enteromorpha intestinalis (L.) Link. 3
E. compresa (L.) Grev. 4
E. linza (L.) Ag. 5
E. flexuosa (Wulf.) Ag. 6
E. prolifera (O.Múll) J. Ag
7
Cladophorales
Urospora penicilliformis (Roth.) Aresh
8
Cladophora vagabunda (L.) Hoek. 9
C. sericea (Huds.) Kütz. 10
C. albida (Huds.) Kütz. 11. Bryopsidales
Bryopsis plumosa (Huds.) Ag. 12
B. hypnoides Lamour
ISOGENERATAE - PHAEOPHYTA
13
Ectocarpales
Ectocarpus siliculosus (Dillw.) Lyngb. CYCLOSPOREAE - PHAEOPHYTA
14
Fucales
Cystoseira barbata (Good et Wood) Ag. FLORIDEOPHYCEAE-RHODOPHYTA
15
Ceramiales
Callithamnion corymbosum (Smith.) Lyngb. 16
Ceramium rubrum (Huds) Ag. 17
Ceramium elegans (Roth.) Ducl. Table 4. The decrease of the number of macrophyte algae species during 1977-2007
(data after Sava [19], [18], [25 - 28])
Phyllum
After data:
Bavaru
1977
Vasiliu
1980-1995
Sava
2007
Chlorophyta
31
22
16
Phaeophyta
14
9
5
Rhodophyta
41
24
10
Total
86
55
30 Table 4. The decrease of the number of macrophyte algae species during 1977-2007 onclusion Results and Discussions 10
C. albida (Huds.) Kütz. 11. Bryopsidales
Bryopsis plumosa (Huds.) Ag. 12
B. hypnoides Lamour
ISOGENERATAE - PHAEOPHYTA
13
Ectocarpales
Ectocarpus siliculosus (Dillw.) Lyngb. CYCLOSPOREAE - PHAEOPHYTA
14
Fucales
Cystoseira barbata (Good et Wood) Ag. FLORIDEOPHYCEAE-RHODOPHYTA
15
Ceramiales
Callithamnion corymbosum (Smith.) Lyngb. 16
Ceramium rubrum (Huds) Ag. 17
Ceramium elegans (Roth.) Ducl. Table 4. The decrease of the number of macrophyte algae species during 1977-2007
(data after Sava [19], [18], [25 - 28])
Phyllum
After data:
Bavaru
1977
Vasiliu
1980-1995
Sava
2007
Chlorophyta
31
22
16
Phaeophyta
14
9
5
Rhodophyta
41
24
10
Total
86
55
30
Conclusion Table 3. The most abundant algae species identified in algae agglomerations on the shore
(after Sava, [18], [25 - 28])
Nr. crt. Taxonomic group
Species
CHLOROPHYCEAE
1
Ulvales
Ulva rigida (lactuca) (L.)
2
Enteromorpha intestinalis (L.) Link. 3
E. compresa (L.) Grev. 4
E. linza (L.) Ag. 5
E. flexuosa (Wulf.) Ag. 6
E. prolifera (O.Múll) J. Ag
7
Cladophorales
Urospora penicilliformis (Roth.) Aresh
8
Cladophora vagabunda (L.) Hoek. 9
C. sericea (Huds.) Kütz. 10
C. albida (Huds.) Kütz. 11. Bryopsidales
Bryopsis plumosa (Huds.) Ag. 12
B. hypnoides Lamour
ISOGENERATAE - PHAEOPHYTA
13
Ectocarpales
Ectocarpus siliculosus (Dillw.) Lyngb. CYCLOSPOREAE - PHAEOPHYTA
14
Fucales
Cystoseira barbata (Good et Wood) Ag. FLORIDEOPHYCEAE-RHODOPHYTA
15
Ceramiales
Callithamnion corymbosum (Smith.) Lyngb. 16
Ceramium rubrum (Huds) Ag. 17
Ceramium elegans (Roth.) Ducl. Table 4. The decrease of the number of macrophyte algae species during 1977-2007
(data after Sava [19], [18], [25 - 28])
Phyllum
After data:
Bavaru
1977
Vasiliu
1980-1995
Sava
2007
Chlorophyta
31
22
16
Phaeophyta
14
9
5
Rhodophyta
41
24
10
Total
86
55
30
Conclusion Table 3. The most abundant algae species identified in algae agglomerations on the shore Table 3. The most abundant algae species identified in algae agglomerations on the shore Table 3. The most abundant algae species identified in algae agglomerations on the sho
(after Sava, [18], [25 - 28])
Nr. crt. Taxonomic group
Species
CHLOROPHYCEAE
1
Ulvales
Ulva rigida (lactuca) (L.)
2
Enteromorpha intestinalis (L.) Link. 3
E. compresa (L.) Grev. 4
E. linza (L.) Ag. 5
E. flexuosa (Wulf.) Ag. 6
E. prolifera (O.Múll) J. Ag
7
Cladophorales
Urospora penicilliformis (Roth.) Aresh
8
Cladophora vagabunda (L.) Hoek. 9
C. sericea (Huds.) Kütz. 10
C. albida (Huds.) Kütz. 11. Bryopsidales
Bryopsis plumosa (Huds.) Ag. 12
B. hypnoides Lamour
ISOGENERATAE - PHAEOPHYTA
13
Ectocarpales
Ectocarpus siliculosus (Dillw.) Lyngb. Results and Discussions collection: the sample square” for qualitative and quantitative determinations of the macroalgal flora: a. the choice
of transects perpendicular to the shore line; b. the “sample square” method; c. sampling by corer for quantitative
determinations in the depth of the column with algal substrate and fauna associated to this substrate (Photo: a. Vama Veche - 2 Mai; b. Vama Veche and Mangalia; Paraschiv, Sava, Negreanu), [25 – 28]
a. b. c. Fig. 3. Sample a. a. a. b. c. b. c. Fig. 3. Sample collection: the sample square” for qualitative and quantitative determinations of the macroalgal flora: a. the choice
of transects perpendicular to the shore line; b. the “sample square” method; c. sampling by corer for quantitative
determinations in the depth of the column with algal substrate and fauna associated to this substrate (Photo: a. Vama Veche - 2 Mai; b. Vama Veche and Mangalia; Paraschiv, Sava, Negreanu), [25 – 28] 38 38 European Journal of Medicine and Natural Sciences All shoreline protection works (against beaches erosion and for tourist activities) caused changes in the movement of littoral
currents, being created areas with low dynamic of water bodies and thus eliminated rheophile/oxygenophile species in
these areas. Today only about one third of the total number of macro-algae species is encountered, compared to species cited 50 years
ago; this has allowed the mass development of cosmopolitan, opportunistic, short life cycle species, especially belonging
to the group Chlorophyta (green macro-algae); the most significant decrease is recorded for red (31 species in this group
no longer being found on the Romanian seaside in the past 50 years) and brown macro-algae species (9 species). An
important ecological niche for the development of marine benthos on hard substrate of the littoral part from the south of
Constanta was represented by the "field of Cystoseira barbata"; currently in this field have left only small "oasis" with a
much reduced surface [Sava et. al., (2007)]. much reduced surface [Sava et. al., (2007)]. Table 3. The most abundant algae species identified in algae agglomerations on the shor
(after Sava, [18], [25 - 28])
Nr. crt. Taxonomic group
Species
CHLOROPHYCEAE
1
Ulvales
Ulva rigida (lactuca) (L.)
2
Enteromorpha intestinalis (L.) Link. 3
E. compresa (L.) Grev. 4
E. linza (L.) Ag. 5
E. flexuosa (Wulf.) Ag. 6
E. prolifera (O.Múll) J. Ag
7
Cladophorales
Urospora penicilliformis (Roth.) Aresh
8
Cladophora vagabunda (L.) Hoek. 9
C. sericea (Huds.) Kütz. Acknowledgments Scientific investigations were funded by Norway Grants Program – Innovation Norway, “Norwegian Coop Scientific investigations were funded by Norway Grants Program – Innovation Norway, “Norwegian Cooperation
Programmes for Economic Growth and Sustainable Development in Bulgaria and Romania”,
Project no. KNRIN
2008/115241. Conclusion The most important features of macro-algal communities in the southern Romanian Black Sea Coast are: 39 ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online)
European Journal of
Medicine and Natural Sciences
July - December 2019
Volume 2, Issue 2
•
reduced number of species in groups of red and brown macro-algae;
•
proliferation of opportunistic species of green macro-algae group, with short life cycle and which can
develop impressive biomass in a relatively short time; these few species occupies 80% area of shallow
sea bottom;
•
reduce the area occupied by perennial macro-algae, Cystoseira and Phyllophora. •
To improve the existing situation is necessary to popularize the importance of species (rare species and
especially of perennial ones) on one hand, and to recover large amounts of macro-algae biomass produced
during summer on the other hand. European Journal of July - December 2019
Volume 2, Issue 2 Medicine and Natural Sciences reduced number of species in groups of red and brown macro-algae; •
proliferation of opportunistic species of green macro-algae group, with short life cycle and which can
develop impressive biomass in a relatively short time; these few species occupies 80% area of shallow
sea bottom; reduce the area occupied by perennial macro-algae, Cystoseira and Phyllophora. •
To improve the existing situation is necessary to popularize the importance of species (rare species and
especially of perennial ones) on one hand, and to recover large amounts of macro-algae biomass produced
during summer on the other hand. References [1] Bavaru, A., Contribution of algal association study from rocky substratum of Black Sea coast, PhD Thesis, Ed. Bucuresti University, 1977, 195 pp. [1] Bavaru, A., Contribution of algal association study from rocky substratum of Black Sea coast, PhD Thesis, Ed. Bucuresti University, 1977, 195 pp. [2] Băcescu, M.C., Substratum; Marine Ecology, vol. I, part. 3, London, 1972, 1291-1314 pp. [3] Băcescu, M., Müller, G.I., Gomoiu M.T., Cercetari de ecologie bentală în Marea Neagră. Analiza cantitativă, calitativă
şi comparată a faunei bentale pontice. Ecologie marină 1971, 4, 1-357 pp. [4] Bologa, A.S., Destruction of marine biodiversity – a case study of the Black Sea. IOI-Pacem in Maribus XXVII
Conference, Proceedings, 2001, 249-254 pp. [5] Bologa, A.S., Sava, D, Progressive decline and present tend of Romanian Black Sea macroalgal flora – Marine
Research, 2006, 36: 31-60 pp. [6] Celan, M, Şerbănescu, G, Sur les Ceramium de la mer Noire- Lucr. Ser. St. Stat. Zool. Mar. „Prof. I. Borcea”, Agigea,
1959, 531-56 pp. [7] Dumitrache, C., Present state of the zoobenthos from the Romanian Black Sea continental shelf. Cercetari marine –
Recherches marines, IRCM Constanta, 1996-1997, 29-30: 141-151 pp. [8] Godeanu, S., Botnariuc, N., Petran, A., Caracterizarea ecologica generală a ecosistemelor acvatice; Pontus Euxinus,
Cercetari si studii, II, 1982, 258-270 pp. [9] Godeanu, S., Paraschiv, G.M., Compendiu de Ecologie Aplicată/Caiet de lucrări practice, 198 p., Ed. Bucura Mond,
2005, 181 pp. [10] Gomoiu, M.-T., Marine Eutrofication Syndrome in the Northwestern Part of the Black Sea. Science of the Total
Environmental, Supp. Else. Scie. Publ. B. V., Amsterdam, 1978, 683-692 pp. [11] ***Some problems concerning actual ecological changes in the Black Sea. Cercetari Marine – Recherches marines,
IRCM Constanta, 1981, 14: 109-127 pp. [12] Kinne, O., Marine Ecology: Zonation and Organismic Assemblages; In. Vol. V, Part 1; Ed. John Wiley &Sons-New
York, 1982, 267-508 pp. [13] Panin, N., On the Geomorphological and Geological Evolution of the River Danube – Black Sea Interaction Zone;
GeoEcoMarina 2: Fluvial-Marine Interactions, Bucuresti, 1997, 31-40 pp. 40 40 40 ISSN 2601-6397 (Print)
ISSN 2601-6400 (Online) European Journal of Medicine and Natural Sciences [17] Sava, D., Pollution Ecological Assessment of Macrophytic Cenosis From Rocky Black Sea Coast, PhD Thesis,
“Ovidius” University Constanţa, 2002, 233 pp. [17] Sava, D., Pollution Ecological Assessment of Macrophytic Cenosis From Rocky Black Sea Coast, PhD Thesis,
“Ovidius” University Constanţa, 2002, 233 pp. [18] ***Macrofitic algal from Romanian Black Sea, Ed. References Ex Ponto, „Ovidius” University Press, Constanta, 2006, 147 pp. [19] Sava, D. Samargiu, M.D., Paraschiv, G.M., Macroalgal Flora from the Romanian Black Sea Coast – Diversity,
Ecology, present tend; The 8th National Conference of Environmental Protection and 5th National Conference of
Ecosangenesis – May 2007: 100-104. [20] Vasiliu, F., Macrophytic Algal Production from Romanian Black Sea Coast; PhD Thesis, Bucuresti University, 1984,
210 pp. [21] ***Ecological Consideration of Macrophytic Species List from Romanian Black Sea Coast; Naturalia – Piteşti, St. cerc. II-III, 1996, 432-444 pp. [22] Ţigănuş, V., Modifications dans la structure de la biocenose des sables a Corbula mediterranea (Costa) du littoral
roumain. Rapp.Comm.int.mer Medit., 1982b, 28: 205-206 pp. [23] Ţigănuş, V., Evolution des peuplements macrobenthiques du substrat sablonneux sur le littoral roumain. Rapp.Comm.int.mer Medit., 1990, 32, 1:22. [24] Ţigănuş, V., Dumitrache C., Sur la diversite actuelle de la macrofaune benthique du littoral roumain. Rapp. Comm. int. mer Medit., 1995, 34: 45. [25] Negreanu-Pîrjol, T., Negreanu-Pîrjol, B., Năstac, M., Paraschiv, G.M., Qualitative data about shallow waters
macroalgal resources from South Romanian Black Sea Coast”, International Conference on the Conservation and
Sustainable Use of Wild Plant Diversity - CSUWPD 2010, 4-8 May 2010, Kolympari, Chania, Crete, Greece, Section:
Wild Plant in Scientific Research and Development (SRD), Abstracts, p. 55. [26] Negreanu-Pîrjol, B., Negreanu-Pirjol, T., Paraschiv, G., Bratu, M., Sirbu, R., Roncea, F., Meghea, A., Physical-
chemical characterization of some green and red macrophyte algae from Romanian Black Sea littoral, Scientific
Study & Research-Chemistry & Chemical Engineering, Biotechnology, Food industry, 2011, 12 (2), pp. 173 – 184. [27] Paraschiv, G.M., Negreanu-Pirjol, T., Negreanu-Pirjol, B., Sirbu, R., Study of the invertebrates fauna associated of
the macroalgal biomass from the Romanian Black Sea Coast, 12th International Multidisciplinary Scientific
GeoConference „Modern Management of Mine Production, Geology and Environmental Protection” – SGEM 2012,
17 – 23 June 2012, Albena, Bulgaria, Conference Proceedings, Volume V, Section „Ecology and Environmental
protection”, pp. 801-808. [28] Paraschiv, G.M., Negreanu-Pîrjol, B.-Ş., Arpenti, M., Jurja, S., Mireşan, H., Negreanu-Pîrjol, T., Evaluation of physic-
chemical and biological conditions from the psammic habitats that are populated by interstitial cnidarian species
(cnidaria-hydrozoa) from Vama Veche, Romanian Black Sea Coast, 14th International Multidisciplinary Scientific
GeoConferences „Surveying Geology & mining Ecology Management – SGEM 2014”, 17 – 26 June 2014, Albena,
Bulgaria, Conference Proceedings, Volume II, Section: „Water Resources, Forest, Marine and Ocean Ecosystems”,
pp. 601 – 606. 41 41
|
https://openalex.org/W2102937843
|
http://threatenedtaxa.org/index.php/JoTT/article/download/880/1575
|
English
| null |
Garra dampaensis, a new ray-finned fish species (Cypriniformes: Cyprinidae) from Mizoram, northeastern India
|
Journal of threatened taxa
| 2,013
|
cc-by
| 6,389
|
ISSN
Online 0974-7907
Print 0974-7893
OPEN ACCESS ISSN
Online 0974-7907
Print 0974-7893
OPEN ACCESS ournal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377 Communication Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377 Abstract: Garra dampaensis, a new cyprinid fish species, is described from the Seling River, a t Keywords: Dampa Tiger Reserve, Karnaphuli, Khawthlang Tuipui, new species, Seling. Abbreviations: HL - Head length; SL - Standard length; MUMF - Manipur University Museum of Fishes, Manipur, India; PUCMF - Pachhunga
University College Museum of Fishes, Mizoram, India; ZSI - Zoological Survey of India, Kolkata, India. Mizo Abstract: Garra dampaensis, nghalim chhungkaw zinga mi, nghazawngek chi thar chu Seling lui, Khawthlang Tuipui (Karnaphuli),
Mizoram, India atanga hmuhchhuah a ni. He sangha chi thar hian a mei ah W ang tak thil dum in rin a nei a, chutiang inrin chu nghazawng
ek chi dang, heng, G. abhoyai, G. lissorhynchus, G. nambulica, G. paralissorhynchus leh G. rupecula, te chauhin an nei ve a ni. Heng
nghazawngek chi 5 tarlante nen an danglamna chu, a awm leh dulah te phuhlip a nei bik, a mawngkua leh a mawng pangparh inkar hlat
zawng a tawi bik, tin, a taksa dungzui zawnga phuhlip intlar thla a tlem bik a ni (27–29 vs. 29 aia tam vek). Nghazawngek (Lissorhynchus
complex) ho hriathran theihna tur pek a ni bawk. doi: http://dx.doi.org/10.11609/JoTT.o3141.4368-77 | ZooBank: urn:lsid:zoobank.org:pub:CF728AC6-0507-452B-B753-A82FED642D48 Samuel Lalronunga 1, Lalnuntluanga 2 & Lalramliana 3 Samuel Lalronunga 1, Lalnuntluanga 2 & Lalramliana 3 1,2 Department of Environmental Science, Mizoram University, Aizawl, Mizoram 796009, India
3 Department of Zoology, Pachhunga University College, Aizawl, Mizoram 796001, India
1 samuellrna@gmail.com, 2 tluanga_249@rediffmail.com, 3 lrl_zoo@yahoo.co.in (corresponding author Abstract: Garra dampaensis, a new cyprinid fish species, is described from the Seling River, a tributary of the Khawthlang Tuipui (Karnaphuli
River), in Mizoram, India. The species can be distinguished from all other Garra species, except G. abhoyai, G. lissorhynchus, G. nambulica,
G. paralissorhynchus and G. rupecula by the presence of a distinct W-shaped black band on the caudal fin. It can be distinguished from the
above mentioned five species in having scales on the breast and belly, shorter vent to anal distance, and by having fewer lateral line scales
(27–29 vs. more than 29 in all other species). A key to the species of Garra in the Lissorhynchus complex is provided. Description Biometric data are given in Table 1. Head depressed;
body small, compressed and elongate. Dorsal profile
gently rising from tip of snout to origin of dorsal fin then
sloping gently towards caudal peduncle, body depth
greatest at dorsal fin base. Ventral surface flattened
from head to anal fin base. Eye ovoid, moderately
large, not visible from ventral view, located in middle
or slightly posterior of head length. Snout rounded
without transverse groove, minute tubercles clustered
(6–9) at anterior base of rostral barbels and sparsely
extending on tip of snout, rostral lobe short. Head wider
than deep. Date of publication: 26 May 2013 (online & print) Date of publication: 26 May 2013 (online & print) Manuscript details: Ms # o3141 | Received 29 March 2012 | Final received 07 May 2013 | Finally accepted 09 May 2013 Citation: Lalronunga, S., Lalnuntluanga & Lalramliana (2013). Garra dampaensis, a new ray-finned fish species (Cypriniformes: Cyprinidae) from Mizoram,
northeastern India. Journal of Threatened Taxa 5(9): 4368–4377; http://dx.doi.org/10.11609/JoTT.o3141.4368-77 Copyright: © Lalronunga et al. 2013. Creative Commons Attribution 3.0 Unported License. JoTT allows unrestricted use of this article in any medium, reproduction
and distribution by providing adequate credit to the authors and the source of publication. Funding: The study was funded by University Grant Commission-North Eastern Regional Office and Zoram Educational
Trust. SLRN is awardee of Mizoram University Research Scholars Fellowship. Competing Interest: None. Acknowledgements: We are grateful to Director Zoological Survey of India, Kolkata for the facilities provided; Subrata Kar (ZSI) and Waikom Vishwanath (MUMF)
for access to material under their care. Mizoram State Forest and Wildlife Department, especially, Mr. Laltlanhlua Zathang, Field Director, Dampa Tiger Reserve,
for permission to survey. Funding for LRL from University Grant Commission-North Eastern Regional Office, Zoram Educational Trust, Mizoram, and SLRN from
Mizoram University, Mizoram; facilities provided by Dr Tawnenga, Principal, Pachhunga University College, Aizawl, Mizoram are acknowledged here. Author Contribution: SLRN - detailed examination of Garra species of Mizoram and comparison with specimens in ZSI and in other museums; LNT - supervision
in identification of freshwater fish species, interpretation of the result and discusses taxonomic status; LRL - supervision in establishing new species, comparison
with available literature, discusses taxonomic status, preparation of drawings and comparison with specimens in MUMF. Author Details: Samuel Lalronunga is a research scholar, registered for PhD degree under the Department of Envinonmental Science, Mizoram University. He
is working on diversity of fishes of Mizoram, northeastern India and their phylogenetic analysis. Lalnuntluanga is an Associate Professor in the Department
of Environmental Science, Mizoram University and his field of specialization is Biodiversity. He is presently engaged in taxonomy and systematics of freshwater
organisms of Mizoram. Lalramliana is an Assistant Professor in the Department of Zoology, Pachhunga University College, Mizoram and his field of specialization
is fish and fisheries. He is presently engaged in molecular characterization and phylogeny of freshwater fishes of Mizoram. 4368 Garra dampaensis sp. nov. Lalronunga et al. Material examined Holotype: PUCMF 12001, 22.vii.2011, 45.6mm SL,
Seling River, a tributary of Khawthlang Tuipui (Karnaphuli
River) in the vicinity of Damparengpui, Mizoram, India,
23040’51”N & 92022’35”E, coll. Samuel Lalronunga &
Lalnuntluanga. Paratypes: PUCMF 12002, 10 exs., 40.6–51.9 mm SL,
same data as holotype; PUCMF 12003, 2 exs., 42.0–48.9
mm SL, same data as holotype (dissected for gonadal
studies); PUCMF 12004, 3 exs., 36.5–41.4 mm SL, same
data as holotype (dissected and preserved in glycerin
with thymol for bone study). The Karnaphuli River, locally known as the
Khawthlang Tuipui, in Mizoram, is located between
the Ganga-Brahmaputra and the Kolodyne drainages. Originating from the hills of the Mizoram-Tripura border
in India, it flows along the Mizoram-Bangladesh border
and then southwest through the Chittagong Hill tract
and Chittagong and ultimately joins the Bay of Bengal. No previous reports have been made on any Garra
species from the Karnaphuli drainage of Mizoram. Recent freshwater faunal surveys conducted in the
Karnaphuli drainage of Dampa Tiger Reserve, Mizoram,
India, resulted in the collection of specimens of Garra. Detailed studies and comparison of this material with
congeners revealed it to belong to an unnamed species
which is herein described as Garra dampaensis sp. nov. Diagnosis A small species of Garra with the following
combination of characters: no transverse groove and
proboscis on the snout; tip of dorsal fin falcate; long
axillary scale present at the base of pelvic fin, reaching
the base of last pelvic fin ray; 27–29 lateral-line scales,
10–11 regularly arranged predorsal scales; W-shaped
black band across the middle of caudal fin and presence
of scales on the breast and belly. Additional characters
useful for diagnosing this species are outlined in the
discussion. Garra dampaensis sp. nov.
(Image 1 A&B; Image 2 A&B) urn:lsid:zoobank.org:act:6C1E6C12-F00B-4A9F-9E1E-55F39DA1E85E Introduction Weberian apparatus (assumed to contain four vertebrae). Numbers in parentheses after a meristic value indicate
the frequency of that value. Specimens examined for
the study are deposited in Pachhunga University College
Museum of Fishes (PUCMF), Mizoram, India. Species of the genus Garra Hamilton, 1822 are hill
stream bottom dwelling cyprinids currently consisting
of more than 85 described species (Chen et al. 2009),
usually found in fast flowing rivers and streams adhering
to submerged rocks with the help of a sucking disc
present on the ventral surface of the head, just behind
the mouth. The genus occurs widely from south China,
Borneo and south Asia through Burma (now Myanmar),
India, the Middle East, Arabian Peninsula and East Africa
to West Africa (Menon 1964). During the last decade,
several descriptions (Kottelat 2000; Vishwanath &
Kosygin 2000; Gopi 2001; Zhang & Chen 2002; Zhang
et al. 2002; Kullander & Fang 2004; Vishwanath &
Joyshree 2005; Vishwanath & Shanta 2005; Zhang 2005,
2006; Zhou et al. 2005; Li et al. 2008; Vishwanath &
Linthoingambi 2008; Chen et al. 2009; Nebeshwar et al. 2009) and revisions (Zhang et al. 2002; Zhou et al. 2005)
on Garra species have been made from Asia. Material and methods Dorsal fin with ii,6 (16) rays, falcate with sub-acuminate
tip, first branched ray longest; origin closer to snout tip
than caudal fin base, origin anterior to pelvic fin origin
and over 10th lateral line scales; posterior margin slightly
concave. Pectoral fin sub-acuminate with i,12 (16) rays
(two to three small unbranched rays posterior to the last
branched ray not counted), fourth and fifth branched
ray longest, adpressed fin tip reaching beyond half the
distance between pectoral fin origin and pelvic fin origin
or reached 9th lateral line scale. Pelvic fin subacuminate,
with i,6 (16) rays (one small unbranched ray posterior to
the last branched ray not counted), second branched ray
longest, adpressed fin tip reaching beyond vent but not
reaching base of anal fin, axillary scale present at base
of pelvic fin, reaching base of last pelvic fin ray. Vent
closer to anal fin base than base of last pelvic fin ray. Anal fin sub-acuminate, with ii, 4(16) rays, first branched
ray longest, adpressed fin tip almost reaching base of
caudal fin. Caudal fin deeply emarginated, lobe tips
blunt, principle caudal rays 10+9 (16), 10th ray shortest,
upper lobe slightly shorter than lower. Table 1. Biometric data for Garra dampaensis sp. nov. (n=16). All
ratios expressed as percent of SL, HL, or ventral-anal length. Material and methods The specimens were preserved in 10% formalin and
later on transferred to 70% alcohol. Measurements
and counts follow Kullander & Fang (2004), and that
of ventral to anal fin and vent to anal fin, Menon
(1964). Lateral transverse scales rows count and other
additional measurements follow Nebeshwar et al. (2009). Measurements were taken point to point with
digital calipers rounded to the nearest 0.1mm. Fin
rays and numbers of scales were counted under stereo
zoom microscope. For vertebral count, three paratype
specimens were cleared and stained following Taylor &
van Dyke (1985). Abdominal vertebrae count include the Anterior barbel short, not reaching margin of rostral
cap. Rostral cap connected with lower lip at corners of
mouth. Upper jaw entirely covered by rostral cap. No Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377 4369 Garra dampaensis sp. nov. Lalronunga e
Image 1. Holotype of Garra dampaensis sp. nov. (PUCMF 11012), 46.5mm SL (A) Lateral and (B) Ventral view. A
B
© Lalramliana A
© Lalramliana A Image 1. Holotype of Garra dampaensis sp. nov. (PUCMF 11012), 46.5mm SL (A) Lateral and (B) Ventral view. B B Image 1. Holotype of Garra dampaensis sp. nov. (PUCMF 11012), 46.5mm SL (A) Lateral and (B) Ventral view. Image 2. Holotype of Garra dampaensis sp. nov. (PUCMF 11012), 46.5mm SL Head in (A) Lateral and (B) Ventral view. Scale = 2mm
A
B
© Lalramliana B A mage 2. Holotype of Garra dampaensis sp. nov. (PUCMF 11012), 46.5mm SL Head in (A) Lateral and (B) Ventral view. Scale = 2m margin modified to form a transverse skin fold covered
by numerous tiny papillae, anteriorly separated from
lower jaw by a deep groove running along lower jaw and
posteriorly bordered in a deep groove with a central pad. Central pad wider than long, lateral and posterior margin papilliferous tissue on upper jaw. Antero-lateral fold
conspicous between upper and lower lip at corner of
mouth, not extending mediad between exposed lower
jaw and lower lip. Lower lip thick and modified into
sucking disc. Disc elliptical, wider than long; anterior Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377 4370 Lalronunga et al. Table 1. Biometric data for Garra dampaensis sp. nov. (n=16). All
ratios expressed as percent of SL, HL, or ventral-anal length. Etymology The species is named after Dampa Tiger Reserve,
Mizoram. Material and methods Holotype
PUCMF12001
Mean±Sd
Holotype
included
RANGE
Standard Length (SL) (in
mm)
46.5
36.5–51.9
In % SL
Body depth
21.7
21.6±0.8
20.1–22.7
Head length
27.3
27.4±0.6
26.6–28.7
Head height at eye
13.2
13.5±0.3
13.1–13.9
Head height at occiput
15.0
15.5±0.3
15.0–16.0
Head width at opercle
21.3
20.9±0.4
20.0–21.4
Head width at nare
17.7
17.3±0.5
16.2–18.1
Body width at dorsal
17.8
17.3±0.5
16.5–18.1
Body width at anal
10.5
9.6±0.6
8.8–10.5
Caudal peduncle length
18.2
16.5±0.9
15.6–18.2
Caudal peduncle height
13.4
13.5±0.4
12.7–14.2
Dorsal fin length
25.3
24.7±0.9
22.8–26.5
Dorsal fin base length
13.0
13.2±0.8
12.3–14.7
Pectoral fin length
26.2
25.3±1.4
22.9–27.1
Pelvic fin length
22.3
21.9±0.8
20.6–23.2
Anal fin length
20.2
19.8±0.8
18.5–21.0
Anal fin base length
8.4
7.8±0.4
7.0–8.4
Upper caudal fin lobe
length
23.8
25.8±1.6
22.7–28.3
Lower caudal fin lobe
length
24.2
26.3±1.5
24.1–28.5
Median caudal fin rays
length
20.0
21.1±1.4
18.1–22.6
Pre-anal length
75.1
77.0±1.4
75.1–79
Pre-anus length
71.9
72.7±1.2
70.6–74.4
Pre-ventral length
52.9
53.5±1.3
51.5–56.0
Pre-dorsal length
53.3
53.2±0.9
51.5–54.7
Pre-pectoral length
22.8
23.4±0.9
21.6–25.2
In % Ventral to anal fin
Vent to anal fin
17.6
17.9±1.1
15.9–19.6
In % HL
Snout length
52.8
51.5±1.5
48.7–54.4
Eye diameter
20.0
21.0±1.3
18.5–22.8
Inter-orbital space
47.9
48.6±1.3
45.9–50.3
Disc length
35.9
35.7±0.9
34.2–37.2
Disc width
54.7
53.6±2.3
49.0–57.9
Callous pad length
24.5
23.6±1.3
21.4–26.6
Callous pad width
37.2
34.9±1.9
31.9–37.6 Lateral line complete and obvious; scales 27(3), 28(8)
or 29(5); transverse scale rows above lateral line 3½
(14) or 4½ (2); below lateral line from ventral fin origin
3(13) or 4(3); from anal fin origin 3½ (10) or 4½ (6). Circumpeduncular scale rows 16(16). Predorsal scales
10(10) or 11(6) and arranged regularly. Belly and breast
scaled; breast scales in between the pectoral fin base
deeply embedded. Gill rakers 12(3). Vertebrae: 30 (4 + 15 abdominal + 11 caudal) (2) or
31 (4 + 16 abdominal + 11 caudal) (1). Colouration: In 70% alcohol: dorsum, sides and head
dark grey. Ventral side of head, chest, and abdomen
whitish. Black spot immediately at the upper angle of gill
opening. Each scale formed by blackish spot at center,
more conspicuous at the posterior half. Anal, pelvic and
pectoral fins whitish, pectoral fin with a black streak
on each interradial membrane. Dorsal fin greyish with
submarginal black band. Caudal fin grayish with distinct
W-shaped black band. Notes on biology: A dissected paratype 42.0mm SL is
a female with ripe ovulae. Distribution and habitat surrounding central pad papillated, posteriormost
margin almost reaching vertical to posterior margin of
eye. Known only from Seling River, inside Dampa Tiger
Reserve, a tributary of Khawthlang Tuipui (Karnaphuli
drainage) Mizoram, India (Fig. 1). Garra dampaensis Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377 Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377 4371 Garra dampaensis sp. nov. Figure 1. Map of Mizoram, India showing collection localities of (●)
Garra dampaensis sp. nov. A symbol may represent more than one
locality. Lalronunga et al. tributary of Kolodyne) and Kolodyne River, however, the
identity of some of these species needs confirmation. From Manipur, the neighboring state of Mizoram,
India, the following species has been described, namely
Garra abhoyai and G. naganensis (Hora, 1921), G. manipurensis (Vishwanath & Sarojnalini, 1988), G. litanensis (Vishwanath, 1993), G. paralissorhynchus
(Kosygin & Vishwanath, 1998), G. compressus (Vishwanath
& Shanta, 1998), G. elongata (Vishwanath & Kosygin,
2000) and G. nambulica (Vishwanath & Joyshree, 2005). Further, the occurrence of G. lissorhynchus, G. rupecula
McClelland, G. kempi Hora, G. nasuta McClelland, G. gravelyi and G. gotyla has been reported from Manipur
(Vishwanath 1993). Garra abhoyai has been treated as a
junior synonym of G. rupecula (Menon, 1964), however,
Vishwanath & Linthoingambi (2008) resurrected the
species and ruled out the occurrence of G. rupecula in
the Chindwin basin of Manipur. Among the aforementioned species, Garra gotyla
gotyla, G. lamta, G. litanensis, G. elongata, G. arupi and
G. nasuta are closely related to each other in having a
transverse groove and also a weak to well developed
proboscis on the snout. Garra dampaensis clearly differs
from any of them in having a snout without a transverse
groove. Garra dampaensis shares similar characters with
G. annandalei, G. naganensis, G. notata, G. kempi,
G. compressus and G. manipurensis in having a snout
without a transverse groove and a proboscis, and in
certain body proportions and counts. However, it can
be easily distinguished from them by the presence (vs. absence) of a distinct W-shaped black band on the
caudal fin. Figure 1. Map of Mizoram, India showing collection localities of (●)
Garra dampaensis sp. nov. A symbol may represent more than one
locality. i
McClelland
(1839)
described
Gonorhynchus
rupeculus from the Mishmi Hills, Arunachal Pradesh,
India (Brahmaputra basin). Distribution and habitat The description is very brief
and he did not mention the presence or absence of wavy
or W-shaped black bar across the caudal fin, but reported
35 scales along the lateral line and nine rows of scales on
either side between the dorsal and ventral fins; a snout
smooth and broad; a row of open pores extending round
the snout between the nostrils, and another row between
the eyes, besides other characters. Gunther (1868)
and Day (1878), without any comments, considered
it as a synonym of Discognathus lamta Hamilton (now
Garra lamta), a species with a deep transverse groove
separating the snout tip and no wavy or W-shaped
black bar across the caudal fin. Similarly, Platycara
lissorhynchus was described by McClelland (1842) from
Kasyah Mountains, Assam (Bhrahmaputra basin) to
possess a head, flat below, arched and thick above; a has been collected from clear, shallow, moderately fast-
flowing streams with a predominantly rocky bottom. It
is found associated with Devario aequipinnatus, Garra
cf. annandalei and Schistura spp. Discussion Karmakar & Das (2007) and Kar & Sen (2007)
reported eight species of Garra from Mizoram, namely
Garra annandalei Hora, G. gotyla gotyla Gray, G. gravelyi Annandale, G. kempi Hora, G. lamta Hamilton,
G. lissorhynchus McClelland, G. naganensis Hora, and G. notata Blyth from Barak drainage (Brahmaputra basin),
and again G. annandalei, G. gotyla gotyla along with G. lamta and G. naganensis to occur in the Mat River (a Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377 4372 Lalronunga et al. Garra dampaensis sp. nov. disc behind the mouth; a snout smooth and rounded;
and scales large. The two species were recognized and
redescribed as Garra rupecula (as G. rupeculus by Hora
1921) and G. lissorhynchus respectively by Hora (1921)
and Menon (1964), mentioning the absence of scales
on the ventral side (chest and abdomen), presence of
wavy or W-shaped black bar across the caudal fin in
both the species and lateral line scales as 32–34 for G. rupecula and 32–35 for G. lissorhynchus. However, the
descriptions on G. rupecula by Hora (1921) and Menon
(1964) are based on specimens collected from Manipur
valley, which belong to Chindwin drainage (Nebeshwar
et al. 2009). Since the distribution of G. rupecula in
the Chindwin basin is already ruled out (Vishwanath &
Linthoingambi 2008; Nebeshwar et al. 2009), it can be
considered that their examined specimens are totally
different species (probably a mixture of small specimens
of Garra nambulica and G. paralissorhynchus, as
mentioned by Vishwanath & Linthoingambi 2008). It is
thus obvious that the description of G. rupecula available
is the only brief statement by McClelland (1839), and we
therefore consider that a thorough revision is essential
to depict the detail characters of the species. longer dorsal fin (22.8–26.5 % SL vs. 17.4–20.4), longer
pectoral fin (22.9–27.1 % SL vs. 17.0–20.8), longer pelvic
fin (20.6 – 23.2 % SL vs. 15.2-17.9), longer snout (48.7–
54.4 % HL vs. 29.1–33.0) and shorter vent to anal distance
(15.9–19.6 % ventral-anal distance vs. 33.6–43.6). Kullander & Fang (2004) described seven species
of Garra viz. G. propulvinus, G. vittatula, G. rakhinica,
G. flavatra and G. nigricollis from the western slope
of the Rakhine Yoma, while G. spilota and G. poecilura
from the eastern slope of the Irrawaddy drainage. Garra dampaensis sp. nov. differs from all the species
described from Rakhine Yoma and Irrawaddy drainage,
except G. propulvinus and G. Discussion rakhinica, in absence (vs. presence) of a narrow band of papilliferous tissue along
the upper jaw, and a short pleated papilliferous fold that
extends mediad from the corner of the mouth between
the exposed lower jaw and the lower lip. Further, G. dampaensis differs from G. propulvinus in having fewer
vertebrae (26–27 vs. 28–29), fewer unbranched dorsal
fin (2 vs. 3), fewer lateral line scales (27–29 vs. 31),
longer head (26.6–28.7 % SL vs. 23.4–25.3), shallower
body depth (20.1–22.7 % SL vs. 26.6–28.9), shorter
dorsal fin (22.8– 26.5 % SL vs. 31.3–34.2) and shorter
anal fin (18.5–21.0 % SL vs. 23.3–27.5); from G. rakhinica
in having fewer unbranched dorsal fin (2 vs. 3), shallower
body (20.1–22.7 % SL vs. 27.2–28.8), shorter dorsal
fin (22.8–26.5 % SL vs. 28.7–32.3), shorter pectoral fin
(22.9–27.1 % SL vs. 28.6–30.8), shorter anal fin (18.5–
21.0 % SL vs. 23.3–24.7) and also absence (vs. present)
of horizontal black stripes from base of anterior barbel
to preopercle. Menon (1964) grouped Garra species having a dark
streak near the free margin of the dorsal fin, W-shaped
band on the caudal fin and naked breast and belly in the
Lissorhynchus complex. Species which can be put under
this group are G. lissorhynchus, G. rupecula, G. abhoyai,
G. paralissorhynchus and G. nambulica. The species
under description shares similar characters with them
in having a dark streak near the free margin of dorsal
fin and distinct W-shaped black band on the caudal
fin. However, it can be easily distinguished from them
in having scales on breast and belly (vs. absent in all)
(see Table 2 for comparison). It further differs from G. lissorhynchus in having fewer lateral line scales (27–29
vs. 34–35) and fewer predorsal scales (10–11 vs. 14–15);
from G. rupecula, as mentioned by McClelland (1839),
in having fewer lateral line scales (27–29 vs. 35); from
G. abhoyai in having deeper body (20.1–22.7 % SL vs. 17.6–18.7), longer head (26.6–28.7% SL vs. 22.0–23.5),
longer dorsal fin (22.8–26.5 % SL vs. 11.7–14.8), longer
pectoral fin (22.9–27.1 % SL vs. 19.7–22.0), longer pelvic
fin (20.6–23.2 % SL vs. 16.5–18.2) and regularly arranged
10–11 predorsal scales (vs. appears to be naked due
to thick mucous cover); from G. paralissorhynchus in
having more gill rakers (12 vs. 6) and shorter vent to anal
distance (15.9–19.6% ventral-anal distance vs. 25.0–
30.8); and from G. nambulica in having fewer lateral line
scales (27–29 vs. Discussion 34–35), fewer predorsal scales (10–11
vs. 16–29), longer head (26.6 –28.7 % SL vs. 20.7–25.1), Rahman (2005) listed Garra annandalei and Garra
gotyla gotyla, both from the Brahmaputra basin in
Bangladesh. However, as noted above, both are readily
distinguished from the new species. Data from Kullander & Fang (2004).
Garra rupecula: Data from Mc Clelland (1839) Garra gotyla gotyla: ZSI 9955/1, 1 ex., 102.2mm SL,
Kangra Hill Stream, Punjab. Garra gotyla gotyla: ZSI 9955/1, 1 ex., 102.2mm SL,
Kangra Hill Stream, Punjab. Kangra Hill Stream, Punjab. Garra gravelyi: MUMF 4173, 17.viii.1999, 1 ex., 74.6mm SL, Leimatak River, Manipur, K. Nebeshwar. Garra kempi: Data from Zhang & Chen (2002). Garra lamta: Data from Menon (1964). Garra lissorhynchus: MUMF 4163–4166, 02.ix.2000, Gdam - Garra dampaensis sp. nov.; Gliss - G. lissorhynchus; Grupe - G. rupecula; Gabho - G. abhoyai; Gpara - G. paralissorhynchus; Gnamb - G. nambulica. Garra dampaensis sp. nov. Lalronunga et al. Data from Kullander & Fang (2004). Garra rupecula: Data from Mc Clelland (1839) Data from Kullander & Fang (2004). Garra rupecula: Data from Mc Clelland (1839) Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377
4374 Comparative material Garra abhoyai: MUMF 6296–6305, 17.i.2003, 10
exs., 50.6–55.7 mm SL, Iril River, Phungdhar, Manipur, K. Nebeshwar, M. Shantakumar & I. Linthoingambi. Garra abhoyai: MUMF 6296–6305, 17.i.2003, 10
exs., 50.6–55.7 mm SL, Iril River, Phungdhar, Manipur, K. Nebeshwar, M. Shantakumar & I. Linthoingambi. Garra annandalei: MUMF 5088–5090, 20.iii.2000,
3 exs., 52.1–68.2 mm SL, Tuivai River, Churachandpur,
Shanta Devi. Garra
compressus:
MUMF
2316
(holotype),
17.iii.1998, 69.6mm SL, MUMF 2314–2315, paratype,
2 exs., 80.7–84.2 mm SL, Wanze Stream at Khamson,
Ukhrul District, Manipur (Chindwin basin), L. Kosygin. Garra elongata: MUMF 2311 (holotype), 12.xi.1997,
87.7mm SL; MUMF 2308–2310, paratypes, 3 exs., 74.1–
82.8mm SL, a small stream near Tolloi, Ukhrul District,
Manipur (Chindwin Basin), L. Kosygin. Garra elongata: MUMF 2311 (holotype), 12.xi.1997,
87.7mm SL; MUMF 2308–2310, paratypes, 3 exs., 74.1–
82.8mm SL, a small stream near Tolloi, Ukhrul District,
Manipur (Chindwin Basin), L. Kosygin. Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377 4373 SP.J.1141.2009.04438 Day, F. (1878). The Fishes of India: Being a Natural History of The Fishes
Known to Inhabit The Seas and Freshwaters of India, Burma and
Ceylon. Berdnard Quaritch, London, i-xx+778pp. Garra
litanensis:
MUMF-68/1
(holotype),
16.iii.1986, 90.1mm SL, Litan Stream, Litan, Manipur, W. Vishwanath. Ceylon. Berdnard Quaritch, London, i-xx+778pp. y
,
,
pp
Gopi, K.C. (2001). Garra periyarensis, a new cyprinid fish from Periyar i
Tiger Reserve, Kerala, India. Journal of the Bombay Natural Historical
Society 98: 80–83. i Garra naganensis: MUMF 4156–4159, 20.xi.1999,
4 exs., 78.2–103.4 mm SL, Barak River, Vanchengphai
Village, Tamenglong District, Manipur (Brahmaputra
basin); K. Nebeshwar. Günther, A. (1868). Catalogue of The Fishes in The British Museum. Department of Zoology, British Museum (Natural History), London
7: i-xx+512pp. Hora, S.L. (1921). Indian cyprinoid fishes belonging to the genus Garra,
with notes on related species from other countries. Records of
Indian Museum 22: 633–687. G. nambulica: MUMF 8004–8008, 5 exs., 41.5–58.7
mm SL, Conchak lok, stream of Nambul River, Manipur
(Chindwin basin). Kar, D. & N. Sen (2007). Systematic list and distribution of fishes in
Mizoram, Tripura and Barak drainage of northeastern India. Zoos’
Print Journal 22(3): 2599–2607; http://dx.doi.org/10.11609/JoTT. ZPJ.1571a.2599-607 Garra nasuta: MUMF 4079, 10.xi.1999, 3 exs., 115.2–
118.7 mm SL, Barak River at Khunphung, Manipur, K. Nebeshwar. Karmakar, A.K. & A. Das (2007). Fishes. In: Fauna of Mizoram, State
Fauna Series 14, Part 1. Zoological Survey of India, Kolkata, 691pp. t Garra notata: Data from Menon (1964). Kottelat, M. (2000). Diagnoses of a new genus and 64 new species
of fishes from Laos (Teleostei: Cyprinidae, Balitoridae, Bagridae,
Syngnathidae, Chaudhuriidae and Tetraodontidae). Journal of South
Asian Natural History 5: 37–82. Garra paralissorhynchus: MUMF 5054 (holotype),
25.vii.2000, 64.2mm SL, Khuga River, Churchanpur
District, Manipur (Chindwin Basin); L. Shanta Devi. Additional data from Vishwanath & Shanta (2005).t Garra paralissorhynchus: MUMF 5054 (holotype),
25.vii.2000, 64.2mm SL, Khuga River, Churchanpur
District, Manipur (Chindwin Basin); L. Shanta Devi. Additional data from Vishwanath & Shanta (2005).t Kullander, S.O. & F. Fang (2004). Seven new species of Garra
(Cyprinidae: Cyprininae) from the Rakhine Yoma, southern Myanmar. Ichthyological Exploration of Freshwaters 15: 257–278.i Garra propulvinus, G. vittatula, G. rakhinica,
G.flavatra, G. nigricollis, G. spilota, and G. poecilura: Garra propulvinus, G. vittatula, G. rakhinica,
G.flavatra, G. nigricollis, G. spilota, and G. poecilura: Li, F., W. Zhou & Q. Fu (2008). Garra findolabium, a new species of
cyprinid fish (Teleostei: Cypriniformes) from the Red River drainage Table 2. References (
)
Garra lissorhynchus: MUMF 4163–4166, 02.ix.2000, Chen, Z., S. Zhao & J. Yang (2009). A new species of the genus Garra
from Nujiang River Basin, Yunnan, China (Teleostei: Cyprinidae). Zoological Research 30(4): 438–444; http://dx.doi.org/10.3724/
SP.J.1141.2009.04438 4 exs., 69.2–87.5 mm SL, Iyei River at Noney, Tamenglong
District (Brahmaputra Basin), K. Nebeshwar. Gdam - Garra dampaensis sp. nov.; Gliss - G. lissorhynchus; Grupe - G. rupecula; Gabho - G. abhoyai; Gpara - G. paralissorhynchus; Gnamb - G. na Journal of Threatened Taxa | www.threatenedtaxa.org | 2
4374 Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377 Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9
4374 Garra dampaensis sp. nov. Garra dampaensis sp. nov. Lalronunga et al. Keys to the species of Garra in the Lissorhynchus complex
1. Breast and belly scaled; Lateral line with 27–29 scales ....................................................................... G. dampaensis sp. nov. -
Breast and belly naked; Lateral line with more than 29 scales ............................................................................................... 2
2. Lateral line with 30–31 scales; 11–12 predorsal scales ….......................................................................... G. paralissorhynchus
-
Lateral line with or more than 30 scales ….............................................................................................................................. 3
3. Lateral line with 30–33; predorsal region covered by thick mucous, scales irregularly arranged …......................... G. abhoyai
-
Lateral line with 34–35 scales; 16–29 predorsal scales ......................................................................................… G. nambulica
4. Lateral line with 34–35 scales; 14–15 predorsal scales ….................................................................................. G. lissorhynchus
-
Row of open pores on inter-orbital, and on inter-narial region …........................................................................... G. rupecula Keys to the species of Garra in the Lissorhynchus complex Keys to the species of Garra in the Lissorhynchus complex
1. Breast and belly scaled; Lateral line with 27–29 scales ....................................................................... G. dampaensis sp. nov. -
Breast and belly naked; Lateral line with more than 29 scales ............................................................................................... 2
2. Lateral line with 30–31 scales; 11–12 predorsal scales ….......................................................................... G. paralissorhynchus
-
Lateral line with or more than 30 scales ….............................................................................................................................. 3
3. Lateral line with 30–33; predorsal region covered by thick mucous, scales irregularly arranged …......................... G. abhoyai
-
Lateral line with 34–35 scales; 16–29 predorsal scales ......................................................................................… G. nambulica
4. Lateral line with 34–35 scales; 14–15 predorsal scales ….................................................................................. G. lissorhynchus
-
Row of open pores on inter-orbital, and on inter-narial region …........................................................................... G. rupecula Vishwanath, W. & I. Linthoingambi (2008). Redescription of Garra
abhoyai Hora (Teleostei: Cyprinidae: Garrinae) with a note on Garra
rupecula from Manipur, India. Journal of the Bombay Natural History
Society 105(1): 101–104. McClelland, J. (1839). Indian Cyprinidae. Asiatic Researches 19(2):
217–471. McClelland, J. (1839). Indian Cyprinidae. Asiatic Researches 19(2):
217–471.i McClelland, J. (1842). On the fresh-water fishes collected by William
Griffith, Esq., F. L. S. Madras Medical Service, during his travels under
the orders of the Supreme Government of India, from 1835 to 1842. Calcutta Journal of Natural History 2(8): 560–589. i McClelland, J. (1842). On the fresh-water fishes collected by William
Griffith, Esq., F. L. S. Madras Medical Service, during his travels under
the orders of the Supreme Government of India, from 1835 to 1842. Calcutta Journal of Natural History 2(8): 560–589. i Vishwanath, W. & L. Kosygin (2000). SP.J.1141.2009.04438 Comparison of Garra dampaensis sp. nov. with related species. Gdam
Gliss
Grupe
Gabho
Gpara
Gnamb
In % SL
Body depth
20.1–22.7
18.2–20.8
–
17.6–18.7
19.3–25.7
16.4–20.5
Head length
26.6–28.7
23.1–23.6
–
22.0–23.5
20.0–26.8
20.7–25.1
Dorsal fin length
22.8–26.5
18.5–19.4
–
11.7–14.8
19.9
17.4–20.4
Pectoral fin length
22.9–27.1
20.4–22.2
–
19.7–22.0
21.7
17.0–20.8
In % ventral-anal
Vent- anal distance
15.9–19.6
24.6–26.9
–
37.6–46.0
25.0–30.8
34.0–43.4
In% HL
Snout length
48.7–54.4
45.8–53.5
–
44.0–48.0
46.8–57.7
29.1–33.0
Meristic count
Lateral line scales
27–29
34–35
35
30–33
30–31
34–35
Predorsal scales
10–11
14–15
–
–
11–12
16–29
Circumpeduncular scales
16
16
16
16
16
16
Gill rakers
12
12
–
–
6
10
Scales on chest
present
absent
absent
absent
absent
absent
Table 2. Comparison of Garra dampaensis sp. nov. with related species. Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377 4374 Garra dampaensis sp. nov. Garra elongata, a new species
of the subfamily Garrinae from Manipur, India (Cyprinidae,
Cypriniformes). Journal of the Bombay Natural Historical Society 97:
408–414. Menon, A.G.K. (1964). Monograph of the cyprinid fishes of the genus
Garra, Hamilton. Memoirs of the Indian Museum 14(4): 173–260. Vishwanath, W. & K. Shanta (2005). A new species of Garra Hamilton-
Buchanan (Cypriniformes: Cyprinidae) from Manipur, India. Journal
of the Bombay Natural Historical Society 102(1): 86–88.i Nebeshwar, K., W. Vishwanath & D.N. Das (2009). Garra arupi,
a new cyprinid fish species (Cypriniformes: Cyprinidae) from
upper Brahmaputra basin in Arunachal Pradesh, India. Journal of
Threatened Taxa 1(4): 197–202; http://dx.doi.org/10.11609/JoTT. o1842.197-202 Zhang, E. (2005). Garra bispinosa, a new species of cyprinid fish
(Teleostei: Cypriniformes) from Yunnan, southwest China. Raffles
Bulletin of Zoology (Supplement) 13: 9–15. Rahman, A. K. A. (2005). Freshwater Fishes of Bangladesh (Second
edition). The Zoological Society of Bangladesh, Department of
Zoology, University of Dhaka, Dhaka, 394pp. i
Zhang, E. & Y.Y. Chen (2002). Garra tengchongensis, a new cyprinid
species from the upper Irrawaddy River basin in Yunnan, China
(Pisces: Teleostei). Raffles Bulletin of Zoology 50: 459–464. Taylor, W.R. & G.G. van Dyke (1985). Revised procedures for staining
and clearing small fishes and other vertebrates for bone and
cartilage study. Cybium 9: 107–119. Zhang, E., S.P. He & Y.Y. Chen (2002). Revision of the Cyprinid genus
Placocheilus Wu, 1977 in China, with description of a new species
from Yunnan. Hydrobiologia 487: 207–217.t Zhou, W., X.F. Pan & M. Kottelat (2005). Species of Garra and
Discogobio (Teleostei: Cyprinidae) in Yuanjiang (Upper Red River)
drainage of Yunnan Province, China with description of a new
species. Zoological Studies 44: 445–453. Vishwanath, W. & H. Joyshree (2005). A new species of the genus Garra
Hamilton-Buchanan (Teleostei: Cyprinidae) from Manipur, India. Zoos’ Print Journal 20(4): 1832–1834; http://dx.doi.org/10.11609/
JoTT.ZPJ.1228.1832-4 4375 Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377 Lalronunga et al. Garra dampaensis sp. nov. Jo rnal
f Threatened Ta a |
th
t
dt
| 26 M
2013 | 5(9) 4368 4377
ra dampaensis sp. nov. Lalronunga et al. Garra dampaensis sp. nov. 76
Holotype
(PUCMF 12001)
Paratypes
(PUCMF 12002)
Paratypes
(PUCMF 12003)
Paratypes
(PUCMF 12004)
A
C
D
E
F
G
H
I
K
M
J
N
L
O
P
Standard length (in mm)
46.5
45.6
40.9
41.9
41.6
48.2
42.8
45.2
43.9
51.9
41.7
42
48.9
40.6
36.5
41.4
In % SL
Body depth
21.7
20.2
22.1
21.2
21.4
22.1
22.2
21.5
22.7
22.6
21.9
20.9
20.6
20.1
21.7
21.8
Head length
27.3
26.6
27.5
27.3
27
27.8
28.1
27.2
27.1
26.9
27.5
26.8
27.1
28.7
27.6
26.6
Head height at eye
13.2
13.1
13.6
13.3
13.9
13.6
13.5
13.25
13.3
13.1
13.7
13.7
13.3
13.5
13.2
13.9
Head height at occiput
15
15.1
16
15.6
15.9
15.5
15.9
15.3
15.5
15.6
15.7
15.3
15.2
15.5
15.8
15.1
Head width at opercle
21.3
20
21
20.6
20.9
21.4
21
20.9
20.5
21.2
20.9
20.2
21.4
21.4
20.4
20.5
Head width at nare
17.7
16.9
16.8
16.9
17.3
17.6
18.1
16.2
17.7
17.4
16.9
17.4
16.6
17.3
17.8
17.3
Body width at dorsal
17.8
16.5
17.7
17.1
16.8
17.7
17.9
16.8
17.4
18.1
16.9
16.9
16.5
17
17.9
17.5
Body width at anal
10.5
9.2
9.6
9
8.7
10.2
10.1
9.4
9.3
10.5
9.3
9.7
8.9
8.9
10.1
9.9
Caudal peduncle length
18.2
17
16
16.2
15.6
17.6
15.6
15.6
15.8
18
16.6
16.2
15.9
15.8
16.9
16.6
Caudal peduncle height
13.4
12.7
12.9
13.6
13.4
13.6
13.9
14
13.6
14.2
13.5
13.5
13
13.9
13.7
13.9
Dorsal fin length
25.3
24.9
24.3
22.8
23.9
26.5
24.6
24.5
23.9
26.3
24.8
24.1
24
24.7
24.7
26.2
Dorsal fin base length
13
12.4
13.9
13.7
12.6
14.7
13.1
13.8
12.3
14.2
13
12.7
13.5
12.7
14.1
12.4
Pectoral fin length
26.2
22.9
26.1
25.1
23.7
27.1
24.9
26.2
23.4
26.6
26.8
24.8
26.9
25.3
25.7
23.6
Pelvic fin length
22.3
21.2
22.1
20.9
20.6
22.5
21.8
22.1
20.8
23.2
22.9
22
21.5
21.7
22.9
22.7
Anal fin length
20.2
19.1
20.6
19.5
19
20.7
18.5
20.2
18.6
21
19.8
19.8
20.8
20.3
19.6
19.5
Anal fin base length
8.4
7.7
8.3
7.9
7.5
7.8
7
8.3
7.2
8.3
7.6
7.6
8.1
7.6
8.3
7.5
Upper caudal fin lobe length
23.8
22.7
25.2
25.3
24.3
26.6
27.6
27.3
26.2
28.3
26.4
25.3
26.6
26.9
26.4
23.2
Lower caudal fin lobe length
24.2
24.1
24.9
25.5
25.6
25.5
28
27.4
26.7
28.5
28.4
25.5
24.4
27.5
26.8
28.1
Median caudal fin rays length
20
18.1
21.7
19.7
20.7
21.4
22.6
22.4
21.6
22
22.6
19.4
22.1
21.6
21.5
19.3
Pre-anal length
75.1
76.3
76.5
77.9
77.2
75.7
79
78.5
78.2
75.3
77.4
75.5
75.4
78.7
77.5
78
Pre-anus length
71.9
72.5
72
72.9
72.8
71.1
74.2
73.7
74.4
70.6
72.4
72.1
71.8
74.4
71.9
73.7
Pre-ventral length
52.9
51.6
53.4
54.3
54.3
51.9
54.8
54.3
56
51.5
52.9
53.2
52.7
54.1
53.9
54.7
Pre-dorsal length
53.3
52.3
52.9
53.1
53.2
52.4
53.3
53.8
54.6
52.8
54.7
51.5
52.7
54.3
53.4
53
Pre-pectoral length
22.8
22.9
23.4
25.2
24.4
21.6
22.9
23.9
23.5
22.9
23.4
22.9
22.1
24.9
23.6
24.2
In % Ventral to anal fin
24.3
23.8
25.5
25
24
25.3
25.2
24.3
Vent to anal fin
17.6
16.8
19
17.8
19
18.9
19.1
17
17.3
19.6
18.4
15.9
16.5
17.3
17.9
18.9
In % HL ric characters of Garra dampaensis sp. nov. Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377 Lalronunga et al. Garra dampaensis sp. nov. Holotype
(PUCMF 12001)
Paratypes
(PUCMF 12002)
Paratypes
(PUCMF 12003)
Paratypes
(PUCMF 12004)
A
C
D
E
F
G
H
I
K
M
J
N
L
O
P
Snout length
52.8
50.7
51.6
51.6
51.7
52.3
48.7
49.7
52.8
51.3
51.8
54.4
49.5
50
53.2
51.5
Eye diameter
20
18.5
20.9
20.8
22.1
19.6
22.1
20.5
22.5
20.7
22.8
22.8
19.7
19.9
21.6
22.3
Inter-orbital space
47.9
50.1
49.5
48.8
50.1
47.2
48.1
48.8
47
45.9
49.2
50.2
47.9
48.5
48.6
50.3
Disc length
35.9
35.5
34.2
36.2
37
34.7
36.4
37.2
36
35.2
35.1
34.9
35.6
36
35.3
36.7
Disc width
54.7
52.4
50.8
49
54.4
57.9
54.6
55.3
53.8
54.3
53.8
54.2
55.2
50.8
51.1
55.7
Callous pad length
24.5
23.9
22.2
24.3
23.6
23.8
24.6
26.6
23.1
23.5
22.8
21.4
22.7
23
25.3
23
Callous pad width
37.2
34.1
32.2
34
34.3
36.5
37.6
36.6
35.2
36.6
33.8
33.2
32.9
31.9
36.8
35.7 Holotype
(PUCMF 12001)
Paratypes
(PUCMF 12002)
Paratypes
(PUCMF 12003)
Paratypes
(PUCMF 12004)
A
C
D
E
F
G
H
I
K
M
J
N
L
O
P
Snout length
52.8
50.7
51.6
51.6
51.7
52.3
48.7
49.7
52.8
51.3
51.8
54.4
49.5
50
53.2
51.5
Eye diameter
20
18.5
20.9
20.8
22.1
19.6
22.1
20.5
22.5
20.7
22.8
22.8
19.7
19.9
21.6
22.3
Inter-orbital space
47.9
50.1
49.5
48.8
50.1
47.2
48.1
48.8
47
45.9
49.2
50.2
47.9
48.5
48.6
50.3
Disc length
35.9
35.5
34.2
36.2
37
34.7
36.4
37.2
36
35.2
35.1
34.9
35.6
36
35.3
36.7
Disc width
54.7
52.4
50.8
49
54.4
57.9
54.6
55.3
53.8
54.3
53.8
54.2
55.2
50.8
51.1
55.7
Callous pad length
24.5
23.9
22.2
24.3
23.6
23.8
24.6
26.6
23.1
23.5
22.8
21.4
22.7
23
25.3
23
Callous pad width
37.2
34.1
32.2
34
34.3
36.5
37.6
36.6
35.2
36.6
33.8
33.2
32.9
31.9
36.8
35.7 4377 Journal of Threatened Taxa | www.threatenedtaxa.org | 26 May 2013 | 5(9): 4368–4377
|
https://openalex.org/W4214484173
|
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0264314&type=printable
|
English
| null |
Health care seeking behaviour and financial protection of patients with hypertension: A cross-sectional study in rural West Bengal, India
|
PloS one
| 2,022
|
cc-by
| 7,588
|
Background Elevated blood pressure or hypertension is responsible for around 10 million annual deaths
globally, and people residing in low and middle-income countries are disproportionately
affected by it. India is no exception, where low rate of treatment seeking for hypertension
coupled with widespread out-of-pocket payments (OOPs) have been a challenge. This
study assessed the pattern of health care seeking behaviour and financial protection along
with the associated factors among hypertensive individuals in rural West Bengal, India. OPEN ACCESS Citation: Chakraborty S, Rai RK, Biswas AK, Barik
A, Gurung P, Praveen D (2022) Health care seeking
behaviour and financial protection of patients with
hypertension: A cross-sectional study in rural West
Bengal, India. PLoS ONE 17(2): e0264314. https://
doi.org/10.1371/journal.pone.0264314 PLOS ONE RESEARCH ARTICLE Sandipta ChakrabortyID1,2, Rajesh Kumar RaiID3,4,5,6*, Asit Kumar Biswas1,
Anamitra Barik3,7, Preeti Gurung8, Devarsetty Praveen9,10,11 1 Institute of Public Health, Kalyani, West Bengal, India, 2 Department of Preventive and Social Medicine, All
India Institute of Hygiene and Public Health, West Bengal, India, 3 Society for Health and Demographic
Surveillance, Suri, West Bengal, India, 4 Department of Global Health and Population, Harvard T.H. Chan
School of Public Health, Boston, Massachusetts, United States of America, 5 Department of Economics,
University of Goettingen, Goettingen, Germany, 6 Centre for Modern Indian Studies, University of
Goettingen, Goettingen, Germany, 7 Suri District Hospital, Suri, West Bengal, India, 8 Medecins Sans
Frontieres, Manipur, India, 9 Primary Health Care Research, The George Institute for Global Health,
Hyderabad, Telangana, India, 10 Faculty of Medicine, University of New South Wales, Kensington, NSW,
Australia, 11 Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, India a1111111111
a1111111111
a1111111111
a1111111111
a1111111111 * rajesh.iips28@gmail.com Editor: Khurshid Alam, Murdoch University,
AUSTRALIA Received: February 25, 2021
Accepted: February 8, 2022
Published: February 25, 2022 * rajesh.iips28@gmail.com Health care seeking behaviour and financial
protection of patients with hypertension: A
cross-sectional study in rural West Bengal,
India Sandipta ChakrabortyID1,2, Rajesh Kumar RaiID3,4,5,6*, Asit Kumar Biswas1,
Anamitra Barik3,7, Preeti Gurung8, Devarsetty Praveen9,10,11 Sandipta ChakrabortyID1,2, Rajesh Kumar RaiID3,4,5,6*, Asit Kumar Biswas1,
Anamitra Barik3,7, Preeti Gurung8, Devarsetty Praveen9,10,11 PLOS ONE PLOS ONE Introduction Globally, non-communicable diseases (NCDs) contribute to a major share of the disease bur-
den, where countries with differential level of development and varied phases of epidemiologi-
cal transition have witnessed a significant rise in overall morbidity and mortality from NCDs
[1–3]. Among all NCDs, cardiovascular diseases (ischaemic heart disease and stroke) are listed
as the major cause of death worldwide, with hypertension (commonly defined as a systolic
blood pressure 140 or diastolic blood pressure 90) being the most important risk factor
causing significant amount of premature deaths globally [4, 5]. According to World Health
Organization estimations, the number of adults aged 30–79 years having hypertension is 1.28
billion worldwide. Majority of them (two-thirds) are from low-and middle-income countries
(LMICs) and only less than half are taking treatment [5]. Despite the high burden of hyperten-
sion, health system responses like health service delivery, health information and health
financing for hypertension is suboptimal, especially in LMICs [6–10]. Evidence suggests that
people seeking health care for NCDs bear significant and unjustified financial burden charac-
terised by huge out-of-pocket payments (OOPs), often leading to irregular and absence of
treatment seeking due to financial difficulties [10, 11]. In addition, studies show that overall
health care seeking behaviour for blood pressure management is low and shared among public
and non-public facilities [12, 13]. In India, between one-quarter to one-third of adults, aged 18 years or more, have hyperten-
sion. This is a major public health concern and threat to Indian healthcare system [14–16]. In
the year 2010, to combat the emerging NCDs and its risk factors, the federal Indian govern-
ment introduced the National Programme for Prevention and Control of Cancer, Diabetes,
Cardiovascular Diseases and Stroke (NPCDCS) with hypertension and diabetes as the main
focus areas. In addition, in 2017, the government launched the National Health Policy target-
ing 25% reduction in premature mortality occurring from cardiovascular diseases, cancer, dia-
betes or chronic respiratory diseases by 2025 [17, 18]. But the impacts of these program and
policy level initiatives are not evaluated extensively. The main focus for research on hyperten-
sion in India is primarily on the risk factors of hypertension while few actually explored the
health care utilization and service expenses and overall health system performance among
hypertensive individuals, as evidenced from the PubMed/MEDLINE database search [19–22]. PLOS ONE PLOS ONE Health care seeking behaviour and financial protection aCoefflower-middle 7.83, CI 0.65,15.00 and aCoeffupper-middle 7.25, CI: 0.80,13.70) had higher
relative expenditure. aCoefflower-middle 7.83, CI 0.65,15.00 and aCoeffupper-middle 7.25, CI: 0.80,13.70) had higher
relative expenditure. the form of funds to RKR. The funders had no role
in study design, data collection, and analysis,
decision to publish, or preparation of the
manuscript. the form of funds to RKR. The funders had no role
in study design, data collection, and analysis,
decision to publish, or preparation of the
manuscript. Conclusion Competing interests: The authors have declared
that no competing interests exist. This study suggests that individuals with hypertension had poor health care seeking behav-
iour, preferred non-public health facilities and had suboptimal financial protection. Economi-
cally poorer individuals had higher burden of health expenditure for treatment of
hypertension, which indicated gaps in equitable health care delivery for the control of
hypertension. Abbreviations: aOR, adjusted odds ratio; BIRPOP,
Birbhum Population Project; CI, confidence
interval; NCDs, non-communicable diseases;
OOPs, out of pocket payments; OR, odds ratio;
uOR, unadjusted odds ratio. Method and findings Copyright: © 2022 Chakraborty 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. A cross-sectional study was conducted in Birbhum district of the state of West Bengal, India,
during 2017–2018, where 300 individuals were recruited randomly from a list of hyperten-
sives in a population cohort. Healthcare seeking for hypertension and related financial pro-
tection in terms of–OOPs and expenses relative to monthly per-capita family expenditure,
were analysed. Findings indicated that 47% of hypertensives were not on treatment. Among
those under treatment, 80% preferred non-public facilities, and 91% of them had wide-
spread OOPs. Cost of medication was a major share of expenses followed by transportation
cost to access public health care facility. Multivariable logistic regression analysis indicated
longer duration of disease (adjusted odds ratio (aOR): 5.68, 95% Confidence Interval
(CI) 1.24–25.99) and health care seeking from non-public establishment (aOR: 34.33,
CI: 4.82–244.68) were associated with more incident of OOPs. Linear regression with gen-
eralized linear model revealed presence of co-morbidities (adjusted coefficient (aCoeff)
10.28, CI: 4.96,15.61) and poorer economic groups (aCoeffpoorest 11.27, CI 3.82,18.71; Data Availability Statement: Data are of the
COHESION study (the complete dissertation work)
is available on Zenodo: https://zenodo.org/record/
3911117#.YDZ6D3lX42w (http://doi.org/10.5281/
zenodo.3911117). Funding: This study was supported by the
Department of Health and Family Welfare,
Government of West Bengal, India in the form of a
fellowship to SC. This study was also supported by
the Open Access Publication Funds of the
University of Goettingen, Goettingen, Germany in 1 / 16 PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 Study setting, design and sampling COHESION study is a population-based cross-sectional study, conducted between November
2017 and February 2018 in a population cohort of Birbhum Population Project (BIRPOP), a
health and demographic surveillance system (HDSS) functioning under the ambit of Society
for Health and Demographic Surveillance (http://www.shds.co.in/), located in the Birbhum
district of the state of West Bengal, India,. BIRPOP spreads over four administrative blocks
(namely Suri I, Sainthia, Mohammad Bazar and Rajnagar) out of a total of 19 blocks in district
Birbhum. At its inception in 2008, BIRPOP included a sample of over 12,000 households
selected by multistage stratified sampling method and has been periodically collecting infor-
mation on indicators related to public health and demography. Until inception of the present
study, BIRPOP had completed three rounds of follow-up surveys, in 2008–09, 2012–13, and
2016–17 [23]. COHESION study was based on BIRPOP’s 2016–17 survey where blood pres-
sure was measured for 12,255 individuals aged 18 years. Those recorded with high blood
pressure (systolic blood pressure (SBP) 140 mm of Hg and/or diastolic blood pressure (DBP)
90 mm of Hg) or reported taking anti-hypertensive medication of any form were included in
the hypertensive cohort [23, 24]. Details about the blood pressure measurement survey at BIR-
POP has previously been published elsewhere [25]. From the list of all hypertensive individu-
als, 310 were selected by simple random sampling for this study. Sample size was calculated
using CDC Epi-infoTM version 7.2, assuming 50% prevalence for hypertension control among
all hypertensives, 7.5% of error and confidence interval of 99%. With the addition of 5% non-
response rate, final sample size was 310 individuals of which 300 interviews were conducted. Terminally ill and mentally challenged individuals, diagnosed by a physician, were not consid-
ered for participation in the study. In case, if more than one individual had been selected from
same family, it was planned to replace the latter one. Data were collected by trained surveyors
with pre-designed and pretested questionnaire using Computer Assisted Personal Interview
(CAPI) technique [26]. A rigorous protocol for survey monitoring was followed to assure the
quality of the data being collected. Introduction From the perspective of health system strengthening and population health management,
understanding the local preferences and health system capacity is essential. Considering dearth
of literature in this field, a study, Capacity of Health Systems to combat the Emergence of
Hypertension (COHESION), was designed to assess the status of blood pressure control,
health care seeking and financial protection among hypertensive individuals along with the
health system responsiveness towards them. Here, we present a component of COHESION PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 2 / 16 PLOS ONE Health care seeking behaviour and financial protection study to elicit the pattern of health care seeking, determine financial protection and its associ-
ated factors among patients with hypertension in rural West Bengal. The study aimed to
understand how background socio-demographic characteristics, co-morbid conditions, health
seeking pattern could be associated with financial protection related to heath care seeking and
whether the issue of fair financing distributed with equity among the participants. PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 Outcome measurement Health care seeking for chronic NCDs, like hypertension comprises of a complex dynamic
interplay between medicine intake, visit to health care professional and regularity of both the
components within a reference time period (Fig 1). To understand the health care seeking
behaviour, patients were asked if they were taking any medication for blood pressure control
and have been visiting any healthcare provider. Patients with a history of intake of daily medi-
cation for hypertension in the preceding four weeks were considered to be on regular medica-
tion. Those with a history of visit to any health care provider at least once in the last six
months for treatment or follow-up care of hypertension, were considered to have regular med-
ical consultation. Patients who had both of the above (regular medication and regular medical
consultation) were labelled as having ‘regular treatment for hypertension’. Those who reported
only regular medication but not regular medical consultation was identified as having ‘regular
medication only’. Patients currently not on any medication or consultation for last one year or 3 / 16 PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 PLOS ONE Health care seeking behaviour and financial protection Fig 1. Construct of health care seeking behaviour for hypertension among the participants. https://doi.org/10.1371/journal.pone.0264314.g001 Fig 1. Construct of health care seeking behaviour for hypertension among the participants. never sought any treatment for hypertension, were labelled as ‘not on treatment’. The rest
were categorised as ‘patients on irregular treatment’ (Fig 1). Two outcomes in relation to cost of treatment, were analysed in this study–i) Out-of-pocket
payments (OOPs), and ii) expenses relative to monthly per-capita family expenditure, henceforth
termed as ‘relative expenditure’. Considering the varied practice of health care seeking behaviour,
expected monthly OOPs were calculated assuming an ideal month when complete health care
(consultation by a physician and regular medicine intake) was sought. Thus, total expected OOPs
for a month were calculated considering summative expenses that included expenses paid for
medical consultation, transport and others, like food, lodging etc. during the consultation in the
last medical visit, and cost of blood pressure lowering medication if taken for a month. Monthly
per capita expenditure (MPCE) was calculated as monthly total consumer expenditure in a house-
hold over all items of consumption divided by the household size (total number of persons in the
household) and was used as the proxy measure of the economic status [27]. Outcome measurement Based on the MPCE,
the participants were divided into four quartile classes and categorised into relative economic
groups: poorest, lower-middle, upper-middle and richest class. Relative expenditure for an indi-
vidual for a month was defined as percentage of MPCE incurred for OOPs [19]. Covariates Based on existing literature from developing countries, a range of potential covariates were
considered. 4 / 16 PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 PLOS ONE Health care seeking behaviour and financial protection Socio-demographic characteristics. This included age in completed years (later catego-
rised based on tertile distribution- <50, 50–63, >63), gender (female and male), educational
attainment (secondary and above, upper primary, primary, and illiterate/below primary),
social group (other backward classes, scheduled castes/ scheduled tribes and others), religion
(Hinduism and Islam), civil status (living with partner, and not living with partner), employ-
ment status (service/business, labourer, homemaker/retired/student, and unemployed), and
economic status based on MPCE quartile distribution (high, upper-middle, lower-middle, and
poor). Hypertension related variables. This included duration of hypertension (<5 years, 5
years, and not sure/don’t know), co-morbidity (no and yes), regularity of treatment of hyper-
tension (as elaborated before in Fig 1), type of health facility accessed (public, i.e. all govern-
ment and semi-government health facilities and non-public), and healthcare provider like,
public physician, private physician, AYUSH (Ayurveda, Yoga and Naturopathy, Unani, Siddha
and Homoeopathy) doctor, and informal health care practitioner (Quack) [28]. Comorbidity
refers to self-report about any of the diseases like diabetes, dyslipidaemia, chronic kidney dis-
ease or cardiovascular disease in addition to hypertension. Statistical analysis Bivariate and multivariable analyses were performed to attain the study objectives. Means and
proportions were presented with 95% confidence intervals. Based on existing evidences, a
Directed Acyclic Graph (DAG) was developed, using causal diagram theory [29]. The DAG
illustrated the pathways of possible association with directed arrows, between the variables
incorporated in the study. This diagram served as an overall theoretical framework along with
a guide for constructing various regression models used in the analysis (Fig 2). Binary logistic
regression was deployed to understand the predictors of OOPs, whereas linear regression by
generalized linear models (GLM) was used to assess the relative expenditure. Measures of asso-
ciation were presented as odds ratio (OR) with 95% confidence interval (CI) with value “1” as
the null point. GLM was preferred because of abundance of zero values in relative cost data
and a possible non-parametric distribution of the relative expenditure [30]. With the linear
modelling, the association is expressed with the estimated coefficient (Coeff) and associated
95% CI. “Zero” was considered as the null point. Data analysis were carried out using a statisti-
cal package—Stata, version 12.0. Alpha level was assumed as 0.05, p value 0.05 was consid-
ered to interpret the significance of observed association in general. Although qualitative
interpretation based on p value (significant/non-significant based on conventional cut off) was
judged cautiously, keeping with the sample size, study design, limitations and considering the
effect size based on respective 95%CI of the measures of association. Ethics statement Ethical approval was granted by institutional review board of Society for health and Demo-
graphic Surveillance. Written informed consent was obtained from all participants prior to
enrolment in the study. Irrespective of their participation status, all, who were approached to
participate in the study were provided with a leaflet on healthy lifestyle, health education
related to hypertension and other NCDs written in local language. PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 Results In total, 310 were approached to participate in this study, and 300 finally participated. Table 1
outlines the descriptive characteristics of all the participants. The mean age of the participants
was 55.99 ± 12.46 years. More than half of the participants were female and were illiterate or 5 / 16 PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 PLOS ONE Health care seeking behaviour and financial protection Fig 2. Directed acyclic graph: Illustrating associations between variables. https://doi.org/10.1371/journal.pone.0264314.g002 Fig 2. Directed acyclic graph: Illustrating associations between variables. https://doi.org/10.1371/journal.pone.0264314.g002 https://doi.org/10.1371/journal.pone.0264314.g002 PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 6 / 16 PLOS ONE Health care seeking behaviour and financial protection Table 1. Characteristics of the study participants (N = 300). Background characteristics
N
Mean or Percentage (95%
CI)
Age
300
55.99 (54.58–57.41)
Total expected cost of seeking complete care for hypertension in a month
(₹)
159
306.49 (257.65–355.33)
Relative expenditure (%) for treatment of hypertension with respect to
MPCE
159
13.52 (11.13–15.90)
Age group (years)
< 50
101
33.67 (28.29–39.04)
50–63
107
35.67 (30.22–41.12)
>63
92
30.67 (25.42–35.91)
Education
Completed Secondary or above
48
16.00 (11.83–20.17)
Completed Upper-primary
46
15.33 (11.23–19.43)
Completed Primary
56
18.67 (14.23–23.10)
Illiterate/Below primary
150
50.00 (44.31–55.69)
Sex
Female
183
61.00 (55.45–66.55)
Male
117
39.00 (33.45–44.55)
Social group
Others
140
46.67 (40.99–52.34)
OBC
42
14.00 (10.05–17.95)
SC/ST
118
39.33 (33.77–44.89)
Religion+
Hinduism
225
75.25 (70.33–80.17)
Islam
74
24.75 (19.83–29.67)
Civil status
Living with partner
195
65.00 (59.57–70.43)
Not living with partner
105
35.00 (29.57–40.43)
Occupation
Service/Business
65
21.67 (16.98–26.36)
Labourer
47
15.67 (11.53–19.80)
Homemaker/Retired/ Student
160
53.33 (47.66–59.01)
Unemployed
28
9.33 (6.02–12.64)
Economic Class
Richest
75
25.00 (20.07–29.93)
Upper Middle
79
26.33 (21.32–31.35)
Lower-middle
70
23.33 (18.52–28.15)
Poorest
76
25.33 (20.38–30.28)
Duration of Hypertension (years)
<5
141
47.00 (41.32–52.68)
5
106
35.33 (29.89–40.77)
Not sure/don’t know
53
17.67 (13.32–22.01)
Co-morbidity
No
240
80.00 (75.45–84.55)
Yes
60
20.00 (15.45–24.55)
Regular treatment for hypertension
On regular consultation & medication
71
23.67 (18.83–28.50)
On regular medication only
39
13.00 (9.17–16.83)
(Continued) PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 7 / 16 PLOS ONE Health care seeking behaviour and financial protection Table 1. Results (Continued)
Background characteristics
N
Mean or Percentage (95%
CI)
On irregular treatment
49
16.33 (12.13–20.54)
Not on treatment
141
47.00 (41.32–52.68)
Place of treatment for hypertension
Public
31
19.50 (13.27–25.72)
Non-public
128
80.50 (74.28–86.73)
Health care provider
Public physician
30
18.87 (12.72–25.02)
Private physician
63
39.62 (31.94–47.31)
AYUSH doctor/ Other
19
11.95 (6.85–17.05)
Informal healthcare provider
47
29.56 (22.39–36.73)
OPP
Absent
15
9.43 (4.84–14.03)
Present
144
90.57 (85.97–95.16)
₹: Indian National Rupee; CI: Confidence Interval; OBC: Other backward classes; SC: Scheduled caste; ST: Scheduled
tribe; AYUSH: Ayurveda, Yoga and Naturopathy, Unani, Siddha and Homoeopathy; OOPs: Out of Pocket Payments;
MPCE: Monthly per capita expenditure. Sample characteristics is based on 159 participants representing patients seeking treatment for hypertension. + One person did not share information on religion. https://doi.org/10.1371/journal.pone.0264314.t001 ₹: Indian National Rupee; CI: Confidence Interval; OBC: Other backward classes; SC: Scheduled caste; ST: Scheduled
tribe; AYUSH: Ayurveda, Yoga and Naturopathy, Unani, Siddha and Homoeopathy; OOPs: Out of Pocket Payments;
MPCE: Monthly per capita expenditure. https://doi.org/10.1371/journal.pone.0264314.t001 had not completed their primary education. Majority of the participants were Hindus and
homemaker/retired/students by profession. Over 35% (n = 106) of participants had hyperten-
sion for 5 years, and 20% (n = 60) had a co-morbid condition. Over 47% (n = 141) of the par-
ticipants were not on treatment, and among individuals receiving treatment, over 80%
(n = 128) sought healthcare from non-public healthcare provider. Over 90% (n = 144) of those
who sought care for blood pressure treatment incurred some OOPs. Expected cost for seeking
complete care for hypertension per month was over ₹ 306 (> $4.5) and relative expenditure
was 13.5% of the MPCE (Table 1). Further analysis revealed that the median of relative expen-
diture was higher for those seeking care from non-public healthcare facility (median: 10.7%)
compared to the public healthcare establishments (2.1%). Purchase of medicines (47.7%)
accounted for the largest median share of OOPs in non-public healthcare, while it was for
transport and other costs (51.3%) followed by purchase of medicines (37.5%) in the public
healthcare facilities (Fig 3). g
Fifteen individuals were reported incurring no OOPs for the usual treatment for hyperten-
sion. Results Median of OOPs share (%) and relative expenditure across the public and non-public health establishments (N = 159). https://doi.org/10.1371/journal.pone.0264314.g003 Linear regression with GLM (Table 3) demonstrated lower relative expenditure among
people with primary or below level of schooling, compared to highest educational group;
(Adjusted Coefficient (aCoeff) completed primary -10.65 (CI: -19.78, -1.51) and aCoeffno formal edu-
cation/below primary -11.60 (CI: -20.88, -2.32)). The unemployed individuals had more relative
expenditure compared to those engaged in service/business (Unadjusted Coefficient (uCoeff)u-
nemployed 8.71 (CI: 0.04,17.38) and aCoeffunemployed 9.34 (CI: -1.74,20.43)). The poorest, lower-
middle and upper-middle class had 11, 8 and 7 units of more relative expenditure respectively,
compared to the richest economic class (aCoeffpoorest 11.27 (CI: 3.82,18.71); aCoefflower-middle
7.83 (CI: 0.65,15.00) and aCoeffupper-middle 7.25 (CI: 0.80,13.70)) (Fig 4). Presence of co-mor-
bidity and visiting non-public establishments both were associated with higher relative expen-
diture (aCoeffone or more co-morbidity 10.28 (CI: 4.96,15.61); reference group: no co-morbidity
and aCoeffnon-public establishment 11.55 (CI: 5.74,17.37); reference group: public establishment). Similarly, seeking treatment from private doctors, informal practitioners and AYUSH doctors/
others were associated with more relative expenditure (aCoeffprivate Doctors 18.43 (CI: 12.13,
24.73), aCoeffinformal healthcare provider 5.96 (CI: -0.36, 12.28), aCoeffAYUSH/ Other 10.28 (CI: 2.56,
17.99)) when compared to those seeking treatment from government doctors. Results Majority (n = 9) were female, aged between 50 to 63 years (n = 9), Hindu (n = 12), general
caste (n = 9) with below primary or no formal education (n = 10), home maker/ retired (n = 10)
and belongs to upper-middle class (n = 6) of the economic strata of the study population. Table 2 shows lower odds of having OOPs among participants aged 50–63 years and 63
years and above compared to participants below 50 years. Males when compared to females,
and homemaker/retired /student, labourer and unemployed when compared to those in ser-
vice/business had relatively lower odds of incurring any OOPs. Compared to the richest eco-
nomic class the poorest had lower odds of having any OOPs, in unadjusted model (uOR poorest
0.22 (CI: 0.04–1.21)). Having hypertension for five years or more (uOR 5.14 (CI: 1.39–19.01)
and aOR 5.68 (CI: 1.24–25.99)) and seeking treatment from non-public establishments (uOR
26.32 (CI: 6.80–101.93) and aOR 34.33 (CI: 4.82–244.68)) were positively associated with
OOPs. Fifteen individuals were reported incurring no OOPs for the usual treatment for hyperten-
sion. Majority (n = 9) were female, aged between 50 to 63 years (n = 9), Hindu (n = 12), general
caste (n = 9) with below primary or no formal education (n = 10), home maker/ retired (n = 10)
and belongs to upper-middle class (n = 6) of the economic strata of the study population. Table 2 shows lower odds of having OOPs among participants aged 50–63 years and 63
years and above compared to participants below 50 years. Males when compared to females,
and homemaker/retired /student, labourer and unemployed when compared to those in ser-
vice/business had relatively lower odds of incurring any OOPs. Compared to the richest eco-
nomic class the poorest had lower odds of having any OOPs, in unadjusted model (uOR poorest
0.22 (CI: 0.04–1.21)). Having hypertension for five years or more (uOR 5.14 (CI: 1.39–19.01)
and aOR 5.68 (CI: 1.24–25.99)) and seeking treatment from non-public establishments (uOR
26.32 (CI: 6.80–101.93) and aOR 34.33 (CI: 4.82–244.68)) were positively associated with
OOPs. 8 / 16 PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 PLOS ONE Health care seeking behaviour and financial protection Fig 3. Median of OOPs share (%) and relative expenditure across the public and non-public health establishments (N = 159). https://doi.org/10.1371/journal.pone.0264314.g003 Fig 3. Discussion India has witnessed an increasing burden of hypertension, which demands urgent attention
from the public health researchers, program and policy makers. To add on to the existing body
of literature on prevention of hypertension in India, this study aims to understand characteris-
tics of healthcare seeking and financial protection among hypertensive population in West 9 / 16 PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 Health care seeking behaviour and financial protection PLOS ONE PLOS ONE Table 2. Factors associated with out of pocket payments: Logistic regression analysis (N = 159). Unadjusted
Adjusted
OR (95% CI)
p
OR (95% CI)
p
Age group (years)
< 50
1.00
1.00
50–63
0.14 (0.02–1.13)
0.06
0.14 (0.02–1.38)
0.09
>63
0.29 (0.03–2.60)
0.27
0.47 (0.04–5.88)
0.56
Education
Completed Secondary or above
1.00
1.00
Completed Upper-primary
0.89 (0.05–15.00)
0.93
0.39 (0.01–12.94)
0.60
Completed Primary
0.33 (0.03–3.41)
0.35
0.20 (0.01–4.22)
0.30
Illiterate/Below primary
0.24 (0.03–2.00)
0.19
0.09 (0.00–2.49)
0.15
Sex
Female
1.00
1.00
Male
0.70 (0.24–2.10)
0.53
0.08 (0.01–0.71)
0.02
Social group
Others
1.00
1.00
OBC
2.19 (0.26–18.37)
0.47
3.13 (0.28–34.91)
0.35
SC/ST
1.09 (0.34–3.43)
0.89
3.36 (0.60–18.97)
0.17
Religion
Hinduism
1.00
1.00
Islam
1.40 (0.37–5.22)
0.62
2.30 (0.40–13.39)
0.35
Civil status
Living with partner
1.00
1.00
Not living with partner
0.82 (0.28–2.37)
0.71
0.95 (0.25–3.66)
0.94
Occupation
Service/Business
1.00
1.00
Labourer
0.16 (0.01–1.91)
0.15
0.08 (0.00–1.65)
0.10
Homemaker/Retired/ Student
0.27 (0.03–2.18)
0.22
0.04 (0.00–0.79)
0.03
Unemployed
0.25 (0.02–2.97)
0.27
0.17 (0.01–3.65)
0.26
Economic Class
Richest
1.00
1.00
Upper Middle
0.27 (0.05–1.42)
0.12
0.47 (0.07–3.04)
0.42
Lower-middle
0.57 (0.08–4.28)
0.59
1.14 (0.12–11.18)
0.91
Poorest
0.22 (0.04–1.21)
0.08
0.40 (0.06–2.91)
0.37
Co-morbidity
No
1.00
1.00
Yes
0.74 (0.24–2.31)
0.61
0.54 (0.13–2.24)
0.39
Duration of Hypertension (years)
<5
1.00
1.00
5
5.14 (1.39–19.01)
0.01
5.68 (1.24–25.99)
0.03
Place of treatment seeking for hypertension
Public
1.00
1.00
Non-public
26.32 (6.80–101.93)
<0.01
34.33(4.82–244.68)
<0.01
CI: Confidence Interval; OBC: Other backward classes; SC: Scheduled caste; ST: Scheduled tribe; OR: Odds ratio. https://doi.org/10.1371/journal.pone.0264314.t002 Table 2. Factors associated with out of pocket payments: Logistic regression analysis (N = 159). Bengal, India. The state of West Bengal recorded nearly 25% of total annual deaths and 13% of
disability adjusted life years (DALYs) attributed to hypertension [15, 31]. This study revealed
poor health care seeking behaviour, preference of non-public health facilities and high OOPs Bengal, India. The state of West Bengal recorded nearly 25% of total annual deaths and 13% of
disability adjusted life years (DALYs) attributed to hypertension [15, 31]. This study revealed
poor health care seeking behaviour, preference of non-public health facilities and high OOPs PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 10 / 16 Health care seeking behaviour and financial protection PLOS ONE Table 3. Factors associated with relative expenditure: Linear regression with GLM. Unadjusted
Adjusted
β (95% CI)
p
β (95% CI)
p
Age group (years)
< 50
0.00
0.00
50–63
-2.39 (-8.55,3.77)
0.45
-3.22 (-9.84,3.40)
0.34
>63
0.28 (-5.78,6.33)
0.93
-1.66 (-8.51,5.19)
0.64
Education
Completed Secondary or above
0.00
0.00
Completed Upper-primary
-2.58 (-10.82,5.67)
0.54
-5.17 (-14.14,3.80)
0.26
Completed Primary
-3.15 (-11.02,4.73)
0.43
-10.65 (-19.78,-1.51)
0.02
Illiterate/Below primary
-1.06 (-7.69,5.56)
0.75
-11.60 (-20.88,-2.32)
0.01
Sex
Female
0.00
0.00
Male
-0.94 (-5.99,4.10)
0.71
-3.39 (-10.90,4.13)
0.38
Social group
Others
0.00
0.00
OBC
0.43 (-6.95,7.82)
0.91
-2.02 (-9.58,5.55)
0.60
SC/ST
3.44 (-1.78,8.66)
0.20
5.36 (-1.27,11.98)
0.11
Religion
Hinduism
0.00
0.00
Islam
-0.07 (-5.54,5.40)
0.98
3.23 (-3.37,9.82)
0.34
Civil status
Living with partner
0.00
0.00
Not living with partner
1.11(-3.68,5.90)
0.65
1.85 (-3.62,7.32)
0.51
Occupation
Service/Business
0.00
0.00
Labourer
5.57 (-4.40,15.54)
0.27
5.88 (-5.04,16.79)
0.29
Homemaker/Retired/Student
1.59 (-4.38,7.56)
0.60
0.85 (-7.88,9.59)
0.85
Unemployed
8.71 (0.04,17.38)
0.05
9.34 (-1.74,20.43)
0.09
Economic Class
Richest
0.00
0.00
Upper Middle
5.54 (-0.38,11.46)
0.07
7.25 (0.80,13.70)
0.03
Lower-middle
5.73 (-0.97,12.43)
0.09
7.83 (0.65,15.00)
0.03
Poorest
10.39 (3.82,16.95)
0.00
11.27 (3.82,18.71)
0.00
Co-morbidity
No
0.00
0.00
Yes
7.74 (2.59,12.89)
0.00
10.28 (4.96,15.61)
<0.01
Duration of Hypertension (years)
<5
0.00
0.00
5
1.64 (-3.10,6.37)
0.50
2.17 (-2.62,6.97)
0.37
Place of treatment seeking for hypertension
Public
0.00
0.00
Non-public
9.35(3.56,15.14)
0.00
11.55 (5.74,17.37)
<0.01
Health care provider
Public physician
0.00
0.00
Private physician
14.38 (8.24,20.51)
<0.01
18.43 (12.13,24.73)
<0.01
AYUSH doctor/Other
5.39 (-2.72,13.50)
0.19
10.28 (2.56,17.99)
0.01
(Continued) Table 3. Factors associated with relative expenditure: Linear regression with GLM. PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 11 / 16 Health care seeking behaviour and financial protection PLOS ONE Table 3. (Continued)
Unadjusted
Adjusted
β (95% CI)
p
β (95% CI)
p
Informal healthcare provider
3.40 (-3.07,9.86)
0.30
5.96 (-0.36,12.28)
0.06
GLM: Generalised Linear Model; CI: Confidence Interval; OBC: Other backward classes; SC: Scheduled caste; ST: Scheduled tribe; AYUSH: Ayurveda, Yoga and
Naturopathy, Unani, Siddha and Homoeopathy; OPP: Out of Pocket Payments; β: Coefficient. https://doi.org/10.1371/journal.pone.0264314.t003 Table 3. (Continued)
Unadjusted
Adjusted
β (95% CI)
p
β (95% CI)
p
Informal healthcare provider
3.40 (-3.07,9.86)
0.30
5.96 (-0.36,12.28)
0.06
GLM: Generalised Linear Model; CI: Confidence Interval; OBC: Other backward classes; SC: Scheduled caste; ST: Scheduled tribe; AYUSH: Ayurveda, Yoga and
Naturopathy, Unani, Siddha and Homoeopathy; OPP: Out of Pocket Payments; β: Coefficient. https://doi.org/10.1371/journal.pone.0264314.t003 GLM: Generalised Linear Model; CI: Confidence Interval; OBC: Other backward classes; SC: Scheduled caste; ST: Scheduled tribe; AYUSH: Ayurveda, Yoga and
Naturopathy, Unani, Siddha and Homoeopathy; OPP: Out of Pocket Payments; β: Coefficient. https://doi.org/10.1371/journal.pone.0264314.t003 GLM: Generalised Linear Model; CI: Confidence Interval; OBC: Other backward classes; SC: Scheduled caste; ST: Sched
Naturopathy, Unani, Siddha and Homoeopathy; OPP: Out of Pocket Payments; β: Coefficient. among patients who sought care for hypertension. Regression analysis adjusted for potential
covariates indicate that OOPs are associated with age, sex, occupation, duration of hyperten-
sion, and place of treatment seeking for hypertension, while relative expenditure is associated
with education, occupation, economic class, comorbidity, place of treatment and healthcare
provider. The population under study were relatively older, female predominated, had low education
level, and majority were retired/homemaker. This distribution was similar to other studies
where hypertension prevalence was more among elderly, females, and in poor socio-economic
strata [32, 33]. The findings of poor health care seeking for blood pressure control, was perhaps
due to lack of awareness, affordability and availability of health care services as evidenced from
the findings of COHESION study but not elaborated here. Among the hypertensives seeking
treatment, OOPs were extensively reported. This scenario corroborates with previous findings
of sub-optimal health system response for blood pressure control care [10, 11, 13, 14, 20, 34–
37]. However better system response was associated with substantial improvement in Fig 4. PLOS ONE Relative expenditure for care seeking across the economic strata with reference to richest economic class: Findings from linear
regression (N = 159) PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 12 / 16 PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 PLOS ONE Health care seeking behaviour and financial protection indicators like awareness, treatment and control of hypertension in a few developed countries
[38]. Similar to other studies, non-public establishments were major places for seeking treat-
ment and public institutions played a minor role for management of hypertension. Similarly,
majority sought consultation from private physicians and informal healthcare providers [13,
20, 22]. The presence of OOPs and extent of relative expenditure varied between service utili-
zation from public to non-public health facilities as well as with different service providers. The findings related to OOPs in this study are in line with previous reports including a report
of the WHO, Study on global AGEing and adult health (SAGE) but the significant variation
observed in OOPs across public and non-public institutions in this study is found to be novel
[19, 20]. Earlier studies found medicine purchase as the major share for OOPs [19–21] which
corroborates with the findings from this study, however transport and other costs are also
found to impose a substantial share of OOPs in public set-up, possibly indicating better acces-
sibility for the non-public establishments in local level compared to public institutions. This
could also justify the increased usage of non-public facilities for hypertension management. Contrasting with findings from other studies, the present study reported lower incident of
OOPs among male and those belonging to 50 years or above age group [10, 20]. More relative
expenditure was associated with higher level of education, whereas it was found to be inversely
related with disadvantageous economic class. These findings point towards potential issues of
social justice and inequity which share a complex interrelationship [19, 20]. This might be
related to poor treatment seeking behaviour among patients with low education and economic
status (jointly the lower socio-economic class) owing to low awareness, financial constraint
and limited access to healthcare, which may have led to lower possibility of having OOPs. But
despite these barriers, patients who sought treatment experienced inequitable financial bur-
den. Similar explanation may be applied for the unemployed group, having more extent of rel-
ative expenditure while seeking care but lower odds of OOPs. PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 PLOS ONE Lower OOPs among
homemaker/retired individuals was perhaps due to better utilization of public health facilities,
compared to the service holders/businessmen who generally have less opportunity to visit pub-
lic outpatient services due to its fixed schedule. Longer duration of hypertension and existence
of comorbid conditions require more intense therapy resulting in more possibility of having
OOPs and more relative expenditure [10]. homemaker/retired individuals was perhaps due to better utilization of public health facilities,
compared to the service holders/businessmen who generally have less opportunity to visit pub-
lic outpatient services due to its fixed schedule. Longer duration of hypertension and existence
of comorbid conditions require more intense therapy resulting in more possibility of having
OOPs and more relative expenditure [10]. The existing national health program NPCDSC, for prevention and control of NCDs, offers
provision of treatment for hypertensives along with other NCDs. In the state of West Bengal,
the NCD clinics operational under all public health facilities offers consultation and commonly
prescribed medication at free of cost. Despite that, we observed poor preference to public
establishment and people visiting non-public establishments with more OOPs. The present
study indicated that the major share of OOPs in the public facilities were due to transport and
other costs (51.28%). Decentralization of NCD clinics up to Health Sub-centre level, mobile
clinics may invite more individual to seek care from public facilities including those who are
not seeking treatment for accessibility. Study also suggests a substantial amount of OOPs from
medicine purchase even in public facilities. Local public health system must ensure a continu-
ous logistic supply including medicines to mitigate the issue of affordability among care seeker. Responsiveness of the respective health system might also play some role which justify prefer-
ence towards non-public facilities. Findings from this study indicates further research on
health care seeking pattern with objectives to understand the reason of specific pattern. Limitation of the study should be interpreted in light of the results. Firstly, being a cross-
sectional study, temporal ambiguity cannot be ruled out. Secondly, as most of variables under
study are information based on recall, some chances for recall errors may be present. Thirdly,
measurement of exact expenditure and assessing economic status could be debated. Acknowledgments Authors are indebted to the members of Society for Health and Demographic Surveillance,
West Bengal, India, for helping execute the study. PLOS ONE To
counter the variability of health care seeking, health care expenditure related to hypertension PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 13 / 16 PLOS ONE Health care seeking behaviour and financial protection management was calculated as expected cost for having complete care. This may have over-
represented the relative expenditure for treatment to some extent. Effects of residual con-
founding also cannot be ruled out. Within purview of limitations, considering the geographic
and demographic uniqueness of the Birbhum population, the findings of this study should be
interpreted cautiously for other settings. Despite these limitations, the study contributes tre-
mendously to the existing literature in terms of unique study setting and use of pre-tested and
validated study tools. The findings from the study suggest suboptimal financial protection of
population for hypertension care. The aspect of awareness generation and evaluation of exist-
ing programs on NCDs might be needed for a better financial protection mechanism to people
with hypertension. Author Contributions Conceptualization: Sandipta Chakraborty, Rajesh Kumar Rai, Asit Kumar Biswas. Data curation: Sandipta Chakraborty, Anamitra Barik. Formal analysis: Sandipta Chakraborty, Anamitra Barik. Investigation: Sandipta Chakraborty, Rajesh Kumar Rai. Methodology: Sandipta Chakraborty, Asit Kumar Biswas. Project administration: Sandipta Chakraborty, Rajesh Kumar Rai, Asit Kumar Biswas, Ana-
mitra Barik. Resources: Sandipta Chakraborty, Rajesh Kumar Rai, Asit Kumar Biswas, Anamitra Barik. Software: Sandipta Chakraborty. Supervision: Sandipta Chakraborty, Rajesh Kumar Rai, Asit Kumar Biswas, Anamitra Barik. Validation: Sandipta Chakraborty, Preeti Gurung, Devarsetty Praveen. Visualization: Sandipta Chakraborty, Preeti Gurung, Devarsetty Praveen. Writing – original draft: Sandipta Chakraborty, Rajesh Kumar Rai, Preeti Gurung, Devarsetty
Praveen. Writing – review & editing: Sandipta Chakraborty, Rajesh Kumar Rai, Asit Kumar Biswas,
Anamitra Barik, Preeti Gurung, Devarsetty Praveen. Conceptualization: Sandipta Chakraborty, Rajesh Kumar Rai, Asit Kumar Biswas. Conceptualization: Sandipta Chakraborty, Rajesh Kumar Rai, Asit Kumar Biswas. Data curation: Sandipta Chakraborty, Anamitra Barik. Formal analysis: Sandipta Chakraborty, Anamitra Barik. Investigation: Sandipta Chakraborty, Rajesh Kumar Rai. Methodology: Sandipta Chakraborty, Asit Kumar Biswas. Project administration: Sandipta Chakraborty, Rajesh Kumar Rai, Asit Kumar Biswas, Ana-
mitra Barik. Resources: Sandipta Chakraborty, Rajesh Kumar Rai, Asit Kumar Biswas, Anamitra Barik. Software: Sandipta Chakraborty. Supervision: Sandipta Chakraborty, Rajesh Kumar Rai, Asit Kumar Biswas, Anamitra Barik. Supervision: Sandipta Chakraborty, Rajesh Kumar Rai, Asit Kumar Biswas, Anamitra Barik. Validation: Sandipta Chakraborty, Preeti Gurung, Devarsetty Praveen. Validation: Sandipta Chakraborty, Preeti Gurung, Devarsetty Praveen. Visualization: Sandipta Chakraborty, Preeti Gurung, Devarsetty Praveen. Writing – original draft: Sandipta Chakraborty, Rajesh Kumar Rai, Preeti Gurung, Devarsetty
Praveen. Writing – review & editing: Sandipta Chakraborty, Rajesh Kumar Rai, Asit Kumar Biswas,
Anamitra Barik, Preeti Gurung, Devarsetty Praveen. References 1. Abubakar I, Tillmann T, Banerjee A. Global, regional, and national age-sex specific all-cause and
cause-specific mortality for 240 causes of death, 1990–2013: a systematic analysis for the Global Bur-
den of Disease Study 2013. Lancet. 2015; 385(9963):117–71. https://doi.org/10.1016/S0140-6736(14)
61682-2 PMID: 25530442 2. Habib SH, Saha S. Burden of non-communicable disease: global overview. Diabetes & Metabolic Syn-
drome: Clinical Research & Reviews. 2010; 4(1):41–7. 3. Murray CJ, Ezzati M, Flaxman AD, Lim S, Lozano R, Michaud C, et al. GBD 2010: design, definitions,
and metrics. Lancet. 2012; 380(9859):2063–6. https://doi.org/10.1016/S0140-6736(12)61899-6 PMID:
23245602 PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 14 / 16 PLOS ONE Health care seeking behaviour and financial protection 4. World Health Organization. The top 10 causes of death 2020 [updated 9 December 2020; cited 2021,
13 September]. [Available from: https://www.who.int/news-room/fact-sheets/detail/the-top-10-causes-
of-death]. 5. World Health Organization. Hypertension 2021 [updated 25 August 2021; cited 2021, 13 September]. [Available from: https://www.who.int/news-room/fact-sheets/detail/hypertension]. 6. Alshamsan R, Lee JT, Rana S, Areabi H, Millett C. Comparative health system performance in six mid-
dle-income countries: cross-sectional analysis using World Health Organization study of global ageing
and health. Journal of the Royal Society of Medicine. 2017; 110(9):365–75. https://doi.org/10.1177/
0141076817724599 PMID: 28895493 7. Feng XL, Pang M, Beard J. Health system strengthening and hypertension awareness, treatment and
control: data from the China Health and Retirement Longitudinal Study. Bull World Health Organ. 2014;
92(1):29–41. https://doi.org/10.2471/BLT.13.124495 PMID: 24391298 8. Ibrahim MM, Damasceno A. Hypertension in developing countries. Lancet. 2012; 380(9841):611–9. https://doi.org/10.1016/S0140-6736(12)60861-7 PMID: 22883510 9. Peck R, Mghamba J, Vanobberghen F, Kavishe B, Rugarabamu V, Smeeth L, et al. Preparedness of
Tanzanian health facilities for outpatient primary care of hypertension and diabetes: a cross-sectional
survey. Lancet Glob Health. 2014; 2(5):e285–92. https://doi.org/10.1016/S2214-109X(14)70033-6
PMID: 24818084 10. Wang Q, Fu AZ, Brenner S, Kalmus O, Banda HT, De Allegri M. Out-of-pocket expenditure on chronic
non-communicable diseases in sub-Saharan Africa: the case of rural Malawi. PLoS One. 2015; 10(1):
e0116897. https://doi.org/10.1371/journal.pone.0116897 PMID: 25584960 11. World Health Organization. Impact of out-of-pocket payments for treatment of non-communicable dis-
eases in developing countries: a review of literature. 2011. 12. Bovet P, Gervasoni JP, Mkamba M, Balampama M, Lengeler C, Paccaud F. Low utilization of health
care services following screening for hypertension in Dar es Salaam (Tanzania): a prospective popula-
tion-based study. BMC Public Health. 2008; 8(1):407. 13. Baliga SS, Gopakumaran PS, Katti SM, Mallapur MD. References The Seventh Report of
the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pres-
sure: the JNC 7 report. JAMA. 2003; 289(19):2560–72. https://doi.org/10.1001/jama.289.19.2560
PMID: 12748199 25. Ghosh S, Mukhopadhyay S, Barik A. Sex differences in the risk profile of hypertension: a cross-sec-
tional study. BMJ Open. 2016; 6(7):e010085. https://doi.org/10.1136/bmjopen-2015-010085 PMID:
27466234 26. Baker RPJSSCR. New technology in survey research: Computer-assisted personal interviewing
(CAPI). 1992; 10(2):145–57. 27. Howe LD, Galobardes B, Matijasevich A, Gordon D, Johnston D, Onwujekwe O, et al. Measuring socio-
economic position for epidemiological studies in low- and middle-income countries: a methods of mea-
surement in epidemiology paper. Int J Epidemiol. 2012; 41(3):871–86. https://doi.org/10.1093/ije/
dys037 PMID: 22438428 28. Das J, Chowdhury A, Hussam R, Banerjee AV. The impact of training informal health care providers in
India: A randomized controlled trial. Science (New York, NY). 2016; 354(6308). https://doi.org/10.1126/
science.aai9379 PMID: 27846485 29. Glymour MM, Greenland S. Causal Diagrams. In: Rothman KJ, Greenland S, Lash TL, editors. Modern
epidemiology. 3 ed. New Delhi: Wolters Kluwer (India) Pvt Ltd; Eighth Indian Reprint 2016. p. 183–
209. 30. Matsaganis M, Mitrakos T, Tsakloglou P. Modelling health expenditure at the household level in
Greece. The European Journal of Health Economics. 2009; 10(3):329–36. https://doi.org/10.1007/
s10198-008-0137-y PMID: 19037671 31. Institute for Health Metrics and Evaluation (IHME). GBD India Compare | Viz Hub 2019 [cited 2021 Feb-
ruary 22]. [Available from: https://vizhub.healthdata.org/gbd-compare/india]. 32. Irazola VE, Gutierrez L, Bloomfield GS, Carrillo-Larco RM, Dorairaj P, Gaziano T, et al. Hypertension
Prevalence, Awareness, Treatment, and Control in Selected Communities of Nine Low-and Middle
Income Countries: Results From the NHLBI/UHG Network of Centers of Excellence for Chronic Dis-
eases. Global heart. 2016; 11(1):47. https://doi.org/10.1016/j.gheart.2015.12.008 PMID: 27102022 33. Sarki AM, Nduka CU, Stranges S, Kandala NB, Uthman OA. Prevalence of Hypertension in Low- and
Middle-Income Countries: A Systematic Review and Meta-Analysis. Medicine (Baltimore). 2015; 94
(50):e1959. https://doi.org/10.1097/MD.0000000000001959 PMID: 26683910 34. Chow CK, Teo KK, Rangarajan S, Islam S, Gupta R, Avezum A, et al. Prevalence, awareness, treat-
ment, and control of hypertension in rural and urban communities in high-, middle-, and low-income
countries. JAMA. 2013; 310(9):959–68. https://doi.org/10.1001/jama.2013.184182 PMID: 24002282 35. Kaur P, Rao SR, Radhakrishnan E, Rajasekar D, Gupte MD. Prevalence, awareness, treatment, control
and risk factors for hypertension in a rural population in South India. Int J Public Health. 2012; 57(1):87–
94. https://doi.org/10.1007/s00038-011-0303-3 PMID: 21947549 36. Singh AK, Kalaivani M, Krishnan A, Aggarwal P, Gupta SK. References Treatment seeking behavior and health care
expenditure incurred for hypertension among elderly in urban slums of Belgaum City. Community Med. 2013; 4(2):227–30. 14. Anchala R, Kannuri NK, Pant H, Khan H, Franco OH, Di Angelantonio E, et al. Hypertension in India: a
systematic review and meta-analysis of prevalence, awareness, and control of hypertension. J Hyper-
tens. 2014; 32(6):1170–7. https://doi.org/10.1097/HJH.0000000000000146 PMID: 24621804 15. Indian Council of Medical Research; Public Health Foundation of India and Institute for Health Metrics
and Evaluation. India: Health of Nation’s States—The India State- level Disease Burden Initiative. New
Delhi, India: ICMR, PHFI and IHME; 2017. 2017. 16. Gupta R, Gaur K, CV SR. Emerging trends in hypertension epidemiology in India. J Hum Hypertens. 2019; 33(8):575–87. https://doi.org/10.1038/s41371-018-0117-3 PMID: 30254382 17. Directorate General of Health Services; Ministry of Health & Family Welfare Government of India. National Programme for Prevention and Control of Cancer, Diabetes, Cardiovascular Diseases and
Stroke (NPCDCS) 2017 [updated 26 August 2020; cited 2021 February 22]. [Available from: http://
dghs.gov.in/content/1363_3_NationalProgrammePreventionControl.aspx]. 18. Ministry of Health & Family Welfare GoI. National Health Policy 2017 [cited 2021 February 22]. [Avail-
able from: https://www.nhp.gov.in/nhpfiles/national_health_policy_2017.pdf]. 19. Bhojani U, Thriveni B, Devadasan R, Munegowda C, Devadasan N, Kolsteren P, et al. Out-of-pocket
healthcare payments on chronic conditions impoverish urban poor in Bangalore, India. BMC Public
Health. 2012; 12(1):990. https://doi.org/10.1186/1471-2458-12-990 PMID: 23158475 20. Brinda EM, Kowal P, Attermann J, Enemark U. Health service use, out-of-pocket payments and cata-
strophic health expenditure among older people in India: The WHO Study on global AGEing and adult
health (SAGE). J Epidemiol Community Health. 2015; 69(5):489–94. https://doi.org/10.1136/jech-2014-
204960 PMID: 25576563 21. Engelgau MM, Karan A, Mahal A. The Economic impact of Non-communicable Diseases on house-
holds in India. Global Health. 2012; 8(1):9. https://doi.org/10.1186/1744-8603-8-9 PMID: 22533895 22. Kanungo S, Mahapatra T, Bhowmik K, Saha J, Mahapatra S, Pal D, et al. Patterns and predictors of
undiagnosed and uncontrolled hypertension: observations from a poor-resource setting. J Hum Hyper-
tens. 2017; 31(1):56–65. https://doi.org/10.1038/jhh.2016.30 PMID: 27193382 23. Ghosh S, Barik A, Majumder S, Gorain A, Mukherjee S, Mazumdar S, et al. Health & Demographic Sur-
veillance System Profile: The Birbhum population project (Birbhum HDSS). Int J Epidemiol. 2015; 44
(1):98–107. https://doi.org/10.1093/ije/dyu228 PMID: 25540150 15 / 16 PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 PLOS ONE Health care seeking behaviour and financial protection 24. Chobanian AV, Bakris GL, Black HR, Cushman WC, Green LA, Izzo JL Jr., et al. PLOS ONE | https://doi.org/10.1371/journal.pone.0264314
February 25, 2022 References Prevalence, awareness, treatment and con-
trol of hypertension among elderly persons in an urban slum of Delhi, India. Indian Journal of Medical
Specialities. 2014; 5(1):7–10. 37. Tocci G, Ferrucci A, Pontremoli R, Ferri C, Rosei E, Morganti A, et al. Blood pressure levels and control
in Italy: comprehensive analysis of clinical data from 2000–2005 and 2005–2011 hypertension surveys. Journal of human hypertension. 2015; 29(11):696. https://doi.org/10.1038/jhh.2015.4 PMID: 25673112 38. Joffres M, Falaschetti E, Gillespie C, Robitaille C, Loustalot F, Poulter N, et al. Hypertension preva-
lence, awareness, treatment and control in national surveys from England, the USA and Canada, and
correlation with stroke and ischaemic heart disease mortality: a cross-sectional study. BMJ Open. 2013; 3(8):e003423. https://doi.org/10.1136/bmjopen-2013-003423 PMID: 23996822 16 / 16
|
https://openalex.org/W2964280833
|
https://europepmc.org/articles/pmc6642529?pdf=render
|
English
| null |
Proximity-dependent biotinylation screening identifies NbHYPK as a novel interacting partner of ATG8 in plants
|
BMC plant biology
| 2,019
|
cc-by
| 9,924
|
Macharia et al. BMC Plant Biology (2019) 19:326
https://doi.org/10.1186/s12870-019-1930-8 Macharia et al. BMC Plant Biology (2019) 19:326
https://doi.org/10.1186/s12870-019-1930-8 Open Access Abstract Background: Autophagy is a conserved, highly-regulated catabolic process that plays important roles in growth,
development and innate immunity in plants. In this study, we compared the rate of autophagy induction in Nicotiana
benthamiana plants infected with Tobacco mosaic virus or the TMV 24A + UPD mutant variant, which replicates at a
faster rate and induces more severe symptoms. Using a BirA* tag and proximity-dependent biotin identification (BioID)
analysis, we identified host proteins that interact with the core autophagy protein, ATG8 in TMV 24A + UPD infected
plants. By combining the use of a fast replicating TMV mutant and an in vivo protein-protein screening technique, we
were able to gain functional insight into the role of autophagy in a compatible virus-host interaction. Results: Our study revealed an increased autophagic flux induced by TMV 24A + UPD, as compared to TMV in
N. benthamiana. Analysis of the functional proteome associated with ATG8 revealed a total of 67 proteins, 16 of which
are known to interact with ATG8 or its orthologs in mammalian and yeast systems. The interacting proteins were
categorized into four functional groups: immune system process, response to ROS, sulphur amino acid metabolism and
calcium signalling. Due to the presence of an ubiquitin-associated (UBA) domain, which is demonstrated to interact
with ATG8, the Huntingtin-interacting protein K-like (HYPK) was selected for validation of the physical interaction and
function. We used yeast two hybrid (Y2H), bimolecular fluorescence complementation (BiFC) and subcellular
localization to validate the ATG8-HYPK interaction. Subsequent down-regulation of ATG8 by virus-induced gene silencing
(VIGS) showed enhanced TMV symptoms, suggesting a protective role for autophagy during TMV 24A + UPD infection. Conclusion: This study presents the use of BioID as a suitable method for screening ATG8 interacting proteins in planta. We have identified many putative binding partners of ATG8 during TMV 24A + UPD infection in N. benthamiana plants. In addition, we have verified that NbHYPK is an interacting partner of ATG8. We infer that autophagy plays a protective
role in TMV 24A + UPD infected plants. Keywords: BioID, Autophagy, ATG8, TMV, TMV 24A + UPD, Protein-protein interaction, HYPK Keywords: BioID, Autophagy, ATG8, TMV, TMV 24A + UPD, Protein-protein interaction, HYPK studies have continued to elucidate roles of autophagy, its
basic mechanism and interaction with other host compo-
nents during virus infection in plants. © The Author(s). 2019 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. Proximity-dependent biotinylation screening
identifies NbHYPK as a novel interacting
partner of ATG8 in plants ercy W. Macharia1, Wilfred Y. Z. Tan1, Prem P. Das1, Naweed I. Naqvi1,2 and Sek-Man Wong1,2,3* Abstract ATG8 directly inter-
acts and facilitates elimination of Cotton leaf curl Multan
virus (CLCuMuV) virulence factor [5] and Cauliflower
mosaic virus (CaMV) capsid protein P4 [6]. Calmodulin-
like protein NbCaM, interacts with N. benthamiana
Suppressor of Gene Silencing 3 (NbSGS3) and pro-
motes autophagic degradation during geminivirus in-
fection
[7]. During
Turnip
mosaic
virus
(TuMV)
infection, selective autophagy cargo receptor NBR1 tar-
gets the RNA silencing suppressor HCpro, thus sup-
pressing viral accumulation [8]. ATG6 interacts with Background
d
f Induction of autophagic vesicles has been reported with
infection of several viruses in both plant and animal cells
[1–4]. Unless impaired, autophagy pathways endeavour to
actively eliminate intracellular invaders to promote cell
survival [2]. Studies have revealed an important role of au-
tophagy in plant innate immunity, programme cell death,
plant resistance and viral RNA silencing [4–6]. Recent * Correspondence: dbswsm@nus.edu.sg
1Department of Biological Sciences, National University of Singapore,
Singapore 119543, Singapore
2Temasek Life Sciences Laboratory, Singapore 117604, Singapore
Full list of author information is available at the end of the article Page 2 of 11 Page 2 of 11 Macharia et al. BMC Plant Biology (2019) 19:326 TuMV RNA-dependent RNA polymerase (RdRp) and
restricts its infection [9]. TuMV RNA-dependent RNA polymerase (RdRp) and
restricts its infection [9]. TuMV RNA-dependent RNA polymerase (RdRp) and
restricts its infection [9]. does not influence viral symptoms in test plants. The full
length primary sequences of mammalian HYPK and
NbHYPK-like proteins share a 57% similarity of conserved
and similar amino acids. Both of the proteins have a con-
served UBA domain at the C terminus. This shared simi-
larity suggests that NbHYPK may play a role similar to the
mammalian ortholog. The mammalian HYPK is an intrin-
sically unstructured chaperone that interacts with Hun-
tingtin (HTT) and it enhances autophagy flux and
increases in conversion of ATG8 to the lipidated/active
ATG8-PE (LC3I to LC3II) [18]. RNA viruses exploit cellular machinery into virus
assembly complexes through various compositions of
protein-RNA, protein-lipid and protein-protein compo-
nents [10]. Their interaction with plant autophagy is
largely unexploited. Therefore, there is a need to identify
major host proteins that are involved in autophagy during
compatible RNA virus-host interaction. Autophagy in-
duces
the
formation
of
autophagosomes
which
are
double-membrane vesicles that engulf cargoes such as
proteins, damaged organelles and pathogens and transport
them to the vacuoles for degradation [11]. ATG8 is a core
protein associated with maturation of the autophagosome
[12]. Therefore, screening for ATG8 interacting proteins is
crucial in understanding the basic mechanism of autopha-
gosome formation and processing during viral infection. TMV 24A + UPD induced autophagosome biogenesis and
autophagic flux TMV 24A + UPD replicated faster and induced more
severe symptoms, as compared to TMV [14]. We hy-
pothesized that rapid virus replication could increase au-
tophagy and/or autophagic flux. To determine whether
autophagy is triggered upon infection by TMV and
TMV 24A + UPD, we detected autophagic flux by con-
firming the presence of ATG8-II at 2 and 3 dpi (Fig. 1a;
Additional file 1: Figure S1). Next, we investigated the
ultrastructural changes in infected leaves by transmission
electron microscopy (TEM). Membranous vesicles resem-
bling autophagosome-like structures were observed in ul-
trathin sections of TMV 24A + UPD infected leaves
(Fig. 1b). To verify autophagy induction, we infiltrated
RFP-ATG8 into virus-infected N. benthamiana leaves,
and quantified the number of epifluorescent foci (Fig. 1c). Tobacco mosaic virus (TMV) is a positive sense RNA
virus that is compatible with certain genotypes of tobacco
plants. It has an upstream pseudo-knot domain (UPD) at
the 3′ end that plays a crucial role during virus translation
and expression [13]. TMV 24A + UPD, a mutant engi-
neered by introducing an internal poly (A) tract (24 nucleo-
tides) upstream of the TMV UPD induced earlier and more
severe necrotic symptoms [14]. Using this mutant, we
investigated autophagy induction and flux in infected N. benthamiana plants. We screened for host proteins that
interact with ATG8 during mutant virus infection in
planta. In this report, we showed that TMV 24A + UPD, a
faster replicating mutant, enhanced autophagy induction
and flux, as compared to TMV. We employed the BioID
technique by fusing the biotin ligase BirA* to ATG8. The
technique was initially used in mammalian cells [15] and
more recently used in rice protoplasts [16] and detached
leaf tissues [17]. The BirA* releases biotinyl-5′-AMP which
chemically attaches biotin to proteins that are located
within 10 nm of its proximity. Subsequently, proteins that
are close to or interacting with the target protein ATG8 are
biotinylated. They can be purified using streptavidin and
analysed by tandem mass spectrometry (MS/MS). The number of autophagosome-like structures
in
TMV
24A + UPD
infected
plants
were
significantly
higher than those in TMV infected plants (Fig. 1d). A
significantly higher number of RFP-ATG8 labelled aggre-
gate structures were observed in TMV 24A + UPD, as
compared to that of TMV (Fig. 1e). Results TMV 24A + UPD induced autophagosome biogenesis and
autophagic flux Identification of biotinylated proteins RFP-ATG8a autophagosomes were significantly enhanced by infection with TMV24A + UPD (*p < 0.05). The asterisks
indicate significant differences by unpaired sample t test. The scale bar represents 1 μm
A
B
C
Fig. 2 Immunoblot analysis of BioID fusion proteins and total biotinylated proteins. a Western blots were carried out using anti-ATG8, or anti-mCherry
antisera to ascertain fusion protein expression. b Streptavidin-HRP blot of crude protein lysate. c Strep-HRP blot after Dynabeads™purification. Lower
panels show Ponceau S stained blot membranes to confirm equal loading of total proteins A
B
C
D
E
Fig. 1 Autophagy activation in response to TMV and TMV24A + UPD infection in N. benthamiana. a Immunoblot analysis using ATG8 antibody. Molecular weight of the bands detected at ~ 16 kDa. The Ponceau S staining served as a loading control (lower panel, Ponceau S). b Representative
electron micrographs showing infected plants at 3 dpi (days post inoculation). Arrows show membranous autophagosome-like structures. Abbreviations; S, starch, C, cytoplasm. c Representative images of RFP-ATG8 labelled autophagosomes at 3 dpi. d The number of autophagosome-like
structures was obtained from ~ 100μm2 section for each experiment. Autophagosome-like structures were significantly enhanced by infection with
TMV 24A + UPD (*p < 0.05). e The mean number of fluorescent puncta/aggregates were obtained from sections with approximately equal number of
cells (~ 100) for each experiment. RFP-ATG8a autophagosomes were significantly enhanced by infection with TMV24A + UPD (*p < 0.05). The asterisks
indicate significant differences by unpaired sample t test. The scale bar represents 1 μm D D A B B E E C C Fig. 1 Autophagy activation in response to TMV and TMV24A + UPD infection in N. benthamiana. a Immunoblot analysis using ATG8 antibody. Molecular weight of the bands detected at ~ 16 kDa. The Ponceau S staining served as a loading control (lower panel, Ponceau S). b Representative
electron micrographs showing infected plants at 3 dpi (days post inoculation). Arrows show membranous autophagosome-like structures. Abbreviations; S, starch, C, cytoplasm. c Representative images of RFP-ATG8 labelled autophagosomes at 3 dpi. d The number of autophagosome-like
structures was obtained from ~ 100μm2 section for each experiment. Autophagosome-like structures were significantly enhanced by infection with
TMV 24A + UPD (*p < 0.05). e The mean number of fluorescent puncta/aggregates were obtained from sections with approximately equal number of
cells (~ 100) for each experiment. Identification of biotinylated proteins y
p
After determining that TMV 24A + UPD induced autoph-
agic flux, we sought to identify ATG8 interacting proteins
during infection. Two plasmids, PXY01-RFP-HA-BirA*
(BirA*) used as a control and PXY01-RFP-HA-BirA*-
ATG8 (BirA*-ATG8) used as baits, were constructed
(Additional file 1: Figure S2a). Expression of BirA* and
BirA*-ATG8 were successful for both constructs (Fig. 2a;
Additional file 1: Figure S2b, 2c, 2d, 2e). N. benthamiana
leaves were agroinfiltrated either with BirA* or BirA*-
ATG8 vectors, with agroinfiltration buffer supplemented
with 2 mM biotin. Biotinylated proteins were detected by
Western blot and purified using Magnetic Dynabeads™
coated with streptavidin (Fig. 2b, c; Additional file 1:
Figure
S3a,
b). The
BirA*-ATG8
bound
fraction
showed multiple biotinylated protein bands (Fig. 2c;
Additional file 1: Figure S3c). This suggests that there A total of 67 proteins were identified, most of which are
previously unknown to interact with autophagy proteins
in plants. Sixteen of the proteins have been previously
shown to directly or indirectly associate with autophagy
pathway in animal and/or yeast system. Due to the pres-
ence of the UBA domain, which is known to interact with
ATG8, the Huntingtin-interacting protein K-like (HYPK)
was selected for further validation. Using yeast-two-hybrid
(Y2H),
biomolecular
fluorescence
complementation
(BiFC) and subcellular co-localization, we showed that
HYPK and ATG8 interacted in N. benthamiana plants. Knockdown of NbHYPK did not enhance viral symptoms,
in contrast to the observed decrease in symptoms upon
autophagy knockdown, suggesting that NbHYPK alone Page 3 of 11 Macharia et al. BMC Plant Biology (2019) 19:326 Macharia et al. BMC Plant Biology A
B
C
D
E
Fig. 1 Autophagy activation in response to TMV and TMV24A + UPD infection in N. benthamiana. a Immunoblot analysis using ATG8 antibody. Molecular weight of the bands detected at ~ 16 kDa. The Ponceau S staining served as a loading control (lower panel, Ponceau S). b Representative
electron micrographs showing infected plants at 3 dpi (days post inoculation). Arrows show membranous autophagosome-like structures. Abbreviations; S, starch, C, cytoplasm. c Representative images of RFP-ATG8 labelled autophagosomes at 3 dpi. d The number of autophagosome-like
structures was obtained from ~ 100μm2 section for each experiment. Autophagosome-like structures were significantly enhanced by infection with
TMV 24A + UPD (*p < 0.05). e The mean number of fluorescent puncta/aggregates were obtained from sections with approximately equal number of
cells (~ 100) for each experiment. NbHYPK interacts with ATG8 NbHYPK interacts with ATG8
NbHYPK was identified from BioID screening and verified
by cDNA cloning and sequencing. NbHYPK is a small
protein spanning 109 amino acids. It has a UBA domain
between amino acids 68–109 and is denoted as UBA_
NbHYPK. In order to test if the UBA domain is required
for its interaction with ATG8, it was deleted from the
NbHYPK gene and referred to as NbHYPKΔUBA (1–67
aa). We confirmed expression of full length and truncated
fusion proteins of HYPK-GFP and RFP-ATG8 by Western
blotting (Additional file 1: Figure S4a). We then con-
ducted a co-localization assay After NbHYPK-GFP /
NbHYPKΔUBA-GFP/ UBA_NbHYPK-GFP and mCherry-
ATG8 were co-infiltrated into N. benthamiana leaves and
transiently expressed, aggregates were observed only in
leaves co-expressing NbHYPK-GFP and mCherry-ATG8
(Fig. 4a), but with no aggregates observed in leaves ex-
pressing NbHYPKΔUBA or UBA_NbHYPK-GFP and
mCherry-ATG8 (Additional file 1: Figure S4b). To further
confirm the interaction between NbHYPK and ATG8, we
performed a BiFC assay. Constructs with NbHYPK fused
to the C-terminus of yellow fluorescent protein (NbHYPK
-Yc) and ATG8 fused to the N-terminus of YFP (ATG8-
Yn) were co-expressed in N. benthamiana leaves and re-
sulted in reconstitution of YFP (Fig. 4b). Leaves expressing
ATG8-Yn with UBA_NbHYPK –Yc, NbHYPKΔUBA -Yc
or other empty vector controls failed to generate epifluor-
escent signals (Additional file 1: Figure S4c). A
B
Fig. 3 Statistics of proteins identified and Gene ontology (GO)
enrichment analysis of unique BirA*-ATG8 proteins. aVenn diagrams
showing unique and shared proteins between BirA* and BirA*-ATG8. b Interactive graphs of proteins that were identified with BirA*-ATG8
during TMV 24A + UPD infection. The sizes of the circles are proportional
to the number of proteins associated with the specific term. The
interactive network were summarized and plotted following published
REVIGO protocol (http://revigo.irb.hr/) A A B
Fig. 3 Statistics of proteins identified and Gene ontology (GO)
enrichment analysis of unique BirA*-ATG8 proteins. aVenn diagrams
showing unique and shared proteins between BirA* and BirA*-ATG8. b Interactive graphs of proteins that were identified with BirA*-ATG8
during TMV 24A + UPD infection. The sizes of the circles are proportional
to the number of proteins associated with the specific term. The
interactive network were summarized and plotted following published
REVIGO protocol (http://revigo.irb.hr/) B g
(
g
)
Additionally, we employed Y2H to confirm the inter-
action between NbHYPK and ATG8. Identification of biotinylated proteins RFP-ATG8a autophagosomes were significantly enhanced by infection with TMV24A + UPD (*p < 0.05). The asterisks
indicate significant differences by unpaired sample t test. The scale bar represents 1 μm A
B
C
Fig. 2 Immunoblot analysis of BioID fusion proteins and total biotinylated proteins. a Western blots were carried out using anti-ATG8, or anti-mCherry
antisera to ascertain fusion protein expression. b Streptavidin-HRP blot of crude protein lysate. c Strep-HRP blot after Dynabeads™purification. Lower
panels show Ponceau S stained blot membranes to confirm equal loading of total proteins B C B A C A Fig. 2 Immunoblot analysis of BioID fusion proteins and total biotinylated proteins. a Western blots were carried out using anti-ATG8, or anti-mCherry
antisera to ascertain fusion protein expression. b Streptavidin-HRP blot of crude protein lysate. c Strep-HRP blot after Dynabeads™purification. Lower
panels show Ponceau S stained blot membranes to confirm equal loading of total proteins Page 4 of 11 Macharia et al. BMC Plant Biology (2019) 19:326 Macharia et al. BMC Plant Biology (2019) 19:326 Macharia et al. BMC Plant Biology were more biotinylated proteins in the beads fraction of
BirA*-ATG8 samples, as compared to the control. interact with the autophagy pathway (Table 1). Proteins 17
to 30 have not been shown to interact with autophagy pro-
cesses but have biological roles in plant defense and may
likely interact with the core autophagy components. We
selected the HYPK protein for validation of ATG8 inter-
action because it contains a UBA domain which has been
demonstrated to interact with ATG8. NbHYPK interacts with ATG8 ATG8 was fused to
the binding domain (BD) and tested for its interaction
with NbHYPK fused to the activation domain (AD). Y2H
assays validated the physical interaction between NbHYPK
and ATG8 (Fig. 4c). We also constructed two other plas-
mids, NbHYPKΔUBA and UBA_NbHYPK, into the AD
and tested for their interactions with BD-ATG8. No inter-
action was evident (Fig. 4c). Taken together, we conclude
that the newly identified host protein NbHYPK physically
interacts with ATG8 in vitro and in vivo. In addition, we
demonstrated that the UBA domain in NbHYPK is essen-
tial for such physical interaction with ATG8. Fig. 3 Statistics of proteins identified and Gene ontology (GO)
enrichment analysis of unique BirA*-ATG8 proteins. aVenn diagrams
showing unique and shared proteins between BirA* and BirA*-ATG8. b Interactive graphs of proteins that were identified with BirA*-ATG8
during TMV 24A + UPD infection. The sizes of the circles are proportional
to the number of proteins associated with the specific term. The
interactive network were summarized and plotted following published
REVIGO protocol (http://revigo.irb.hr/) Fig. 3 Statistics of proteins identified and Gene ontology (GO)
enrichment analysis of unique BirA*-ATG8 proteins. aVenn diagrams
showing unique and shared proteins between BirA* and BirA*-ATG8. b Interactive graphs of proteins that were identified with BirA*-ATG8
during TMV 24A + UPD infection. The sizes of the circles are proportional
to the number of proteins associated with the specific term. The
interactive network were summarized and plotted following published
REVIGO protocol (http://revigo.irb.hr/) ATG8 potentially interacts with a network of proteins
involved in plant defense Subsequent bioinformatics analysis of MS/MS results re-
vealed 5 proteins that were shared between the BirA* and
BirA*-ATG8 extracts and 67 proteins were unique to
BirA*-ATG8 (Fig. 3a). Gene ontology analysis categorized
BirA*-ATG8-identified proteins into 4 functional groups
namely: immune system process, response to ROS, sulphur
amino acid metabolism and calcium ion signalling (Fig. 3b). Of these proteins, 14 were uncharacterized and 23 were
not reported to be involved in autophagy or plant defense
(Additional file 2: Table S1). Therefore, they were not
selected as candidates for further validation. The rest of
the proteins identified were deemed significant, based on
published literature (Table 1). These proteins may interact
directly or indirectly with ATG8 in N. benthamiana plants. The first 16 proteins have been previously shown to Autophagy protects N. benthamiana plants against rapid
cell death induced by TMV 24A + UPD Autophagy protects N. benthamiana plants against rapid
cell death induced by TMV 24A + UPD To test whether autophagy was required for TMV 24A +
UPD induced cell death, we silenced ATG5, ATG7 and Page 5 of 11 Macharia et al. BMC Plant Biology (2019) 19:326 Table 1 BirA*-ATG8 associated proteins identified via BioID
No. Accession
Protein name
1. I7GVS5
Heat shock protein 70 (Hsp70) [18, 19] . 2
A2PYH3
Alpha chain of nascent polypeptide associated complex (NAC) [20]. 3
A0A1J6JLR9
Eukaryotic translation initiation factor 4 g [21]. 4
A0A1P8SF07
TOM1-like protein 2 (Tom1L2) [22]
5
Q4QXL9
Autophagy-related Protein 3 (ATG3) [23, 24]. 6
A0A1U7YMI0
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) [24]. 7
A0A1S3ZA42
FK506-binding protein 5 (FKBP5)-like isoform X2 [25]. 8
A0A1U7XHY8
Subtilisin-like protease (SLP) [26]. 9
Q8W183
Carbonic anhydrase [27]. 10
Q76MF3
Calmodulin [28]. 11
A0A1U7YG19
Serine hydroxymethyltransferase (SHMT) [29]. 12
A0A1U7VJK4
Plasminogen activator inhibitor 1 (PAI-1) RNA-binding protein-like [30]. 13
A8UDS9
Copper/zinc superoxide dismutase (SOD1) [31]. 14
A0A1U7XPN3
Huntingtin-interacting protein K (HYPK) [32] . 15
A0A1S3XIE4
Acyl-CoA-binding domain-containing protein 3-like [33]. 16
A0A1U7XC68
Clathrin light chain [34]. 17
A0A1P8SF08
AvrPto-interacting protein 1 (Api1)
18
A0A1J6K7H0
Elongation factor 1-alpha (eEF1A)
19
A0A1U7XRQ0
H/ACA ribonucleoprotein (RNP) complex subunit 1-like isoform X2 [35]. 20
Q9SXX4
Fructose-bisphosphate aldolase [36]
21
A0A1U7YCY5
Epidermal growth factor receptor substrate 15 (EPS15)-like 1
22
Q6K0Q3
Chloroplast glutamine synthetase (GS) [37, 38]. 23
C9DFB0
ASR
24
Q8LKF9
SGT1-like protein
25
A0A1U7YZQ4
probable ADP-ribosylation factor GTPase-activating protein (Arf GAP) AGD6
26
A0A1U7YFQ9
ATP-dependent RNA helicase SUPV3L1, mitochondrial-like
27
A0A1U7XQL2
40S ribosomal protein S20–2 (RPS20)
28
A0A1U7WRW2
40S ribosomal protein S6 (RPS6) [39]
29
A0A1U7VRZ1
Charged multi-vesicular body protein 5 (CHMP5)-like
30
A0A1U7VDD8
Actin cytoskeleton-regulatory complex protein PAN1-like isoform X1 [40]. Table 1 BirA*-ATG8 associated proteins identified via BioID ATG8, which are core components of autophagy. Such
autophagy silenced plants infected with TMV showed in-
creased chlorosis but did not show severe cell death symp-
toms (Fig. 5a). Cell death triggered by TMV 24A + UPD
was markedly increased in ATG5 and ATG7 silenced
plants (Fig. 5b). Despite targeting the conserved regions of
ATG8 isoforms, ATG8 silencing was less efficient, as com-
pared to ATG5 and ATG7 in both TMV and TMV 24A +
UPD infected plants (Additional file 1: Figure S5a, b). Per-
haps transient ATG8 silencing was less efficient as ATG8
has 8 isoforms in N. benthamiana [41]. Autophagy protects N. benthamiana plants against rapid
cell death induced by TMV 24A + UPD The silenced
TMV 24A + UPD infected plants showed enhanced cell
death symptoms in the newly emerged leaves (Fig. 5b). We infer that autophagy plays a protective role in TMV
24A + UPD infected plants. NbHYPK-silenced plants did
show slight but not any obvious differences in viral symptoms, as compared to the normal NbHYPK express-
ing plants (Fig. 6a). No significant difference was found in
coat protein gene expression between NbHYPK-silenced
and control plants (Additional file 1: Figure S6a), as quan-
tified by ImageJ [42]). Discussion Several studies have defined autophagy in yeast and mam-
malian systems [25, 29]. However, autophagy pathways in
plants have not been elucidated extensively. In this study,
we compared the autophagy induction and flux by TMV
and a fast replicating mutant TMV 24A + UPD in N. benthamiana plants. An increase of autophagy flux was
detected at 2 and 3 dpi (Fig. 1a). Significantly higher num-
ber of autophagosome-like structures were detected in
plants infected with the faster replicating TMV 24A + Page 6 of 11 Macharia et al. BMC Plant Biology (2019) 19:326 Macharia et al. BMC Plant Biology A
C
B
Fig. 4 ATG8 directly interacts with NbHYPK. a GFP labelled NbHYPK, NbHYPKΔUBA and UBA-NbHYPK was co-infiltrated with RFP-labelled ATG8
and localized by confocal microscopy. b Bimolecular fluorescence complementation (BiFC) analysis, ATG8-Yn or x-Yn(empty vector) was co-
expressed with NbHYPK-Yc, NbHYPKΔUBA-Yc and UBA-NbHYPK-Yc or x-Yc (empty vector). Fluorescent signals were visualized after 3 dpi by
confocal microscopy. Bar = 1 μm. c Analysis of interaction between ATG8 and NbHYPK by Yeast two hybrid assay. Plasmids expression full length
NbHYPK or the UBA domain or NbHYPKΔUBA or empty vector were transformed into AH109 yeast and mated with yeast expressing plasmids
containing ATG8 or an empty vector and grown in amino acid drop out YPDA media
A
B
Fig. 5 Silencing important gene(s) essential for autophagy, accelerated TMV 24A + UPD cell death symptoms. aTMV infected plants showing
chlorosis in autophagy silenced plants. Inset is an enlarged section of ATG7-silenced plants. b TMV 24A + UPD showing accelerated cell death in
autophagy silenced plants. An enlarged ATG7 silenced plant showing accelerated cell death in the emerged leaves A
C
B
Fig. 4 ATG8 directly interacts with NbHYPK. a GFP labelled NbHYPK, NbHYPKΔUBA and UBA-NbHYPK was co-infiltrated with RFP-labelled ATG8
and localized by confocal microscopy. b Bimolecular fluorescence complementation (BiFC) analysis, ATG8-Yn or x-Yn(empty vector) was co-
expressed with NbHYPK-Yc, NbHYPKΔUBA-Yc and UBA-NbHYPK-Yc or x-Yc (empty vector). Fluorescent signals were visualized after 3 dpi by
confocal microscopy. Bar = 1 μm. c Analysis of interaction between ATG8 and NbHYPK by Yeast two hybrid assay. Discussion Plasmids expression full length
NbHYPK or the UBA domain or NbHYPKΔUBA or empty vector were transformed into AH109 yeast and mated with yeast expressing plasmids
containing ATG8 or an empty vector and grown in amino acid drop out YPDA media A
B A B B A C C C C Fig. 4 ATG8 directly interacts with NbHYPK. a GFP labelled NbHYPK, NbHYPKΔUBA and UBA-NbHYPK was co-infiltrated with RFP-labelled ATG8
and localized by confocal microscopy. b Bimolecular fluorescence complementation (BiFC) analysis, ATG8-Yn or x-Yn(empty vector) was co-
expressed with NbHYPK-Yc, NbHYPKΔUBA-Yc and UBA-NbHYPK-Yc or x-Yc (empty vector). Fluorescent signals were visualized after 3 dpi by
confocal microscopy. Bar = 1 μm. c Analysis of interaction between ATG8 and NbHYPK by Yeast two hybrid assay. Plasmids expression full length
NbHYPK or the UBA domain or NbHYPKΔUBA or empty vector were transformed into AH109 yeast and mated with yeast expressing plasmids
containing ATG8 or an empty vector and grown in amino acid drop out YPDA media A
B
Fig. 5 Silencing important gene(s) essential for autophagy, accelerated TMV 24A + UPD cell death symptoms. aTMV infected plants showing
chlorosis in autophagy silenced plants. Inset is an enlarged section of ATG7-silenced plants. b TMV 24A + UPD showing accelerated cell death in
autophagy silenced plants. An enlarged ATG7 silenced plant showing accelerated cell death in the emerged leaves A A B
Fig. 5 Silencing important gene(s) essential for autophagy, accelerated TMV 24A + UPD cell death symptoms. aTMV infected plants showing
chlorosis in autophagy silenced plants. Inset is an enlarged section of ATG7-silenced plants. b TMV 24A + UPD showing accelerated cell death in
autophagy silenced plants. An enlarged ATG7 silenced plant showing accelerated cell death in the emerged leaves B Fig. 5 Silencing important gene(s) essential for autophagy, accelerated TMV 24A + UPD cell death symptoms. aTMV infected plants showing
chlorosis in autophagy silenced plants. Inset is an enlarged section of ATG7-silenced plants. b TMV 24A + UPD showing accelerated cell death in
autophagy silenced plants. An enlarged ATG7 silenced plant showing accelerated cell death in the emerged leaves Page 7 of 11 Macharia et al. BMC Plant Biology (2019) 19:326 (2019) 19:326 Macharia et al. BMC Plant Biology A A
B
Fig. 6 TMV 24A + UPD symptoms and gene expression analysis in VIGS-NbHYPK plants. a VIGS-silenced plants showed no significant difference in
viral symptoms as compared to non-silenced plants. Discussion b Quantitative real-time (qrtPCR) analysis of NbHYPK gene in control and VIGS-NbHYPK plants A B Fig. 6 TMV 24A + UPD symptoms and gene expression analysis in VIGS-NbHYPK plants. a VIGS-silenced plants showed no significant difference in
viral symptoms as compared to non-silenced plants. b Quantitative real-time (qrtPCR) analysis of NbHYPK gene in control and VIGS-NbHYPK plants independent functions of ATG8 in maintaining lipid drop-
let integrity in yeast and in apicoplast formation in malaria
[44–46]. Perhaps ATG8 isoform(s) also play an autoph-
agy-independent role in plants. Some proteins that inter-
act with ATG8, such as ATG4 and ATG7, were not
identified through MS/MS. Some autophagy proteins may
be difficult to purify as they unstable [47]. In addition,
some proteins not interacting with ATG8 were also bio-
tinylated due to their incidental proximity to the BirA*-
ATG8 fusion protein in cells, an inherent limitation of the
BioID technique. Therefore, interaction studies such as
Y2H, BiFC and co-localization were further considered to
confirm the physical interactions. UPD variant (Fig. 1b - e). This indicates that induction of
autophagy is likely accelerated by increased viral load due
to a more rapidly replicating TMV virus. Out of the 67 putative ATG8 interacting proteins identi-
fied through BioID screening, 16 proteins were directly
associated with autophagy pathways (Table 1). Among
these, ATG3 and calmodulin have been shown to interact
directly with ATG8 and autophagosomes in N. benthami-
ana plants [7, 23]. A subtilisin-like protease implicated in
programmed cell death and defense signaling in plants,
plays a role in animal autophagy [25, 41, 42]. Acyl-CoA-
binding domain-containing protein 3-like has been shown
to disrupt autophagosome formation and increase ATG8
degradation in plants [33]. Most of the other proteins
identified in this group are involved with autophagy in
mammalian systems but have not been reported in plants. On the other hand, proteins 17 to 30 (Table 1) are in-
volved in autophagy-associated functions such as patho-
gen defense, stress signalling, and hypersensitive response
(HR) [4, 42, 43]. Proteins 1 to 24 (Additional file 2: Table
S1) have biological functions that are not associated with
autophagy. Recent
studies have
revealed autophagy- High throughput protein-protein interaction studies
are crucial in narrowing down candidates to study au-
tophagy. ATG8 interacting proteins typically possess an
AIM/LIR motif. While this motif is used to select candi-
dates, it does not always represent functionality of the
motif [48]. Plant materials, plasmid construction and agrobacterium
infiltration g
y
Although down-regulation of NbHYPK using VIGS pro-
duced no significant difference in viral symptoms and cell
death in NbHYPK-silenced plants, silencing NbHYPK may
not produce phenotypes but may have an effect on other
cellular processes, as evidenced by the mammalian HYPK
ortholog. The mammalian huntingtin-interacting protein K
(HYPK) has chaperone-like properties and is involved in
cell death, unfolded protein response, cell cycle and cell
growth [52]. Overexpressing HYPK increased conversion
of the mammalian homologues of ATG8 and ATG8-PE,
LC3I to LC3II, respectively [18]. Interestingly, the Hunting-
tin protein itself (HTT) has been shown to interact with
ATG8 and is important for autophagy in Drosophila [32]. We do not rule out the redundancy in chaperone functions
in targeting ATG8. Nicotiana benthamiana seeds were obtained from Profes-
sor Dawei Li of China Agricultural University, Beijing,
PRC. Seedlings and plants were grown in pots placed in
growth rooms at 25 °C under a 16-h-light/8-h-dark cycle. NbATG8a (referred to as ATG8) was amplified using
primers in Additional file 3: Table S2. The cDNA clone
was used to construct vector PXY01 -35S-mCherry-
ATG8a. The construct was transformed into Agrobacter-
ium. For VIGS experiment, ATG5, ATG7 and ATG8
targets were amplified using primers listed in Additional
file 3: Table S2. The resulting fragments were inserted into
pTRV2. Together, pTRV1 and pTRV2 were introduced
into Agrobacterium as previously described [56]. Down-
regulation of the gene expression for NbHYPK, ATG5,
ATG7 and ATG8 was confirmed by qRT-PCR/RT-PCR
(Fig. 6b; Additional file 1: Figure S5, S6b). Cloning was
done using either ligation of restriction enzyme generated
sticky ends (enzyme sites underlined) or Gibson Assembly®
cloning kit from NEB kit, see primers (prefix GA is used)
in Additional file 3: Table S2. On the other hand, knockdown of ATG5, ATG7 and
ATG8 revealed that autophagy plays a protective role
against TMV 24A + UPD induced cell death. Although au-
tophagy seems to serve as an antiviral mechanism against
TMV, it is still intriguing that there is no significant au-
tophagic flux, as compared to TMV 24A + UPD. Autoph-
agy has been shown to play an antiviral role [8], thus, it is
possible that TMV subverts autophagy by an as yet un-
known mechanism. A recent study has shown that Barley
stripe mosaic virus (BSMV) interrupts autophagy by dis-
rupting the interaction between ATG8 and ATG7 [47]. Discussion Therefore, additional criteria are employed,
such as structural and biological aspects of the proteins. Autophagy receptors Joka2, P62 and NBR1 have UBA-
like domain(s) that are crucial in their interaction with Macharia et al. BMC Plant Biology (2019) 19:326 Macharia et al. BMC Plant Biology (2019) 19:326 Page 8 of 11 Page 8 of 11 Conclusion ATG8 [49]. Analysis of the ATG8 interactor NbHYPK
(this study) revealed that the primary sequence does not
contain a conventional AIM motif. However, it con-
tained a UBA domain in the C-terminus. Thus, we opted
to further validate NbHYPK interaction with ATG8
using the aforementioned analyses. Using the BioID technique, we have identified 67 proteins
that interact with ATG8 in N. benthamiana plants infected
with TMV and its more rapidly replicating mutant TMV
24A + UPD. A new ATG8 interacting protein, NbHYPK,
was identified and verified for its interaction with ATG8. The interaction requires the presence of the UBA domain
in NbHYPK. A recent study has described a new class of
ATG8 adapters and receptors that exploit ubiquitin-
interacting motif sequences for high-affinity binding [55]. Our results showed that NbHYPK and NbATG8 inter-
acted physically. The interaction of NbHYPK and ATG8
requires the UBA domain. The UBA domain of NbHYPK
has high similarity with another cytosolic chaperone, nas-
cent polypeptide-associated complex proteins (NAC),
which is associated with post translational processes of
nascent proteins emerging from the ribosomes [50]. We
also identified the alpha chain of nascent polypeptide
associated complex protein (Table 1). The mammalian
Plic-2 protein possesses a UBA domain and it is involved
in autophagy [51]. Plic-2 has played a protective role dur-
ing starvation and requires ATG5 and ATG7 proteins. It
directly interacts with ATG8 (LC3) and plays a role in fu-
sion of autophagosomes to lysosomes [51]. In summary, NbHYPK is involved in and may regulate
autophagic processes by ATG8 during viral/TMV infec-
tion. Future studies will focus on elucidating the bio-
logical significance of NbHYPK chaperone activity and
its relationship with other novel interacting partners
identified in the functional proteome associated with
ATG8 in N. benthamiana plants. Yeast two hybrid (Y2H) assays Yeast two hybrid (Y2H) assays
The genes of interest (Additional file 3: Table S2) were
cloned into either PGADT7 (AD) or PGBKT7 (BD) yeast
plasmid. The recombinant vectors were transformed into
AH109 yeast using lithium chloride as described by
Matchmaker® Yeast 2 Hybrid protocol. Transformed yeast
colonies were grown in liquid media and diluted into 10-,
100- and 1,000-fold and spread over on SD/−Trp/−Leu,
SD/−His/−Trp/−Leu
and
SD/−His/−Trp/−Leu/−Ade
plates. The plates were incubated at 30 °C until colonies
appeared 3 days later. Colonies that formed on more strin-
gent selection using SD/−His/−Trp/−Leu and SD/−His/
−Trp/−Leu/−Ade plates indicated physical interaction be-
tween the bait and prey proteins. BioID sample preparation and MS/MS analysis The protein lysate was subjected to phenol extraction. The resulting pellet was dissolved in lysis buffer (0.4%
SDS, 500 mM Nacl, 5 mM EDTA, 1 mM DTT, 50 mM
Tris-HCL, pH 7.4). Protein concentration was deter-
mined using Bradford assay. Streptavidin-coated Dyna-
beads (200 μl) was gently added into 100 μg of total
proteins. The mixture was incubated at 4 °C overnight
with gentle shaking. The beads containing bound bio-
tinylated proteins were separated from unbound proteins
using a magnetic stand. An aliquot of the unbound pro-
teins was saved for Western blot. Plant materials, plasmid construction and agrobacterium
infiltration It
is also plausible that the induction of autophagy flux by
TMV 24A + UPD is a result of an altered host-pathogen
interaction. Reactive oxygen species (ROS) can induce au-
tophagy in mammalian and plant cells [53, 54]. Autophagy
plays a significant role to alleviate oxidative damage by re-
ducing ROS [53, 54]. Future studies will aim at identifying
whether early infection by TMV 24A + UPD elicits an in-
creased ROS which likely results in accelerated cell death. E. coli biotin ligase BirA* was amplified from pcDNA
3.1
myc
BioID
plasmid
using
appropriate
primers
(Additional file 3: Table S2). Xba1 RE site and HA tag se-
quences were included in the forward primer while Sma1
was included in the reverse primer. The resulting frag-
ment was digested with appropriate enzymes and inserted
into vector PXY0 -35S-mCherry-ATG8. The resulting
vector
PXY01-mCherry-HABirA*-ATG8
(BirA*-ATG8)
was confirmed by DNA sequencing. For the control plas-
mid, the fragment was inserted into PXY01-mCherry-X
and
resulted
into
PXY01-mCherry-HABirA*
(BirA*). BioID clones were transformed into agrobacterium, and
2.5 mM
biotin incorporated into
the
agroinfiltration Page 9 of 11 Macharia et al. BMC Plant Biology (2019) 19:326 buffer. The clones were agroinfiltrated into fully expanded
leaves and 2.5 μg in vitro transcribed TMV 24A + UPD
viral RNA was mechanically inoculated into the plants. The leaves were collected at 3dpi and total proteins ex-
tracted. Protein expression was verified by immunoblot
using mCherry and ATG8 antibodies. For BiFC and subcel-
lular localization, PCR fragments were amplified with
primers shown in Additional file 3: Table S2 and cloned
into respective vectors. BiFC vectors were transformed into
Agrobacterium. The two cultures, nYFP-ATG8 and cYFP
–NbHYPK, were mixed at a ratio of 1:1 and co-inoculated
into N. benthamiana plants as previously described [28]. For subcellular co-localization, NbHYPK-GFP and RFP-
ATG8 vectors were also co-cultured as above. buffer. The clones were agroinfiltrated into fully expanded
leaves and 2.5 μg in vitro transcribed TMV 24A + UPD
viral RNA was mechanically inoculated into the plants. The leaves were collected at 3dpi and total proteins ex-
tracted. Protein expression was verified by immunoblot
using mCherry and ATG8 antibodies. For BiFC and subcel-
lular localization, PCR fragments were amplified with
primers shown in Additional file 3: Table S2 and cloned
into respective vectors. BiFC vectors were transformed into
Agrobacterium. Western blotting
T
l Total proteins were extracted from N. benthamiana
leaves and separated by SDS-PAGE for immunoblot ana-
lysis with appropriate antibody. After proteins were
transferred to nitrocellulose membrane, Ponceau S was
used to stain proteins for loading control, according to
manufacturer’s protocol, before proceeding with block-
ing and antibody incubation. Protein gel band images
were captured and converted into JPEG format and sub-
jected to digital image analysis using ImageJ software
version 1.52a [42]. Plant materials, plasmid construction and agrobacterium
infiltration The two cultures, nYFP-ATG8 and cYFP
–NbHYPK, were mixed at a ratio of 1:1 and co-inoculated
into N. benthamiana plants as previously described [28]. For subcellular co-localization, NbHYPK-GFP and RFP-
ATG8 vectors were also co-cultured as above. acetone for 20 min and then embedded in Spurr® resin. The resin blocks were trimmed and ultrathin sectioned. After staining with 2% uranyl acetate and 1% alkaline
lead citrate, the ultrathin sections were observed under a
TEM (model JEOL JEM-1230). Confocal microscopy For autophagosome visualization, fully expanded leaves
were agroinfiltrated with RFP-ATG8. After 24 h, the infil-
trated leaves were inoculated mechanically with 2.5 μg in
vitro transcribed RNA in GKP buffer (50 mM glycine; 30
mM K2HPO4, pH 9.2; 1% bentonite; 1% celite). After 3 days,
leaves were syringe-infiltrated with 5 uM of autophagy in-
hibitor E64d for 12 h, immediately followed by confocal mi-
croscopy. For subcellular localization and BiFC, leaves were
observed for fluorescence 3 days after agroinfiltration. The beads were washed several times (in 1 ml of 1 X
PBS per wash with gently shaking, 5 min at room
temperature), once in 2% SDS, once in 1% SDS, twice in
1% NP-40 and twice with 1 X PBS. The beads were left
in the final wash. An aliquot of the beads was saved for
Western blot analysis using streptavidin antibody (1:
2000). The beads were then subjected to MS analysis. Briefly, the beads were resuspended in 200 μl triethylam-
monium bicarbonate. Live cell images were acquired from abaxial leaf epider-
mal cells using a Zeiss LSM510 microscope. GFP and RFP
probes were excited at 488 and 561 nm, respectively, and
their fluorescent emissions detected at 495–550 and
570–610 nm, respectively. YFP was excited at 514 nm with
an emission of 527 nm. Confocal images were processed
with ZEN (version 2011) and 578 Image J (version 1.48v)
software. (TEAB) (0.5 M, pH 8.5) with 4 μl Tris(2-carboxyethyl)-
phosphine (TCEP) (100 mM stock) by gently mixing at
65 °C for 1 h. Four μl methyl methanethiosulfonate
(MMTS) (200 mM stock) was added into the mixture
above and incubated at room temperature for 15 min. Tryspin was added into the beads at 12.5 ng/μl and incu-
bated at 37 °C for 16 h with gentle shaking. The beads
were pelleted and the supernatant subjected to MS
analysis. MS/MS data was searched against database of
Nicotiana proteins using ProteinPilot™. Data cleaning
was carried out to remove insignificant hits. BirA*- Funding This work was financially supported by Singapore Ministry of Education through
National University of Singapore research grant R-154-000-B23–114, Suzhou
Bureau of Science and Technology grant SNG2018039, National Natural Science
Foundation of China grant 31872639 and NUS-SINGA scholarship to Mercy W. Macharia. N. Naqvi acknowledges intramural funding from the Temasek Life
Sciences Laboratory, Singapore. All funding played a role in the design of the
study and collection, analysis, and interpretation of data and in writing the
manuscript. Tem Virus infected and/or autophagy inhibitor treated leaf
samples were fixed in fixation medium (2% paraformal-
dehyde (w/v), 2.5% glutaraldehyde (v/v) in phosphate
buffer (0.1 M, pH 7.0) overnight and post-fixed with 1%
OsO4 in the phosphate buffer for 2 h. After a series of
ethanol dehydration, leaf samples were transferred to Page 10 of 11 Page 10 of 11 Macharia et al. BMC Plant Biology (2019) 19:326 Macharia et al. BMC Plant Biology (2019) 19:326 ATG8 proteins that overlapped with the control BirA*
proteins were also removed. Redundant and low quality
proteins were excluded from the final analysis. The pro-
teins were functionally classified. Gene ontology inter-
active network were summarized and plotted following
published REVIGO protocol (http://revigo.irb.hr/ dia-
grams
were
generated
using
UGen
Venn
software
(http://bioinformatics.psb.ugent.be/webtools/Venn/). Abbreviations
ATG8 A
h ATG8: Autophagy 8; BioID: Proximity dependent biotin identification;
BirA*: Biotin protein ligase; G/Y/RFP: Green/Yellow/Red Fluorescent protein;
HYPK: Huntingtin Interacting Protein K-like; MMTS: Methyl
methanethiosulfonate; MS: Mass spectrometry; ROS: Reactive oxygen species;
TCEP: Tris(2-carboxyethyl)phosphine; TEAB: Triethylammonium bicarbonate;
TEM: Transmission electron microscope; UBA: Ubiquitin associated domain;
VIGS: Virus induced gene silencing 7. Li F, Zhao N, Li Z, Xu X, Wang Y, Yang X, et al. A calmodulin-like protein
suppresses RNA silencing and promotes geminivirus infection by degrading
SGS3 via the autophagy pathway in Nicotiana benthamiana. PLoS Pathog. 2017;13(2):e1006213. 8. Hafrén A, Üstün S, Hochmuth A, Svenning S, Johansen T, Hofius D. Turnip
mosaic virus counteracts selective autophagy of the viral silencing
suppressor HCpro. Plant Physiol. 2017;176(1):649–62. 8. Hafrén A, Üstün S, Hochmuth A, Svenning S, Johansen T, Hofius D. Turnip
mosaic virus counteracts selective autophagy of the viral silencing
suppressor HCpro. Plant Physiol. 2017;176(1):649–62. Received: 18 January 2019 Accepted: 9 July 2019 Received: 18 January 2019 Accepted: 9 July 2019 Received: 18 January 2019 Accepted: 9 July 2019 References 1. Nakashima A, Tanaka N, Tamai K, Kyuuma M, Ishikawa Y, Sato H, et al. Survival of parvovirus B19-infected cells by cellular autophagy. Virology. 2006;349(2):254–63. 2. Hofius D, Munch D, Bressendorff S, Mundy J, Petersen M. Role of autophagy
in disease resistance and hypersensitive response-associated cell death. Cell
Death Differ. 2011;18(8):1257–62. 2. Hofius D, Munch D, Bressendorff S, Mundy J, Petersen M. Role of autophagy
in disease resistance and hypersensitive response-associated cell death. Cell
Death Differ. 2011;18(8):1257–62. protein expression as detected by anti-TMV antibody. TMV coat protein
is ~ 17.5 kDa. Statistical significance was determined by Student’s t test
(p = .39). (b) Semi-quantitative qRT-PCR analysis of NbHYPK expression in
VIGS silenced and non-silenced Nicotiana benthamiana plants. (ZIP 3798 kb) 3. Liu Y, Schiff M, Czymmek K, Talloczy Z, Levine B. Dinesh-Kumar S autophagy
regulates programmed cell death during the plant innate immune
response. Cell. 2005;121(4):567–77. 4. Agius C, Eamens AL, Millar AA, Watson JM, Wang MB. RNA silencing and
antiviral defense in plants. Methods Mol Biol. 2012;894(1):17–38. Additional file 2: Table S1. Proteins identified through BioID (DOCX 16 kb) Additional file 2: Table S1. Proteins identified through BioID (DOCX 16 kb) Additional file 2: Table S1. Proteins identified through BioID (DOCX 16 kb) 5. Haxim Y, Ismayil A, Jia Q, Wang Y, Zheng X, Chen T, et al. Autophagy
functions as an antiviral mechanism against geminiviruses in plants. eLife. 2017;6(10):e23897. Additional file 3: Table S2. List of primers used in this study (DOCX 18 kb) Additional file 3: Table S2. List of primers used in this study (DOCX 18 kb) Additional file 3: Table S2. List of primers used in this study (DOCX 18 kb) 6. Hafren A, Macia JL, Love AJ, Milner JJ, Drucker M, Hofius D. Selective
autophagy limits Cauliflower mosaic virus infection by NBR1-mediated
targeting of viral capsid protein and particles. Proc Natl Acad Sci U S A. 2017;114(10):E2026–e2035. Authors’ contribution MWM performed experiments, analysed and writing the manuscript. WZYT
conducted the BioID experiments and analysed the data. PPD assisted in
designing experiments and optimization of protocols. NIN and SMW assisted
in design of the study, discussing the results and editing the manuscript. All authors have read and approved the manuscript. Additional files (a) Graphical representation of
control BirA*and experimental plasmids
BirA*-ATG8. Full gel image for Fig. 2a carried out using anti-mCherry antiseri,
for both (b) & (c) and anti-ATG8 antiserum (* indicates a weak band). (d) to
ascertain fusion protein expression. (e) Detection of RFP signals from
agroinfiltrated N.benthamiana leaves to confirm
expression of RFP-fused BirA* and BirA*-ATG8. Figure S3. Full gel
Immunoblot analysis of total biotinylated proteins for Fig. 2b and c. (a)
Streptavidin-HRP blot of crude protein lysate. (b)Strep-HRP blot after
DynabeadsTM purification. Abbreviations: b, beads; s, supernatant. Lane 1. WT- Biotin only. Lanes 2–3,-BirA*, lanes 4–5, BirA*-ATG8, lane 6-BirA*, lane 7,
BirA*-ATG8, lane 8, BirA*, lane 9, BirA*-ATG8. Different treatments as follows:
Samples 2–5, biotin was infiltrated 3 days after agroinfiltration. Samples
6–9, biotin-infiltrated concurrently with agroinfiltration buffer. Samples
6 and 7, proteins extracted 3 dpi and samples 8 and
9 were collected 4 dpi. Treatments 6 and 7 were used for the final
experiment. Figure S4. ATG8 directly interacts with NbHYPK but not
NbHYPKΔUBA and UBA-NbHYPK (Fig. 4). (a) GFP-NbHYPK, GFP-NbHYPKΔUBA,
GFP-UBA-HYPK and RFP-ATG8 fusion proteins were detected in Western
blot using GFP and RFP antibodies, respectively. (b) RFP-ATG8 aggregates
with GFP-NbHYPK but not GFP -NbHYPKΔUBA or GFP-UBA-NbHYPK. (c)
Bimolecular fluorescence complementation (BiFC) analysis showed that
ATG8 was able to associate with NbHYPK but ATG8-Yn did not associate
with x-Yc (plasmid without insert). NbHYPK-Yc also did not associate with
x-Yn (plasmid without insert). Figure S5. Analysis of gene down-regulation
in ATG5/7/8-VIGS plants (Fig. 5). (a) Semi-quantitative RT-PCR expression
analysis of ATG8 isoforms in ATG8-silenced and non-silenced Nicotiana
benthamiana plants. (b) qRT-PCR analysis of ATG5 and ATG7 genes in
control and VIGS-plants. Figure S6. TMV accumulation and NbHYPK relative
expression in VIGS-NbHYPK plants (Fig. 6). (a) TMV coat
protein expression as detected by anti-TMV antibody. TMV coat protein
is ~ 17.5 kDa. Statistical significance was determined by Student’s t test
(p = .39). (b) Semi-quantitative qRT-PCR analysis of NbHYPK expression in
VIGS silenced and non-silenced Nicotiana benthamiana plants. (ZIP 3798 kb)
Additional file 2: Table S1 Proteins identified through BioID (DOCX 16 kb) Additional file 1: Figure S1. Full immunoblot images for Fig. 1a using
ATG8 antibody. (a) Mock. (b) TMV. (c) TMV 24A + UPD. Figure S2. Consent for publication
N/A Consent for publication
N/A Competing interests
h
h
d
l
h p
g
The authors declare that they have no competing interests. Author details
1
f 9 were collected 4 dpi. Treatments 6 and 7 were used for the final
experiment. Figure S4. ATG8 directly interacts with NbHYPK but not
NbHYPKΔUBA and UBA-NbHYPK (Fig. 4). (a) GFP-NbHYPK, GFP-NbHYPKΔUBA,
GFP-UBA-HYPK and RFP-ATG8 fusion proteins were detected in Western
blot using GFP and RFP antibodies, respectively. (b) RFP-ATG8 aggregates
with GFP-NbHYPK but not GFP -NbHYPKΔUBA or GFP-UBA-NbHYPK. (c)
Bimolecular fluorescence complementation (BiFC) analysis showed that
ATG8 was able to associate with NbHYPK but ATG8-Yn did not associate
with x-Yc (plasmid without insert). NbHYPK-Yc also did not associate with
x-Yn (plasmid without insert). Figure S5. Analysis of gene down-regulation
in ATG5/7/8-VIGS plants (Fig. 5). (a) Semi-quantitative RT-PCR expression
analysis of ATG8 isoforms in ATG8-silenced and non-silenced Nicotiana
benthamiana plants. (b) qRT-PCR analysis of ATG5 and ATG7 genes in
control and VIGS-plants. Figure S6. TMV accumulation and NbHYPK relative
expression in VIGS-NbHYPK plants (Fig. 6). (a) TMV coat Singapore 119543, Singapore. 2Temasek Life Sciences Laboratory, Singapore
117604, Singapore. 3National University of Singapore Research Institute, uzhou, Jiangsu 215123, People’s Republic of China. Availability of data and materials All data generated or analysed during this study are included in this published
article [and its supplementary information files]. Ethics approval and consent to participate
N/A Ethics approval and consent to participate Additional files Additional file 1: Figure S1. Full immunoblot images for Fig. 1a using
ATG8 antibody. (a) Mock. (b) TMV. (c) TMV 24A + UPD. Figure S2. Expression of BirA* and BirA_ATG8 constructs. (a) Graphical representation of
control BirA*and experimental plasmids
BirA*-ATG8. Full gel image for Fig. 2a carried out using anti-mCherry antiseri,
for both (b) & (c) and anti-ATG8 antiserum (* indicates a weak band). (d) to
ascertain fusion protein expression. (e) Detection of RFP signals from
agroinfiltrated N.benthamiana leaves to confirm
expression of RFP-fused BirA* and BirA*-ATG8. Figure S3. Full gel
Immunoblot analysis of total biotinylated proteins for Fig. 2b and c. (a)
Streptavidin-HRP blot of crude protein lysate. (b)Strep-HRP blot after
DynabeadsTM purification. Abbreviations: b, beads; s, supernatant. Lane 1. WT- Biotin only. Lanes 2–3,-BirA*, lanes 4–5, BirA*-ATG8, lane 6-BirA*, lane 7,
BirA*-ATG8, lane 8, BirA*, lane 9, BirA*-ATG8. Different treatments as follows:
Samples 2–5, biotin was infiltrated 3 days after agroinfiltration. Samples
6–9, biotin-infiltrated concurrently with agroinfiltration buffer. Samples
6 and 7, proteins extracted 3 dpi and samples 8 and
9 were collected 4 dpi. Treatments 6 and 7 were used for the final
experiment. Figure S4. ATG8 directly interacts with NbHYPK but not
NbHYPKΔUBA and UBA-NbHYPK (Fig. 4). (a) GFP-NbHYPK, GFP-NbHYPKΔUBA,
GFP-UBA-HYPK and RFP-ATG8 fusion proteins were detected in Western
blot using GFP and RFP antibodies, respectively. (b) RFP-ATG8 aggregates
with GFP-NbHYPK but not GFP -NbHYPKΔUBA or GFP-UBA-NbHYPK. (c)
Bimolecular fluorescence complementation (BiFC) analysis showed that
ATG8 was able to associate with NbHYPK but ATG8-Yn did not associate
with x-Yc (plasmid without insert). NbHYPK-Yc also did not associate with
x-Yn (plasmid without insert). Figure S5. Analysis of gene down-regulation
in ATG5/7/8-VIGS plants (Fig. 5). (a) Semi-quantitative RT-PCR expression
analysis of ATG8 isoforms in ATG8-silenced and non-silenced Nicotiana
benthamiana plants. (b) qRT-PCR analysis of ATG5 and ATG7 genes in
control and VIGS-plants. Figure S6. TMV accumulation and NbHYPK relative
expression in VIGS-NbHYPK plants (Fig. 6). (a) TMV coat
protein expression as detected by anti-TMV antibody. TMV coat protein
is ~ 17.5 kDa. Statistical significance was determined by Student’s t test
(p = .39). (b) Semi-quantitative qRT-PCR analysis of NbHYPK expression in
VIGS silenced and non-silenced Nicotiana benthamiana plants. (ZIP 3798 kb) Additional file 1: Figure S1. Full immunoblot images for Fig. 1a using
ATG8 antibody. (a) Mock. (b) TMV. (c) TMV 24A + UPD. Figure S2. Expression of BirA* and BirA_ATG8 constructs. Acknowledgements Chloroplasts are partially mobilized to the vacuole by
autophagy. Autophagy. 2008;4(7):961–2. 37. Ishida H, Yoshimoto K. Chloroplasts are partially mob
autophagy. Autophagy. 2008;4(7):961–2. 38. Izumi M, Wada S, Makino A, Ishida H. The autophagic degradation of
chloroplasts via rubisco-containing bodies is specifically linked to leaf
carbon status but not nitrogen status in Arabidopsis. Plant Physiol. 2010;
154(3):1196–209. 15. Roux KJ, Kim DI, Raida M, Burke B. A promiscuous biotin ligase fusion
protein identifies proximal and interacting proteins in mammalian cells. J
Cell Biol. 2012;196(6):801. 16. Lin Q, Zhou Z, Luo W, Fang M, Li M, Li H. Screening of proximal and
interacting proteins in Rice protoplasts by proximity-dependent
Biotinylation. Front Plant Sci. 2017;8(10):749. 39. Blommaart EF, Luiken JJ, Blommaart PJ, van Woerkom GM, Meijer AJ. Phosphorylation of ribosomal protein S6 is inhibitory for autophagy in
isolated rat hepatocytes. J Biol Chem. 1995;270(5):2320–6. 17. Khan M, Youn J-Y, Gingras A-C, Subramaniam R, Desveaux D. In planta
proximity dependent biotin identification (BioID). Sci Rep. 2018;8(1):9212. 40. Monastyrska I, He C, Geng J, Hoppe AD, Li Z, Klionsky DJ. Arp2 links autophagic
machinery with the actin cytoskeleton. Mol Biol Cell. 2008;19(5):1962–75. 18. Choudhury KR, Bucha S, Baksi S, Mukhopadhyay D. Bhattacharyya. Chaperone-like protein HYPK and its interacting partners augment
autophagy. Eur J Cell Biol. 2016;95(6–7):182–94. 41. Kellner R, De la Concepcion JC, Maqbool A, Kamoun S, Dagdas YF. ATG8 expansion: a driver of selective autophagy diversification? Trends
Plant Sci. 2017;22(3):204–14. 19. Pimkina J, Murphy ME. Murphy, interaction of the ARF tumor suppressor
with cytosolic HSP70 contributes to its autophagy function. Cancer Biol
Ther. 2011;12(6):503–9. 42. Schneider CA, Rasband WS, Eliceiri KW. NIH image to ImageJ: 25 years of
image analysis. Nat Methods. 2012;9(7):671. 43. Hofius D, Schultz-Larsen T, Joensen J, Tsitsigiannis DI, Petersen NH, Mattsson
O, et al. Autophagic components contribute to hypersensitive cell death in
Arabidopsis. Cell. 2009;137(4):773–83. 20. Guo B, Huang J, Wu W, Feng D, Wang X, Chen Y, et al. The nascent
polypeptide-associated complex is essential for autophagic flux. Autophagy. 2014;10(10):1738–48. 44. Maeda Y, Oku M, Sakai Y. Autophagy-independent function of Atg8 in lipid
droplet dynamics in yeast. J Biochem. 2017;161(4):339–48. 21. Ramírez-Valle F, Braunstein S, Zavadil J, Formenti SC, Schneider RJ. eIF4GI
links nutrient sensing by mTOR to cell proliferation and inhibition of
autophagy. J Cell Biol. 2008;181(2):293. 45. Ichimura Y, Kirisako T, Takao T, Satomi Y, Shimonishi Y, Ishihara N, et al. Acknowledgements A ubiquitin-like system mediates protein lipidation. Nature. 2000;
408(6811):488–92. 22. Tumbarello DA, Waxse BJ, Arden SD, Bright NA, Kendrick-Jones J, Buss F. Autophagy receptors link myosin VI to autophagosomes to mediate Tom1-
dependent autophagosome maturation and fusion with the lysosome. Nat
Cell Biol. 2012;14(10):1024–35. 46. Ketelaar T, Voss C, Dimmock SA, Thumm M, Hussey PJ. Arabidopsis
homologues of the autophagy protein Atg8 are a novel family of
microtubule binding proteins. FEBS Lett. 2004;567(2):302–6. 23. Yamaguchi M, Noda NN, Nakatogawa H, Kumeta H, Ohsumi Y, Inagaki
F. Autophagy-related protein 8 (Atg8) family interacting motif in Atg3
mediates the Atg3-Atg8 interaction and is crucial for the cytoplasm-
to-vacuole targeting pathway. J Biol Chem. 2010;285(38):29599–607. 47. Yang M, Zhang Y, Xie X, Yue N, Li J, Wang XB, et al. Barley stripe mosaic
virus gammab protein subverts autophagy to promote viral infection
by disrupting the ATG7-ATG8 interaction. Plant Cell. 2018;30(7):1582–95. 48. Popelka H, Klionsky DJ. Analysis of the native conformation of the LIR/
AIM motif in the Atg8/LC3/GABARAP-binding proteins. Autophagy. 2015;11(12):2153–9. 24. Han S, Wang Y, Zheng X, Jia Q, Zhao J, Bai F, et al. cytoplastic
Glyceraldehyde-3-Phosphate Dehydrogenases Interact with ATG3 to
Negatively Regulate Autophagy and Immunity in Nicotiana benthamiana. Plant Cell. 2015;27(4):1316. 49. Zientara-Rytter K, Sirko A. Significant role of PB1 and UBA domains in
multimerization of Joka2, a selective autophagy cargo receptor from
tobacco. Front Plant Sci. 2014;5(10):13. 25. Gassen NC, Hartmann J, Schmidt MV, Rein T. FKBP5/FKBP51 enhances autophagy
to synergize with antidepressant action. Autophagy. 2015;11(3):578–80. 50. Arnesen T, Starheim KK, Van Damme P, Evjenth R, Dinh H, Betts MJ, et al. The chaperone-like protein HYPK acts together with NatA in cotranslational
N-terminal acetylation and prevention of huntingtin aggregation. Mol Cell
Biol. 2010;30(8):1898–909. 26. Takeshige K, Baba M, Tsuboi S, Noda T, Ohsumi Y. Autophagy in yeast
demonstrated with proteinase-deficient mutants and conditions for its
induction. J Cell Biol. 1992;119(2):301–11. 27. Du A, Huang S, Zhao X, Feng K, Zhang S, Huang J, et al. Suppression of
CHRN endocytosis by carbonic anhydrase CAR3 in the pathogenesis of
myasthenia gravis. Autophagy. 2017;13(11):1981–94. 51. N'Diaye EN, Kajihara KK, Hsieh I, Morisaki H, Debnath J, Brown EJ. PLIC
proteins or ubiquilins regulate autophagy-dependent cell survival during
nutrient starvation. EMBO Rep. 2009;10(2):173–9. 28. Xu G, Wang S, Han S, Xie K, Wang Y, Li J, et al. Plant Bax Inhibitor-1
interacts with ATG6 to regulate autophagy and programmed cell death. Autophagy. 2017;13(7):1161–75. 28. Acknowledgements Xu G, Wang S, Han S, Xie K, Wang Y, Li J, et al. Plant Bax Inhibitor-1
interacts with ATG6 to regulate autophagy and programmed cell death. Autophagy. 2017;13(7):1161–75. 52. Choudhury KR, Raychaudhuri S, Bhattacharyya N. Identification of HYPK-
interacting proteins reveals involvement of HYPK in regulating cell
growth, cell cycle, unfolded protein response and cell death. PLoS One. 2012;7(12):e51415. 29. Xu M, Moresco JJ, Chang M, Mukim A, Smith D, Diedrich JK, et al. SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 tat K63-
ubiquitylation and destruction by autophagy. PLoS Pathog. 2018;14(5):
–e1007071. 53. Chen YF, Liu H, Luo XJ, Zhao Z, Zou ZY, Li J, et al. The roles of reactive
oxygen species (ROS) and autophagy in the survival and death of leukemia
cells. Crit Rev Oncol Hematol. 2017;112:21–30. 30. Wang Z-H, Ren W-Y, Zhu L, Hu L-J. Plasminogen activator inhibitor-1
regulates LPS induced inflammation in rat macrophages through
autophagy activation. Sci World J. 2014;2014(189168):1–12. 54. Xiong Y, Contento AL, Bassham DC. Disruption of autophagy results
in constitutive oxidative stress in Arabidopsis. Autophagy. 2007;3(3):257–8. 55. Marshall RS, Hua Z, Mali S, McLoughlin F, Vierstra RD. ATG8-binding UIM
proteins define a new class of autophagy adaptors and receptors. Cell. 2019;
In press. https://doi.org/10.1016/j.cell.2019.02.009. 31. Ramesh N, Pandey UB. Autophagy dysregulation in ALS: when protein
aggregates get out of hand. Front Mol Neurosci. 2017;10(33):263. 32. Ochaba J, Lukacsovich T, Csikos G, Zheng S, Margulis J, Salazar L, et al. Potential function for the huntingtin protein as a scaffold for selective
autophagy. Proc Natl Acad Sci U S A. 2014;111(47):16889–94. 56. Liu Y, Schiff M. Dinesh-Kumar S virus-induced gene silencing in tomato. Plant J. 2002;31(6):777–86. 33. Xiao S, Gao W, Chen Q-F, Chan S-W, Zheng S-X, Ma J, et al. Overexpression of Arabidopsis acyl-CoA binding protein ACBP3
promotes starvation-induced and age-dependent leaf senescence. Plant
Cell. 2010;22(5):1463–82. Acknowledgements 9. Li F, Zhang C, Li Y, Wu G, Hou X, Zhou X, et al. Beclin1 restricts RNA virus
infection in plants through suppression and degradation of the viral
polymerase. Nature Comm. 2018;9(1):1268. 9. Li F, Zhang C, Li Y, Wu G, Hou X, Zhou X, et al. Beclin1 restricts RNA virus
infection in plants through suppression and degradation of the viral
polymerase. Nature Comm. 2018;9(1):1268. Acknowledgements
The authors would like to thank Mr. Teck Kwang Lim at Protein and Proteomics
Center, Department of Biological Sciences, NUS and Ms. Shaalini D/O
Subramaniam and Mr. Ouyang Xuezhi at the TEM facility, Temasek Life Sciences
Laboratory, Singapore, for their technical support. The authors would like to thank Mr. Teck Kwang Lim at Protein and Proteomics
Center, Department of Biological Sciences, NUS and Ms. Shaalini D/O
Subramaniam and Mr. Ouyang Xuezhi at the TEM facility, Temasek Life Sciences
Laboratory, Singapore, for their technical support. 10. Wang RY, Li K. Host factors in the replication of positive-strand RNA viruses
Chang Gung Med J. 2012;35(2):111–24. Page 11 of 11 Page 11 of 11 Macharia et al. BMC Plant Biology (2019) 19:326 Macharia et al. BMC Plant Biology (2019) 19:326 11. Lieberthal W. Macroautophagy: a mechanism for mediating cell death or for
promoting cell survival? Kidney Int. 2008;74(5):555–7. 34. Lin MH, Liu YC, Liu SY, Chen FC, Yang PJ, Li GH, et al. Clathrin-mediated
endocytosis is required for ANE 30-100K-induced autophagy. J Oral Pathol
Med. 2018;47(1):25–31. 12. Fracchiolla D, Sawa-Makarska J, Martens S. Beyond Atg8 binding: the role of
AIM/LIR motifs in autophagy. Autophagy. 2017;13(5):978–9. 35. Lin P, Mobasher ME, Hakakian Y, Kakarla V, Naseem AF, Ziai H, et al. Differential requirements for H/ACA ribonucleoprotein components in cell
proliferation and response to DNA damage. Histochem Cell Biol. 2015;
144(6):543–58. 13. Zeenko VV, Ryabova LA, Spirin AS, Rothnie HM, Hess D, Browning KS, et al. Eukaryotic elongation factor 1A interacts with the upstream pseudoknot
domain in the 3′ untranslated region of Tobacco mosaic virus RNA. J Virol. 2002;76(11):5678–91. 36. Lenk SE, Susan PP, Hickson I, Jasionowski T, Dunn WA Jr. Ubiquitinated
aldolase B accumulates during starvation-induced lysosomal proteolysis. J
Cell Physiol. 1999;178(1):17–27. 14. Guo S, Kierzek E, Chen G, Zhou YJ, Wong SM. TMV mutants with
poly(a) tracts of different lengths demonstrate structural variations in
3'UTR affecting viral RNAs accumulation and symptom expression. Sci
Rep. 2015;5:18412. 37. Ishida H, Yoshimoto K. 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.
|
https://openalex.org/W4327941887
|
https://www.nature.com/articles/s41598-023-31318-z.pdf
|
English
| null |
Author Correction: Myxozoan infection in thinlip mullet Chelon ramada (Mugiliformes: Mugilidae) in the Sea of Galilee
|
Scientific reports
| 2,023
|
cc-by
| 1,745
|
www.nature.com/scientificreports www.nature.com/scientificreports In the Abstract, “These catadromous species do not reproduce in the lake, consequently, fingerlings have been introduced every
year since 1958. Following a survey of myxozoan infections in the Sea of Galilee, we described Myxobolus pup-
koi n. sp. infecting the gill arches, and reported Myxobolus exiguus from visceral peritoneum and gall bladder
of C. ramada. The prevalence of infection of both Myxobolus pupkoi n. sp. and M. exiguus were 11.5% (2/23). Our study indicates that the parasites infecting C. ramada belong to a lineage of myxozoans infecting mugilids” Aditya Gupta , Michal Haddas‑Sasson , Kfir Gayer & Dorothée Huchon Aditya Gupta , Michal Haddas‑Sasson , Kfir Gayer & Dorothée Huchon Correction to: Scientific Reports https://doi.org/10.1038/s41598-022-13215-z, published online 16 June 202 The original version of this Article contained errors. Illumina sequencing of the DNA extract of Myxobolus pupkoi led us to discover that the host of this species is
not Chelon ramada, but rather C. labrosus. The morphological identification error stemmed from the fact that C. labrosus is extremely rare in the Sea of Galilee, and thus its identification was overlooked. We only sequenced
the COI gene of a single fish specimen among the 23 fish sampled to confirm the morphological identification. Unlike C. ramada, C. labrosus was never voluntarily introduced to the Sea of Galilee, but rather was a hitchhiker
introduced together with C. ramada1. In absence of reproduction in the lake, its population size is very small1. We assembled the complete mitochondrial genome of C. labrosus from the Illumina data obtained from the
sequencing of the M. pupkoi sample (deposited under accession OX417109). We also confirmed using PCR
amplifications that the fish host of M. exiguus studied in our work is C. ramada (deposited under accessions
OX417110-1). This misidentification that we here correct does not affect the main conclusions of our manuscript. Like C. ramada, C. labrosus is an alien species and its infection took place in the Mediterranean Sea, where the fingerlings
were caught. Additionally, the differences in spore morphology between M. pupkoi and other Myxobolus parasites
of the genus Chelon warrant the description of a new species. The authors apologize for the misidentification
and any confusion caused. Corresponding text modifications are indicated below. In the Abstract, Figure 3. Phylogenetic relationships within the mugiliform-infecting lineage inferred from 18S rRNA
sequences under the ML criterion (TVM + F + R3 model). The new sequences of M. exiguus (OL604467 and
OM065835) and M. pupkoi (OL605966) are indicated in bold and with a yellow background. Branch supports
(i.e. ML bootstrap percentages [BP] above 50/posterior probabilities [PP] above 0.5) are indicated near the
corresponding nodes. Maximal support values (BP = 100/PP = 1.0) are indicated by an asterisk. A dash indicates
BP < 50 or PP < 0.5. The sequences identified as M. muelleri in NCBI, but recognized to be M. exiguus10,43, are
indicated within brackets. should read: “These catadromous species do not reproduce in the lake, consequently, fingerlings have been introduced every
year since 1958. Few additional mugilid species have been introduced unintentionally together with these two
species, including C. labrosus. Following a survey of myxozoan infections in the Sea of Galilee, we described
Myxobolus pupkoi n. sp. infecting the gill arches of C. labrosus, and reported Myxobolus exiguus from visceral
peritoneum and gall bladder of C. ramada. Our study indicates that the parasites infecting C. ramada and C. labrosus belong to a lineage of myxozoans infecting mugilids.” In the Results section, under the subheading ‘Myxobolus exiguus Thélohan, 1895 from the Sea of Galilee’, | https://doi.org/10.1038/s41598-023-31318-z Scientific Reports | (2023) 13:4565 www.nature.com/scientificreports/ Figure 3. Phylogenetic relationships within the mugiliform-infecting lineage inferred from 18S rRNA
sequences under the ML criterion (TVM + F + R3 model). The new sequences of M. exiguus (OL604467 and
OM065835) and M. pupkoi (OL605966) are indicated in bold and with a yellow background. Branch supports
(i.e. ML bootstrap percentages [BP] above 50/posterior probabilities [PP] above 0.5) are indicated near the
corresponding nodes. Maximal support values (BP = 100/PP = 1.0) are indicated by an asterisk. A dash indicates
BP < 50 or PP < 0.5. The sequences identified as M. muelleri in NCBI, but recognized to be M. exiguus10,43, are
indicated within brackets. www.nature.com/scientificreports/ www.nature.com/scientificreports/ Table 2. Comparative description of Myxobolus pupkoi n. sp. with myxobolid species infecting Chelon ramada
(measurements in micrometer). Species
Host
Site of infection
Locality
Myxospores
Polar capsule
No. of coils
Parietal folds
LS/WS ratio
Myxobolus pupkoi
n. sp. (present
study)
Chelon ramada
Gill arch
Sea of Galilee,
Israel
5.84 ± 0.13 × 5.41 ± 0.09
2.44 ± 0.20 × 1.34 ± 0.19
4–5
Present
1.07
M. exiguus (pre-
sent study)
C. ramada
Gall bladder
Sea of Galilee,
Israel
7.80 ± 0.35 × 6.60 ± 0.24
3.79 ± 0.13 × 2.54 ± 0.07
3–4
Absent
1.18
M. exiguus (pre-
sent study)
C. ramada
Visceral perito-
neum
Sea of Galilee,
Israel
6.63 ± 0.25 × 6.01 ± 0.30
3.41 ± 0.19 × 2.16 ± 0.10
3–4
Absent
1.10
M. adeli8
C. auratus
Digestive tract,
swim bladder, gills,
muscle
Mediterranean Sea
off Spain, Azov
and Black Sea
6.2 ± 0.3 × 7.2 ± 0.3
3.1 ± 0.3 × 1.8 ± 0.2
4
Absent
0.86
M. adiposus10
C. ramada
Adipose tissue
River Minho,
Portugal
9.1 ± 0.3 × 9.0 ± 0.3
4.6 ± 0.3 × 3.0 ± 0.3
6–7
Present
1.01
M. cerveirensis10
C. ramada
Intestine
River Minho,
Portugal
8.1 ± 0.2 × 6.8 ± 0.2
4.2 ± 0.2 × 2.8 ± 0.2
4–5
Present
1.19
M. episquamalis18
C. ramada, M. cephalus
Scales
Off Japan, Egypt
8.6 ± 0.2 × 6.8 ± 0.1
4.4 × 2.2
–
Present
1.26
M. exiguus15
C. ramada, pos-
sibly also in C. auratus, C. saliens,
C. labrosus and M. cephalus
Visceral perito-
neum
France, Tunisia,
Portugal
9.3 ± 0.6 × 8.2 ± 0.5
4.8 ± 0.2 × 2.8 ± 0.3
5
Absent
1.13
M. hepatobiliaris10
C. ramada
Liver and gall
bladder
River Minho,
Portugal
6.6 ± 0.3 × 5.20.3
3.0 ± 0.2 × 1.7 ± 0.2
4
Present
1.27
M. labrosus10
C. labrosus
Urinary bladder
River Minho,
Portugal
10 ± 0.2 × 8.1 ± 0.3
4.5 ± 0.2 × 2.5 ± 0.2
5–7
Present
1.23
M. mugauratus19
C. auratus
Abdominal serosa
Black Sea off
Ukraine
6.5 × 5.0
4.0 × 3.0
–
Absent
1.3
M. mugchelo23
C. ramada, C. labrosus
Gills or mesentery
Off Italy
6.06 ± 0.4 × 3.48 ± 0.9
2.19 ± 0.5 × 1.59 ± 0.3
5–6
Absent
1.74
M. muscularis10
C. should read: Because of fish misidentification the prevalence of infection cannot be computed. Because of fish misidentification the prevalence of infection cannot be computed. In the Results section, under subheading ‘Myxobolus pupkoi n. sp.’, “Type host: Chelon ramada (Risso, 1827), vern. thinlip mullet, Family: Mugilidae.”
should read: “Type host: Chelon ramada (Risso, 1827), vern. thinlip mullet, Family: Mugilidae.”
should read: https://doi.org/10.1038/s41598-023-31318-z Scientific Reports | (2023) 13:4565 | “Myxobolus pupkoi n. sp. parasite of the gill arch of Chelon labrosus.” Finally, the original Figure 3 and Table 2 showing the incorrect host name appear below as Figure 3 and Table 2,
respectively. The original Article has been corrected. Reference
1. Golani, D. & Mires, D. Introduction of fishes to the freshwater system of Israel. Isr. J. Aquac. Bamidgeh 52, 47–60 (2000) © The Author(s) 2023 www.nature.com/scientificreports/ ramada
Skeletal and heart
muscle
River Minho,
Portugal
9.1 ± 0.6 × 7.0 ± 0.6
4.3 ± 0.3 × 2.7 ± 0.2
5–6
Present
1.3
M. parsi21
C. parsia
Gills
India
9.1 × 8.1
4.4 × 2.8
5
Present
1.12
M. parenzani16
C. labrosus
Gills
Off Italy
5.4 × 5.4
~ 2
–
–
1.0
M. parvus13
M. cephalus, C. auratus, C. saliens,
P. haematocheila
Gills, kidney, liver,
mesentery, gall
bladder, intestine,
lower jaw
China, Ukraine,
Black Sea, Indian
Ocean
6.5–7.0 × 5.5–6.0
3.8–4.2 × 2.0
6–7
–
1.17
M. peritonaeum10
C. labrosus
Visceral perito-
neum
River Minho,
Portugal
8.1 ± 0.2 × 7.1 ± 0.2
3.8 ± 0.2 × 2.4 ± 0.2
4–5
Present
1.14
M. pharyngob-
ranchialis10
C. ramada
Pharyngobranchial
organ
River Minho,
Portugal
9.3 ± 0.4 × 7.7 ± 0.4
4.7 ± 0.3 × 2.9 ± 0.2
6–7
Present
1.20
M. ramadus10
C. ramada
Gill lamellae
River Minho,
Portugal
8.2 ± 0.5 × 7.9 ± 0.2
4.2 ± 0.2 × 3.0 ± 0.2
5–6
Absent
1.03
M. renalis10
C. ramada
Kidney
River Minho,
Portugal
6.7 ± 0.2 × 5.8 ± 0.2
3.1 ± 0.2 × 1.9 ± 0.2
4
Present
1.15 Table 2. Comparative description of Myxobolus pupkoi n. sp. with myxobolid species infecting Chelon ramada
(measurements in micrometer). “Type host: Chelon labrosus (Risso, 1827), vern. thicklip grey mullet, Family: Mugilidae.”
“Prevalence of infection: 11.5% (02/23).” Because of fish misidentification the prevalence of infection cannot be computed. “M. pupkoi n. sp. and M. parenzani infect different hosts: C. ramada and C. labrosus, respectively.”
should read: “M. pupkoi n. sp. and M. parenzani infect different hosts: C. ramada and C. labrosus, respectively.”
should read: “Although M. pupkoi n. sp. and M. parenzani infect the same host the morphological differences mentioned
above justify the definition of a novel species.” Although M. pupkoi n. sp. and M. parenzani infect the same host the morphological differences mentioned
bove justify the definition of a novel species.” Scientific Reports | (2023) 13:4565 | https://doi.org/10.1038/s41598-023-31318-z www.nature.com/scientificreports/ www.nature.com/scientificreports/ “Myxobolus pupkoi n. sp. parasite of the gill arch of Chelon ramada.”
should read: “Myxobolus pupkoi n. sp. parasite of the gill arch of Chelon ramada.” “Myxobolus pupkoi n. sp. parasite of the gill arch of Chelon labrosus.” Reference
l Reference
1. Golani, D. & Mires, D. Introduction of fishes to the freshwater system of Israel. Isr. J. Aquac. Bamidgeh 52, 47–60 (2000). 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/. https://doi.org/10.1038/s41598-023-31318-z Scientific Reports | (2023) 13:4565 |
|
https://openalex.org/W2947063958
|
https://peerj.com/articles/6946v0.3/submission
|
English
| null |
Peer Review #1 of "Gene expression in Tribolium castaneum life stages: Identifying a species-specific target for pest control applications (v0.1)"
| null | 2,019
|
cc-by
| 17,838
|
Manuscript to be reviewed Gene expression in Tribolium castaneum life stages:
Identifying a species-specific target for pest control
applications Lindsey C Perkin
Corresp., 1 , Brenda Oppert
2 Lindsey C Perkin
Corresp., 1 , Brenda Oppert
2 1 Southern Plains Agricultural Research Center, USDA, Agricultural Research Service, College Station, TX, United States
2 Center for Grain and Animal Health Research, USDA, Agricultural Research Service, Manhattan, KS, United States
Corresponding Author: Lindsey C Perkin
Email address: lindsey.perkin@ars.usda.gov 1 Southern Plains Agricultural Research Center, USDA, Agricultural Research Service, College Station, TX, United States
2 Center for Grain and Animal Health Research, USDA, Agricultural Research Service, Manhattan, KS, United States
Corresponding Author: Lindsey C Perkin
Email address: lindsey.perkin@ars.usda.gov The red flour beetle, Tribolium castaneum, is a major agricultural pest of post-harvest
products and stored grain. Control of T. castaneum in stored products and grain is
primarily by fumigants and sprays, but insecticide resistance is a major problem, and new
control strategies are needed. T. castaneum is a genetic model for coleopterans, and the
reference genome can be used for discovery of candidate gene targets for molecular-
based control, such as RNA interference. Gene targets need to be pest specific, and
ideally, they are expressed at low levels for successful control. Therefore, we sequenced
the transcriptome of four major life stages of T. castaneum, sorted data into groups based
on high or low expression levels, and compared relative gene expression among all life
stages. We narrowed our candidate gene list to a cuticle protein gene (CPG) for further
analysis. We found that the CPG sequence was unique to T. castaneum and expressed only
in the larval stage. RNA interference targeting CPG in newly-emerged larvae caused a
significant (p<0.05) decrease in CPG expression (1,491-fold) compared to control larvae
and 64% mortality over 18 d. RNA-Seq of survivors after 18 d identified changes in the
expression of other genes as well, including 52 long noncoding RNAs. Expression of three
additional cuticle protein genes were increased and two chitinase genes were decreased in
response to injection of CPG dsRNA. The data demonstrate that RNA-Seq can identify
genes important for insect survival and thus may be used to develop novel biologically-
based insect control products. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Manuscript to be reviewed 1
Gene expression in Tribolium castaneum life stages: Identifying a species-specific target for
2
pest control applications
3
4
Lindsey C. Perkin§, and Brenda Oppert
5
6
USDA, Agricultural Research Service, Southern Plains Agricultural Research Center, 2881 F&B
7
Road, College Station, TX 77845
8
USDA, Agricultural Research Service, Center for Grain and Animal Health Research, 1515
9
College Avenue, Manhattan, KS 66502
10
11
12
Running title: Tribolium castaneum life stage gene expression
13
14
§Corresponding author
15
Email addresses:
16
LCP: lindsey.perkin@ars.usda.gov
17
BO: brenda.oppert@ars.usda.gov
18 18 PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) 40
Introduction 40
Introduction
41
The red flour beetle, Tribolium castaneum, is a pest of stored grain commodities. Traditional
42
control methods for T. castaneum and other stored product beetles are rapidly becoming less
43
effective, mostly because insect populations are developing resistance to pesticide treatments
44
(Boyer et al. 2012). For example, storage pests around the globe are developing high resistance
45
levels to one of the most common grain fumigants, phosphine (Opit et al., 2012; Pimentel et al.,
46
2010). Thus, there is a need for new pest control strategies, and we are evaluating genetic-based
47
treatments with target specificity and less damage to the environment, including the application
48
of RNA interference (RNAi; Baum et al., 2007; Noh et al., 2012). 49
50
T. castaneum is a useful model to identify candidate genes because it has a sequenced genome
51
(Tribolium Genome Sequencing Consortium, 2008) and responds well to RNAi when dsRNA is
52
injected (RNAi; Brown et al., 1999; Tomoyasu & Denell, 2004; Aronstein et al., 2011; Miller et
53
al., 2012). Oral RNAi was successful in T. castaneum larvae against genes encoding vATPase
54
(Whyard et al., 2009), inhibitor of apoptosis (Cao et al., 2018), and a voltage-gated sodium ion
55
channel (Haim et al., 2016). However, we and others have not had success with oral RNAi in T. 56
castaneum (unpublished data, Palli, 2014). Many factors may influence RNAi efficacy in
57
insects, such as target sequence specificity, concentration and length of dsRNA, persistence of
58
silencing effect in the target pest, and nucleases counteracting the effect of dsRNA (Huvenne &
59
Smagghe 2010; Allen & Walker, 2012; Lomate & Bonning, 2016; Guan et al., 2018, Cao et al.,
60
2018). In the meantime, we have focused on the identification of gene targets with low
61
expression requiring lower doses of dsRNA, and those that are expressed in critical feeding
62
stages (larvae and adults) to improve the efficacy of oral RNAi. 41
The red flour beetle, Tribolium castaneum, is a pest of stored grain commodities. Traditional
42
control methods for T. castaneum and other stored product beetles are rapidly becoming less
43
effective, mostly because insect populations are developing resistance to pesticide treatments
44
(Boyer et al. 2012). PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) 19
Abstract 19
Abstract
20
The red flour beetle, Tribolium castaneum, is a major agricultural pest of post-harvest products
21
and stored grain. Control of T. castaneum in stored products and grain is primarily by fumigants
22
and sprays, but insecticide resistance is a major problem, and new control strategies are needed. 23
T. castaneum is a genetic model for coleopterans, and the reference genome can be used for
24
discovery of candidate gene targets for molecular-based control, such as RNA interference. 25
Gene targets need to be pest specific, and ideally, they are expressed at low levels for successful
26
control. Therefore, we sequenced the transcriptome of four major life stages of T. castaneum,
27
sorted data into groups based on high or low expression levels, and compared relative gene
28
expression among all life stages. We narrowed our candidate gene list to a cuticle protein gene
29
(CPG) for further analysis. We found that the CPG sequence was unique to T. castaneum and
30
expressed only in the larval stage. RNA interference targeting CPG in newly-emerged larvae
31
caused a significant (p<0.05) decrease in CPG expression (1,491-fold) compared to control
32
larvae and 64% mortality over 18 d. RNA-Seq of survivors after 18 d identified changes in the
33
expression of other genes as well, including 52 long noncoding RNAs. Injection of CPG dsRNA
34
also resulted in increased expression of three additional cuticle protein genes and reduced
35
expression of two chitinase genes in T. castaneum larvae. The data demonstrate that RNA-Seq
36
can identify genes important for insect survival and thus may be used to develop novel
37
biologically-based insect control products. 39 PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) 40
Introduction For example, storage pests around the globe are developing high resistance
45
levels to one of the most common grain fumigants, phosphine (Opit et al., 2012; Pimentel et al.,
46
2010). Thus, there is a need for new pest control strategies, and we are evaluating genetic-based
47
treatments with target specificity and less damage to the environment, including the application
48
of RNA interference (RNAi; Baum et al., 2007; Noh et al., 2012). 41
The red flour beetle, Tribolium castaneum, is a pest of stored grain commodities. Traditional
42
control methods for T. castaneum and other stored product beetles are rapidly becoming less
43
effective, mostly because insect populations are developing resistance to pesticide treatments
44
(Boyer et al. 2012). For example, storage pests around the globe are developing high resistance
45
levels to one of the most common grain fumigants, phosphine (Opit et al., 2012; Pimentel et al.,
46
2010). Thus, there is a need for new pest control strategies, and we are evaluating genetic-based
47
treatments with target specificity and less damage to the environment, including the application
48
of RNA interference (RNAi; Baum et al., 2007; Noh et al., 2012). 50
T. castaneum is a useful model to identify candidate genes because it has a sequenced genome
51
(Tribolium Genome Sequencing Consortium, 2008) and responds well to RNAi when dsRNA is
52
injected (RNAi; Brown et al., 1999; Tomoyasu & Denell, 2004; Aronstein et al., 2011; Miller et
53
al., 2012). Oral RNAi was successful in T. castaneum larvae against genes encoding vATPase
54
(Whyard et al., 2009), inhibitor of apoptosis (Cao et al., 2018), and a voltage-gated sodium ion
55
channel (Haim et al., 2016). However, we and others have not had success with oral RNAi in T. 56
castaneum (unpublished data, Palli, 2014). Many factors may influence RNAi efficacy in
57
insects, such as target sequence specificity, concentration and length of dsRNA, persistence of
58
silencing effect in the target pest, and nucleases counteracting the effect of dsRNA (Huvenne &
59
Smagghe 2010; Allen & Walker, 2012; Lomate & Bonning, 2016; Guan et al., 2018, Cao et al.,
60
2018). In the meantime, we have focused on the identification of gene targets with low
61
expression requiring lower doses of dsRNA, and those that are expressed in critical feeding
62
stages (larvae and adults) to improve the efficacy of oral RNAi. Manuscript to be reviewed 63
64
The iBeetle project (http://ibeetle-base.uni-goettingen.de) conducted a large-scale RNAi screen
65
in T. castaneum larvae and pupae with injected dsRNA, and various phenotypes were observed,
66
including mortality and developmental abnormalities (Schmitt-Engel et al., 2015). From this
67
screen, eleven genes were identified as potential pest control targets (Donitz et al., 2015; Ulrich
68
et al., 2015). These genes encode mostly products with GO terms related to the proteasome, and
69
mortality was observed after injection of larvae, pupae and adults. Some of these genes have
70
orthologs in other species, such as Drosophila melanogaster, Aedes aegypti, Apis mellifera, and
71
Acyrthosiphon pisum, and therefore RNAi or other molecular strategies based on these genes
72
may not be species-specific and may not be practical for insect control. Knorr et al. (2018)
73
selected 50 genes from the iBeetle study that resulted in 90% mortality to evaluate for RNAi in
74
Diabrotica vigifera vigifera and found that feeding adults dsRNA targeting 20 genes resulted in
75
mortality, and 36 retarded growth. While this work is important to highlight genes that have
76
application across species, the usefulness in the field may be limited due to off-target effects. 77
78
Previously, we applied RNA-Seq to the major developmental stages of T. castaneum to identify 63
64
The iBeetle project (http://ibeetle-base.uni-goettingen.de) conducted a large-scale RNAi screen
65
in T. castaneum larvae and pupae with injected dsRNA, and various phenotypes were observed,
66
including mortality and developmental abnormalities (Schmitt-Engel et al., 2015). From this
67
screen, eleven genes were identified as potential pest control targets (Donitz et al., 2015; Ulrich
68
et al., 2015). These genes encode mostly products with GO terms related to the proteasome, and
69
mortality was observed after injection of larvae, pupae and adults. Some of these genes have
70
orthologs in other species, such as Drosophila melanogaster, Aedes aegypti, Apis mellifera, and
71
Acyrthosiphon pisum, and therefore RNAi or other molecular strategies based on these genes
72
may not be species-specific and may not be practical for insect control. Knorr et al. (2018)
73
selected 50 genes from the iBeetle study that resulted in 90% mortality to evaluate for RNAi in
74
Diabrotica vigifera vigifera and found that feeding adults dsRNA targeting 20 genes resulted in
75
mortality, and 36 retarded growth. 40
Introduction PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Manuscript to be reviewed While this work is important to highlight genes that have
76
application across species, the usefulness in the field may be limited due to off-target effects. 77
78
Previously, we applied RNA-Seq to the major developmental stages of T. castaneum to identify
79
highly expressed cysteine peptidase genes in feeding stages (larvae and adults) with likely
80
digestive functions (Perkin et al., 2016). A similar approach was used across the life stages of D. 81
melanogaster to reveal new transcribed regions and small non-coding RNAs, demonstrating that
82
transcriptome sequencing can discover new elements and help to annotate genomes of even the
83
most well studied insects (Graveley et al., 2011). Transcriptome sequencing of developmental
84
stages of the non-model oriental fruit fly, Bactocera dorsalis, and the harlequin bug, Murgantia 63 63
64
The iBeetle project (http://ibeetle-base.uni-goettingen.de) conducted a large-scale RNAi screen
65
in T. castaneum larvae and pupae with injected dsRNA, and various phenotypes were observed,
66
including mortality and developmental abnormalities (Schmitt-Engel et al., 2015). From this
67
screen, eleven genes were identified as potential pest control targets (Donitz et al., 2015; Ulrich
68
et al., 2015). These genes encode mostly products with GO terms related to the proteasome, and
69
mortality was observed after injection of larvae, pupae and adults. Some of these genes have
70
orthologs in other species, such as Drosophila melanogaster, Aedes aegypti, Apis mellifera, and
71
Acyrthosiphon pisum, and therefore RNAi or other molecular strategies based on these genes
72
may not be species-specific and may not be practical for insect control. Knorr et al. (2018)
73
selected 50 genes from the iBeetle study that resulted in 90% mortality to evaluate for RNAi in
74
Diabrotica vigifera vigifera and found that feeding adults dsRNA targeting 20 genes resulted in
75
mortality, and 36 retarded growth. While this work is important to highlight genes that have
76
application across species, the usefulness in the field may be limited due to off-target effects. 77 PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 85
histrionica, led to a list of candidate developmental and insecticide resistance genes for
86
downstream studies (Shen et al., 2011; Sparks et al., 2017). 87
88
In the present study, we examined gene expression patterns in T. castaneum life stages (adults,
89
eggs, larvae, and pupae), and used statistical analysis to sort expression patterns into groups of
90
low and high expression. Our hypothesis was that genes with low expression can be more
91
successfully targeted with RNAi or other applied control methods because the dose of dsRNA
92
required to knockdown transcript expression will be lower, and highly expressed genes and gene
93
expression patterns may be useful in understanding the physiology of the insect, or to identify
94
promoters for transgenic applications. Previously, we found that some genes with high
95
expression (i.e. those encoding cysteine peptidases) were important to insect physiology and
96
were duplicated in the genome, and complete knockdown of these genes induced a compensation
97
response and upregulation of other closely related genes (Perkin et al., 2016). Through screening
98
of potential targets in the present study, we identified a unique cuticle protein gene (CPG)
99
expressed in larvae, and we provide functional evidence for its potential as a molecular target for
100
pest control. We further evaluated the effect of CPG RNAi on the expression of other genes,
101
defining new potential metabolic connections between CPG and other genes. 102 85
histrionica, led to a list of candidate developmental and insecticide resistance genes for
86
downstream studies (Shen et al., 2011; Sparks et al., 2017). 85
histrionica, led to a list of candidate developmental and insecticide resistance genes for
86
downstream studies (Shen et al., 2011; Sparks et al., 2017). 87
88
In the present study, we examined gene expression patterns in T. castaneum life stages (adults,
89
eggs, larvae, and pupae), and used statistical analysis to sort expression patterns into groups of
90
low and high expression. Our hypothesis was that genes with low expression can be more
91
successfully targeted with RNAi or other applied control methods because the dose of dsRNA
92
required to knockdown transcript expression will be lower, and highly expressed genes and gene
93
expression patterns may be useful in understanding the physiology of the insect, or to identify
94
promoters for transgenic applications. Previously, we found that some genes with high
95
expression (i.e. Manuscript to be reviewed those encoding cysteine peptidases) were important to insect physiology and
96
were duplicated in the genome, and complete knockdown of these genes induced a compensation
97
response and upregulation of other closely related genes (Perkin et al., 2016). Through screening
98
of potential targets in the present study, we identified a unique cuticle protein gene (CPG)
99
expressed in larvae, and we provide functional evidence for its potential as a molecular target for
100
pest control. We further evaluated the effect of CPG RNAi on the expression of other genes,
101
defining new potential metabolic connections between CPG and other genes. 102
103
Materials & Methods
104
Insects
105
Insect strains and collection protocols were as previously described (Perkin et al., 2016). 106
Briefly, the T. castaneum lab colony used in this study was originally collected from a grain bin
107
in Kansas and has been maintained on 95% wheat flour and 5% brewer’s yeast at 28C, 75% 01
defining new potential metabolic connections between CPG and other genes. Manuscript to be reviewed 108
R.H., 0L:24D. Insects were subcultured from the laboratory colony, and specific life stages were
109
removed. Adults were collected at 3-7 days post-eclosion and were mixed sex. Eggs were sifted
110
from diet 24-48 hours after oviposition and were separated from the fine particulate with a brush. 111
Larvae were collected at a late instar stage that was actively feeding (approximately 14 days post
112
hatch). Pupae included those with pigmentation in the eye, but not the elytra. 113
114
Library preparation and RNA sequencing of life stages
115
RNA was collected as three independent biological replicates from mixed sex groups of each life
116
stage (10 adults, approximately 500 eggs, 10 larvae, and 10 pupae per replicate). Tissue was
117
pulverized in TRIZOL (BulletBlender, Next Advance Inc., Averill Park, NY, USA) at speed 8
118
for 2 min with RNAse-free ziroconium oxide beads. RNA extraction and purification were with
119
a Zymo mini prep kit (Irvine, CA, USA). From the total RNA, DIRECTbeads (Agilient, Santa
120
Clara, CA, USA) were used to isolate polyA mRNA, and libraries were made with a 200 bp
121
RNA-Seq v2 kit (Life Technologies, Grand Island, NY, USA). Samples were sequenced on
122
318v2 chips on the Ion Torrent Personal Genome Machine (PGM, Life Technologies). Each run
123
provided approximately 1-5 million reads, with a total of 5-12 million reads per life stage (Perkin
124
et al., 2016). Life stage sequences were deposited at NCBI SRA as part of BioProject
125
PRJNA299695. 126
127
Data analysis 108
R.H., 0L:24D. Insects were subcultured from the laboratory colony, and specific life stages were
109
removed. Adults were collected at 3-7 days post-eclosion and were mixed sex. Eggs were sifted
110
from diet 24-48 hours after oviposition and were separated from the fine particulate with a brush. 111
Larvae were collected at a late instar stage that was actively feeding (approximately 14 days post
112
hatch). Pupae included those with pigmentation in the eye, but not the elytra. 112
hatch). Pupae included those with pigmentation in the eye, but not the elytra. 113
114
Library preparation and RNA sequencing of life stages
115
RNA was collected as three independent biological replicates from mixed sex groups of each life
116
stage (10 adults, approximately 500 eggs, 10 larvae, and 10 pupae per replicate). Manuscript to be reviewed Tissue was
117
pulverized in TRIZOL (BulletBlender, Next Advance Inc., Averill Park, NY, USA) at speed 8
118
for 2 min with RNAse-free ziroconium oxide beads. RNA extraction and purification were with
119
a Zymo mini prep kit (Irvine, CA, USA). From the total RNA, DIRECTbeads (Agilient, Santa
120
Clara, CA, USA) were used to isolate polyA mRNA, and libraries were made with a 200 bp
121
RNA-Seq v2 kit (Life Technologies, Grand Island, NY, USA). Samples were sequenced on
122
318v2 chips on the Ion Torrent Personal Genome Machine (PGM, Life Technologies). Each run
123
provided approximately 1-5 million reads, with a total of 5-12 million reads per life stage (Perkin
124
et al., 2016). Life stage sequences were deposited at NCBI SRA as part of BioProject
125
PRJNA299695. 126
127
Data analysis
128
Relative gene expression was analyzed using ArrayStar (Lasergene Genomics Suite v14,
129
DNASTAR, Madison, WI, USA) by mapping reads to the NCBI Tcas5.2 genome build. Read
130
counts were normalized by Reads Per Kilobase of template per Million mapped reads (RPKM,
PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) 114
Library preparation and RNA sequencing of life stages 114
Library preparation and RNA sequencing of life stages
115
RNA was collected as three independent biological replicates from mixed sex groups of each life
116
stage (10 adults, approximately 500 eggs, 10 larvae, and 10 pupae per replicate). Tissue was
117
pulverized in TRIZOL (BulletBlender, Next Advance Inc., Averill Park, NY, USA) at speed 8
118
for 2 min with RNAse-free ziroconium oxide beads. RNA extraction and purification were with
119
a Zymo mini prep kit (Irvine, CA, USA). From the total RNA, DIRECTbeads (Agilient, Santa
120
Clara, CA, USA) were used to isolate polyA mRNA, and libraries were made with a 200 bp
121
RNA-Seq v2 kit (Life Technologies, Grand Island, NY, USA). Samples were sequenced on
122
318v2 chips on the Ion Torrent Personal Genome Machine (PGM, Life Technologies). Each run
123
provided approximately 1-5 million reads, with a total of 5-12 million reads per life stage (Perkin
124
et al., 2016). Life stage sequences were deposited at NCBI SRA as part of BioProject
125
PRJNA299695. 129
DNASTAR, Madison, WI, USA) by mapping reads to the NCBI Tcas5.2 genome build. Read
130
counts were normalized by Reads Per Kilobase of template per Million mapped reads (RPKM, PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 131
Mortazavi et al., 2008). All data were filtered to groups with low expression (RPKM greater
132
than 2 less than 8 log2; i.e., the log2 of the RPKM value was between 2 and 8, not inclusive) and
133
high expression (RPKM greater than 8 log2) for comparisons and biological screening. We use a
134
cutoff of RPKM greater than 2 to avoid underrepresented genes that can skew data. 135
136
Gene ontology (GO) terms were obtained and enrichment of GO terms was analyzed in
137
BLAST2GO PRO (version 4.1.5, Valencia, Spain, Götz et al., 2008). Over-representation tests
138
were performed with GO terms associated with genes in low and high categories in each life
139
stage, using the program g:Profiler and the g:GOSt function, which provides statistical
140
enrichment analysis (http://biit.cs.ut.ee/gprofiler/index.cgi; (Reimand et al., 2011). In g:Profiler,
141
results were limited to T. castaneum and the main GO categories: biological process (BP),
142
molecular function (MF) and cellular component (CC). Significance was determined using the
143
False Discovery Rate (FDR) multiple-testing correction threshold of 0.05 (Benjamini and
144
Hochberg 1995). Enriched GO terms also were obtained from the pairwise comparison of gene
145
expression in larvae injected with cuticle protein gene (CPG, LOC103313766) dsRNA compared
146
to mock-injected, where the test set was the significant (p<0.05) differentially expressed genes,
147
and the reference set was expression from all genes. GO terms were limited to p<0.05 (after
148
FDR correction) and collapsed to the most specific description of each term. 149
150
Candidate gene selection
151
Genes were first filtered to only include those with expression levels between RPKM 2 and 8 131
Mortazavi et al., 2008). All data were filtered to groups with low expression (RPKM greater
132
than 2 less than 8 log2; i.e., the log2 of the RPKM value was between 2 and 8, not inclusive) and
133
high expression (RPKM greater than 8 log2) for comparisons and biological screening. We use a
134
cutoff of RPKM greater than 2 to avoid underrepresented genes that can skew data. 151
Genes were first filtered to only include those with expression levels between RPKM 2 and 8
152
(log2). The resulting gene list included 181 genes. We then filtered to only include genes
153
expressed at low levels in larvae because a field application would rely on genes expressed PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 154
during the most active feeding stage, reducing the list to 139 genes. Our next filter was a
155
manually curated gene set and was based on GO analysis and gene annotations, selecting genes
156
with a function potentially necessary for survival. 157
158
The final filter submitted potential genes to the program OfftargetFinder (Good et al., 2016). 159
This program checks gene specificity by searching 101 arthropod transcriptomes, 21mers at a
160
time, to the 1000 Insect Transcriptome Evolution (1KITE) dataset (http://www.1kite.org) and is
161
specifically designed to identify potential problems in designing dsRNA for insect control. The
162
algorithm provides visualization of specific regions of the target gene that may cause off-target
163
effects and allows for dsRNA to be designed to regions with increased specificity to the target
164
pest. This filter limited our gene list to only three genes. We selected CPG as our primary target
165
because the 3’ region of CPG was unique to T. castaneum, and this region was used to design
166
primers for dsRNA. 167
168
RNAi
169
Primers for dsRNA targeting CPG were designed similar to Perkin et al. (2017a) via Primer-
170
BLAST (http://www.ncbi.nlm.nih.gov/tools/primer-blast/) using default parameters, and primer
171
specificity was evaluated against the T. castaneum genome. A primary set of primers was
172
designed to amplify CPG, and secondary primers were designed to amplify the 3’ region to
173
minimize off-target effects.. 174
175
The primary set of primers (Forward: ATAATCAAGCCCGTTTCCAACA, Reverse:
176
AATCACGACTACAAACATTCTTAGG) amplified CPG in 25 l PCR reactions using 154
during the most active feeding stage, reducing the list to 139 genes. Our next filter was a
155
manually curated gene set and was based on GO analysis and gene annotations, selecting genes
156
with a function potentially necessary for survival. 157
158
The final filter submitted potential genes to the program OfftargetFinder (Good et al., 2016). 159
This program checks gene specificity by searching 101 arthropod transcriptomes, 21mers at a
160
time, to the 1000 Insect Transcriptome Evolution (1KITE) dataset (http://www.1kite.org) and is
161
specifically designed to identify potential problems in designing dsRNA for insect control. The
162
algorithm provides visualization of specific regions of the target gene that may cause off-target
163
effects and allows for dsRNA to be designed to regions with increased specificity to the target
164
pest. This filter limited our gene list to only three genes. Manuscript to be reviewed We selected CPG as our primary target
165
because the 3’ region of CPG was unique to T. castaneum, and this region was used to design
166
primers for dsRNA. 154
during the most active feeding stage, reducing the list to 139 genes. Our next filter was a
155
manually curated gene set and was based on GO analysis and gene annotations, selecting genes
156
with a function potentially necessary for survival. 154
during the most active feeding stage, reducing the list to 139 genes. Our next filter was a
155
manually curated gene set and was based on GO analysis and gene annotations, selecting genes
156
with a function potentially necessary for survival. 158
The final filter submitted potential genes to the program OfftargetFinder (Good et al., 2016). 159
This program checks gene specificity by searching 101 arthropod transcriptomes, 21mers at a
160
time, to the 1000 Insect Transcriptome Evolution (1KITE) dataset (http://www.1kite.org) and is
161
specifically designed to identify potential problems in designing dsRNA for insect control. The
162
algorithm provides visualization of specific regions of the target gene that may cause off-target
163
effects and allows for dsRNA to be designed to regions with increased specificity to the target
164
pest. This filter limited our gene list to only three genes. We selected CPG as our primary target
165
because the 3’ region of CPG was unique to T. castaneum, and this region was used to design
166
primers for dsRNA. 158
The final filter submitted potential genes to the program OfftargetFinder (Good et al., 2016). 159
This program checks gene specificity by searching 101 arthropod transcriptomes, 21mers at a
160
time, to the 1000 Insect Transcriptome Evolution (1KITE) dataset (http://www.1kite.org) and is
161
specifically designed to identify potential problems in designing dsRNA for insect control. The
162
algorithm provides visualization of specific regions of the target gene that may cause off-target
163
effects and allows for dsRNA to be designed to regions with increased specificity to the target
164
pest. This filter limited our gene list to only three genes. We selected CPG as our primary target
165
because the 3’ region of CPG was unique to T. castaneum, and this region was used to design
166
primers for dsRNA. 168
RNAi
169
Primers for dsRNA targeting CPG were designed similar to Perkin et al. Manuscript to be reviewed (2017a) via Primer-
170
BLAST (http://www.ncbi.nlm.nih.gov/tools/primer-blast/) using default parameters, and primer
171
specificity was evaluated against the T. castaneum genome. A primary set of primers was
172
designed to amplify CPG, and secondary primers were designed to amplify the 3’ region to
173
minimize off-target effects.. Manuscript to be reviewed 177
genomic DNA template from the lab strain (2.5 l 10X buffer, 2.0 l 2.5 mM dNTP, 0.5 l 10
178
M forward primer, 0.5 l 10 M reverse primer, 0.125 l JumpStart AccuTaq DNA
179
polymerase (Sigma-Aldrich, Saint Louis, MO, USA), 2 l genomic DNA, 17.375 l nuclease-
180
free water) and thermal cycle conditions as specified by the JumpStart AccuTaq DNA
181
polymerase product information guide (denaturation for 30 sec at 95C, 30 cycles of 95C for 30
182
sec, primer annealing at Tm 55.5C for 30 sec, and extension at 68C for 30 sec, final extension
183
at 68C for 5 min, and hold at 4C). The product was assessed on a 1% agarose E-gel
184
(ThermoFisher, Waltham, MA, USA) to ensure the amplified region was the correct size. 185
186
A second round of PCR was done with the secondary set of primers (Forward:
187
TATTCGTCTGTCGTCGCTCC, Reverse: AATCACGACTACAAACATTCTTAGG) for
188
specific targeting of CPG. The secondary PCR reaction was 100 l and the product from the
189
primary PCR reaction was used as the template (10 l 10X buffer, 8 l 2.5 mM dNTP, 2 l T7
190
forward primer, 2 l T7 reverse primer, 0.5 l JumpStart AccuTaq DNA polymerase, 10 l
191
primary PCR product, 67.5 l nuclease-free water). The thermal reaction profile was as follows:
192
denaturation for 30 sec at 95C, 5 cycles of 95C for 30 sec, primer Tm for 30 sec, 72C for 30
193
sec, 29 cycles of 95C for 30 sec, primer Tm plus 5C for 30 sec, and 72C for 30 sec, extension
194
for 5 min at 68C and hold at 4C. The secondary PCR primers had a T7 construct attached to
195
the 5’ end (TAATACGACTCACTATAGGG), and thus 5C was added to the second round of
196
amplification as suggested in the kit manual. The secondary PCR products were checked again
197
via 1% agarose E-gel for appropriate length (150 bp) and sufficient amplification. Manuscript to be reviewed 199
PCR products from the secondary amplification were used to make dsRNA via MEGAscript T7
200
kit (ThermoFisher) according to the kit protocol (8 l dNTP mix, 2 l 10X reaction buffer, 8 l
201
secondary PCR products with T7 construct, 2 l enzyme mix), and after a 6 h incubation period
202
at 37C with constant mixing, products were purified via MEGAclear kit (ThermoFisher). Size
203
and quantity were verified on a digital nanophotometer (Implen, Westlake Village, CA, USA)
204
and TapeStation (Agilent). 205
206
Micro-injected dsRNA
207
Immediately before injection, dsRNA solution was mixed with blue dye (1:20) to aid in
208
visualization of the injected liquid as in Perkin et al. (2017a). Larvae used in injections were
209
briefly put on ice, transferred to a microscope slide with double-sided tape for stabilization, and
210
the entire slide was placed on top of a small ice block. Thirty individuals were injected with 200
211
ng of dsRNA in triplicate. CPG-dsRNA was injected into larvae weighing approximately 1 mg. 212
Each treatment injection had a corresponding control injection of dye only (Mock) and a non-
213
injection control (Control). Injections were with a Drummond Nanoject (Drummond Scientific
214
Co., Broomall, PA, USA) set at 69 nl and fast injecting speed with a “bee-stinger” needle. 215
Needles were made with 3.5 Drummond glass capillary tubes (3-000-203-G) and a micropipette
216
puller (Sutter Instrument Co. Model P-97, Novato, CA, USA) using the program: heat 750, pull
217
100, velocity 8, time 250, and pressure 500. After injection, each group was allowed to recover
218
for 2 h at room temperature, and then were covered with diet (95% wheat flour, 5% brewer’s
219
yeast) and kept at 28C, 75% R.H., 0L:24D. All treatments and controls were followed for 18
220
days to monitor mortality and/or developmental abnormalities. 199
PCR products from the secondary amplification were used to make dsRNA via MEGAscript T7
200
kit (ThermoFisher) according to the kit protocol (8 l dNTP mix, 2 l 10X reaction buffer, 8 l
201
secondary PCR products with T7 construct, 2 l enzyme mix), and after a 6 h incubation period
202
at 37C with constant mixing, products were purified via MEGAclear kit (ThermoFisher). Size
203
and quantity were verified on a digital nanophotometer (Implen, Westlake Village, CA, USA)
204
and TapeStation (Agilent). Manuscript to be reviewed 198 177
genomic DNA template from the lab strain (2.5 l 10X buffer, 2.0 l 2.5 mM dNTP, 0.5 l 10
178
M forward primer, 0.5 l 10 M reverse primer, 0.125 l JumpStart AccuTaq DNA
179
polymerase (Sigma-Aldrich, Saint Louis, MO, USA), 2 l genomic DNA, 17.375 l nuclease-
180
free water) and thermal cycle conditions as specified by the JumpStart AccuTaq DNA
181
polymerase product information guide (denaturation for 30 sec at 95C, 30 cycles of 95C for 30
182
sec, primer annealing at Tm 55.5C for 30 sec, and extension at 68C for 30 sec, final extension
183
at 68C for 5 min, and hold at 4C). The product was assessed on a 1% agarose E-gel
184
(ThermoFisher, Waltham, MA, USA) to ensure the amplified region was the correct size. 185
186
A second round of PCR was done with the secondary set of primers (Forward:
187
TATTCGTCTGTCGTCGCTCC, Reverse: AATCACGACTACAAACATTCTTAGG) for 186
A second round of PCR was done with the secondary set of primers (Forward: 187
TATTCGTCTGTCGTCGCTCC, Reverse: AATCACGACTACAAACATTCTTAGG) for
188
specific targeting of CPG. The secondary PCR reaction was 100 l and the product from the
189
primary PCR reaction was used as the template (10 l 10X buffer, 8 l 2.5 mM dNTP, 2 l T7
190
forward primer, 2 l T7 reverse primer, 0.5 l JumpStart AccuTaq DNA polymerase, 10 l
191
primary PCR product, 67.5 l nuclease-free water). The thermal reaction profile was as follows:
192
denaturation for 30 sec at 95C, 5 cycles of 95C for 30 sec, primer Tm for 30 sec, 72C for 30
193
sec, 29 cycles of 95C for 30 sec, primer Tm plus 5C for 30 sec, and 72C for 30 sec, extension
194
for 5 min at 68C and hold at 4C. The secondary PCR primers had a T7 construct attached to
195
the 5’ end (TAATACGACTCACTATAGGG), and thus 5C was added to the second round of
196
amplification as suggested in the kit manual. The secondary PCR products were checked again
197
via 1% agarose E-gel for appropriate length (150 bp) and sufficient amplification. 198 PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 207
Immediately before injection, dsRNA solution was mixed with blue dye (1:20) to aid in
208
visualization of the injected liquid as in Perkin et al. (2017a). Larvae used in injections were
209
briefly put on ice, transferred to a microscope slide with double-sided tape for stabilization, and
210
the entire slide was placed on top of a small ice block. Thirty individuals were injected with 200
211
ng of dsRNA in triplicate. CPG-dsRNA was injected into larvae weighing approximately 1 mg. 212
Each treatment injection had a corresponding control injection of dye only (Mock) and a non-
213
injection control (Control). Injections were with a Drummond Nanoject (Drummond Scientific
214
Co., Broomall, PA, USA) set at 69 nl and fast injecting speed with a “bee-stinger” needle. 221 221 PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 222
Library preparation and RNA sequencing and data analysis after RNAi 223
We validated knockdown of CPG with RNA-Seq as previously (Perkin et al., 2017b). Eight
224
individuals from each treatment and control were flash frozen in liquid nitrogen on day 18 post
225
injection. Total RNA was extracted by Trizol (Thermo Fisher Scientific, Waltham, MA USA)
226
and Quick-RNA Mini Prep kit (Zymo Research, Irvine, CA USA). Libraries were made on the
227
NeoPrep (200 bp insert) and sequenced on a Mi-Seq (2x300, Illumina, San Diego, CA USA). 228
Three independent biological replicates of all groups and 3-4 technical replicates of CPG
229
dsRNA-injected larvae were sequenced (metrics are found in Supplemental File 5). Sequence
230
reads were deposited at NCBI SRA as PRJNA520884. 231
Arraystar (DNAStar, Madison, WI USA) was used to calculate RPKM and fold change between
232
treatment and control groups by mapping reads to the Tcas5.2 genome. We also used Arraystar
233
for statistical analysis, student t-tests between treatments and ANOVA among treatments. Genes
234
were filtered to only include those that had >8-fold difference between treatments, and
235
significant at p<0.01 after FDR correction. To classify ncRNA, sequences were submitted to
236
RNAcon (website: http://crdd.osdd.net/raghava/rnacon/submit.html) for prediction using SVM
237
scores (default of 0.0; Panwar et al., 2014). 238
239
Cuticle protein tree
240
NCBI RefseqRNA was searched with term “cuticle protein” and limited to T. castaneum, which
241
returned a list of 160 genes which we then manually curated to only include relevant genes with
242
a chitin domain (pfam00379). This resulted in a total of 125 sequences in the final data set. 243
Protein sequences from the selected genes were used as input in MEGA X (version 10.0.5;
244
Kumar et al., 2018). Protein sequences were aligned using ClustalW. The evolutionary history 231
Arraystar (DNAStar, Madison, WI USA) was used to calculate RPKM and fold change between
232
treatment and control groups by mapping reads to the Tcas5.2 genome. We also used Arraystar
233
for statistical analysis, student t-tests between treatments and ANOVA among treatments. Genes
234
were filtered to only include those that had >8-fold difference between treatments, and
235
significant at p<0.01 after FDR correction. To classify ncRNA, sequences were submitted to
236
RNAcon (website: http://crdd.osdd.net/raghava/rnacon/submit.html) for prediction using SVM
237
scores (default of 0.0; Panwar et al., 2014). Manuscript to be reviewed 231
Arraystar (DNAStar, Madison, WI USA) was used to calculate RPKM and fold change between
232
treatment and control groups by mapping reads to the Tcas5.2 genome. We also used Arraystar
233
for statistical analysis, student t-tests between treatments and ANOVA among treatments. Genes
234
were filtered to only include those that had >8-fold difference between treatments, and
235
significant at p<0.01 after FDR correction. To classify ncRNA, sequences were submitted to
236
RNAcon (website: http://crdd.osdd.net/raghava/rnacon/submit.html) for prediction using SVM
237
scores (default of 0.0; Panwar et al., 2014). PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 245
of cuticle proteins was inferred using the Maximum Likelihood method, JTT matrix-based
246
model, and 500 bootstrap iterations (Jones et al., 1992), using the tree with the highest log
247
likelihood. 248
249
Results
250
In the following sections, transcriptome datasets of gene expression in four developmental stages
251
of T. castaneum were analyzed by sorting genes into categories of high and low expression
252
levels. Gene Ontology (GO) terms were associated with each group, and overrepresented terms
253
were identified by enrichment analysis. A cuticle protein gene was selected as a gene expressed
254
at low levels only in larvae and was evaluated via RNAi as a gene with critical function for
255
insect survival. 256
257
Life stage expression analysis – genes expressed at high levels
258
Analysis of T. castaneum genes with high expression levels (RPKM >8, log2) in all life stages
259
indicated there were 101, 290, 238, and 54 genes uniquely expressed in adults, eggs, larvae, and
260
pupae, respectively (Fig. 1, Supplemental File 1). Eggs and larvae stages shared the most
261
commonly expressed genes (162), followed by adults and larvae (48), and adults and eggs (29). 262
Genes common to eggs and larvae included 44 ribosomal proteins (large and small subunits),
263
indicative of the high degree of protein production occurring in these stages. Adults and larvae
264
feeding stages shared two digestive cathepsin L genes (LOC659441 and LOC659502; Martynov
265
et al., 2015; Perkin et al., 2016) and two chitinase precursor genes (Cht8 and Cht11). Only
266
LOC663906 encoding a single-stranded DNA-binding protein was commonly expressed in eggs
267
and pupae. Twelve genes were highly expressed in all stages, including those encoding two
Manuscript to be reviewe PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 245
of cuticle proteins was inferred using the Maximum Likelihood method, JTT matrix-based
246
model, and 500 bootstrap iterations (Jones et al., 1992), using the tree with the highest log
247
likelihood. 245
of cuticle proteins was inferred using the Maximum Likelihood method, JTT matrix-based
246
model, and 500 bootstrap iterations (Jones et al., 1992), using the tree with the highest log
247
likelihood. 245
of cuticle proteins was inferred using the Maximum Likelihood method, JTT matrix-based
246
model, and 500 bootstrap iterations (Jones et al., 1992), using the tree with the highest log
247
likelihood. 257
Life stage expression analysis – genes expressed at high levels
258
Analysis of T. castaneum genes with high expression levels (RPKM >8, log2) in all life stages
259
indicated there were 101, 290, 238, and 54 genes uniquely expressed in adults, eggs, larvae, and
260
pupae, respectively (Fig. 1, Supplemental File 1). Eggs and larvae stages shared the most
261
commonly expressed genes (162), followed by adults and larvae (48), and adults and eggs (29). 262
Genes common to eggs and larvae included 44 ribosomal proteins (large and small subunits),
263
indicative of the high degree of protein production occurring in these stages. Adults and larvae
264
feeding stages shared two digestive cathepsin L genes (LOC659441 and LOC659502; Martynov
265
et al., 2015; Perkin et al., 2016) and two chitinase precursor genes (Cht8 and Cht11). Only
266
LOC663906 encoding a single-stranded DNA-binding protein was commonly expressed in eggs
267
and pupae. Twelve genes were highly expressed in all stages, including those encoding two PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Manuscript to be reviewed 268
elongation factors, three ribosomal proteins, a cathepsin L (26-29-p), glyceraldehyde-3-
269
phosphase dehydrogenase 2, NADH dehydrogenase subunit 2, ATP synthase, cytochrome c and
270
cytochrome b, and I-rRNA (Table 1). 271
272
In the highly-expressed gene group, the top Molecular Function (MF) GO terms for each life
273
stage varied, but adults and larvae had shared term “nucleotide binding”, whereas eggs and
274
larvae shared “hydrolase activity” (Fig. 2). “Oxidoreductase activity” was common to larvae,
275
pupae and adults. An enrichment analysis found 16 MF terms belonging to “structural
276
constituent of the ribosome” (p=1.07x10-11) and 62 with “catalytic activity” (p=0.028) enriched
277
only in adults. 278
279
We also examined the most highly expressed genes in each developmental stage. The top 10
280
most highly expressed genes in adults included those encoding an odorant binding protein,
281
protamine, and cytochrome c oxidase subunit II (RPKM 7,694-20,300), and the highest
282
expressed genes in eggs had similar function, including chemosensory protein 2, I-rRNA and
283
cytochrome c oxidase subunit I and II (RPKM 7,960-26,611; Supplemental File 1). These genes
284
also were highly expressed in larvae, along with cathepsin L genes involved in digestion of
285
cereal proteins (RPKM 13,248-43,202; Martynov et al., 2015; Perkin et al., 2016). Highly
286
expressed genes in pupae encoded two cuticular proteins and a conserved cathepsin L, 26-29-p
287
(RPKM 3,576-13,818). 288 268
elongation factors, three ribosomal proteins, a cathepsin L (26-29-p), glyceraldehyde-3-
269
phosphase dehydrogenase 2, NADH dehydrogenase subunit 2, ATP synthase, cytochrome c and
270
cytochrome b, and I-rRNA (Table 1). 268
elongation factors, three ribosomal proteins, a cathepsin L (26-29-p), glyceraldehyde-3-
269
phosphase dehydrogenase 2, NADH dehydrogenase subunit 2, ATP synthase, cytochrome c and
270
cytochrome b, and I-rRNA (Table 1). 278
279
We also examined the most highly expressed genes in each developmental stage. The top 10
280
most highly expressed genes in adults included those encoding an odorant binding protein,
281
protamine, and cytochrome c oxidase subunit II (RPKM 7,694-20,300), and the highest
282
expressed genes in eggs had similar function, including chemosensory protein 2, I-rRNA and
283
cytochrome c oxidase subunit I and II (RPKM 7,960-26,611; Supplemental File 1). These genes
284
also were highly expressed in larvae, along with cathepsin L genes involved in digestion of
285
cereal proteins (RPKM 13,248-43,202; Martynov et al., 2015; Perkin et al., 2016). Manuscript to be reviewed Highly
286
expressed genes in pupae encoded two cuticular proteins and a conserved cathepsin L, 26-29-p
287
(RPKM 3,576-13,818). 289
Life stage expression analysis – genes expressed at low levels PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 290
A comparison of genes with low expression levels (RPKM between 2-8 log2) revealed
291
expression of 273 genes unique to adults, 167 to eggs, 139 to larvae, and 14 to pupae (Fig. 3;
292
Supplemental File 2). Adults and larvae shared 138 genes including chitin deacetylase 7 (Cda7)
293
and two chitinase precursors (Cht4 and Cht9). Larvae and pupae shared a single gene,
294
LOC664054 encoding pathogenesis-related protein 5, which also was expressed in adults but at
295
higher levels and thus was not part of the low expression group. Nine genes expressed at low
296
levels were common across all life stages, four of which had uncharacterized functions (Table 1). 297
The other five included genes encoding maternal protein tudor (Tctud), poly(A) polymerase type
298
3, THO complex subunit 2, transmembrane protein 35, and sentrin-specific protease. 299
300
A GO analysis of each group of unique genes indicated differences in top level functions among
301
stages, with more similar expression in the adults and larval stages, sharing MF terms “serine-
302
type endopeptidase activity”, “oxidoreductase activity”, and “transition metal ion binding” (Fig. 303
4). However, an enrichment analysis indicated that serine-type endopeptidases were
304
overrepresented only in the adults stage (p=0.005), and substrate-specific transporter activity was
305
overrepresented in the larval stage (p=0.04). Still, these two life stages shared 138 genes
306
expressed at low levels, not unexpected since both stages are active and feeding. Pupae had the
307
least number of genes and GO terms and included those with MF term “serine-type
308
endopeptidase activity”, and two unique terms: “NADH dehydrogenase activity”, and “structural
309
constituent of cuticle”. Enrichment analysis for pupae indicated overrepresentation of negative
310
regulation of programmed cell death (BP; p=0.002), which was due to reads mapping to the gene
311
LOC663274 that encodes fas apoptotic inhibitory molecule 1, consistent with cell division and
312
tissue rearrangement occurring during this stage. Genes expressed in eggs were associated with 290
A comparison of genes with low expression levels (RPKM between 2-8 log2) revealed
291
expression of 273 genes unique to adults, 167 to eggs, 139 to larvae, and 14 to pupae (Fig. 3;
292
Supplemental File 2). Adults and larvae shared 138 genes including chitin deacetylase 7 (Cda7)
293
and two chitinase precursors (Cht4 and Cht9). Larvae and pupae shared a single gene, PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 313
terms “sequence-specific DNA binding” and “transcription factor activity sequence-specific
314
DNA binding”. The most enriched categories in eggs were BP anatomical structure development
315
(p=0.002), sex determination (p=0.011), and cell differentiation (p=0.006), consistent with
316
highly complex developmental processes during embryogenesis. 317
318
Selection of candidate gene
319
To find candidate genes for RNAi, we manually curated genes unique to each life stage and
320
expressed at low levels (Supplemental File 2). Six cuticle genes were expressed only in larvae,
321
but unfortunately many cuticle genes have orthologs in other species. However, a BLAST of
322
CPG (LOC103313766) indicated no hits to other species (data not shown). In examining
323
previous data (Morris et al., 2009), CPG was found to be moderately expressed in the larval gut
324
(relative to other gut-expressed genes). Unfortunately, this gene was not analyzed by the iBeetle
325
project (Schmitt-Engel et al., 2015). We then submitted the sequence to OffTargetFinder and
326
found hits to only four other insect species which were focused to the 5’ and middle regions,
327
leaving the 3’ as a unique portion of the sequence (Supplemental Fig. 1). So, we chose
328
LOC103313766 CPG to evaluate as a potential candidate, since it met our criteria of uniquely
329
expressed in T. castaneum larvae, contained regions where dsRNA would minimize off target
330
effects, and was expressed in the larval gut. 331
332
RNAi validation of CPG 313
terms “sequence-specific DNA binding” and “transcription factor activity sequence-specific
314
DNA binding”. The most enriched categories in eggs were BP anatomical structure development
315
(p=0.002), sex determination (p=0.011), and cell differentiation (p=0.006), consistent with
316
highly complex developmental processes during embryogenesis. 313
terms sequence-specific DNA binding and transcription factor activity sequence-specific
314
DNA binding”. The most enriched categories in eggs were BP anatomical structure development
315
(p=0.002), sex determination (p=0.011), and cell differentiation (p=0.006), consistent with
316
highly complex developmental processes during embryogenesis. 317
318
Selection of candidate gene
319
To find candidate genes for RNAi, we manually curated genes unique to each life stage and
320
expressed at low levels (Supplemental File 2). Six cuticle genes were expressed only in larvae,
321
but unfortunately many cuticle genes have orthologs in other species. However, a BLAST of
322
CPG (LOC103313766) indicated no hits to other species (data not shown). PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 337
larvae and controls (mock-injected “Mock” and noninjected “Control”) 18 d post injection. The
338
RNAi treatment significantly reduced the expression of CPG target transcript 1,491-fold
339
compared to Control (p=2.17x10-7) and 284-fold compared to Mock (p=7.14x10-7). An ANOVA
340
comparing the RPKM values of Mock, Control, and CPG treatments also was significantly
341
different (Fig. 5A; p=2.64x10-5). The large decrease in expression was biologically significant
342
because 64% mortality was observed in the CPG dsRNA treatment group compared to the non-
343
injected control at day 18 post-injection (Fig. 5B; p=0.057). We also observed 29% mortality in
344
Mock, but it was not significant when compared to Control mortality (19%; p=0.79). 345
346
RNA-Seq analysis of larvae injected with CPG dsRNA compared to Mock resulted in 449
347
significantly differentially expressed genes (p<0.01 and at least 8-fold change; Supplemental Fig. 348
2 and Supplemental File 3). Of those genes, 100 were uncharacterized, and 20 were annotated as
349
hypothetical proteins. Most (62%) had decreased expression, and the 10 most highly repressed
350
genes were uncharacterized except the target gene and LOC100142553 adenylate kinase. Of
351
those with increased expression, the most highly increased was Jtb, which encodes an orphan
352
receptor with unknown function, LOC662244 F-box SPRY that contributes to ubiquitin-protein
353
transferase activity, and BBIP1 which is a chromosome associated protein. Other up regulated
354
genes related to transcription/translation included LOC107398339 (splicing factor for mRNA),
355
LOC103313738 (a repressor of developmentally regulated gene expression), and LOC664045,
356
involved in chromatin silencing. In response to knockdown of CPG, three other cuticle protein
357
genes were significantly increased: LOC100141875 cuticle 19-like, LOC103313752 cuticle
358
protein 70, and LOC655183 cuticle protein. 337
larvae and controls (mock-injected “Mock” and noninjected “Control”) 18 d post injection. The
338
RNAi treatment significantly reduced the expression of CPG target transcript 1,491-fold
339
compared to Control (p=2.17x10-7) and 284-fold compared to Mock (p=7.14x10-7). An ANOVA
340
comparing the RPKM values of Mock, Control, and CPG treatments also was significantly
341
different (Fig. 5A; p=2.64x10-5). The large decrease in expression was biologically significant
342
because 64% mortality was observed in the CPG dsRNA treatment group compared to the non-
343
injected control at day 18 post-injection (Fig. 5B; p=0.057). We also observed 29% mortality in
344
Mock, but it was not significant when compared to Control mortality (19%; p=0.79). Manuscript to be reviewed In examining
323
previous data (Morris et al., 2009), CPG was found to be moderately expressed in the larval gut
324
(relative to other gut-expressed genes). Unfortunately, this gene was not analyzed by the iBeetle
325
project (Schmitt-Engel et al., 2015). We then submitted the sequence to OffTargetFinder and
326
found hits to only four other insect species which were focused to the 5’ and middle regions,
327
leaving the 3’ as a unique portion of the sequence (Supplemental Fig. 1). So, we chose 319
To find candidate genes for RNAi, we manually curated genes unique to each life stage and
320
expressed at low levels (Supplemental File 2). Six cuticle genes were expressed only in larvae,
321
but unfortunately many cuticle genes have orthologs in other species. However, a BLAST of
322
CPG (LOC103313766) indicated no hits to other species (data not shown). In examining
323
previous data (Morris et al., 2009), CPG was found to be moderately expressed in the larval gut
324
(relative to other gut-expressed genes). Unfortunately, this gene was not analyzed by the iBeetle
325
project (Schmitt-Engel et al., 2015). We then submitted the sequence to OffTargetFinder and
326
found hits to only four other insect species which were focused to the 5’ and middle regions,
327
leaving the 3’ as a unique portion of the sequence (Supplemental Fig. 1). So, we chose 333
To demonstrate that this was a biological target, we used RNAi to knockdown expression of
334
CPG in T. castaneum larvae. We injected dsRNA into early stage larvae (2nd-3rd instar), which
335
we hypothesized would have the most impact on transcript abundance. Knockdown and off
336
target effects were evaluated by another round of RNA-Seq on RNA isolated from the injected Manuscript to be reviewed 345 346
RNA-Seq analysis of larvae injected with CPG dsRNA compared to Mock resulted in 449
347
significantly differentially expressed genes (p<0.01 and at least 8-fold change; Supplemental Fig. 348
2 and Supplemental File 3). Of those genes, 100 were uncharacterized, and 20 were annotated as
349
hypothetical proteins. Most (62%) had decreased expression, and the 10 most highly repressed
350
genes were uncharacterized except the target gene and LOC100142553 adenylate kinase. Of
351
those with increased expression, the most highly increased was Jtb, which encodes an orphan
352
receptor with unknown function, LOC662244 F-box SPRY that contributes to ubiquitin-protein
353
transferase activity, and BBIP1 which is a chromosome associated protein. Other up regulated
354
genes related to transcription/translation included LOC107398339 (splicing factor for mRNA),
355
LOC103313738 (a repressor of developmentally regulated gene expression), and LOC664045,
356
involved in chromatin silencing. In response to knockdown of CPG, three other cuticle protein
357
genes were significantly increased: LOC100141875 cuticle 19-like, LOC103313752 cuticle
358
protein 70, and LOC655183 cuticle protein. 359 PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 360
There were 52 genes in this dataset that were annotated as noncoding RNA (ncRNA), 25 with
361
increased and 27 with decreased expression (Supplemental File 4). All were preliminarily
362
characterized as long ncRNAs since they were greater than 200 nt. All ncRNAs were screened
363
through RNAcon (Panwar et al., 2014) to predict the classification of each. There were 10 SSU-
364
rRNA5, three Intron-GP-1, and one IRESe; the remaining sequences were below the default
365
Support Vector Machines (SVM) threshold (0.0) and were classified as coding mRNA. 366
However, these sequences were characterized by NCBI as ncRNA, probably due to unusual
367
structure. Regardless, our transcriptome data suggests that ncRNA are actively transcribed in
368
response to RNAi, as has been described previously (Ji et al., 2015). 369
370
A GO term enrichment analysis of significantly decreased gene expression in response to CPG
371
RNAi identified functions involved in chitin breakdown (BP GO:0006032 and MF GO:0004568;
372
p=0.04 and 0.04, respectively). LOC107398196 and Cht13, both encoding chitinases, were
373
responsible for these enriched GO terms. In contrast, the GO term aspartic-type endopeptidase
374
activity (p=8.28x10-5) was significantly enriched in up regulated genes. 375
376
Characterization of CPG
377
To gain insight into the function of the CPG target gene, a maximum likelihood tree was
378
constructed with T. castaneum protein sequences annotated as ‘cuticle protein’ (Fig. 6). CPG
379
predicted protein (XP_008196095, highlighted with a yellow box) was most similar to cuticle
380
proteins 16.5 (XP_015833062) and 19.8 (XP_976285). Interestingly, the target CPG protein also
381
was found in the same major clade as the up regulated cuticle protein 70 gene LOC103313752
382
(XP_008196069, highlighted in red), and found in close proximity on LG3 (Table 2). Another 360
There were 52 genes in this dataset that were annotated as noncoding RNA (ncRNA), 25 with
361
increased and 27 with decreased expression (Supplemental File 4). All were preliminarily
362
characterized as long ncRNAs since they were greater than 200 nt. All ncRNAs were screened
363
through RNAcon (Panwar et al., 2014) to predict the classification of each. There were 10 SSU-
364
rRNA5, three Intron-GP-1, and one IRESe; the remaining sequences were below the default
365
Support Vector Machines (SVM) threshold (0.0) and were classified as coding mRNA. Manuscript to be reviewed 377
To gain insight into the function of the CPG target gene, a maximum likelihood tree was
378
constructed with T. castaneum protein sequences annotated as ‘cuticle protein’ (Fig. 6). CPG
379
predicted protein (XP_008196095, highlighted with a yellow box) was most similar to cuticle
380
proteins 16.5 (XP_015833062) and 19.8 (XP_976285). Interestingly, the target CPG protein also
381
was found in the same major clade as the up regulated cuticle protein 70 gene LOC103313752
382
(XP_008196069, highlighted in red), and found in close proximity on LG3 (Table 2). Another 377
To gain insight into the function of the CPG target gene, a maximum likelihood tree was
378
constructed with T. castaneum protein sequences annotated as ‘cuticle protein’ (Fig. 6). CPG
379
predicted protein (XP_008196095, highlighted with a yellow box) was most similar to cuticle
380
proteins 16.5 (XP_015833062) and 19.8 (XP_976285). Interestingly, the target CPG protein also
381
was found in the same major clade as the up regulated cuticle protein 70 gene LOC103313752
382
(XP_008196069, highlighted in red), and found in close proximity on LG3 (Table 2). Another PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 383
cuticle protein gene with increased expression, LOC655183 (XP_008190752) also on LG3, was
384
related to those encoding resilin proteins. The protein product of the cuticle gene with highest
385
increased expression, LOC100141875 (XP_001809825), was related to cuticle protein 7
386
(XP_008193006) encoded by LOC656347, and both genes were found on LG5. 387
388
Discussion
389
Current control methods for T. castaneum and other stored product pests are becoming less
390
effective due to development of insecticide resistance (Collins, 1990; Jagadeesan et al., 2012;
391
Opit et al., 2012). Alternative management strategies are limited, and new molecular-based
392
controls are needed because they offer increased efficacy and selectivity, and targeted
393
approaches to combatting resistance. There are major hurdles in developing molecular-based
394
strategies in T. castaneum. The first step is to identify a target gene that can be effectively
395
knocked-down. The target gene should be specific to the pest or a narrow range of pests. The
396
most difficult challenge is delivery, whether it is topical or oral RNAi, or another mechanism. In
397
this study, we evaluated molecular targets by injection of dsRNA prior to attempts of topical or
398
oral delivery. 399 383
cuticle protein gene with increased expression, LOC655183 (XP_008190752) also on LG3, was
384
related to those encoding resilin proteins. The protein product of the cuticle gene with highest
385
increased expression, LOC100141875 (XP_001809825), was related to cuticle protein 7
386
(XP_008193006) encoded by LOC656347, and both genes were found on LG5. 384
related to those encoding resilin proteins. The protein product of the cuticle gene with highest
385
increased expression, LOC100141875 (XP_001809825), was related to cuticle protein 7
386
(XP_008193006) encoded by LOC656347, and both genes were found on LG5. 387
388
Discussion
389
Current control methods for T. castaneum and other stored product pests are becoming less
390
effective due to development of insecticide resistance (Collins, 1990; Jagadeesan et al., 2012;
391
Opit et al., 2012). Alternative management strategies are limited, and new molecular-based
392
controls are needed because they offer increased efficacy and selectivity, and targeted
393
approaches to combatting resistance. There are major hurdles in developing molecular-based
394
strategies in T. castaneum. The first step is to identify a target gene that can be effectively
395
knocked-down. The target gene should be specific to the pest or a narrow range of pests. Manuscript to be reviewed 406
and may be the ancestral cathepsin L gene, but it most likely functions in development and
407
immunity (Perkin et al., 2016). While this gene may not be useful for species-specific pest
408
control because of the conservation of sequence among insects, its function in T. castaneum and
409
other insects is of biological interest, as it appears to provide critical function(s) throughout
410
development. 411
412
Nine genes were commonly expressed at low levels in all developmental stages, including Tctud
413
(maternal protein tudor). Tctud has been found in many eukaryotes and has been implicated in
414
protein-protein interactions, where methylated substrates bind to the tudor domain. In D. 415
melanogaster, tudor proteins are found in chromatin, small nuclear RNA assembly, RNA-
416
induced silencing complex, and germ granules (Ying & Chen, 2012). Similar to Tctud, temporal
417
expression data shows low to moderately high expression of Dmtud in early fly embryos through
418
30-day old adults in both males and females (flybase.org, modENCODE temporal expression
419
data, Gramates et al., 2017). Additionally, mutants of various alleles caused lethality of early
420
embryos through maternal effects, and both male and female sterility (Thomson & Lasko, 2004;
421
flybase.org, Summary of Phenotypes, Gramates et al., 2017). We submitted Tctud nucleotide
422
sequence to OffTargetFinder and found multiple 21mer hits to 35 other species (data not shown),
423
and therefore the gene was not selected for RNAi. 424
425
We have found that validation of RNAi knockdown through RNA Seq can provide unique 406
and may be the ancestral cathepsin L gene, but it most likely functions in development and
407
immunity (Perkin et al., 2016). While this gene may not be useful for species-specific pest
408
control because of the conservation of sequence among insects, its function in T. castaneum and
409
other insects is of biological interest, as it appears to provide critical function(s) throughout
410
development. 406
and may be the ancestral cathepsin L gene, but it most likely functions in development and
407
immunity (Perkin et al., 2016). While this gene may not be useful for species-specific pest
408
control because of the conservation of sequence among insects, its function in T. castaneum and
409
other insects is of biological interest, as it appears to provide critical function(s) throughout
410
development. Manuscript to be reviewed The
396
most difficult challenge is delivery, whether it is topical or oral RNAi, or another mechanism. In
397
this study, we evaluated molecular targets by injection of dsRNA prior to attempts of topical or
398
oral delivery. 399
400
An RNA-Seq analysis of the four major life stages of T. castaneum identified twelve genes that
401
were highly expressed in all developmental stages. One gene was a cathepsin L named 26-29-p. 402
Cathepsin L genes in T. castaneum are part of a gene expansion group that are expressed at high
403
levels in adults and larvae for the digestion of cereal proteins (Goptar et al., 2012; Oppert et al.,
404
2010; Oppert et al., 2003; Oppert et al., 1993; Perkin et al., 2016; Perkin et al., 2017a;
405
Vinokurov et al., 2009). Based on phylogenetic analysis, 26-29-p is conserved across insects 405
Vinokurov et al., 2009). Based on phylogenetic analysis, 26-29-p is conserved across insects 405
Vinokurov et al., 2009). Based on phylogenetic analysis, 26-29-p is conserved across insects PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 411
412
Nine genes were commonly expressed at low levels in all developmental stages, including Tctud
413
(maternal protein tudor). Tctud has been found in many eukaryotes and has been implicated in
414
protein-protein interactions, where methylated substrates bind to the tudor domain. In D. 415
melanogaster, tudor proteins are found in chromatin, small nuclear RNA assembly, RNA-
416
induced silencing complex, and germ granules (Ying & Chen, 2012). Similar to Tctud, temporal
417
expression data shows low to moderately high expression of Dmtud in early fly embryos through
418
30-day old adults in both males and females (flybase.org, modENCODE temporal expression
419
data, Gramates et al., 2017). Additionally, mutants of various alleles caused lethality of early
420
embryos through maternal effects, and both male and female sterility (Thomson & Lasko, 2004;
421
flybase.org, Summary of Phenotypes, Gramates et al., 2017). We submitted Tctud nucleotide
422
sequence to OffTargetFinder and found multiple 21mer hits to 35 other species (data not shown),
423
and therefore the gene was not selected for RNAi. 425
We have found that validation of RNAi knockdown through RNA-Seq can provide unique
426
insights into function. Previously, we used RNA-Seq to validate knockdown of aspartate 1-
427
decarboxylase (ADC) in T. castaneum larvae, resulting in the identification of additional gene
428
interconnectivity (Perkin et al., 2017b). Not only was the significant knockdown of ADC PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 429
confirmed through RNA-Seq, a previously unknown interaction between ADC and dopamine
430
receptor 2 also was discovered. This information led to biological assays that determined that
431
the reduction of ADC transcripts via RNAi resulted in adults with decreased mobility. Therefore,
432
we used the same approach in the present study to evaluate knock down of a target gene and also
433
understand the overall impact to the transcriptome of reduced gene expression. 434
435
To isolate a candidate gene that could be used as a molecular-based pest control target, we
436
sought genes unique to a feeding stage (i.e. larvae or adults) and expressed at low levels. 437
Through manual curation of life stage transcriptome data, we found CPG was uniquely expressed
438
in larvae at low levels and lacked an ortholog in other species at the 3’ end of the gene; in fact,
439
BLAST did not return any hits at the mRNA level. We were encouraged that this target also has
440
potential as an oral RNAi product, since the gene was moderately expressed in the larval gut. 441
The protein product of this gene, XP_008196095, is a peptide of 61 amino acids, with 41%
442
identity to a neuropeptide-like precursor from the flesh fly, Sacrophaga crassipalpis (Li et al.,
443
2009). Additionally, Bhatia and Bhattacharya (2018) found that knockdown of a related cuticle
444
protein gene in the green peach aphid (Myzus persicae) through oral delivery of dsRNA
445
expressed in Arabidopsis thaliana resulted in reduced fecundity. We did not investigate whether
446
the T. castaneum target cuticle protein also had neuropeptide properties or whether reduced gene
447
expression caused a reduction in fecundity, but our functional test with RNAi demonstrated that
448
decreased gene expression in early stage larvae resulted in significant mortality compared to
449
Control and Mock. Thus, this gene is a candidate target for oral delivery of dsRNA. 429
confirmed through RNA-Seq, a previously unknown interaction between ADC and dopamine
430
receptor 2 also was discovered. This information led to biological assays that determined that
431
the reduction of ADC transcripts via RNAi resulted in adults with decreased mobility. Therefore,
432
we used the same approach in the present study to evaluate knock down of a target gene and also
433
understand the overall impact to the transcriptome of reduced gene expression. Manuscript to be reviewed 451
RNA-Seq analysis of the transcriptome after RNAi knockdown of CPG identified three other
452
cuticle genes with increased expression and two chitinase genes with decreased expression
453
compared to Mock. The cuticle genes with increased expression included one encoding cuticle
454
protein 70 (XP_008196069), clustering in the same major clade as the target cuticle protein gene,
455
suggesting similar function and perhaps an indication of redundancy in function as has
456
previously been noted with gene expansion groups. In fact, this redundancy may explain
457
survivors in the dsRNA-injected larvae, albeit a low percentage (32%), and it may complicate
458
oral RNAi if there is compensation response similar to that previously identified in attempting to
459
target cysteine protease genes via RNAi (Perkin et al., 2017a). Another cuticle protein gene
460
LOC655183 also was up regulated after RNAi treatment, and this gene product (XP_008190752)
461
clustered with resilin proteins. Resilin is a specialized cuticle protein that is found in soft parts
462
of the adult insect allowing for movement of wings (Andersen & Weis-Fogh, 1964). 463
LOC655183 is an ortholog to a gene in Drosophila melanogaster encoding cuticular protein 56F, 451
RNA-Seq analysis of the transcriptome after RNAi knockdown of CPG identified three other
452
cuticle genes with increased expression and two chitinase genes with decreased expression
453
compared to Mock. The cuticle genes with increased expression included one encoding cuticle
454
protein 70 (XP_008196069), clustering in the same major clade as the target cuticle protein gene,
455
suggesting similar function and perhaps an indication of redundancy in function as has
456
previously been noted with gene expansion groups. In fact, this redundancy may explain
457
survivors in the dsRNA-injected larvae, albeit a low percentage (32%), and it may complicate
458
oral RNAi if there is compensation response similar to that previously identified in attempting to
459
target cysteine protease genes via RNAi (Perkin et al., 2017a). Another cuticle protein gene
460
LOC655183 also was up regulated after RNAi treatment, and this gene product (XP_008190752)
461
clustered with resilin proteins. Resilin is a specialized cuticle protein that is found in soft parts
462
of the adult insect allowing for movement of wings (Andersen & Weis-Fogh, 1964). 470
Opposite in response to the increased expression of cuticle protein genes, Cht13, a chitinase, was
471
decreased in response to the injection of CPG dsRNA. Manuscript to be reviewed 429
confirmed through RNA-Seq, a previously unknown interaction between ADC and dopamine
430
receptor 2 also was discovered. This information led to biological assays that determined that
431
the reduction of ADC transcripts via RNAi resulted in adults with decreased mobility. Therefore,
432
we used the same approach in the present study to evaluate knock down of a target gene and also
433
understand the overall impact to the transcriptome of reduced gene expression. 437
Through manual curation of life stage transcriptome data, we found CPG was uniquely expressed
438
in larvae at low levels and lacked an ortholog in other species at the 3’ end of the gene; in fact,
439
BLAST did not return any hits at the mRNA level. We were encouraged that this target also has
440
potential as an oral RNAi product, since the gene was moderately expressed in the larval gut. 441
The protein product of this gene, XP_008196095, is a peptide of 61 amino acids, with 41%
442
identity to a neuropeptide-like precursor from the flesh fly, Sacrophaga crassipalpis (Li et al.,
443
2009). Additionally, Bhatia and Bhattacharya (2018) found that knockdown of a related cuticle
444
protein gene in the green peach aphid (Myzus persicae) through oral delivery of dsRNA 445
expressed in Arabidopsis thaliana resulted in reduced fecundity. We did not investigate whether
446
the T. castaneum target cuticle protein also had neuropeptide properties or whether reduced gene
447
expression caused a reduction in fecundity, but our functional test with RNAi demonstrated that
448
decreased gene expression in early stage larvae resulted in significant mortality compared to
449
Control and Mock. Thus, this gene is a candidate target for oral delivery of dsRNA. 450 PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Cht13 is predicted to be part of group IV
472
chitinases expressed in the gut or fat body and expressed in response to feeding in larval and
473
adult stages (Zhu et al., 2008). All differentially expressed chitin-related genes are apparently PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Manuscript to be reviewed 474
interconnected through a regulatory pathway that responds to the loss of function of CPG by
475
RNAi. 476
477
We were surprised at the number of long ncRNAs (52) that were differentially expressed at a
478
significant level (p<0.01) in surviving T. castaneum larvae that were injected with CPG dsRNA. 479
Most ncRNA were not classified as typical ncRNAs and may represent new classes, or
480
alternatively may be miss-annotated. However, differentially expressed long ncRNA have been
481
implicated in human disease states, particularly cancer (Ma et al., 2015). Of relevance to this
482
study, differentially-expressed long ncRNAs can impose epigenetic changes that alter the
483
transcription of other genes, including silencing (Tufarelli et al., 2003). Therefore, we can
484
speculate that the large number of differentially expressed genes in this study (449) may have
485
been regulated in part by ncRNAs. While not to the same degree, ncRNAs were implicated in a
486
previous RNAi study, in which LOC107398253 ncRNA (decreased 12.3-fold, p=0.001, in the
487
current study) was decreased 593-fold in response to RNAi of ADC (Perkin et al., 2017b). This
488
particular ncRNA was annotated as an U3 snoRNA, predicted to be involved in site-specific
489
cleavage of ribosomal RNA (rRNA) during pre-rRNA processing (Clery et al., 2007). More
490
work is needed to understand the relationship of ncRNAs and RNAi in insects. 491
492
Conclusions PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Manuscript to be reviewed 496
was expressed at low levels overall and moderate levels in the larval gut, oral delivery methods
497
for CPG dsRNA have the potential to control damage by T. castaneum larvae. 498
499
Acknowledgements
500
The authors would like to thank technicians Ken Friesen and Tom Morgan for their contribution,
501
injecting larvae and RNA extraction and library preparation, respectively. Mention of trade
502
names or commercial products in this publication is solely for the purpose of providing specific
503
information and does not imply recommendation or endorsement by the U.S. Department of
504
Agriculture. USDA is an equal opportunity provider and employer. 496
was expressed at low levels overall and moderate levels in the larval gut, oral delivery methods
497
for CPG dsRNA have the potential to control damage by T. castaneum larvae. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 528
and ingenstion of analogous dsRNAs. International Journal of Molecular Sciences. 19:
529
1079, doi:10.3390/ijms19041079. 530
Clery, A., Senty-Segault, V., Leclerc, F., Raue, H.A. and Branlant, C. 2007. Analysis of 528
and ingenstion of analogous dsRNAs. International Journal of Molecular Sciences. 19:
529
1079, doi:10.3390/ijms19041079. 529
1079, doi:10.3390/ijms19041079. 530
Clery, A., Senty-Segault, V., Leclerc, F., Raue, H.A. and Branlant, C. 2007. Analysis of
531
sequence and structural features that identify the B/C motif of U3 small nucleolar RNA
532
as the recognition site for the Snu13p-Rrp9p protein pair. Molecular and Cell Biology
533
27:1191-1206. 530
Clery, A., Senty-Segault, V., Leclerc, F., Raue, H.A. and Branlant, C. 2007. Analysis of
531
sequence and structural features that identify the B/C motif of U3 small nucleolar RNA
532
as the recognition site for the Snu13p-Rrp9p protein pair. Molecular and Cell Biology
533
27:1191-1206. 534
Collins, P.J. 1990. A new resistance to pyrethroids in Tribolium castaneum (herbst). Journal of
535
Pesticide Science 28:101-115. ,
py
(
)
535
Pesticide Science 28:101-115. 536
Ditzel, N., Andersen, S. O. and Højrup, P. 2003. Cuticular proteins from the horseshoe crab,
537
Limulus Polyphemus. Comparative Biochemistry and Physiology Part B 134(3):489-497. 538
Donitz, J , Schmitt-Engel, C , Grossmann, D , Gerischer, L , Tech, M , Schoppmeier, M , 536
Ditzel, N., Andersen, S. O. and Højrup, P. 2003. Cuticular proteins from the horseshoe crab,
537
Limulus Polyphemus. Comparative Biochemistry and Physiology Part B 134(3):489-497. 538
Donitz, J., Schmitt-Engel, C., Grossmann, D., Gerischer, L., Tech, M., Schoppmeier, M.,
539
Klingler, M. and Bucher, G. 2015. iBeetle-Base: a database for RNAi phenotypes in the
540
red flour beetle Tribolium castaneum. Nucleic Acids Research 43: D720-725. 539
Klingler, M. and Bucher, G. 2015. iBeetle-Base: a database for RNAi phenotypes in the
540
red flour beetle Tribolium castaneum. Nucleic Acids Research 43: D720-725. 541
El Halim, H.M.A., Alshukri, B.M.H., Ahmad, M.S., Nakasu, E.Y.T., Awwad, M.H., Salama, 542
E.M., Gatehouse, A.M.R., and Edwards, M.G. 2016. RNAi-mediated knockdown of the 542
E.M., Gatehouse, A.M.R., and Edwards, M.G. 2016. RNAi-mediated knockdown of the
543
voltage gated sodium ion channel TcNav causes mortality in Tribolium castaneum. 542
E.M., Gatehouse, A.M.R., and Edwards, M.G. 2016. RNAi-mediated knockdown of the
543
voltage gated sodium ion channel TcNav causes mortality in Tribolium castaneum. 544
Scietific Reports 6:29301, doi:10.1038/srep29301. 543
voltage gated sodium ion channel TcNav causes mortality in Tribolium castaneum. 544
Scietific Reports 6:29301, doi:10.1038/srep29301. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) 505
References 506
Allen, M.L. and Walker, W.B., 3rd. 2012. Saliva of Lygus lineolaris digests double stranded
507
ribonucleic acids. Journal of Insect Physiology 58: 391-396. 508
Andersen, S. O. and Weis-Fogh, T. 1964. Reslin. A rubberlike protein in arthropod cuticle. 509
Advances in Insect Physiology 2:1-65. 510
Aronstein, K., Oppert, B. and Lorenzen, M. 2011. RNAi in agriculturally-important arthropods. 511
In: RNA Processing (Grabowski, PP, ed.), pp. 157-180. InTech. 512
Baum, J.A., Bogaert, T., Clinton, W., Heck, G.R., Feldmann, P., Ilagan, O., Johnson, S., 513
Plaetinck, G., Munyikwa, T., Pleau, M., Vaughn, T. and Roberts, J. 2007. Control of
514
coleopteran insect pests through RNA interference. Nature Biotechnology 25: 1322-1326. 515
Benjamini, Y. and Hochberg, Y. 1995. Controlling the false discovery rate: a practical and
516
powerful approach to multiple testing. Journal of Royal Statistics Society B
517
Methodololgy 57:289-300. 513
Plaetinck, G., Munyikwa, T., Pleau, M., Vaughn, T. and Roberts, J. 2007. Control of
514
coleopteran insect pests through RNA interference Nature Biotechnology 25: 1322 1326 515
Benjamini, Y. and Hochberg, Y. 1995. Controlling the false discovery rate: a practical and
516
powerful approach to multiple testing. Journal of Royal Statistics Society B
517
Methodololgy 57:289-300. 518
Bhatia, V. and Bhattacharya, R. 2018. Host mediated RNAi of cuticular protein gene impaired
519
fecundity in green peach aphid Myzus persicae. Pest Management Science. 520
10.1002/ps.4900. 521
Boyer, S., Zhang, H. and Lemperiere, G. 2012. A review of control methods and resistance
522
mechanisms in stored-product insects. Bullin Entomology Resources 102:213-29. 523
Brown, S.J., Mahaffey, J.P., Lorenzen, M.D., Denell, R.E., and Mahaffey, J.W. 1999. Using
524
RNAi to investigate orthologous homeotic gene function during development of distantly
525
related insects. Evolution and Development 1:11-15. 526
Cao, M., Gatehouse, J.A., and Fitches, E.C. 2018. A systematic study of RNAi effects and
527
dsRNA stability in Tribolium castaneum and Acyrthosiphon pisum, following injection PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 544
Scietific Reports 6:29301, doi:10.1038/srep29301. 545
Good, R.T., Varghese, T., Golz, J.F., Russell, D.A., Papanicolaou, A., Edwards, O. and Robin,
546
C. 2016. OfftargetFinder: a web tool for species-specific RNAi design. Bioinformatics
547
32:1232-1234. 548
Goptar, I.A., Semashko, T.A., Danilenko, S.A., Lysogorskaya, E.N., Oksenoit, E.S., Zhuzhikov,
549
D.P., Belozersky, M.A., Dunaevsky, Y.E., Oppert, B., Filippova, I.Y. and Elpidina, E.N. 550
2012. Cysteine digestive peptidases function as post-glutamine cleaving enzymes in PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Manuscript to be reviewed 551
tenebrionid stored-product pests. Comp Biochem Physiol B Biochem Mol Biol 161: 148-
552
154. 553
Götz, S., Garcia-Gomez, J.M., Terol, J., Williams, T.D., Nagaraj, S.H., Nueda, M.J., Robles, M.,
554
Talon, M., Dopazo, J. and Conesa, A. 2008. High-throughput functional annotation and
555
data mining with the Blast2GO suite. Nucleic Acids Research 36:3420-3435. 556
Gramates, L.S., Marygold, S.J., Santos, G.D., Urbano, J.M., Antonazzo, G., Matthews, B.B.,
557
Rey, A.J., Tabone, C.J., Crosby, M.A., Emmert, D.B., Falls, K., Goodman, J.L., Hu, Y.,
558
Ponting, L., Schroeder, A.J., Strelets, V.B., Thurmond, J., Zhou, P. and the FlyBase, C. 559
2017. FlyBase at 25: looking to the future. Nucleic Acids Research 45:D663-D671. 560
Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G.,
561
van Baren, M.J., Boley, N., Booth, B.W., Brown, J.B., Cherbas, L., Davis, C.A., Dobin,
562
A., Li, R., Malone, J.H., Mattiuzzo, N.R., Miller, D., Sturgill, D., Tuch, B.B., Zaleski, C.,
563
Zhang, D., Blanchette, M., Dudoit, S., Eads, B., Green, R.E., Hammonds, A., Jiang, L.,
564
Kapranov, P., Langton, L., Perrimon, N., Sandler, J.E., Wan, K.H., Willingham, A.,
565
Zhang, Y., Zou, Y., Andrews, J., Bickel, P.J., Brenner, S.E., Brent, M.R., Cherbas, P.,
566
Gingeras, T.R., Hoskins, R.A., Kaufman, T.C., Oliver, B. and Celniker, S.E. 2011. The
567
development transcriptome of Drosophila melanogaster. Nature 471:473-479. 568
Guan, R.B., Li, H.C., Fan, Y.J., Hu, S.R., Christiaens, O., Smagghe, G., and Miao, X.X 2018. A
569
nuclease specific to lepidopteran insects suppresses RNAi. Journal of Biological
570
Chemistry jbc.RA117.001553. 571
Huvenne, H. and Smagghe, G. 2010. Mechanisms of dsRNA uptake in insects and potential of
572
RNAi for pest control: a review Journal of Insect Physiology 56:227-235 551
tenebrionid stored-product pests. Comp Biochem Physiol B Biochem Mol Biol 161: 148-
552
154. 556
Gramates, L.S., Marygold, S.J., Santos, G.D., Urbano, J.M., Antonazzo, G., Matthews, B.B., 558
Ponting, L., Schroeder, A.J., Strelets, V.B., Thurmond, J., Zhou, P. and the FlyBase, C. 559
2017. FlyBase at 25: looking to the future. Nucleic Acids Research 45:D663-D671. Manuscript to be reviewed 560
Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G.,
561
van Baren, M.J., Boley, N., Booth, B.W., Brown, J.B., Cherbas, L., Davis, C.A., Dobin,
562
A., Li, R., Malone, J.H., Mattiuzzo, N.R., Miller, D., Sturgill, D., Tuch, B.B., Zaleski, C.,
563
Zhang, D., Blanchette, M., Dudoit, S., Eads, B., Green, R.E., Hammonds, A., Jiang, L.,
564
Kapranov, P., Langton, L., Perrimon, N., Sandler, J.E., Wan, K.H., Willingham, A.,
565
Zhang, Y., Zou, Y., Andrews, J., Bickel, P.J., Brenner, S.E., Brent, M.R., Cherbas, P.,
566
Gingeras, T.R., Hoskins, R.A., Kaufman, T.C., Oliver, B. and Celniker, S.E. 2011. The
567
development transcriptome of Drosophila melanogaster. Nature 471:473-479. A., Li, R., Malone, J.H., Mattiuzzo, N.R., Miller, D., Sturgill, D., Tuch, B.B., Za 568
Guan, R.B., Li, H.C., Fan, Y.J., Hu, S.R., Christiaens, O., Smagghe, G., and Miao, X.X 2018. A
569
nuclease specific to lepidopteran insects suppresses RNAi. Journal of Biological
570
Chemistry jbc.RA117.001553. 571
Huvenne, H. and Smagghe, G. 2010. Mechanisms of dsRNA uptake in insects and potential of
572
RNAi for pest control: a review. Journal of Insect Physiology 56:227-235. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be Manuscript to be reviewed Manuscript to be reviewed 573
Jagadeesan, R., Collins, P.J., Daglish, G.J., Ebert, P.R., Schlipalius, D.I. 2012. Phosphine
574
resistance in the rust red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae):
575
inheritance, gene interactions and fitness costs. PloS one 7:e31582. 576
Ji, Z., Song, R., Regev, A. and Struhl, K. 2015. Many lncRNAs, 5'UTRs, and pseudogenes are
577
translated and some are likely to express functional proteins. eLife 4:e08890. 578
Jones D.T., Taylor W.R., and Thornton J.M. 1992. The rapid generation of mutation data
579
matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282. 580
Knorr, E., Fishilevich, E., Tenbusch, L., Frey, M.L.F., Rangasamy, M., Billion, A., Worden,
581
S.E., Gandra, P., Arora, K., Lo, W., Schulenberg, G., Valverde-Garcia, P., Vilcinskas, A. 582
and Narva, K.E. 2018. Gene silencing in Tribolium castaneum as a tool for the targeted
583
identification of candidate RNAi targets in crop pests. Scientific Reports 8:2061,
584
doi:10.1038/s41589-018-20416-y. 585
Kumar S., Stecher G., Li M., Knyaz C., and Tamura K. 2018. MEGA X: Molecular Evolutionary
586
Genetics Analysis across computing platforms. Molecular Biology and Evolution
587
35:1547-1549. 588
Li, A., Rinehart, J.P. and Denlinger, D.L. 2009. Neuropeptide-like precursor 4 is uniquely
589
expressed during pupal diapause in the flesh fly. Peptides 30:518-521. 590
Lomate, P.R. and Bonning, B.C. 2016. Distinct properties of proteases and nucleases in the gut,
591
salivary gland and saliva of southern green stink bug, Nezara viridula. Scientific Report
592
6:27587. 593
Loktev, A.V., Zhang, Q., Beck, J.S., Searby, C.C., Scheetz, T.E., Bazan, J.F., Slusarski, D.C.,
594
Sheffield, V.C., Jackson, P.K. and Nachury, M.V. 2008. A BBSome subunit links
595
ciliogenesis, microtubule stability, and acetylation. Developmental Cell 15:854-865. 573
Jagadeesan, R., Collins, P.J., Daglish, G.J., Ebert, P.R., Schlipalius, D.I. 2012. Phosphine
574
resistance in the rust red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae):
575
inheritance, gene interactions and fitness costs. PloS one 7:e31582. 576
Ji, Z., Song, R., Regev, A. and Struhl, K. 2015. Many lncRNAs, 5'UTRs, and pseudogenes are
577
translated and some are likely to express functional proteins. eLife 4:e08890. 578
Jones D.T., Taylor W.R., and Thornton J.M. 1992. The rapid generation of mutation data
579
matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282. 580
Knorr, E., Fishilevich, E., Tenbusch, L., Frey, M.L.F., Rangasamy, M., Billion, A., Worden,
581
S.E., Gandra, P., Arora, K., Lo, W., Schulenberg, G., Valverde-Garcia, P., Vilcinskas, A. 582
and Narva, K.E. 2018. Manuscript to be reviewed Gene silencing in Tribolium castaneum as a tool for the targeted
583
identification of candidate RNAi targets in crop pests. Scientific Reports 8:2061,
584
doi:10.1038/s41589-018-20416-y. 585
Kumar S., Stecher G., Li M., Knyaz C., and Tamura K. 2018. MEGA X: Molecular Evolutionary 576
Ji, Z., Song, R., Regev, A. and Struhl, K. 2015. Many lncRNAs, 5'UTRs, and pseudogenes are
577
translated and some are likely to express functional proteins. eLife 4:e08890. 585
Kumar S., Stecher G., Li M., Knyaz C., and Tamura K. 2018. MEGA X: Molecular Evolutionary
586
Genetics Analysis across computing platforms. Molecular Biology and Evolution
587
35:1547-1549. 588
Li, A., Rinehart, J.P. and Denlinger, D.L. 2009. Neuropeptide-like precursor 4 is uniquely
589
expressed during pupal diapause in the flesh fly. Peptides 30:518-521. 590
Lomate, P.R. and Bonning, B.C. 2016. Distinct properties of proteases and nucleases in the gut,
591
salivary gland and saliva of southern green stink bug, Nezara viridula. Scientific Report
592
6:27587. 593
Loktev, A.V., Zhang, Q., Beck, J.S., Searby, C.C., Scheetz, T.E., Bazan, J.F., Slusarski, D.C.,
594
Sheffield, V.C., Jackson, P.K. and Nachury, M.V. 2008. A BBSome subunit links
595
ciliogenesis, microtubule stability, and acetylation. Developmental Cell 15:854-865. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Manuscript to be reviewed 596
Ma, L., Li, A., Zou, D., Xu, X., Xia, L., Yu, J., Bajic V.B. and Zhang, Z. 2015. LncRNAWiki:
597
harnessing community knowledge in collaborative curation of human long non-coding
598
RNAs Nucleic Acids Research 43:187-192. 599
Martynov, A.G., Elpidina, E.N., Perkin, L. and Oppert, B. 2015. Functional analysis of C1
600
family cysteine peptidases in the larval gut of Tenebrio molitor and Tribolium castaneum 599
Martynov, A.G., Elpidina, E.N., Perkin, L. and Oppert, B. 2015. Functional analysis of C1 600
family cysteine peptidases in the larval gut of Tenebrio molitor and Tribolium castaneum. 601
BMC Genomics 16:75. 602
Morris, K., Lorenzen, M.D., Hiromasa, Y., Tomich, J.M., Oppert, C., Elpidina, E.N., Vinokurov,
603
K., Jurat-Fuentes, J.L., Fabrick, J. and Oppert, B. 2009. Tribolium castaneum Larval Gut
604
Transcriptome and Proteome: A Resource for the Study of the Coleopteran Gut. Journal
605
Proteome Research 8:3889-3898. 602
Morris, K., Lorenzen, M.D., Hiromasa, Y., Tomich, J.M., Oppert, C., Elpidina, E.N., Vinokurov, 606
Miller, S.C., Miyata, K., Brown, S.J. and Tomoyasu, Y. 2012. Dissecting systemic RNA
607
interference in the red flour beetle Tribolium castaneum: parameters affecting the
608
efficiency of RNAi. PLoS One 7:e47431. 609
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. and Wold, B. 2008. Mapping and
610
quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5:621-628. 611
Noh, M.Y., Beeman, R.W. and Arakane, Y. 2012. RNAi-based functional genomics in Tribolium
612
castaneum and possible application for controlling insect pests. Entomology Research
613
42:1-10. 614
Noh, M.Y., Kramer, K.J., Muthukrishnan, S., Beeman, R.W., Kanost, M.R. and Arakane, Y. 614
Noh, M.Y., Kramer, K.J., Muthukrishnan, S., Beeman, R.W., Kanost, M.R. and Arakane, Y. 614
Noh, M.Y., Kramer, K.J., Muthukrishnan, S., Beeman, R.W., Kanost, M.R. and Arakane, Y. 615
2015. Loss of function of the yellow-e gene causes dehydration-induced mortality of
616
adult Tribolium castaneum. Developmental Biology 399:315-324. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 617
Opit, G.P., Phillips, T.W., Aikins, M.J. and Hasan, M.M. 2012. Phosphine resistance in
618
Tribolium castaneum and Rhyzopertha dominica from stored wheat in Oklahoma. Journal
619
of Economic Entomology 105:1107-1114. 620
Oppert, B., Elpidina, E.N., Toutges, M. and Mazumdar-Leighton, S. 2010. Microarray analysis
621
reveals strategies of Tribolium castaneum larvae to compensate for cysteine and serine
622
protease inhibitors. Comparitive Biochemistry and Physiology Part D Genomics
623
Proteomics 5:280-287. 624
Oppert, B., Morgan, T., Hartzer, K., Lenarcic, B., Galesa, K., Brzin, J., Turk, V., Yoza, K.,
625
Ohtsubo, K. and Kramer, K. 2003. Effects of proteinase inhibitors on digestive
626
proteinases and growth of the red flour beetle, Tribolium castaneum (Herbst)(Coleoptera:
627
Tenebrionidae). Comparitive Biochemistry and Physiology Part C Toxicology and
628
Pharmacology 134:481-490. 629
Oppert, B., Morgan, T.D., Culbertson, C. and Kramer, K.J. 1993. Dietary mixtures of cysteine
630
and serine proteinase inhibitors exhibit synergistic toxicity toward the red flour beetle,
631
Tribolium castaneum. Comparitive Biochemistry and Physiology Part C: Comparative
632
Pharmacology 105:379-385. 617
Opit, G.P., Phillips, T.W., Aikins, M.J. and Hasan, M.M. 2012. Phosphine resistance in
618
Tribolium castaneum and Rhyzopertha dominica from stored wheat in Oklahoma. Journal
619
of Economic Entomology 105:1107-1114. 620
Oppert, B., Elpidina, E.N., Toutges, M. and Mazumdar-Leighton, S. 2010. Microarray analysis
621
reveals strategies of Tribolium castaneum larvae to compensate for cysteine and serine
622
protease inhibitors. Comparitive Biochemistry and Physiology Part D Genomics
623
Proteomics 5:280-287. 620
Oppert, B., Elpidina, E.N., Toutges, M. and Mazumdar-Leighton, S. 2010. Microarray analysis
621
reveals strategies of Tribolium castaneum larvae to compensate for cysteine and serine
622
protease inhibitors. Comparitive Biochemistry and Physiology Part D Genomics
623
Proteomics 5:280-287. 624
Oppert, B., Morgan, T., Hartzer, K., Lenarcic, B., Galesa, K., Brzin, J., Turk, V., Yoza, K.,
625
Ohtsubo, K. and Kramer, K. 2003. Effects of proteinase inhibitors on digestive
626
proteinases and growth of the red flour beetle, Tribolium castaneum (Herbst)(Coleoptera:
627
Tenebrionidae). Comparitive Biochemistry and Physiology Part C Toxicology and
628
Pharmacology 134:481-490. 624
Oppert, B., Morgan, T., Hartzer, K., Lenarcic, B., Galesa, K., Brzin, J., Turk, V., Yoza, K.,
625
Ohtsubo, K. and Kramer, K. 2003. Effects of proteinase inhibitors on digestive
626
proteinases and growth of the red flour beetle, Tribolium castaneum (Herbst)(Coleoptera:
627
Tenebrionidae). Comparitive Biochemistry and Physiology Part C Toxicology and
628
Pharmacology 134:481-490. 629
Oppert, B., Morgan, T.D., Culbertson, C. and Kramer, K.J. 1993. Manuscript to be reviewed Dietary mixtures of cysteine
630
and serine proteinase inhibitors exhibit synergistic toxicity toward the red flour beetle,
631
Tribolium castaneum. Comparitive Biochemistry and Physiology Part C: Comparative
632
Pharmacology 105:379-385. 633
Palli, S. R. 2014. RNA interference in Colorado potato beetle: steps toward development of
634
dsRNA as a commercial insecticide. Current Opinion Insect Science 6:1-8. 635
Panwar, B., Arora, A. and Raghava, G.P.S. 2014. Prediction and classification of ncRNAs using
636
structural information. BMC Genomics 15:127. 637
Perkin, L., Elpidina, E.N. and Oppert, B. 2016. Expression patterns of cysteine peptidase genes
638
across the Tribolium castaneum life cycle provide clues to biological function. PeerJ
639
4:e1581. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 640
Perkin, L.C., Elpidina, E.N. and Oppert, B. 2017a. RNA interference and dietary inhibitors
641
induce a similar compensation response in Tribolium castaneum larvae. Insect Molecular
642
Biology 26:35-45. 643
Perkin, L.C., Gerken, A.R., Oppert, B. 2017b. RNA-Seq validation of RNAi identifies additiona
644
gene connectivity in Tribolium castaneum (Coleoptera: Tenebrionidae). Journal of Insect
645
Science 17:1-7. 646
Pimentel, M.A., D'A Faroni, L.R., Da Silva, F.H., Batista, M.D. and Guedes, R.N.C. 2010. 647
Spread of phosphine resistance among Brazilian populations of three species of stored
648
product insects. Neotropical Entomology 39:101-107. 649
Reimand, J., Arak, T. and Vilo, J. 2011. g:Profiler--a web server for functional interpretation of
650
gene lists (2011 update). Nucleic Acids Research 39:W307-315. 651
Schmitt-Engel, C., Schultheis, D., Schwirz, J., Strohlein, N., Troelenberg, N., Majumdar, U.,
652
Dao, V.A., Grossmann, D., Richter, T., Tech, M., Donitz, J., Gerischer, L., Theis, M.,
653
Schild, I., Trauner, J., Koniszewski, N.D., Kuster, E., Kittelmann, S., Hu, Y., Lehmann,
654
S., Siemanowski, J., Ulrich, J., Panfilio, K.A., Schroder, R., Morgenstern, B., Stanke, M. 655
Buchhholz, F., Frasch, M., Roth, S., Wimmer, E.A., Schoppmeier, M., Klingler, M. and
656
Bucher, G. 2015. The iBeetle large-scale RNAi screen reveals gene functions for insect
657
development and physiology. Nature Communications 6:7822. 658
Sparks, M.E., Rhoades, J.H., Nelson, D.R., Kuhar, D., Lancaster, J., Lehner, B., Tholl, D.,
659
Weber, D.C. and Gundersen-Rindal, D.E. 2017. A Transcriptome Survey Spanning Life
660
Stages and Sexes of the Harlequin Bug, Murgantia histrionica. Insects 8. 640
Perkin, L.C., Elpidina, E.N. and Oppert, B. 2017a. RNA interference and dietary inhibitors
641
induce a similar compensation response in Tribolium castaneum larvae. Insect Molecular
642
Biology 26:35-45. 643
Perkin, L.C., Gerken, A.R., Oppert, B. 2017b. RNA-Seq validation of RNAi identifies additional
644
gene connectivity in Tribolium castaneum (Coleoptera: Tenebrionidae). Journal of Insect
645
Science 17:1-7. 646
Pimentel, M.A., D'A Faroni, L.R., Da Silva, F.H., Batista, M.D. and Guedes, R.N.C. 2010. 647
Spread of phosphine resistance among Brazilian populations of three species of stored
648
product insects. Neotropical Entomology 39:101-107. 649
Reimand, J., Arak, T. and Vilo, J. 2011. g:Profiler--a web server for functional interpretation of
650
gene lists (2011 update). Nucleic Acids Research 39:W307-315. Manuscript to be reviewed 661
Shen, G., Dou, W., Niu, J., Jiang, H., Yang, W., Jia, F., Hu, F., Cong, L. and Wang, J. 2011. 662
Transcriptome analysis of the Oriental fruit fly (Bactrocera dorsalis). PLoS one
663
6:e29127. 664
Thomson, T. and Lasko, P. 2004. Drosophila tudor is essential for polar granule assembly and
665
pole cell specification, but not for posterior patterning. Genesis 40:164-170. 666
Tomoyasu, Y. and Denell, R.E. 2004. Larval RNAi in Tribolium (Coleoptera) for analyzing
667
adult development. Developmental Genes and Evolution 214;575-578. 668
Tribolium Genome Sequencing Consortium. 2008. The genome of the model beetle and pest
669
Tribolium castaneum. Nature 452:949-955. 670
Tufarelli, C., Stanley, J.A., Garrick D, Sharpe, J.A., Ayyub, H., Wood, W.G. and Higgs, D.R. 671
2003. Transcription of antisense RNA leading to gene silencing and methylation as a
672
novel cause of human genetic disease. Nature Genetics 34:157-165. 673
Ulrich, J., Dao, V.A., Majumdar, U., Schmitt-Engel, C., Schwirz, J., Schultheis, D., Strohlein,
674
N., Troelenberg, N., Grossmann, D., Richter, T., Donitz, J., Gerischer, L., Leboulle, G.,
675
Vilcinskas, A., Stanke, M. and Bucher, G. 2015. Large scale RNAi screen in Tribolium
676
reveals novel target genes for pest control and the proteasome as prime target. BMC
677
Genomics 16:674. 678
Vinokurov, K.S., Elpidina, E.N., Zhuzhikov, D.P., Oppert, B., Kodrik, D. and Sehnal, F. 2009. 679
Digestive proteolysis organization in two closely related Tenebrionid beetles: red flour
680
beetle (Tribolium castaneum) and confused flour beetle (Tribolium confusum). Archives
681
in Insect Biochemistry 70:254-279. 682
Whyard, S., Singh, A.D., and Wong, S. 2009. Ingested double-stranded RNAs can act as specie
683
specific insecticides. Insect Biochemistsry and Molecular Biology 39:824-832. 661
Shen, G., Dou, W., Niu, J., Jiang, H., Yang, W., Jia, F., Hu, F., Cong, L. and Wang, J. 2011. 661
Shen, G., Dou, W., Niu, J., Jiang, H., Yang, W., Jia, F., Hu, F., Cong, L. an 662
Transcriptome analysis of the Oriental fruit fly (Bactrocera dorsalis). PLoS one
663
6:e29127. 664
Thomson, T. and Lasko, P. 2004. Drosophila tudor is essential for polar granule assembly and
665
pole cell specification, but not for posterior patterning. Genesis 40:164-170. 666
Tomoyasu, Y. and Denell, R.E. 2004. Larval RNAi in Tribolium (Coleoptera) for analyzing 666
Tomoyasu, Y. and Denell, R.E. 2004. Larval RNAi in Tribolium (Coleoptera) for analyzing
667
adult development. Developmental Genes and Evolution 214;575-578. 667
adult development. Developmental Genes and Evolution 214;575-578. Manuscript to be reviewed 651
Schmitt-Engel, C., Schultheis, D., Schwirz, J., Strohlein, N., Troelenberg, N., Majumdar, U.,
652
Dao, V.A., Grossmann, D., Richter, T., Tech, M., Donitz, J., Gerischer, L., Theis, M.,
653
Schild, I., Trauner, J., Koniszewski, N.D., Kuster, E., Kittelmann, S., Hu, Y., Lehmann, 640
Perkin, L.C., Elpidina, E.N. and Oppert, B. 2017a. RNA interference and dietary inhibitors
641
induce a similar compensation response in Tribolium castaneum larvae. Insect Molecular
642
Biology 26:35-45. 643
Perkin, L.C., Gerken, A.R., Oppert, B. 2017b. RNA-Seq validation of RNAi identifies additional
644
gene connectivity in Tribolium castaneum (Coleoptera: Tenebrionidae). Journal of Insect
645
Science 17:1-7. 646
Pimentel, M.A., D'A Faroni, L.R., Da Silva, F.H., Batista, M.D. and Guedes, R.N.C. 2010. 647
Spread of phosphine resistance among Brazilian populations of three species of stored
648
product insects. Neotropical Entomology 39:101-107. 649
Reimand, J., Arak, T. and Vilo, J. 2011. g:Profiler--a web server for functional interpretation of
650
gene lists (2011 update). Nucleic Acids Research 39:W307-315. 651
Schmitt-Engel, C., Schultheis, D., Schwirz, J., Strohlein, N., Troelenberg, N., Majumdar, U.,
652
Dao, V.A., Grossmann, D., Richter, T., Tech, M., Donitz, J., Gerischer, L., Theis, M.,
653
Schild, I., Trauner, J., Koniszewski, N.D., Kuster, E., Kittelmann, S., Hu, Y., Lehmann,
654
S., Siemanowski, J., Ulrich, J., Panfilio, K.A., Schroder, R., Morgenstern, B., Stanke, M.,
655
Buchhholz, F., Frasch, M., Roth, S., Wimmer, E.A., Schoppmeier, M., Klingler, M. and
656
Bucher, G. 2015. The iBeetle large-scale RNAi screen reveals gene functions for insect
657
development and physiology. Nature Communications 6:7822. 657
development and physiology. Nature Communications 6:7822. 658
Sparks, M.E., Rhoades, J.H., Nelson, D.R., Kuhar, D., Lancaster, J., Lehner, B., Tholl, D., 659
Weber, D.C. and Gundersen-Rindal, D.E. 2017. A Transcriptome Survey Spanning Life
660
Stages and Sexes of the Harlequin Bug, Murgantia histrionica. Insects 8. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Manuscript to be reviewed 668
Tribolium Genome Sequencing Consortium. 2008. The genome of the model beetle and pest
669
Tribolium castaneum. Nature 452:949-955. 670
Tufarelli, C., Stanley, J.A., Garrick D, Sharpe, J.A., Ayyub, H., Wood, W.G. and Higgs, D.R. 671
2003 Transcription of antisense RNA leading to gene silencing and methylation as a 670
Tufarelli, C., Stanley, J.A., Garrick D, Sharpe, J.A., Ayyub, H., Wood, W.G. and Higgs, D.R. 670
Tufarelli, C., Stanley, J.A., Garrick D, Sharpe, J.A., Ayyub, H., Wood, W.G. and Higgs, D.R. 671
2003. Transcription of antisense RNA leading to gene silencing and methylation as a
672
novel cause of human genetic disease. Nature Genetics 34:157-165. 671
2003. Transcription of antisense RNA leading to gene silencing and methylation as a
672
novel cause of human genetic disease. Nature Genetics 34:157-165. 673
Ulrich, J., Dao, V.A., Majumdar, U., Schmitt-Engel, C., Schwirz, J., Schultheis, D., Strohlein,
674
N., Troelenberg, N., Grossmann, D., Richter, T., Donitz, J., Gerischer, L., Leboulle, G.,
675
Vilcinskas, A., Stanke, M. and Bucher, G. 2015. Large scale RNAi screen in Tribolium
676
reveals novel target genes for pest control and the proteasome as prime target. BMC
677
Genomics 16:674. 678
Vinokurov, K.S., Elpidina, E.N., Zhuzhikov, D.P., Oppert, B., Kodrik, D. and Sehnal, F. 2009. 679
Digestive proteolysis organization in two closely related Tenebrionid beetles: red flour
680
beetle (Tribolium castaneum) and confused flour beetle (Tribolium confusum). Archives
681
in Insect Biochemistry 70:254-279. 682
Whyard, S., Singh, A.D., and Wong, S. 2009. Ingested double-stranded RNAs can act as species-
683
specific insecticides. Insect Biochemistsry and Molecular Biology 39:824-832. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Table 1(on next page) Manuscript to be reviewed 684
Ying, M. and Chen, D. (2012) Tudor domain-containing proteins of Drosophila melanogaster. 685
Developmental Growth & Differentiation 54:32-43. 686
Zhu, Q., Arakane, Y., Banerjee, D., Beeman, R.W., Kramer, K.J., and Muthukrishnan, S. 2008. 687
Domain organization and phylogenetic analysis of the chitinase-like family of proteins in
688
three species of insects. Insect Biochemistry and Molecular Biology 38: 452-466 685
Developmental Growth & Differentiation 54:32-43. 686
Zhu, Q., Arakane, Y., Banerjee, D., Beeman, R.W., Kramer, K.J., and Muthukrishnan, S. 2008. 687
Domain organization and phylogenetic analysis of the chitinase-like family of proteins in
688
three species of insects. Insect Biochemistry and Molecular Biology 38: 452-466 PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Manuscript to be reviewed Table 1(on next page) Table 1(on next page) Genes that were expressed at high and low levels in all life stages. List of genes that were expressed at high (top) and low (bottom) levels in all life stages of T. castaneum. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed 1
Tables
2
Table 1. Genes that were expressed at high (top) and low (bottom) levels in all life stages of T. castaneum. Average RPKM
Name
Description
Adult
Egg
Larvae
Pupae
LOC656235
Elongation factor 1-gamma
1,560
1,334
657
6,278
RpS3
Ribosomal protein S3
3,953
2,663
1,475
263
26-29-p
Cathepsin L
369
281
261
5,710
LOC659992
40S ribosomal protein S29
1,135
1,443
626
3,238
LOC663023
Glyceraldehyde-3-phosphate dehydrogenase 2
2,405
812
2,135
2,375
LOC660435
60S ribosomal protein L11
2,673
2,134
1,096
6,999
Efa1
Elongation factor 1-alpha
2,253
2,541
1,762
3,576
ND2
NADH dehydrogenase subunit 2
1,081
1,457
1,000
401
ATP6
ATP synthase F0 subunit 6
5,442
4,960
4,555
270
COX3
Cytochrome c oxidase subunit III
4,267
3,923
6,559
857
CYTB
Cytochrome b
3,181
4,829
7,123
558
I-rRNA
I-rRNA
16,635
11,824
34,216
11,020
LOC103315067
Uncharacterized
5.91
57.1
7.30
18.7
LOC103312214
Uncharacterized
10.3
89.0
8.11
24.6
LOC103315070
Uncharacterized
17.5
94.1
16.9
26.9
LOC107399196
Uncharacterized
25.5
181
9.69
22.7
LOC103312419
Maternal protein tudor
5.25
15.3
5.34
5.45
LOC103312455
poly(A) polymerase type 3
9.11
65.5
13.0
15.0
LOC663288
THO complex subunit 2
7.55
61.8
8.69
10.6
LOC659780
Transmembrane protein 35
240
7.72
241
179
LOC103313244
Sentrin-specific protease
10.5
74.6
35.0
9.45
3 1
Tables PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Table 2(on next page) Differentially expressed cuticle genes. Differentially expressed cuticle genes in T. castaneum larvae injected with CPG dsRNA. Shaded row indicates target gene. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Manuscript to be reviewed y expressed cuticle genes in T. castaneum larvae injected with LOC103313766 cuticle protein dsRNA. Shaded
gene. Table 2. Differentially expressed cuticle genes in T. castaneum larvae injected with LOC103313766 cuticle protein dsRNA. Shaded
2
row indicates target gene. 3 3
4
Gene
LG
Coordinate
Start
Coordinate
Stop
Protein
Annotation
Fold
Change
Expression
LOC103313766
3
4099231
4115167
XP_008196095
Cuticle protein
1,491
LOC658110
3
4097672
4112513
XP_015833062
Cuticle protein 16.5
2.51
LOC658489
3
4077823
4109423
XP_976285
Cuticle protein 19.8
1.44
LOC103313752
3
4114536
4126952
XP_008196069
Cuticle protein 70
10.8
LOC655183
3
2446367
2620651
XP_008190752
Cuticle protein
4.01
LOC100141875
5
3608978
3616499
XP_001809825
Cuticle protein
16.9
LOC656347
5
3612511
3613210
XP_008193006
Cuticle protein 7
4.89
LOC107399215
2
6796409
6962942
XP_015840495
Larval cuticle protein A2B-like
25.1
5 6 PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Manuscript to be reviewed Figure 1 Venn diagram comparing genes expressed in T. castaneum life stages: adult, egg,
larvae, and pupae with high expression values (>8 log2 RPKM). Shades of grey indicate the relative number of genes in each comparison. Dark grey
indicates a higher number of genes and lighter shades represent comparisons with fewer
genes. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Figure 2 Top GO terms for genes with high expression in each life stage. Each pie chart identifies the top GO terms for each life stage; (A) Egg, (B) Larvae, (C) Pupae,
(D) Adult. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed Manuscript to be reviewed Figure 3 Venn diagram comparing genes between all T. castaneum life stages: adult, egg, larvae,
and pupae with low expression values (2-8 log2 RPKM). Shades of grey indicate the relative number of genes in each comparison. Dark grey
indicates a higher number of genes and lighter shades represent comparisons with fewer
genes. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Figure 5 Effects of injection of CPG dsRNA in T. castaneum larvae. Figure 4 Top GO terms for genes with low expression in each T. castaneum life stage. Each pie chart identifies the top GO terms for each life stage; (A) Egg, (B) Larvae, (C) Pupae,
(D) Adult. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Effects of injection of CPG dsRNA in T. castaneum larvae. (A) Average expression of CPG in control, mock, and dsRNA-injected T. castaneum larvae 18
d following RNAi application. (B) Percent survival of T. castaneum larvae following RNAi
treatment. Manuscript to be reviewed PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Figure 6 Manuscript to be reviewed Manuscript to be reviewed Figure 6 T. castaneum cuticle protein maximum likelihood tree. CPG (XP_008196095) is highlighted with a yellow box, and proteins from the three cuticle
genes with increased expression (XP_008196069, XP_001809825, XP_008190752) are
highlighted with a red box. PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) Manuscript to be reviewed PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019) PeerJ reviewing PDF | (2018:11:32938:2:0:NEW 4 Apr 2019)
|
https://openalex.org/W4382195895
|
https://www.frontiersin.org/articles/10.3389/fimmu.2023.1159337/pdf
|
English
| null |
Strategies to improve γδTCRs engineered T-cell therapies for the treatment of solid malignancies
|
Frontiers in immunology
| 2,023
|
cc-by
| 7,109
|
TYPE Opinion
PUBLISHED 27 June 2023
DOI 10.3389/fimmu.2023.1159337 Introduction After the overwhelming clinical success of targeting hematological malignancies with
CAR-T cells (1), the first signals of treatment are seen for solid tumors targeted by
engineered immune cells (2). However, targeting solid tumors with this kind of
immunotherapy still remains a challenge (3, 4). There are multiple mechanisms that
make it difficult for adoptive cellular therapies to effectively target solid tumors. First, most solid tumors lack homogeneous expression of a tumor-specific antigen
making it difficult to find appropriate receptors to target them (5). The selection of
targetable tumor antigens needs careful consideration to avoid targeting of healthy tissue,
especially when considering engineered cellular therapies against solid cancers, where
potent and safe antigens are rare (6). Additionally, the microenvironment of solid tumors
holds unique features such as expression of immunosuppressive molecules and hypoxia
that have a huge impact on T cell fitness (4, 7, 8). Finally, a combination of extracellular
matrix deposition and anti-inflammatory signals, like attracting mesenchymal derived
suppressor cells (MDSCs), prevent effective infiltration of T cells towards the tumor site (9). In this article we will further discuss the roadblocks facing successful implementation
of T cell therapies for the treatment of solid malignancies focusing on gdT cells and their
receptors since they provide a new avenue to target novel tumor antigens. Characterization
of these cells and their receptors holds the potential to generate novel strategies for
targeting cancer and provide new engineering strategies to potentially overcome
these hurdles. First, most solid tumors lack homogeneous expression of a tumor-specific antigen
making it difficult to find appropriate receptors to target them (5). The selection of
targetable tumor antigens needs careful consideration to avoid targeting of healthy tissue,
especially when considering engineered cellular therapies against solid cancers, where
potent and safe antigens are rare (6). Additionally, the microenvironment of solid tumors
holds unique features such as expression of immunosuppressive molecules and hypoxia
that have a huge impact on T cell fitness (4, 7, 8). Finally, a combination of extracellular
matrix deposition and anti-inflammatory signals, like attracting mesenchymal derived
suppressor cells (MDSCs), prevent effective infiltration of T cells towards the tumor site (9). In this article we will further discuss the roadblocks facing successful implementation
of T cell therapies for the treatment of solid malignancies focusing on gdT cells and their
receptors since they provide a new avenue to target novel tumor antigens. KEYWORDS CITATION
Meringa AD, Herna´ ndez-Lo´ pez P, Cleven A,
de Witte M, Straetemans T, Kuball J,
Beringer DX and Sebestyen Z (2023)
Strategies to improve gdTCRs engineered
T-cell therapies for the treatment of
solid malignancies. Front. Immunol. 14:1159337. T-cell therapy, gdTCR, cancer, immune therapy, antigen, fitness, TME (tumor
microenvironment), migration Front. Immunol. 14:1159337. doi: 10.3389/fimmu.2023.1159337 © 2023 Meringa, Herna´ndez-Lo´ pez, Cleven,
de Witte, Straetemans, Kuball, Beringer and
Sebestyen. 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. OPEN ACCESS OPEN ACCESS
EDITED BY
Maria Themeli,
Amsterdam University Medical Center,
Netherlands
REVIEWED BY
Jonathan Fisher,
University College London,
United Kingdom
*CORRESPONDENCE
Z. Sebestyen
z.sebestyen@umcutrecht.nl
†These authors have contributed equally to
this work
RECEIVED 05 February 2023
ACCEPTED 09 June 2023
PUBLISHED 27 June 2023
CITATION
Meringa AD, Herna´ ndez-Lo´ pez P, Cleven A,
de Witte M, Straetemans T, Kuball J,
Beringer DX and Sebestyen Z (2023)
Strategies to improve gdTCRs engineered
T-cell therapies for the treatment of
solid malignancies. Front. Immunol. 14:1159337. doi: 10.3389/fimmu.2023.1159337 OPEN ACCESS
EDITED BY
Maria Themeli,
Amsterdam University Medical Center,
Netherlands
REVIEWED BY
Jonathan Fisher,
University College London,
United Kingdom
*CORRESPONDENCE
Z. Sebestyen
z.sebestyen@umcutrecht.nl
†These authors have contributed equally to
this work
RECEIVED 05 February 2023
ACCEPTED 09 June 2023
PUBLISHED 27 June 2023
CITATION
Meringa AD, Herna´ ndez-Lo´ pez P, Cleven A,
de Witte M, Straetemans T, Kuball J,
Beringer DX and Sebestyen Z (2023)
Strategies to improve gdTCRs engineered
T-cell therapies for the treatment of
solid malignancies. Front. Immunol. 14:1159337. doi: 10.3389/fimmu.2023.1159337 EDITED BY
Maria Themeli,
Amsterdam University Medical Center,
Netherlands
REVIEWED BY
Jonathan Fisher,
University College London,
United Kingdom
*CORRESPONDENCE
Z. Sebestyen
z.sebestyen@umcutrecht.nl A. D. Meringa 1†, P. Herna´ndez-Lo´ pez 1†, A. Cleven 1†,
M. de Witte 1,2, T. Straetemans 1,2, J. Kuball 1,2,
D. X. Beringer 1 and Z. Sebestyen 1* D. X. Beringer 1 and Z. Sebestyen 1* 1Center for Translational Immunology, University Medical Center Utrecht, Utrecht University,
Utrecht, Netherlands, 2Department of Hematology, University Medical Center Utrecht, Utrecht
University, Utrecht, Netherlands T-cell therapy, gdTCR, cancer, immune therapy, antigen, fitness, TME (tumor
microenvironment), migration Improving T-cell fitness for durable
tumor control T cell dysfunction has been one of the major causes of failure of
CAR-T cell treatments as it results in poor T cell expansion and
short-term persistence resulting in reduced anti-tumor efficacy (8,
49). Despite efforts to improve CAR designs, CAR-T cell exhaustion
remains one of the main limitations of this kind of therapy (50–52). Thus, although CAR-T field has significantly growth in the last years,
some studies advocate for the use of natural TCR signaling to reduce
exhaustion of T cells (53, 54). The main reason for this is that CAR’s
artificial design accelerates exhaustion of T cells when compared to
TCR based therapies, mostly due to the described tonic signaling in
the absence of antigen (54–56). In this line, several designs have been
explored to make CAR more TCR-like, such as HLA-independent
TCR (HIT) or synthetic TCR and antigen receptor (STAR) (57, 58). The CAR scFv sequence in these receptors is fused to the constant
domains of an abTCR, thereby preserving TCR signaling while using
the CAR’s ability to recognize tumors in an HLA independent way. An elegant alternative to these designs is engineering ab T cells to
express tumor-reactive Vg9Vd2 TCRs (called TEGs) (41, 59). In this
way, the use of gdTCRs in T cell therapy appear to be advantageous
when compared with CARs or abTCRs, as they supply T cells with
natural TCR signaling while preserving the ability of recognize
tumors in an HLA-independent way (44). Unlike above discussed Vd2- T cells, Vd2+ T cells, also referred
as Vg9Vd2 T cells are mainly present in blood and their role of
cancer immune surveillance have been studied the most among all
gdT cells (33). The process of identifying the ligand complex for the
invariant Vg9Vd2 TCRs has been a long and winding path, that
started with the identification of phosphoantigens (34) that are
bound by the intracellular domain of butrophylin 3A1 (BTN3A1)
(35). This process leads to a re-localization of BTN3A1 to the cell
surface (36, 37), where it can form a complex with BTN2A1 (38–
40). Only when this phosphoantigen driven complex of BTN3A1
and BTN2A1 is formed on the plasma membrane, Vg9Vd2 TCRs Optimal co-stimulation has been described as key to overcome
exhaustion and improve T cell fitness and persistence in the context
of cancer (60–62). Gamma delta T cells as source of
novel tumor-targeting receptors can be activated. This multistep ligand complex formation serves a
safety threshold that prevents Vg9Vd2 TCR mediated toxicity
towards healthy tissue but enables the eradication of tumors in
many preclinical models (41–43). The infiltration of gdT cell in tumors has been associated in
many studies to have a favorable impact on patient survival (10–16),
while some other studies made in murine models report that
interleukin-17 (IL-17) producing gdT cells are tumor promoting
(17, 18). While these data are very insightful, it has to be carefully
handled when translating it to human clinical practices given that
human and mouse gdT cell repertoires and functions are not fully
compatible. Regardless of the ultimate effector function, activation
of gdT cells is contingent upon the engagement of their surface
receptors with antigens on the tumor cell. gd T cells can be divided
into two groups, Vd2+ and Vd2-, with Vd1 forming the majority of
Vd2- T-cells. Vd2- T cells are predominantly found in peripheral
tissue and have also been shown to be enriched in carcinomas (11,
19–21). Multiple studies reported a correlating favorable clinical
outcome either with the presence of Vd2- T-cells (12, 13) or with
gdT in general (13). This tissue-association might be advantageous
for targeting and infiltrating solid tumors when using Vd1TCR T
cells as effector cells. Vd2- TCRs can recognize a wide variety of
ligands that are expressed on infected and malignant cells (22). A
large number of studies have shown that numerous Vd2- TCRs can
recognize nonpolymorphic MHC I-like molecules MR1 and CD1
(23, 24). Most CD1 isoforms, CD1a, CD1b, and CD1c, are mainly
found on cells of hematological origin and declassify them as
potential ligands for solid tumors (25), but both MR1 as CD1d
have been found to be expressed on solid tumors (25, 26). Other
gdTCR ligands expressed on solid tumors and are recognized by
specific Vd2- TCR clones are endothelial protein C receptor (EPCR)
(27), Annexin A2 (28), and EphA2 (29). Based on the wide breath of
ligands recognized by Vd2- TCRs (22), it is to be expected that many
more ligands for this subset will be identified in the future. While
many of these Vd2- TCR ligands are also expressed on the surface
healthy cells, such as EPCR on endothelial cells (30) and CD1d on
APCs (31), no major safety concerns have been reported. Gamma delta T cells as source of
novel tumor-targeting receptors For
example, a study demonstrating that while an EPCR reactive Vd2-
TCR clone recognized cytomegalovirus (CMV)-infected or
malignant endothelial cells it was not reactive against normal
endothelial cells, due to increased expression of immune
modulating molecules such as CD54 and CD58 (27). Additionally, to avoid toxicity towards healthy, antigen presenting
cells (APCs), lipid-specific CD1d reactive Vd2- TCRs can be
used (32). While gdT cells have their natural potential to target cancer, as
described above, the most clinical trials to date, that have assessed
the efficacy and safety of gdT cells as adoptive cellular therapy did
show moderate clinical efficacy (44–47) where only incidentally e.g. prolonged survival of patients has been reported (46). However, the
potential of natural, tumor infiltrating gdT cells has recently been
demonstrated in colorectal cancer (10) and kidney cancer (16),
supporting the idea to further investigate the details of receptors
present on gdT cells for the treatment of cancer. While providing an
emerging universe of tumor specific receptors, one has to carefully
assess possible toxicity against healthy tissues in advanced 3-
dimensional preclinical models (41, 42, 48) that resemble the
homeostatic environment of the human body. Introduction Characterization
of these cells and their receptors holds the potential to generate novel strategies for
targeting cancer and provide new engineering strategies to potentially overcome
these hurdles. Frontiers in Immunology Frontiers in Immunology 01 frontiersin.org Meringa et al. 10.3389/fimmu.2023.1159337 Frontiers in Immunology Improving T-cell fitness for durable
tumor control Therefore, as costimulatory signals are highly
involved in T cell metabolic reprogramming (63, 64) and T cell
exhaustion is closely related with metabolic dysfunction,
manipulation of co-stimulation in T cell therapies will result in
improved metabolic T cell fitness, which is key to achieve robust
anti-tumor responses (63). One example is the addition of co-
stimulatory domains to the first generation of CARs, which has
shown to improve persistence of these cells (65, 66). This led to the
development of second and third generation of CARs with Frontiers in Immunology 02 frontiersin.org Meringa et al. 10.3389/fimmu.2023.1159337 10.3389/fimmu.2023.1159337 improved proliferation ability. Therefore, combining natural
TCR signaling properties, by using gdTCRs to target tumors,
with improved co-stimulation might be the answer to CAR-
T limitations. Modulation of the chemokine signaling of the tumor-reactive T
cells can lead to improved T cell infiltration by increasing
chemotaxis towards the tumor site. For example, expression of
the colony stimulating factor receptor (CSF-R) in CAR-T cells
improved migration towards solid tumor models producing CSF
(84). Arming T cells with other chemokine receptors have shown
similar results where CCR4, CCR2b and CXCR3 overexpression in
the T cell products led to increased infiltration in the TME and
thereby increased tumor targeting (85–87). One way to improve the co-stimulation of T cells can be
achieved by expressing chimeric costimulatory receptors (CCRs)
in combination with a CAR or a TCR (67–70). These receptors
preserve the structure of conventional second-generation CARs but
lack the CD3z domain, therefore providing only costimulatory
signals to the T cell. Uncoupling of signal 1 (CD3 signal) and
signal 2 (co-stimulation) by this dual targeting has been shown to be
beneficial (71–73) as T cells will only activate once synergistic
signals are delivered upon encounter of both antigens. While these
receptors improve T cell proliferation, they also reduce exhaustion
(71) thereby improving T cell persistence in the tumor niche and
leading to an improved therapeutic effect (71, 74). y
g
g
Upon infiltration of immune cells in the TME, multiple
mechanisms can render the T cells inactive via expression of
immunosuppressive molecules. Well-known checkpoint molecules
such as PD-1 and TIM3 are not only affecting ab T cells but also act
on gd T cells as has been recently shown (10) in colorectal cancer. Improving T-cell fitness for durable
tumor control However, gd T cells are also often regulated by unique sets of
inhibitory natural killer (NK) receptors: for example, tumor and
stromal cells can express ligands for immune checkpoints in T cells
like HLA-E binding NKG2A on gd tumor infiltrating lymphocytes
(TILs) (88). To overcome this, numerous cytokines have been tested
to make armed CAR-T cells also known as T cell redirected for
antigen-unrestricted cytokine-initiated killing (TRUCKs) (89). CAR-T cells targeting different solid tumor models were shown to
improve their anti-tumor activity, increase their resistance to
regulatory T cell signaling and improve local proliferation upon
arming the T cells with IL-12 expression (90–92). Expression of
other cytokines such as IL-7, IL-15 and IL-18 have shown to provide
similar results by increasing therapy efficacy via increasing local
inflammation in the TME (92–94). Chemokine and cytokine
arming of gdTCR based T cell therapies could increase efficacy
since other T cell engineering approaches for CAR-T cells. A type of CCRs are the so-called switch chimeric co-receptors
(75–78), which use the extracellular domain of a described
inhibitory receptor (such as PD-1 or TIGIT) and link it to the
intracellular domain of activating costimulatory receptors (such as
CD28 or 4-1BB) or eventually DAP10, when expressed in gdT cells
(70). Thus, these receptors turn inhibitory signals, that would
normally induce exhaustion of T cells, into activating signals. This strategy improves not only T cell fitness, by improving co-
stimulation, but also makes engineered T cells resistant to tumor
microenvironment immunosuppressive factors. Finally, it is important to further investigate the mechanisms
that impact T cell fitness as not all the T cells subsets respond equal
to the same stimulus. For example, TGF-b has been shown to
improve cytotoxic activity of Vd2+ T cells (79) while it is been
described to suppress ab T cells function (80). Furthermore, IL-15
has been shown to improve tumor killing capacity of gdT cells
isolated from AML patients (81). Therefore, comprehensive studies
and rational engineering it is key to develop effective therapies. In
conclusion, to achieve durable anti-tumor responses the next
generation of T cell-based immunotherapies should include fine-
tuning of co-stimulation, to preserve T cell fitness, ensure
persistence, and skew the T cells to the most potent phenotype. Additionally, CAR-T cells can be engineered to express ECM-
modifying enzymes to facilitate better penetration to the tumor site. Improving T-cell fitness for durable
tumor control Heparinase expressing GD2 CAR-T cells improved their infiltrating
capacity in solid tumor models compared to CAR-T cells lacking
heparin expression (95, 96). Arming CAR-T cell with prolyl
endopeptidase is another approach for targeting the ECM in the
TME (97). Expression of prolyl endopeptidase in CAR-T cells
improved their anti-tumor activity, however some toxicity
towards healthy tissue was observed with both ECM targeting
approaches. Introducing these types of modifications could be
very promising for improving the therapeutic effect of gdTCR T
cells in solid tumors. Tackling the tumor microenvironment The lack of efficacy observed for different T cell treatments
targeting various antigens in solid tumors suggest the presence of
general barriers that inhibit the efficacy of these immunotherapies. The cellular and extra-cellular composition of the tumor
microenvironment can influence the tumor biology and response
to immune therapy (82). The dense extracellular matrix (ECM) of
solid tumors is a physical barrier for T cells to penetrate leading
to low numbers of infiltrating, endogenous T cells in solid tumors
(4). Meanwhile, immunosuppressive cells such as myeloid-
derived suppressive cells and regulatory T cells in the tumor
microenvironment (TME) inhibit antitumor activity of T cells
that do infiltrate in the TME (83). Different engineering strategies
are being developed to overcome these general barriers of T-cell
therapies in solid malignancies. Frontiers in Immunology Funding This work was supported by grants KWF 11979, KWF 11393,
KWF 12586, KWF 13043, KWF 13493 to authors JK, ZS and DB from
the Dutch Cancer Society KWF. In conclusion, promising approaches for improving the efficacy
and scope of T cell therapies are being developed to overcome the
current roadblocks in the treatment of solid malignancies. Using
gdTCRs as tumor-reactive receptors, and combining these with
appropriate co-stimulation via expression of additional chimeric
costimulatory receptor to improve fitness and providing additional
mechanisms to improve gdTCR T-cell infiltration like boosting
chemotaxis, will be key assets to enhance efficacy of T cell therapies
for solid malignancies. While further modifying the T cells does Author contributions All authors listed have made a substantial, direct, and intellectual
contribution to the work and approved it for publication. Future perspectives Current developments in the field of engineered adoptive
cellular therapies, especially CAR-T cell therapies show promising
results in the treatment of haematological malignancies; more
specifically B cell-derived tumors. However, adapting these T cells
therapies to solid tumor treatments options requires overcoming
certain impediments posed by solid malignancies and their TME
(Figure 1). Fortunately, these T cells-based therapies allow for ex
vivo modifications of the treatment to address these tumor-specific
challenges posed in the TME of solid tumors where lesson learned
from tumor specific gdT may provide a possible solution. Frontiers in Immunology frontiersin.org 03 Meringa et al. 10.3389/fimmu.2023.1159337 FIGURE 1
Schematic representation of T-cell engineering approaches. Biological mechanisms that prevent effective adoption of gd T-cell therapies for the
treatment of solid malignancies and suggested engineering strategies to overcome these hurdles are shown. FIGURE 1
Schematic representation of T-cell engineering approaches. Biological mechanisms that prevent effective adoption of gd T-cell therapies for the
treatment of solid malignancies and suggested engineering strategies to overcome these hurdles are shown. Selection of the tumor-reactive receptor and the tumor specific/
associated antigen remains the first important step in optimizing T cell
therapies in solid tumors. To this end, gdTCRs are an interesting option
due to their unique recognition patterns. Secondly, the addition of a co-
stimulatory signal, especially in combination with a naturally low
affinity gdTCR can help improve T cell fitness via either one of the
three suggested signalling approaches. Expressing a chimeric
costimulatory receptor to mimic signal 2 will help the T cells to retain
their anti-tumor activity upon prolonged exposure in the TME. Furthermore, the induction of inflammation via secretion of cytokines
such as at the tumor site can help the tumor infiltrating gdTCR T cells to
overcome the immunosuppressive signals present in the TME. Finally,
expression of chemokine(receptors) or ECM modifying molecules can
help increase T cell infiltration in the solid tumor microenvironment. contain risks, these solutions will help to optimize efficacy of
engineered T cell therapies and introduce this technology for a
more widespread use in anticancer therapy. Frontiers in Immunology Conflict of interest JK, ZS and DB are inventors on various patents regarding T cell
immune therapies, JK is shareholder at Gadeta BV. The remaining 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. frontiersin.org 04 Meringa et al. Meringa et al. 10.3389/fimmu.2023.1159337 10.3389/fimmu.2023.1159337 Publisher’s note organizations, or those of the publisher, the editors and the
reviewers. Any product that may be evaluated in this article, or
claim that may be made by its manufacturer, is not guaranteed or
endorsed by the publisher. All claims expressed in this article are solely those of the
authors and do not necessarily represent those of their affiliated References lymphocytes mediate antitumor reactivity. Cancer Immunol Res (2020) 8(4):530–43. doi: 10.1158/2326-6066.CIR-19-0513 1. Roschewski M, Longo DL, Wilson WH. CAR T-cell therapy for Large b-cell
lymphoma - who, when, and how? N Engl J Med (2022) 386(7):692–6. doi: 10.1056/
NEJMe2118899 22. Willcox BE, Willcox CR. Gammadelta TCR ligands: the quest to solve a 500-
million-year-old mystery. Nat Immunol (2019) 20(2):121–8. doi: 10.1038/s41590-018-
0304-y 2. Majzner RG, Ramakrishna S, Yeom KW, Patel S, Chinnasamy H, Schultz LM,
et al. GD2-CAR T cell therapy for H3K27M-mutated diffuse midline gliomas. Nature
(2022) 603(7903):934–41. doi: 10.1038/s41586-022-04489-4 23. Van Rhijn I, Le Nours J. CD1 and MR1 recognition by human gammadelta T
cells. Mol Immunol (2021) 133:95–100. doi: 10.1016/j.molimm.2020.12.008 3. MarofiF, Motavalli R, Safonov VA, Thangavelu L, Yumashev AV, Alexander M,
et al. CAR T cells in solid tumors: challenges and opportunities. Stem Cell Res Ther
(2021) 12(1):81. doi: 10.1186/s13287-020-02128-1 24. Castro CD, Boughter CT, Broughton AE, Ramesh A, Adams EJ. Diversity in
recognition and function of human gammadelta T cells. Immunol Rev (2020) 298
(1):134–52. doi: 10.1111/imr.12930 4. Hou AJ, Chen LC, Chen YY. Navigating CAR-T cells through the solid-tumour
microenvironment. Nat Rev Drug Discov (2021) 20(7):531–50. doi: 10.1038/s41573-
021-00189-2 25. Consonni M, Dellabona P, Casorati G. Potential advantages of CD1-restricted T
cell immunotherapy in cancer. Mol Immunol (2018) 103:200–8. doi: 10.1016/
j.molimm.2018.09.025 5. Wagner J, Wickman E, DeRenzo C, Gottschalk S. CAR T cell therapy for solid
tumors: bright future or dark reality? Mol Ther (2020) 28(11):2320–39. doi: 10.1016/
j.ymthe.2020.09.015 26. Crowther MD, Dolton G, Legut M, Caillaud ME, Lloyd A, Attaf M, et al. Genome-wide CRISPR-Cas9 screening reveals ubiquitous T cell cancer targeting via the
monomorphic MHC class I-related protein MR1. Nat Immunol (2020) 21(2):178–85. doi: 10.1038/s41590-019-0578-8 6. Bailey SR, Berger TR, Graham C, Larson RC, Maus MV. Four challenges to CAR
T cells breaking the glass ceiling. Eur J Immunol (2022) p:e2250039. doi: 10.1002/
eji.202250039 27. Willcox CR, Pitard V, Netzer S, Couzi L, Salim M, Silberzahn T, et al. Cytomegalovirus and tumor stress surveillance by binding of a human gammadelta
T cell antigen receptor to endothelial protein c receptor. Nat Immunol (2012) 13
(9):872–9. doi: 10.1038/ni.2394 7. Gao TA, Chen YY. Engineering next-generation CAR-T cells: overcoming tumor
hypoxia and metabolism. Annu Rev Chem Biomol Eng (2022) 13:193–216. doi: 10.1146/
annurev-chembioeng-092120-092914 8. Gumber D, Wang LD. Improving CAR-T immunotherapy: overcoming the
challenges of T cell exhaustion. EBioMedicine (2022) 77:103941. References doi: 10.1016/
j.ebiom.2022.103941 28. Marlin R, Pappalardo A, Kaminski H, Willcox CR, Pitard V, Netzer S, et al. Sensing of cell stress by human gammadelta TCR-dependent recognition of annexin
A2. Proc Natl Acad Sci USA (2017) 114(12):3163–8. doi: 10.1073/pnas.1621052114 9. Lanitis E, Dangaj D, Irving M, Coukos G. Mechanisms regulating T-cell
infiltration and activity in solid tumors. Ann Oncol (2017) 28(suppl_12):xii18–32. doi: 10.1093/annonc/mdx238 29. Harly C, Joyce SP, Domblides C, Bachelet T, Pitard V, Mannat C, et al. Human
gammadelta T cell sensing of AMPK-dependent metabolic tumor reprogramming
through TCR recognition of EphA2. Sci Immunol (2021) 6(61). doi: 10.1126/
sciimmunol.aba9010 10. de Vries NL, van de Haar J, Veninga V, Chalabi M, Ijsselsteijn ME, Ploeg der van
M, et al. Gammadelta T cells are effectors of immunotherapy in cancers with HLA class
I defects. Nature (2023) 613(7945):743–50. doi: 10.1038/s41586-022-05593-1 30. Laszik Z, Mitro A, Taylor FB Jr, Ferrell G, Esmon CT. Human protein c receptor
is present primarily on endothelium of large blood vessels: implications for the control
of the protein c pathway. Circulation (1997) 96(10):3633–40. doi: 10.1161/
01.CIR.96.10.3633 11. Gherardin NA, et al. Gammadelta T cells in merkel cell carcinomas have a
proinflammatory profile prognostic of patient survival. Cancer Immunol Res (2021) 9
(6):612–23. doi: 10.1158/2326-6066.CIR-20-0817 31. Brigl M, Brenner MB. CD1: antigen presentation and T cell function. Annu Rev
Immunol (2004) 22:817–90. doi: 10.1146/annurev.immunol.22.012703.104608 12. Donia M, Ellebaek E, Straten Pt Andersen MH, Svane IM. Analysis of Vdelta1 T
cells in clinical grade melanoma-infiltrating lymphocytes. Oncoimmunology (2012) 1
(8):1297–304. doi: 10.4161/onci.21659 32. Luoma AM, Castro CD, Mayassi T, Bembinster LA, Bai L, Picard D, et al. Crystal
structure of Vdelta1 T cell receptor in complex with CD1d-sulfatide shows MHC-like
recognition of a self-lipid by human gammadelta T cells. Immunity (2013) 39(6):1032–
42. doi: 10.1016/j.immuni.2013.11.001 13. Gentles AJ, Newman AM, Liu CL, Bratman SV, Feng W, Kim D, et al. The
prognostic landscape of genes and infiltrating immune cells across human cancers. Nat
Med (2015) 21(8):938–45. doi: 10.1038/nm.3909 33. Sebestyen Z, Prinz I, Déchanet-Merville J, Silva-Santos B, Kuball J. Translating
gammadelta (gammadelta) T cells and their receptors into cancer cell therapies. Nat
Rev Drug Discov (2020) 19(3):169–84. doi: 10.1038/s41573-019-0038-z 14. Zakeri N, Hall A, Swadling L, Pallett LJ, Schmidt NM, Diniz MO, et al. Characterisation and induction of tissue-resident gamma delta T-cells to target
hepatocellular carcinoma. Nat Commun (2022) 13(1):1372. doi: 10.1038/s41467-022-
29012-1 34. References Tanaka Y, Morita CT, Tanaka Y, Nieves E, Brenner MB, Bloom BR, et al. Natural and synthetic non-peptide antigens recognized by human gamma delta T cells. Nature (1995) 375(6527):155–8. doi: 10.1038/375155a0 15. Rosso DA, Rosato M, Iturrizaga J, González N, Shiromizu CM, Keitelman IA,
et al. Glioblastoma cells potentiate the induction of the Th1-like profile in
phosphoantigen-stimulated gammadelta T lymphocytes. J Neurooncol (2021) 153
(3):403–15. doi: 10.1007/s11060-021-03787-7 35. Harly C, Guillaume Y, Nedellec S, Peigné C-M, Mönkkönen H, Mönkkönen J,
et al. Key implication of CD277/butyrophilin-3 (BTN3A) in cellular stress sensing by a
major human gammadelta T-cell subset. Blood (2012) 120(11):2269–79. doi: 10.1182/
blood-2012-05-430470 16. Rancan C, Arias-Badia M, Dogra P, Chen B, Aran D, Yang H, et al. Exhausted
intratumoral Vdelta2(-) gammadelta T cells in human kidney cancer retain effector
function. Nat Immunol (2023) 24:612–24. doi: 10.1038/s41590-023-01448-7 36. Vantourout P, Laing A, Hayday AC. Heteromeric interactions regulate
butyrophilin (BTN) and BTN-like molecules governing gammadelta T cell biology. Proc Natl Acad Sci USA (2018) 115(5):1039–44. doi: 10.1073/pnas.1701237115 17. Coffelt SB, Kersten K, Doornebal CW, Weiden J, Vrijland K, Hau C-S, et al. IL-
17-producing gammadelta T cells and neutrophils conspire to promote breast cancer
metastasis. Nature (2015) 522(7556):345–8. doi: 10.1038/nature14282 37. Vyborova A, Beringer +DX, Fasci D, Karaiskaki F, Diest van E, Kramer L, et al. gamma9delta2T cell diversity and the receptor interface with tumor cells. J Clin Invest
(2020) 130(9):4637–51. doi: 10.1172/JCI132489 18. Lo Presti E, Toia F, Oieni S, Buccheri S, Turdo A, Mangiapane LR, et al. Squamous cell tumors recruit gammadelta T cells producing either IL17 or IFNgamma
depending on the tumor stage. Cancer Immunol Res (2017) 5(5):397–407. doi: 10.1158/
2326-6066.CIR-16-0348 38. Rigau M, Ostrouska S, Fulford TS, Johnson DN, Woods K, Ruan Z, et al. Butyrophilin 2A1 is essential for phosphoantigen reactivity by gammadelta T cells. Science (2020) 367(6478). doi: 10.1126/science.aay5516 19. Hidalgo JV, Bronsert P, Orlowska-Volk M, Dı́az LB, Stickeler E, Werner M, et al. Histological analysis of gammadelta T lymphocytes infiltrating human triple-negative
breast carcinomas. Front Immunol (2014) 5:632. doi: 10.3389/fimmu.2014.00632 39. Karunakaran MM, Willcox CR, Salim M, Paletta D, Fichtner AS, Noll A, et al. Butyrophilin-2A1 directly binds germline-encoded regions of the Vgamma9Vdelta2
TCR and is essential for phosphoantigen sensing. Immunity (2020) 52(3):487–498 e6. doi: 10.1016/j.immuni.2020.02.014 20. Dadi S, Chhangawala S, Whitlock BM, Franklin RA, Luo CT, Oh SA, et al. Cancer immunosurveillance by tissue-resident innate lymphoid cells and innate-like T
cells. References Sadelain M, Brentjens R, Rivière I. The basic principles of chimeric antigen
receptor design. Cancer Discov (2013) 3(4):388–98. doi: 10.1158/2159-8290.CD-12-
0548 46. Xu Y, et al. Allogeneic Vgamma9Vdelta2 T-cell immunotherapy exhibits
promising clinical safety and prolongs the survival of patients with late-stage lung or
liver cancer. Cell Mol Immunol (2021) 18(2):427–39. doi: 10.1038/s41423-020-0515-7 70. Fisher J, Sharma R, Don Wisidagamage D, Barisa M, Hurtado MO, Abramowski
P, et al. Engineering gammadeltaT cells limits tonic signaling associated with chimeric
antigen receptors. Sci Signal (2019) 12(598). doi: 10.1126/scisignal.aax1872 47. Fournie JJ, Sicard H, Poupot M, Bezombes C, Blanc A, Romagné F, et al. What
lessons can be learned from gammadelta T cell-based cancer immunotherapy trials? Cell Mol Immunol (2013) 10(1):35–41. doi: 10.1038/cmi.2012.39 71. Wilkie S, Schalkwyk van MCI, Hobbs S, Davies DM, Stegen der van SJC, Pereira
ACP, et al. Dual targeting of ErbB2 and MUC1 in breast cancer using chimeric antigen
receptors engineered to provide complementary signaling. J Clin Immunol (2012) 32
(5):1059–70. doi: 10.1007/s10875-012-9689-9 48. Braham MVJ, Minnema MC, Aarts T, Sebestyen Z, Straetemans T, Vyborova A,
et al. Cellular immunotherapy on primary multiple myeloma expanded in a 3D bone
marrow niche model. Oncoimmunology (2018) 7(6):e1434465. doi: 10.1080/
2162402X.2018.1434465 72. Liao Q, Mao Y, He H, Ding X, Zhang X, Xu J, et al. PD-L1 chimeric costimulatory
receptor improves the efficacy of CAR-T cells for PD-L1-positive solid tumors and
reduces toxicity in vivo. biomark Res (2020) 8(1):57. doi: 10.1186/s40364-020-00237-w 49. Fraietta JA, Lacey SF, Orlando EJ, Pruteanu-Malinici I, Gohil M, Lundh S, et al. Determinants of response and resistance to CD19 chimeric antigen receptor (CAR) T
cell therapy of chronic lymphocytic leukemia. Nat Med (2018) 24(5):563–71. doi:
10.1038/s41591-018-0010-1 73. Lanitis E, Poussin M, Klattenhoff AW, Song D, Sandaltzopoulos R, June CH,
et al. Chimeric antigen receptor T cells with dissociated signaling domains exhibit
focused antitumor activity with reduced potential for toxicity in vivo. Cancer Immunol
Res (2013) 1(1):43–53. doi: 10.1158/2326-6066.CIR-13-0008 50. Kouro T, Himuro H, Sasada T. Exhaustion of CAR T cells: potential causes and
solutions. J Transl Med (2022) 20(1):239. doi: 10.1186/s12967-022-03442-3 74. Halim L, Das KK, Larcombe-Young D, Ajina A, Candelli A, Benjamin R, et al. Engineering of an avidity-optimized CD19-specific parallel chimeric antigen receptor
that delivers dual CD28 and 4-1BB Co-stimulation. Front Immunol (2022) 13:836549. doi: 10.3389/fimmu.2022.836549 51. Wherry EJ, Kurachi M. Molecular and cellular insights into T cell exhaustion. Nat Rev Immunol (2015) 15(8):486–99. References doi: 10.1038/nri3862 75. Vienot A, Pallandre J-R, Renaude E, Viot J, Bouard A, Spehner L, et al. Chemokine switch regulated by TGF-b1 in cancer-associated fibroblast subsets
determines the efficacy of chemo-immunotherapy. Oncoimmunology (2022) 11
(1):2144669. doi: 10.1080/2162402X.2022.2144669 52. Poorebrahim M, Melief J, Coaña Pico Y, Wickström SL, Cid-Arregui A,
Kiessling R, et al. Counteracting CAR T cell dysfunction. Oncogene (2021) 40
(2):421–35. doi: 10.1038/s41388-020-01501-x 53. Salter AI, Rajan A, Kennedy JJ, Ivey RG, Shelby SA, Leung I, et al. Comparative
analysis of TCR and CAR signaling informs CAR designs with superior antigen
sensitivity and in vivo function. Sci Signal (2021) 14(697). doi: 10.1126/
scisignal.abe2606 76. Supimon K, Sangsuwannukul T, Sujjitjoon J, Chieochansin T, Junking M, P-T,
et al. Cytotoxic activity of anti-mucin 1 chimeric antigen receptor T cells expressing
PD-1-CD28 switch receptor against cholangiocarcinoma cells. Cytotherapy (2022)
25:148–61. doi: 10.1016/j.jcyt.2022.10.006 54. Wachsmann TLA, Wouters AK, Remst DFG, Hagedoorn RS, Meeuwsen MH,
Diest van E, et al. Comparing CAR and TCR engineered T cell performance as a
function of tumor cell exposure. Oncoimmunology (2022) 11(1):2033528. doi: 10.1080/
2162402X.2022.2033528 77. Chen C, Gu Y-M, Zhang F, Zhang Z-C, Zhang Y-T, He Y-D, et al. Construction
of PD1/CD28 chimeric-switch receptor enhances anti-tumor ability of c-met CAR-T in
gastric cancer. Oncoimmunology (2021) 10(1):1901434. doi: 10.1080/2162402X. 2021.1901434 55. Calderon H, Mamonkin M, Guedan S. Analysis of CAR-mediated tonic
signaling. Methods Mol Biol (2020) 2086:223–36. doi: 10.1007/978-1-0716-0146-4_17 78. Hoogi S, Eisenberg V, Mayer S, Shamul A, Barliya T, Cohen CJ, et al. A TIGIT-
based chimeric co-stimulatory switch receptor improves T-cell anti-tumor function. J Immunother Cancer (2019) 7(1):243. doi: 10.1186/s40425-019-0721-y 56. Gomes-Silva D, Mukherjee M, Srinivasan M, Krenciute G, Dakhova O, Zheng Y,
et al. Tonic 4-1BB costimulation in chimeric antigen receptors impedes T cell survival
and is vector-dependent. Cell Rep (2017) 21(1):17–26. doi: 10.1016/j.celrep.2017.09.015 79. Peters C, Meyer A, Kouakanou L, Feder J, Schricker T, Lettau M, et al. TGF-b
enhances the cytotoxic activity of Vd2 T cells. Oncoimmunology (2019) 8(1):e1522471. doi: 10.1080/2162402X.2018.1522471 57. Mansilla-Soto J, Eyquem J, Haubner S, Hamieh M, Feucht J, Paillon N, et al. HLA-independent T cell receptors for targeting tumors with low antigen density. Nat
Med (2022) 28(2):345–52. doi: 10.1038/s41591-021-01621-1 80. Dahmani A, Delisle JS. TGF-b in T cell biology: implications for cancer
immunotherapy. Cancers (Basel) (2018) 10(6). doi: 10.3390/cancers10060194 58. Liu Y, Liu G, Wang J, Zheng Z-Y, Jia L. References Cell (2016) 164(3):365–77. doi: 10.1016/j.cell.2016.01.002 40. Hsiao CHC, Nguyen K, Jin Y, Vinogradova O, Wiemer AJ. Ligand-induced
interactions between butyrophilin 2A1 and 3A1 internal domains in the HMBPP
receptor complex. Cell Chem Biol (2022) 29(6):985–995 e5. doi: 10.1016/
j.chembiol.2022.01.004 21. Janssen A, Hidalgo JV, Beringer DX, Dooremalen van S, Fernando F, Diest van
E, et al. Gammadelta T-cell receptors derived from breast cancer-infiltrating T Frontiers in Immunology 05 frontiersin.org Meringa et al. 10.3389/fimmu.2023.1159337 Meringa et al. memory development in CAR T cells. Immunity (2016) 44(2):380–90. doi: 10.1016/
j.immuni.2016.01.021 41. Johanna I, Straetemans T, Heijhuurs S, Aarts-Riemens T, Norell H, Bongiovanni
L, et al. Evaluating in vivo efficacy - toxicity profile of TEG001 in humanized mice
xenografts against primary human AML disease and healthy hematopoietic cells. J Immunother Cancer (2019) 7(1):69. doi: 10.1186/s40425-019-0558-4 65. Tokarew N, Ogonek J, Endres S, Bergwelt-Baildon von M, Kobold S. Teaching
an old dog new tricks: next-generation CAR T cells. Br J Cancer (2019) 120(1):26–37. doi: 10.1038/s41416-018-0325-1 42. van Diest E, López Hernández P, Meringa AD, Vyborova A, Karaiskaki F,
Heijhuurs S, et al. Gamma delta TCR anti-CD3 bispecific molecules (GABs) as novel
immunotherapeutic compounds. J Immunother Cancer (2021) 9(11). doi: 10.1136/jitc-
2021-003850 66. Imai C, Sjöstrand M, Naik J, Mansilla-Soto J, Kefala D, Kladis G, et al. Chimeric
receptors with 4-1BB signaling capacity provoke potent cytotoxicity against acute
lymphoblastic leukemia. Leukemia (2004) 18(4):676–84. doi: 10.1038/sj.leu.2403302 43. De Gassart A, Le K-S, Brune P, Agaugué S, Sims J, Goubard A, et al. Development of ICT01, a first-in-class, anti-BTN3A antibody for activating
Vgamma9Vdelta2 T cell-mediated antitumor immune response. Sci Transl Med
(2021) 13(616):eabj0835. doi: 10.1126/scitranslmed.abj0835 67. Katsarou A, Guo HF, Latouche JB, Tan C, Cheung NK, Sadelain M, et al. Combining a CAR and a chimeric costimulatory receptor enhances T cell sensitivity to
low antigen density and promotes persistence. Sci Transl Med (2021) 13(623):
eabh1962. doi: 10.1126/scitranslmed.abh1962 44. Sebestyen Z, Prinz I, Déchanet-Merville J, Silva-Santos B, Kuball J. Translating
gammadelta (gd) T cells and their receptors into cancer cell therapies. Nat Rev Drug
Discov (2020) 19(3):169–84. doi: 10.1038/s41573-019-0038-z 68. Krause A, et al. Antigen-dependent CD28 signaling selectively enhances survival
and proliferation in genetically modified activated human primary T lymphocytes. J Exp Med (1998) 188(4):619–26. doi: 10.1084/jem.188.4.619 45. Mensurado S, Blanco-Dominguez R, Silva-Santos B. The emerging roles of
gammadelta T cells in cancer immunotherapy. Nat Rev Clin Oncol (2023) 20:178–91. doi: 10.1038/s41571-022-00722-1 69. References Chimeric STAR receptors using TCR
machinery mediate robust responses against solid tumors. Sci Transl Med (2021) 13
(586). doi: 10.1126/scitranslmed.abb5191 81. Van Acker HH, Anguille S, Willemen Y, Bergh den Van JM, Berneman ZN, Lion
E, et al. Interleukin-15 enhances the proliferation, stimulatory phenotype, and
antitumor effector functions of human gamma delta T cells. J Hematol Oncol (2016)
9(1):101. doi: 10.1186/s13045-016-0329-3 59. Marcu-Malina V, Heijhuurs S, Buuren van M, Hartkamp L, Strand S, Sebestyen
Z, et al. Redirecting alphabeta T cells against cancer cells by transfer of a broadly tumor-
reactive gammadeltaT-cell receptor. Blood (2011) 118(1):50–9. doi: 10.1182/blood-
2010-12-325993 82. Junttila MR, de Sauvage FJ. Influence of tumour micro-environment
heterogeneity on therapeutic response. Nature (2013) 501(7467):346–54. doi:
10.1038/nature12626 60. Long AH, Haso WM, Shern JF, Wanhainen KM, Murgai M, Ingaramo M, et al. 4-1BB costimulation ameliorates T cell exhaustion induced by tonic signaling of
chimeric antigen receptors. Nat Med (2015) 21(6):581–90. doi: 10.1038/nm.3838 83. Verma NK, Wong BHS, Poh ZS, Udayakumar A, Verma R, Goh RKJ, et al. Obstacles for T-lymphocytes in the tumour microenvironment: therapeutic challenges,
advances and opportunities beyond immune checkpoint. EBioMedicine (2022)
83:104216. doi: 10.1016/j.ebiom.2022.104216 61. Guedan S, Posey AD Jr, Shaw C, Wing A, Da T, Patel PR, et al. Enhancing CAR
T cell persistence through ICOS and 4-1BB costimulation. JCI Insight (2018) 3(1). doi:
10.1172/jci.insight.96976 84. Lo AS, Taylor JR, Farzaneh F, Kemeny DM, Dibb NJ, Maher J, et al. Harnessing
the tumour-derived cytokine, CSF-1, to co-stimulate T-cell growth and activation. Mol
Immunol (2008) 45(5):1276–87. doi: 10.1016/j.molimm.2007.09.010 62. Kowolik CM, Topp MS, Gonzalez S, Pfeiffer T, Olivares S, Gonzalez N, et al. CD28 costimulation provided through a CD19-specific chimeric antigen receptor
enhances in vivo persistence and antitumor efficacy of adoptively transferred T cells. Cancer Res (2006) 66(22):10995–1004. doi: 10.1158/0008-5472.CAN-06-0160 85. Di Stasi A, Angelis De B, Rooney CM, Zhang L, Mahendravada A, Foster AE,
et al. T Lymphocytes coexpressing CCR4 and a chimeric antigen receptor targeting
CD30 have improved homing and antitumor activity in a Hodgkin tumor model. Blood
(2009) 113(25):6392–402. doi: 10.1182/blood-2009-03-209650 85. Di Stasi A, Angelis De B, Rooney CM, Zhang L, Mahendravada A, Foster AE,
et al. T Lymphocytes coexpressing CCR4 and a chimeric antigen receptor targeting
CD30 have improved homing and antitumor activity in a Hodgkin tumor model. Blood
(2009) 113(25):6392–402. doi: 10.1182/blood-2009-03-209650 63. Pellegrino M, Bufalo Del F, Angelis De B, Quintarelli C, Caruana I, Billy E, et al. 95. Caruana I, Savoldo B, Hoyos V, Weber G, Liu H, Kim ES, et al. Heparanase
promotes tumor infiltration and antitumor activity of CAR-redirected T lymphocytes.
Nat Med (2015) 21(5):524–9. doi: 10.1038/nm.3833 96. Mardomi A, Abediankenari S. Matrix metalloproteinase 8: could it benefit the
CAR-T cell therapy of solid tumors?- a- commentary on therapeutic potential. Cancer
Microenviron (2018) 11(1):93–6. doi: 10.1007/s12307-018-0208-2 91. Koneru M, Purdon TJ, Spriggs D, Koneru S, Brentjens RJ. IL-12 secreting
tumor-targeted chimeric antigen receptor T cells eradicate ovarian tumors in
vivo. Oncoimmunology (2015) 4(3):e994446. doi: 10.4161/2162402X.2014.
994446 94. Chmielewski M, Abken H. CAR T cells releasing IL-18 convert to T-bet(high)
FoxO1(low) effectors that exhibit augmented activity against advanced solid tumors.
Cell Rep (2017) 21(11):3205–19. doi: 10.1016/j.celrep.2017.11.063 References Manipulating the metabolism to improve the efficacy of CAR T-cell immunotherapy. Cells (2020) 10(1). doi: 10.3390/cells10010014 86. Nagarsheth N, Wicha MS, Zou W. Chemokines in the cancer microenvironment
and their relevance in cancer immunotherapy. Nat Rev Immunol (2017) 17(9):559–72. doi: 10.1038/nri.2017.49 86. Nagarsheth N, Wicha MS, Zou W. Chemokines in the cancer microenvironment
and their relevance in cancer immunotherapy. Nat Rev Immunol (2017) 17(9):559–72. doi: 10.1038/nri.2017.49 64. Kawalekar OU, RS, Fraietta JA, Guo L, McGettigan SE, Posey AD Jr, et al. Distinct signaling of coreceptors regulates specific metabolism pathways and impacts Frontiers in Immunology 06 frontiersin.org Meringa et al. 10.3389/fimmu.2023.1159337 Meringa et al. 87. Craddock JA, Lu A, Bear A, Pule M, Brenner MK, Rooney CM, et al. Enhanced
tumor trafficking of GD2 chimeric antigen receptor T cells by expression of the
chemokine receptor CCR2b. J Immunother (2010) 33(8):780–8. doi: 10.1097/
CJI.0b013e3181ee6675 92. Yeku OO, Purdon TJ, Koneru M, Spriggs D, Brentjens RJ. Armored CAR T cells
enhance antitumor efficacy and overcome the tumor microenvironment. Sci Rep (2017)
7(1):10541. doi: 10.1038/s41598-017-10940-8 93. Hoyos V, Savoldo B, Hoyos V, Weber G, Liu H, Kim ES, et al. Engineering
CD19-specific T lymphocytes with interleukin-15 and a suicide gene to enhance their
anti-lymphoma/leukemia effects and safety. Leukemia (2010) 24(6):1160–70. doi:
10.1038/leu.2010.75 93. Hoyos V, Savoldo B, Hoyos V, Weber G, Liu H, Kim ES, et al. Engineering
CD19-specific T lymphocytes with interleukin-15 and a suicide gene to enhance their
anti-lymphoma/leukemia effects and safety. Leukemia (2010) 24(6):1160–70. doi:
10.1038/leu.2010.75 88. Cazzetta V, Bruni E, Terzoli S, Carenza C, Franzese S, Piazza R, et al. NKG2A
expression identifies a subset of human Vdelta2 T cells exerting the highest
antitumor effector functions. Cell Rep (2021) 37(3):109871. doi: 10.1016/
j.celrep.2021.109871 94. Chmielewski M, Abken H. CAR T cells releasing IL-18 convert to T-bet(high)
FoxO1(low) effectors that exhibit augmented activity against advanced solid tumors. Cell Rep (2017) 21(11):3205–19. doi: 10.1016/j.celrep.2017.11.063 94. Chmielewski M, Abken H. CAR T cells releasing IL-18 convert to T-bet(high)
FoxO1(low) effectors that exhibit augmented activity against advanced solid tumors. Cell Rep (2017) 21(11):3205–19. doi: 10.1016/j.celrep.2017.11.063 89. Chmielewski M, Hombach AA, Abken H. Of CARs and TRUCKs: chimeric
antigen receptor (CAR) T cells engineered with an inducible cytokine to
modulate the tumor stroma. Immunol Rev (2014) 257(1):83–90. doi: 10.1111/
imr.12125 95. Caruana I, Savoldo B, Hoyos V, Weber G, Liu H, Kim ES, et al. 97. Tran E, Chinnasamy D, Yu Z, Morgan RA, Lee Richard C-C, Restifo NP, et al.
Immune targeting of fibroblast activation protein triggers recognition of multipotent
bone marrow stromal cells and cachexia. J Exp Med (2013) 210(6):1125–35. doi:
10.1084/jem.20130110 92. Yeku OO, Purdon TJ, Koneru M, Spriggs D, Brentjens RJ. Armored CAR T cells
enhance antitumor efficacy and overcome the tumor microenvironment. Sci Rep (2017)
7(1):10541. doi: 10.1038/s41598-017-10940-8
93. Hoyos V, Savoldo B, Hoyos V, Weber G, Liu H, Kim ES, et al. Engineering
CD19-specific T lymphocytes with interleukin-15 and a suicide gene to enhance their
anti-lymphoma/leukemia effects and safety. Leukemia (2010) 24(6):1160–70. doi:
10.1038/leu.2010.75
94. Chmielewski M, Abken H. CAR T cells releasing IL-18 convert to T-bet(high)
FoxO1(low) effectors that exhibit augmented activity against advanced solid tumors.
Cell Rep (2017) 21(11):3205–19. doi: 10.1016/j.celrep.2017.11.063
95. Caruana I, Savoldo B, Hoyos V, Weber G, Liu H, Kim ES, et al. Heparanase
promotes tumor infiltration and antitumor activity of CAR-redirected T lymphocytes.
Nat Med (2015) 21(5):524–9. doi: 10.1038/nm.3833
96. Mardomi A, Abediankenari S. Matrix metalloproteinase 8: could it benefit the
CAR-T cell therapy of solid tumors?- a- commentary on therapeutic potential. Cancer
Microenviron (2018) 11(1):93–6. doi: 10.1007/s12307-018-0208-2
97. Tran E, Chinnasamy D, Yu Z, Morgan RA, Lee Richard C-C, Restifo NP, et al.
Immune targeting of fibroblast activation protein triggers recognition of multipotent
bone marrow stromal cells and cachexia. J Exp Med (2013) 210(6):1125–35. doi:
10.1084/jem.20130110 References Heparanase
promotes tumor infiltration and antitumor activity of CAR-redirected T lymphocytes. Nat Med (2015) 21(5):524–9. doi: 10.1038/nm.3833 90. Pegram HJ, Lee J C, Hayman EG, Imperato GH, Tedder TF, Sadelain M, et al. Tumor-targeted T cells modified to secrete IL-12 eradicate systemic tumors without
need for prior conditioning. Blood (2012) 119(18):4133–41. doi: 10.1182/blood-2011-
12-400044 96. Mardomi A, Abediankenari S. Matrix metalloproteinase 8: could it benefit the
CAR-T cell therapy of solid tumors?- a- commentary on therapeutic potential. Cancer
Microenviron (2018) 11(1):93–6. doi: 10.1007/s12307-018-0208-2 91. Koneru M, Purdon TJ, Spriggs D, Koneru S, Brentjens RJ. IL-12 secreting
tumor-targeted chimeric antigen receptor T cells eradicate ovarian tumors in
vivo. Oncoimmunology (2015) 4(3):e994446. doi: 10.4161/2162402X.2014. 994446 97. Tran E, Chinnasamy D, Yu Z, Morgan RA, Lee Richard C-C, Restifo NP, et al. Immune targeting of fibroblast activation protein triggers recognition of multipotent
bone marrow stromal cells and cachexia. J Exp Med (2013) 210(6):1125–35. doi:
10.1084/jem.20130110 07 07 Frontiers in Immunology frontiersin.org
|
https://openalex.org/W2132284333
|
https://isprs-archives.copernicus.org/articles/XL-5/451/2014/isprsarchives-XL-5-451-2014.pdf
|
English
| null |
Photogrammetry applied to Problematic artefacts
|
The international archives of the photogrammetry, remote sensing and spatial information sciences/International archives of the photogrammetry, remote sensing and spatial information sciences
| 2,014
|
cc-by
| 4,616
|
1. INTRODUCTION The paper investigate this issue and reports the use of close-
range photogrammetry for the generation of 3D models of
artefacts stored in a museum which can result problematic due
to their material – reflective, translucent and homogenous
surfaces. The aim of this work is to show how a careful
planning and a correct imaging acquisition allow to generate
accurate and faithful 3D textured models of small exhibits even
in loco (without moving the object from the museum) and with
low-cost photographic equipment. 3D digitization applications in the world of historical patrimony
are directly connected to research and study, with the primary
goal
of
producing
heterogeneous
material
useful
for
documentation, restoration and as well valorization purposes. At
the same time 3D data can be used for the creation of virtual
models, reachable on digital media or on the web, thus intended
both as a virtual version of a proper museum, but as well as a
copy to study an archaeological artefact or a remote site. Digital
representations are pushing a deep transformation in the cultural
heritage domain and they are bringing new paths for generating
social and economic benefits in the scientific community, in
museums, as well as in the immediate surroundings. Surveying artefacts in museums can be a hard task due to many
constraints dictated by the location characteristics (i.e. restricted
spaces, unfavorable lighting conditions, etc.). Indeed passive
techniques are very dependent on ambient lighting conditions,
more than active sensors. External lights coming from windows
or mixed color light temperature caused by different light
sources hitting the object must be removed especially when
reflective surfaces are being surveyed. A proper inspection of
the location is therefore mandatory to reach the needed light
control over the artefact and define the available space around
the object. Although the process of creating 3D models from surveyed data
has represented a great benefit within the heritage field and a lot
of one-click solutions are nowadays available, there are still
many open issues raised by the design and implementation of a
project (Remondino et al., 2013), by software solutions
(Remondino et al., 2012; Koutsoudis et al., 2013) but also by
artefacts with challenging texture and material, such as marble,
metal surfaces, glass, etc. (Guidi et al., 2013). These problems
apply both to photogrammetry and range sensors. KEY WORDS: photogrammetry, cultural heritage, marble, ceramics, reflective, bronze KEY WORDS: photogrammetry, cultural heritage, marble, ceramics, reflective, bronze ABSTRACT: The process of creating 3D accurate and faithful textured models from 2D images has been a major endeavor within
the cultural heritage field. This field has general requirements, such as accuracy, portability and costs, that are often integrated by
more specific needs such as the integration of color information. The aim of this paper is to show how photogrammetry can be a valid
and reliable techniques for creating 3D models of museum artefacts even in case of objects with materials featuring difficult optical
properties (absorptivity, reflectivity, scattering), challenging texture and complex shape/geometry. The main objective is to establish
some core specifications for data acquisition and modeling, in order to guarantee the scientific quality of data and the interoperability
of 3D models with the archaeologists and conservators. All these aspects are taken into consideration and presented with three study
cases (two statues - one made of marble and one made of bronze - and a restored ceramic jug). The established, comprehensive and
accessible pipeline for the creation of complex artefacts 3D models in the field of cultural heritage is presented and discussed. a Romanian National History Museum, 12 Calea Victoriei, 030026, Bucharest, Romania –
mariacorinanicolae@gmail.com b 3D Optical Metrology (3DOM) unit, Bruno Kessler Foundation (FBK), via Sommarive 18, 38123, Trento, Italy –
<nocerino, fmenna, remondino>@fbk.eu cal Metrology (3DOM) unit, Bruno Kessler Foundation (FBK), via Sommarive 18, 38123, Trento, Italy –
<nocerino, fmenna, remondino>@fbk.eu PHOTOGRAMMETRY APPLIED TO PROBLEMATIC ARTEFACTS C. Nicolae a, E. Nocerino b, F. Menna b, F. Remondino b C. Nicolae a, E. Nocerino b, F. Menna b, F. Remondino b a Romanian National History Museum, 12 Calea Victoriei, 030026, Bucharest, Romania –
mariacorinanicolae@gmail.com 1. INTRODUCTION doi:10.5194/isprsarchives-XL-5-451-2014 451 The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL-5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL-5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy Figure 1: The two surveyed statues. Examples of very short depth of field on marble and bronze objects. The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL 5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy Figure 1: The two surveyed statues. Examples of very short depth of field on marble and bronze objects. - dense matching and 3D reconstruction for the generation of
dense point clouds;
- polygonal model generation and texture mapping for analyses
and visualization. - dense matching and 3D reconstruction for the generation of
dense point clouds; function of the object’s shape and the minimum base-to-
distance ratio that is planned between the photographs. For
objects of more complex shape it must be carefully selected and
can be also kept not constant in a complete turn (depending on
the complexity of the artefact). Several turns at different heights
may be necessary to cover the whole object and also strengthen
the camera network. Additional pictures for scaling the object
may be also required if the scale bar is not clearly visible in the
acquired images. - polygonal model generation and texture mapping for analyses
and visualization. 1. INTRODUCTION In this study, three artefacts belonging to the Archaeological
Collections of the Buonconsiglio castle in Trento (Italy) were
taken into consideration. The three case studies, two statues -
one of marble and one of bronze - and a restored ceramic jug
are all of small size. Consequently, very close-range
photogrammetry in quasi-macro regime was planned to be used. At small ranges from the objects, additional difficulties arise
due to the limited depth of field (Fig. 1) that demands good
photographic expertise to capture sharp and contrasted images,
mandatory for accurate 3D reconstruction (Menna et al., 2012). Marble is a translucent surface, bronze is reflective while in the
case of the ceramic vessel, approximately 30% of the object is
restored, thus textureless. pp y
p
g
y
g
For small objects, like many of the exhibits preserved in
museums, active triangulation sensors (laser or structured light)
are likely the most feasible and reliable digitization solutions. Unfortunately, these systems are usually quite expensive and
not all museums can afford such costs. Therefore, as in many
other applications, photogrammetry is a valuable and attractive
alternative. Photogrammetry is a 3D surveying and modelling
method which has the major advantage of being low-cost,
portable, flexible and able to deliver, at the same time, highly
detailed geometries and textures. The objects best suited for
automated image-based 3D reconstruction methods “have
amorphous geometries, structured surfaces, many edges, many
corresponding image points and an inhomogeneous coloring. Objects that produce rather bad or no results have unstructured,
monochrome, translucent, reflective, and/or self-resembling
surfaces” (Schaich, 2013). Nevertheless, most of the cultural
heritage artefacts fall in the second category, being therefore
problematic for image-based 3D modeling techniques. The undertaken work will be presented in three sections, each
section corresponding to one artefact, focusing more on the
winning methodology and lesson learnt than on the employed
software. The photogrammetric workflow consisted of: - image acquisition with a SLR digital camera; - camera calibration and image orientation, using automated
procedures able to extract homologues points between the
images and the unknown camera parameters; This contribution has been peer-reviewed. 2. SELECTION OF THE PHOTOGRAMMETRIC
PROCEDURES doi:10.5194/isprsarchives-XL-5-451-2014 452 The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL-5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy Front view
Side view
Back view
Enlargement of the object’s texture
Figure 2: Marble male torso (Collections of Castello del Buonconsiglio Museum, Trento, Italy). The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL-5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL-5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy Enlargement of the object’s texture Enlargement of the object’s texture Front view Front view Side view Back view Figure 2: Marble male torso (Collections of Castello del Buonconsiglio Museum, Trento, Italy Figure 2: Marble male torso (Collections of Castello del Buonconsiglio Museum, Trento, Italy). a)
b)
c)
Figure 3: Imaging network for the marble torso (a). Mesh (b) and textured 3D model (c). a) b) c) b)
c)
). Mesh (b) and textured 3D model (c). b)
c)
Figure 3: Imaging network for the marble torso (a). Mesh (b) and textured 3D model (c). which is a crystalline rock aggregation of small packed grains of
calcite, is known to generate errors and noise in range
measurements
when
using
an
active
sensor
due
to
heterogeneous reflection properties encountered on the marble
surface within the area illuminated (Godin et al., 2001; Guidi et
al., 2009). A set of 53 photos was acquired with a 14.2
Megapixel DX-format sensor Nikon D3100 (pixel size of 5.26
m) mounting a 35 mm Nikkor lens with the focus locked. The
imaging acquisition distance was about 520 mm, implying an
image scale of about 1:15 and a GSD of about 0.08 mm. The
obtained camera network is shown in Fig. 3a. The final mesh
model (Fig. 3b) and external texture (Fig. 3c) were generated
with an average resolution (mean triangle side length) of 0.3
mm and a mean GSD of 0.2 mm, respectively. imaging acquisition, attention should be paid in optimizing the
field of view, trying to cover the great part of the sensor with
the object of interest. 2. SELECTION OF THE PHOTOGRAMMETRIC
PROCEDURES In order to exploit the cost-effectiveness of most recent
photogrammetric developments, a quasi-automatic procedure
was selected. The photogrammetric acquisition was carried out
in a museum room during the closing day. Due to very long
exposure time required by dim lights present in the museum, the
camera was mandatorily mounted on a stable tripod. Indeed
large f-numbers used to guarantee a sufficient depth of field
yielded to very long exposure times. The advantage of rotating the object (when allowed) with
respect to rotating the camera around it is that the space needed
for the photographic acquisition can be significantly reduced -
an important factor considering the limited space normally
available in deposits and conservation labs. At the same time,
with this procedure, especially when photographing with limited
depth of field, the camera-to-object distance can be controlled
much more efficiently with respect to move the camera and the
tripod around the object especially when photographic lamps on
their stands are used. This results in a significant time saving. On the other hand the disadvantage when using turning tables is
that within the imaged scene there are relative movements
between the artefacts and the surrounding environment. Therefore, if automatic photogrammetric orientation is used,
images have to be properly masked for removing parts of the
images not belonging to the artefacts. When possible, setting up
a homogeneous background (e.g. a backcloth) can solve the
problem. Furthermore, in the In the case of the marble object, it was considered sufficient to
use the museum illumination, since it produced a quite
homogeneous illumination on the object, without strong shades
and reflections. For the other two artefacts, it was necessary to
use two photographic lamps mounted on tripods. The
availability of sufficient and safe space for the photographic
acquisition was a non-trivial issue. Indeed, the risk of hitting
and damaging other heritage assets when moving around with
bulky equipment can be really high and must not be
underestimated. Each artefact was placed on a turning table and rotated every
time of at least 1/16 of a round angle. In general, the angle is This contribution has been peer-reviewed. doi:10.5194/isprsarchives-XL-5-451-2014 This contribution has been peer-reviewed. 4. STUDY CASE 2 – BRONZE WARRIOR a reference scale bar was marked on the images in order to
scale the photogrammetric model; The second artefact taken into consideration is a small bronze
statuette, about 150 mm high, depicting Mars, the Roman God
of war (Fig. 4). The bronze statue represents a challenging
object because of its material and size. In this case, the museum
lights were not suitable for the survey, since they produced
several specular reflections on the shiny bronze object. To avoid
specular highlight that can compromise the photogrammetric
process and produce a not faithful texture, some cold lamps
were used and circular polarized filters were applied to camera
lens and lamps. Cross polarization indeed reduces the amount of
light hitting the sensor, requiring lower aperture number and/or
higher exposure time. With matted surfaces, cross-polarization
removes veiling glare and increases saturation and contrast. an automatic dense image matching process was run; the derived dense point cloud was triangulated to obtain a
mesh model; the mesh model was opportunely edited to correct for
topological errors; the mesh model was textured with high resolution external
texture generated from the original images. 2. SELECTION OF THE PHOTOGRAMMETRIC
PROCEDURES The three case studies were selected for their characteristics,
very common in the cultural heritage field and also known to be
problematic for non-contact optical measuring systems. For the
three artefacts different angular steps of the rotating table and
acquisition heights were used. At least three additional pictures
were taken for imaging a scale bar. After the image acquisition, the following processing and
modeling workflow was used: After the image acquisition, the following processing and
modeling workflow was used: if necessary, the images were manually edited in order to
mask the background, leaving only the artifact visible on the
pictures; the images were automatically oriented; 3. STUDY CASE 1 – MARBLE TORSO The marble torso has a size of 300x150x100 mm (Fig. 2). The
artifact is dated to the early Roman period (2nd cent. AD) and
was selected for its material and colour. Figure 3 shows a
particular of the material: the grain of the marble makes the
object suitable for photogrammetric process. Indeed, marble, This contribution has been peer-reviewed. doi:10.5194/isprsarchives-XL-5-451-2014 This contribution has been peer-reviewed. doi:10.5194/isprsarchives-XL-5-451-2014 453 The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL-5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL-5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy Front view
Side view
Back view
Enlargement of the object texture with bluish specular
reflections
Figure 4. Bronze statuette depicting Roman Mars (Collections of Castello del Buonconsiglio Museum, Trento, Italy). ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy Enlargement of the object texture with bluish specular
reflections Enlargement of the object texture with bluish specular
reflections Back view Side view Front view Figure 4. Bronze statuette depicting Roman Mars (Collections of Castello del Buonconsiglio Museum, Trento, Italy). a)
b)
c)
Figure 5: Derived camera network for the bronze warrior (a). Mesh model after the triangulation of the dense point cloud (b) and textured model (c). a) b) c) c) time of 5.0 s. The images were taken from a distance of
approximately 63 cm from the object, obtaining a GSD less than
0.04 mm. Instead with certain metals and alloys some specular reflections
still remain, causing artificial bluish colour where the specular
reflections are stronger. This effect is still visible on the bronze
warrior (Fig. 4 right). Thanks to the high number of acquired
images, the effect is significantly reduced on the final 3D
textured model. 35 photos (Fig. 5a) were acquired, using 24
Megapixel Nikon D3X full frame camera (pixel size of 5.95
m), with a 105 mm macro lens, ISO 400, f/16.0, and exposure The final mesh model (Fig. 5b) and external texture (Fig. 5c)
were generated with an average resolution (mean triangle side
length) less than 0.1 mm and a mean GSD of 0.1 mm,
respectively. 3. STUDY CASE 1 – MARBLE TORSO Object
Camera type
Nominal focal
length [mm]
Pixel size
[m]
# images
Image GSD
[mm]
Mesh resolution
[mm]
Texture resolution
[mm]
Marble torso
Nikon D3100
35
5.26
53
0.08
0.3
0.2
Bronze statue
Nikon D3X
105
5.95
35
0.04
0.1
0.1
Ceramic jug
Nikon D3100
35
5.26
55+40
0.1
0.25
0.25 This contribution has been peer-reviewed. doi:10.5194/isprsarchives-XL-5-451-2014
454 This contribution has been peer-reviewed. doi:10.5194/isprsarchives-XL-5-451-2014
454 454 The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL-5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy Right view
Left view
Back view
Enlargement of the featureless restored part without
(left) and with the projected random pattern (right)
Figure 6. Ceramic jug (Collections of Castello del Buonconsiglio Museum, Trento, Italy). The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL-5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL-5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy Right view
Left view
Back view
Enlargement of the featureless restored part without
(left) and with the projected random pattern (right)
Figure 6. Ceramic jug (Collections of Castello del Buonconsiglio Museum, Trento, Italy). Right view
Left view Left view Right view Enlargement of the featureless restored part without
(left) and with the projected random pattern (right) Right view Left view Back view Figure 6. Ceramic jug (Collections of Castello del Buonconsiglio Museum, Trento, Italy). Figure 7: Reconstructed 3D model of the ceramic jug: the white
textureless part was not reconstructed using a standard photographic
equipment and photogrammetric approach. approximately 63 cm giving a GSD of about 0.1 mm. For the
pattern projection, a Dell M109S mini projector was used. A
first complete set of 55 photos of the ceramic jug was acquired,
without pattern projection (green pyramids in Fig. 8a). A second set of 40 images was acquired, divided into five
different strips. From each position two images were acquired:
one with the projected pattern on the object and one without the
pattern (red pyramids, Fig. 8b). It is noteworthy that for each
single strip the relative position between the object and pattern
remained fixed. Between two consecutive strips, the object was
rotated until all the white textureless part was completely
photographed. 5. STUDY CASE 3 – CERAMIC JUG The third case study is represented by a restored ceramic jug
(Fig. 6). According to the form of the pot, it is a kitchen ware,
known as olpe, being employed for liquids. This type of ceramic
is specific for the 1st cent. AD of the Roman Empire. The object
has approximately 30% of its body restored – according to
restoration criteria, for this part it has been used a homogenous
and textureless material (Figure 6). As photogrammetry needs
corresponding features visible in different images in order to
compute the exterior and interior parameters of the camera, the
texture of the object is a primary factor in determining the
future geometry of the imaged object. To test the reliability of
automatic photogrammetric procedures in case of challenging
texture, a first experiment was performed employing minimal
photographic equipment. A 14.2 Megapixel DX-format sensor
Nikon D3100 (pixel size of 5.26 m) mounting a 35 mm Nikkor
lens with the focus locked was used to take 73 photos ISO 1600,
f/11.0, and exposure time of 0.6s-1.3s. In this test, the museum
illumination was used; the camera was put on the tripod and the
object rotated. With this minimal and simple set up, the
restored, white part of the object was not reconstructed (Figure
7). 3. STUDY CASE 1 – MARBLE TORSO All the images without pattern were aligned in
order to derive the interior and exterior camera parameters. Afterwards, for matching purposes, the images with the pattern
were substituted to those from the same position but without
pattern assigning the same camera parameters. Those images
were then employed to reconstruct the geometry of the white
part of the object. After the dense matching, a polygon mesh of
approximately 0.25 mm mean triangle side length (Fig. 8c) and
a high resolution (0.25 mm GSD) texture (Fig. 8d) were
produced. Figure 7: Reconstructed 3D model of the ceramic jug: the white
textureless part was not reconstructed using a standard photographic
equipment and photogrammetric approach. Schaich, M. 2013: Combined 3D scanning and photogrammetry
surveys with 3D database support for archaeology & cultural
heritage. A practice report on ArcTron’s information system
aSPECT3D. Proc. Photogrammetric Week 2013, D. Fritsch (ed.).
Wichmann, Berlin/Offenbach, pp. 233-246. 6. CONCLUSIONS doi:10.5194/isprsarchives-XL-5-451-2014 455 The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL-5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XL-5, 2014
ISPRS Technical Commission V Symposium, 23 – 25 June 2014, Riva del Garda, Italy Figure 8: Imaging configuration for the ceramic jug: main imaging configuration without pattern projected onto the object (a); additional strips with
images acquired with random pattern (b). Mesh model after the triangulation of the dense point cloud (c) and final textured 3D model (d). configuration for the ceramic jug: main imaging configuration without pattern projected onto the object (a); additional strips with
ed with random pattern (b). Mesh model after the triangulation of the dense point cloud (c) and final textured 3D model (d). Figure 8: Imaging configuration for the ceramic jug: main imaging configuration without pattern projected onto the object (a); additional strips with
images acquired with random pattern (b). Mesh model after the triangulation of the dense point cloud (c) and final textured 3D model (d). Lichti, D. D., Harvey, B. R., 2002: The effects of reflecting
surface
properties
on
Time-of-Flight
laser
scanner
measurements. Int. Archives of Photogrammetry, Remote
Sensing and Spatial Information Sciences, Vol. 34(4). As demonstrated in the reported results, although featureless
textures represent a challenge for image-based documentation
methods, there are solutions in order to deliver precise 3D
geometric and textural information of these types of objects. As demonstrated in the reported results, although featureless
textures represent a challenge for image-based documentation
methods, there are solutions in order to deliver precise 3D
geometric and textural information of these types of objects. Koutsoudis, B. Vidmar, F. Arnaoutoglou, 2013: Performance
evaluation of a multi-image 3D reconstruction software on a
low-feature artifact. Journal of Archaeological Science, Vol. 40
pp. 4450-4456, http://dx.doi.org/10.1016/j.jas.2013.07.007. ACKNOWLEDGEMENTS This work was funded by COST-Action TD 1201: Colour and
Space in Cultural Heritage (COSCH) within a Short Term
Scientific Mission grant, performed at 3DOM-FBK, Trento
(Italy), from November-December 2013. The work is also
partially supported by the 3D-ICONS project funded under the
EC’s ICT Policy Support Programme. The authors are also
thankful to the Buonconsiglio Castle personnel for their support
and help during the acquisitions. Menna, F., Rizzi, A., Nocerino, E., Remondino, F., Gruen, A.,
2012: High resolution 3D modeling of the Behaim globe. Int. Archives of Photogrammetry, Remote Sensing and Spatial
Information Sciences, Vol. 39(5), pp. 115-120. XXII ISPRS
Congress, Melbourne, Australia Remondino, F., Del Pizzo, S., Kersten, T., Troisi, S., 2012:
Low-cost and open-source solutions for automated image
orientation – A critical overview. Proc. EuroMed 2012
Conference, LNCS 7616, pp. 40-54. 6. CONCLUSIONS The paper presented the photogrammetric surveying and 3D
modeling of some museum artefacts with challenging texture
and color, complex shape/geometry and material featuring
difficult optical properties (absorptivity, reflectivity, scattering). An automated procedure was assembled in order to achieve
satisfactory results in terms of geometry as well as texture. The
most important aspects are geometry and, more critically, high
fidelity colour information. Close-range photogrammetry was
employed as an effective, low-cost and automated technique. In
contrast to other more complex and expensive system solutions,
close-range
photogrammetry
is
relatively
accessible
to
professionals in non-technical fields - such as curators or
restorers – both in terms of software and hardware. Nevertheless
high attention and experience is needed for the image
acquisition otherwise even the most effective fully automated
procedure will fail. A second test was then carried out using a more sophisticated
photographic configuration. For successfully applying an
automatic and non-invasive photogrammetric processing
without employing targets or directly interact with the object, a
random pattern was projected on the artifact in order to create a
synthetic texture on the featureless material (Figure 6). Images were acquired with the same Nikon D3100 of the first
case study. Additionally, polarized light was used for reducing
the
reflections. The
camera
to
object
distance
was A second test was then carried out using a more sophisticated
photographic configuration. For successfully applying an
automatic and non-invasive photogrammetric processing
without employing targets or directly interact with the object, a
random pattern was projected on the artifact in order to create a
synthetic texture on the featureless material (Figure 6). The first two artefacts highlighted a high level of noise in the
final mesh models, most probably a consequence primarily of
the reduced depth of field (see other experiences in Bitelli and
Girardi, 2010; Gallo et al., 2013) and the material of the object. Having a reduced depth of field, points matching becomes more
difficult and the result is a mesh with high noise level, more
topological errors and a final textured 3D model with some
areas out of focus. Images were acquired with the same Nikon D3100 of the first
case study. Additionally, polarized light was used for reducing
the
reflections. The
camera
to
object
distance
was b) b) d) c) a) This contribution has been peer-reviewed. doi:10.5194/isprsarchives-XL-5-451-2014 This contribution has been peer-reviewed. REFERENCES Bitelli, G., Girardi, F., 2010: Problematiche nel rilievo e
modellazione tridimensionale di oggeti di piccole dimensioni
nel campo dei Beni Culturali. Proc. 14a Conferenza Nazionale
ASITA,
pp. 285-290
(available
at:
http://www.attiasita.it/ASITA2010/Pdf/241.pdf, last accessed
on May 15, 2014). Remondino, F., Menna, F., Koutsoudis, A., Chamzas, C., El-
Hakim, S., 2013: Design and implement a reality-based 3D
digitisation and modelling project. Proc. IEEE Conference
"Digital Heritage 2013", Vol. 1, pp. 137-144. Schaich, M. 2013: Combined 3D scanning and photogrammetry
surveys with 3D database support for archaeology & cultural
heritage. A practice report on ArcTron’s information system
aSPECT3D. Proc. Photogrammetric Week 2013, D. Fritsch (ed.). Wichmann, Berlin/Offenbach, pp. 233-246. Gallo, G., Muzzupappa, A., Bruno, F., 2013: 3D reconstruction
of small sized objects from a sequence of multi-focused images. Journal of Cultural Heritage, Vol. 15(2), pp. 173-182 Guidi, G., Remondino, F., Russo, M., Spinetti, A, 2009: Range
sensors on marble surfaces: quantitative evaluation of artifacts. Proc. Videometrics, Range Imaging and Applications X, Proc. of SPIE Optics+Photonics, Vol. 7447, pp. 744703-744703. Guidi, G., Rodríguez Navarro, O., Gonizzi-Barsanti, S., Micoli,
L.L., Russo, M., 2013: Quick textured mesh generation in
Cultural heritage digitization. Proc. Built Heritage 2013
Conference - Monitoring Conservation and Management, pp. 874-882. Godin, G., Rioux, M., Beraldin, J.-A., Levoy, M., Cournoyer,
L., 2001. An Assessment of Laser Range Measurement of
Marble Surfaces. Proc. of the 5th Conference on Optical 3-D
Measurement Techniques, Vienna, Austria, 49-56. Gordon, S., Lichti, D. D., Stewart, M.P., Tsakiri, M., 2001. Metric performance of a high-resolution laser scanner. Proc. of
Videometrics and Optical Methods for 3D Shape Measurement,
SPIE Vol. 4309, pp. 174-184. This contribution has been peer-reviewed. doi:10.5194/isprsarchives-XL-5-451-2014 This contribution has been peer-reviewed. doi:10.5194/isprsarchives-XL-5-451-2014 456
|
https://openalex.org/W2556949014
|
https://europepmc.org/articles/pmc5100966?pdf=render
|
English
| null |
Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests: A Randomized Clinical Trial
|
PLoS medicine
| 2,016
|
cc-by
| 8,136
|
Background Achieving higher rates of partner HIV testing and couples testing among pregnant and post-
partum women in sub-Saharan Africa is essential for the success of combination HIV pre-
vention, including the prevention of mother-to-child transmission. We aimed to determine
whether providing multiple HIV self-tests to pregnant and postpartum women for secondary
distribution is more effective at promoting partner testing and couples testing than conven-
tional strategies based on invitations to clinic-based testing. Academic Editor: Alexander C. Tsai,
Massachusetts General Hospital, UNITED STATES Academic Editor: Alexander C. Tsai,
Massachusetts General Hospital, UNITED STATES Received: June 20, 2016
Accepted: September 30, 2016
Published: November 8, 2016 Received: June 20, 2016
Accepted: September 30, 2016
Published: November 8, 2016 OPEN ACCESS Citation: Masters SH, Agot K, Obonyo B, Napierala
Mavedzenge S, Maman S, Thirumurthy H (2016)
Promoting Partner Testing and Couples Testing
through Secondary Distribution of HIV Self-Tests:
A Randomized Clinical Trial. PLoS Med 13(11):
e1002166. doi:10.1371/journal.pmed.1002166 Samuel H. Masters1, Kawango Agot2, Beatrice Obonyo2, Sue Napierala Mavedzenge3,
Suzanne Maman4, Harsha Thirumurthy1,5* 1 Department of Health Policy and Management, Gillings School of Global Public Health, University of North
Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America, 2 Impact Research and
Development Organization, Kisumu, Kenya, 3 RTI International, San Francisco, California, United States of
America, 4 Department of Health Behavior, Gillings School of Global Public Health, University of North
Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America, 5 Carolina Population Center,
University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America a1111 * harsha@unc.edu Promoting Partner Testing and Couples
Testing through Secondary Distribution of
HIV Self-Tests: A Randomized Clinical Trial Samuel H. Masters1, Kawango Agot2, Beatrice Obonyo2, Sue Napierala Mavedzenge3,
Suzanne Maman4, Harsha Thirumurthy1,5* RESEARCH ARTICLE * harsha@unc.edu Conclusions Competing Interests: The authors have declared
that no competing interests exist. Competing Interests: The authors have declared
that no competing interests exist. Provision of multiple HIV self-tests to women seeking antenatal and postpartum care was
successful in promoting partner testing and couples testing. This approach warrants further
consideration as countries develop HIVST policies and seek new ways to increase aware-
ness of HIV status among men and promote couples testing. Abbreviations: ANC, antenatal care; HIVST, HIV
self-testing; IPV, intimate partner violence; PPC,
postpartum care; SSA, sub-Saharan Africa. Abbreviations: ANC, antenatal care; HIVST, HIV
self-testing; IPV, intimate partner violence; PPC,
postpartum care; SSA, sub-Saharan Africa. Why Was This Study Done? • Despite progress in recent years, men in sub-Saharan Africa have lower HIV testing
rates than women, and nearly half of all HIV-positive individuals remain unaware of
their HIV status; this represents a key barrier to meeting the UNAIDS 90-90-90 targets
for HIV elimination. • Among pregnant and postpartum women, male partner testing has been encouraged for
HIV prevention purposes but remains uncommon in many countries. • Recent WHO guidelines on HIV testing serviceshave acknowledged the potential of
HIV self-testing as a means to increase testing uptake among those not reached by other
testing services,and have called for additional research to explore the potential benefits
of self-testing. • “Secondary distribution” of self-tests by women visiting health facilities has the potential
to increase access to testing among their male sexual partners and to promote results dis-
closure and safer sexual decision-making. Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests Trial Registration ClinicalTrials.gov NCT02386215. PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 Methods and Findings We conducted a randomized trial in Kisumu, Kenya, between June 11, 2015, and January
15, 2016. Six hundred antenatal and postpartum women aged 18–39 y were randomized to
an HIV self-testing (HIVST) group or a comparison group. Participants in the HIVST group
were given two oral-fluid-based HIV test kits, instructed on how to use them, and encour-
aged to distribute a test kit to their male partner or use both kits for testing as a couple. Par-
ticipants in the comparison group were given an invitation card for clinic-based HIV testing
and encouraged to distribute the card to their male partner, a routine practice in many
health clinics. The primary outcome was partner testing within 3 mo of enrollment. Among
570 participants analyzed, partner HIV testing was more likely in the HIVST group (90.8%,
258/284) than the comparison group (51.7%, 148/286; difference = 39.1%, 95% CI 32.4%
to 45.8%, p < 0.001). Couples testing was also more likely in the HIVST group than the
comparison group (75.4% versus 33.2%, difference = 42.1%, 95% CI 34.7% to 49.6%, p <
0.001). No participants reported intimate partner violence due to HIV testing. This study
was limited by self-reported outcomes, a common limitation in many studies involving
HIVST due to the private manner in which self-tests are meant to be used. Copyright: © 2016 Masters 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: Data from this study
are available on the Odum Institute, HIV self-testing
Dataverse: http://dx.doi.org/10.15139/S3/12409. Funding: The study was funded by the
International Initiative for Impact Evaluation (TW2-
02-02). HT acknowledges support from the Eunice
Kennedy Shriver National Institute of Child Health
and Human Development (K01HD061605). The
funders had no role in study design, data collection
and analysis, decision to publish, or preparation of
the manuscript. 1 / 15 PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 What Do These Findings Mean? • The promising results of this study suggest that secondary distribution of self-tests war-
rants further consideration as countries develop HIV self-testing policies and seek new
ways to promote male partner testing and couples testing. • Additional research is recommended to explore uptake of clinic-based confirmatory
testing among partners who self-test HIV-positive, which was beyond the scope of this
research. • The feasibility of secondary distribution strategies among other populations and settings
should be explored, along with the potential of HIV self-tests to facilitate safer sexual
behaviors. What Did the Researchers Do and Find? • We conducted a randomized trial among 600 women attending antenatal and postpar-
tum clinics in western Kenya to determine whether providing them multiple HIV self-
tests is more effective at promoting partner testing and couples testing than a conven-
tional strategy based on partner invitations to clinic-based testing. • In the three months of follow-up, male partner testing was reported to have occurred for
90% of women in the HIV self-testing group but only 52% of women in the comparison
group, a difference that was statistically significant. • Couples testing was more than twice as likely among women who received multiple HIV
self-tests than women who received invitations for their partners (75% in the HIV self-
testing group versus 33% in the comparison group). • The self-testing intervention was safe and effective at promoting partner HIV testing
among women whose partners had not tested in the past 12 months. 2 / 15 PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 Ethics Statement The study received approval from the Scientific and Ethics Review Unit at the Kenya Medical
Research Institute and the Office of Human Research Ethics at the University of North Caro-
lina at Chapel Hill. Study Setting The study was conducted in urban and peri-urbanareas within Kisumu County, Kenya. Adult
HIV prevalence in Kisumu County is 19.3% [23], the third highest among the counties in the coun-
try. Women visiting ANC and PPC clinics were recruitedfrom three health facilities in Kisumu. Introduction Simple oral-
fluid-basedtests have achieved high sensitivity and specificity, with some studies also having 3 / 15 PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests shown that the tests can be used accurately by individuals [18]. A number of countries in SSA
have developed policies for implementation and support of HIVST [19,20], with Kenya being
the first country in SSA to include HIVST in its national testing guidelines [21]. Recent
research in Kenya has also demonstrated the acceptability and feasibility of a novel “secondary
distribution” strategy that seeks to promote HIV testing among men and in couples through
provision of multiple self-tests to women seeking health services[22]. We conducted a randomized trial in Kenya among women receiving antenatal care (ANC)
or postpartum care (PPC) servicesto test whether the provision of multiple self-tests to women
for distribution to their partners can increase uptake of male partner testing and couples
testing. Introduction Low uptake of HIV testing servicesin sub-Saharan Africa (SSA) is among the key barriers to
meeting the 90-90-90 targets established by UNAIDS and to improving the effectiveness of
HIV treatment as prevention. HIV testing among men in particular remains low in many
countries, as does knowledge of HIV status among HIV-infected persons [1]. Door-to-door
testing and mobile testing strategies have moved testing servicesout of health facilities and into
communities, overcoming barriers related to clinic-based testing and, subsequently, increasing
testing coverage. However, despite these advancements, there remains a need for novel inter-
ventions that can promote testing among men and other hard-to-reach populations [2,3]. In addition to increasing HIV testing uptake among men, achieving higher rates of couples
testing can also contribute to HIV prevention efforts. Low uptake of couples testing is particu-
larly concerning in light of data indicating that four out of every ten new HIV infections occur
within stable heterosexual partnerships and that the majority of persons in sero-discordant
relationships are unaware of their HIV status [4]. The benefits of couples testing may include
safer sexual behavior in couples [5], higher uptake of interventions such as antiretroviral ther-
apy (ART) for HIV-positive partners [6], and pre-exposure prophylaxis (PrEP) among HIV-
negative partners in sero-discordant relationships, as well as increased uptake of and adherence
to prevention of mother-to-child transmission (PMTCT) interventions [7–9]. Given the need
to achieve better PMTCT outcomes and prevent new infections in couples, a number of coun-
tries have sought to promote partner testing and couples testing among pregnant and postpar-
tum women [10]. However, efforts to encourage pregnant and postpartum women to refer
their male partners for HIV testing have had limited success [11,12]. The barriers to testing
among male partners have included stigma, fear of prognosis, lack of awareness of HIV risk,
inconvenience, fear of disclosure, transportation costs, opportunity costs such as time off from
work, and behavioral factors such as a tendency to delay behaviors with immediate costs and
delayed benefits [13,14]. HIV self-testing (HIVST) is a promising approach that addresses many barriers associated
with clinic-based HIV testing and has had high acceptability in SSA [15–17]. Self-tests enable
individuals to test themselves for HIV privately and at their own convenience. Study Design and Participants Trained research assistants screened and enrolled women seeking ANC or PPC at the three
facilities, in a private location away from regular clinic activities. Women were given the oppor-
tunity to enroll in the study if they met the following eligibility criteria: were 18–39 y of age,
reported that their primary partner was not known to be HIV-positive or had not tested in the
past 6 mo, resided in or around Kisumu County, and had no intention of leaving the area
within 3 mo. In addition, at the ANC clinic eligibility was limited to women with gestation
age 20 wk, and at the PPC clinic eligibility was limited to women who had given birth in the
past 6 wk to 12 mo. Following the provision of written informed consent, participants were
administered a baseline questionnaire that measured demographic characteristics, sexual
behavior, HIV testing history, and partner characteristics. All study staff received ethical train-
ing on research with human participants. Randomization Procedures Participants were randomized in a 1:1 ratio using balanced block randomization (block size 20)
to an HIVST group or a comparison group. Sealed randomization envelopes were offered to
participants sequentially, and these revealed the study group assignment to the participant and
study staff simultaneously. Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests undertake couples testing if they felt comfortable doing so; they were also counseled on how to
talk to their partners about HIV testing, the possibility of adverse reactions associated with sug-
gesting HIV testing to their partner, learning their partner’s HIV status, and disclosing their
own HIV status. Following Kenya’s 2015 HIV testing servicesguidelines [19], participants
were informed about the need to seek clinic-based confirmatory testing if a positive (reactive)
self-test result was obtained, and an invitation card for confirmatory testing at a clinic in the
study area was included with each test. Participants in the comparison group were counseled on the importance of partner testing
and provided with an invitation card to give to their partner for HIV testing at a study clinic. The use of invitation cards to promote male partner testing is currently standard practice in
many facilities. The cards mentioned the importance of testing, listed the health facility where
the participant was enrolled, and encouraged the male partner to get tested at the study facility. B
h
i
d i f
i
h
k d i
d
i
f
li i
l Both groups received information on where to seek advice and assistance for clinical,
counseling, and legal support in case of intimate partner violence (IPV). They also were given a
study phone number to call in case they had questions or needed advice about clinic-based test-
ing or self-testing, or IPV or other adverse events. Follow-Up Assessments Follow-up data collection occurred over a 3-mo period. Participants were contacted each
month to determine if they had distributed a self-test kit to their sexual partner (HIVST group)
or if their partner had sought HIV testing at a clinic (comparison group). Research assistants
scheduled and conducted an in-person follow-up interviewwith participants who reported
having distributed a test to their partner or who reported that their partner sought clinic-based
testing, while participants who had not done so or were not reached at 1 and 2 mo were inter-
viewed at 3 mo. If participants were unable to meet with research assistants, a follow-up phone
interviewwas conducted. Participants in both groups were asked whether their partner had
been tested for HIV since study enrollment. PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 Intervention Participants in the HIVST group received two oral-fluid-basedrapid HIV tests (OraQuick
Rapid HIV-1/2 Antibody Test, OraSure Technologies). Each test was accompanied with an
instruction sheet that describedstep-by-step self-testing procedures in multiple languages. Study staff also provided the participants with a brief demonstration of how to use the test. Par-
ticipants were encouraged to distribute a test kit to their male partner or to use both test kits to 4 / 15 PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 Statistical Analyses The unit of analysis was the study participant. All outcomes were self-reportedby study partici-
pants. The primary, prespecified outcome was whether the primary partner of the participant
had an HIV test within 3 mo of enrollment, which was determined from the follow-up survey
question: “Has your partner had an HIV test since you were enrolled in the study?” The pri-
mary analysis compared this outcome in the HIVST and comparison groups using an unad-
justed modifiedPoisson regression with robust standard errors [24]. Our original analysis plan
proposed estimation of a logistic regression model, but ultimately we selected a modifiedPois-
son model because risk ratios can be easier to interpret than odds ratios. We chose to present
both the absolute risk differences between the two study groups and the risk ratios from modi-
fied Poisson regressions. Participants who were not successfully followed up were not included
in the analyses as it was not possible to determine the primary and secondary outcomes for
them. In secondaryanalyses we examined the impact of the intervention on the following six out-
comes reported by participants: (1) discussion of HIV testing with partner, (2) couples testing,
(3) couples testing among participants whose partner tested for HIV, (4) awareness of partner’s
HIV test result, (5) awareness of partner’s HIV test result among participants whose partner
tested for HIV, and (6) partner’s HIV test result. Discussion of HIV testing was defined as hav-
ing occurred if the participant reported that she and her partner had talked about HIV testing
since enrollment in the study. Couples testing was defined as having occurredwhen a 5 / 15 PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests participant reported that she had tested together with her partner at the same time. Awareness
of partner’s HIV test result was defined as the participant having learned her partner’s HIV sta-
tus. Additionally, we examined whether partners of participants in the HIVST group who
tested positive sought confirmatory testing and whether partners in both groups who received
a positive result were reported to be in care at the time of follow-up. We also assessed IPV at
baseline and follow-up using questions adapted from the Kenya Demographic and Health Sur-
vey [25] that asked whether participants experiencedphysical, emotional, verbal, or sexual vio-
lence from their partner. Participant Recruitment and Flow BetweenJune 11, 2015, and October16, 2015, a total of 1,929 women were screened for participa-
tion. Among those, 614 (32%) were determined to be ineligible, 715 declined to participate
(37%), and 600 (31%) were enrolled and randomized (Fig 1). Reasons for ineligibility included
no primary partner (28%), partner HIV-positive (22%), intention of leaving study area during
follow-up period(15%), age of participant (8%), age of child (8%), and fear of IPV due to discuss-
ing HIV testing with partner (5%). Common reasons for refusal included women reporting they
were “in a hurry” or “too busy” (384/715, 53.7%), needing permission from partner to enroll in a
study (54/715, 7.6%), and reporting their partner had tested recently and therefore did not have
interest in participating in the study (111/715, 15.5%). Follow-up interviewswere conducted
until January 15, 2016. One person from the comparison group withdrew from the study during
the follow-up period.Of the 600 participants who were enrolled, follow-up was completed for
570 (95%), 286 (94.4%) in the comparison group and 284 (95.6%) in the HIVST group. Statistical Analyses Participants were coded as having experiencedIPV if they responded
affirmatively to any of the IPV questions. Survey questions used to measure study outcomes
are reported in S1 Table. In order to determine whether there were differences in intervention effectiveness in certain
populations, we estimated modifiedPoisson regression models among participants who were
enrolled at each of the three health facilities, among those whose primary partner had tested
for HIV in the 12 mo prior to enrollment or not, and among those who had experiencedIPV
in the 12 mo prior to enrollment or not. All statistical tests were two-sided, and significance
level was set at p < 0.05. No adjustment was made for multiple testing since the secondary
analyses were considered exploratory. Statistical analyses were performed using Stata 14.1. The planned sample size for the study was 600, with 300 participants in each study group. Power calculations assuming a two-sided unadjusted independent proportions test indicated
that with a sample size of 300 per study group and 20% uptake of partner testing in the com-
parison group, there would be 80% power to detect a difference in partner testing as small as
10%. Participant Characteristics Participants in the two study groups had largely similar characteristics at baseline (Table 1). Their mean age was 24 y, and the vast majority were married. Median monthly earnings was
US$0 since the majority did not report any engagement in income-earning activities during or
after pregnancy. Participants’ self-reported sexual behavior and their reports of their partner’s
HIV testing history were similar in both groups (Table 2). Nearly 4% of all participants self-
reported being HIV-positive. The majority of participants reported that their partner had
tested for HIV in the past 12 mo (56%), and only a small percentage of participants (14%) had
heard of HIVST prior to the study. Nearly 30% of participants reported experiencingIPV in
the past 12 mo. 6 / 15 PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests Male Partner Testing Male partner testing within 3 mo of enrollment was higher in the HIVST group (258/284,
90.8%) than the comparison group (148/286, 51.7%), as shown in Table 3. The difference of
39.1% between the two groups was statistically significant (95% CI 32.4% to 45.8%, p < 0.001). Among participants in the HIVST group whose partners used a self-test, 76% and 17%
reported that their partner found it “very easy” or “somewhat easy,” respectively, to use the
self-test, while 6% reported that their partner found it “somewhat difficult” or “very difficult.”
In the comparison group, 45% (67/148) of partners who tested were reported to have done so
outside of the three study facilities. Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests Table 1. Baseline characteristics of study participants. Characteristic
Comparison Group (n = 286)
HIV Self-Testing Group (n = 284)
Total (n = 570)
Age (years), mean (SD)
24.2 (4.3)
24.2 (4.5)
24.2 (4.4)
Monthly earnings (US dollars), median (IQR)
0 (0–30)
0 (0–40)
0 (0–36)
Ethnic group
Luo
221 (77)
219 (77)
440 (77)
Luhya
33 (12)
43 (15)
76 (13)
Other
32 (11)
22 (8)
54 (9)
Education
Some or completed primary
138 (48)
143 (50)
281 (49)
Some secondary
133 (47)
120 (42)
253 (44)
Completed secondary or greater
15 (5)
21 (7)
36 (6)
Married
266 (93)
266 (94)
532 (93)
Occupation
Non-manual
74 (26)
83 (29)
157 (28)
Manual
19 (7)
28 (10)
47 (8)
Housewife/unemployed
193 (67)
173 (61)
366 (64) Table 1. Baseline characteristics of study participants. −1.1%, 95% CI −4.3% to 2.2%, p = 0.512). Participants in the HIVST group were more likely to
test as a couple than participants in the comparison group (difference = 42.1%, 95% CI 34.7%
to 49.6%, p < 0.001). In addition, among participants whose partner tested for HIV during the
follow-up period, couples testing was more likely in the HIVST group than the comparison
group (difference = 18.8%, 95% CI 9.8% to 27.8%, p < 0.001). For all variables frequencies are presented, with percentages in parentheses, except where otherwise noted. IQR, interquartile range; SD, standard deviation. doi:10.1371/journal.pmed.1002166.t001 −1.1%, 95% CI −4.3% to 2.2%, p = 0.512). Participants in the HIVST group were more likely to
test as a couple than participants in the comparison group (difference = 42.1%, 95% CI 34.7%
to 49.6%, p < 0.001). In addition, among participants whose partner tested for HIV during the
follow-up period, couples testing was more likely in the HIVST group than the comparison
group (difference = 18.8%, 95% CI 9.8% to 27.8%, p < 0.001). Table 2. Self-reported sexual behavior and HIV testing history. Secondary Outcomes Over 95% of participants in both groups reported discussing HIV testing with their partner
since enrollment, and there was no significant difference between the two groups (difference = Fig 1. Assessment of eligibility, randomization, and follow-up. HIVST, HIV self-testing. doi:10.1371/journal.pmed.1002166.g001 Fig 1. Assessment of eligibility, randomization, and follow-up. HIVST, HIV self-testing. doi:10.1371/journal.pmed.1002166.g001 PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 7 / 15 d, with percentages in parentheses, except where otherwise noted. For all variables frequencies are presented, with percentages in parentheses, except where otherwise noted.
SD
d
d d
i
i −1.1%, 95% CI −4.3% to 2.2%, p = 0.512). Participants in the HIVST group were more likely to
test as a couple than participants in the comparison group (difference = 42.1%, 95% CI 34.7%
to 49.6%, p < 0.001). In addition, among participants whose partner tested for HIV during the
follow-up period, couples testing was more likely in the HIVST group than the comparison
group (difference = 18.8%, 95% CI 9.8% to 27.8%, p < 0.001). Behavior or HIV Testing History
Comparison Group (n = 286) HIV Self-Testing Group (n = 284) Total, (n = 570)
Age at first intercourse (years), mean (SD)
17.7 (2.8)
17.9 (2.5)
17.8 (2.7)
Condom used during last sex
54 (19)
46 (16)
100 (18)
Had at least one other sexual partner in the past 12 mo
4 (1)
5 (2)
9 (2)
Number of times been tested for HIV in the past 12 mo, mean
(SD)
2.8 (1.4)
2.8 (1.5)
2.8 (1.4)
Self-reported HIV-positive
10 (3.5)
13 (4.6)
23 (4.1)
Heard of HIV self-testing prior to study
39 (14)
41 (14)
80 (14)
Primary partner ever tested for HIV
Yes
220 (77)
216 (76)
436 (76)
No
19 (7)
21 (7)
40 (7)
Don’t know
47 (16)
47 (17)
94 (16)
Primary partner tested for HIV in the past 12 mo
Yes
173 (60)
149 (52)
322 (56)
No
35 (12)
42 (15)
77 (14)
Don’t know
78 (27)
93 (33)
171 (30)
Know partner’s status
192 (67)
194 (68)
386 (68)
Experienced intimate partner violence in the past 12 mo
76 (27)
78 (27)
154 (27)
For all variables frequencies are presented, with percentages in parentheses, except where otherwise noted. SD, standard deviation. Table 2. Self-reported sexual behavior and HIV testing history. PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 8 / 15 Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests At follow-up, participants in the HIVST group were more likely to know their partner’s
HIV status than those in the comparison group (difference = 39.1%, 95% CI 32.4% to 45.8%,
p < 0.001). However, among participants whose partner tested for HIV during the follow-up
period, participants’ awareness of their partner’s HIV status did not differ significantly between
the two groups (difference = 0.9%, 95% CI −1.8% to 3.5%, p < 0.519), suggesting that the
increase in awareness of partner HIV status in the HIVST group was driven by the greater like-
lihood of partner testing having occurred rather than a greater likelihoodof becoming aware if
a partner did get tested. Among participants whose partner tested for HIV, almost all were
aware of their partner’s HIV test result (98.0% in comparison group, 98.8% in HIVST group). A small number of participants in both groups reported that their partner tested HIV-positive
(1.4% in comparison group, 2.8% in HIVST group). Heterogeneity of Intervention Effectiveness Participants in the HIVST group reported higher partner testing rates than participants in the
comparison group in all subgroups examined (Table 4). While partner testing was significantly
more likely in the HIVST group than the comparison group in all three study sites, the HIVST
intervention was more effective in promoting partner testing in the hospital setting as com-
pared to the urban health clinic setting (p < 0.001). There was no difference in intervention
effectiveness by partner testing status in the past 12 mo (p = 0.172). Similarly, we found no dif-
ference in intervention effectiveness between participants who had experiencedIPV at baseline
and those who had not (p = 0.111). Among the eight partners who tested posi-
tive in the HIVST group, two went for confirmatory testing, were confirmed positive, and were
linked to care. Among the four partners who tested positive in the comparison group, three
were reported to have sought HIV care at the time of the 3-mo interview. No participants in
either group reported IPV due to HIV testing. **Estimates and confidence intervals are risk ratios from unadjusted modified Poisson regression. are marginal effects from unadjusted modified Poisson regression. *Estimates and confidence intervals are marginal effects from unadjusted modified Poisson regression. are risk ratios from unadjusted modified Poisson regression. **Estimates and confidence intervals are risk ratios from unadjusted modified Poisson regression. nfidence intervals are marginal effects from unadjusted modified Poisson regression. doi:10.1371/journal.pmed.1002166.t003 ***Model includes the subset of participants whose partner tested for HIV. Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests Table 4. Comparison of intervention effectiveness in participant subgroups. Subgroup
HIV Testing Uptake, Number/
Total Number (Percent)
Effect of Self-Testing
p-Value for
Interaction**
Comparison
Group
HIV Self-
Testing Group
Absolute Difference,
Percentage Points (95% CI)*
p-Value for
Subgroup*
Study site
Urban health clinic
80/120 (66.7)
117/129 (90.7)
24.0 (14.2 to 33.9)
<0.001
—
Hospital
47/122 (38.5)
97/105 (92.4)
53.9 (43.8 to 63.9)
<0.001
<0.001
Peri-urban health clinic
21/44 (47.7)
44/50 (88.0)
40.3 (22.9 to 57.7)
<0.001
0.093
Partner tested for HIV in 12 mo prior to
enrollment
Tested 1 time
102/173 (59.0)
142/149 (95.3)
36.3 (28.3 to 44.4)
<0.001
—
Did not test
16/35 (45.7)
37/42 (88.1)
42.4 (23.1 to 61.7)
<0.001
0.389
Do not know if tested
30/73 (38.5)
79/93 (84.9)
46.5 (33.5 to 59.5)
<0.001
0.057
Participants reported intimate partner
violence in past 12 mo at baseline
No
114/210 (54.3)
185/206 (89.8)
35.5 (27.6 to 43.4)
<0.001
—
Yes
34/76 (44.7)
73/78 (93.6)
48.9 (36.4 to 61.3)
<0.001
0.111
*Estimates and confidence intervals are marginal effects from a modified Poisson regression of outcome on study group for the subgroup described. **p-Value for interaction coefficient between subgroup and first category (urban health clinic, tested 1 time in past 12 mo, and no IPV). doi:10 1371/journal pmed 1002166 t004 *Estimates and confidence intervals are marginal effects from a modified Poisson regression of outcome on study group for the subgroup described. **p-Value for interaction coefficient between subgroup and first category (urban health clinic, tested 1 time in past 12 mo, and no IPV). doi:10.1371/journal.pmed.1002166.t004 higher couples testing than a more conventional approach of giving women invitation cards
for their male partners to test at health facilities. In the group that received multiple self-tests,
partner testing was reported by 91% of participants who were followed up, and 75% of partici-
pants followed up tested together with their partner. To our knowledge, this is the first ran-
domized trial to test whether provision of multiple self-tests to women promotes partner and
couples testing. In subgroup analyses, the intervention was more effective than the partner
invitation approach even among women who reported a history of IPV at baseline and among
women whose partners had not gone for HIV testing in the past 12 mo. Male partner testing was nearly universal among women who received multiple self-tests. Discussion Provision of multiple self-tests to women led to secondary distribution of the self-tests to their
male partners and ultimately achieved higher HIV testing among their male partners and Table 3. Effects of HIV self-testing intervention within 3 mo. Outcome
Comparison Group,
Number (Percent)
(n = 286)
HIV Self-Testing Group,
Number (Percent)
(n = 284)
Absolute Difference,
Percentage Points
(95% CI)*
Risk Ratio
(95% CI)**
p-Value*
Primary outcome
Male partner HIV testing
148 (51.7)
258 (90.8)
39.1 (32.4 to 45.8)
1.76 (1.56–1.98)
<0.001
Secondary outcomes
Discussed HIV testing with partner
276 (96.5)
271 (95.4)
−1.1 (−4.3 to 2.2)
0.99 (0.96–1.02)
0.512
Couples testing for HIV
95 (33.2)
214 (75.4)
42.1 (34.7 to 49.6)
2.27 (1.90–2.71)
<0.001
Couples testing conditional on partner
HIV testing***
95 (64.2)
214 (82.9)
18.8 (9.8 to 27.8)
1.29 (1.13–1.48)
<0.001
Aware of partner’s HIV test result
145 (50.7)
255 (89.8)
39.1 (32.3 to 45.9)
1.77 (1.57–2.00)
<0.001
Aware of partner’s HIV test result
conditional on partner HIV testing***
145 (98.0)
255 (98.8)
0.9 (−1.8 to 3.5)
1.01 (0.98–1.04)
0.519
Partner tested HIV-positive
4 (1.4)
8 (2.8)
1.4 (−0.9 to 3.8)
2.01 (0.61–6.62)
0.239 Table 3. Effects of HIV self-testing intervention within 3 mo. PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 9 / 15 PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests While prior HIV testing in this urban and peri-urban study setting was fairly high, we
found no difference in the effectiveness of the HIVST intervention based on whether partners
had tested for HIV in the past 12 mo. This result is encouraging since it suggests that the strat-
egy of giving multiple self-tests to women can effectively increase access to HIV testing in
hard-to-reach populations such as men who do not test regularly, and perhaps more generally
in settings where testing rates are not as high as they were in our study setting. In addition, the
large differences in partner testing between the HIVST and comparison groups was observed
in all population subgroups, which suggests broader applicability of this intervention to various
subgroups of pregnant and postpartum women. From a policy standpoint, providing self-tests to women in clinic settings has substantial
appeal not only because it promotes male partner testing but also because it helps women learn
their partner’s HIV status. The intervention’s feasibility is enhanced by the fact that pregnant
and postpartum women represent an easier-to-reach segment of the population by virtue of
their higher utilization of health services.Couples testing, which is recommended by the
World Health Organization and the Kenyan Ministry of Health, is another important benefit
of the intervention. Individuals who test as a couple and mutually disclose their HIV status are
more likely than those testing alone to adopt a range of HIV prevention and care behaviors [5]. Despite these benefits, only 37.2% of people who have tested for HIV in Kenya reported ever
testing together with a sexual partner [28]. Notably, the uptake of couples testing observed
among women given multiple self-tests in this study (75%) was higher than the uptake reported
in the recent pilot study we conducted in the study area, in which women receiving ANC and
PPC tested as couples 47% and 58% of the time, respectively [22]. This study has several limitations that warrant discussion. First, we relied on self-reported
data for the main outcomes. This is a common limitation in many studies involving HIVST
due to the private manner in which self-tests are meant to be used. PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 This
striking result is consistent with findings from a pilot study we previously conducted in the study
region, in which male partner testing was reported to have occurredfor 91% of women seeking
ANC and 86% of women receiving PNC [22]. The study results are also consistent with the high
acceptability of HIVST that has been documented throughout SSA and elsewhere [15–17]. Uptake of partner testing and couples testing in the comparison group that received invita-
tion cards for their male partner was largely similar to what has been reported in two other
recent studies. One study conducted in the same region of Kenya reported that couples testing
occurredamong 36% of pregnant women who received clinic invitation cards for their partner
[26]. Further, a study conducted among HIV-positive pregnant women in Malawi reported
that couples testing occurredamong 52% of women who received invitation cards for their
partner [27]. The similarity in male partner and couples testing levels in the comparison group
of our study with those reported in these other studies of the partner invitation approach pro-
vide further support for the validity of the self-reported measures obtained in our study. In
addition, it is notable that the couples testing rate in the HIVST group of our study was similar
to or exceeded the rates achieved by the interventions tested in the two other studies: home vis-
its and invitations followed by home tracing. While formal cost-effectivenessanalyses are nec-
essary, it is plausible that interventions relying on secondarydistribution of self-tests would
ultimately require fewer resources in total and therefore would have greater sustainability. PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 10 / 15 Despite the potential for
self-reporting to be associated with reporting bias, we believe reporting bias was minimal given
the above-mentioned consistency of our results for partner testing in both study groups with
other studies conducted in SSA [15,18,22,26,27] and given the lack of material incentives tied
to participants’ responses. In addition, any bias in reporting of testing uptake is unlikely to be
differential by study group. Male partners in the comparison group were able to test at multiple
facilities in the study area, and it was as difficult in practice to verify their clinic-based testing
as it was to verify self-test usage by partners in the HIVST group. These factors are likely to
strengthen the validity of comparing self-reported partner testing in the two study groups. Since objective verification of self-test use will remain a challenge, there is a need for larger-
scale studies that examine downstream outcomes such as the proportion of partners linking to
HIV prevention and treatment. Second, our study did not include women who knew their part-
ner was HIV-positive because we believed that a partner testing intervention would have little
additional benefit to them. This feature of the study design, coupled with high rates of HIV
testing in the urban and peri-urban study setting [29], likely led to relatively few HIV-positive
partners being identified in this study. This limited our ability to make statistical inferences
with respect to confirmatory testing and linkage to care. More research is needed to rigorously
assess levels of confirmatory testing and linkage to care following HIVST, as well as to under-
stand the decision-makingprocess of whether or not to seek these services. Finally, the third limitation stems from the fact that roughly one-third of women seeking
ANC or PPC declined to participate in the study, and some were ineligible because they
reported a fear that violence would result from offering a self-test to their partner. Among
women declining participation, the most commonly reported reason was a lack of adequate
time to enroll in the study, but other reasons such as a lack of interest in partner testing likely
played a role. While these two reasons for declining to participate in the study do not impact PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 11 / 15 Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests the internal validity of the study results, they do limit the generalizability of the findings to all
pregnant and postpartum women. Refusal also reinforces the feasibility and safety of offering
multiple self-tests because women demonstrated considerable agency and ability to decide
themselves whether to accept self-tests and offer them to their partner. Prior work has docu-
mented the high acceptability of this intervention among women receiving multiple self-tests
[22], and ongoing qualitative research with women receiving multiple self-tests shows that
women have a strong sense of agency when deciding whether to offer self-tests to others and
appreciate the opportunity to learn their partner’s status. Additional qualitative research will pro-
vide insights and lessons for wider implementation. Given the novelty of HIVST and this particu-
lar strategy for promoting partner testing (i.e., secondarydistribution of self-tests by women
receiving ANC and PPC), it is also likely that the broader acceptability of secondarydistribution
strategies will grow as HIVST becomes more common. Additional research is necessary to assess
the effectivenessof the intervention in other populations and settings outside western Kenya. However, to the extent that men experiencesimilar barriers to clinic-basedHIV testing else-
where, the results from this study could be applicable to other settings and populations. One concern about providing multiple self-tests to women for distribution to partners has
been the possibility of IPV. Despite women reporting high rates of IPV in the past 12 mo at
baseline (27%), it is noteworthy that the intervention was highly effective even among women
who reported a history of IPV at baseline, and there were no cases of IPV due to HIV testing
reported in either study group during the follow-up period. Few male partners had a reactive
self-test result in the study, which may have contributed to the lack of reported IPV due to test-
ing. However, prior research we have conducted with women receiving multiple self-tests—
including female sex workers who identified a greater proportion of HIV-positive partners
than ANC or PPC women in our study—also suggests IPV is rare [22]. The fact that there were
no cases of IPV also suggests that women have the agency and discretion to decide whether to
accept self-tests and whether to offer self-tests to their partner. This study provides key insights on a strategy—secondarydistribution of self-tests to sexual
partners—that may become common in many populations in SSA and elsewhere as HIV self-tests
become more widely available, whether formally endorsed or not. For example, the feasibility of
this approach is also being explored among key populations such as men who have sex with men
[30,31]. The promising results from this study suggest that secondarydistribution of self-tests
warrants further consideration as countries develop HIVST policies and seek new ways to pro-
mote partner testing. Implementing this intervention at scale is feasible as the primary require-
ments are that clinic staff be trained on how to explain self-test use and to offer self-tests to
women. However, there are potential challenges to programmatic implementation of the interven-
tion, such as ensuring adequate counseling when self-tests are offered to women, making counsel-
ing available post-test, and including interventions to achieve high linkage to appropriate services. Ongoing and planned implementation research will assess these issues and further develop strate-
gies for maximizing the potential for HIVST in achieving HIV prevention and care objectives. S1 Table. Outcome and intimate partner violence questions.
(DOCX) S1 Table. Outcome and intimate partner violence questions. (DOCX) 12 / 15 PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests Writing – review& editing: SHM HT KA BO SM SNM. Writing – review& editing: SHM HT KA BO SM SNM. Acknowledgments We are grateful to the patients who participated in the study as well as the staff at the study
facilities. Writing – original draft: SHM HT. Writing – original draft: SHM HT. Conceptualization: HT KA. Data curation: SHM. Project administration: HT. Writing – original draft: SHM HT. PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 References 2004; 37(5):1620–6. Epub 2004/12/04. PubMed Central PMCID: PMCPmc3384734. PMID:
15577420 12. Msuya SE, Mbizvo EM, Hussain A, Uriyo J, Sam NE, Stray-Pedersen B. Low male partner participation
in antenatal HIV counselling and testing in northern Tanzania: implications for preventive programs. AIDS Care. 2008; 20(6):700–9. Epub 2008/06/26. doi: 10.1080/09540120701687059 PMID:
18576172 13. Obermeyer CM, Osborn M. The utilization of testing and counseling for HIV: a review of the social and
behavioral evidence. Am J Public Health. 2007; 97(10):1762–74. Epub 2007/09/01. PubMed Central
PMCID: PMCPMC1994175. doi: 10.2105/AJPH.2006.096263 PMID: 17761565 14. Hutchinson AB, Corbie-Smith G, Thomas SB, Mohanan S, del Rio C. Understanding the patient’s per-
spective on rapid and routine HIV testing in an inner-city urgent care center. AIDS Educ Prev. 2004; 16
(2):101–14. Epub 2004/05/12. PMID: 15134119 15. Choko AT, Desmond N, Webb EL, Chavula K, Napierala-Mavedzenge S, Gaydos CA, et al. The
uptake and accuracy of oral kits for HIV self-testing in high hiv prevalence setting: a cross-sectional
feasibility study in Blantyre, Malawi. PLoS Med. 2011; 8(10):e1001102. doi: 10.1371/journal.pmed. 1001102 PMID: 21990966 16. Figueroa C, Johnson C, Verster A, Baggaley R. Attitudes and acceptability on HIV self-testing among
key populations: a literature review. AIDS Behav. 2015; 19(11):1949–65. PubMed Central PMCID:
PMC4598350. doi: 10.1007/s10461-015-1097-8 PMID: 26054390 17. Napierala Mavedzenge S, Baggaley R, Corbett EL. A review of self-testing for HIV: research and policy
priorities in a new era of HIV prevention. Clin Infect Dis. 2013; 57(1):126–38. doi: 10.1093/cid/cit156
PMID: 23487385 18. Choko AT, MacPherson P, Webb EL, Willey BA, Feasy H, Sambakunsi R, et al. Uptake, accuracy,
safety, and linkage into care over two years of promoting annual self-testing for HIV in Blantyre,
Malawi: a community-based prospective study. PLoS Med. 2015; 12(9):e1001873. Epub 2015/09/09. PubMed Central PMCID: PMCPmc4562710. doi: 10.1371/journal.pmed.1001873 PMID: 26348035 19. National AIDS and STI Control Programme. Guidelines for HIV testing services in Kenya. Nairobi:
National AIDS and STI Control Programme; 2015. 20. World Health Organization. Consolidated guidelines on HIV testing services. Geneva: World Health
Organization; 2015. 21. National AIDS and STI Control Programme, Ministry of Public Health and Sanitation. Guidelines for
HIV testing and counselling in Kenya. Nairobi: National AIDS and STI Control Programme; 2010. 22. Thirumurthy H, Masters S, Napierala Mavedzenge S, Maman S, Omanga E, Agot A. References 1. UNAIDS. 90-90-90: an ambitious treatment target to help end the AIDS epidemic. Geneva: UNAIDS;
2014. 2. Suthar AB, Ford N, Bachanas PJ, Wong VJ, Rajan JS, Saltzman AK, et al. Towards universal voluntary
HIV testing and counselling: a systematic review and meta-analysis of community-based approaches. PLoS Med. 2013; 10(8):e1001496. Epub 2013/08/24. PubMed Central PMCID: PMC3742447. doi: 10. 1371/journal.pmed.1001496 PMID: 23966838 3. Sharma M, Ying R, Tarr G, Barnabas R. Systematic review and meta-analysis of community and facil-
ity-based HIV testing to address linkage to care gaps in sub-Saharan Africa. Nature. 2015; 528(7580):
S77–85. doi: 10.1038/nature16044 PMID: 26633769 4. Gelmon L, Kenya P, Oguya F, Cheluget B, Haile G. Kenya HIV prevention response and modes of
transmission analysis. Nairobi: Kenya National AIDS Control Council; 2009. 5. Allen S, Meinzen-Derr J, Kautzman M, Zulu I, Trask S, Fideli U, et al. Sexual behavior of HIV discor-
dant couples after HIV counseling and testing. AIDS. 2003; 17(5):733–40. doi: 10.1097/01.aids. 0000050867.71999.ed PMID: 12646797 6. Cohen MS, Chen YQ, McCauley M, Gamble T, Hosseinipour MC, Kumarasamy N, et al. Prevention of
HIV-1 infection with early antiretroviral therapy. N Engl J Med. 2011; 365(6):493–505. doi: 10.1056/
NEJMoa1105243 PMID: 21767103 7. Aluisio A, Richardson BA, Bosire R, John-Stewart G, Mbori-Ngacha D, Farquhar C. Male antenatal
attendance and HIV testing are associated with decreased infant hiv infection and increased HIV free
survival. J Acquir Immune Defic Syndr. 2011; 56(1):76–82. doi: 10.1097/QAI.0b013e3181fdb4c4
PMID: 21084999 8. Drake AL, Wagner A, Richardson B, John-Stewart G. Incident HIV during pregnancy and postpartum
and risk of mother-to-child HIV transmission: a systematic review and meta-analysis. PLoS Med. 2014; 11(2):e1001608. doi: 10.1371/journal.pmed.1001608 PMID: 24586123 9. Medley A, Baggaley R, Bachanas P, Cohen M, Shaffer N, Lo Y-R. Maximizing the impact of HIV pre-
vention efforts: interventions for couples. AIDS Care. 2013; 25(12):1569–80. doi: 10.1080/09540121. 2013.793269 PMID: 23656251 10. World Health Organization. Guidance on couples HIV testing and counselling including antiretroviral
therapy for treatment and prevention in serodiscordant couples: recommendations for a public health
approach. Geneva: World Health Organization; 2012. 11. Farquhar C, Kiarie JN, Richardson BA, Kabura MN, John FN, Nduati RW, et al. Antenatal couple
counseling increases uptake of interventions to prevent HIV-1 transmission. J Acquir Immune Defic PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 13 / 15 Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests Syndr. 2004; 37(5):1620–6. Epub 2004/12/04. PubMed Central PMCID: PMCPmc3384734. PMID:
15577420 Syndr. PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 30.
Carballo-Dieguez A, Frasca T, Balan I, Ibitoye M, Dolezal C. Use of a rapid HIV home test prevents
HIV exposure in a high risk sample of men who have sex with men. AIDS Behav. 2012; 16(7):1753–60.
Epub 2012/08/16. PubMed Central PMCID: PMC3458207. doi: 10.1007/s10461-012-0274-2 PMID:
22893194 31.
Carballo-Dieguez A, Frasca T, Dolezal C, Balan I. Will gay and bisexually active men at high risk of
infection use over-the-counter rapid HIV tests to screen sexual partners? J Sex Res. 2012; 49(4):379–
87. Epub 2012/02/02. doi: 10.1080/00224499.2011.647117 PMID: 22293029 PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests References Promoting male
partner HIV testing and safer sexual decision making through secondary distribution of self-tests by
HIV-negative female sex workers and women receiving antenatal and post-partum care in Kenya: a
cohort study. Lancet HIV. 2016; 3(6):e266–74. doi: 10.1016/S2352-3018(16)00041-2 PMID:
27240789 23. National AIDS and STI Control Programme. Kenya HIV county profiles. Nairobi: Ministry of Health;
2014. 24. Zou G. A modified poisson regression approach to prospective studies with binary data. Am J Epide-
miol. 2004; 159(7):702–6. Epub 2004/03/23. PMID: 15033648 25. Kenya National Bureau of Statistics, ICF Macro. Kenya Demographic and Health Survey 2008–09. Calverton (Maryland): ICF Macro; 2010. 26. Osoti AO, John-Stewart G, Kiarie J, Richardson B, Kinuthia J, Krakowiak D, et al. Home visits during
pregnancy enhance male partner HIV counselling and testing in Kenya: a randomized clinical trial. AIDS. 2014; 28(1):95–103. Epub 2013/08/15. PubMed Central PMCID: PMCPmc4337402. doi: 10. 1097/QAD.0000000000000023 PMID: 23942059 27. Rosenberg NE, Mtande TK, Saidi F, Stanley C, Jere E, Paile L, et al. Recruiting male partners for cou-
ple HIV testing and counselling in Malawi’s option B+ programme: an unblinded randomised controlled
trial. Lancet HIV. 2015; 2(11):e483–91. doi: 10.1016/S2352-3018(15)00182-4 PMID: 26520928 28. Ng’ang’a A, Waruiru W, Ngare C, Ssempijja V, Gachuki T, Njoroge I, et al. The status of HIV testing
and counseling in Kenya: results from a nationally representative population-based survey. J Acquir
Immune Defic Syndr. 2014; 66(Suppl 1):S27–36. Epub 2014/04/16. doi: 10.1097/QAI. 0000000000000102 PMID: 24732818 29. Kimanga DO, Ogola S, Umuro M, Ng’ang’a A, Kimondo L, Murithi P, et al. Prevalence and incidence of
HIV infection, trends, and risk factors among persons aged 15–64 years in Kenya: results from a
nationally representative study. J Acquir Immune Defic Syndr. 2014; 66(Suppl 1):S13–26. PubMed
Central PMCID: PMCPMC4794992. doi: 10.1097/QAI.0000000000000124 PMID: 24445338 PLOS Medicine | DOI:10.1371/journal.pmed.1002166
November 8, 2016 14 / 15 Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests 15 / 15
|
https://openalex.org/W3120681140
|
https://dspace.mit.edu/bitstream/1721.1/131333/1/futureinternet-13-00017-v3.pdf
|
English
| null |
E-Mail Network Patterns and Body Language Predict Risk-Taking Attitude
|
Future internet
| 2,021
|
cc-by
| 9,724
|
MIT Open Access Articles The MIT Faculty has made this article openly available. Please share
how this access benefits you. Your story matters. Citation: Future Internet 13 (1): 17 (2021)
As Published: http://dx.doi.org/10.3390/fi13010017
Publisher: Multidisciplinary Digital Publishing Institute
Persistent URL: https://hdl.handle.net/1721.1/131333 Terms of use: Creative Commons Attribution
Citation: Sun, J.; Gloor, P. E-Mail
Network Patterns and Body
Language Predict Risk-Taking
Attitude. Future Internet 2021, 13, 17. https://doi.org/10.3390/fi13010017 Citation: Sun, J.; Gloor, P. E-Mail
Network Patterns and Body
Language Predict Risk-Taking
Attitude. Future Internet 2021, 13, 17. https://doi.org/10.3390/fi13010017 Jiachen Sun 1,2 and Peter Gloor 1,* Jiachen Sun 1,2 and Peter Gloor 1,* 1
MIT Center for Collective Intelligence, MIT’s Sloan School of Management, Cambridge, MA 02142, USA;
sunjch6@mail2.sysu.edu.cn
2
School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510275, China
*
Correspondence: pgloor@mit.edu 1
MIT Center for Collective Intelligence, MIT’s Sloan School of Management, Cambridge, MA 02142, USA;
sunjch6@mail2.sysu.edu.cn
2
School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510275, China
*
Correspondence: pgloor@mit.edu Abstract: As the Enron scandal and Bernie Madoff’s pyramid scheme have shown, individuals’
attitude towards ethical risks can have a huge impact on society at large. In this paper, we com-
pare risk-taking attitudes assessed with the Domain-Specific Risk-Taking (DOSPERT) survey with
individual e-mail networking patterns and body language measured with smartwatches. We find
that e-mail communication signals such as network structure and dynamics, and content features as
well as real-world behavioral signals measured through a smartwatch such as heart rate, accelera-
tion, and mood state demonstrate a strong correlation with the individuals’ risk-preference in the
different domains of the DOSPERT survey. For instance, we found that people with higher degree
centrality in the e-mail network show higher likelihood to take social risks, while using language
expressing a “you live only once” attitude indicates lower willingness to take risks in some domains. Our results show that analyzing the human interaction in organizational networks provides valuable
information for decision makers and managers to support an increase in ethical behavior of the
organization’s members. Keywords: risk-preference; social network analysis; e-mail communication; body language
Citation: Sun, J.; Gloor, P. E-Mail
Network Patterns and Body
Language Predict Risk-Taking
Attitude. Future Internet 2021, 13, 17. https://doi.org/10.3390/fi13010017
Received: 10 December 2020
Accepted: 11 January 2021
Published: 14 January 2021 future internet future internet 1. Introduction The willingness of individuals to take ethical risks for personal gain has led to immense
pain and loss for individuals and society. Understanding the behavior of Enron’s former
CEO, Jeffrey Skilling and former CFO, Andrew Fastow in the Enron scandal, or of Bernie
Madoff, the head of the largest pyramid scheme in world history, and their readiness to take
large ethical risks illustrates that it is of huge importance for society to investigate what
triggers such risky behavior. It would be of great value to get early warning signs based
on hidden “honest signals” of people such as Fastow, Skilling, or Madoff, to discourage
such behavior in the future or stop it from happening in the first place. Generally, the term
“risk-preference” refers to the willingness to engage in rewarding activities which involve
uncertain danger or harm [1]. Given that risk-preference is a fundamental construct
characterizing human behaviors [2], psychologists have proposed many theoretical and
empirical studies of the clues that contribute to individual differences of risk-preference,
such as personality traits [3–5], gender [6–9], age [10,11], and national culture [12,13]. Received: 10 December 2020
Accepted: 11 January 2021
Published: 14 January 2021 Publisher’s Note: MDPI stays neu-
tral with regard to jurisdictional clai-
ms in published maps and institutio-
nal affiliations. Yet, despite a large literature gauging interindividual differences of risk-preference
in psychology, relatively little is known about the hidden cues and predictors for risk-
preference in terms of human daily behavior. Humans’ survival, as an intensely social
species, depends on effective social functioning [14], which is fully reflected in their inter-
personal interaction, spoken language, as well as body language. In recent years, digital
social media have become an indispensable part of modern society [15,16]. By applying the
lens of Social Network Analysis (SNA) and text mining [17–19], seemingly unnoticeable
patterns—“honest signals” embedded in the digital social media affords the researchers a
deep view into the moods, personality, and social influence of people [20]. For instance, Copyright: © 2021 by the authors. Li-
censee MDPI, Basel,
Switzerland. This article is an open access article
distributed under the terms and con-
ditions of the Creative Commons At-
tribution (CC BY)
license (https://
creativecommons.org/licenses/by/
4.0/). https://www.mdpi.com/journal/futureinternet Future Internet 2021, 13, 17. https://doi.org/10.3390/fi13010017 Future Internet 2021, 13, 17 2 of 13
noticea-
search “honest signals” extracted from e-mail communication have successfully predicted per-
sonality characteristics, moral values, and “tribal affiliations” [18,21,22]. 1. Introduction On the other
hand, the rapid growth of sensor technology allows researchers to capture physical body
signals through a variety of wearable sensors in many areas [23–30]. Recently, a body
sensing system called “Happimeter” was proposed to extract “honest signals” in terms
of body movement, physiology, and environmental information, which have been shown
to be useful for predicting happiness, moral values, and creativity [25,31]. Leveraging
well-established social networking and sensor technologies, and given their predictive
power shown in many previous studies mentioned above, it would clearly be useful if we
could utilize e-mail communication and body signals measured through sensors to predict
the risk-taking attitude of an individual. stance, honest signals extracted from e-mail communication have successfully pre-
dicted personality characteristics, moral values, and “tribal affiliations” [18,21,22]. On the
other hand, the rapid growth of sensor technology allows researchers to capture physical
body signals through a variety of wearable sensors in many areas [23–30]. Recently, a
body sensing system called “Happimeter” was proposed to extract “honest signals” in
terms of body movement, physiology, and environmental information, which have been
shown to be useful for predicting happiness, moral values, and creativity [25,31]. Lever-
aging well-established social networking and sensor technologies, and given their predic-
tive power shown in many previous studies mentioned above, it would clearly be useful
if we could utilize e-mail communication and body signals measured through sensors to
predict the risk-taking attitude of an individual. I
thi
k
t
ti
ll
l
t i di id
l ’ i k
f
b
bi i In this work, we systematically evaluate individuals’ risk-preference by combining
SNA, text mining, body signals, and mood data, pursuing two different approaches doc-
umented in two empirical studies. In Study A, we investigate an e-mail communication
network through the mailbox of an active participant, analyzing network structure, digital
“tribes” features, and emotionality from word usage. In Study B, using the Happimeter
system based on smartwatches [25], we collect individuals’ daily records including body
movement, physiology, as well as self-reported mood states. Based on these empirical
data, we find strong correlations between social networking and behavioral variables and
risk-preference, which is measured by the Domain-Specific Risk-Taking (DOSPERT) sur-
vey [32,33] in five specific domains. Our regression results imply that properties obtained
both from social networking and body signals can be good candidates to predict individual
risk-preference. 1. Introduction The overall theoretical framework for this study is shown in Figure 1. In this work, we systematically evaluate individuals’ risk-preference by combining
SNA, text mining, body signals, and mood data, pursuing two different approaches doc-
umented in two empirical studies. In Study A, we investigate an e-mail communication
network through the mailbox of an active participant, analyzing network structure, digital
“tribes” features, and emotionality from word usage. In Study B, using the Happimeter
system based on smartwatches [25], we collect individuals’ daily records including body
movement, physiology, as well as self-reported mood states. Based on these empirical
data, we find strong correlations between social networking and behavioral variables and
risk-preference, which is measured by the Domain-Specific Risk-Taking (DOSPERT) sur-
vey [32,33] in five specific domains. Our regression results imply that properties obtained
both from social networking and body signals can be good candidates to predict individ-
ual risk-preference. The overall theoretical framework for this study is shown in Figure 1. Figure 1. Theoretical framework. In this work we conduct two different case studies. On the one hand, a social network
through e-mail archives is studied by analyzing structural metrics, virtual features, and emotionality. On the other hand,
body-signal data are collected by using the Happimeter system. We then used both data separately to predict each person's
risk-preference through the DOSPERT survey [32,33], in five specific domains. Figure 1. Theoretical framework. In this work we conduct two different case studies. On the one hand, a social network
through e-mail archives is studied by analyzing structural metrics, virtual features, and emotionality. On the other hand,
body-signal data are collected by using the Happimeter system. We then used both data separately to predict each person’s
risk-preference through the DOSPERT survey [32,33], in five specific domains. Figure 1. Theoretical framework. In this work we conduct two different case studies. On the one hand, a social network
through e-mail archives is studied by analyzing structural metrics, virtual features, and emotionality. On the other hand,
body-signal data are collected by using the Happimeter system. We then used both data separately to predict each person's
risk-preference through the DOSPERT survey [32,33], in five specific domains. Figure 1. Theoretical framework. In this work we conduct two different case studies. On the one hand, a social network
through e-mail archives is studied by analyzing structural metrics, virtual features, and emotionality. 2.2.1. Data E-mail data are collected from the personal mailbox of an active participant, as a
proxy for the organizational memory of his community, which mainly consists of aca-
demic/business collaborators in dozens of teams with a variety of topics. The study period
is from 2 January 2019 to 2 February 2020. After removing some invalid and junk e-mail
addresses, there are 912 e-mail accounts including the mailbox owner and 8074 exchanges
of at least one e-mail between two users, which are used to reconstruct the e-mail social
network. Further, we identified 72 active users who have sent at least 50 e-mail messages
during the study period and invited them to complete the online DOSPERT survey on
https://www.happimeter.org/, 34 of whom returned the survey (16 men and 18 women). We measured the e-mail behavior of these 34 users by analyzing their network structure
and content. 2. Data and Methods 2.1. The Measurement of Risk-Preference 1. Introduction On the other hand,
body-signal data are collected by using the Happimeter system. We then used both data separately to predict each person’s
risk-preference through the DOSPERT survey [32,33], in five specific domains. he main contributions of this paper include:
The main contributions of this paper include: The main contributions of this paper include:
The main contributions of this paper include: (1) Combining network theory, text mining, and body-sensing technology, we introduce
a novel interdisciplinary research method for analyzing one’s attitude of risk-taking. (1)
Combining network theory, text mining, and body-sensing technology, we introduce
a novel interdisciplinary research method for analyzing one’s attitude of risk-taking. p
y
y
g
g
p
y
y
g
g
(2)
We validate the utility of the proposed method through two different empirical studies,
using e-mail archives and the Happimeter sensing system, respectively. A strong Future Internet 2021, 13, 17 3 of 13 correlation is found between the empirical signals and individual risk-preference in
the different domains of the DOSPERT survey. (3) (3)
Through empirical evidence, we quantify significant predictors for one’s attitude of
risk-taking based on tribal language features, emotionality, network structure metrics,
and body sensors, which provide valuable information for decision makers and
managers to support an increase in ethical behavior of the organization’s members (3)
Through empirical evidence, we quantify significant predictors for one’s attitude of
risk-taking based on tribal language features, emotionality, network structure metrics,
and body sensors, which provide valuable information for decision makers and
managers to support an increase in ethical behavior of the organization’s members The rest of this paper is organized as follows. In Section 2, we introduce the measure-
ment of risk-preference and the two empirical experiments. In Section 3, we present the
numerical regression results. Discussions are presented in Section 4. Finally, Section 5 lists
limitations and summarizes the paper. 2.1. The Measurement of Risk-Preference We access individual risk-preference through a 30-item version of DOSPERT [33],
one of the most widely used questionnaires. In particular, DOSPERT measures two different
risk-related metrics in five specific domains of life (ethical, financial, recreational, health,
and social). One is the willingness for “risk-taking”, measuring that respondents might
engage in risky behaviors using a 7-point rating scale where higher scores mean higher
likelihood of risk-taking. The other is called “risk-perception”, corresponding to the gut
level assessment of the riskiness of these behaviors, similarly measured from 1 (“not at all
risky”) to 7 (“extremely risky”). Clearly, the sum of “risk-taking” and “risk-perception” is an
intuitive indicator of risk-willingness, i.e., one’s intrinsic risk-preference being influenced
by perception. For example, brave and witty people are generally aware of a risk (high
risk-perception) and still take it (high risk-taking), leading to high risk-willingness. On the
contrary, low risk-willingness corresponds either to someone of impulse and ignorance who
takes a risk without being aware of it, or someone who acts with caution, i.e., fully aware
of a risk and not taking it. Therefore, in this study we extend the original DOSPERT
risk-taking survey and define the individual degree of “risk-willingness” as the sum of the
score of “risk-taking” and that of “risk-perception”. In the following analysis, we investigate the original DOSPERT risk-taking, as well as
the risk-willingness in five domains separately. Additionally, since DOSPERT also permits
the researcher to capture the general dimension of risk-preference [34], we include it in the
analysis by adding the construct of general risk-willingness and risk-taking as the average
value in the five domains. 2.2. Study A: E-Mail Analysis 2.2. Study A: E-Mail Analysis 2.2.3. Content Variables Similar to the structure variables, we employ Condor to calculate content variables
based on the participants’ e-mail messages, which contain virtual “tribe” signals and
emotion signals. •
Contribution signals •
Contribution signals The amount of information contributed by an individual in the e-mail network is
calculated as the number of e-mails sent and received by the individual. Hence, we use the
contribution index metric [18] defined as the balance of messages sent and received by a
user during the study period. It is calculated by subtracting messages received from the
messages sent and then dividing the result by the messages sent added to the messages
received [18]. •
Position signals A static e-mail social network is reconstructed using the filtered 912 nodes (users) and
8074 unique links (the exchange of at least one e-mail between two nodes). The position
of a given node in the network can be characterized by its nodal centrality, which has
been found to be useful in predicting productivity [35], job turnover [36], and individual
performance [37]. In particular, we consider three well-known nodal centralities: (1) De-
gree centrality, i.e., the number of links connected to it, (2) betweenness centrality [38],
measuring the probability with which a node is on the shortest path between other nodes,
and (3) closeness centrality [39], measuring the mean distance from a node to other nodes. Apart from the nodal centrality, we also calculate reach-2 as a proxy for individual social
capital [40], which is the number of other nodes a given node can reach with two steps. 2.2.2. Structure Variables We employed the dynamic social network analysis tool Condor [18] to calculate the
following three kinds of structure variables: Position, contribution, and dynamic signals. Future Internet 2021, 13, 17 4 of 13 •
Dynamic signals •
Dynamic signals E-mail communication is generally a dynamic process, implying that an individual’s
position in the network may change continuously over time. To allow for this, we recon-
struct day-by-day networks by merely including the communications (links) happening
on that particular day, leading to e-mail social networks per day. Based on these net-
works, we calculate individual betweenness oscillation [18] by quantifying the number
of local maxima and minima in the betweenness centrality curve. We also calculate the
contribution index oscillation in a similar way. These metrics’ utility have been validated
repeatedly [41,42]. In addition, we investigate individual responsiveness in e-mail com-
munication, i.e., how fast a responder replies to a sender, which plays an important role
in dynamic communications analysis [43,44]. Specifically, for each user we consider two
different variables, the Average Response Time (ART) defined as the average time needed
for the given user to respond to an e-mail, and the nudges defined as the average number
of pings (e-mails sent) needed to get a response [18]. •
Virtual tribe signals Tribes are groups of people homogenous within themselves and heterogeneous to
other groups. Given that a tribe is generally helpful for reflecting one’s identity, place in so-
ciety, and ethnic partiality [45–47], and has demonstrated usefulness in different scenarios
such as marketing [47] and human resource management [22], it is important to inves-
tigate correlations between the users’ risk-preference and their underlying virtual tribe. To identify the tribes of users in the e-mail network, we employ TribeFinder [47], which is a
novel AI-based tool trained on Twitter. Specifically, TribeFinder finds the different types of
tribes and their leaders on Wikipedia, then looks at the language of the leaders on Twitter. People are then assigned to tribes if their word usage is similar to the aggregate of all
“leaders” of a tribe. We identify tribes for e-mail users according to words usage in their
e-mails, using five pre-existing macro-categories [22]: Alternative Realities, Personality,
Recreation, Ideology, and Lifestyle [47], each of which consists of four dimensions (see
detailed explanations for each dimension within each macro-category in Table 1). For each
user, TribeFinder computes his/her probability of being in a certain dimension. 5 of 13 Future Internet 2021, 13, 17 Table 1. Explanation of five macro-categories of tribe used in this paper, each of them includes four dimensions. 2.3.1. Data To achieve body sensing, we employ an existing app called Happimeter [25] that
allows tracking of instant body physical signals and mood states. We conducted an
experiment with participants at a 3-day international academic conference from 14 to 17
September 2017. During this period, the participants wore Android smartwatches provided
by our research group with the Happimeter app installed and linked to their smartphones. Similar to Study A, they were asked to complete the online DOSPERT test. A total of 23
user’s risk-preference results were collected, from whom three participants had technical
issues connecting the smartwatch to their phones, and five participants have a negligibly
small number of recorded sensor data. Hence, these users were excluded from the body
sensing analysis. From the remaining 15 users (8 men and 7 women), we obtained a total
of 4339 sensor records and 2450 affective records. •
Virtual tribe signals Macro-Category
Dimension
Explanation
Alternative Realities
fatherlanders
extreme patriots whose vision is a recreation of the national states from the 1900s
spiritualism
people who focus on all things spiritual such as soul and mindfulness
nerds
people who believe in advances in technology as a solution for a better future
tree huggers
environmentalists who strive to protect nature from phenomena such as global warming
Personality
stock-traders
people who are willing to take risks to grow their capital
politicians
people who use “political language” rather than simply saying the truth and sticking to the facts
journalists
people who use direct language to report actual events as the opposite to politicians
risk-takers
people who make daring decisions (trained with tweets of wing-suit flyers and cave divers)
Recreation
fashion
people who focus on new fashion styles
art
people who have an interest in art, such as music or painting
travel
people who enjoy travelling around the world
sport
people who enjoy actively engaging in sports
Ideology
liberalism
liberals focusing on enhancing and protecting the freedom of individuals
socialism
people who advocate for more government control to better distribute shared resources
capitalism
people arguing for letting the “invisible hand” take its course through minimal government
intervention in markets
complainers
people who frequently voice their protests and vent their frustrations in public
Lifestyle
yolo
“You only live once” people who want to live life to its fullest extent, even embracing behavior
carrying inherent risk
sedentary
people who spend too much time seated with little exercise or physical activity
fitness
people who favor fitness such as strength training, cardio, and yoga
vegan
people who eat no animal-derived products •
Emotion signals To calculate the e-mail sentiment, we employ Condor’s built-in sentiment analysis
function, which is a Bayesian-based classifier trained on billions of tweets achieving over
80% accuracy on English e-mail corpora [47]. The sentiment score of each e-mail ranges
from 0 (negative) to 1 (positive). A user’s average sentiment is denoted as the mean value
of all sentiment scores from her/his e-mails. In addition, we use TribeFinder to further
quantify each user’s explicit mood state. Similarly, we set up an additional mood “tribe”,
which depicts the individual’s mood by four dimensions (happy, sad, angry, and fear)
through assigning a likelihood of belonging for each dimension. 2.3. Study B: Body Sensing Analysis
2.3.1. Data 2.3.2. Variable The Happimeter app regularly collects the wearer’s sensor data through all the avail-
able sensors of the smartwatch, such as heart rate, accelerometer, GPS coordinates, and light
level. To access a user’s body language, we consider two kinds of sensors. One is the
accelerometer, the most widely used movement sensors for human physical activity moni-
toring [24]. Specifically, the built-in three-axis accelerometer on the smartwatch captures
the users’ acceleration average magnitude per minute, which are measured simultane- Future Internet 2021, 13, 17 6 of 13 ously in three dimensions of physical space (usually labelled as x, y, and z), resulting in
three specific values. The other is the heart rate sensor, i.e., the average number of heart
beats per minute [24]. This is achieved by detecting the amount of blood flowing through
the wearer’s wrist through a green LED light paired with light-sensitive photodiodes on
the smartwatch. In addition, we collect the participant’s momentary self-reports of their mood states
through the Happimeter app. In particular, a user’s affective state is recorded by answer-
ing the following two questions [48] which appear on the smart watch screen: (1) “How
pleasant do you feel?” and (2) “How active do you feel?” The user then chooses his/her
pleasance and activation level with a scale from 0–2, where 0 represents the lowest plea-
sance/activation and 2 represents the highest pleasance/activation [25], resulting in two
affective values. To correlate each user’s DOSPERT survey result with his/her multiple records of
sensor values and mood values which are generated across time, we first aggregate the
Happimeter values by computing the average level of each value for each hour, given that
the participants may not provide their affective information at the same frequency as their
sensor data. Then, for each user, we calculate the mean and variance of each aggregated
value, resulting in a total of 12 Happimeter variables (see Table 2), which are used for
further analysis. Table 2. Explanation of Happimeter variables. 2.3.2. Variable Category
Variable
Definition
Movement sensor
avg-AccX
The mean of user’s acceleration magnitude (aggregated by day) in the physical
space along the x axis
avg-AccY
Similar to avgAcc-x but measured along the y axis
avg-AccZ
Similar to avgAcc-x but measured along the z axis
var-AccX
The variance of acceleration magnitude (aggregated by day) along the x axis
var-AccY
Similar to varAcc-x but measured along the y axis
var-AccZ
Similar to varAcc-x but measured along the z axis
Physiological sensor
avg-bpm
The average number of aggregated-by-day heart rate
var-bpm
The variance of aggregated-by-day heart rate
Mood state
avg-pleasant
The mean value of day-level scores for self-reported pleasance
avg-active
Similar to avg-pleasant but measured for active scores
var-pleasant
The variance of day-level scores for self-reported pleasance
var-active
Similar to var-pleasant but measured for active scores
3. Results
3.1. E-Mail Results
First, we present the qualitative findings of Study A (N = 34). We report the statistical
description of variables in Supplementary Table S1. By correlating the position, content,
and emotion variables computed from the e-mail data with the individual risk-taking
and risk-willingness over six domains, we find strong and significant correlations (see the
Pearson coefficient in Supplementary Table S2), implying a potentially linear relationship
among the variables considered. Then, we employ the Ordinary Least Squares (OLS)
regression to predict the 12 subscales of risk-preference (six for risk taking, six for risk will-
ingness) separately, by choosing corresponding significant variables as predictors. Table 3
reports the regression results, along with the Breusch-Pagan/Cook-Weisberg test [49,50]
employed to check the variance homoscedasticity of the fitted OLS model. Table 2. Explanation of Happimeter variables. Table 2. Explanation of Happimeter variables. 2.3.2. Variable Category
Variable
Definition
Movement sensor
avg-AccX
The mean of user’s acceleration magnitude (aggregated by day) in the physical
space along the x axis
avg-AccY
Similar to avgAcc-x but measured along the y axis
avg-AccZ
Similar to avgAcc-x but measured along the z axis
var-AccX
The variance of acceleration magnitude (aggregated by day) along the x axis
var-AccY
Similar to varAcc-x but measured along the y axis
var-AccZ
Similar to varAcc-x but measured along the z axis
Physiological sensor
avg-bpm
The average number of aggregated-by-day heart rate
var-bpm
The variance of aggregated-by-day heart rate
Mood state
avg-pleasant
The mean value of day-level scores for self-reported pleasance
avg-active
Similar to avg-pleasant but measured for active scores
var-pleasant
The variance of day-level scores for self-reported pleasance
var-active
Similar to var-pleasant but measured for active scores First, we present the qualitative findings of Study A (N = 34). We report the statistical
description of variables in Supplementary Table S1. By correlating the position, content,
and emotion variables computed from the e-mail data with the individual risk-taking
and risk-willingness over six domains, we find strong and significant correlations (see the
Pearson coefficient in Supplementary Table S2), implying a potentially linear relationship
among the variables considered. Then, we employ the Ordinary Least Squares (OLS)
regression to predict the 12 subscales of risk-preference (six for risk taking, six for risk will-
ingness) separately, by choosing corresponding significant variables as predictors. Table 3
reports the regression results, along with the Breusch-Pagan/Cook-Weisberg test [49,50]
employed to check the variance homoscedasticity of the fitted OLS model. 7 of 13 Future Internet 2021, 13, 17 Table 3. Ordinary least squares (OLS) regression on the risk-taking and risk-willingness of Study A (N = 34). The stars
within the bracket correspond to the predictor’s significance level: * p < 0.1, ** p < 0.05, *** p < 0.01. Dependent Variable
Significant Predictor (Coefficient)
Adj. R2
RMSE
Chi-2
(Prob. > Chi-2)
(a) Risk-taking
1. general
Lifestyle-Fitness (−1.27 ***),
Contribution index oscillation (−0.003 **),
ART (−0.01 **),
Recreation-Sport (0.91 **)
0.60
0.27
0.88
(0.35)
2. ethical
Lifestyle-Yolo (−2.37 **),
Personality-Journalist (3.85 **),
Recreation-Sport (1.50 **),
Alternative Realities-Spiritualism (1.41 **)
0.53
0.53
1.26
(0.26)
3. financial
Recreation-Arts (2.88 ***)
0.33
0.74
0.10
(0.76)
4. health
Recreation-Sport (2.91 ***),
Lifestyle-Yolo (−2.32 **),
Lifestyle-Fitness (−1.78 *)
0.54
0.57
1.94
(0.20)
5. 2.3.2. Variable recreational
ART (−0.04 ***),
Personality-Politician (−2.69 ***),
Emotion-Happy (1.79 **),
Contribution index oscillation (−0.006 *)
0.65
0.67
0.72
(0.40)
6. social
Degree centrality (0.003 **),
Alternative Realities-Spiritualism (−1.80 ***)
0.36
0.66
0.63
(0.43)
(b) Risk-willingness
1. general
Lifestyle-Yolo (−4.17 ***),
Ideology-Complainer (13.55 **),
Emotion-Sad (−1.65 **),
Ideology-Liberalism (1.11 **)
0.61
0.60
0.05
(0.82)
2. ethical
Lifestyle-Yolo (−4.83 **),
Personality-Journalist (5.95 **),
Ideology-Complainer (26.37 ***)
0.51
1.00
0.18
(0.67)
3. financial
Lifestyle-Yolo (−6.10 **),
Recreation-Arts (3.26 **),
Reach-2 (−0.01 *)
0.45
1.10
0.39
(0.53)
4. health
Lifestyle-Sedentary (3.77 ***),
Lifestyle-Yolo (−5.09 **),
Lifestyle-Fitness (−3.36 **)
0.50
1.06
0.26
(0.61)
5. recreational
ART (−0.05 ***),
Personality-Politician (−6.77 ***)
0.60
1.16
0.43
(0.51)
6. social
Alternative Realities-Spiritualism (−4.18 ***),
Nudges (−1.53 *)
0.44
0.89
0.03
(0.87)
Importantly from Table 3 we find several significant e mail based predictors for Importantly, from Table 3 we find several significant e-mail-based predictors for
risk-preference scores in certain domains. For example, a faster responsiveness in e-mail
message (i.e., smaller ART) and more stable contribution in the e-mail network (i.e., smaller
contribution index oscillation) correspond to more risk-taking both in general and in the
recreational domain. On the other hand, higher degree centrality in the e-mail network,
i.e., communicating with more different people, indicates higher likelihood to take social
risks. One of the most interesting findings of the virtual tribes is that a more “you live only
once” lifestyle reflected by the e-mail content actually causes less willingness to show risky
behavior in the ethical, financial, and health domains. This means that their assessment
of risk and their willingness to take that risk are more aligned. In other words, “they are Future Internet 2021, 13, 17 8 of 13 willing to put their money where their mouth is”. As for emotion, we find that participants
who are happier (or less sad) in words are more risk-seeking in recreational activities and
show a greater willingness to take risks in general. Overall, the high adjusted R2 and low RMSE reported in Table 3 demonstrate that the
combinations of these variables indeed forecasts the individuals’ risk-preference effectively. In addition, the Breusch-Pagan/Cook-Weisberg test shows a small chi-2 and corresponding
large probability, indicating that the variance is homogenous and thus OLS’s validity is
confirmed. Figure 2 shows the specific predicted result of each participant compared with
the real value over the six domains. 2.3.2. Variable Pearson r = 0.81
General
Risk-taking
Risk-awareness
(a)
(b)
Ethical
Risk-taking
Risk-awareness
(c)
(d)
33
Financial
Risk-taking
Risk-awareness
(e)
(f)
Health
Risk-taking
Risk-awareness
(g)
(h)
3
Recreational
Risk-taking
Risk-awareness
(i)
(j)
3
Social
Risk-taking
Risk-awareness
(k)
(l)
𝑃= 2×10-8
Pearson r = 0.77
𝑃= 3×10-7
Pearson r = 0.60
𝑃= 3×10-4
Pearson r = 0.77
𝑃= 3×10-7
Pearson r = 0.84
𝑃= 2×10-9
Pearson r = 0.63
𝑃= 1×10-4
Pearson r = 0.81
𝑃= 1×10-8
Pearson r = 0.75
𝑃= 9×10-7
Pearson r = 0.71
𝑃= 5×10-6
Pearson r = 0.74
𝑃= 1×10-6
Pearson r = 0.79
𝑃= 5×10-8
Pearson r = 0.69
𝑃= 2×10-5
Figure 2. Comparison between the predicted risk-preference score and the real self-reported value (N = 34) in the general (a,b),
ethical (c,d), financial (e,f), health (g,h), recreational (i,j), and social domains (k,l). Each point corresponds to a specific participant. The predicted value is calculated by using significant predictors and the corresponding coefficients reported in Table 3. Ethical
Risk-taking
Risk-awareness
(c)
(d)
Pearson r = 0.77
𝑃= 3×10-7
Pearson r = 0.75
𝑃= 9×10-7 Pearson r = 0.81
General
Risk-taking
Risk-awareness
(a)
(b)
𝑃= 2×10-8
Pearson r = 0.81
𝑃= 1×10-8 33
Financial
Risk-taking
(e)
Pearson r = 0.60
𝑃= 3×10-4 Health
Risk-taking
Risk-awareness
(g)
(h)
Pearson r = 0.77
𝑃= 3×10-7
Pearson r = 0.74
𝑃= 1×10-6 Risk-awareness
(f)
Pearson r = 0.71
𝑃= 5×10-6 33
Financial
Risk-taking
Risk-awareness
(e)
(f)
Pearson r = 0.60
𝑃= 3×10-4
Pearson r = 0.71
𝑃= 5×10-6 (h) (f) 3
Social
Risk-taking
(k)
Pearson r = 0.63
𝑃= 1×10-4 3
Social
Risk-taking
Risk-awareness
(k)
(l)
Pearson r = 0.63
𝑃= 1×10-4
Pearson r = 0.69
𝑃= 2×10-5 Risk-awareness
(l)
Pearson r = 0.69
𝑃= 2×10-5 Risk-awareness
(j)
Pearson r = 0.79
𝑃= 5×10-8 (l) (j) 3
Recreational
Risk-taking
(i)
Pearson r = 0.84
𝑃= 2×10-9 Figure 2. Comparison between the predicted risk-preference score and the real self-reported value (N = 34) in the general (a,b),
ethical (c,d), financial (e,f), health (g,h), recreational (i,j), and social domains (k,l). Each point corresponds to a specific participant. The predicted value is calculated by using significant predictors and the corresponding coefficients reported in Table 3. 3.2. Body Sensor Results In this section, we demonstrate the predictive effect of the body signals on individuals’
attitude towards the risk of Study B. The dependent variables are the mean and variance
calculated from 4339 sensor records and 2450 affective records of 15 participants. Again,
these variables show a strong correlation with the risk-preference scores in certain domains
(see statistical description of the data and the Pearson coefficient between the body signals
and the risk-preference in Supplementary Tables S3 and S4, respectively). Similar to Study
A, we employ the OLS regression with these significant variables to predict the individuals’
risk-preference. We report the OLS results of Study B in Table 4. We find that the sensor features can reliably distinguish high risk-preference individ-
uals from low risk-preference ones. Specifically, the variability of the heart rate is found
to be a significant indicator to measure one’s risk-preference in the recreational domain. In addition, participants exhibiting a higher average heart rate show stronger willingness
to take ethical risks. The acceleration-related variables also show a significant relationship Future Internet 2021, 13, 17 9 of 13 9 of 13 with risk-preference. For instance, the less consistent the body movement of a participant is
(i.e., high variance of acceleration’s magnitude), the more likely they will take risks in the
ethical and health domains. Regarding the affective states, we find that participants with a
more active sense of self are risk-seeking in financial activities. Finally, we compare the pre-
dicted values of the above variables with the real ones (see Figure 3). It can be seen that the
statistics from sensor and mood data predict well in the general, financial, and recreational
domains, while the prediction is comparatively poorer in the three other domains. ble 4. OLS regression analysis of Study B based on 4339 sensor records and 2450 affective records from 15
he stars within the bracket correspond to the predictor’s significance level: * p < 0.1, ** p < 0.05, *** p < 0.01. alysis of Study B based on 4339 sensor records and 2450 affective records from 15 participants. t correspond to the predictor’s significance level: * p < 0.1, ** p < 0.05, *** p < 0.01. Table 4. OLS regression analysis of Study B based on 4339 sensor records and 2450 affective records from 15 participants. 3.2. Body Sensor Results The stars within the bracket correspond to the predictor’s significance level: * p < 0.1, ** p < 0.05, *** p < 0.01. Dependent Var. Significant Predictor (Coefficient)
Adj. R2
RMSE
Chi-2 (Prob. > Chi-2)
(a) Risk-taking
1. general
var-AccX (0.41 **)
0.33
0.42
1.53 (0.22)
2. ethical
var-AccX (0.47 *)
0.18
0.67
1.67 (0.20)
3. financial
avg-active (1.73 **), var-AccY (−0.89 *)
0.45
0.75
0.25 (0.62)
4. health
var-AccX (0.63 **)
0.27
0.74
2.38 (0.12)
5. recreational
var-bpm (−0.54 ***)
0.50
0.88
1.08 (0.30)
6. social
avg-AccX (0.35 **)
0.37
0.65
0.23 (0.63)
(b) Risk-willingness
1. general
var-bpm (−0.55 **)
0.49
0.90
0.95 (0.33)
2. ethical
avg-bpm (0.11 **)
0.29
1.10
1.99 (0.16)
3. financial
avg-active (3.00 **), avg-AccY (−1.03 **)
0.52
1.20
0.01 (0.95)
4. health
avg-AccY (−1.12 **)
0.23
1.32
0.01 (0.93)
5. recreational
var-bpm (−0.87 ***), avg-AccY (−0.82 *)
0.60
1.33
0.35 (0.55)
6. social
avg-AccX (0.39 **)
0.35
0.89
0.24 (0.62)
Pearson r = 0.61
General
Risk-taking
Risk-awareness
(a)
(b)
Ethical
Risk-taking
Risk-awareness
(c)
(d)
33
Financial
Risk-taking
Risk-awareness
(e)
(f)
Health
Risk-taking
Risk-awareness
(g)
(h)
3
Recreational
Risk-taking
Risk-awareness
(i)
(j)
3
Social
Risk-taking
Risk-
awareness
(k)
(l)
𝑃= 0.015
Pearson r = 0.49
𝑃= 0.06
Pearson r = 0.73
𝑃= 0.002
Pearson r = 0.56
𝑃= 0.03
Pearson r = 0.73
𝑃= 0.002
Pearson r = 0.61
𝑃= 0.016
Pearson r = 0.73
𝑃= 0.002
Pearson r = 0.58
𝑃= 0.02
Pearson r = 0.77
𝑃= 8×10-4
Pearson r = 0.58
𝑃= 0.02
Pearson r = 0.81
𝑃= 2×10-4
Pearson r = 0.58
𝑃= 0.02
Figure 3. Comparison between the predicted risk-preference score and the realistic self-reported value (N = 15) over
six domains of Study B (a,b for general, c,d for ethical, e,f for financial, g,h for health, i,j for recreational, k,l for social). The predicted value is calculated using significant predictors and the corresponding coefficients reported in Table 4. 4. Discussion and Limitations By measuring features of individual language, both verbal and as body language,
we propose a novel way to measure attitudes towards risk. The same approach can also
be used to measure other “soft” personality characteristics such as ethical and moral val-
ues [21,22]. We find, for instance, that someone using a language indicating a fitness-aware
lifestyle is less willing to take general risks, while someone using a language indicating
a preference for “yolo” is less willing to take ethical risks. On the other hand, people
who use a “journalist” such as “matter of fact” language are more willing to take ethical
risks. Similar insights can also be gleaned from the body language of individuals. For in-
stance, the less consistent they move their bodies, i.e., the higher the variance of their arm
movement over time, the higher their willingness to take general risks. On the theoretical
side, insights such as these offer valuable suggestions for personality researchers. On the
practical side, these results permit HR managers to better understand the culture of their
organizations, based on the words that the members of their organization use. g
g
The presented study has some potential areas in need of further investigation. First,
individual risk-preference is measured through self-reported questionnaires, which may
introduce a subjective bias of observed relations due to the common method variance [51]. A more objective alternative is to expose participants to gaming tasks (e.g., the ultimatum
game [52]). Second, a relatively small number of participants inevitably restrict the validity
generalization of our results. Therefore, a larger-scale experiment involving more partici-
pants from a wider range of backgrounds should be done to provide further evidence of
the robustness of our results. In addition, in the social networking part (Study A) of this
study we have mainly focused on e-mail networks, but the proposed methodology could
be extended to online social networks from practically any discipline, such as Facebook
and microblogging platforms. 3.2. Body Sensor Results Ethical
Risk-taking
Risk-awareness
(c)
(d)
Pearson r = 0.49
𝑃= 0.06
Pearson r = 0.58
𝑃= 0.02 Pearson r = 0.61
General
Risk-taking
Risk-awareness
(a)
(b)
𝑃= 0.015
Pearson r = 0.73
𝑃= 0.002 Ethical
Risk-taking
(c)
Pearson r = 0.49
𝑃= 0.06 Health
Risk-taking
Risk-awareness
(g)
(h)
Pearson r = 0.56
𝑃= 0.03
Pearson r = 0.58
𝑃= 0.02 33
Financial
Risk-taking
Risk-awareness
(e)
(f)
Pearson r = 0.73
𝑃= 0.002
Pearson r = 0.77
𝑃= 8×10-4 Risk-awareness
(f)
Pearson r = 0.77
𝑃= 8×10-4 (f) 3
Social
Risk-taking
(k)
Pearson r = 0.61
𝑃= 0.016 Risk-
awareness
(l)
Pearson r = 0.58
𝑃= 0.02 Risk-awareness
)
Pearson r = 0.81
𝑃= 2×10-4 3
Recreational
Risk-taking
(i)
Pearson r = 0.73
𝑃= 0.002 (k) (l) (j) Figure 3. Comparison between the predicted risk-preference score and the realistic self-reported value (N = 15) over
six domains of Study B (a,b for general, c,d for ethical, e,f for financial, g,h for health, i,j for recreational, k,l for social). The predicted value is calculated using significant predictors and the corresponding coefficients reported in Table 4. Future Internet 2021, 13, 17 10 of 13 10 of 13 5. Conclusions Overall, this study makes contributions both to research with direct implications
for current theories of risk-preference in scientific settings and to practice in different
applied settings. In particular, we introduced a novel interdisciplinary research method
for analyzing one’s attitude of risk-taking. To the best of our knowledge, this is the first
empirical analysis to combine network theory, text mining, and body-sensing technology
to access the individuals’ attitude towards risk. Most importantly, through the empirical
evidence of two presented studies, we have shown that one can efficiently predict both the
original DOSPERT risk-taking and the intrinsic risk-willingness in six domains (general,
ethical, health, financial, recreation, social) based on tribal language features, emotionality,
network structure metrics, and body sensors (see the summarized predictors in Figure 4). In conclusion, we have introduced a novel system of practical value both for risk
researchers and decision makers in organizations. For researchers, we provide a novel way
based on “honest signals” [20] to measure “soft” attributes such as attitude towards risk
and ethical values, permitting them to study these personal characteristics without the need
to ask survey questions. Using “honest signals” to predict risk attitudes will also eliminate
the subjectivity bias inherent in surveys. For managers, identifying the risk-preferences
of the members of an organization based on their e-mail networking behavior and body
language enables them to develop risk-mitigation strategies to create more risk-aware and
ethical organizations. Overall, this study makes contributions both to research with direct implications
for current theories of risk-preference in scientific settings and to practice in different
applied settings. In particular, we introduced a novel interdisciplinary research method
for analyzing one’s attitude of risk-taking. To the best of our knowledge, this is the first
empirical analysis to combine network theory, text mining, and body-sensing technology
to access the individuals’ attitude towards risk. Most importantly, through the empirical
evidence of two presented studies, we have shown that one can efficiently predict both the
original DOSPERT risk-taking and the intrinsic risk-willingness in six domains (general,
ethical, health, financial, recreation, social) based on tribal language features, emotionality,
network structure metrics, and body sensors (see the summarized predictors in Figure 4). In conclusion, we have introduced a novel system of practical value both for risk
researchers and decision makers in organizations. study.
D
A
il bili
S
Th
d
d
h
d
l
g
;
g p
,
; pp
2.
Ariely, D. Predictably Irrational; American Psychological Association: Worcester, MA, USA, 2013. 5. Conclusions For researchers, we provide a novel way
based on “honest signals” [20] to measure “soft” attributes such as attitude towards risk
and ethical values, permitting them to study these personal characteristics without the need
to ask survey questions. Using “honest signals” to predict risk attitudes will also eliminate
the subjectivity bias inherent in surveys. For managers, identifying the risk-preferences
of the members of an organization based on their e-mail networking behavior and body
language enables them to develop risk-mitigation strategies to create more risk-aware and
ethical organizations. 11 of 13
11 of 13 Future Internet 2021, 13, 17
Future Internet 2021, 13, x FO Figure 4. Significant predictors of risk-preference. Figure 4. Significant predictors of risk-preference. Figure 4. Significant predictors of risk-preference. Figure 4. Significant predictors of risk-preference. In conclusion, we have introduced a novel system of practical value both for risk
researchers and decision makers in organizations. For researchers, we provide a novel
way based on “honest signals” [20] to measure “soft” attributes such as attitude towards
risk and ethical values, permitting them to study these personal characteristics without
the need to ask survey questions. Using “honest signals” to predict risk attitudes will also
li
i
h
bj
i i
bi
i h
i
F
id
if i
h
i k
f
Supplementary Materials: The following are available online at https://www.mdpi.com/1999-590
3/13/1/17/s1. Table S1: Descriptive analysis of variables of Study A; Table S2: Pearson correlation
between risk-preference scores as dependent variables and communication signals as independent
variables; Table S3: Descriptive analysis of variables of Study B; Table S4: Pearson correlation between
risk-preference scores and body signals in terms of sensor data and mood data. eliminate the subjectivity bias inherent in surveys. For managers, identifying the risk-pref-
erences of the members of an organization based on their e-mail networking behavior and
body language enables them to develop risk-mitigation strategies to create more risk-
aware and ethical organizations
Author Contributions: P.G. conceived the project; J.S. designed the experiments and analyzed the
results; J.S. and P.G. wrote the manuscript. All authors have read and agreed to the published version
of the manuscript. aware and ethical organizations. Supplementary Materials: The following are available online at www.mdpi.com/xxx/s1. Table S1:
Funding: This research was partially funded by Signify (Philips Research), grant number 024826-
00013 and the China Scholarship Council Program, grant number 201906380135. 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 privacy reasons
y
y
y
g
3.
Zuckerman, M.; Kuhlman, D.M. Personality and Risk-Taking: Common Bisocial Factors. J. Pers. 2000, 68, 999–1029. [CrossRef] Data Availability Statement: The data presented in this study are availa
corresponding author The data are not publicly a ailable due to pri acy r
3.
Zuckerman, M.; Kuhlman, D.M. Personality and Risk-Taking: Common Bisocial Factors. J. Pers. 2000, Informed Consent Statement: Informed consent was obtained from all subjects involved in the
study
1.
Kahneman, D.; Tversky, A. Prospect theory: An analysis of decision under risk. In Handbook of the Fundamentals of Financial
Decision Making: Part I; World Scientific: Singapore, 2013; pp. 99–127. 5. Conclusions Descriptive analysis of variables of Study A; Table S2: Pearson correlation between risk-preference
scores as dependent variables and communication signals as independent variables; Table S3: De-
scriptive analysis of variables of Study B; Table S4: Pearson correlation between risk-preference
scores and body signals in terms of sensor data and mood data
Institutional Review Board Statement: The study was conducted according to the guidelines of
the Declaration of Helsinki, and approved by the Institutional Review Board of MIT (protocol code
170181783) on 16 Feburary 2017. Descriptive analysis of variables of Study A; Table S2: Pearson correlation between risk-preference
scores as dependent variables and communication signals as independent variables; Table S3: De-
scriptive analysis of variables of Study B; Table S4: Pearson correlation between risk-preference
scores and body signals in terms of sensor data and mood data
Institutional Review Board Statement: The study was conducted according to the guidelines of
the Declaration of Helsinki, and approved by the Institutional Review Board of MIT (protocol code
170181783) on 16 Feburary 2017. scores and body signals in terms of sensor data and mood data. Author Contributions: P.G. conceived the project; J.S. designed the experiments and analyzed the
Informed Consent Statement: Informed consent was obtained from all subjects involved in the study. Author Contributions: P.G. conceived the project; J.S. designed the experiments and analyzed the
results; J.S. and P.G. wrote the manuscript. All authors have read and agreed to the published ver-
sion of the manuscript. 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 privacy reasons. Funding: This research was partially funded by Signify (Philips Research), grant number 024826-
00013 and the China Scholarship Council Program, grant number 201906380135. Acknowledgments: All the experiments conducted in this work have been approved by the Institu-
tional Review Board (IRB) of the Massachusetts Institute of Technology (MIT). Institutional Review Board Statement: The study was conducted according to the guidelines of the
l
f
l
k
d
d b
h
I
l
d
f
I
l
d
Conflicts of Interest: The authors declare no conflict of interest. Institutional Review Board Statement: The study was conducted
Conflicts of Interest: The authors declare no conflict of interest. Data Availability Statement: The data presented in this study are available on request from
corresponding author The data are not publicly available due to privacy reasons
Kuhlman, D.M. Personality and Risk-Taking: Common Bisocial Factors. J. Pers. 2000, 68, 999–1029. [CrossR study.
D
A
il bili
S
Th
d
d i
hi
d
il bl
f
g p
pp
tably Irrational; American Psychological Association: Worcester, MA, USA, 2013. References Cultural Influences on Entrepreneurial Orientation: The Impact of National
Culture on Risk Taking and Proactiveness in SMEs. Entrep. Theory Pr. 2010, 34, 959–983. [CrossRef] 13. Ashraf, B.N.; Zheng, C.; Arshad, S. Effects of national culture on bank risk-taking behavior. Res. Int. Bus. Financ. 2016, 37, 309–326. [CrossRef] 14. Adolphs, R. Cognitive neuroscience of human social behaviour. Nat. Rev. Neurosci. 2003, 4, 165–178. [CrossRef] [PubMed]
15. Lazer, D.; Pentland, A.S.; Adamic, L.; Aral, S.; Barabasi, A.L.; Brewer, D.; Jebara, T. Life in the network: The coming age of
computational social science. Science 2009, 323, 721–723. [CrossRef] [PubMed] p
g
15. Lazer, D.; Pentland, A.S.; Adamic, L.; Aral, S.; Barabasi, A.L.; Brewer, D.; Jebara, T. Life in the network: The coming age of
computational social science. Science 2009, 323, 721–723. [CrossRef] [PubMed] p
16. Kumar, R.; Novak, J.; Tomkins, A. Structure and Evolution of Online Social Networks. In Link Mining: Models, Algorithms,
and Applications; Springer Science and Business Media LLC: New York, NY, USA, 2010; pp. 337–357. 17. Otte, E.; Rousseau, R. Social network analysis: A powerful strategy, also for the information sciences. J. Inf. Sci. 2002, 28, 441–453. [CrossRef] 18. Gloor, P.A. Sociometrics and Human Relationships; Emerald: Bingley, UK, 2017; pp. 1–23. 19. Newman, M. Networks; Oxford University Press: Oxford, UK, 2018. 20. Pentland, A. Honest Signals: How They Shape our World; MIT Press: Cambridge, MA, USA, 2010. 21. Gloor, P.; Colladon, A.F. Heart Beats Brain: Measuring Moral Beliefs Through E-mail Analysis. In Digital Transformation of
Collaboration; Przegalinska, A., Grippa, F., Gloor, P.A., Eds.; Springer Science and Business Media LLC: Berlin, Germany, 2020;
pp. 85–93. 22. Morgan, L.; Gloor, P. Identifying Virtual Tribes by Their Language in Enterprise Email Archives. In Digital Transformation of
Collaboration; Przegalinska, A., Grippa, F., Gloor, P.A., Eds.; Springer Science and Business Media LLC: Berlin, Germany, 2020;
pp. 95–110. pp
23. Eagle, N.; Pentland, A. (Sandy) Reality mining: Sensing complex social systems. Pers. Ubiquitous Comput. 2005, 10, 255–268. [CrossRef] 24. Chen, K.Y.; Janz, K.F.; Zhu, W.; Brychta, R.J. Re-defining the roles of sensors in objective physical activity monitoring. Med. Sci. Sports Exerc. 2012, 44 (Suppl. 1), S13. [CrossRef] 25. Gloor, P.A.; Colladon, A.F.; Grippa, F.; Budner, P.; Eirich, J. Aristotle said “happiness is a state of activity”—Predicting mood
through body sensing with Smartwatches. J. Syst. Sci. Syst. Eng. 2018, 27, 586–612. [CrossRef] 26. Kreuter, F.; Haas, G.-C.; Keusch, F.; Bähr, S.; Trappmann, M. References Informed Consent Statement: Informed consent was obtained from all subjects involved in the
study
1. Kahneman, D.; Tversky, A. Prospect theory: An analysis of decision under risk. In Handbook of the Fundamentals of Financial
Decision Making: Part I; World Scientific: Singapore, 2013; pp. 99–127. 12 of 13 12 of 13 Future Internet 2021, 13, 17 4. Hoyle, R.H.; Fejfar, M.C.; Miller, J.D. Personality and Sexual Risk Taking: A Quantitative Review. J. Pers. 2000, 68, 1203–1231. [CrossRef] [
]
5. Foster, J.D.; Shenesey, J.W.; Goff, J.S. Why do narcissists take more risks? Testing the roles of perceived risks and benefits of risky
behaviors. Pers. Individ. Differ. 2009, 47, 885–889. [CrossRef] 5. Foster, J.D.; Shenesey, J.W.; Goff, J.S. Why do narcissists take more risks? Testing the roles of perceived risks and benefits of risky
behaviors. Pers. Individ. Differ. 2009, 47, 885–889. [CrossRef]
6. Byrnes, J.P.; Miller, D.C.; Schafer, W.D. Gender differences in risk taking: A meta-analysis. Psychol. Bull. 1999, 125, 367. [CrossRef] ff
6. Byrnes, J.P.; Miller, D.C.; Schafer, W.D. Gender differences in risk taking: A meta-analysis. Psychol. Bull. 1999, 125, 367. [CrossRef]
7. Harris, C.R.; Jenkins, M. Gender differences in risk assessment: Why do women take fewer risks than men? Judgm. Decis. Mak. 2006, 1, 48–63. y
, J
;
,
;
,
g
y
y
,
,
[
]
7. Harris, C.R.; Jenkins, M. Gender differences in risk assessment: Why do women take fewer risks than men? Judgm. Decis. Mak. 2006, 1, 48–63. 7. Harris, C.R.; Jenkins, M. Gender differences in risk assessment: Why do women take fewer risks t
2006, 1, 48–63. 8. Daruvala, D. Gender, risk and stereotypes. J. Risk Uncertain. 2007, 35, 265–283. [CrossRef] 8. Daruvala, D. Gender, risk and stereotypes. J. Risk Uncertain. 2007, 35, 265–283. [CrossRef] 9. Czerwonka, M. Cultural, cognitive and personality traits in risk-taking behaviour: Evidence from Poland and the United States
of America. Econ. Res. Ekon. Istraživanja 2019, 32, 894–908. [CrossRef] Evolutionary hypotheses of risk-sensitive choice: Age differences and perspective change. Evol. Hum. Beha
ossRef] 10. Wang, X. Evolutionary hypotheses of risk-sensitive choice: Age differences and perspective chang
1–15. [CrossRef] 11. Gardner, M.; Steinberg, L. Peer Influence on Risk Taking, Risk Preference, and Risky Decision Making in Adolescence and
Adulthood: An Experimental Study. Dev. Psychol. 2005, 41, 625–635. [CrossRef] [PubMed] p
y
y
12. Kreiser, P.M.; Marino, L.D.; Dickson, P.; Weaver, K.M. 35.
Aral, S.; Brynjolfsson, E.; Van Alstyne, M. Information, Technology, and Information Worker Productivity. Inf. Syst. Res. 2012, 23,
849–867. [CrossRef] 33.
Blais, A.R.; Weber, E.U. A domain-specific risk-taking (DOSPERT) scale for adult populations. Judgm. Decis. Mak. 2006, 1, 33–47.
34.
Highhouse, S.; Nye, C.D.; Zhang, D.C.; Rada, T.B. Structure of the Dospert: Is There Evidence for a General Risk Factor? J. Behav.
Decis. Mak. 2017, 30, 400–406. [CrossRef] References Collecting Survey and Smartphone Sensor Data with an App:
Opportunities and Challenges around Privacy and Informed Consent. Soc. Sci. Comput. Rev. 2018, 38, 533–549. [CrossRef] 27. Akhbarifar, S.; Javadi, H.H.S.; Rahmani, A.M.; Hosseinzadeh, M. A secure remote health monito
diagnosis in cloud-based IoT environment. Pers. Ubiquitous Comput. 2020, 1–17. [CrossRef] g
q
p
,
[
]
28. Shadroo, S.; Rahmani, A.M.; Rezaee, A. The two-phase scheduling based on deep learning in the Internet of Things. Comput. Netw. 2020, 107684, 107684. [CrossRef] 28. Shadroo, S.; Rahmani, A.M.; Rezaee, A. The two-phase scheduling based on deep learning in the Interne
2020, 107684, 107684. [CrossRef] 29. Ali, F.; El-Sappagh, S.; Islam, S.M.R.; Ali, A.; Attique, M.; Imran, M.; Kwak, K.-S. An intelligent healthcare monitoring framework
using wearable sensors and social networking data. Futur. Gener. Comput. Syst. 2021, 114, 23–43. [CrossRef] g
g
p
y
30. Ali, F.; El-Sappagh, S.; Islam, S.R.; Kwak, D.; Ali, A.; Imran, M.; Kwak, K. A smart healthcare monitoring system for heart disease
prediction based on ensemble deep learning and feature fusion. Inf. Fusion 2020, 63, 208–222. [CrossRef] 31. Sun, L.; Gloor, P. Measuring Moral Values with Smartwatch-Based Body Sensors. In Digital Transformation of Collaboration;
Przegalinska, A., Grippa, F., Gloor, P.A., Eds.; Springer Science and Business Media LLC: Berlin, Germany, 2020; pp. 51–66. 32. Weber, E.U.; Betz, N.E. A domain-specific risk-attitude scale: Measuring risk perceptions and risk behaviors. J. Behav. Decis. Mak. 2002, 15, 263–290. [CrossRef] 33. Blais, A.R.; Weber, E.U. A domain-specific risk-taking (DOSPERT) scale for adult populations. Judgm. Decis. Mak. 2006, 1, 33–47. 34. Highhouse, S.; Nye, C.D.; Zhang, D.C.; Rada, T.B. Structure of the Dospert: Is There Evidence for a General Risk Factor? J. Behav. Decis. Mak. 2017, 30, 400–406. [CrossRef] 35. Aral, S.; Brynjolfsson, E.; Van Alstyne, M. Information, Technology, and Information Worker Productivity. Inf. Syst. Res. 2012, 23,
849–867. [CrossRef] 13 of 13 Future Internet 2021, 13, 17 13 of 13 36. Gloor, P.; Colladon, A.F.; Grippa, F.; Giacomelli, G. Forecasting managerial turnover through e-mail based social network analysis. Comput. Hum. Behav. 2017, 71, 343–352. [CrossRef] 36. Gloor, P.; Colladon, A.F.; Grippa, F.; Giacomelli, G. Forecasting managerial turnover through e-mail based social network analysis. Comput. Hum. Behav. 2017, 71, 343–352. [CrossRef] p
37. Ahuja, M.K.; Galletta, D.F.; Carley, K.M. Individual Centrality and Performance in Virtual R&D Groups: An Empirical Study. Manag. Sci. 2003, 49, 21–38. [CrossRef] g
38. Freeman, L.C. References A Set of Measures of Centrality Based on Betweenness. Sociometry 1977, 40. [CrossRef] g
38. Freeman, L.C. A Set of Measures of Cen 38. Freeman, L.C. A Set of Measures of Centrality Based on Betweenness. Sociometry 1977, 40. [CrossRef]
39
Bavelas A Communication Patterns in Task Oriented Groups J Acoust Soc Am 2005 22 725 730 [CrossRef] 38. Freeman, L.C. A Set of Measures of Centrality Based on Betweenness. Sociometry 1977, 40. [CrossRef]
39. Bavelas, A. Communication Patterns in Task-Oriented Groups. J. Acoust. Soc. Am. 2005, 22, 725–730. [CrossRef] y
y
Communication Patterns in Task-Oriented Groups. J. Acoust. Soc. Am. 2005, 22, 725–730. [CrossRef] 39. Bavelas, A. Communication Patterns in Task-Oriented Groups. J. Acoust. Soc. Am. 2005, 22, 725–73 40. Hadley, B.; Gloor, P.A.; Woerner, S.L.; Zhou, Y. Analyzing vc influence on startup success: They might not be good for you. In Proceedings of the COINs Conference, Detroit, MI, USA, 14–16 September 2017; Volume 2017, p. 187. y,
;
,
;
,
;
,
y
g
p
y
g
g
y
In Proceedings of the COINs Conference, Detroit, MI, USA, 14–16 September 2017; Volume 2017, p. 187. 41. Kidane, Y.H.; Gloor, P. Correlating temporal communication patterns of the Eclipse open source community with performance
and creativity. Comput. Math. Organ. Theory 2006, 13, 17–27. [CrossRef] 42. Antonacci, G.; Colladon, A.F.; Stefanini, A.; Gloor, P. It is rotating leaders who build the swarm: Social
growth for healthcare virtual communities of practice. J. Knowl. Manag. 2017, 21, 1218–1239. [CrossRef 43. Jackson, T.; Dawson, R.; Wilson, D. Reducing the effect of email interruptions on employees. Int. J. Inf. Manag. 2003, 23, 55–65. [CrossRef] 44. Kushlev, K.; Dunn, E.W. Checking email less frequently reduces stress. Comput. Hum. Behav. 2015, 43, 220–228. [CrossRef] 44. Kushlev, K.; Dunn, E.W. Checking email less frequently reduces stress. Comput. Hum. Behav. 2015, 43, 220–228. [CrossRef]
45
Maffesoli M The Time of the Tribes: The Decline of Individualism in Mass Society; Sage: Thousand Oaks CA USA 1995 ushlev, K.; Dunn, E.W. Checking email less frequently reduces stress. Comput. Hum. Behav. 2015, 43, 220–228
ff
li M Th Ti
f th T ib
Th D li
f I di id
li
i
M
S
i t
S
Th
d O k
CA USA 44. Kushlev, K.; Dunn, E.W. Checking email less frequently reduces stress. Comput. Hum. Behav. 2015, 43,
45. Maffesoli, M. R.D.; Weisberg, S. Diagnostics for heteroscedasticity in regression. Biometrika 1983, 70, 1–10. [CrossRef] References The Time of the Tribes: The Decline of Individualism in Mass Society; Sage: Thousand Oaks, C 46. Garry, T.; Broderick, A.J.; Lahiffe, K. Tribal motivation in sponsorship and its influence on sponsor relationship development and
corporate identity. J. Mark. Manag. 2008, 24, 959–977. [CrossRef] 47. Gloor, P.; Colladon, A.F.; De Oliveira, J.M.; Rovelli, P. Put your money where your mouth is: Using deep learning to identify
consumer tribes from word usage. Int. J. Inf. Manag. 2020, 51, 101924. [CrossRef] g
f
g
48. Russell, J.A. A circumplex model of affect. J. Personal. Soc. Psychol. 1980, 39, 1161. [CrossRef] 49. Breusch, T.S.; Pagan, A.R. A Simple Test for Heteroscedasticity and Random Coefficient Variation. Econometrica 1979, 47, 1287. [CrossRef] 50. Cook, R.D.; Weisberg, S. Diagnostics for heteroscedasticity in regression. Biometrika 1983, 70, 1–10. [Cr 51. Podsakoff, P.M.; MacKenzie, S.B.; Lee, J.Y.; Podsakoff, N.P. Common method biases in behavioral research: A critical review of
the literature and recommended remedies. J. Appl. Psychol. 2003, 88, 879. [CrossRef] pp
y
52. Nowak, M.A.; Page, K.M.; Sigmund, K. Fairness versus reason in the ultimatum game. Science 2000, 289, 1773–1775. [CrossRef]
[PubMed]
|
https://openalex.org/W3122729181
|
https://www.researchsquare.com/article/rs-11858/v2.pdf
|
English
| null |
Correlation of macular sensitivity measures and visual acuity to vision-related quality of life in patients with age-related macular degeneration
|
BMC ophthalmology
| 2,021
|
cc-by
| 6,469
|
Research article Keywords: Age-related macular degeneration, Early Treatment Diabetic Retinopathy Study, macular
sensitivity, microperimetry, visual acuity, vision-related quality of life, Visual Function Questionnaire 39 Posted Date: July 23rd, 2020 DOI: https://doi.org/10.21203/rs.2.21263/v2 License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. d
ll License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full License Version of Record: A version of this preprint was published on March 23rd, 2021. See the published
version at https://doi.org/10.1186/s12886-021-01901-x. Page 1/17 Page 1/17 Abstract Background: Visual acuity is commonly used as a functional outcome measure in patients with age-
related macular degeneration (AMD), despite having a weak correlation with self-perceived visual quality
of life. Microperimetry is a useful method of detecting loss of macular function. We wanted to investigate
the relationship between these two objective visual outcome measures and subjective vision-related
quality of life, finding out which objective measure is more patient-relevant. Methods: Fifty-six consecutive patients with AMD were recruited to the study. Participants were required to
complete the Visual Function Questionnaire 39, the Early Treatment Diabetic Retinopathy Study visual
acuity examination and a microperimetry assessment using the Micro Perimeter 3. One patient withdrew
consent and seven patients dropped out due to cooperation difficulties under microperimetry. Forty-eight
patients with AMD were included in the study: thirty-three patients with late AMD (exudative AMD and/or
geographic atrophy) and fifteen patients with early (non-exudative) AMD. The right eye was included as
standard, as was the eye with the best-corrected visual acuity. Results: There was a higher correlation between vision-related quality of life and macular sensitivity
(rho=0.371; p=0.034) than between vision-related quality of life and visual acuity (rho=0.334; p=0.058) in
patients with late AMD. These correlations were not statistically significant in patients with early AMD. Composite score (rho=0.405; p=0.019) and near-distance activities score (rho=0.469; p=0.006) correlated
highest with the nasal inner macular sub-region in patients with late AMD. Correlations between
composite score and macular sub-regions in patients with early AMD were not significant, but near-
distance activities score correlated highest with the nasal outer macular sub-region in these patients
(rho=0.735; p=0.002). Conclusions: Macular sensitivity as measured using microperimetry correlates significantly better with
vision-related quality of life than visual acuity, showing it to be a more patient-relevant outcome measure
in patients with late AMD. Furthermore, the nasal sub-regions of the macula appear to be preferred retinal
loci in patients with AMD. (330 words) Background Age-related macular degeneration (AMD) is the leading cause of vision loss in the developed world [1]. The disease impacts vision-related quality of life, as well as having a substantial medical cost [2-5]. In
clinical practice, monitoring of AMD is most often reliant on visual acuity and optical coherence
tomography (OCT) even though it is known that both these measures have a relatively weak correlation
with measures of patient self-reporting such as the Visual Function Questionnaire (VFQ) [3, 6]. Outcome
measures that are more patient-relevant are being sought after in clinical trials, but since patient relevance
can be difficult to quantify, it is important to identify the objective measure of visual function most closely
aligned with subjective experience. Page 2/17 Page 2/17 Microperimetry is a non-invasive measure of macular sensitivity that can provide valuable information
about visual dysfunction in patients with AMD, including location and size of lesions in the macula and
how they affect fixation [3, 4, 7-9]. Studies involving patients with diabetic retinopathy have suggested
that microperimetry could be a better objective measure in quantifying visual function than visual acuity
[10, 11], a claim supported by studies investigating AMD [12, 13]. We wanted to investigate the
relationship between vision-related quality of life measured using VFQ and objective measures of visual
function, namely, visual acuity and microperimetry. In this, the first study of its kind, our primary aim was
to find the objective measure that is most patient-relevant in patients with AMD. Microperimetry can measure the function of different areas of the macula and studies have shown
differences in the way in which patients with AMD fixate compared with individuals without vitreoretinal
disease [14, 15]. As an additional aim, we wanted to investigate if different areas of the macula correlated
better with VFQ, and if certain areas of the macula are more important than others in patients with AMD. Study design and participants Telephone interviews w
and were conducted within one week of the patient visit. A
research room and a clear interview guide was used. Interv
felt it necessary to have their next of kin present. In such c
during and after the interview. The VFQ lasts approximately twenty minutes and consists of thirty-nine items concerning the self-reported
visual health status of an individual. The overall VFQ composite score and the near activities sub-score
were included in our analysis of results. VFQ investigations were performed by one of the authors, T.R.J.F.,
preferably face-to-face, or by telephone. Interviews were conducted by telephone when patient limitations
such as advanced age and disability did not allow completion of both the questionnaire and the
microperimetry investigation during the same visit and when geographical distance and transport costs
rendered a second visit unfeasible. Telephone interviews were permitted to provide flexibility in this regard
and were conducted within one week of the patient visit. All interviews were conducted in a designated
research room and a clear interview guide was used. Interviews were one-to-one unless a study participant
felt it necessary to have their next of kin present. In such cases, the investigator made a note of this both
during and after the interview. Visual acuity Visual acuity was examined according to departmental guidelines using the Early Treatment Diabetic
Retinopathy (ETDRS) method. Some participants only had best-corrected visual acuity (BCVA) reported in
Snellen; these values were converted to ETDRS before performing statistical analysis. Snellen to ETDRS
conversion was performed for five participants in the AMD group and twelve participants in the group
without vitreoretinal disease. Study design and participants Based on previous studies [16-18] and with a given significance value of 0.05 and a power of 80%, we
calculated that thirty-four patients with AMD were required to undergo retinal function testing. Due to the
risk of dropout, the minimum number required was increased to forty. From October 2017 to March 2019
fifty-six consecutive patients with AMD were recruited from the outpatient department of Zealand
University Hospital. A consultant ophthalmologist performed a full ocular examination at the start of the study. Although
patients had been diagnosed with AMD in the years prior to the study, fundus examination and OCT were
used to confirm the diagnosis. No patients recently diagnosed with AMD were included in this study. Patients with a vitreoretinal pathology other than AMD, glaucoma with visual field defect, amblyopia or
cognitive deficit were excluded from the study. One patient withdrew consent and seven patients dropped
out from the study for failing to complete the microperimetry assessment. Of these seven, five were
unable to fixate on the target during the investigation, one fell asleep and one had a stiff neck and found
the chin rest to be too uncomfortable. Forty-eight patients with AMD were therefore included in the study. These were: thirty-three patients with late AMD (exudative AMD and/or geographic atrophy) and fifteen
patients with early (non-exudative) AMD. Additionally, for the purposes of investigating how patients with AMD differ in the way in which they fixate
compared with individuals with healthy retina, we included thirty-two individuals without vitreoretinal
disease as a control group. These individuals were also recruited from the outpatient department of our
university teaching hospital. Measurement of Vision-related Quality of Life Measurement of Vision-related Quality of Life Page 3/17 Vision-related quality of life was measured using the National Eye Institute Visual Function Questionnaire-
39 (VFQ). Several instruments for measuring vision-related quality of life exist, but we chose the National
Eye Institute Visual Function Questionnaire-39 (VFQ) because our patients are Danish speakers and a
Danish language version of this questionnaire exists that is validated for use in patients with AMD [19]. The VFQ lasts approximately twenty minutes and consists
visual health status of an individual. The overall VFQ com
were included in our analysis of results. VFQ investigation
preferably face-to-face, or by telephone. Interviews were co
such as advanced age and disability did not allow comple
microperimetry investigation during the same visit and wh
rendered a second visit unfeasible. Microperimetry Microperimetry is a useful method of detecting loss of macular function in patients with AMD [5]. All
microperimetry investigations were performed by one of the authors, T.R.J.F. using a single Nidek Micro
Perimeter 3 (MP-3) (Nidek Co., Ltd. Gamagori, Japan) according to the operator instructions. The
assessments were conducted in a dark room while the contralateral eye was patched. In the case of
significant eye movements, which occurred often due to poor fixation in patients with AMD, the test was
paused automatically. Moreover, the test was paused if the patient needed a break. The test could then
resume after successful realignment of the study eye. Microperimetry measures differential light sensitivity (DLS) in decibels at thirty-three different points in the
region of the macula. DLS defines as the “minimal luminance of a white spot stimulus superimposed on a
white background of uniform luminance necessary to perceive the stimulus” [7]. We calculated the mean
overall macular sensitivity for each eye using 95% confidence intervals and we performed local analysis
of macular sensitivity by macular sub-region. Page 4/17 To study the individual macular sub-regions, we superimposed a standard ETDRS grid onto a fundus
image obtained by microperimetry. The ETDRS macular grid [20] is a tool that allows the macula to be
divided into sub-regions when projected onto a fundus image [21, 22]. The macular subfields defined by
the ETDRS grid are: the fovea, superior inner, temporal inner, inferior inner, nasal inner, superior outer,
temporal outer, inferior outer, and nasal outer [7]. Each DLS point corresponds with a number that
determines which ETDRS sub-region it falls into. (Figure 1) Using Microsoft Excel (Microsoft Co. Redmond, WA), we calculated the mean of the DLS points within
each macular sub-region with 95% confidence intervals. The fovea was comprised of a single, central DLS
point; the four inner sub-regions each contained three DLS points and the four outer sub-regions each
contained four DLS points. Four DLS points fell outside of the superimposed ETDRS grid and were
therefore excluded from local analysis but were included in the overall mean macular sensitivity
calculation. Finally, we correlated data from the overall macula and the individual macular subfields with visual
function as defined by the VFQ. Data Analysis Results were analysed using two different methods: standard eye analysis and best eye analysis. (Table
1) Standard eye analysis used data from the right eye, as far as possible. Exceptions to this rule were:
cases in which a patient had clinical evidence of AMD only in the left eye on ophthalmic examination
and/or a missing or incomplete right eye microperimetry investigation. A patient’s best eye was defined as
the eye with highest BCVA. Best eye analysis was required to correlate BCVA and macular sensitivity to VFQ. Objective means of
measurement of visual function do not always correlate with patients’ self-perceived visual abilities [19],
but it seemed likely that the better-seeing eye would be the more important eye in terms of subjective
visual function. Best eye analysis was therefore used to determine if BCVA or macular sensitivity related
better to vision-related quality of life. Best eye analysis was also used to investigate the correlation
between different macular sub-regions and VFQ and to show how specific areas of the macula relate to
aspects of visual function. Standard eye analysis was performed to avoid selection bias when
investigating the effects of AMD on macular sensitivity. We used this method to compare the different
ETDRS subfields to find out which areas of the macula are more important in patients with AMD. Data Analysis was performed using SPSS Statistical Analysis Software (IBM Corporation Armonk, NY). We assessed distribution using bar charts and distribution curves. In the case of normal distribution,
parametric tests (Pearson’s coefficient; independent samples t-test) were used. In the absence of normal
distribution, non-parametric tests were used (Spearman’s rho coefficient; Mann-Whitney U-test). A p value
of <0.05 was considered statistically significant. Results Page 5/17 Page 5/17 We included fifteen patients with early AMD (mean age: 77.5±7.2 years), thirty-three patients with late
AMD (mean age: 79±5.2 years), and thirty-two individuals without vitreoretinal disease (mean age:
71.7±7.8 years) as a control group. The control group was significantly younger than the group with AMD
(p<0.001; independent samples test). Demographic data is available as an additional file (see Additional
file 1). Visual acuities are reported in Table 1. We included fifteen patients with early AMD (mean age: 77.5±7.2 years), thirty-three patients with late
AMD (mean age: 79±5.2 years), and thirty-two individuals without vitreoretinal disease (mean age:
71.7±7.8 years) as a control group. The control group was significantly younger than the group with AMD
(p<0.001; independent samples test). Demographic data is available as an additional file (see Additional
file 1). Visual acuities are reported in Table 1. With regards the main aim of this study, there was a positive correlation between VFQ composite score
and BCVA in patients with late AMD (rho=0.334; p=0.058; Spearman’s Correlation), but the correlation
between VFQ composite score and overall macular sensitivity in these patients was higher (rho=0.371;
p=0.034). (Figure 2) The correlations between VFQ composite score and BCVA and VFQ composite score
and overall macular sensitivity in patients with early AMD were not statistically significant. There were no
significant differences between males and females in the VFQ scores and their association with visual
acuity and microperimetry measures. Full correlation data for early and late AMD are shown in Table 2
and Table 3 respectively. To address the secondary purpose of this study, which was to investigate how patients with AMD differ
from those with healthy retina in terms of how they preferentially recruit sub-regions of the macula, we
obtained macular sensitivities measured in decibels for eyes with AMD and eyes without vitreoretinal
disease. The overall macular sensitivities were 21.9 (interquartile range (IQR): 8.8) in the early AMD sub-
group and 17.3 (IQR: 10.9) in the late AMD sub-group, compared with 22.61 (IQR: 7) in the healthy retina
group (p<0.001; Mann-Whitney U-test). In patients with AMD and individuals without vitreoretinal disease, the area of the macula with the highest
macular sensitivity was the temporal outer sub-region. Results The macular sensitivities in this area were: 23.0
(IQR: 7) in the early AMD sub-group and 21.0 (IQR: 9.25) in the late AMD sub-group compared with 23.59
(IQR: 7) in the healthy retina group, a difference that was not statistically significant (p=0.145; Mann-
Whitney U-test). Macular sensitivity results are provided as an additional file (see Additional file 2). When we correlated the different ETDRS subfields with VFQ, the VFQ composite score correlated highest
with the nasal inner macular sub-region (rho=0.405; p=0.019) in patients with late AMD, suggesting that
this area of the macula is most important in terms of vision-related quality of life in these patients. Correlations between composite score and macular sub-regions in patients with early AMD and
individuals with healthy retina were not significant. The VFQ near-distance activities sub-score correlated highest with the nasal inner macular sub-region in
patients with late AMD (rho=0.469; p=0.006), and with the nasal outer sub-region in patients with early
AMD (rho=0.735; p=0.002), suggesting that the nasal macula is most important to this aspect of visual
functioning in patients with AMD. Correlations between near-distance activities sub-score and macular
sub-regions in individuals with healthy retina were not significant. Full correlation data is available as an
additional file (see Additional file 3). Page 6/17 Page 6/17 BCVA is commonly used as an outcome measure in clinical studies and as a general measure of visual
function. The need for an objective method of testing visual outcome, such as BCVA, in response to
treatment is widely accepted. BCVA has a low correlation with VFQ [19]. Microperimetry has been shown
to correlate significantly with visual acuity (p=0.0001) [23]. Our results now suggest that microperimetry
could be a superior measure of visual outcome than visual acuity because it correlates better with VFQ. BCVA is commonly used as an outcome measure in clinical studies and as a general measure of visual
function. The need for an objective method of testing visual outcome, such as BCVA, in response to
treatment is widely accepted. BCVA has a low correlation with VFQ [19]. Microperimetry has been shown
to correlate significantly with visual acuity (p=0.0001) [23]. Our results now suggest that microperimetry
could be a superior measure of visual outcome than visual acuity because it correlates better with VFQ. The importance of VFQ as a subjective method of vision assessment is accepted and it is acknowledged
that responses may differ depending on how the questionnaire is administered [24]. Most studies that
compare different modes of administration find a small or negligible impact on the results [25, 26],
although one study reported that telephone administration is associated with more positive quality of life
scores [27]. However, limitations due to disability should not be a factor in determining whether an
individual is eligible to be interviewed, and it makes sense to provide flexibility in this regard by
interviewing over the phone [28]. Nevertheless, face-to-face interviews are often preferable as this mode
allows for the observation of non-verbal cues, providing a more natural type of interchange between the
interviewer and the subject [29]. Responses can be influenced either over the phone or face-to-face,
through inflections of the voice, gestures and facial expressions [30] and it is therefore important that an
interviewer maintains the neutral tone of voice and style of delivery set out by the interview guide when
administering the VFQ. Unlike microperimetry, which uses decibels, visual acuity has no standardised measurement as distances
can be measured in feet or metres. In addition, there are several different methods of visual acuity
examination in clinical use [6, 31, 32], making it difficult to directly compare results from different clinics
and research centres. Page 6/17 Visual acuity measures a person’s ability to discriminate between stimuli when
presented on a highly contrasted background [6]. For routine visual acuity assessment in daily clinical
practice, the Snellen Visual Acuity Chart or the ETDRS Chart is generally used [32]. Previous studies recommend the ETDRS method of visual acuity measurement in patients with AMD
because it has better accuracy and reproducibility than Snellen, particularly in patients with advanced
disease [6, 31, 33]. This is especially relevant as visual acuity may not be affected in patients with AMD
until the disease has progressed into the late stage [3, 9, 12]. The ETDRS chart measures visual acuity
from a distance of four metres, so a specially adapted room is required, which is not the case when using
microperimetry. Moreover, the accuracy of the visual acuity assessment is often dependent on the
competency level of the examiner, leading to inter-observer variability [32]. Unlike the visual acuity
assessment, microperimetry is an automated functional test, meaning that the investigator does not run
the same risk of acquiring unreliable data. Microperimetry is a non-invasive procedure to assess macular sensitivity while the fundus is directly
examined through live imaging [5]. Other clinical tests of visual function have been found to be useful
measures in AMD. These include: contrast sensitivity [34]; dark adaptation [35] and electroretinography
(ERG) [36]. Unlike in ERG, there is no standardised protocol in microperimetry. For example, no
recommendations exist on whether patients should be examined with their pupils dilated or undilated, Page 7/17 Page 7/17 although a recent study found that patients may be tested with or without pupil dilation as both scenarios
produce consistent and interchangeable results [37]. Microperimetry enables clinicians to directly relate
visual function to underlying fundus morphology, giving insight into the pathophysiology and natural
history of retinal disease. Even in the presence of relatively good visual acuity, such as in the early stage
of AMD, microperimetry can provide relevant information regarding macular dysfunction [7, 8]. Sugawara
et al. have already shown a significant positive correlation (p=0.0003) between macular sensitivity as
measured by microperimetry and vision-related quality of life in patients with retinitis pigmentosa [38];
now our correlations reveal that macular sensitivity relates more closely to vision-related quality of life in
patients with AMD than does the ETDRS measurement of visual acuity. Page 6/17 Microperimetry technology contains an eye-tracking system that automatically corrects the position of the
stimulus when a patient changes their fixation. The Nidek MP-3 has an eye tracking system that
automatically registers the position of the eye relative to anatomical landmarks twenty-five times per
second [6]. Additionally, microperimetry has been shown to have high test-retest reliability even when
visual acuity is poor, and fixation is unstable and eccentric [39]. Microperimetry is therefore proven to be a
useful tool in tracking disease progression when looking at treatment efficacy or performing a longitudinal
study [3, 40]. The Nidek MP-3 microperimeter can provide an overall macular sensitivity by calculating the mean of all
DLS points inside the region of the macula. Patients with AMD may show macular dysfunction that
precedes noticeable vision loss [3, 40] and our results show that overall macular sensitivity is reduced in
early and late AMD compared with eyes with healthy retina. Therefore, microperimetry may be a more
sensitive screening tool for early disease than visual acuity. In patients with AMD, DLS points can vary greatly in terms of their retinal sensitivity. This produces a wide
range of results within the same macula: for example, a clinically significant difference in retinal
sensitivity is found at the border of a scotoma. Analysis of retinal sensitivity at individual DLS points
therefore allows for a more localised assessment of macular function [3, 7, 40] that can be helpful in the
management of retinal pathology [9]. Macular subfield analysis can be used clinically in the management
of patients with AMD to determine the impact of the disease on specific areas of the macula. Although macular sensitivity is more closely aligned with vision-related quality of life than the ETDRS
method of visual acuity testing, microperimetry is not without limitations. The investigation can be time
consuming and it requires good patient cooperation. Microperimetry in patients with AMD with unstable
fixation can be even more time-consuming as in order for the investigation to proceed to eventual
completion, eye movements must be either corrected automatically by the microperimeter or manually by
the technician. Furthermore, microperimetry equipment comes at a cost to the healthcare provider [41],
although we might reasonably expect the apparatus to become less expensive over time. Page 6/17 We chose to correlate macular subfields with the near-distance activities sub-score of the VFQ because
the inability of patients with AMD to maintain steady fixation is strongly associated with slower reading
[42]. This particular aspect of visual function can affect quality of life in patients with AMD [43]. Page 8/17 In both AMD sub-groups, we observed that the nasal macula strongly correlated with VFQ composite and
near activities scores. A person with healthy retina would normally use their fovea to perform near-
distance activities, but patients with macular dysfunction typically recruit a parafoveal region of the
macula as their preferred retinal locus for fixating and scanning text [10, 11, 44]. The strong correlation
between the nasal macular sensitivity and the VFQ near activities sub-score in particular suggests that the
nasal outer and inner sub-regions are preferred retinal loci in patients with early and late AMD respectively. This is suggestive of a pattern of disease-mediated photoreceptor loss, but further studies are required to
investigate the possible clinical implications of this finding. In both AMD sub-groups, we observed that the nasal macula strongly
near activities scores. A person with healthy retina would normally use
distance activities, but patients with macular dysfunction typically rec
macula as their preferred retinal locus for fixating and scanning text [1
between the nasal macular sensitivity and the VFQ near activities sub
nasal outer and inner sub-regions are preferred retinal loci in patients
This is suggestive of a pattern of disease-mediated photoreceptor los
investigate the possible clinical implications of this finding. There were no statistically significant correlations observed in the group without vitreoretinal disease. This
may be due to a ceiling-effect caused by a narrow range of retinal sensitivities among those without
vitreoretinal disease. Indeed, a similar trend was observed by Barboni et al. in the control group of their
study [40]. AMD is a heterogenous disease and a strength of this study is that we divided patients by stage: those
with either neovascular AMD and/or geographic atrophy were allocated one sub-group, while those with
non-neovascular AMD without geographic atrophy were allocated another. A limitation of this study is that
we did not correlate functional outcome measures with lesion size in the patients with geographic
atrophy. Future studies could seek to correlate retinal function with disease morphology in these patients. Page 6/17 Our study did not divide the patients according to severity or phenotype: future studies could repeat our
experiment with the addition of an intermediate AMD sub-group and compare patients with neovascular
AMD to those with non-neovascular AMD. Furthermore, in this study the AMD group and the healthy retina
group were not age-matched. This is an inherent difficulty in case-control studies involving AMD, as it is
estimated that up to one third of the population older than 60 years have drusen clinically, and perhaps all
elderly people have drusen histologically [45]. Conclusions Our findings show that mean macular sensitivity relates better to vision-related quality of life than BCVA
using the ETDRS method of testing. Microperimetry is arguably superior to visual acuity as a measure of
visual outcome and we therefore recommend the implementation of microperimetry in clinical practice in
order to improve the management of patients with AMD. Use of microperimetry can also potentiate further
studies that aim to investigate macular morphology and function in greater detail. In the future it may be
possible to use microperimetry as a prognostic tool for predicting vision-related quality of life in patients
with AMD by analysing areas of reduced macular sensitivity. Declarations Ethics approval and consent to participate Acknowledgements Thanks to Grace Chandler for help with figures. The authors also gratefully acknowledge Christopher Rue
Molbech and Yousif Subhi for their assistance with statistics. Authors’ contributions TLS designed the study. TRJF and AKP collected the patient data. All authors analysed and interpreted the
data and were major contributors in writing the manuscript. All authors read and approved the final
manuscript. Abbreviations AMD = age-related macular degeneration; BCVA = best-corrected visual acuity; DLS = differential light
sensitivity; ERG = electroretinography; ETDRS = Early Treatment Diabetic Retinopathy Study; IQR =
interquartile range; OCT = optical coherence tomography; VFQ = visual function questionnaire. Competing interests Competing interests The authors declare that they have no competing interests. This study was supported by the Danish Eye Research Foundation, Synoptik Foundation, Fight for Sight
Denmark, and the Jascha Fund. The funding bodies had no influence on: the design of the study; the
collection, analysis and interpretation of the data; the preparation of the manuscript; or the decision to
publish. Ethics approval and consent to participate Ethics approval and consent to participate This study was conducted in accordance with the ethical principles stated in the Declaration of Helsinki. The study was approved by the Ethics Committee of Region Zealand, Denmark (Den Videnskabsetiske Page 9/17 Page 9/17 Page 9/17 Komité for Region Sjælland) with reference number SJ-618. Informed oral and written consent was
obtained from all participants. Consent for publication Consent for publication Not applicable. Availability of data and materials All data generated or analysed during this study are included in this published article and its
supplementary information files. References 1. Prokofyeva E, Zrenner E. Epidemiology of major eye diseases leading to blindness in Europe: a
literature review. Ophthalmic Res. 2012;47:171-188. Page 10/17 Page 10/17 Page 10/17 2. Mitchell J, Bradley C. Quality of life in age-related macular degeneration: a review of the literature. Health and quality of life outcomes. Health Qual Life Outcomes. 2006;4:97. 3. Chandramohan A, Stinnett SS, Petrowski JT, Schuman SG, Toth CA, Cousins SW et al. Visual function
measures in early and intermediate age-related macular degeneration. Retina. 2016;36:1021-1031. 4. Taylor DJ, Hobby AE, Binns AM, Crabb DP. How does age-related macular degeneration affect real-
world visual ability and quality of life? A systematic review. BMJ open. 2016;6:e011504. 5. Laishram M, Srikanth K, Rajalakshmi AR, Nagarajan S, Ezhumalai G. Microperimetry - A new tool for
assessing retinal sensitivity in macular diseases. Journal of Clinical and Diagnostic Research. 2017;11:8-11. 6. Falkenstein IA, Cochran DE, Azen SP, Dustin L, Tammewar AM, Kozak I, et al. Comparison of visual
acuity in macular degeneration patients measured with snellen and early treatment diabetic
retinopathy study charts. Ophthalmology. 2008;115:319-23. 7. Cassels NK, Wild JM, Margrain TH, Chong V, Acton JH. The use of microperimetry in assessing visual
function in age-related macular degeneration. Surv Ophthalmol. 2017;63:40-55. 7. Cassels NK, Wild JM, Margrain TH, Chong V, Acton JH. The use of microperimetry in assessing visual
function in age-related macular degeneration. Surv Ophthalmol. 2017;63:40-55. 8. Nagpal M, Khandelwal J, Juneja R, Mehrotra N. Correlation of optical coherence tomography
angiography and microperimetry (MP-3) features in wet age-related macular degeneration. Indian J
Ophthalmol. 2018;66:1790-1795. 9. Crossland M, Jackson M, Seiple WH. Microperimetry: A review of fundus related perimetry. Optometry
Reports. 2012;2:11-15. 9. Crossland M, Jackson M, Seiple WH. Microperimetry: A review of fundus related perimetry. Optometry
Reports. 2012;2:11-15. 10. Midena E, Vujosevic S. Microperimetry in diabetic retinopathy. Saudi Journal of Ophthalmology. 2011;25:131–135 10. Midena E, Vujosevic S. Microperimetry in diabetic retinopathy. Saudi Journal of Ophthalmology. 2011;25:131–135 11. Vujosevic S, Casciano M, Pilotto E, Boccassini B, Varano M, Midena E. Diabetic macular edema:
fundus autofluorescence and functional correlations. Invest Ophthalmol Vis Sci. 2011;52:442-448. 11. Vujosevic S, Casciano M, Pilotto E, Boccassini B, Varano M, Midena E. Diabetic macular edema:
fundus autofluorescence and functional correlations. Invest Ophthalmol Vis Sci. 2011;52:442-448. 12. Midena E, Vujosevic S, Convento E, Manfre' A, Cavarzeran F, Pilotto E. Microperimetry and fundus
autofluorescence in patients with early age-related macular degeneration. Br J Ophthalmol. 2007;91:1499-1503. 12. Surg. 2015;41:1248-1255. Surg. 2015;41:1248-1255. 18. Pedersen, KB, Sjølie AK, Vestergaard AH, Andréasson S, Møller F. Fixation stability and implication for
multifocal electroretinography in patients with neovascular age-related macular degeneration after
anti-VEGF treatment Arch Clin Exp Ophthalmol. 2016;254:1897-1908. 19. Sørensen MS, Andersen, S, Henningsen GO, Larsen CT, Sørensen TL. Danish version of Visual
Function Questionnaire-25 and its use in age-related macular degeneration. Dan Med Bull. 2011;58:1-
5. 20. Age-Related Eye Disease Study Research Group. The Age-Related Eye Disease Study System for
classifying age-related macular degeneration from stereoscopic color fundus photographs: the Age-
Related Eye Disease Study Report Number 6. Am J Ophthalmol. 2001;132:668-681. 21. Kim MS, Kim DY, Jo YJ, Kim JY. The Effect of Machine Aging on the Measurements of Optical
Coherency Tomography. Journal of the Korean Ophthalmological Society. 2016;57:1087-1092. 22. Kafieh R, Rabbani H, Hajizadeh F, Abramoff MD, Sonka M. Thickness mapping of eleven retinal layers
segmented using the diffusion maps method in normal eyes. Journal of Ophthalmology. 2015;2015:1-14 23. Okada K, Yamamoto S, Mizunoya A, Hoshino A, Arai M, Takatsuna Y. Correlation of Retinal Sensitivity
Measured with Fundus-related Microperimetry to Visual Acuity and Retinal Thickness in Eyes with
Diabetic Macular Edema. Eye (Lond). 2006;20:805-809. 24. Boynton PM, Wood GW, Greenhalgh T. Reaching beyond the white middle classes. BMJ. 2004;328:1433-1436. 25. McColl E, Fayers PM. Context effects and proxy assessments. In: Fayers PM and Hays RD (eds),
Assessing Quality of Life in Clinical Trials: Methods and Practice (2nd ed.). Oxford: Oxford University
Press, 2005. 26. Gundy C and Aaronson NK. Effects of mode of administration (MOA) on the measurement properties
of the EORTC QLQ‐C30: a randomized study. Health Qual Life Outcomes. 2010;8:35. 26. Gundy C and Aaronson NK. Effects of mode of administration (MOA) on the measurement properties
of the EORTC QLQ‐C30: a randomized study. Health Qual Life Outcomes. 2010;8:35. 27. Hays RD, Kim W, Spritzer KL, et al. Effects of mode and order of administration on generic health‐
related quality of life scores. Value Health. 2009;12:1035–1039. 27. Hays RD, Kim W, Spritzer KL, et al. Effects of mode and order of administration on generic health‐
related quality of life scores. Value Health. 2009;12:1035–1039. 28. Schechter S, Blair J, Hey JV. Conducting Cognitive Interviews To Test Self-Administered and
Telephone Surveys: Which Method Should We Use? Proceedings of the Section on Survey Methods
Research, American Statistical Association. American Statistical Association, 1996. 29. Willis GB. Cognitive Interviewing – “How To” Guide. References Midena E, Vujosevic S, Convento E, Manfre' A, Cavarzeran F, Pilotto E. Microperimetry and fundus
autofluorescence in patients with early age-related macular degeneration. Br J Ophthalmol. 2007;91:1499-1503. 13. Schmitz-Valckenberg S, Bültmann S, Dreyhaupt J, Bindewald A, Holz FG, Rohrschneider K. Fundus
autofluorescence and fundus perimetry in the junctional zone of geographic atrophy in patients with
age-related macular degeneration. Invest Ophthalmol Vis Sci. 2004;45:4470-4476. 13. Schmitz-Valckenberg S, Bültmann S, Dreyhaupt J, Bindewald A, Holz FG, Rohrschneider K. Fundus
autofluorescence and fundus perimetry in the junctional zone of geographic atrophy in patients with
age-related macular degeneration. Invest Ophthalmol Vis Sci. 2004;45:4470-4476. 14. Shima N, Markowitz SN, Reyes SV Concept of a functional retinal locus in age-related macular
degeneration. Can J Ophthalmol. 2010;45:62-66. 14. Shima N, Markowitz SN, Reyes SV Concept of a functional retinal locus in age-related macular
degeneration. Can J Ophthalmol. 2010;45:62-66. 15. Midena E, Pilotto E. Microperimetry in age: related macular degeneration. Eye (Lond). 2017;31:985-
994. 15. Midena E, Pilotto E. Microperimetry in age: related macular degeneration. Eye (Lond). 2017;31:985-
994. 16. Pedersen KB, Møller F, Sjølie AK, Andréasson S. Electrophysiological assessment of retinal function
during 6 months of bevacizumab treatment in neovascular age-related macular degeneration. Retina. 2010;30:1025-1033. 16. Pedersen KB, Møller F, Sjølie AK, Andréasson S. Electrophysiological assessment of retinal function
during 6 months of bevacizumab treatment in neovascular age-related macular degeneration. Retina. 2010;30:1025-1033. Page 11/17
17. Ma Y, Huang J, Zhu B, Sun Q, Miao Y, Zou H. Cataract surgery in patients with bilateral advanced age-
related macular degeneration: Measurement of visual acuity and quality of life. J Cataract Refract Page 11/17
17. Ma Y, Huang J, Zhu B, Sun Q, Miao Y, Zou H. Cataract surgery in patients with bilateral advanced age-
related macular degeneration: Measurement of visual acuity and quality of life. J Cataract Refract Surg. 2015;41:1248-1255. Research Triangle Institute, 1999. Available at:
https://www.hkr.se/contentassets/9ed7b1b3997e4bf4baa8d4eceed5cd87/gordonwillis.pdf accessed
on 05.07.2020. 30. Houtkoop-Steenstra H. Interaction and the standardised survey interview: the living questionnaire. Cambridge: Cambridge University Press, 2000. 30. Houtkoop-Steenstra H. Interaction and the standardised survey interview: the living questionnaire. Cambridge: Cambridge University Press, 2000. 31. Shamir RR, Friedman Y, Joskowicz L, Mimouni M, Blumenthal EZ. Comparison of Snellen and Early
Treatment Diabetic Retinopathy Study charts using a computer simulation. International Journal of
Ophthalmology. 2016;9:119-123. Page 12/17 Page 12/17 32. Kaiser PK. Prospective evaluation of visual acuity assessment: a comparison of Snellen versus
ETDRS charts in clinical practice (An AOS Thesis). Trans Am Ophthalmol Soc. 2009;107:311-324. 33. Cocce KJ, Stinnett SS, Luhmann UFO, Vajzovic L, Horne A, Schuman SG, et al. Visual Function Metrics
in Early and Intermediate Dry Age-related Macular Degeneration for Use as Clinical Trial Endpoints. Am J Ophthalmol. 2018;189:127-138. 34. Faria BM, Duman F, Zheng CX, et al. Evaluating Contrast Sensitivity in Age-related Macular
Degeneration Using a Novel Computer-Based Test, The Spaeth/Richman Contrast Sensitivity Test. Retina. 2015;35:1465-1473. 35. Laíns I, Miller JB, Park DH et al. Structural Changes Associated with Delayed Dark Adaptation in Age-
Related Macular Degeneration. Ophthalmology. 2017;124:1340–1352. 36. Gerth, C. The role of the ERG in the diagnosis and treatment of Age-Related Macular Degeneration. Documenta Ophthalmologica. 2009;118:63–68. 37. Han RC, Jolly JK, Xue K, MacLaren RE. Effects of pupil dilation on MAIA microperimetry. Clin Exp
Ophthalmol. 2017;45:489-495. 38. Sugawara T, Sato E, Baba T, Hagiwara A, Tawada A, Yamamoto S. Relationship between Vision-
related quality of life and Microperimetry-determined Macular Sensitivity in Patients with Retinitis
Pigmentosa. Jpn J Ophthalmol. 2011;55:643-646. 39. Weingessel B, Sacu S, Vecsei-Mailovits PV, Weingessel A, Richter-Mueksch S, Schmidt-Erfurth U. Interexaminar and intraexaminar reliability of the microperimeter MP-1. Eye (Lond). 2009;23:1052-
1058 40. Barboni, M, Szepessy, Z, Ventura, DF, & Németh, J. Individual Test Point Fluctuations of Macular
Sensitivity in Healthy Eyes and Eyes with Age-Related Macular Degeneration Measured with
Microperimetry. Translational Vision Science & Technology. 2018;7:1-12. 41. Wu Z, Ayton LN, Guymer RH, Luu CD. Low-luminance visual acuity and microperimetry in age-related
macular degeneration. Ophthalmology. 2014;121:1612-1619. 42. Crossland MD, Dunbar HMP, Rubin GS. Fixation stability measurement using the MP1 microperimeter. Retina. 2009;29:651-656 43. Kaltenegger K, Kuester S, Altpeter-Ott E, Eschweiler GW, Cordey A, Ivanov IV, et al. Effects of home
reading training on reading and quality of life in AMD – a randomized and controlled study. Graefes
Arch Clin Exp Ophthalmol. Surg. 2015;41:1248-1255. 2019;257:1499-1512. 44. Raasch TW. What we don't know about eccentric viewing. Br J Ophthalmol. 2004;88:443. 45. Ferris, FL. Senile macular degeneration: Review of epidemiologic features. Am J Epidemiol. 1983;118:132–151. List Of Additional Files Additional file 1: Word.docx; Patient characteristics; table Page 13/17 Additional file 2: Word.docx; Median macular sensitivities in age-related macular degeneration and healthy
retina using right eye as standard; table
Additional file 3: Word.docx; Visual Function Questionnaire sub-scores correlated with macular
sensitivities by sub-region; table
Additional file 4: Word.doc; Consolidated criteria for reporting qualitative studies checklist; table
Table
Table 1
Comparison between best eye analysis and standard eye analysis data
Best Eye Analysis*
Standard Eye Analysis†
Early AMD
Group
Late AMD
Group
Healthy
Retina Group
p
value
Early AMD
Group
Late AMD
Group
Healthy
Retina
Group
p
value
Visual acuity
74.7 SD:
±5.3 ETDRS
(6/9.5
Snellen)
65.7 SD:
±14.8 ETDRS
(6/15
Snellen)
73.5 SD:
±8.7 ETDRS
(6/9 Snellen)
<
0.001
71.5 SD:
±6.8 ETDRS
(6/12
Snellen)
57.2 SD:
±23.2 ETDRS
(6/24
Snellen)
73.5 SD:
±8.7 ETDRS
(6/9
Snellen)
0.001
Total macular
sensitivity
(dB)
21.9
IQR: 8.8
17.3
IQR: 10.9
22.61
IQR: 7
<
0.001
21.9
IQR: 8.8
15.2
IQR: 13
22.61
IQR: 7
<
0.001
*Eye with best-corrected visual acuity used
†Right eye used as standard
AMD = age-related macular degeneration; dB = decibels; ETDRS = Early Treatment Diabetic Retinopathy
Study; IQR = interquartile range; SD = standard deviation Figures Page 14/17 igure 1 Figure 2 Visual Function Questionnaire and visual acuity and macular sensitivity correlations in late age-related
macular degeneration. Figure 1 Diagram of a fundus image with superimposed Early Treatment of Diabetic Retinopathy Study macular
grid. Numbered dots show the locations of the individual retinal sensitivity measurements or differential
light sensitivity points. Note that four differential light sensitivity points numbered 7; 15; 23 and 31 lie
outside the Early Treatment of Diabetic Retinopathy Study grid. Page 15/17 Page 15/17 Supplementary Files Page 16/17 This is a list of supplementary files associated with this preprint. Click to download. This is a list of supplementary files associated with this preprint. Click to download. Additionalfile3.docx
Additionalfile4.docx
Additionalfile1revised.docx
Additionalfile2revised.docx Additionalfile3.docx Additionalfile4.docx Additionalfile1revised.docx Additionalfile2revised.docx Page 17/17
|
https://openalex.org/W3198939481
|
https://trialsjournal.biomedcentral.com/track/pdf/10.1186/s13063-021-05566-1
|
English
| null |
Normalising comparative effectiveness trials as clinical practice
|
Trials
| 2,021
|
cc-by
| 3,129
|
© The Author(s). 2021 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. Briffa et al. Trials (2021) 22:620
https://doi.org/10.1186/s13063-021-05566-1 Briffa et al. Trials (2021) 22:620
https://doi.org/10.1186/s13063-021-05566-1 Open Access Normalising comparative effectiveness trials
as clinical practice Tom Briffa1, Tanya Symons2, Nikolajs Zeps3, Nicola Straiton2,4*
, William Odita Tarnow-Mordi2, John Simes2,
Ian A. Harris5, Melinda Cruz2,6, Steven A. Webb7, Edward Litton8, Alistair Nichol7 and Christopher M. Williams9 Abstract There is a lack of high-quality evidence underpinning many contemporary clinical practice guidelines embedded in
the healthcare systems, leading to treatment uncertainty and practice variation in most medical disciplines. Comparative effectiveness trials (CETs) represent a diverse range of research that focuses on optimising health
outcomes by comparing currently approved interventions to generate high-quality evidence to inform decision
makers. Yet, despite their ability to produce real-world evidence that addresses the key priorities of patients and
health systems, many implementation challenges exist within the healthcare environment. This manuscript aims to highlight common barriers to conducting CETs and describes potential solutions to
normalise their conduct as part of a learning healthcare system. y
y
p
g
This manuscript aims to highlight common barriers to conducting CETs and describes potential solutions t
normalise their conduct as part of a learning healthcare system. Keywords: Comparative effectiveness, Pragmatic, Trials, High-quality evidence, Clinical care, Embed Background approaches to evidence generation are needed to expand
and strengthen the quality of recommendations in
CPGs. Many
recommendations
contained
in
contemporary
clinical practice guidelines (CPG) are not supported by
high quality evidence [1]. In Australia, almost three in
ten evidence statements covering 748 graded recommen-
dations from ten CPGs are low quality or consensus-
based. Less than half are based on high quality evidence
derived from randomised controlled trials (RCTs) or sys-
tematic review of these trials. Further afield, the picture
is even more concerning. In many medical specialities,
in North America and Europe, less than 20% of recom-
mendations are supported by high quality evidence [1–
3] and in specialities such as cardiology, little has chan-
ged in the last 10 years [3]. As a result, clinicians, pa-
tients, health systems and the public are unable to
determine the comparative safety and efficacy of ac-
cepted
treatments
[4]. Clearly,
more
progressive Comparative effectiveness trials (CETs) address this
conundrum by randomising participants to usual care al-
ternatives in order to generate unbiased, high-quality
evidence of the relative effectiveness of existing treat-
ments [5]. Their purpose is to assist clinicians, health-
care
providers,
policy
makers
and
patients
make
informed decisions that improve health care at both the
individual and population level. CETs often adopt prag-
matic designs, and their key features are illustrated in
Fig. 1. As the treatment options investigated are widely used
in practice, the additional risk to patients is low. Fur-
thermore, public opinion polls repeatedly confirm that
patients want their health systems to be ‘research active’
so that they are better informed about the benefits and
risks of different treatments [4–6]. It seems likely, there-
fore, that working to normalise the conduct of CETs in
clinical practice will help strengthen the clinician-patient
relationship,
especially
when
health
systems
are * Correspondence: nicola.straiton@clinicaltrialsalliance.org.au
2University of Sydney, Sydney, New South Wales, Australia
4Australian Clinical Trials Alliance, Suite 1, Level 2, 24 Albert Road, Melbourne,
VIC 3205, Australia
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 Briffa et al. Trials (2021) 22:620 Page 2 of 4 Fig. 1 Key features of pragmatic comparative effectiveness trials Fig. 1 Key features of pragmatic comparative effectiveness trials Fig. 1 Key features of pragmatic comparative effectiveness trials encouraged to partner with consumers to create learning
healthcare systems (LHS), where the conduct of CETs and
other high-quality research is routine, embedded and con-
tinuous [7]. The concept of an LHS was first introduced
by the Institute of Medicine [8] to combat the unsustain-
able growth in US healthcare spending, but despite CETs
being considered an essential component of an LHS, their
embedding into routine practice has proven challenging. This perspective illustrates these barriers and summarises
commentary on the mechanisms that could support their
embedding into the health system. One of the most significant barriers to the adoption of
CETs for contemporary evidence generation is the ab-
sence of proportionate approaches to trial governance. p
p
pp
g
Currently, the policy framework and governance ar-
rangements applied to CETs are largely identical to
those for trials involving novel interventions. For ex-
ample, some CETs compare interventions in which ver-
bal consent to treatment would have been obtained
outside the trial setting. Yet, when formally comparing
two standard treatments, lengthy, legalistic
consent
forms are mandated, despite growing evidence that pa-
tients prefer simpler ways to be informed about such re-
search that do not overinflate the perception of risk [10,
11]. Therefore, a range of consent models that reflect
the extent to which a trial departs from usual care seem
appropriate. Some countries, including Australia, en-
dorse a proportionate approach to trial consent [9] but
uptake is still low due to fear of censure. Many factors have stymied attempts to integrate CETs
into clinical care. Indeed, the characteristics that support
their pragmatism can also hamper their conduct. For ex-
ample, to preserve external validity, CETs necessarily
avoid certain design features required for high internal
validity, (blinding, strict inclusion criteria and a highly
controlled setting) [9]. However, the large sample sizes re-
quired to account for this make some trials prohibitively
expensive. In response trialists have dispensed with the
costly, parallel infrastructure that is set up for each trial
and instead, collect data straight from medical records
and utilise front-line clinicians to undertake study activ-
ities such as informed consent. Solutions to normalise the conduct of CETs Efforts to develop, design and conduct CETs will con-
tinue to require creative approaches to overcome com-
mon challenges. Table 1 describes commentary on these
challenges and possible solutions so enable the embed-
ding of CETs into the health system. But front-line clinicians
can be reticent to involve themselves in trials, partly be-
cause there are few financial (or other) incentives, and
partly because they fear that such involvement may overly
disrupt their clinical workflows. Very few, therefore, rec-
ommend trial participation to their patients leading to a
lack of trial awareness amongst the population. Possible solutions The lack of a culture of continuous improvement where knowledge
creation is explicitly recognised as a core activity of the health system The lack of a culture of continuous improvement where knowledge
creation is explicitly recognised as a core activity of the health system - Incentivise Chief Executive Officers and board members to advance the
role of research in their organisations. - Improve health system leader buy-in by more closely aligning research ac-
tivity with health system priorities. - Improve stakeholder buy-in by structuring learning to focus on the out-
comes of care delivery, increasing return on investment, and decreasing
costs. - Engage all stakeholders to create widespread awareness of the pivotal role
clinical research plays in the generation of high-quality evidence and im-
proved health outcomes. p
- Restructure workflow to incorporate research activity with protected time
and provide incentives for clinicians who contribute to research-driven clin-
ical improvements. p
- Support studies conducted by investigator networks to address real-world
evidence gaps. Failure to apply risk-proportionate governance practices to CET - Ensure proportionate approaches to trial ethics and governance approval
that expedite study approval when trial risks are low - Utilise existing flexibilities in trial regulation to improve trial conduct (e.g. the use of flexible, patient-supported approaches to informed consent). - Ensure governance arrangements for CETs balance a trial’s risk against the
risks posed by current, unresearched care. - Ensure that patients are involved in trial governance decisions and the
design of research ethics and regulatory systems. Difficulties designing and conducting large, efficient CETs - Harmonise requirements for trial conduct to facilitate international
collaboration. - Ensure trial networks collaborate with consumers and frontline clinicians to
share expertise and knowledge and to drive more efficient trial practices. p
g
p
- Utilise novel trial designs that minimise disruption to clinical workflows. g
- Utilise trial platforms to create a coordinated approach to evidence
generation g
- Incorporate implementation science strategies into CETs to facilitate uptake
of evidence-based practice. of evidence-based practice. - A cost-effectiveness analysis into, or alongside trials. Limited engagement from patients and the public as active partners
in advancing the delivery of care - Introduce health system accreditation for ‘partnering with consumers’ to
develop clinical trials operations so that research policies and practices
reflect the needs and preferences reflect the needs and preferences of
service users. Acknowledgements
k
l d
h We acknowledge the Australian Clinical Trials Alliance (ACTA) for their
support of the investigator-led clinical trials sector and activities to further
embed clinical trials into routine care. Possible solutions - Co-design with patients a communication strategy to widely broadcast re-
search as a core activity of the health system and that data and tissue is
used to improve care within a framework that safeguards privacy and
confidentiality. y
- Assist/enable patients to prioritise research questions so that the questions
investigated, and the outcomes chosen are those most important to them. - Involve patients in the design of research so that it is conducted in ways
that are sensitive to participants’ needs (e.g. by minimising the burden of
participation). Adapted from Symons et al. 2021. Making the move to a learning healthcare system: has the pandemic brought us one step
closer? (https://doi.org/10.1071/AH21076) Adapted from Symons et al. 2021. Making the move to a learning healthcare system: has the pandemic brought us one step
closer? (https://doi.org/10.1071/AH21076) Although some progress has been made, few health-
care organisations have successfully transitioned into
LHSs that conduct trials as an integral part of the deliv-
ery of high-quality care. Despite progress in areas such
as trial design, lingering challenges remain, not least, the
need to develop risk-proportionate regulatory and gov-
ernance frameworks that facilitate the conduct of large,
pragmatic CET by them being less expensive and cum-
bersome to conduct. activity of the health system will require disruptive
change, but without such change, the widespread use
of low-value or suboptimal treatments will remain
unchecked. Conclusion - Ensure that patients are involved in trial governance de
design of research ethics and regulatory systems. Difficulties designing and conducting large, efficient CETs
- Harmonise requirements for trial conduct to facilitate in
collaboration. - Ensure trial networks collaborate with consumers and f
share expertise and knowledge and to drive more effic
- Utilise novel trial designs that minimise disruption to cl
- Utilise trial platforms to create a coordinated approach
generation
- Incorporate implementation science strategies into CET
of evidence-based practice. - A cost-effectiveness analysis into, or alongside trials. Limited engagement from patients and the public as active partners
in advancing the delivery of care
- Introduce health system accreditation for ‘partnering w
develop clinical trials operations so that research policie
reflect the needs and preferences reflect the needs and
service users. - Co-design with patients a communication strategy to w
search as a core activity of the health system and that
used to improve care within a framework that safeguar
confidentiality. - Assist/enable patients to prioritise research questions so
investigated, and the outcomes chosen are those most
- Involve patients in the design of research so that it is c
that are sensitive to participants’ needs (e.g. by minimis
participation). Adapted from Symons et al. 2021. Making the move to a learning healthcare system: has the pandemic brought us one step
closer? (https://doi.org/10.1071/AH21076) Conclusion The failure of health systems to ground everyday treat-
ments in sound science impacts the quality of care pro-
vided to patients and contributes to health system waste. Conducting CETs that provide robust and generalisable
evidence to guide practice is a public good. Importantly,
patients recognise this and consistently confirm that
they want their health systems to be research-active. Health system leaders too are reluctant to allocate re-
sources to support trial activity, perhaps because the re-
search agenda has historically been driven by academics
and the trials conducted within their institutions have
not always been in line with health system priorities. Page 3 of 4 Briffa et al. Trials (2021) 22:620 Briffa et al. Trials (2021) 22:620 Table 1 Solutions for embedding CETs
Barriers to embedding
The lack of a culture of continuous improvement where knowledge
creation is explicitly recognised as a core activity of the health system
Failure to apply risk-proportionate governance practices to CET
Difficulties designing and conducting large, efficient CETs
Limited engagement from patients and the public as active partners
in advancing the delivery of care
Adapted from Symons et al. 2021. Making the move to a learning healthcare
closer? (https://doi.org/10.1071/AH21076) Table 1 Solutions for embedding CETs
Barriers to embedding
Possible solutions
The lack of a culture of continuous improvement where knowledge
creation is explicitly recognised as a core activity of the health system
- Introduce health system accreditation acknowledging c
based on indicators of research activities. - Incentivise Chief Executive Officers and board members
role of research in their organisations. - Improve health system leader buy-in by more closely a
tivity with health system priorities. - Improve stakeholder buy-in by structuring learning to f
comes of care delivery, increasing return on investmen
costs. - Engage all stakeholders to create widespread awarenes
clinical research plays in the generation of high-quality
proved health outcomes. - Restructure workflow to incorporate research activity w
and provide incentives for clinicians who contribute to
ical improvements. - Support studies conducted by investigator networks to
evidence gaps. Failure to apply risk-proportionate governance practices to CET
- Ensure proportionate approaches to trial ethics and go
that expedite study approval when trial risks are low
- Utilise existing flexibilities in trial regulation to improve
the use of flexible, patient-supported approaches to inf
- Ensure governance arrangements for CETs balance a tr
risks posed by current, unresearched care. Authors information
Correspondence to Professor Tom Briffa tom.briffa@uwa.edu.au. Correspondence to Professor Tom Briffa tom.briffa@uwa.edu.au. Funding g
is project received grant funding from the Australian Government Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. Availability of data and materials Availability of data and materials
Not applicable. Availability of data and materials
Not applicable. Consent for publication
Not applicable. Consent for publication
Not applicable. Consent for publication
Not applicable. Competing interests TS provides clinical research consulting services in Australia and the UK;
however, no organisation controlled or influenced the development of this
manuscript. The other authors have no competing interests. Received: 13 May 2021 Accepted: 24 August 2021 Received: 13 May 2021 Accepted: 24 August 2021 Authors’ contributions Implementing solutions that address the factors that
currently prevent the embedding of CETs as a core TB and TS led the writing group on normalising comparative effectiveness
trials as clinical practice. CW, NZ, and NS all co-wrote the perspective; WOT- Briffa et al. Trials (2021) 22:620 Briffa et al. Trials (2021) 22:620 Page 4 of 4 Page 4 of 4 M, JS, IAH, MC, SAW, EL, and AN all contributed to writing the perspective. All authors conceived, read, and approved the final perspective. All authors
read and approved the final manuscript. 10. Ramsberg J, Platt R. Opportunities and barriers for pragmatic embedded
trials: triumphs and tribulations. Learn Health Syst. 2018;2(1):e10044. https://
doi.org/10.1002/lrh2.10044. 11. Angus DC. Optimizing the trade-off between learning and doing in a
pandemic. JAMA. 2020;323(19):1895–6. https://doi.org/10.1001/jama.2020.4
984. Author details
1 1University of Western Australia, Perth, Western Australia, Australia. 2University
of Sydney, Sydney, New South Wales, Australia. 3Epworth HealthCare,
Richmond, Victoria, Australia. 4Australian Clinical Trials Alliance, Suite 1, Level
2, 24 Albert Road, Melbourne, VIC 3205, Australia. 5Ingham Institute,
Liverpool, New South Wales, Australia. 6University of New South Wales,
Sydney, New South Wales, Australia. 7Monash University, Melbourne, Victoria,
Australia. 8Fiona Stanley Hospital, Murdoch, Western Australia, Australia. 9University of Newcastle, Callaghan, New South Wales, Australia. Received: 13 May 2021 Accepted: 24 August 2021 10.
Ramsberg J, Platt R. Opportunities and barriers for pragmatic embedded
trials: triumphs and tribulations. Learn Health Syst. 2018;2(1):e10044. https://
doi.org/10.1002/lrh2.10044. Declarations Ethics approval and consent to participate
Not applicable. References 1. Australian Commission on Safety and Quality in Healthcare. The National
Clinical Trials Governance Framework and User Guide for Health Service
Organisations Conducting Clinical Trials 2020. Available at https://www.sa
fetyandquality.gov.au/publications-and-resources/resource-library/national-
clinical-trials-governance-framework-and-user-guide. Accessed 5 Aug 2021. 1. Australian Commission on Safety and Quality in Healthcare. The National
Clinical Trials Governance Framework and User Guide for Health Service
Organisations Conducting Clinical Trials 2020. Available at https://www.sa
fetyandquality.gov.au/publications-and-resources/resource-library/national-
clinical-trials-governance-framework-and-user-guide. Accessed 5 Aug 2021. 2. Institute of Medicine. Integrating research and practice: health system
leaders working toward high-value care: workshop summary. Washington
DC: The National Academies Press; 2015. 3. Califf RM, Robb MA, Bindman AB, et al. Transforming evidence generation
to support health and health care decisions. N Engl J Med. 2016;375:24. 4. Australian Clinical Trials Alliance. International Best Practice Towards a
Learning Healthcare System: a scoping activity to map international
approaches to embed clinical trials into the healthcare system. 2018. Available at https://clinicaltrialsalliance.org.au. Accessed 22 July 2021. 5. Psek W, Davis FD, Gerrity G, Stametz R, Bailey-Davis L, Henninger D, et al. Leadership perspectives on operationalizing the learning health care system
in an integrated delivery system. eGEMS. 2016;4(3):6. https://doi.org/10.13
063/2327-9214.1233. 6. Psek WA, Stametz RA, Bailey-Davis LD, et al. Operationalizing the learning
health care system in an integrated delivery system. eGEMs (Generating
Evidence & Methods to improve patient outcomes). 2015;3(1):6. 7. Gelijns AC, Gabriel SE. Looking beyond translation — integrating clinical
research with medical practice. N Engl J Med. 2012;366(18):1659–61. https://
doi.org/10.1056/NEJMp1201850. 8. Symons T, Webb S, Zalcberg J. Putting the “good” into Good Clinical
Practice. Med J Aus. 2021;214(2):62–65.e1. 9. Webster M, Stewart R, Aagaard N, McArthur C. The learning health system:
trial design and participant consent in comparative effectiveness research. Eur Heart J. 2019;40(15):1236–40. https://doi.org/10.1093/eurheartj/ehy235.
|
W2896287217.txt
|
https://www.degruyter.com/document/doi/10.1515/jisys-2018-0020/pdf
|
en
|
FCNB: Fuzzy Correlative Naive Bayes Classifier with MapReduce Framework for Big Data Classification
|
Journal of intelligent systems
| 2,018
|
cc-by
| 6,603
|
J. Intell. Syst. 2020; 29(1): 994–1006
Chitrakant Banchhor* and N. Srinivasu
FCNB: Fuzzy Correlative Naive Bayes
Classifier with MapReduce Framework
for Big Data Classification
https://doi.org/10.1515/jisys-2018-0020
Received December 6, 2017; previously published online October 22, 2018.
Abstract: The term “big data” means a large amount of data, and big data management refers to the efficient
handling, organization, or use of large volumes of structured and unstructured data belonging to an organization. Due to the gradual availability of plenty of raw data, the knowledge extraction process from big data
is a very difficult task for most of the classical data mining and machine learning tools. In a previous paper,
the correlative naive Bayes (CNB) classifier was developed for big data classification. This work incorporates
the fuzzy theory along with the CNB classifier to develop the fuzzy CNB (FCNB) classifier. The proposed FCNB
classifier solves the big data classification problem by using the MapReduce framework and thus achieves
improved classification results. Initially, the database is converted to the probabilistic index table, in which
data and attributes are presented in rows and columns, respectively. Then, the membership degree of the
unique symbols present in each attribute of data is found. Finally, the proposed FCNB classifier finds the
class of data based on training information. The simulation of the proposed FCNB classifier uses the localization and skin segmentation datasets for the purpose of experimentation. The results of the proposed FCNB
classifier are analyzed based on the metrics, such as sensitivity, specificity, and accuracy, and compared with
the various existing works.
Keywords: Big data, classification, correlative naive Bayes classifier, fuzzy theory, MapReduce.
1 Introduction
Data mining [6] has become a prevailing technique for the discovery of valuable information available on
network platforms. Big data [6] significantly promotes the traditional industries to achieve better progressiveness, and hence data retrieval from the big data environment is necessary. The term “big data” is derived
from the phrase “a large amount of data,” usually in zettabytes processed in a year. Hence, data management
options should be openly available to each organization for better handling of big data [15, 22]. The data can
be concluded as big data based on the factors of volume, velocity, variety, and veracity. Also, big data from
Internet sources arrives in a continuous pattern, and thus the processing of data is more difficult [5].
Data mining schemes come under two major categories: clustering and classification. Various classifiers,
such as support vector machine [13], naive Bayes (NB) [24], and extreme learning machine (ELM) [12] primarily contribute toward big data classification [9, 11]. The ELM [5] algorithm provides multiclassification of data
rather than binary classification [6]. While processing data with high volume, the computational complexity
of algorithms is increased [1]. The supervised classification approaches classify big data through a learning
algorithm, and thus finds the suitable classes for the database [7]. The prevailing problem by the large size
of data can be solved by introducing MapReduce schemes. Google introduces the MapReduce [1, 3, 14, 25, 29]
*Corresponding author: Chitrakant Banchhor, Research Scholar, Computer Science and Engineering Department, Koneru
Lakshmaiah Education Foundation, Vaddeswaram, Guntur, India, e-mail: banchhorchitrakant@gmail.com
N. Srinivasu: Computer Science and Engineering Department, Koneru Lakshmaiah Education Foundation, Vaddeswaram,
Guntur, India
Open Access. © 2020 Walter de Gruyter GmbH, Berlin/Boston.
4.0 Public License.
This work is licensed under the Creative Commons Attribution
C. Banchhor and N. Srinivasu: Fuzzy Correlative Naive Bayes Classifier
|
995
framework for mining data of size larger than petabytes. MapReduce contains the mapper and reducer for the
parallel processing of the datasets [4].
Big data include the collection of data from different fields, and the employment of the classification
algorithm solves the data mining issues in big data. The main idea behind the classification task is to build a
model (classifier) that classifies the data with the goal to accurately predict the target class for each item in
the data [14]. There are many techniques, such as decision trees, Bayes networks, genetic algorithms, genetic
programming, and so on, to comply with the classification of big data [1]. The properties, such as continuity
and distributed blocks, present in the big data pose additional challenges to the ELM algorithms [5]. The big
data also has imbalanced datasets and the fuzzy rule-based classification systems (FRBCS) [17, 18], denoted
as Chi-FRBCS-Big Data CS, have achieved significant results during the classification of the imbalanced big
data [18]. Literature work has also discussed the MapReduce-based fuzzy c-means clustering [19], k-nearest
neighbor algorithm [20], fuzzy associative classifier [23], machine learning tools [28], and Chi-FRBCS-BigData
algorithm [8] for big data classification.
The primary contribution of this research is the development of the fuzzy correlative NB classifier (FCNB)
for big data classification. The proposed model permits the MapReduce framework to deal with the big data.
The paper organization is done in the following manner: Section 1 presents the introduction to the big
data classification model. Section 2 presents the proposed FCNB algorithm along with the MapReduce framework for the big data classification. Section 3 presents various simulation results obtained for the proposed
FCNB classifier based on the evaluation metrics. Section 4 concludes the research work.
2 Proposed Method: Proposed FCNB Classifier with the
MapReduce Framework for Big Data Classification
This research work deals with big data classification with the proposed FCNB classifier. The proposed FCNB
classifier is the extensive work of the correlative NB (CNB) classifier defined in Ref. [2]. The FCNB classifier is
developed by integrating the CNB classifier and the fuzzy theory [9]. Also, this work includes the MapReduce
framework for dealing with the big data. In data mining and the cloud environment, there is a continuous flow
of data. The existing fuzzy NB (FNB) classifier has various merits, such as dealing with the missing attributes
of the data sample, incremental learning, and performing the training with low data samples. In the proposed work, the FNB classifier is modified by adding the correlation between the data samples. This makes
the proposed FCNB algorithm a dependent hypothesis. As the research allows the classification of big data,
the inclusion of the MapReduce framework is necessary. The MapReduce framework eliminates the problem
of the classification of a large dataset and the storage problems.
2.1 Algorithmic Description of the Proposed FCNB Classifier
The proposed FCNB classifier gets the training data from various sources as the input. The training data needs
to be represented as the probability index table. The probability index table represents the data samples as
the data matrix. The rows and columns of the probability index table represent the data and their respective
attributes. The training sample for the proposed FCNB classifier is represented as follows:
⎧
⎫
⎨T p,q ; 1 ≤ p ≤ d ⎬
T=
,
(1)
⎩
1≤q≤a⎭
where the term T p,q represents the pth data sample in the qth attribute of the probability index table. The
terms d and a represent the total data samples and the attributes present in the training dataset, respectively.
The proposed model aims at classifying the data samples into various classes. Equation (2) expresses the
classes indicated in the vector form:
G = {g p ; 1 ≤ p ≤ d},
(2)
996 | C. Banchhor and N. Srinivasu: Fuzzy Correlative Naive Bayes Classifier
where the term gp represents the class of the pth data sample. The attributes present in the data sample contribute more toward the data classification. Consider the training data sample having a number of attributes;
hence, the attributes of the data sample are represented as follows:
H = {h q ; 1 ≤ q ≤ a},
(3)
where the term hq represents the qth attribute of the data sample. The data samples categorized under
each attribute have unique symbols. The proposed FCNB classifier calculates the fuzzy membership degree
depending on the unique data symbols within the attribute. Consider that there is S number of unique data
symbols within the attribute. For the calculation of the membership degree of the proposed FCNB classifier,
consider the qth attribute in the training sample that contains s number of unique symbols. The symbols in
the qth attribute are indicated by h q ∈ m s , and the value of s varies in the range 1 ≤ s ≤ S. The expression
for the membership degree of training samples provided to the proposed FCNB classifier is represented by
the following expression:
⃒ s⃒
⃒m q ⃒
s
,
(4)
µq =
d
where the term µ sq shows the membership degree of the sth symbol present in the qth attribute of the
⃒ ⃒
training sample. Also, the term ⃒m sq ⃒ represents the total occurrence of the sth symbol in the qth attribute
and d indicates the data sample in the attribute. The proposed FCNB classifier classifies the data samples
into K number of classes. The variation of the total number of classes is represented as Gk , and the value
of k is in the range 1 ≤ k ≤ K. The proposed FCNB classifier also calculates the membership degree of each
class for the ground truth information. The membership degree for the kth class provided with the ground
truth information is represented as follows:
⃒ ⃒
⃒ k⃒
⃒m ⃒
k
µc =
,
(5)
d
⃒ ⃒
⃒ ⃒
where the term ⃒m k ⃒ represents the total occurrence of the kth class in the ground truth information. The
membership degree acts as a prime factor in the data classification. The model size of both the member1ship degrees derived in Eqs. (4) and (5) is expressed as [(a * S) + K ], where K is the total number of
classes, S represents the number of unique data symbols, and a is the number of attributes.
2.1.1 Adapting the FNB Classifier with the Correlation Function
The existing FNB classifier utilizes the NB and the fuzzy-based approaches for the data classification. In
this work, the proposed FCNB classifier adapts the FNB classifier with the virtual correlation function to
make the proposed algorithm dependent on the hypothesis. Also, the correlation function makes the proposed algorithm an incremental learner. The proposed FCNB classifier finds the virtual correlation factor for
each attribute present in the training database. Equation (6) expresses the virtual correlation between each
attribute of the training data:
C k = f (h1 , h2 , h3 , . . . .h q , . . . , h a ),
(6)
where the term Ck represents the virtual correlation of the attributes in the kth class. The term f (.) represents
the correlation function. The correlation function between the attributes of the data samples is constructed
by representing the attributes and the symbols of the training sample as the diagonal matrix. Equation (7)
represents the correlation function between the attributes of the training data:
f (h1 , h2 , h3 , . . . h q , . . . h a ) =
a
a
∑︁
∑︁
1
r(h e , h q ),
1 + 2 + . . . + (a − 1)
q=1 s=q+1
(7)
C. Banchhor and N. Srinivasu: Fuzzy Correlative Naive Bayes Classifier
|
997
where the term r(h e , h q ) represents the correlation between the eth and the qth attributes. The term 1 + 2 +
based on the triangular number series [10]. Now, Eq. (7)
. . . + (a − 1) in Eq. (7) can be expressed as a(a−1)
2
can be rewritten as
f (h1 , h2 , h3 , . . . h q , . . . , h a ) =
f (h1 , h2 , h3 , . . . h q , . . . , h a ) =
1
a
a
∑︁
∑︁
a(a−1)
q=1 s=q+1
2
r(h s , h q ).
a
a
∑︁
∑︁
2
r(h s , h q ).
a(a − 1)
(8)
(9)
q=1 s=q+1
In this research work, the proposed FCNB classifier considers the correlation factor for finding the relation between the data samples present in the training data. The proposed FCNB classifier finds the correlation
of the independent data sample present in the training set. The correlation factor for finding the relation
between the unique symbols present in the attributes is represented as follows:
[︂
]︂
correlative(h s , h q ) + 1
r(h s , h q ) =
,
(10)
2
where the function correlative(h s , h q ) indicates the Pearson’s correlation coefficient [16]. The function
correlative(h s , h q ) finds the linear correlation between the data samples. The general expression for the
Pearson’s correlation coefficient is expressed by the following equation:
∑︀d
p=1 (t pq − t̄ q )(t ps − t̄ s )
√︁
,
(11)
correlative(h s , h q ) = √︁∑︀
2 ∑︀d
2
d
(t
−
t̄
)
(t
−
t̄
)
pq
q
ps
s
p=1
p=1
where the term t̄ q indicates the average of the data samples present in the qth attribute and the term t̄ s represents the average of the unique data symbols in the qth attribute. The final output from the training of the
proposed FCNB classifier contains the membership degree from the attribute, membership degree from the
ground truth information, and the correlation factor. The output of the proposed FCNB classifier is expressed
as follows:
{︁
}︁
FCNB = µ kq , µ kc , C .
(12)
The membership degree for the attributes has the size of (d * S), while the membership degree for the
ground truth information has the size of (1 * K). The correlation factor between the unique symbols of the
attributes represented by each class has the size of (1 * K). The results of the training of the proposed FCNB
classifier have the total size of (d * S + 2K).
2.2 Testing of the Proposed FCNB Classifier
This section presents the testing phase of the proposed FCNB classifier. The proposed FCNB algorithm utilizes the posterior probability of the NB classifier, the fuzzy membership degree, and the correlation function
to classify the test data. For the training phase, the proposed FCNB classifier is provided with the test data
represented as X. The proposed FCNB algorithm tries to classify the test data into K number of classes. The
output of the proposed FCNB classifier is represented as follows:
G = arg Max
k=1 to K
P(g k |X ) * C k ,
(13)
where the term P(g k |X ) defines the posterior probability based on the test data X for the class gk and the
term Ck represents the correlation for the class k. The value of P(g k |X ) is represented based on the following
expression:
P(g k |X ) = P(g k )
a [︂
∏︁
P(h q |g k )
q=1
P(h q )
]︂
* µq ,
(14)
998 | C. Banchhor and N. Srinivasu: Fuzzy Correlative Naive Bayes Classifier
where P(h q |g k ) and P(h q ) represent the posterior probability for the attribute hq based on the class k and
the probability of occurrence of the attribute hq in the class. The proposed FCNB model uses the Laplacian
correction [2] in the above expression for avoiding the missing of the attributes during the training phase.
The adjustment is done based on the following expressions:
[︁∑︀
]︁
X
k
µ
·
µ
q
X +1
X∈d
]︀
P(X|g k ) = [︀∑︀
,
(15)
k
X∈d µ X + |dom(h q )|
[︁∑︀
]︁
k
X∈d µ X + 1
,
(16)
P(g k ) =
d + |dom(G)|
where the term dom(G) represents the total number of classes and the term dom(hq ) represents the total
number of data symbols present in the qth attribute.
2.3 Pseudo Code of the Proposed FCNB Classifier
This section presents the pseudo code of the proposed FCNB classifier. As shown in Algorithm 1, the proposed
FCNB classifier classifies the data into K number of classes. In the training phase, the proposed FCNB classifier gets the training data T as the input. For the training data, the membership degree and the correlative
function are calculated. In the testing phase, the probability index of the test data is calculated and based on
the classification output in Eq. (13), the class of the test data is found by the proposed FCNB classifier.
2.4 Adapting the FCNB Classifier in the MapReduce Framework
The application of the proposed FCNB classifier to the concept of the big data classification can be achieved
by introducing the MapReduce framework in the proposed FCNB classifier. The MapReduce framework has
the mapper and the reducer that allow the simultaneous functioning of the large dataset. This research
performs big data classification through the training and testing phases of the proposed FCNB classifier.
Algorithm 1: Pseudo Code of the Proposed FCNB Classifier.
Algorithm: FCNB classifier
Serial no.
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
Steps
Input: Data sample: T
Output: class: G = {G1 , G2 , ..., G K }
Begin
// Training phase
Read the training data T
For (p = 1 to d)
Read the data samples
For (q = 1 to a)
Read the attributes
Calculate the membership degree of the qth attribute
Calculate the membership degree of the ground value
Calculate the correlation factor C k
End for
End for
//Testing phase
Read the test input X
Calculate the probability index of the class P(g k |X )
Find the class G for the test data using Eq. (13)
Return the class G
End
C. Banchhor and N. Srinivasu: Fuzzy Correlative Naive Bayes Classifier
Q1
Q2
Q3
U1
U2
U3
Training data
|
999
QU
UU
Reducer V
V k(i)
Figure 1: Training of the FCNB-Based MapReduce Framework.
In the training phase, the training data T is fed to the MapReduce function. Figure 1 presents the architecture
of the proposed FCNB classifier enabled with the MapReduce for the training phase.
2.4.1 Training Phase
Training of the mapper: The mapper present in Figure 2 gets the training data as the input. The training
data is represented in the matrix, with the rows indicating the data and the columns indicating the attributes.
X1
X2
X3
XU
Testing data
U1
U2
U3
UU
V1
V2
V3
Vk
G1
G2
G3
GK
Figure 2: Testing of the FCNB-Based MapReduce Framework.
1000 | C. Banchhor and N. Srinivasu: Fuzzy Correlative Naive Bayes Classifier
The training data to the mapper of the proposed FCNB classifier is represented as given in Eq. (17). As the data
that arrives at the proposed classifier is a continuous data, the size of the data is very large. Hence, the data
requires partitioning. In this work, the training data sample T is partitioned into U parts. Each part of the
training sample is represented by the following expression:
T = {Q i ; 1 ≤ i ≤ U},
(17)
where the term Qi represents the ith part of the data matrix. Each partitioned data is provided to the mapper of
the proposed model. Hence, the number of mappers in the model equals the number of data sample parts.
Consider that the proposed model has U mappers and V reducers. The data present in the mapper is
represented by the following expression:
Qi =
⎧
⎫
⎨n b,q ; 1 ≤ b ≤ A i ⎬
1≤q≤a ⎭
⎩
,
(18)
where the term nb,q represents the part of the data provided to the ith mapper. The value of b varies based
on the data present in the mapper Ai . The mappers present in the proposed classification model find the
classes from the training data. Each mapper provides the data to the reducer of size (d * S) + 2K. The mapper
generates the probability index table for the training sample, and it is represented as follows:
U i = {µ q (i), µ c (i), C(i), A i },
(19)
where µq (i) represents the membership degree of the qth attribute for the data sample i, µc (i) shows the
membership degree for the ground value, C(i) represents the correlation factor, and the term Ai indicates
the number of data present in the mapper i.
Training of the reducer: For the training of the reducer, the outputs of each mapper are provided to the V
reducers in the proposed model. The probability index table obtained from the mapper is of size (d * S) + 2K.
The reducer tries to merge the probability index table from the mapper to a single function of size (d * S) + 2K.
The reducer uses the aggregation mechanism to merge the outputs of the mapper. The membership degree
present in the mapper output is reduced at the reducer phase based on the following expressions:
µ kq
µ kc
∑︀U
µ kq (i)
,
U
∑︀U
k
i=1 µ c (i)
=
,
U
=
i=1
(20)
(21)
where the terms µ kq and µ kc represent the membership degrees of the attribute and the ground information
of the data part i, respectively. The classified information from each mapper is merged in the reducer and is
expressed as follows:
Vk =
∑︀U
V k (i)
,
U
i=1
(22)
where the term Vk (i) represents the classified output of the data part i.
2.4.2 Testing Phase
The testing phase of the proposed FCNB classifier with the MapReduce is explained in this section. Figure 2
presents the MapReduce framework with the proposed FCNB classifier during the testing phase. For the
testing, the test data X is provided to the MapReduce framework.
C. Banchhor and N. Srinivasu: Fuzzy Correlative Naive Bayes Classifier
|
1001
Testing of the mapper: The test data provided to the mapper is represented as X. Initially, the test data X is
subjected for the partitioning and is expressed as follows:
X = {X x ; 1 ≤ x ≤ U},
(23)
where the term Xx represents the xth part of the test data X. The test data contains d number of data samples and a number of attributes. For the test data, the membership degree, the correlative function, and the
number of data for each mapper are calculated. Finally, the mapper provides the information to the reducer.
Testing of the reducer: In the testing phase, the output of the mapper is fed to the reducer. The reducer
merges the information and provides the information about the class variable of each part of the test data
sample. The reducer provides K number of classes and is represented as follows:
G = {G1 , G2 , . . . , G K }.
(24)
3 Results and Discussion
The simulation results achieved by the proposed FCNB classifier are presented in this section, which also
contains the results of the comparative discussion achieved by analyzing the results of various comparative
models.
3.1 Experimental Setups
Experimental setup 1: The experimentation setup 1 contains a set of four mappers for analyzing the
performance of different algorithms.
Experimental setup 2: The experimentation setup 2 contains a set of five mappers for the simulation
purpose.
The entire experimentation is done on the Java platform installed in a personal computer with the
following configurations: Windows 10 OS, 4 GB Ram, and Intel I3 processor.
3.2 Dataset Description
The experimentation of the proposed FCNB classifier is done with the standard dataset localization dataset
[16] and the skin segmentation dataset [26] utilized from the University of California, Irvine (UCI) machine
repository, and their descriptions are provided as follows:
Localization dataset [16]: The localization dataset from the UCI machine repository contains information
about the activities of the person, and is obtained through the observation of various persons wearing the
data tag on their ankle, leg, etc. The localization dataset contains a large set of instances (total of 164,860)
under eight attributes. Table 1 shows the description of the localization database.
Table 1: Description of Localization Dataset.
Dataset characteristics
Univariate, sequential, time series
Number of instances
Area
Attribute characteristics
Number of attributes
Associated tasks
Missing values
164,860
Life
Real
8
Classification
N/A
1002 | C. Banchhor and N. Srinivasu: Fuzzy Correlative Naive Bayes Classifier
Table 2: Description of Skin Segmentation Dataset.
Dataset characteristics
Univariate
Number of instances
Area
Attribute characteristics
Number of attributes
Associated tasks
Missing values
245,057
Computer
Real
4
Classification
N/A
Skin segmentation dataset [26]: This dataset is collected from people of various age groups with different
skin colors. The learning sample taken for the experimentation varies as 245,057, and they are grouped under
four attributes. This dataset is more suitable for big data classification as the simulation results can be categorized under the skin set and the non-skin set. Table 2 shows the description of the skin segmentation
dataset.
3.3 Comparative Models
The performance of the proposed FCNB classifier for big data classification is compared with various methods, such as NB [27], CNB [2], gray wolf optimization-based CNB (GWO-CNB), cuckoo gray wolf-based CNB
(CGCNB), and FNB classifier [27]. The NB classifier performs data classification by defining the probabilistic definition, and the CNB classifier uses the correlative function along with the NB for making the suitable
decision. Incorporating the GWO [21] with the CNB leads to the formation of the GWO-CNB classifier, and the
optimization scheme is used for defining the class. The CGCNB classifier is designed with the integration of
the cuckoo search (CS) algorithm and the GWO algorithm with the CNB. The FNB classifier uses the fuzzy
theory along with the NB for the classification purpose.
3.4 Comparative Analysis
Comparative analysis is done by varying the training percentage of the localization and the skin datasets
for the various numbers of mappers, and the performance of each model is measured by the sensitivity,
specificity, and accuracy.
3.4.1 Analysis Based on Accuracy
Figure 3 presents the comparative analysis of the proposed FCNB classifier based on the accuracy metric for
the varying training percentages of the dataset and the mapper. Figure 3A presents the performance of the
classifiers with the mapper size of 4 and varying training percentages of the localization dataset. For 90%
training of the localization dataset, the existing NB, CNB, GWO-CNB, CGCNB, and FNB classifiers achieved
accuracy values of 76.504%, 77.9505%, 79.862%, 80.8977%, and 72.33%, respectively, while the proposed
FCNB classifier had an improved accuracy value of 91.7816%. Figure 3B presents the performance analysis
of the classifiers in the skin dataset with mapper = 4. Here, the comparative models NB, CNB, GWO-CNB,
CGCNB, and FNB classifiers achieved the accuracy values of 75.723%, 76.636%, 77.770%, 79.327%, and 53.45%,
respectively; however, the proposed FCNB classifier achieved the accuracy value of 91.7817%. Figure 3C
and D present the performance analysis of the classifiers in the localization and skin datasets for
mapper = 5. For 90% training of the localization dataset, the existing NB, CNB, GWO-CNB, CGCNB, and FNB
classifiers with five mappers achieved the accuracy values of 76.996%, 77.808%, 79.7638%, 80.6568%, and
72.3310%, respectively, while the proposed FCNB achieved the high accuracy value of 91.78164%. For the
skin dataset, the proposed FCNB with mapper = 5 achieved an accuracy value of 91.78165%.
C. Banchhor and N. Srinivasu: Fuzzy Correlative Naive Bayes Classifier
75
80
85
Training (%)
Accuracy
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
100
90
80
70
60
50
40
30
20
10
0
90
C
Accuracy
1003
B
100
90
80
70
60
50
40
30
20
10
0
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
75
80
85
Training (%)
90
D
100
90
80
70
60
50
40
30
20
10
0
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
75
80
85
Training (%)
Accuracy
Accuracy
A
|
90
100
90
80
70
60
50
40
30
20
10
0
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
75
80
85
Training (%)
90
Figure 3: Comparative Analysis of the FCNB Classifier Based on Accuracy.
For mapper = 4 in (A) localization dataset and (B) skin dataset. For mapper = 5 in (C) localization dataset and (D) skin dataset.
3.4.2 Analysis Based on Sensitivity
Figure 4 presents the comparative analysis of the proposed FCNB classifier based on the sensitivity metric for the varying training percentages of the dataset and the mapper. Figure 4A presents the analysis of the classifiers based on sensitivity with the mapper size of 4 and varying training percentages of
the localization dataset. For 90% training of the localization dataset, the existing NB, CNB, GWO-CNB,
A
B
120
80
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
60
40
20
0
75
80
85
Training (%)
Sensitivity
Sensitivity
100
90
C
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
75
80
85
Training (%)
90
D
120
80
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
60
40
20
0
75
80
85
Training (%)
90
Sensitivity
100
Sensitivity
100
90
80
70
60
50
40
30
20
10
0
100
90
80
70
60
50
40
30
20
10
0
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
75
80
85
Training (%)
90
Figure 4: Comparative Analysis of the FCNB Classifier Based on Sensitivity.
For mapper = 4 in (A) localization dataset and (B) skin dataset. For mapper = 5 in (C) localization dataset and (D) skin dataset.
1004 | C. Banchhor and N. Srinivasu: Fuzzy Correlative Naive Bayes Classifier
CGCNB, and FNB classifiers achieved a sensitivity of 80.699%, 81.899%, 83.2474%, 84.399%, and 99.986%,
respectively, while the proposed FCNB classifier achieved a sensitivity value of 94.79%, which was less than
that of the FNB classifier. This is due to the factor that the training data taken for the classification is classified
toward the same class. Figure 4B presents the performance of the classifiers in the skin dataset along with
mapper = 4 based on sensitivity. Here, the comparative models NB, CNB, GWO-CNB, CGCNB, and FNB classifiers achieved the sensitivity value of 80.845%, 81.845%, 82.466%, 84.2254%, and 36.811%, respectively;
however, the proposed FCNB classifier achieved the sensitivity value of 94.79%. Figure 4C and D present the
performance of the classifiers in the localization and skin datasets for mapper = 5 based on the sensitivity
metric. For 90% training of the localization dataset, the existing NB, CNB, GWO-CNB, CGCNB, and FNB classifiers with five mappers achieved the sensitivity value of 80.879%, 81.4741%, 83.447%, 84.478%, and 99.98%,
respectively, while the proposed FCNB achieved the sensitivity value of 94.79%. Similarly, for the 90% training of the skin dataset, the existing NB, CNB, GWO-CNB, CGCNB, and FNB classifiers achieved the sensitivity
values of 80.960%, 81.986%, 82.918%, 84.316%, and 34.76%, respectively. For the same dataset, the proposed
FCNB with mapper = 5 achieved an accuracy value of 94.79%. From the analysis, the proposed FCNB seems
to have the sensitivity value of 94.79% for both the localization and skin datasets.
3.4.3 Analysis Based on Specificity
Figure 5 presents the comparative analysis of the proposed FCNB classifier based on the specificity metric for
the varying training percentages of the dataset and the mapper. Figure 5A presents the performance of the
classifiers with the mapper size of 4 and varying training percentages of the localization dataset based on the
specificity metric. For 90% training of the localization dataset, the existing NB, CNB, GWO-CNB, CGCNB, and
FNB classifiers achieved specificity values of 72.884%, 73.953%, 75.9060%, 76.9617%, and 36.12%, respectively, while the proposed FCNB classifier had improved specificity value of 88.891%. Figure 5B presents
the performance of the classifiers in the skin dataset along with mapper = 4 based on specificity. Here,
the comparative models NB, CNB, GWO-CNB, CGCNB, and FNB classifiers achieved the specificity value of
70.8791%, 71.8203%, 72.7240%, 74.2836%, and 70.67%, respectively; however, the proposed FCNB classifier
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
75
80
85
Training (%)
90
C
Specificity
Specificity
B
100
90
80
70
60
50
40
30
20
10
0
100
90
80
70
60
50
40
30
20
10
0
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
75
80
85
Training (%)
90
D
100
90
80
70
60
50
40
30
20
10
0
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
75
80
85
Training (%)
90
Specificity
Specificity
A
100
90
80
70
60
50
40
30
20
10
0
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
75
80
85
Training (%)
90
Figure 5: Comparative Analysis of the FCNB Classifier Based on Specificity.
For mapper = 4 in (A) localization dataset and (B) skin dataset. For mapper = 5 in (C) localization dataset and (D) skin dataset.
C. Banchhor and N. Srinivasu: Fuzzy Correlative Naive Bayes Classifier
|
1005
Table 3: Time Complexity of the Comparative Methods.
Methods
NB
CNB
GWO-CNB
CGCNB
FNB
Proposed FCNB
Time complexity (s)
7.4
8.2
7
6.8
6.3
5
had the specificity value of 88.891%. Figure 5C presents the performance of the classifiers in the localization for mapper = 5 based on the specificity metric. For 90% training of the localization dataset, the NB,
CNB, GWO-CNB, CGCNB, and FNB classifiers with five mappers achieved the specificity value of 72.7007%,
73.8631%, 75.8758%, 76.991%, and 36.127%, respectively, while the proposed FCNB had a high specificity
value of 88.89%. Figure 5D presents the performance of the classifiers in the skin dataset for mapper = 5
based on the specificity metric. For the skin dataset, the proposed FCNB with mapper = 5 achieved a
specificity value of 88.8912%.
3.4.4 Analysis Based on Time Complexity
Table 3 shows the time complexity of the comparative methods. The time complexity of the proposed FCNB
is 5 s; on the other hand, the time complexity of the existing methods, such as NB, CNB, GWO-CNB, CGCNB,
and FNB, is 7.4, 8.2, 7, 6.8, and 6.3 s, respectively. The time complexity of the proposed method is less when
compared to the existing methods, which shows the effectiveness of the proposed method.
4 Conclusion
This work introduces the classification algorithm based on the fuzzy network, called FCNB, for data classification in the big data framework. The proposed FCNB classifier is designed through the integration of
the correlation and the fuzzy theory, along with the MapReduce framework. As the proposed FCNB combines the fuzzy theory and the NB, it has improved classification performance in the large data framework.
The proposed FCNB classifier is used along with the MapReduce framework for dealing with the large data
environment. The simulation of the proposed FCNB classifier is done by considering the localization and
skin segmentation datasets from the UCI repository. Also, the performance of the proposed FCNB classifier is compared against the existing NB, CNB, GWO-CNB, CGCNB, and FNB classifiers. From the simulation
results, the proposed FCNB classifier shows improved performance in both the localization and skin segmentation datasets under the conditions of mapper = 4 and mapper = 5. For the skin segmentation, the FCNB
classifier has high values of 91.78166%, 94.79%, and 88.8912% for accuracy, sensitivity, and specificity,
respectively.
Bibliography
[1] Á. Arnaiz-González, A. González-Rogel, J. F. Díez-Pastor and C. López-Nozal, MR-DIS: democratic instance selection for big
data by MapReduce, Progr. Artif. Intell. 6 (2017), 211–219.
[2] C. Banchhor and N. Srinivasu, CNB-MRF: adapting correlative naive Bayes classifier and MapReduce framework for big
data classification, Int. Rev. Comput. Softw. (IRECOS) 11 (2016).
[3] A. Bechini, F. Marcelloni and A. Segatori, A MapReduce solution for associative classification of big data, Inform. Sci. 332
(2016), 33–55.
[4] R. Bhukya and J. Gyani, Fuzzy associative classification algorithm based on MapReduce framework, in: Proceedings of the
International Conference on Applied and Theoretical Computing and Communication Technology (iCATccT), pp. 357–360,
Davangere, 2015.
1006 | C. Banchhor and N. Srinivasu: Fuzzy Correlative Naive Bayes Classifier
[5] J. Chen, H. Chen, X. Wan and G. Zheng, MR-ELM: a MapReduce-based framework for large-scale ELM training in big data
era, Neural Comput. Appl. 27 (2016), 101–110.
[6] M. Duan, K. Li, X. Liao and K. Li, A parallel multiclassification algorithm for big data using an extreme learning machine,
IEEE Trans. Neural Netw. Learn. Syst. 29 (2017), 2337–2351.
[7] M. Elkano, M. Galar, J. Sanz and H. Bustince, CHI-BD: a fuzzy rule-based classification system for big data classification
problems, Fuzzy Sets Syst. 348 (2018), 75–101.
[8] A. Fernández, S. del Río, A. Bawakid and F. Herrera, Fuzzy rule based classification systems for big data with MapReduce:
granularity analysis, Adv. Data Anal. Classif. 11 (2017), 711–730.
[9] A. Haque, B. Parker, L. Khan and B. Thuraisingham, Evolving big data stream classification with MapReduce, in:
Proceedings of IEEE 7th International Conference on Cloud Computing, pp. 570–577, Anchorage, AK, 2014.
[10] M. Hazewinkel, Arithmetic series, in: Encyclopedia of Mathematics, Springer, Netherlands, 2001.
[11] O. Hegazy, S. Safwat and M. E. Bakry, A MapReduce fuzzy techniques of big data classification, in: Proceedings of the SAI
Computing Conference (SAI), pp. 118–128, London, 2016.
[12] G. B. Huang, Q. Y. Zhu and C. K. Siew, Extreme learning machine: theory and applications, Neurocomputing 70 (2006),
489–501.
[13] X. Huang, L. Shi and J. A. K. Suykens, Support vector machine classifier with pinball loss, IEEE Trans. Pattern Anal. Mach.
Intell. 36 (2014), 984–997.
[14] M. S. Kamal, S. Parvin, A. S. Ashour, F. Shi and N. Dey, De-Bruijn graph with MapReduce framework towards metagenomic
data classification, Int. J. Inform. Technol. 9 (2017), 59–75.
[15] W. Lin, Z. Wu, L. Lin, A. Wen and J. Li, An ensemble random forest algorithm for insurance big data analysis, IEEE Access 5
(2017), 16568–16575.
[16] Localization dataset from https://archive.ics.uci.edu/ml/datasets/Localization+Data+for+Person+Activity, Accessed on
October 2017.
[17] V. Lopez, S. del Rio, J. M. Benitez and F. Herrera, On the use of MapReduce to build linguistic fuzzy rule based classification systems for big data, in: Proceedings of the IEEE International Conference on Fuzzy Systems (FUZZ-IEEE),
pp. 1905–1912, Beijing, 2014.
[18] V. López, S. del Río, J. M. Benítez and F. Herrera, Cost-sensitive linguistic fuzzy rule based classification systems under
the MapReduce framework for imbalanced big data, Fuzzy Sets Syst. 258 (2015), 5–38.
[19] S. A. Ludwig, MapReduce-based fuzzy c-means clustering algorithm: implementation and scalability, Int. J. Mach. Learn.
Cybernet. 6 (2015), 923–934.
[20] J. Maillo, I. Triguero and F. Herrera, A MapReduce-based k-nearest neighbor approach for big data classification, in: IEEE
Trustcom/BigDataSE/ISPA, pp. 167–172, Helsinki, 2015.
[21] S. Mirjalili, S. M. Mirjalili and A. Lewis, Grey wolf optimizer, Adv. Eng. Softw. 69 (2014), 46–61.
[22] S. S. Patil and S. P. Sonavane, Enriched over_sampling techniques for improving classification of imbalanced big data,
in: Proceedings of IEEE Third International Conference on Big Data Computing Service and Applications (BigDataService),
pp. 1–10, San Francisco, CA, 2017.
[23] B. Pei, F. Wang and X. Wang, Research on MapReduce-based fuzzy associative classifier for big probabilistic numerical
data, in: Proceedings of the IEEE International Conference on Internet of Things (iThings) and IEEE Green Computing and
Communications (GreenCom) and IEEE Cyber, Physical and Social Computing (CPSCom) and IEEE Smart Data (SmartData),
pp. 903–906, Chengdu, 2016.
[24] G. Santafe, J. A. Lozano and P. Larranaga, Bayesian model averaging of naive Bayes for clustering, IEEE Trans. Syst. Man
Cybernet. Pt. B (Cybernetics) 36 (2006), 1149–1161.
[25] A. Segatori, F. Marcelloni and W. Pedrycz, On distributed fuzzy decision trees for big data, IEEE Trans. Fuzzy Syst. 26
(2018), 174–192.
[26] Skin segmentation dataset from https://archive.ics.uci.edu/ml/datasets/skin+segmentation, Accessed on October 2017.
[27] H. Storr, A compact fuzzy extension of the naive Bayesian classification algorithm, in: Intelligent Systems in e-Commerce
(ISeC), 2002.
[28] I. Triguero, D. Peralta, J. Bacardit, S. García and F. Herrera, MRPR: a MapReduce solution for prototype reduction in big
data classification, Neurocomputing 150 (2015), 331–345.
[29] J. Zhai, S. Zhang and C. Wang, The classification of imbalanced large data sets based on MapReduce and ensemble of ELM
classifiers, Int. J. Mach. Learn. Cybernet. 8 (2017), 1009–1017.
|
|
https://openalex.org/W3019216653
|
https://www.researchsquare.com/article/rs-9106/v3.pdf
|
English
| null |
Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema
|
BMC infectious diseases
| 2,020
|
cc-by
| 8,166
|
Longitudinal assessment of antibiotic resistance
gene profiles in gut microbiomes of infants at risk
of eczema Longitudinal assessment of antibiotic resis
gene profiles in gut microbiomes of infants
of eczema
Evelyn Loo(Former Corresponding Author)
Singapore Institute of Clinical Sciences
https://orcid.org/0000-0001-7690-3191
Amanda Zain
National University Singapore Yong Loo Lin School of Medicine
Gaik Chin Yap
National University Singapore Yong Loo Lin School of Medicine
Rikky W Purbojati
Nanyang Technological University
Daniela I Drautz-Moses
Nanyang Technological University
Yan Qing koh
Nanyang Technological University
Yap Seng Chong
National University Singapore Yong Loo Lin School of Medicine
Kok Hian Tan
KK Women's and Children's Hospital
Peter D Gluckman
Singapore Institute for Clinical Sciences
Fabian Yap
KK Women's and Children's Hospital
Johan Gunnar Eriksson
National University Singapore Yong Loo Lin School of Medicine
Elizabeth Tham
National University Singapore Yong Loo Lin School of Medicine
lynette shek
National University Singapore Yong Loo Lin School of Medicine
Staffan kjelleberg
Nanyang Technological University
Stephan C Schuster
Nanyang Technological University Daniela I Drautz-Moses
Nanyang Technological University Yan Qing koh
Nanyang Technological University Peter D Gluckman
Singapore Institute for Clinical Sciences Fabian Yap
KK Women's and Children's Hospital Page 1/25
KK Womens and Childrens Hospital
Johan Gunnar Eriksson
National University Singapore Yong Loo Lin School of Medicine
Elizabeth Tham
National University Singapore Yong Loo Lin School of Medicine
lynette shek
National University Singapore Yong Loo Lin School of Medicine
Staffan kjelleberg
Nanyang Technological University
Stephan C Schuster
Nanyang Technological University
Ritu Banerjee Vanderbilt University Medical Center
Bee Wah Lee(New Corresponding Author)
(
paeleebw@nus.edu.sg
) Vanderbilt University Medical Center
Bee Wah Lee(New Corresponding Author)
(
paeleebw@nus.edu.sg
) Elizabeth Tham Page 1/25 Research article Keywords: Antibiotic resistance genes, resistome, infancy, birth cohort, ESBL producing
Enterobacteriaceae Posted Date: March 31st, 2020 License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full License Version of Record: A version of this preprint was published at BMC Infectious Diseases on April 28th,
2020. See the published version at https://doi.org/10.1186/s12879-020-05000-y. Page 2/25 Abstract Background While there is increasing knowledge about the gut microbiome, the factors influencing and
the significance of the gut resistome are still not well understood. Infant gut commensals risk transferring
multidrug-resistant antibiotic resistance genes (ARGs) to pathogenic bacteria. The rapid spread of
multidrug-resistant pathogenic bacteria is a worldwide public health concern. Better understanding the
naïve infant gut resistome may build the evidence base for antimicrobial stewardship in both humans
and in the food industry. Given the high carriage rate of extended spectrum beta-lactamase (ESBL)-
producing Enterobacteriaceae in Asia, we aimed to evaluate community prevalence, dynamics, and
longitudinal changes in antibiotic resistance gene (ARG) profiles and prevalence of ESBL-producing E. coli and K. pneumoniae in the intestinal microbiome of infants participating in the Growing Up in
Singapore Towards Healthy Outcomes (GUSTO) study, a longitudinal cohort study of pregnant women
and their infants. Methods: We analysed ARGs in the first year of life among 75 infants at risk of eczema
who had stool samples collected at multiple timepoints using metagenomics. Results: The mean number
of ARGs per infant increased with age. The most common ARGs identified confer resistance to
aminoglycoside, beta-lactam, macrolide and tetracycline antibiotics; all infants harboured these antibiotic
resistance genes at some point in the first year of life. Few ARGs persisted throughout the first year of life. Beta-lactam resistant Escherichia coli and Klebsiella pneumoniae were detected in 4 (5.3%) and 32
(42.7%) of subjects respectively. Conclusion: In this longitudinal cohort study of infants living in a region
with high endemic antibacterial resistance, we demonstrate that majority of the infants harboured several
antibiotic resistance genes in their gut and showed that the infant gut resistome is diverse and dynamic
over the first year of life. Background The rapid spread of multidrug- resistant pathogenic bacteria that are no longer susceptible to treatment
with common antibiotics is a global public health concern. The lack of efficacy of currently available
antibiotics and the paucity of new antibiotic development may potentially result in a situation akin to the
pre-antibiotic era where minor infections may become life-threatening conditions (1-3). The human gastrointestinal tract hosts a diversity of microbiota which are responsible for important
functions such as stimulation of intestinal angiogenesis, protection against cell injury and regulation of
fat storage. However, the gut microbiota is a reservoir for antibiotic resistance genes (ARGs). ARGs have
been identified in the intestinal microbiomes from adults as well as infants as early as the first month of
life (4-9). Alarmingly, ARGs in commensal human gut microbiota can be transferred to pathogenic strains
of bacteria that can cause disease (10). There is significant geographic variation in the prevalence and type of ARGs in microbiota, implying that
there may be environmental and lifestyle factors affecting the prevalence of ARGs. Hu and colleagues
reported regional differences in ARG abundance; Chinese individuals have the greatest number of ARGs,
followed by Danish and Spanish counterparts (11). Page 3/25 Page 3/25 Page 3/25 Southeast and South Asian countries are considered epicentres of antibiotic resistant bacteria (12) with
high prevalence of extended spectrum beta- lactamase (ESBL) producing Enterobacteriaceae. In
particular, the prevalence of ESBL E. coli has been reported to be as high as 50% in the Vietnamese
general population (13), and even higher among infants hospitalized in a neonatal intensive care unit in
Taiwan (14, 15). In a recent study of healthy infants from Bangladesh, 82% had stool samples
containing third generation cephalosporin-resistant E coli, the majority of which were multidrug - resistant
and ESBL- producers (16). Despite the high prevalence of drug-resistant bacteria in community and hospital settings in Southeast
Asia, most literature to date has focused on selected bacteria such as E coli (17). This is the first study in
the region describing changes in the total antibiotic resistance gene (ARG) profile (also known as the
resistome) of healthy infants over time. We aimed to evaluate changes in ARGs over the first year of life
in the gut microbiome of infants from the Growing Up in Singapore Towards Healthy Outcomes (GUSTO)
study, the largest longitudinal birth cohort study including pregnant women and their infants in
Singapore. Background We also aimed to evaluate the role of demographic and social factors on development of the
infant gut resistome. Singapore. We also aimed to evaluate the role of demographic and social factors on development of the
infant gut resistome. Study population The study cohort and methodology of the GUSTO study has been described in detail previously (18). Briefly, we recruited pregnant mothers aged 18 and above, attending their first trimester antenatal dating
scan from the two major maternity units in Singapore who agreed to enrol their offspring for future
longitudinal follow-up. Mothers receiving chemotherapy, taking psychotrophic drugs or who had type 1
diabetes mellitus were excluded from the study. Information about subject demographics, family history
of allergy, hospitalization, illnesses, social data and lifestyle factors was collected. Structured The study cohort and methodology of the GUSTO study has been described in detail previously (18). Briefly, we recruited pregnant mothers aged 18 and above, attending their first trimester antenatal dating
scan from the two major maternity units in Singapore who agreed to enrol their offspring for future
longitudinal follow-up. Mothers receiving chemotherapy, taking psychotrophic drugs or who had type 1
diabetes mellitus were excluded from the study. Information about subject demographics, family history
of allergy, hospitalization, illnesses, social data and lifestyle factors was collected. Structured
questionnaires were administered at 3 weeks, 3 months, 6 months and 12 months to collect information
on each child’s health. Stool samples from enrolled infants were collected at 3 weeks (W3), 3 months
(M3), 6 months (M6), and 12 months (M12). We analysed the presence of ARGs in the first year of life, in
a subset of 75 infants at risk of eczema from the GUSTO birth cohort. The original aim of the study was
to evaluate and compare stool microbiota in infants with eczema vs. those without eczema. Briefly,
eczema subjects were selected based on parental report of physician-diagnosed eczema in the first 18
months of life and/ or had SCORAD scores at 18 or 36 months (19). Non-eczema subjects were matched
with eczema subjects based on age, mode of delivery (caesarean/ vaginal delivered), usage of antibiotics
at labour (yes/no), mode of feeding in first 6 months of life (exclusively breastfeeding/ partial
breastfeeding/ total formula feeding) and usage of antibiotics in the first year of life (yes/no). We
included 40 non-eczema subjects and 35 eczema subjects. The study flowchart is presented in Figure 1. Genomic DNA Extraction Page 4/25 Genomic DNA was extracted from approximately 100-150 mg of stool from each specimen with the ZR
Fecal DNA MicroPrep Kit (Zymo Research, USA) according to the manufacturer’s instructions. Metagenomic sequencing & Bioinformatics Analysis For each stool sample, a sequencing library was first constructed using Illumina’s Truseq Nano DNA
Library Preparation Kit (Illumina, San Diego, USA). The samples were sheared on a Covaris E220 to
~450bp, following the manufacturer’s recommendation, and uniquely tagged with one of Illumina’s
TruSeq HT DNA barcode combinations to enable sample pooling for sequencing. The finished libraries were quantitated using Invitrogen’s Picogreen assay and the average library size
was determined on Bioanalyzer 2100, using a DNA 7500 chip (Agilent). Library concentrations were then
normalized to 4nM and validated by qPCR on a ViiA-7 real-time thermocycler (Applied Biosystems), using
qPCR primers recommended in Illumina’s qPCR protocol, and Illumina’s PhiX control library as standard. The libraries were then pooled at equimolar concentrations and sequenced on an Illumina HiSeq2500
sequencer in rapid mode at a read-length of 250bp paired-end. Approximately 5Gb of sequencing data
were obtained per sample so as to capture most of the novelty (20). Genomic DNA sequences obtained from Illumina HiSeq paired-end sequencing were analyzed as follows:
(i) Sequence quality check, (ii) Reads to protein alignment, and (iii) Taxonomical classification. To
perform a quality check, reads shorter than 30bp and low-quality sequences (<Q20 score) were removed. As elaborated by Illumina Inc. (2018), a sequencing quality score of 20 (Q20) represents an average error
rate of 1 in 100 bases. Therefore, removal of any sequence with a higher error rate than 1% (i.e., <Q20 score) allows for a
corresponding call accuracy of at least 99%. Thereafter, metagenomic reads were obtained by aligning the high-quality reads against human reference
genome (hg19), whereby reads that were aligned to hg19 were discarded. The non-human metagenomic
reads were then run on ResFinder 2.1. to check for the ARG’s conferring resistance to: aminoglycoside,
tetracycline, beta-lactam, colistin, fosfomycin, fusidic acid, macrolide, nitroimidazole, oxazolidinone,
phenicol, quinolone, rifampicin, sulphonamide, trimethoprim, and glycopeptide antibiotics. Lastly, a lowest common ancestor (LCA)-based Taxonomical Classification of the aligned sequence reads
was carried out on MEGAN6 (MEtaGenome Analyzer 6) using a bitscore cut-off of 100. A simple
algorithm is utilized by MEGAN to assign each read to the LCA of the set of taxa that it hits in the
comparison, whereby species-specific sequence reads will be assigned to the species taxon, while widely
conserved sequence reads will be assigned to the high-order taxa (21). Study population and Clinical Characteristics The majority of the subjects included in this study were healthy full-term infants (72/75, 96.0%), while 2
were delivered at 36 weeks and 1 at 35 weeks. Out of these 75 infants, 33.3% were delivered by caesarean
delivery (Table 1). The proportion of female and male infants were similar and the majority were of
Chinese ethnicity [42 (56%)]. Antibiotics were taken by 35 (46.7%) mothers during pregnancy and/or
labour. Out of the 14 mothers that took antibiotics during pregnancy, 3 took it during the first trimester, 6
during second trimester and 5 during third trimester. A minority of the infants [16 (21.3%)] were prescribed
antibiotics during the first year of life. The subjects included in this study were similar to the larger
GUSTO cohort in all characteristics except consumption of antibiotics, illness and hospitalisation
(Additional Table 1, Supplementary Data) Statistical Analysis Univariate analysis using Pearson chi-square test was performed to assess associations between ARGs
and demographic, lifestyle and clinical factors. Page 5/25 Page 5/25 From the absolute number of normalized reads obtained from the LCA based Taxonomical Classification
on MEGAN6, the relative abundance of each bacterial phylum, family, genus and species were calculated. Shannon and Simpson’s Diversity Indices were then calculated using relative abundance obtained at the
species taxon. For all statistical analysis, IBM SPSS Statistics (Version 24.0) was used (IBM Corporation, New York,
USA), with two-tailed statistical tests and confidence intervals of 95% (i.e., p-value < 0.05). All graphical
figures were plotted using Microsoft Excel 2017 (Microsoft Corporation, Washington, USA) and GraphPad
Prism Version 7 (GraphPad Software, California USA). Antibiotic resistance gene profile There were 188 available stool samples from 75 infants; 28 at week 3, 41 at month 3, 58 at month 6 and
61 at month 12. Eight (10.7%) subjects had stool samples available at all 4 timepoints. There were 228
unique ARGs detected among all samples. The mean number of ARGs per infant increased with age (23.0
at W3, 25.0 at M3, 25.4 at M6 and 26.0 at M12, p <0.05, Figure 2a) Microbial diversity of the stool
samples also increased over time, as measured by the Shannon diversity index (Figure 2b). The most common ARGs identified confer resistance to aminoglycoside, beta-lactam, macrolide and
tetracycline antibiotics; all infants harboured these ARGs at some point in the first year of life (Additional
Figure 1, Supplementary Data). Overall, the most common ARGs were fosA, blaZ, tet (M) and mef (A),
conferring fosfomycin, beta-lactam, tetracycline and macrolide resistance, respectively (Table 2). The
most common ARGs detected varied over time. At week 3, the most prevalent ARGs were fosA and blaZ
which were present in more than 95% of infants, while at month 12 the most prevalent ARG was mefA,
found in 93.4% of infants (Table 2). Association between usage of beta-lactam class of antibiotics during pregnancy and/or labour and
acquisition of beta-lactam resistance genes in the offspring Association between usage of beta-lactam class of antibiotics during pregnancy and/or labour and
acquisition of beta-lactam resistance genes in the offspring Page 6/25 Among the 35 women receiving antibiotics during pregnancy and/or labour, beta-lactam antibiotics were
the most commonly given antibiotic class [30/35 (85.7%)] (Table 1). Details of the antibiotics used are
presented in Additional Tables 2 and 3, Supplementary Data. Given the high usage of the beta-lactam class of antibiotics during pregnancy and/or labour, we next
determined if this affected the acquisition of beta -lactam resistance genes in the offspring. All ARGs that
conferred beta-lactam resistance were analysed. Offspring of mothers exposed to beta-lactam antibiotics
during pregnancy and/or labour had significantly increased detection of the beta-lactam-resistance
conferring genes, cepA-44 (9/80, 11.3%) and cfxA (14/80, 17.5%), in their stool samples compared to
offspring of mothers who did not take these antibiotics (1/101, 1.0%; 6/101, 5.9% respectively p<0.01). There were no significant associations between the use of beta-lactam antibiotics during pregnancy
and/or labour and other ARGs conferring beta-lactam resistance in the first year of life. The presence of
specific ARGs were not significantly associated with gender, race, delivery mode, postnatal antibiotics use
and eczema diagnosis in infancy. Beta-lactamase type We next characterized the type of beta-lactamase genes; the majority were ESBLs [CTX-M beta
lactamases (classA), OXA beta-lactamases (class D), SHV beta-lactamases (classA) and TEM beta-
lactamases (classA), Table 3]. The most common ESBL genes was blaTEM-1B, present in 10 (35.7%)
subjects at week 3, 22 subjects (53.7%) at month 3, 34 subjects (58.6%) at month 6, and 29 subjects
(47.5%) at month 12. Carbapenemase detection was rare and only CMY (class C) carbapenemases were
detected. Among stool samples at each time point, carbapenemase genes were found in 1 (3.6%) at W3,
4 (9.8%) at M3, 7 (12.0%) at month 6 and 4 (6.6%) at month 12. Most carbapenemase genes (blaCMY-34,
blaCMY-49, blaCMY-83, blaCMY-98) were detected at 1 timepoint only for a given infant, suggesting that
they do not persist with time. blaCMY-2 was detected in multiple infants including 1 subject at week 3, 2
at month 3, 4 at month 6 and 2 at month 12. NDM and KPC type carbapenemases were not detected in
the infants. Dynamics of ARGs over time We next analysed the most commonly-detected ARGs from early life (3
weeks) up to 12 months of age. The analysis was performed among 22 infants who had stool samples
at both week 3 (first timepoint) and month 12 (last timepoint). Among these infants, there were 3 ARGs
that were present in both samples. These ARGs were mef(A) conferring macrolide resistance, aadE
conferring aminoglycoside resistance, and msr(D) which conferred macrolide, lincosamide and
streptogramin B resistance (Table 4). Among infants who harboured ESBL genes at week 3, we found
blaTEM-1b present at month 12 in 6/9 (67%) subjects and blaOXA-347 in 2/2 (100%) subjects (Table 5). An additional subgroup analysis was performed among infants who had stool samples collected at all
timepoints. Among the 8 infants who had stool samples analysed at all 4 timepoints, there were 9 ARGs
that were present at both week 3 and month 3 samples. These ARGs were lsa(A), mef(A), msr(D), sul2,
tet(O), tet(Q), tet (W), blaTEM-1B and aadE which conferred macrolide, macrolide, sulphonamide, Page 7/25 Page 7/25 tetracycline, beta-lactam, aminoglycoside, macrolide, lincosamide and streptogramin B resistance
respectively. There were 4 ARGs that were present at all timepoints from week 3 to month 6 and they were
tet(O), tet(Q), tet (W), blaTEM-1B, which confer tetracycline and beta-lactam resistance. Beta-lactamase type There were only 2
ARGs that were present at all timepoints from week 3 to month 12: tet(Q) from Bacteroides and tet (W)
from Bifidobacterium, both conferring tetracycline resistance (Table 4). Beta-lactam resistant E. coli and K. pneumoniae Beta-lactam resistant E. coli, which is endemic in Singapore, was detected in 4 (5.3%) subjects at different
timepoints, including, 1 subject at week 3, 2 at month 3 and 2 at month 6 respectively. No beta-lactam
resistant E. coli was detected at month 12. There were 3 ESBL genes detected in E. coli, namely blaCMY-2,
blaCTX-M15 and blaTEM-1b (Table 6). In contrast, beta-lactam resistant K. pneumoniae was more
common and was detected in 32 (42.7%) subjects at any time point. The prevalence of beta-lactam
resistant K. pneumoniae declined over time; it was found in 13 subjects at week 3, 10 at month 3, 11 at
month 6, 8 at month 12. Among these K. pneumoniae, there were 9 ESBLs detected, all of which were
SHV beta-lactamases (class A) (Table 6). Discussion We report the first longitudinal cohort study in Southeast Asia to evaluate the diversity and dynamics of
the infant gut resistome over the first year of life. We observed that in an area with high endemic bacterial
drug resistance, the infant gut harbours a wide diversity of ARGs from early in infancy (4, 6-9). We also
observed significant differences among the ARGs prevalent in early infancy compared to those prevalent
at 1 year of life. Generally, the number of ARGs per infant stool specimen increased over time during the
first year of life. This increasing prevalence may be due to environmental acquisition of some genes or
the emergence of resistance among normal flora. A minority of ARGs persisted through the first year of
life, demonstrating a highly dynamic infant resistome (22, 23). Our findings are supported by studies from other parts of the world. Gosalbes and colleagues found a
high prevalence of resistance to beta-lactam antibiotics and tetracycline in both meconium and stool
samples from 1-week-old infants, suggesting the acquisition of the infant gut resistance reservoir even
before birth (23). A functional screen for ARGs in the gut microbiota of 22 healthy 6-month old infants
from Ireland, who had not received any prior antibiotics, demonstrated the presence of a variety of genes
encoding resistance to aminoglycosides and beta-lactams (24). Nogacka and colleagues also found a
higher occurrence of some beta-lactamase encoding genes in vaginally-delivered term Spanish infants
whose mothers received intra-partum antimicrobial prophylaxis, compared to those whose mothers did
not receive intra-partum antibiotics (25). Wintersdorff et al. also noted increasing prevalence of ARGs
over time in infants, in Germany (26). Page 8/25
The prevalence of ARGs encoding resistance to antibiotics that are rarely used in humans, such as
chloramphenicol, may imply selection pressure from the environment, or food and agriculture, possibly
via maternal diet. If so, this is likely to vary across different regions throughout the world. Early in infancy, certain ARGs may be easily acquired from breast milk or even environmental contaminants of formula
milk (27, 28). Later on, as infants are weaned and begin eating table foods, ARGs may be acquired from
ingesting meat and vegetables. It is known that antibiotics are often used in livestock for growth
promotion and disease prevention, particularly in settings of intensive animal production (29). Discussion This has
been known to be implicated in the development of antimicrobial-resistant bacteria that can be spread to
humans. The tendency to acquire or lose ARGs may be additionally affected by a complex interaction of
epigenetic factors, but the large diversity of ARGs may make it challenging to find significant
associations between specific ARGs and the various clinical variables studied. certain ARGs may be easily acquired from breast milk or even env
milk (27, 28). Later on, as infants are weaned and begin eating tab
ingesting meat and vegetables. It is known that antibiotics are oft
promotion and disease prevention, particularly in settings of inten
been known to be implicated in the development of antimicrobial-
humans. The tendency to acquire or lose ARGs may be additional
epigenetic factors, but the large diversity of ARGs may make it cha
associations between specific ARGs and the various clinical varia We observed that maternal beta-lactam exposure during pregnancy or delivery was associated with the
detection of beta-lactam resistance genes among infants. This is consistent with the work by Nogacka et
al (25), who found that intra-partum antibiotics affect the composition of the infant gut microbiome. Surprisingly, we did not observe any association between the mode of delivery and acquisition of ARGs in
the offspring. This finding differs from a previous study which showed that tetracycline resistance genes
such as tet(M), tet(O), tet(W), and tet(Q) were identified in maternal vaginal flora, and that their
transmission to offspring was dependent on mode of delivery; 50% of the infants delivered vaginally
harboured tetracycline resistance genes tet(M) and tet(O) found in mothers, while 16% and 13% of infants
delivered by C-section had tet(O) and tet(W) respectively (9). The prevalence of ARGs in the gut resistome did not always correlate with common multidrug resistance
phenotypes in the community. For example, mecA, which confers resistance to all beta-lactam antibiotics
and is found in most methicillin-resistant Staphylococcus aureus (MRSA) strains, was not prevalent in the
infant resistome despite its high incidence in adults in the hospital and community (30). Similarly, beta-
lactam-resistant E. coli, which is endemic in Singapore, was only found in 5% of the infants. In contrast,
beta-lactam-resistant K. pneumoniae, which is also common in the community, was found in 42% of the
infants. Discussion In our study, we also found several ESBL genes in infants’ stools in the first year of life, independent of
the selection pressure of antibiotic exposure. This highlights the endemicity of these strains in Singapore,
and the global problem of transmission of multi-drug antibiotic resistant bacteria. Surprisingly few
infants harboured drug-resistant E. coli, despite widespread dissemination of drug-resistant E. coli
sequence types in Singapore (31-34). In contrast, drug-resistant K. pneumoniae was detected in a number
of infants from the GUSTO cohort. K. pneumoniae is known to acquire ARGs via de novo mutations,
plasmid dissemination and transfer of ARGs. This underscores the potential for the infant gut resistome
to facilitate the rise of extremely drug resistant (XDR) strains carrying ‘super resistomes’ (35). In our study, we also found several ESBL genes in infants’ stools in the first year of life, independent of
the selection pressure of antibiotic exposure. This highlights the endemicity of these strains in Singapore,
and the global problem of transmission of multi-drug antibiotic resistant bacteria. Surprisingly few
infants harboured drug-resistant E. coli, despite widespread dissemination of drug-resistant E. coli
sequence types in Singapore (31-34). In contrast, drug-resistant K. pneumoniae was detected in a number
of infants from the GUSTO cohort. K. pneumoniae is known to acquire ARGs via de novo mutations,
plasmid dissemination and transfer of ARGs. This underscores the potential for the infant gut resistome
to facilitate the rise of extremely drug resistant (XDR) strains carrying ‘super resistomes’ (35). The infant gut microbiome in dysbiosis has been implicated in diseases such as necrotizing enterocolitis
and allergic disease. However, the significance of the infant gut resistome specifically and its role in
human disease is still unclear. It is not known what constitutes a “healthy” resistome and the implications
of ARG diversity in the infant gut. It may be a reflection of our antimicrobial use not just in pregnancy but
also in the food industry. It may have longer lasting implications on the nature and severity of bacterial infections acquired later on in life. Potentially, the infant gut resistome can influence the incidence of
multi-drug resistant (MDR) infections, by harbouring ARGs in commensals that transfer to pathogenic
bacteria (30). Better understanding of the naïve infant gut resistome may help to build the evidence base
for antimicrobial stewardship. List Of Abbreviations Antibiotic resistance genes (ARGs) Extended spectrum beta- lactamases (ESBL) Growing Up in Singapore Towards Healthy Outcomes (GUSTO) Conclusion In conclusion, this study describes the diversity and dynamic nature of the infant gut resistome in a
region with high endemic resistance rates, and the paucity of known variables that affect the diversity of
the gut resistome. Future work should focus on the mode of acquisition, transmission, and persistence of
these ARGs. Metagenomic comparisons between microbiota in infants and their adult household
contacts would also help elucidate factors influencing the establishment of the infant gut resistome. Discussion The strengths of this study are the longitudinal collection of infants’ stool specimens and follow up of the
infants by structured questionnaires in early life. In addition, the large sample size and higher endemic
resistance rates in Singapore are also strengths compared to earlier studies. However, a limitation of this
study is that maternal stool specimens and infant stool specimens at birth were not available. It is hence
not possible to identify which ARGs were likely to have been vertically transmitted. In addition, not all
infants had stool samples available at all time points, thereby limiting analyses of ARG persistence over
time. The large diversity of ARGs may also make it challenging to find clinically significant associations
between specific ARGs and demographic and clinical variables. Our studied population also
overrepresents subjects with eczema, limiting its generalizability as they may carry a higher risk of ARG
carriage than the baseline population. Declarations Ethics approval and consent to participate Ethics approval and consent to participate Ethics approval was obtained from the Domain Specific Review Board of Singapore National Healthcare
Group and the Centralised Institutional Review Board of SingHealth. Conduct of the study was based on
the guidelines in the Declaration of Helsinki. Written informed consent was obtained from all participants. Consent for publication Consent for publication
Not applicable Consent for publication Page 10/25 Availability of data and materials Availability of data and materials Availability of data and materials The datasets used and/or analysed during the current study are available from the corresponding author
on reasonable request. Funding The study was supported by the National Medical Research Council Clinician Scientists Individual
Research Grant (R-178-000-222-511) provided by the Ministry of Health (Singapore). This research is also
supported by the Singapore National Research Foundation under its Translational and Clinical Research
(TCR) Flagship Programme and administered by the Singapore Ministry of Health’s National Medical
Research Council (NMRC), Singapore- NMRC/TCR/004-NUS/2008; NMRC/TCR/012-NUHS/2014. Additional funding is provided by the Singapore Institute for Clinical Sciences, Agency for Science
Technology and Research (A*STAR), Singapore. The funders are not involved in the design and conduct
of the study, data analysis and preparation of manuscript. Authors' contributions EXL and AZ analysed, interpreted the data and wrote the manuscript. GCY analysed and interpreted the
data. RWP, DIDM, YQK, SK and SCS analysed the data. YSC, KHT, PDG, FY, JGE and LPS were involved in
the design of the study. ET revised the manuscript. RB and BWL supervised the research and revised the
manuscript. All authors reviewed the manuscript and approved the submitted version. Competing interests YSC has received reimbursement for speaking at conferences sponsored by Abbott Nutrition, Nestle, and
Danone. LPS has received reimbursement for speaking at conferences sponsored by Danone and Nestle
and consulting for Mead Johnson and Nestle. YSC is part of an academic consortium that has received research funding from Abbot Nutrition, Nestle
and Danone. LPS has received research funding from Danone. Acknowledgements Elaine Kwang Hsia Tham, Elaine Phaik Ling Quah, Evelyn Chung Ning Law, Evelyn Xiu Ling Loo, Fabian
Kok Peng Yap, Faidon Magkos, Falk Mueller-Riemenschneider, George Seow Heong Yeo, Hannah Ee Juen
Yong, Helen Yu Chen, Heng Hao Tan, Hong Pan, Hugo P S van Bever, Hui Min Tan, Iliana Magiati, Inez Bik
Yun Wong, Ivy Yee-Man Lau, Izzuddin Bin Mohd Aris, Jeannie Tay, Jeevesh Kapur, Jenny L. Richmond,
Jerry Kok Yen Chan, Jia Xu, Joanna Dawn Holbrook, Joanne Su-Yin Yoong, Joao Nuno Andrade Requicha
Ferreira, Jonathan Tze Liang Choo, Jonathan Y. Bernard, Jonathan Yinhao Huang, Joshua J. Gooley, Jun
Shi Lai, Karen Mei Ling Tan, Keith M. Godfrey, Kenneth Yung Chiang Kwek, Keri McCrickerd, Acknowledgements We thank the GUSTO study group and all clinical and home-visit staff involved. The voluntary
participation of all subjects is greatly appreciated. The GUSTO study group includes Airu Chia, Allan Sheppard, Amutha Chinnadurai, Anna Magdalena
Fogel, Anne Eng Neo Goh, Anne Hin Yee Chu, Anne Rifkin-Graboi, Anqi Qiu, Arijit Biswas, Bee Wah Lee,
Birit Froukje Philipp Broekman , Bobby Kyungbeom Cheon, Boon Long Quah, Candida Vaz, Chai Kiat
Chng, Cheryl Shufen Ngo, Choon Looi Bong, Christiani Jeyakumar Henry, Ciaran Gerard Forde, Claudia
Chi, Daniel Yam Thiam Goh, Dawn Xin Ping Koh, Desiree Y. Phua, Doris Ngiuk Lan Loh, E Shyong Tai, Page 11/25 Page 11/25 Page 11/25 Elaine Kwang Hsia Tham, Elaine Phaik Ling Quah, Evelyn Chung Ning Law, Evelyn Xiu Ling Loo, Fabian
Kok Peng Yap, Faidon Magkos, Falk Mueller-Riemenschneider, George Seow Heong Yeo, Hannah Ee Juen
Yong, Helen Yu Chen, Heng Hao Tan, Hong Pan, Hugo P S van Bever, Hui Min Tan, Iliana Magiati, Inez Bik
Yun Wong, Ivy Yee-Man Lau, Izzuddin Bin Mohd Aris, Jeannie Tay, Jeevesh Kapur, Jenny L. Richmond,
Jerry Kok Yen Chan, Jia Xu, Joanna Dawn Holbrook, Joanne Su-Yin Yoong, Joao Nuno Andrade Requicha
Ferreira, Jonathan Tze Liang Choo, Jonathan Y. Bernard, Jonathan Yinhao Huang, Joshua J. Gooley, Jun
Shi Lai, Karen Mei Ling Tan, Keith M. Godfrey, Kenneth Yung Chiang Kwek, Keri McCrickerd,
Kothandaraman Narasimhan, Krishnamoorthy Naiduvaje, Kuan Jin Lee, Leher Singh, Li Chen, Lieng Hsi
Ling, Lin Lin Su, Ling-Wei Chen, Lourdes Mary Daniel, Lynette Pei-Chi Shek, Marielle V. Fortier, Mark
Hanson, Mary Foong-Fong Chong, Mary Rauff, Mei Chien Chua, Melvin Khee-Shing Leow, Michael J. Meaney, Michelle Zhi Ling Kee, Min Gong, Mya Thway Tint, Navin Michael, Neerja Karnani, Ngee Lek, Oon
Hoe Teoh, P. C. Wong, Paulin Tay Straughan, Pratibha Keshav Agarwal, Priti Mishra, Queenie Ling Jun Li,
Rob Martinus van Dam, Salome A. Rebello, Sambasivam Sendhil Velan, Seang Mei Saw, See Ling Loy,
Seng Bin Ang, Shang Chee Chong, Sharon Ng, Shiao-Yng Chan, Shirong Cai, Shu-E Soh, Sok Bee Lim,
Stella Tsotsi, Stephen Chin-Ying Hsu , Sue-Anne Ee Shiow Toh, Suresh Anand Sadananthan, Swee Chye
Quek, Varsha Gupta, Victor Samuel Rajadurai, Walter Stunkel, Wayne Cutfield, Wee Meng Han, Wei Wei
Pang, Wen Lun Yuan, Yanan Zhu, Yin Bun Cheung, Yiong Huak Chan, Yung Seng Lee. References 1. Warnes SL, Highmore CJ, Keevil CW. Horizontal transfer of antibiotic resistance genes on abiotic
touch surfaces: implications for public health. MBio. 2012;3(6):e00489-12. 1. Warnes SL, Highmore CJ, Keevil CW. Horizontal transfer of antibiotic resistance genes on abiotic
touch surfaces: implications for public health. MBio. 2012;3(6):e00489-12. 2. Bush K, Fisher JF. Epidemiological expansion, structural studies, and clinical challenges of new β-
lactamases from gram-negative bacteria. Annual Review of Microbiology. 2011;65:455-78. 3. Bonomo RA. New Delhi metallo-β-lactamase and multidrug resistance: a global SOS? Clinical
Infectious Diseases. 2011;52(4):485-7. 3. Bonomo RA. New Delhi metallo-β-lactamase and multidrug resistance: a global SOS? Clinical
Infectious Diseases. 2011;52(4):485-7. 4. Gueimonde M, Salminen S, Isolauri E. Presence of specific antibiotic (tet) resistance genes in infant
faecal microbiota. FEMS Immunology & Medical Microbiology. 2006;48(1):21-5. 5. Islam MA, Amin MB, Roy S, Asaduzzaman M, Islam MR, Navab-Daneshmand T, et al. Fecal
Colonization With Multidrug-Resistant E. coli Among Healthy Infants in Rural Bangladesh. 2019;10(640). 6. Mitsou E, Kirtzalidou E, Pramateftaki P, Kyriacou A. Antibiotic resistance in faecal microbiota of Greek
healthy infants. Beneficial Microbes. 2010;1(3):297-306. 6. Mitsou E, Kirtzalidou E, Pramateftaki P, Kyriacou A. Antibiotic resistance in faecal microbiota of Greek
healthy infants. Beneficial Microbes. 2010;1(3):297-306. 7. De Vries LE, Vallès Y, Agersø Y, Vaishampayan PA, García-Montaner A, Kuehl JV, et al. The gut as
reservoir of antibiotic resistance: microbial diversity of tetracycline resistance in mother and infant. PloS one. 2011;6(6):e21644. 7. De Vries LE, Vallès Y, Agersø Y, Vaishampayan PA, García-Montaner A, Kuehl JV, et al. The gut as
reservoir of antibiotic resistance: microbial diversity of tetracycline resistance in mother and infant. PloS one. 2011;6(6):e21644. 8. Zhang L, Kinkelaar D, Huang Y, Li Y, Li X, Wang HH. Acquired antibiotic resistance: are we born with
it? Applied and Environmental Microbiology. 2011:AEM. 05087-11. 8. Zhang L, Kinkelaar D, Huang Y, Li Y, Li X, Wang HH. Acquired antibiotic resistance: are we born with
it? Applied and Environmental Microbiology. 2011:AEM. 05087-11. Page 12/25 Page 12/25 9. Alicea-Serrano AM, Contreras M, Magris M, Hidalgo G, Dominguez-Bello MG. Tetracycline resistance
genes acquired at birth. Archives of Microbiology. 2013;195(6):447-51. 10. Baron SA, Diene SM, Rolain J-M. Human microbiomes and antibiotic resistance. Human Microbiome
Journal. 2018;10:43-52. 11. Hu Y, Yang X, Qin J, Lu N, Cheng G, Wu N, et al. Metagenome-wide analysis of antibiotic resistance
genes in a large cohort of human gut microbiota. Nature Communications. 2013;4:2151. 12. Jean SS, Hsueh PR. References High burden of antimicrobial resistance in Asia. International journal of
antimicrobial agents. 2011;37(4):291-5. 13. Bui TM, Hirai I, Ueda S, Bui TK, Hamamoto K, Toyosato T, et al. Carriage of Escherichia coli Producing
CTX-M-Type Extended-Spectrum beta-Lactamase in Healthy Vietnamese Individuals. Antimicrobial
agents and chemotherapy. 2015;59(10):6611-4. 14. Tsai M-H, Chu S-M, Hsu J-F, Lien R, Huang H-R, Chiang M-C, et al. Risk factors and outcomes for
multidrug-resistant Gram-negative bacteremia in the NICU. Pediatrics. 2014;133(2):e322-9. 15. Folgori L, Bielicki J, Heath PT, Sharland M. Antimicrobial-resistant Gram-negative infections in
neonates: burden of disease and challenges in treatment. Current Opinion in Infectious Diseases. 2017;30(3):281-8. 16. Islam MA, Amin MB, Roy S, Asaduzzaman M, Islam MR, Navab-Daneshmand T, et al. Fecal
Colonization With Multidrug-Resistant E. coli Among Healthy Infants in Rural Bangladesh. Front
Microbiol. 2019;10:640. 17. Hetzer B, Orth-Holler D, Wurzner R, Kreidl P, Lackner M, Muller T, et al. "Enhanced acquisition of
antibiotic-resistant intestinal E. coli during the first year of life assessed in a prospective cohort
study". Antimicrob Resist Infect Control. 2019;8:79. 18. Soh SE, Lee SSM, Hoon SW, Tan MY, Goh A, Lee BW, et al. The methodology of the GUSTO cohort
study: a novel approach in studying pediatric allergy. Asia Pacific Allergy. 2012;2(2):144-8. 19. European Task Force on Atopic Dermatitis. Severity scoring of atopic dermatitis: the SCORAD index. Consensus Report of the European Task Force on Atopic Dermatitis. Dermatology. 1993;186(1):23-
31. 20. Qin, J., Li, R., Raes, J. et al. A human gut microbial gene catalogue established by metagenomic
sequencing. Nature. 2010;464:59–65. 20. Qin, J., Li, R., Raes, J. et al. A human gut microbial gene catalogue established by metagenomic
sequencing. Nature. 2010;464:59–65. 21. Huson, D.H., et al. Integrative analysis of environmental sequences using MEGAN4. Genome
Research. 2011;21(9):1552-1560. 21. Huson, D.H., et al. Integrative analysis of environmental sequences using MEGAN4. Genome
Research. 2011;21(9):1552-1560. 22. Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, et al. Dynamics and
Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host & Microbe. 2015;17(5):690-703. 23. Gosalbes M, Vallès Y, Jiménez-Hernández N, Balle C, Riva P, Miravet-Verde S, et al. High frequencies
of antibiotic resistance genes in infants’ meconium and early fecal samples. Journal of
Developmental Origins of Health and Disease. 2016;7(1):35-44. 23. Gosalbes M, Vallès Y, Jiménez-Hernández N, Balle C, Riva P, Miravet-Verde S, et al. References Staphylococcus aureus among households: A Systematic Review. Int J Infect Dis. 2020 Jan 13. 31. Teo JW, Tan P, La MV, Krishnan P, Tee N, Koh TH, et al. Surveillance trends of carbapenem-resistant
Enterobacteriaceae from Singapore, 2010-2013. Journal of global antimicrobial resistance. 2014;2(2):99-102. 32. Teo JQ, Cai Y, Lim TP, Tan TT, Kwa AL. Carbapenem Resistance in Gram-Negative Bacteria: The Not-
So-Little Problem in the Little Red Dot. Microorganisms. 2016;4(1). 33. Teo J, Ngan G, Balm M, Jureen R, Krishnan P, Lin R. Molecular characterization of NDM-1 producing
Enterobacteriaceae isolates in Singapore hospitals. Western Pacific surveillance and response
journal : WPSAR. 2012;3(1):19-24. 34. Koh TH. Gram-negative resistance in Singapore: a historical perspective. Annals of the Academy of
Medicine, Singapore. 2008;37(10):847-54. 35. Navon-Venezia S, Kondratyeva K, Carattoli A. Klebsiella pneumoniae: a major worldwide source and
shuttle for antibiotic resistance. FEMS Microbiology Reviews. 2017;41(3):252-75. References High frequencies
of antibiotic resistance genes in infants’ meconium and early fecal samples. Journal of
Developmental Origins of Health and Disease. 2016;7(1):35-44. Page 13/25 Page 13/25 24. Fouhy F, Ogilvie LA, Jones BV, Ross RP, Ryan AC, Dempsey EM, et al. Identification of aminoglycoside
and β-lactam resistance genes from within an infant gut functional metagenomic library. PLoS One. 2014;9(9):e108016. 25. Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, et al. Impact of intrapartum
antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance
genes in vaginally delivered full-term neonates. Microbiome. 2017;5(1):93. 25. Nogacka A, Salazar N, Suárez M, Milani C, Arboleya S, Solís G, et al. Impact of intrapartum
antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance
genes in vaginally delivered full-term neonates. Microbiome. 2017;5(1):93. 26. Wintersdorff CJv, Wolffs PF, Savelkoul PH, Nijsen RR, Lau S, Gerhold K, et al. The gut resistome is
highly dynamic during the first months of life. Future Microbiology. 2016;11(4):501-10. 26. Wintersdorff CJv, Wolffs PF, Savelkoul PH, Nijsen RR, Lau S, Gerhold K, et al. The gut resistome is
highly dynamic during the first months of life. Future Microbiology. 2016;11(4):501-10. 27. Pärnänen K, Karkman A, Hultman J, Lyra C, Bengtsson-Palme J, Larsson DJ, et al. Maternal gut and
breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements. Nature
Communications. 2018;9(1):3891. 27. Pärnänen K, Karkman A, Hultman J, Lyra C, Bengtsson-Palme J, Larsson DJ, et al. Maternal gut and
breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements. Nature
Communications. 2018;9(1):3891. 28. Yassour M, Vatanen T, Siljander H, Hämäläinen A-M, Härkönen T, Ryhänen SJ, et al. Natural history of
the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and
stability. Sci Transl Med. 2016;8(343):343ra81-ra81. 28. Yassour M, Vatanen T, Siljander H, Hämäläinen A-M, Härkönen T, Ryhänen SJ, et al. Natural history of
the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and
stability. Sci Transl Med. 2016;8(343):343ra81-ra81. 29. World Health Organization. Antimicrobial resistance in the food chain. 2017. 29. World Health Organization. Antimicrobial resistance in the food chain. 2017. https://www.who.int/foodsafety/areas_work/antimicrobial-resistance/amrfoodchain/en/. Accessed
23 May 2019. https://www.who.int/foodsafety/areas_work/antimicrobial-resistance/amrfoodchain/en/. Accessed
23 May 2019. 30. Shankar N, Soe PM, Tam CC. Prevalence and risk of acquisition of Methicillin-resistant
Staphylococcus aureus among households: A Systematic Review. Int J Infect Dis. 2020 Jan 13. Table 3. Detected beta-lactamase genes. Tables Table 1. Baseline demographic and clinical characteristics of subjects. Table 1. Baseline demographic and clinical characteristics of subjects. Page 14/25 Page 14/25 Baseline Demographics
No. of subjects (n=75)
n (%)
Gender
Male
38 (50.7%)
Female
37 (49.3%)
Presence of siblings
46 (61.3%)
Mode of delivery
Caesarean
25 (33.3%)
Vaginal
50 (66.7%)
Gestational age
Term (≥37 weeks)
72 (96.0%)
Preterm
3 (4.0%)
Ethnicity
Chinese
42 (56%)
Malay
21 (28%)
Indian
12 (16%)
Household monthly income
0-$999
2 (2.8%)
$1000-$1999
9 (12.7%)
$2000-$3999
25 (35.2%)
$4000-$5999
13 (18.3%)
>$6000
22 (31%)
Maternal Tertiary Education
46 (61.3%)
Antibiotics during pregnancy and/or labour
35 (46.7%)
Class of antibiotics used during pregnancy and/ or labour
Beta-lactam
30 (40%)
Macrolide, beta-lactam
1 (1.3%)
Macrolide
3 (4.0%)
Lincosamide
1 (1.3%)
Postnatal antibiotics within first 12 months
16 (21.3%)
Childcare attendance in first year
7 (14%)
Pet ownership at 12months
3 (6%)
Smoking exposure in first year
1 (1.3%)
Maternal history of atopy
18 (24%)
Paternal history of atopy
20 (26.7%)
Eczema up to 18 months
35 (46.7%)
Rhinitis up to 18 months
21 (28.4%)
Wheeze with nebulizer use up to 18 months
5 (7%)
Allergen sensitization at 18 months
15 (23.1%)
Hospitalisation in the first year
5 (6.7%)
Illness diagnosed in the first year
38 (50 7%) Baseline Demographics Page 15/25 Table 2. Most commonly detected antibiotic resistance genes and associated antibiotic resistance phenotypes by time
point. Page 16/25 Antibiotic resistance profile and associated antibiotic resistance
genes
Timepoint
W3
(n=28)
No. (%)
M3
(n=41)
No. (%)
M6
(n=58)
No. (%)
M12
(n=61)
No. (%)
Fosfomycin
fosA
27
(96.43%)
34
(82.93%)
47
(81.03%)
37
(60.66%)
Beta-lactam
blaZ
27
(96.43%)
16
(39.02%)
12
(20.69%)
8 (13.11%)
Tetracycline
tet(M)
20
(71.43%)
26
(63.41%)
35
(60.34%)
38
(62.30%)
Macrolide
mef(A)
19
(67.86%)
31
(75.61%)
46
(79.31%)
57
(93.44%)
Quinolone
oqxB
19
(67.86%)
24
(58.54%)
23
(39.66%)
14
(22.95%)
Quinolone
msr(D)
18
(64.29%)
28
(68.29%)
47
(81.03%)
53
(86.89%)
Macrolide
erm(B)
17
(60.71%)
26
(63.41%)
48
(82.76%)
54
(88.52%)
Macrolide
lsa(A)
17
(60.71%)
32
(78.05%)
29 (50%)
5 (8.20%)
Tetracycline
tet(W)
15
(53.57%)
31
(75.61%)
51
(87.93%)
50
(81.97%)
Aminoglycoside
aac(6')-aph(2'')
15
(53.57%)
10
(24.39%)
21
(36.21%)
34
(55.74%)
The number and percentage of subjects with the antibiotic resistance genes are shown. he number and percentage of subjects with the antibiotic resistance genes are shown The number and percentage of subjects with the antibiotic resistance genes are shown. Table 5. Presence of extended spectrum beta-lactamase (ESBL) resistance genes in the first year of life. The number of subjects with beta lactam resistance genes detected in their stool samples at each time point are shown. Table 4. Presence of antibiotic resistance genes (ARGs) at time points during the first year of life. Tables Page 17/25 Page 17/25 Page 18/25 Beta-lactam resistance genes
W3
n=28
M3
n=41
M6
n=58
M12
n=61
Carbapenemases
CMY (Class C)
blaCMY-2
1
2
4
2
blaCMY-34
0
0
0
1
blaCMY-49
0
1
0
0
blaCMY-76
0
0
2
1
blaCMY-83
0
0
1
0
blaCMY-98
0
1
0
0
Extended spectrum beta-lactamases
CTX-M beta lactamases (Class A)
blaCTX-M-14
0
1
1
0
blaCTX-M-15
0
1
0
1
blaCTX-M-27
0
1
1
0
blaCTX-M-40
0
0
1
1
blaCTX-M-78
0
0
0
1
blaCTX-M-8
0
0
2
1
OXA beta-lactamases (class D)
blaOXA-1
0
0
1
2
blaOXA-10
0
1
0
0
blaOXA-116
1
0
0
0
blaOXA-120
0
0
1
0
blaOXA-184
0
0
0
1
blaOXA-347
2
9
11
14
blaOXA-85
1
0
1
0
SHV beta-lactamases (Class A)
blaSHV-1
9
9
7
3
blaSHV-108
0
0
1
0
blaSHV-11
5
8
7
4
blaSHV-142
1
0
0
0
blaSHV-26
1
0
0
0
blaSHV-27
0
0
0
4 blaSHV-63
0
0
0
1
blaSHV-75
0
0
1
0
blaSHV-83
1
2
0
0
blaSHV-85
0
0
0
1
blaSHV-93
0
1
1
0
TEM beta-lactamases (Class A)
blaTEM-176
1
1
1
2
blaTEM-1B
10
22
34
29
blaTEM-1C
0
0
0
3
blaTEM-1D
0
0
0
1 The number of subjects with beta lactam resistance genes detected in their stool samples at each time point are shown. a lactam resistance genes detected in their stool samples at each time point are shown Table 4. Presence of antibiotic resistance genes (ARGs) at time points during the first year of life. # subjects with stool samples at both week 3 and month 12 (N =22). # subjects with stool samples at both week 3 and month 12 (N =22). *subjects with stool samples at all timepoints (N= 8). *subjects with stool samples at all timepoints (N= 8). # subjects with stool samples at both week 3 and month 12 (N= 22) *subjects with stool samples at all timepoints (N= 8). . Extended spectrum beta-lactamase genes found in E. coli and Klebsiella pneumoniae # subjects with stool samples at both week 3 and month 12 (N= 22) Table 6. Extended spectrum beta-lactamase genes found in E. coli and Klebsiella pneumoniae. samples at both week 3 and month 12 (N= 22) Tables Page 20/25 Number of
subjects#
% of subjects with
ARG present at
time points
Number of subjects*
% of subjects
with ARG present
at time points
Antibiotic resistance
genotype
ARG
W3
W3
and
M12
W3 and M12
W3
W3
to
M3
W3
to
M6
W3
to
M12
W3
to
M3
W3
to
M6
W3
to
M12
Fosfomycin
fosA
21
11
52%
8
7
6
4
88%
75%
50%
Beta-lactam
blaZ
21
2
10%
7
1
1
0
14%
14%
0%
Aminoglycoside
aac(6')-
aph(2'')
11
5
45%
5
1
0
0
20%
0%
0%
Macrolide
lsa(A)
13
2
15%
5
5
3
1
100%
60%
20%
Quinolone
oqxB
14
4
29%
5
4
1
1
80%
20%
20%
Macrolide
erm(B)
13
11
85%
4
2
2
2
50%
50%
50%
Macrolide
erm(X)
6
5
83%
4
3
2
1
75%
50%
25%
Macrolide
mef(A)
15
15
100%
4
4
3
3
100%
75%
75%
Macrolide,
Lincosamide and
Streptogramin B
msr(D)
14
14
100%
4
4
2
2
100%
50%
50%
Tetracycline
tet(M)
15
11
73%
4
2
1
1
50%
25%
25%
Aminoglycoside
aph(3')-
III
7
5
71%
3
2
1
1
67%
33%
33%
Sulphonamide
sul2
8
4
50%
3
3
2
2
100%
67%
67%
Tetracycline
tet(O)
6
4
67%
3
3
3
2
100%
100%
67%
Tetracycline
tet(Q)
5
4
80%
3
3
3
3
100%
100%
100%
Tetracycline
tet(W)
11
10
91%
3
3
3
3
100%
100%
100%
Beta-lactam
blaTEM-
1b
9
6
67%
2
2
2
1
100%
100%
50%
Aminoglycoside
aadE
1
1
100%
1
1
0
0
100%
0%
0% Page 21/25 Number of
subjects#
Presence
Number of subjects*
Presence
Extended Spectrum Beta-
lactamases
W3
W3 and
M12
W3 and
M12
W3
W3 to
M3
W3 to
M6
W3 to
M12
W3 to
M3
W3 to
M6
W3 to
M12
blaTEM-1b
9
6
67%
2
2
2
1
100%
100%
50%
blaSHV-1
8
1
13%
2
0
0
0
0%
0%
0%
blaSHV-11
3
0
33%
1
1
0
0
100%
0%
0%
blaSHV-142
1
0
0%
1
0
0
0
0%
0%
0%
blaSHV-83
1
0
0%
1
0
0
0
0%
0%
0%
blaOXA-116
1
0
0%
1
0
0
0
0%
0%
0%
blaOXA-347
2
2
100%
1
1
1
1
100%
100%
100% # subjects with stool samples at both week 3 and month 12 (N= 22 Page 22/25 Page 22/25 Extended-Spectrum Beta-lactam resistance genes
Species
W3
M3
M6
M12
CMY (Class C)
blaCMY-2
Escherichia coli
1
1
1
0
CTX-M beta lactamases (Class A)
blaCTX-M15
Escherichia coli
0
1
0
0
SHV beta-lactamases (Class A)
blaSHV-1
Klebsiella pneumoniae
6
7
4
2
blaSHV-108
Klebsiella pneumoniae
0
0
1
0
blaSHV-11
Klebsiella pneumoniae
5
2
4
3
blaSHV-142
Klebsiella pneumoniae
1
0
0
0
blaSHV-26
Klebsiella pneumoniae
1
0
0
0
blaSHV-27
Klebsiella pneumoniae
0
0
0
2
blaSHV-38
Klebsiella pneumoniae
0
0
1
0
blaSHV-85
Klebsiella pneumoniae
0
0
0
1
blaSHV-93
Klebsiella pneumoniae
0
1
1
0
TEM beta-lactamases (Class A)
blaTEM-1b
Escherichia coli
0
0
1
0 Extended-Spectrum Beta-lactam resistance genes
Species W3
M3
M6
M12 Supplementary Data.DOCX Supplementary Data.DOCX Additional file contains the following supplementary figures and tables: Additional file contains the following supplementary figures and tables: Additional Table 1. Comparison of demographic variables between subjects included and excluded from
study. Additional Table 1. Comparison of demographic variables between subjects included and excluded from
study. Additional Figure 1. Antibiotic resistance genotypes over time. The percentage of subjects with the
antibiotic resistance genotype are presented over time. Additional Figure 1. Antibiotic resistance genotypes over time. The percentage of subjects with the
antibiotic resistance genotype are presented over time. Additional Table 2. Maternal antibiotic exposures during pregnancy. Additional Table 2. Maternal antibiotic exposures during pregnancy. Additional Table 3. Maternal antibiotic exposures during labour. Additional Table 3. Maternal antibiotic exposures during labour. Figures Page 23/25 Figure 1 Flow chart of subject selection Page 24/25 Page 24/25 Page 24/25 Figure 2 Figure 2 Figure 2 2a. Mean number of ARGs per infant over time. 2b Microbial diversity of stool samples over time as
determined by Simpsons Diversity Index Supplementary Files This is a list of supplementary files associated with this preprint. Click to download. This is a list of supplementary files associated with this preprint. Click to download. ARGpaperSupplementaryDataclean130220.docx Page 25/25
|
https://openalex.org/W2956100226
|
https://link.springer.com/content/pdf/10.1007/s00894-019-4075-7.pdf
|
English
| null |
The nature of the T=T double bond (T = B, Al, Ga, In) in dialumene and its derivatives: topological study of the electron localization function (ELF)
|
Journal of molecular modeling
| 2,019
|
cc-by
| 8,658
|
Journal of Molecular Modeling (2019) 25: 211
https://doi.org/10.1007/s00894-019-4075-7 Journal of Molecular Modeling (2019) 25: 211
https://doi.org/10.1007/s00894-019-4075-7 ORIGINAL PAPER Abstract The local electronic structure of the Al=Al bond was studied in dialumene and derivatives of dialumene in which the Al atoms
were substituted by B, Ga, or In atoms. DFT calculations were performed using the B3LYP, B3PW91, PBE0, M06-L, and M06-
2X functionals. Topological analysis of the electron localization function described the covalent bonds mentioned above using
the disynaptic basins Vi=1,2(B,B), Vi=1,2(Al,Al), V(Ga,Ga), and Vi=1,2(In,In). The basin populations were smaller than 4 e, as
expected for a double bond: B=B 2.97 e, Al=Al 3.44–3.5 e, Ga=Ga 3.58 e, and In=In 3.86 e. The Al=Al, Ga=Ga, and In=In bonds
were found to be intermediate in character between single and double bonds. Topological analysis of the ρ(r) field for dialumene
showed a non-nuclear attractor along the Al=Al bond, with a pseudoatom basin population of 0.937 e. NBO analysis suggested
that a double bond occurred only in the molecules containing Al, Ga, or In atoms. The character of the Ga=Ga bond was observed
to be strongly dependent on the effective core potential used in the calculations. Keywords Triels . Boron group . Dialumene . Electron density . Electron localization function . ELF The nature of the T=T double bond (T = B, Al, Ga, In) in dialumene
and its derivatives: topological study of the electron localization
function (ELF) Michal Michalski1 & Agnieszka J. Gordon1 & Slawomir Berski1 Received: 9 April 2019 /Accepted: 27 May 2019 /Published online: 4 July 2019
# The Author(s) 2019 1
Faculty of Chemistry, University of Wroclaw, 14 F. Joliot-Curie,
54-210 Wroclaw, Poland * Slawomir Berski
slawomir.berski@chem.uni.wroc.pl This paper belongs to the Topical Collection Zdzislaw Latajka 70th
Birthday Festschrift Introduction trigonal planar coordination. Dialumene has been reacted with
ethylene and phenyl acetylene in order to demonstrate the pres-
ence of an Al=Al double bond. The 1H NMR was used to show
that a [2 + 2] cycloaddition reaction took place, leading to the
formation of dialuminacyclobutane. Similarly, the reaction of
phenyl acetylene with dialumene in toluene proceeds via both
[2 + 2] cycloaddition and terminal C−H insertion. The most
interesting observation made during those experimental studies
was the unusual aluminum bond length. Single-crystal X-ray
analysis showed that the homoatomic aluminum bond was
2.394(16) Å in length, which is outside the typical range for
Al–Al single bonds [7]. Boron-containing compounds have fascinated researchers over
the years [1–4], but research into homoatomic multiply bonded
compounds has been fairly limited. There are several examples
of boron molecules with homoatomic multiple bonding. Wang
et al. [5] presented a neutral compound with the homoatomic
B=B double bond, R(H)B=B(H)R (R = :C{N(2,6-
iPr2C6H3)CH}2). A stable diborene at room temperature was
reported by Braunschweig et al. [6]. The first stable molecule to
be found to possess a formal double bond between aluminum
atoms (i.e., Al=Al), dialumene, was synthesized and character-
ized by Bag et al. [7] using X-ray crystallographic and 1H NMR
analysis (Scheme 1). This molecule possesses a trans-planar
geometry in the solid state. Each aluminum atom adopts a Among the most recently developed computational
methods for the electronic structure analysis of molecules
are the electron localization function (ELF), η(r), as pro-
posed by Becke and Edgecombe [8], and topological anal-
ysis of the ELF, as developed by Silvi and Savin [9]. A
high value of the ELF corresponds to high electron local-
ization. An ELF value of 0.5 corresponds to that of a
uniform electron gas. Topological analysis of the ELF
allows us to identify basins corresponding to attractors,
which are chemically significant. The average population
of an ELF basin is calculated by integrating the electron
density over that basin [10]. This paper belongs to the Topical Collection Zdzislaw Latajka 70th
Birthday Festschrift * Slawomir Berski
slawomir.berski@chem.uni.wroc.pl 211
Page 2 of 11 J Mol Model (2019) 25: 211 Scheme 1 Approximate Lewis formula for the dialumene molecule
(Me – methyl, iPr – isopropyl, tBu – tert-butyl) (keyword ‘stable’), and no instabilities were observed. All
molecules were investigated in the singlet electronic state,
using the closed-shell RHF formalism. Geometric structures The structure of the dialumene molecule, which formally con-
tains a double Al=Al bond, was optimized using density func-
tional theory employing the 6-311++G(d,p) basis set and five
exchange-correlation functionals: B3LYP, B3PW91, PBE0,
M06-L, and M06-2X. Dialumene derivatives in which the
Al atoms were substituted by B, Ga, and In atoms were opti-
mized at the DFT(M06-L)/6-311++G(d,p) level. Selected
bond lengths for all of the optimized compounds are presented
in Table 1. The geometric structure of dialumene following
optimization at the DFT(M06-L)/6-311++G(d,p) computa-
tional level is shown in Fig. 1. Introduction Topological analyses of η(r) and the electron density ρ(r)
were carried out using the Multiwfn [27] and TopMod 09 [28]
packages. When analyzing the Ga and In derivatives, extend-
ed wavefunction files were acquired using the ‘wfnx’ key-
word. Topological analyses of η(r) and ρ(r) were implemented
using a grid of points with a step size of 0.05 bohr. The total
population of two Vi=1,2(T,T) basins (T = B, Al, Ga, In) was
estimated as the sum of the V1(T,T) and V2(T,T) basin
populations. Graphical representations of optimized structures,
isosurfaces, and 2D ELF plots were prepared using the
Chimera [29] and Multiwfn programs. Scheme 1 Approximate Lewis formula for the dialumene molecule
(Me – methyl, iPr – isopropyl, tBu – tert-butyl) The Cambridge Structural Database (CSD; version 5.39,
November 2017 [30]) was used to analyze B–B and Al–Al
contacts. The work reported in the current paper focused on the local
nature of the homoatomic Al=Al bond in neutral dialumene. The electronic structures of similar homoatomic bonds (B=B,
Ga=Ga, and In=In) were also investigated in order to establish
general trends in the properties of interest. Electronic struc-
tures were studied by considering the topology of the ELF, the
electron density, natural bond orbital (NBO) theory [11], and
Wiberg bond indices (WBIs) [12]. Computational details The software Gaussian 09 (version E.01), G09 E.01 [13] was
used to obtain the optimized structure of dialumene by apply-
ing the exchange-correlation functionals B3LYP [14],
B3PW91 [15], PBE0 [16], M06-L, and M06-2X [17]. The
standard Pople basis set [18, 19] 6-311++G(d,p) was used as
implemented in G09. Molecules containing B, Ga, and In as
their central atoms were studied at the DFT(M06-L) level
using the 6-311++G(d,p) basis set for H, C, and N atoms. For gallium and indium derivatives, the LANL2DZ effective
core potential (ECP) [20] was applied with the equivalent
basis set. In order to examine the influence of the ECP type,
other ECPs – ECP10MDF for the Ga atom, ECP28MDF for
the In atom [21], and CRENBL for both metal atoms [22,
23] – were also used. Single-point energy calculations were
subsequently carried out using the optimized structures. The
LANL2DZ, ECP10MDF, ECP28MDF, and CRENBL ECPs
were obtained from the EMSL Basis Set Library using the
Basis Set Exchange software [24, 25]. Analysis of natural
bond orbitals was carried out for all optimized structures using
the Natural Bond Orbital (NBO 3.1) program in G09 [26]. All
optimized structures were verified by vibrational analysis,
which did not yield any imaginary frequencies. Additionally,
wavefunction stability was tested for each optimized structure To facilitate comparison, we have also obtained B–B and Al–
Al contact distances in crystal structures from CSD data, and the
distributions of these contact distances are presented in Fig. 2. In
the solid state, most of the B–B interactions occur at contact
distances of between 1.7 and 1.8 Å (~70%), while the Al–Al
interactions occur at contact distances of 2.6–2.8 Å (~65%). Optimized Al=Al bond lengths were between 2.389 Å (M06-
2X) and 2.441 Å (B3PW91) and were noticeably shorter than the
Al–Al contacts found in the CSD data (2.50–3.00 Å). The opti-
mized B=B, Ga=Ga, and In=In bond lengths were 1.628, 2.392,
and 2.757 Å, respectively. Thus, the B=B and Al=Al bonds in
the molecules were found to be shorter than the contact distances
of the most frequent triel interactions that occur in crystal struc-
tures. The reported B=B bond length is also much shorter than
the single B–B bond in the planar B2H4 molecule (1.752 Å) [31]. The Ga=Ga bond length is 0.007 Å shorter than the Al=Al bond. This could be an effect of the LANL2DZ effective core potential
used. Computational details Such a quantitative
Table 1
Optimized T=T, T–Si, and T–C bond lengths (in Å; T = B, Al, Ga, In) calculated using several DFT functionals and the 6-311++G(d,p) basis
set
Bond
B
Al
Ga
In
M06-L
B3LYP
B3PW91
PBE0
M06-L
M06-2X
M06-L
M06-L
T=T
1.628
2.435
2.441
2.431
2.399
2.389
2.392
2.757
T–Si
2.047
2.537
2.530
2.517
2.467
2.481
2.471
2.665
T–C
1.597
2.108
2.097
2.086
2.067
2.089
2.122
2.359 Computational details Page 3 of 11
211 J Mol Model (2019) 25: 211 Table 1
Optimized T=T, T–Si, and T–C bond lengths (in Å; T = B, Al, Ga, In) calculated using several DFT functionals and the 6-311++G(d,p) basis
set
Bond
B
Al
Ga
In
M06-L
B3LYP
B3PW91
PBE0
M06-L
M06-2X
M06-L
M06-L
T=T
1.628
2.435
2.441
2.431
2.399
2.389
2.392
2.757
T–Si
2.047
2.537
2.530
2.517
2.467
2.481
2.471
2.665
T–C
1.597
2.108
2.097
2.086
2.067
2.089
2.122
2.359 Analysis of the bonding
Classical insights into the nature of the T=T bonding in the
molecules of interest were obtained using the natural bond
orbital method. The NBOs were studied using all the of den-
sity functionals mentioned above and the 6-311++G(d,p) basis
set (see the “Computational details” section). The B, Ga, and
In derivatives were studied at the DFT(M06-L)/6-311++
G(d,p) level. The LANL2DZ effective core potential was ap-
plied to the Ga and In atoms. Electron occupancy values for the NBOs in dialumene and
its derivatives (T = B, Ga, In) are presented in Table 2. NBO
pairs were obtained for the T=T (T = Al, Ga, In) bonds, so
they exhibit double-bond character. The population of the
Al=Al σ bond is 1.89 e or 1.90 e, and this bond is formed
by the overlap of two sp1.23–1.26 natural hybrid orbitals. Occupancy of the π bond varies from 1.71 e to 1.77 e, and
the bond is formed by pure Al p orbitals (at all computational
levels). The double Ga=Ga bond is formed by the overlap of
the sp1.37 hybrids in the σ bond with pure p orbitals (95%) in
the π bond. In the In compound, the σ bond is formed by the
overlap of the sp1.53 orbitals of the In atoms, and 87% of the π
bond is contributed by the p orbital, a smaller proportion than
for the corresponding Ga=Ga bond. The most interesting re-
sults were obtained for the B–B bond. NBO analysis showed
that only σ bond was present, formed through the overlap of
sp1.30 and sp1.31 hybrids (43% s orbital and 57% p orbital). There was no indication of π bond. Analysis of the bonding 2 Histograms of the B–B (a) and Al–Al (b) contact distances for the molecules deposited in the Cambridge Stru difference in bonding nature between the formal B=B bond
and the NBO results for the T=T (T = Al, Ga, In) bonds should
be reflected in topological analyses of the η(r) and ρ(r) fields. Moving down the periodic table, the calculated Wiberg bond
indices (WBIs) ranged from 1.55 (B=B) to 1.45 (In=In). Thus,
there was no indication of a pure double bond; the bonds ap-
peared to be intermediate in character between single and double
bonds (see Table 2). The calculated WBI for the Al=Al bond
ranged between 1.60 (M06-L) and 1.66 (B3LYP and M06-2X). A slightly smaller value (1.55) was obtained for the B=B bond,
similar to that calculated for the Ga=Ga bond (1.57). Thus, the
B=B bond was similar in character to the Al=Al bond, but with
less double-bond character. It is worth emphasizing that the WBI
analysis did not point to any qualitative difference between B=B
and the other T=T (T = Al, Ga, In) bonds, in contrast to what was
found using the NBO method. basins in all of the molecules are presented, along with the
topological bond orders, in Table 3. difference in bonding nature between the formal B=B bond
and the NBO results for the T=T (T = Al, Ga, In) bonds should
be reflected in topological analyses of the η(r) and ρ(r) fields. The electronic structure of dialumene was found to be char-
acterized by 48 core and 138 valence attractors (local maxima
of the η(r) field). Similar numbers of attractors were obtained
for the dialumene derivatives with B, Ga, and In atoms. The
Al=Al bond is characterized by two bonding disynaptic
attractors with disynaptic basins V1(Al,Al) and V2(Al,Al), re-
spectively. The concept of basin synapticity has been ex-
plained by Silvi [32]. Each Vi=1,2(Al,Al) localization basin
has a surface in common with two C(Al) core basins. According to the interpretation proposed by Silvi and Savin
[33], shared-electron interactions such as covalent, dative, and
metallic bonds occur when there is at least one bond attractor
between the core attractors of the atoms involved in the bond. Thus, the localization of the Vi=1,2(Al,Al) attractors yields
proof that the Al–Al interaction is covalent, with shared electron
density. Analysis of the bonding Al=Al σ bond is 1.89 e or 1.90 e, and this bond is formed
by the overlap of two sp1.23–1.26 natural hybrid orbitals. Classical insights into the nature of the T=T bonding in the
molecules of interest were obtained using the natural bond
orbital method. The NBOs were studied using all the of den-
sity functionals mentioned above and the 6-311++G(d,p) basis
set (see the “Computational details” section). The B, Ga, and
In derivatives were studied at the DFT(M06-L)/6-311++
G(d,p) level. The LANL2DZ effective core potential was ap-
plied to the Ga and In atoms. Occupancy of the π bond varies from 1.71 e to 1.77 e, and
the bond is formed by pure Al p orbitals (at all computational
levels). The double Ga=Ga bond is formed by the overlap of
the sp1.37 hybrids in the σ bond with pure p orbitals (95%) in
the π bond. In the In compound, the σ bond is formed by the
overlap of the sp1.53 orbitals of the In atoms, and 87% of the π
bond is contributed by the p orbital, a smaller proportion than
for the corresponding Ga=Ga bond. The most interesting re-
sults were obtained for the B–B bond. NBO analysis showed
that only σ bond was present, formed through the overlap of
sp1.30 and sp1.31 hybrids (43% s orbital and 57% p orbital). There was no indication of π bond. Such a quantitative Electron occupancy values for the NBOs in dialumene and
its derivatives (T = B, Ga, In) are presented in Table 2. NBO
pairs were obtained for the T=T (T = Al, Ga, In) bonds, so
they exhibit double-bond character. The population of the Fig. 1 Optimized geometric
structure of dialumene following
optimization at the DFT(M06-L)/
6-311++G(d,p) computational
level (H atoms are omitted for
clarity) Fig. 1 Optimized geometric
structure of dialumene following
optimization at the DFT(M06-L)/
6-311++G(d,p) computational
level (H atoms are omitted for
clarity) J Mol Model (2019) 25: 211 211
Page 4 of 11 Fig. 2 Histograms of the B–B (a) and Al–Al (b) contact distances for the molecules deposited in the Cambridge Structural Database ms of the B–B (a) and Al–Al (b) contact distances for the molecules deposited in the Cambridge Structural Database Fig. For B=B V(B,C), otherwise V(C) J Mol Model (2019) 25: 211 Fig. 3 Graphical representation
of the ELF localization domains
(ELF = 0.795) for dialumene,
labeled with the positions of
valence attractors and basin
populations. Calculations were
carried out at the DFT(M06-L)/6-
311++G(d,p) computational
level. Valence domains for
hydrogens are omitted from the
graphic for the sake of clarity Fig. 3 Graphical representation
of the ELF localization domains
(ELF = 0.795) for dialumene,
labeled with the positions of
valence attractors and basin
populations. Calculations were
carried out at the DFT(M06-L)/6-
311++G(d,p) computational
level. Valence domains for
hydrogens are omitted from the
graphic for the sake of clarity Al–Si plane. Two attractors are observed, which may correspond
to two Al=Al bonds (σ, π). In a seminal paper on the electronic
structures of delocalized bonds, Savin et al. [10] showed two
Vi=1,2(C,C) attractors for ethylene localized in the C=C bonding
region. However, the localization of multiple bonding attractors
is not regarded as proof of multiple bonding [34]. The topology
of ELF in the region of the Al–Al interaction is indicative of a
local symmetry rather than a double bond. For the B=B and
In=In bonds, the local topology of ELF again includes two bond-
ing disynaptic attractors, Vi=1,2(T,T). The Ga=Ga bond is an ex-
ception, as it includes only a single bonding attractor, V(Ga,Ga). Thus, the B=B, Ga=Ga, and In=In bonds exhibit covalent char-
acter, as also observed for the Al=Al bond. topological approach partially supports the idea that this is a
double bond, bearing in mind that the formal value of 4 e for
such bond is idealized anyway. The basin population for the C=C
bond in ethylene, a prototypical molecule with a double bond, is
found to be 3.40 e at the DFT(M06-L)/6-311++G(d,p) compu-
tational level, suggesting that we should expect some similarity
between the Al=Al and C=C bonds. For the B=B, Ga=Ga, and
In=In bonds, as shown in Table 3, the total population of the
bond increases from 2.97 e (B) to 3.86 e (In). The value
of 3.58 e is concentrated in the single-valence bonding basin
V(Ga,Ga). It is worth emphasizing that, for the In–In interaction,
the bond character interpreted from the ELF is very close to the
formal character (i.e., a double bond). It is possible that more
polarizable atoms (Ga: 8.12 Å3, In: 9.1 Å3) [35] containing larger
numbers of diffuse atomic orbitals contribute more electron den-
sity to localization basins during the bond formation process. Analysis of the bonding Two bonding attractors Vi=1,2(Al,Al) are localized ap-
proximately perpendicular to the neighboring bonds and in the
regions with high electron localization. Pauli repulsion between
electron clouds from the Al=Al, Al–C, and Al–Si bonds in those
areas is bound to be smaller than that in the Al–C, Al=Al, and Moving down the periodic table, the calculated Wiberg bond
indices (WBIs) ranged from 1.55 (B=B) to 1.45 (In=In). Thus,
there was no indication of a pure double bond; the bonds ap-
peared to be intermediate in character between single and double
bonds (see Table 2). The calculated WBI for the Al=Al bond
ranged between 1.60 (M06-L) and 1.66 (B3LYP and M06-2X). A slightly smaller value (1.55) was obtained for the B=B bond,
similar to that calculated for the Ga=Ga bond (1.57). Thus, the
B=B bond was similar in character to the Al=Al bond, but with
less double-bond character. It is worth emphasizing that the WBI
analysis did not point to any qualitative difference between B=B
and the other T=T (T = Al, Ga, In) bonds, in contrast to what was
found using the NBO method. The next step in our investigation of the local electronic
structure of dialumene and its derivatives with B=B, Ga=Ga,
and In=In bonds was to perform topological analysis of the
ELF. Figure 3 illustrates the localization domains for the Al
compound; the positions of the valence attractors are marked. The mean electron populations, N, for the core and valence Table 2
Calculated electron occupancy values for the σ and π bonds for the T=T bonds in the dialumene molecule (T = Al) and its derivatives (T = B,
Ga, In), as well as Wiberg bond indices (WBI)
Parameter
B
Al
Ga
In
M06-L
B3LYP
B3PW91
PBE0
M06-L
M06-2X
M06-L
M06 L
σ bond
1.86
1.90
1.90
1.90
1.89
1.90
1.89
1.82
π bond
–
1.75
1.75
1.75
1.71
1.77
1.70
1.71
WBI
1.55
1.66
1.65
1.65
1.60
1.66
1.57
1.45
Calculations were carried out using DFT employing the B3LYP, B3PW91, PBE0, M06-L, and M06-2X electron density functionals and the 6-311++
G(d,p) basis set Calculations were carried out using DFT employing the B3LYP, B3PW91, PBE0, M06-L, and M06-2X electron den
G(d,p) basis set Page 5 of 11
211 J Mol Model (2019) 25: 211 The calculations for dialumene were performed using wavefunctions approximated with different DFT functionals and the 6-311++G(d,p) basis set.
Calculations for B=B, Ga=Ga, and In=In were performed at the DFT(M06-L)/6-311++G(d,p) computational level J Mol Model (2019) 25: 211 The C–Al bond is formally (i.e.,
in the Lewis structure presented in Scheme 1) a covalent da-
tive bond, where two electrons are donated to the Al valence
shell (C →Al). Our study was extended to examine the local
electronic structures of the T–C (T = B, Al, Ga, In) bonds in all
of the derivatives of dialumene. The BCP shows a high ρ(3,−1)(r) value for the B=B bond,
0.152 e/au3, and a low negative value for the Laplacian,
−0.308 e/au5. This indicates that the B=B bond is covalent
in character, in agreement with the NBO and ELF results. In
the dialumene molecule, two nuclear attractors (Al atoms) are
connected by two BCPs and one (3,−3) point that is not related
to the nuclear position and is called a non-nuclear attractor
(NNA). Similar NNAs were obtained for the M–M bond by
Li et al. [39] for (η5-C5H5)2M2 (M = Be, Mg, Ca) molecules. The basin associated with NNA is shown in Fig. 4. The pop-
ulation of the pseudoatom associated with NNA is 0.937 e. The electron densities of the two BCPs are smaller than that
for the NNA and range between 0.055 e/au3 (B3PW91) and
0.058 e/au3 (M06-2X). The negative value of ∇2ρ(3,−1)(r) is
near to zero and ranges between −0.027 e/au5 (B3LYP) and
−0.007 e/au5 (M06-L). For the Ga=Ga and In=In bonds, only
a single (3,−1) critical point was localized, similar to the B–B
bond. The values of ρ(3,−1)(r) for the Ga=Ga and In=In bonds
(0.063 e/au3 and 0.046 e/au3, respectively) are similar to that
for the Al=Al bond and are both much lower than the value
obtained for the B=B bond. The values of ∇2ρ(3,−1)(r) are very
small and positive, which suggests that the bonding character
changes upon shifting from B to In atoms. However, it is
worth remembering that those values were calculated using For the molecule in which the Al atoms are substituted by B
atoms, topological analysis of the η(r) function of the C–B bond
reveals a single disynaptic bonding attractor, V(B,C). Thus, the
bond has covalent character, with electron density shared by the
B and C atoms. Interestingly, different local ELF topologies are
observed for the molecules with Al=Al, Ga=Ga, and In=In
bonds. The C →Al bond is characterized by the monosynaptic
nonbonding attractor V(C) only; no disynaptic attractor V(T,C) is
present. J Mol Model (2019) 25: 211 In summary, analysis of atomic contributions to the V(C)
and V(B,C) basins shows that the binding between the triel
and C atoms is dominated by electron density from the
carbon atom, despite the different characteristics obtained
with the synapticity concept. Basins with larger populations correspond to more covalent
chemical bonds. The topological bond order, TBO (see Table 3), for the
B=B bond is 1.49. For Al=Al, the TBO value is not very
sensitive to the functional used: it ranges between 1.72 and
1.77. The TBO for B=B is 1.49 (M06-L), which is 0.23 small-
er than that calculated for Al=Al (M06-L), suggesting rather
different bond character. The TBOs for Ga=Ga and In=In are
similar to that for Al=Al (1.79 and 1.73, respectively). Thus,
the TBOs confirm the double-bond character of the Al=Al,
Ga=Ga, and In=In interactions. The B=B bond is different;
based on the topological analysis of ELF, it should not be
formally categorized as a double bond. The standard deviation, σ, obtained for a localization basin
can be interpreted as a measure of the electron delocalization
[36]. The values of σ for the T=T bonding basins are presented
in Table 3. The Vi=1,2(B,B), Vi=1,2(Al,Al), and Vi=1,2(In,In) ba-
sins yield values of between 0.85 and 1. The V(Ga,Ga) basin
yields a significantly larger σ value, 1.18. This might be due to
the fact that the Ga=Ga bond is described only by a single basin,
V(Ga,Ga). Since these σ values are smaller than those for the N,
the electron density is well localized in the T=T bonding region. This feature is typical of standard covalent bonds, i.e., those
with basin populations much larger than 1 e. To gain further insight into the nature of the T=T bonds,
topological analysis of the ρ(r) field developed by Bader [38]
was carried out. The values calculated for the (3,−1) bond
critical points (BCPs) of the T=T bonds, i.e., ρ(3,−1)(r), and
the Laplacian of the electron density, ∇2ρ(3,−1)(r), are collected
in Table 5. As described by Bag et al. [7], the double Al=Al bond in
dialumene is bound to two stabilizing substituents at each
end – the silyl group (tBu2MeSi) and N-heterocyclic carbene
((CH3)2C3N2(iPr)2). We therefore decided that it was worth
investigating the nature of the C–Al and Si–Al bonds from an
ELF topological perspective. J Mol Model (2019) 25: 211 The total basin population for the Al=Al bond (see the
“Computational details” section) varies from 3.44 e to 3.50 e,
depending on the DFT functional used (see Table 3). Thus, the Table 3
Basin population values, N (e), standard deviations of N (σ), and topological bond orders (TBOs) for the T=T bonds in the dialumene
molecule (T = Al) and its derivatives (T = B, Ga, In)
Parameter
B
Al
Ga
In
M06-L
B3LYP
B3PW91
PBE0
M06-L
M06-2X
M06-L
M06-L
V1(T,T)
1.60
1.75
1.74
1.74
1.72
1.77
3.58
1.92
V2(T,T)
1.37
1.75
1.75
1.74
1.72
1.77
1.94
V(T,Si)
2.20
2.12
2.13
2.13
2.14
2.12
2.15
2.06
V(T,C)a
2.64
2.61
2.62
2.60
2.67
2.59
2.60
2.58
σ
0.97
0.93
0.98
0.98
0.99
0.99
0.98
0.99
0.98
0.99
0.85
0.85
1.18
1.00
1.00
TBO
1.49
1.75
1.75
1.74
1.72
1.77
1.79
1.73
The calculations for dialumene were performed using wavefunctions approximated with different DFT functionals and the 6-311++G(d,p) basis set. Calculations for B=B, Ga=Ga, and In=In were performed at the DFT(M06-L)/6-311++G(d,p) computational level
a For B=B V(B C) otherwise V(C) 211
Page 6 of 11 J Mol Model (2019) 25: 211 211
Page 6 of 11 in Table 4. The contribution of the boron atom to the
V(B,C) basin of the B–C bond is 0.21 e (~8%) smaller than
that of the C atom, 2.42 e (~92%). The covalent B–C bond
is polarized towards the C atom, and the polarity index pCB
is 0.84. The value of the polarity index ranges between 0
for homopolar bonds and 1 for idealized ionic bonds. The
bond has high covalent and polarized character. Analysis
of the molecules containing Al, Ga, and In atoms shows
that the contribution of the metal to the V(C) basin, 0.11 e,
is smaller than that found for the B-substituted derivative,
0.21, and the participation of the C atom is greater: 2.47–
2.54 e (4%) for Al, 2.46 e (4%) for Ga, and 2.44 e (4%) for
In. Such a result confirms that V(C) is a monosynaptic
basin, since the atomic contribution, 4%, is very
small – approximately half that calculated for the covalent
B–C bond. Nevertheless, to the best of our knowledge,
there is no study in which the atomic contribution is cor-
related with topological characteristics such as synapticity. J Mol Model (2019) 25: 211 Therefore, from an electron density perspective, the covalent
character of the homoatomic T=T bond in the compound di-
minishes due to decreasing electron density and an increasing
Laplacian as the atomic size of T increases. Since the results for the Ga and In derivatives were obtain-
ed with the effective core potential (ECP) approximation, the
qualitative influence of the type of ECP applied on the NBO,
η(r), and ρ(r) results should be considered. Hence, the calcu-
lations were repeated using three additional
ECPs – ECP10MDF, ECP28MDF, and CRENBL – and se-
lected results of the calculations are presented in Table 7. The
populations of the atomic cores of Ga and In were found to be
9.50 e, 9.94 e (CRENBL) and 17.79 e, 17.88 e (ECP10MDF,
ECP28MDF), respectively. p
The delocalization index, DI, is a quantitative measure
of the number of electron pairs that are delocalized be-
tween two atomic basins. It is often considered to be equiv-
alent to the topological bond order [40]. DI values for the
molecules of interest are presented in Table 6. For the B=B,
Ga=Ga, and In=In bonds, the index gradually decreases
from 1.230 to 1.055 to 0.916, respectively. Those values
suggest the presence of a single bond rather than a typical
double bond. Similar calculations performed for the C2H4
molecule at the DFT(M06-L)/6-311++G(d,p) computation-
al level yield a DI of 1.894. For the Al=Al bond with a
NNA localized on the bond, we cannot interpret the DI as
simply being equivalent to the topological bond order. All
possible values for delocalization between the pseudoatom
and the atomic basins are presented in Table 6. The number
of electron pairs exchanged between the atomic basin of Al The NBO populations of the Ga=Ga and In=In σ bonds
were found to be 1.85 e and 1.76 e, respectively, using the
ECP10MDF/ECP28MDF and CRENBL approximations. A
small decrease in electron occupancy is apparent when those
values are compared with those calculated for the σ bonds
using LANL2DZ (1.89 e and 1.82 e). J Mol Model (2019) 25: 211 Thus, based on Silvi and Savin’s interpretation [33], the
C →Al bonds are not classically covalent bonds with a shared
electron density. Those bonds are more of the donor–acceptor
type, where electron density of the carbon atom is donated to the
valence shell of the heavier triel atom (Al, Ga, or In). The results
support Bag et al. interpretation of the dative character of the C–
Al bond [7]. Analysis of atomic contributions to the localization ba-
sins proposed by Raub and Jansen [37] partially confirms
this interpretation. Atomic contribution results are shown Page 7 of 11
211 J Mol Model (2019) 25: 211 Table 4
Atomic contributions (in e) to the V(T,C) and V(C) localization basins in dialumene and its derivatives, T = (B, Al, Ga, In)
Parameter
B
Al
Ga
In
M06-L
B3LYP
B3PW91
PBE0
M06-L
M06-2X
M06-L
M06-L
N [T|V(C)]
–
0.11
0.11
0.11
0.11
0.11
0.11
0.11
N [C|V(C)|
–
2.47
2.48
2.46
2.54
2.46
2.46
2.44
N [T|V(T,C)]
0.21
–
–
–
–
–
–
–
N [C|V(T,C)]
2.42
–
–
–
–
–
–
–
Calculations were performed using wavefunctions approximated by the DFT method employing various electron density functionals and the 6-311++
G(d,p) basis set Calculations were performed using wavefunctions approximated by the DFT method employing various electron den
G(d,p) basis set Calculations were performed using wavefunctions approximated by the DFT method employing various electron density functionals and the 6-311++
G(d,p) basis set the ECPs for Ga and In. The sign of ∇2ρ(3,−1)(r) suggests that
electron density is concentrated around the BCP of B=B and
Al=Al and is depleted in the Ga=Ga and In=In bonds. the ECPs for Ga and In. The sign of ∇2ρ(3,−1)(r) suggests that
electron density is concentrated around the BCP of B=B and
Al=Al and is depleted in the Ga=Ga and In=In bonds. Therefore, from an electron density perspective, the covalent
character of the homoatomic T=T bond in the compound di-
minishes due to decreasing electron density and an increasing
Laplacian as the atomic size of T increases. and the pseudoatom ranges between 0.451 (B3LYP) and
0.474 (PBE0) depending on the level of theory applied. Less electron density is involved in the delocalization be-
tween the two atomic basins of Al; the value of DI ranges
between 0.467 (M06-L) and 0.588 (B3LYP). J Mol Model (2019) 25: 211 4 Basin of the non-nuclear attractor (NNA) of the Al=Al bond in
dialumene. Calculations were carried out at the DFT(M06-L)/6-311++
G(d,p) computational level Total populations for the Vi=1,2(Ga,Ga) basins (Table 7) are
especially dependent on the pseudopotential applied; the
values are 3.74 e using ECP10MDF and 4.47 e using
CRENBL, which are higher than that obtained using
LANL2DZ (3.58 e). Higher values were also obtained using
ECP28MDF and CRENBL for the Vi=1,2(In,In) basins: 3.97 e
and 3.85 e, respectively. However, these results are rather
similar. The standard deviations of the basin populations are
close to those calculated using LANL2DZ (see Table 3). Thus,
the effect of the ECP used on the ELF does not contradict the
conclusions of our analysis performed using the LANL2DZ
pseudopotential for the Ga and In atoms. Although the total
basin populations for Vi=1,2(Ga,Ga) and Vi=1,2(In,In) differ
from those calculated at the LANL2DZ level, the Ga=Ga
and In=In bonds are still found to have double-bond character. respectively. For the In derivative, the populations of the π
bond were found to be 1.68 e and 1.69 e, respectively, using
the ECP28MDF and CRENBL approximations. Analysis of
the WBIs for the Ga and In derivatives revealed smaller values
than those obtained using LANL2DZ. Thus, the influence of
the ECP type on the NBO results is insignificant, and the
results obtained with the LANL2DZ pseudopotential seem
to be reliable. The type of approximation used for the effective core
potential has a significant influence on the results obtained
for the topology of the ELF. The following discussion will
concentrate on the T=T (T = Ga, In) molecular fragment. 2D
ELF maps for the Ga atoms that were calculated using the
CRENBL and ECP10MDF pseudopotentials are shown in
Fig. 5b and c. J Mol Model (2019) 25: 211 Lower values were also
obtained using the ECP10MDF and CRENBL approxima-
tions for the π bond of the Ga derivative: 1.69 e and 1.70 e, Table 5
Calculated values for the bond critical points (BCPs) of the T=T (T = B, Al, Ga, In) bonds in the dialumene molecule (T = Al) and its
derivatives (T = B, Ga, In)
Parameter
B
Al
Ga
In
M06-L
B3LYP
B3PW91
PBE0
M06-L
M06-2X
M06-L
M06-L
ρ(3,−1)(r) (e/au3)
0.152b
0.058a
0.057b
0.057b
0.056a
0.055b
0.055b
0.057a
0.056b
0.056b
0.058a
0.057b
0.057b
0.059a
0.058b
0.058b
0.063b
0.046b
∇2ρ(3,-1)(r) (e/au5)
−0.308b
−0.080a
−0.027b
−0.027b
−0.075a
−0.022b
−0.022b
−0.077a
−0.017b
−0.017b
−0.081a
−0.007b
−0.007b
−0.084a
−0.019b
−0.019b
0.003b
0.040b
Calculations were performed using DFT employing several electron density functionals and the 6-311++G(d,p) basis set
Here, ρ(3,−1)(r) is the electron density at the BCP and ∇2 ρ(3,−1)(r) is the Laplacian of the electron density at the BCP
a NNA (non-nuclear attractor)
b BCP (bond critical point) J Mol Model (2019) 25: 211 211
Page 8 of 11 Fig. 4 Basin of the non-nuclear attractor (NNA) of the Al=Al bond in
dialumene. Calculations were carried out at the DFT(M06-L)/6-311++
G(d,p) computational level ELF topology for the Ga=Ga bond. Instead of the single
V(Ga,Ga) attractor obtained using the LANL2DZ ECP (see
Fig. 5a), two Vi=1,2(Ga,Ga) bonding attractors are found
using CRENBL and ECP10MDF. The value of the ELF also
depends on the ECP used, and it decreases for the
Vi=1,2(Ga,Ga) and Vi=1,2(In,In) attractors in the order 0.939
(LANL2DZ) > 0.911 (CRENBL) > 0.841 (ECP10MDF) and
0.968 (LANL2DZ) > 0.878 (CRENBL) > 0.865
(ECP28MDF), respectively. Detailed analysis of the ELF
distributions obtained with ECP10MDF, ECP28MDF, and
CRENBL showed that the (3,+1) CP along the imaginary
line joining the Ga nuclei has an ELF value of 0.528
(CRENBL) or 0.645 (ECP10MDF). Similar analysis per-
formed for the In=In bond also showed that the (3,+1) CP
had an ELF value of 0.445 (CRENBL) or 0.405
(ECP10MDF) – slightly smaller than the ELF values for
the Vi=1,2(In,In) attractors. Analysis of the ELF field using
the LANL2DZ pseudopotential revealed that the (3,−1) CP
situated along the imaginary line joining the nuclei had an
ELF value of 0.528 (Ga) or 0.645 (In). In both cases, the
values obtained reveal that calculations performed on cores
with fewer electrons treated explicitly yield reduced electron
localization in the T=T bonding region. Fig. J Mol Model (2019) 25: 211 The effect of the approximation adopted for
the core regions can be observed as changes to the local The effect of the choice of ECP on the topology of the ρ(r)
field was also been studied in relation to the ρ(3,−1)(r) and Table 6
Delocalization indices (DI) for T=T bonds (T = B, Al, Ga, In) and T–NNA interactions
Bond/interaction
B
Al
Ga
In
M06-L
B3LYP
B3PW91
PBE0
M06-L
M06-2X
M06-L
M06-L
T=T
1.23
0.588
0.553
0.519
0.467
0.531
1.055
0.916
T–NNA
–
0.451
0.462
0.474
0.473
0.452
–
–
NNA–T
–
0.451
0.462
0.474
0.473
0.452
–
–
Calculations were performed using wavefunctions approximated with DFT employing various electron density functionals and the 6-311++G(d,p) basis
set. Calculations for the B, Ga, and In derivatives were performed at the DFT(M06-L)/6-311++G(d,p) computational level
NNA non-nuclear attractor Table 6
Delocalization indices (DI) for T=T bonds (T = B, Al, Ga, In) and T–NNA interactions Calculations were performed using wavefunctions approximated with DFT employing various electron density functionals and the 6-311++G(d,p) basis
set. J Mol Model (2019) 25: 211 The value
of ∇2ρ(3,−1)(r) given by ECP28MDF or CRENBL was smaller
(by 0.007 or 0.013 e/au5, respectively) than that given by
LANL2DZ. J Mol Model (2019) 25: 211 Calculations for the B, Ga, and In derivatives were performed at the DFT(M06-L)/6-311++G(d,p) computational level Page 9 of 11
211 J Mol Model (2019) 25: 211 Table 7
Electron occupancies for the σ and π bonds, Wiberg bond indices (WBIs), basin populations, N (e) values for the T=T (T = Ga, In) bonding
basins, their standard deviations (σ), and ρ(3,−1)(r) and ∇2ρ(3,−1)(r) values for (3,−1) critical points of the T=T bonds
Parameter
ECP
Ga (ECP10MDF)
Ga (CRENBL)
In (ECP28MDF)
In (CRENBL)
Natural bond orbital
σ bond
1.85
1.85
1.76
1.76
π bond
1.70
1.69
1.69
1.68
WBI
1.52
1.54
1.35
1.37
Electron localization function
V1(T,T)
1.87
2.23
1.99
1.93
V2(T,T)
1.87
2.24
1.98
1.92
σ
1.11
1.11
1.22
1.22
1.16
1.16
1.13
1.13
Electron density
ρ(3,−1)(r) (e/au3)
0.065
0.058
0.047
0.045
∇2ρ(3,−1)(r) (e/au5)
−0.011
0.036
0.033
0.027
Calculations were performed with ECP10MDF or CRENBL for Ga-substituted dialumene and ECP28MDF or CRENBL for the In-substituted
dialumene along with the 6-311++G(d,p) basis set Table 7
Electron occupancies for the σ and π bonds, Wiberg bond indices (WBIs), basin populations, N (e) values for the T=T (T = Ga, In) bonding
basins, their standard deviations (σ), and ρ(3,−1)(r) and ∇2ρ(3,−1)(r) values for (3,−1) critical points of the T=T bonds Calculations were performed with ECP10MDF or CRENBL for Ga-substituted dialumene and ECP28MDF or CRENBL for the In-substituted
dialumene along with the 6-311++G(d,p) basis set ∇2ρ(3,−1)(r) values calculated for the Ga=Ga and In=In bonds. No significant influence of the particular ECP chosen was
observed for the ρ(3,−1)(r) values of either bond, since similar
values were obtained regardless of the ECP applied: 0.058–
0.065 e/au3 (Ga=Ga) and 0.045–0.047 e/au3 (In=In). A more
significant effect on the ∇2ρ(3,−1)(r) values was noted, as using
ECP10MDF resulted in a value with a different sign (−0.011
e/au5) for the Ga-containing molecule. The Laplacian for the
Ga=Ga BCP was smaller when calculated with the smallest
ECP core (ECP10MDF) than with LANL2DZ. When more of
the core electrons are replaced by pseudopotentials (i.e., when
CRENBL is used), a higher ∇2ρ(3,−1)(r) value is obtained. Thus, the character of the Ga=Ga bond is uncertain at this
level of calculation. Analysis of the data obtained for the In-
containing molecule showed that a positive value of
∇2ρ(3,−1)(r) was obtained in all cases, so the ECP type did not have a significant impact on the ρ(r) topology. Conclusions Braunschweig H, Dewhurst RD, Hammond K, Mies J, Radacki K,
Vargas A (2012) Ambient-temperature isolation of a compound
with a boron–boron triple bond. Science 336:1420–1422 7. Bag P, Porzelt A, Altmann PJ, Inoue S (2017) A stable neutral
compound with an aluminum–aluminum double bond. J Am
Chem Soc 139:14384–14387 8. Becke AD, Edgecombe KE (1990) A simple measure of electron
localization in atomic and molecular systems. J Chem Phys 92:
5397–5403 9. Savin A, Becke AD, Flad J, Nesper R, Preuss H, Schnering HG
(1991) A new look at electron localization. Angew Chem Int Ed
Eng 30:409–412 10. Savin A, Silvi B, Colonna F (1996) Topological analysis of the
electron localization function applied to delocalized bonds. Can J
Chem 74:1088–1096 Topological analysis of the ρ(r) field showed a single bond
critical point at the midpoints of the B–B, Ga=Ga, and In=In
bonds and a non-nuclear attractor along the Al=Al bond. The
population of the pseudoatom associated with the NNA was
calculated as 0.937 e. The ρ(3,−1)(r) values for the Al=Al,
Ga=Ga, and In=In bonds were found to be smaller than that
for the B–B bond. The delocalization indices for the B=B,
Ga=Ga, and In=In bonds gradually decreased from 1.230 to
1.055 to 0.916, respectively, suggesting the presence of a sin-
gle bond rather than a typical double bond. 11. Reed AE, Curtiss LA, Weinhold F (1988) Intermolecular interac-
tions from a natural bond orbital, donor–acceptor viewpoint. Chem
Rev 88:899–926 12. Wiberg KB (1966) Application of the Pople–Santry–Segal CNDO
method to the cyclopropylcarbinyl and cyclobutyl cation and to
bicyclobutane. Tetrahedron 24:1083–1096 13. Conclusions J Am Chem Soc 129:12412–12413 (
,
,
)
Analysis of the topology of the ELF showed that all of the
T=T (T = B, Al, Ga, In) bonds were represented by bonding
disynaptic attractors, Vi=1,2(T,T). Thus, they have covalent
character, with shared electron density. The B=B bond, with
a population of 2.98 e, appears to be intermediate between a
single and double bond, and its population is clearly smaller
than those of the other T=T bonds: 3.44 e (Al), 3.58 e (Ga),
and 3.86 e (In), which clearly have strong double-bond char-
acter. The largest population was obtained for the In=In bond. Thus, the results from the topological analysis of the ELF
support the conclusions of the NBO analysis. Both methods
yield results that highlight the differences in electronic struc-
ture between the bonds formed by the B, Al, Ga, and In atoms. Topological analysis of the ρ(r) field showed a single bond
critical point at the midpoints of the B–B, Ga=Ga, and In=In
bonds and a non-nuclear attractor along the Al=Al bond. The
population of the pseudoatom associated with the NNA was
calculated as 0.937 e. The ρ(3,−1)(r) values for the Al=Al,
Ga=Ga, and In=In bonds were found to be smaller than that
for the B–B bond. The delocalization indices for the B=B,
Ga=Ga, and In=In bonds gradually decreased from 1.230 to
1.055 to 0.916, respectively, suggesting the presence of a sin-
gle bond rather than a typical double bond. Analysis of the topology of the ELF showed that all of the
T=T (T = B, Al, Ga, In) bonds were represented by bonding
disynaptic attractors, Vi=1,2(T,T). Thus, they have covalent
character, with shared electron density. The B=B bond, with
a population of 2.98 e, appears to be intermediate between a
single and double bond, and its population is clearly smaller
than those of the other T=T bonds: 3.44 e (Al), 3.58 e (Ga),
and 3.86 e (In), which clearly have strong double-bond char-
acter. The largest population was obtained for the In=In bond. Thus, the results from the topological analysis of the ELF
support the conclusions of the NBO analysis. Both methods
yield results that highlight the differences in electronic struc-
ture between the bonds formed by the B, Al, Ga, and In atoms. 6. Conclusions Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA,
Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson
GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF,
Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K,
Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O,
Nakai H, Vreven T, Montgomery Jr JA, Peralta JE, Ogliaro F,
Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN,
Keith T, Kobayashi R, Normand J, Raghavachari K, Rendell A,
Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM,
Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J,
Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R,
Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski
VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD,
Farkas O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2013)
GAUSSIAN 09, revision E.01. Gaussian, Inc., Wallingford uda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O Nakai H, Vreven T, Montgomery Jr JA, Peralta JE, Ogliaro F, earpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov V Acknowledgements The authors thank the Wroclaw Centre for
Networking and Supercomputing for their generous allocation of com-
puter time. Keith T, Kobayashi R, Normand J, Raghavachari K, Rendell A, urant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam J Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, omperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi Compliance with ethical standards Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski Conflict of interests
The authors declare no conflict of interest with
regard to the publication of this article. 14. 14. Becke AD (1993) Density-functional thermochemistry. III. The role
of exact exchange. J Chem Phys 98:5648–5652 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 appro-
priate credit to the original author(s) and the source, provide a link to the
Creative Commons license, and indicate if changes were made. 15. Becke AD (1988) Density-functional exchange-energy approxima-
tion with correct asymptotic behavior. Phys Rev A 38:3098–3100 16. Adamo C, Barone V (1999) Toward reliable density functional
methods without adjustable parameters: the PBE0 model. J Chem
Phys 110:6158–6170 17. Zhao Y, Truhlar DG (2008) The M06 suite of density functionals
for main group thermochemistry, thermochemical kinetics,
noncovalent interactions, excited states, and transition elements:
two new functionals and systematic testing of four M06-class func-
tionals and 12 other functionals. Theor Chem Accounts 120:215–
241 1.
Olah GA (1965) Friedel–Crafts and related reactions. Interscience,
New York Conclusions Application of the NBO method to and topological analyses of
the η(r) and ρ(r) fields for the newly synthesized metalorganic
dialumene and its derivatives enabled precise characterization
of the local electronic structures of the T=T and T–C bonds
(T = B, Al, Ga, In). We have shown that, in some respects, the
molecular orbital theory approach and real functions yield
complementary insights. Furthermore, the results highlight
considerable differences between the local electronic structure Fig. 5 2D ELF plots for the Ga derivative, as calculated at the DFT(M06-L)/6-311++G(d,p) + ECP computational level, where the ECP is LANL2DZ
(a), CRENBL (b), or ECP10MDF (c). The Ga=Ga bond is in the plane of the plot Fig. 5 2D ELF plots for the Ga derivative, as calculated at the DFT(M06-L)/6-311++G(d,p) + ECP computational level, where the ECP is LANL2DZ
(a), CRENBL (b), or ECP10MDF (c). The Ga=Ga bond is in the plane of the plot 211
Page 10 of 11 J Mol Model (2019) 25: 211 2. Chu T, Korobkov I, Nikonov GI (2014) Oxidative addition of σ
bonds to an Al(I) center. J Am Chem Soc 136:9195–9202 of the nonmetal boron atoms and the local electronic struc-
tures of other metal atoms (Al, Ga, In) in these molecules. 3. Woodward S, Dagorne S (2013) Preface. In: Modern
organoaluminum reagents: preparation, structure, reactivity and
use. Springer, Berlin NBO analysis revealed that the Al=Al, Ga=Ga, and In=In
interactions each included both σ and π bonds, indicating that
they all have double-bond character. However, the B–B inter-
action was characterized as including only σ bond. The WBIs
for these bonds, which ranged from 1.55 (B=B) to 1.45
(In=In), did not point to any qualitative difference between
B–B and other T=T (T = Al, Ga, In) bonds. 4. Holzmann N, Stasch A, Jones C, Frenking G (2011) Structures and
stabilities of group 13 adducts [(NHC)(EX3)] and [(NHC)2(E2Xn)]
(E = B to In; X = H, Cl; n = 4, 2, 0; NHC = N-heterocyclic carbene)
and the search for hydrogen storage systems: a theoretical study. Chem: Eur J 17:13517–13525 5. Wang Y, Quillian B, Wei P, Wannere CS, Xie Y, King RB, Schaefer
HF, Schleyer PR, Robinson GH (2007) A stable neutral diborene
containing a BB double bond. References 18. Krishnan R, Binkley JS, Seeger R, Pople JA (1980) Self-consistent
molecular orbital methods. XX. A basis set for correlated
wavefunctions. J Chem Phys 72:650–654 1. Olah GA (1965) Friedel–Crafts and related reactions. Interscience,
New York J Mol Model (2019) 25: 211 Page 11 of 11
211 Cambridge Structural Database and visualizing crystal structures. Acta Crystallogr Sect B 58:389–397 19. Frisch MJ, Pople JA, Binkley JS (1984) Self-consistent molecular
orbital methods 25. Supplementary functions for Gaussian basis
sets. J Chem Phys 80:3265–3269 31. Szabó A, Kovács A, Frenking G (2005) Theoretical studies of in-
organic compounds. 341) energy decomposition analysis of E–E
bonding in planar and perpendicular X2E−EX2 (E = B, Al, Ga, In,
Tl; X = H, F, Cl, Br, I). Z Anorg Allg Chem 631:1803–1809 20. Hay PJ, Wadt WR (1985) Ab initio effective core potentials for
molecular calculations. Potentials for the transition metal atoms
Sc to Hg. J Chem Phys 82:270–283 21. Peterson KA (2003) Systematically convergent basis sets with rel-
ativistic pseudopotentials. I. Correlation consistent basis sets for the
post-d group 13–15 elements. J Chem Phys 119:11099–11112 32. Silvi B (2002) The synaptic order: a key concept to understand
multicenter bonding. J Mol Struct 614:3–10 33. Silvi B, Savin A (1994) Classification of chemical bonds based on
topological analysis of electron localization functions. Nature 371:
683–686 22. Hurley MM, Pacios LF, Christiansen PA, Ross RB, Ermler WC
(1986) Ab initio relativistic effective potentials with spin-orbit op-
erators. II. K through Kr. J Chem Phys 84:6840–6853 34. Silvi B, Fourré I, Alikhani ME (2005) The topological analysis of
the electron localization function. A key for a position space repre-
sentation of chemical bonds. Monatsh Chem 136:855–879 23. LaJohn LA, Christiansen PA, Ross RB, Atashroo T, Ermler WC
(1987) Ab initio relativistic effective potentials with spin–orbit op-
erators. III. Rb through Xe. J Chem Phys 87:2812–2824 35. Nagle JK (1990) Atomic polarizability and electronegativity. J Am
Chem Soc 112:4741–4747 24. Schuchardt KL, Didier BT, Elsethagen T, Sun L, Gurumoorthi V,
Chase J, Li J, Windus TL (2007) Basis set exchange: a community
database for computational sciences. J Chem Inf Model 47:1045–
1052 36. Silvi B (2004) How topological partitions of the electron distribu-
tions reveal delocalization. Phys Chem Chem Phys 6:256–260 37. Raub S, Jansen G (2001) A quantitative measure of bond polarity
from the electron localization function and the theory of atoms in
molecules. References Theor Chem Accounts 106:223–232 25. Feller D (1996) The role of databases in support of computational
chemistry calculations. J Comput Chem 17:1571–1586 26. Glendening ED, Reed AE, Carpenter JE, Weinhold F (1998) NBO
version 3.1. TCI, University of Wisconsin, Madison 38. Bader RFW (1990) Atoms in molecules: a quantum theory. Oxford
University Press, Oxford 27. Lu T, Chen F (2011) Multiwfn: a multifunctional wavefunction
analyzer. J Comput Chem 33:580–592 39. Li X, Huo S, Zeng Y, Sun Z, Zheng S (2013) Metal–metal and
metal–ligand bonds in (η5-C5H5)2M2 (M = Be, Mg, Ca, Ni, Cu,
Zn). Organometallics 32:1060–1066 28. Noury S, Krokidis X, Fuster F, Silvi B (1999) Computational tools
for the electron localization function topological analysis. Comput
Chem 23:597–604 40. Fradera X, Austen MA, Bader RFW (1999) The Lewis model and
beyond. J Phys Chem A 103:304–314 29. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM,
Meng EC, Ferrin TE (2004) UCSF Chimera—a visualization sys-
tem for exploratory research and analysis. J Comput Chem 25:
1605–1612 Publisher’s note Springer Nature remains neutral with regard to
jurisdictional claims in published maps and institutional affiliations. 30. Bruno IJ, Cole JC, Edgington PR, Kessler M, Macrae C, McCabe P,
Pearson J, Taylor R (2008) New software for searching the
|
https://openalex.org/W4285790025
|
https://journal.unnes.ac.id/sju/index.php/jere/article/view/33507/14152
|
English
| null | null |
Journal of Research and Educational Research Evaluation/Journal of research and educational research evaluation
| 2,019
|
cc-by
| 4,296
|
Universitas Negeri Semarang, Indonesia Article Info
________________
Article history:
Received 3 January
2019
Approved 02 August
2019
Published 23 August
2019
________________
Keywords:
Test instrument, three
tier multiple choice
____________________
Abstract
Weaknesses and strengths of mastery of the material students in the learning process
can be identified using diagnostic tests. This study aims to determine the
appropriateness of the contents of the test instrument three tier multiple choice (3TMC)
for students' misconceptions analysis. The method used is Research and Development
(R&D) with a 4D model consisting of define, design, development and desemination. The analysis technique used is the content validity, content reliability, different power
and difficulty level. Analysis of the content validity of the 3TMC test instrument uses
the Aiken formula, the reliability test of the 3TMC test instrument uses Interclass
Correlation Coefficient (ICC), while the difference power test and difficulty level use
Anates. Content validation data was obtained from 5 validators consisting of 3 expert
lecturers and 2 PPKn teachers. The results of expert validation of the 3TMC test
instruments obtained 20 valid 3TMC items with 19 items having a value of v of 1.00, 1
item with a value of v of 0.60 in item 14. The results of inter-rater reliability analysis
showed an Alpha value of 0.938 with avalue Single Measures of 0.750 ≥ 0.5, so it can
be seen that the rater agreed in providing an assessment with the criteria of High
Reliability. Based on the results of the study it was found that the developed 3TMC test
products are valid with little revision and are reliable for use, so that the 3TMC test
instrument can be used for the analysis of students' misconceptions on PPKn subjects. © 2019 Universitas Negeri Semarang
Alamat korespondensi
Kampus Unnes Kelud Raya, Semarang, 50233
E-mail: suciwidiyana.sw@gmail.com
p-ISSN 2252-6420
e-ISSN 2503-1732 Article Info
________________
Article history:
Received 3 January
2019
Approved 02 August
2019
Published 23 August
2019
________________
Keywords:
Test instrument, three
tier multiple choice Weaknesses and strengths of mastery of the material students in the learning process
can be identified using diagnostic tests. This study aims to determine the
appropriateness of the contents of the test instrument three tier multiple choice (3TMC)
for students' misconceptions analysis. The method used is Research and Development
(R&D) with a 4D model consisting of define, design, development and desemination. The analysis technique used is the content validity, content reliability, different power
and difficulty level. Alamat korespondensi
Kampus Unnes Kelud Raya, Semarang, 50233
E-mail: suciwidiyana.sw@gmail.com JERE 8 (2) (2019) 91 - 97 Universitas Negeri Semarang, Indonesia Analysis of the content validity of the 3TMC test instrument uses
the Aiken formula, the reliability test of the 3TMC test instrument uses Interclass
Correlation Coefficient (ICC), while the difference power test and difficulty level use
Anates. Content validation data was obtained from 5 validators consisting of 3 expert
lecturers and 2 PPKn teachers. The results of expert validation of the 3TMC test
instruments obtained 20 valid 3TMC items with 19 items having a value of v of 1.00, 1
item with a value of v of 0.60 in item 14. The results of inter-rater reliability analysis
showed an Alpha value of 0.938 with avalue Single Measures of 0.750 ≥ 0.5, so it can
be seen that the rater agreed in providing an assessment with the criteria of High
Reliability. Based on the results of the study it was found that the developed 3TMC test
products are valid with little revision and are reliable for use, so that the 3TMC test
instrument can be used for the analysis of students' misconceptions on PPKn subjects. © 2019 Universitas Negeri Semarang © 2019 Universitas Negeri Semarang p-ISSN 2252-6420
e-ISSN 2503-1732 p-ISSN 2252-6420
e-ISSN 2503-1732 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 level which is a multiple choice question that asks the
reason, and the third level which is a scale that asks
the level of student confidence for the answers given
to the two questions above. Student answers for each
item are considered correct when both the choices
and the correct reasons are given with a high level of
confidence. The three-tier test considered more
accurate in capturing students' misconceptions,
because they can detect a lack of knowledge
percentage by using a level of trust (Gurel, D., K.,
Eryilmaz, A., & McDermott, L., C, 2015). Universitas Negeri Semarang, Indonesia In
Pancasila and Citizenship Education subjects, the
use of diagnostic tests can improve the mastery of
PPKn subject matter with a score of 84.15 higher
than the score of students who do not use diagnostic
tests that is 72.35 (Wirasini, Rasyid, & Winarno,
2017, p .464). INTRODUCTION Citizenship education is a very important
education for students and society in general. Citizenship education has the main components
ofcivic knowledge,civic skillsandcivic disposition. The three components of citizenship according to
Winarno (2013, p. 26) are closely related to the goal
of personal formation of citizens. Thus, evaluation of
learning becomes very important to be developed in
the subjects of Pancasila Education and Citizenship. The results of the evaluation can be a guide for
teachers to focus more attention on students who
have not mastered the subject matter as well as to
find out the learning difficulties of students. Learning difficulties for students one of them
when
students
experience
misconceptions. Misconception is an understanding of concepts
contained in the minds of students that are contrary
to scientific concepts, which are influenced by the
experience of students (Hammer in Mubarak, 2016,
p. 102). Teachers
must
be
sensitive
to
misconceptions that occur in students, so that
teachers are able to design effective learning
processes to overcome these misconceptions, thus
misconceptions must be identified so that action can
be taken to help students replace them with more
scientific concepts (Tuysuz, 2009). This study aims to developinstrument design
three-tier multiple choice a valid and reliableto
identify the profile of students' misconceptions in
PPKn class X SMK subjects. So, it can help PPKn
teachers in revealing the profile of understanding of
students at the vocational level. METHODS Study was conducted at SMK Negeri Moenadi
and SMK Negeri 1 Bawen. This type of research is
development research. The development model used
is a 4-D model with a modification of the Tessmer
formative research type. The development model
used is a 4-D model consists of four stages: define,
design, develop, and dissemination (Thiagarajan,
Semmel, & Semmel, 1974, p.5). In the study of the
use of the development model used is a 4-D model
carried out to thestage develop. The stages of the
research consisted of define in the form of needs
analysis and literature study, thestage design in the
form of developing a prototype of the diagnostic test
instrument and thestage developing in the form of
validation, product assessment and small-scale and
large-scale product testing. The product produced in
this study is atest instrument three tier multiple
choice
to
identify
the
profile
of
students' One way to identify misconceptions is to use a
diagnostic test instrument that is given to students
after the learning process is carried out. Diagnostic
tests are used to determine which parts of a subject
have weaknesses and provide tools to find the causes
of these deficiencies and are used to find out the
strengths and weaknesses of students in learning
(Suwarto, 2013). Rusilowati (2015, p.2) revealed that
diagnostic tests are tests that are used to find out the
strengths and weaknesses of students when learning
something, so the results can be used as a basis for
giving follow up. Diagnostic test three-tier multiple choice is one
type of diagnostic test that can be used to identify
and measure the misconceptions on the learner. The
three-tier test has three levels; the first level which
includes a regular multiple choice test, the second 91 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 misconceptions on national integration material in
the frame of Bhineka Tunggal Ika. achievement, time allocation, learning activities and
learning resources. The syllabus is then used as a
reference in compiling the instrument lattice. METHODS The
material used as a study in this study is national
integration material within the frame of Bhineka
Tunggal Ika. Each question was compiled by
following Bloom's cognitive domain in the revised
cognitive domain of Anderson and Krathwohl (2017,
p.99-133). The research subjects in this study were grade
X students of SMK N H. Moenadi and SMK N 1
Bawen Agribusiness and Horticulture Study Program
2018/2019. The research object is a test instrument
for misconception analysis with a three tier multiple
choice test (3TMC) model. The sampling technique
is random. Validation of the 3TMC test instrument
consists of 3 aspects of assessment namely material,
constructive, and language aspects. Validity test
conducted by 5 experts consisting of three academics
and two practitioners, can be seen in Table 1. Data collection methods used in the form of
tests,
questionnaires,
and
observations. Questionnaires
were
distributed
to
students,
consisting of assessment questionnaires and response
questionnaires. The assessment questionnaire was
distributed to small-scale trial subjects and the
response questionnaire was distributed to large-scale
trial subjects. Data collection instruments included a
3TMC model misconception analysis product, an
expert validation sheet, and a student response
questionnaire. The data analysiswas conducted by
validity test expert technique, reliability test, different
power, difficulty level and students' response analysis
to 3TMC test instrument products. Table 1. Expert Data on Test Validity Content
Expert
Competency
Expert
Educational
Description
Expert
1
Academics
and
Practitioners
S3
Lecture
Expert
2
Academics
and
Practitioners
S3
Lecture
Expert
3
Academics
and
Practitioners
S2
Lecture
Expert
4
Practitioners
S2
Teacher
Expert
5
Practitioners
S2
Teacher Table 1. Expert Data on Test Validity Content Contents Validity of the 3TMC Diagnostic Test
Instrument The 3TMC Diagnostic test is a test with the first level
being an ordinary multiple choice test, the second
level is a question containing the reasons for the
reasons for the first level, and the third level is a scale
regarding the level of trust or confidence of students
in answering questions and reasons on the two levels
above. Researchers compile for a level of confidence
consisting of 6 scales that are very very unsure, very
unsure, not sure, sure, very sure, and very very sure. The
experts
gave
responses
from
the
instrument of content validity to the diagnostic test
instrument of three tier multiple choice PPKn class X
SMK subjects. the results of the analysis of expert
response data can be seen in table 2. The instrument was developed based on the
Core Competencies and Basic Competencies that
have been set, which are then used to compile the
syllabus of subjects. Syllabus is the main reference for
the preparation of diagnostic test instruments
developed, the syllabus covers the identity of
subjects, core competencies, basic competencies,
learning
materials,
indicators
of
competency 92 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 Table 2. Analysis Results of the Validity of Content
Ite
m
Aike
n V
Inde
x
Concluci
ons
Ite
m
Aike
n V
Inde
x
Concluci
ons
1
1,00
Valid
11
1,00
Valid
2
1,00
Valid
12
1,00
Valid
3
1,00
Valid
13
1,00
Valid
4
1,00
Valid
14
0,60
Valid
5
1,00
Valid
15
1,00
Valid
6
1,00
Valid
16
1,00
Valid
7
1,00
Valid
17
1,00
Valid
8
1,00
Valid
18
1,00
Valid
9
1,00
Valid
19
1,00
Valid
10
1,00
Valid
20
1,00
Valid judgment is reliable with high criteria. ICC value ≥
0.5, it can be said that the rater agreed in providing
an assessment with high reliable criteria. The 3TMC diagnostic test instrument in the
revised PPKn class X vocational subjects based on
expert advice, was then tested on a large scale subject
of 214 students. Students carry out the test for 90
minutes and work on 18 items. The 3TMC
diagnostic test instrument in PPKn subjects in class
X Vocational High School has a fairly high reliability
coefficient of 0.75. The instruments compiled have a
level of reliability and consistency of measurements
(Azwar, 2016, p.111). Contents Validity of the 3TMC Diagnostic Test
Instrument The 3TMC Instruments that have a
reliability coefficient close to number 1 then the
instrument has a high level of reliability and
consistency of judgment. Based on the analysis of the data in Table 2, it
can be obtained information on expert attachment. The validity of the contents of the 3TMC diagnostic
test instrument in PPKn Vocational Class X subjects
was obtained that 19 items were declared valid with
a V of 1.00. 1 item is declared valid with a value of
0.60 in item 14, with moderate criteria. Item 14
continues to be used with improvements based on
advice from experts. The validity of the content is
related to the rational analysis of the domain to be
measured to determine the representation of the
instrument with the ability to be measured
(Retnawati, 2016, p.17). Furthermore, Budiman &
Jailani's research (2014) shows that the instrument is
feasible to use if the coefficient of Aiken's V is more
than 0.3. Instrument Analysis ofanalysis of different power is
performed twice, namely on a small scale and large
scale. On a small scale consisting of 30 students and
on a large scale consisting of 214 students. The
results of different power analyzes in small scale
trials can be seen in Table 3. Table 3. Results of Small Scale Difference Power
Analysis
Ite
m
Difere
ntial
Power
Informa
tion
Ite
m
Difere
ntial
Power
Informa
tion
1
0,62
Questio
ns
received
11
0,12
Questio
ns
discarde
d
2
0,62
Questio
ns
received
12
0,75
Questio
ns
received
3
0,50
Questio
ns
received
13
0,50
Questio
ns
received
4
0,50
Questio
ns
received
14
0,37
Questio
ns
accepte
d need Table 3. Results of Small Scale Difference Power Instrument Reliability is the level of questionin assessing
what you want to assess. A test can be said to be
reliable if it always gives the same results when tested
on the same group at different times or opportunities
(Arifin, 2009). The reliability test of the 3TMC
diagnostic test instrument in PPKn subjects uses the
SPSS 16 application. Based on the analysis, the
results show that the Alpha reliability coefficient is
0.938 and Single Measures shows a value of 0.750. Alpha reliability ≥ 0.7, it can be said that expert 93 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 ni Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 to
be
correcte
d
5
0,00
Questio
ns
discarde
d
15
0,37
Questio
ns
accepte
d need
to
be
correcte
d
6
0,25
Questio
ns
accepte
d need
to
be
correcte
d
16
0,62
Questio
ns
received
7
0,62
Questio
ns
received
17
0,25
Questio
ns
correcte
d
8
0,62
Questio
ns
received
18
0,50
Questio
ns
received
9
0,25
Soal
diterim
a perlu
diperbai
ki
19
0,75
Questio
ns
received
10
0,5
Questio
ns
received
20
0,62
Questio
ns
received
The results of the analysis of the different
power of thediagnostic test instrument three tier
multiple choice in PPKn class X SMK subjects
showed that from 20 items there were 13 items
received, 4 items were accepted with revision, 1 item
was
corrected
and
2
items
were
discarded. Researchers make improvements in accordance with
the results of the analysis of different power and
discard items that are not able to distinguish the
ability of different power and discard items that are
not able to distinguish the ability of students. The
researcher discards item number 5 and 11. The
researcher discards 2 item that is unable to
distinguish
ability
because
each
achievement
indicator is still represented. The instrument will be
revised before large-scale trials are carried out. The
results of different power analyzes in large scale trials
can be seen in Table 4. Table 4. Instrument Results of Large Scale Difference Power
Analysis
Ite
m
Difere
ntial
Power
Informa
tion
Ite
m
Difere
ntial
Power
Informa
tion
1
0,48
Questio
ns
Receive
d
10
0,47
Questio
ns
Receive
d
2
0,48
Questio
ns
Receive
d
11
0,57
Questio
ns
Receive
d
3
0,35
Questio
ns
received
need to
be
correcte
d
12
0,75
Questio
ns
Receive
d
4
0,35
Questio
ns
received
need to
be
correcte
d
13
0,47
Questio
ns
Receive
d
5
0,31
Questio
ns
received
need to
be
correcte
d
14
0,60
Questio
ns
Receive
d
6
0,41
Questio
ns
Receive
d
15
0,64
Questio
ns
Receive
d researcher discards 2 item that is unable to
distinguish
ability
because
each
achievement
indicator is still represented. The instrument will be
revised before large-scale trials are carried out. The
results of different power analyzes in large scale trials
can be seen in Table 4. Table 4. Results of Large Scale Difference Power
Analysis 94 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 7
0,50
Questio
ns
Receive
d
16
0,64
Questio
ns
Receive
d
8
0,50
Questio
ns
Receive
d
17
0,43
Questio
ns
Receive
d
9
0,43
Questio
ns
Receive
d
18
0,50
Questio
ns
Receive
d
7
0,37
Medium
17
0,43
Medium
8
0,40
Medium
18
0,53
Medium
9
0,30
Difficult
19
0,53
Medium
10
0,33
Medium
20
0,53
Medium
The analysis shows that of the 20 items there
are 1 item that has difficulty in the Easy category,
namely number 3. 15 items have difficulty in the
Medium category, namely numbers 1, 2, 4, 6, 7,
8,10, 11, 12 , 14, 16, 17, 18, 19, and 20. 4 items have
difficulty levels in the Difficult category namely
numbers 5, 9, 13, and 15. The researcher analyzes the level of The analysis shows that of the 20 items there
are 1 item that has difficulty in the Easy category,
namely number 3. 15 items have difficulty in the
Medium category, namely numbers 1, 2, 4, 6, 7,
8,10, 11, 12 , 14, 16, 17, 18, 19, and 20. 4 items have
difficulty levels in the Difficult category namely
numbers 5, 9, 13, and 15. Instrument The researcher analyzes the level of
difficulty from the results of large-scale trials. The
analysis showed that 18 items had varying degrees of
difficulty in the easy, medium, and difficult
categories. The results of the analysis of the difficulty
level of large-scale trials can be seen in Table 6. The results of the analysis of the
large scale difference power test of the 3TMC
diagnostic test instrument in the PPKn subjects in
class X SMK showed that out of 18 items there were
15 items accepted, and 3 items were accepted with
revision. Table 6. Results of Analysis of Large-Scale
Difficulties Table 6. Results of Analysis of Large-Scale
Difficulties
Ite
m
Diffic
ulty
Level
Informa
tion
Ite
m
Diffic
ulty
Level
Informa
tion
1
0,38
Medium
10
0,59
Medium
2
0,49
Medium
11
0,30
Difficult
3
0,70
Easy
12
0,51
Medium
4
0,48
Medium
13
0,38
Medium
5
0,45
Medium
14
0,70
Medium
6
0,52
Medium
15
0,43
Medium
7
0,45
Medium
16
0,46
Medium
8
0,51
Medium
17
0,70
Medium
9
0,49
Medium
18
0,60
Medium REFERENCES Anderson, L. W., & Krathwohl, D. R. 2017. Kerangka Landasan Untuk Pembelajaran,
Pengajaran, dan Aasesmen (Revisi Taksonomi
Pendidikan Bloom). Yogyakarta: Pustaka
Pelajar. The distinguishing features of thediagnostic
test instruments three tier multiple choice developed
were mostly in the accepted and accepted categories
with
improvements. Problems
with
good
differentiation can distinguish smart students and
students who are not good enough. This is consistent
with what was expressed by Arikunto (2009) that the
power of differentiation is used to see the extent to
which the ability of the item is able to distinguish
between high-capacity students and low-ability
students. A good test question is one that can
distinguish students who really master the material
or not, if the test questions cannot distinguish
students who are smart and those who are not smart
then the test objectives will not be achieved. Arifin, Z. 2009. Evaluasi Pembelajaran. Bandung:
Rosda. Arikunto,
S. 2009. Dasar-Dasar
Evaluasi
Pendidikan.Yogjakarta: Bumi Aksara Azwar
S. (2016). Reliabilitas
dan
Validitas. yogyakarta: pustaka pelajar. Budiman, A. & Jailani. 2014. Pengembangan
Instrumen Asesmen Higher Order Thinking
Skill
(HOTS)
Pada
Mata
Pelajaran
Matematika SMP Kelas VIII Semester 1. Gurel, D., K., Eryilmaz, A., & McDermott, L., C. 2015. A
Review
and
Comparison
of
Diagnostic Instruments to Identify Students’
Misconceptions in Science. Eurasia Journal of
Mathematics,
Science
&
Technology
Education. 11(5), 989-1008. Characteristics of 3TMC diagnostic Test items good test questions must be valid
and reliable, in addition to that test questions must
have a good level of difficulty and differentiation. Difficulty level and distinguishing features are
characteristic test items, includingdiagnostic test
questions three tier multiple choice. Difficulty level analysis is carried out twice,
namely on a small scale and large scale. On a small
scale consisting of 30 students and on a large scale
consisting of 214 students. The results of different
power analyzes in small scale trials can be seen in
Table 5. Table 5. Results of Small Scale Difficulty Analysis
Results
Ite
m
Diffic
ulty
Level
Informa
tion
Ite
m
Diffic
ulty
Level
Informa
tion
1
0,40
Medium
11
0,43
Medium
2
0,37
Medium
12
0,50
Medium
3
0,80
Easy
13
0,20
Difficult
4
0,33
Medium
14
0,40
Medium
5
0,23
Difficult
15
0,27
Difficult
6
0,33
Medium
16
0,70
Medium Table 5. Results of Small Scale Difficulty Analysis
Results The analysis shows that of the 18 items there
are 1 item that has difficulty in the Easy category,
namely number 3. 16 items have difficulty in the
Medium category, namely numbers 1, 2, 4, 5, 6, 7, 8,
9, 10 , 12, 13, 14, 15, 16, 17, and 18. 1 item has a
difficulty level in the ifficult category namely number
11. Characteristics of the 3TMC diagnostic test
instrument in PPKn subjects in class X SMK large-
scale trial trials are divided into two analyzes namely
analysis of different power and difficulty levels. 95 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 forgetting the researchers' gratitude to Mr Rodhi and
Mrs. Isnanti
for
providing
support
for
the
implementation of this research. Based on Table 4, 18 items have varying degrees of
difficulty in the difficult, medium, and easy
categories. The level of difficulty of the items has a
purpose to determine the possibility of items that are
biased and can assemble tests that have the accuracy
of the question data (Rusilowati, 2017, p.36). CONCLUSIONS The
3TMC
instrument
developed
for
analyzing students' misconceptions in XK Vocational
High School subjects was said to be feasible based on
the results of validation obtained 20 items of 3TMC
valid questions with 19 items having a v value of
1.00, 1 item with a value of v of 0.60 in item 14. The
results of the analysis reliability between rater
showed Alpha value of 0.938 with Single Measures
value of 0.750 ≥ 0.5, so it can be seen that rater
agreed in providing an assessment with the criteria of
High Reliability. The results of the different power
analysis showed that 15 items were accepted and 3
items were accepted with revision. Difficulty level
analysis results showed 18 items had varying degrees
of difficulty in the difficult, medium, and easy
categories. Mubarak, S., Endang, S., & Edy, C. 2016. Pengembangan Tes Diagnostik Three Tier
Multiple
Choice
Untuk
Mengidentifikasi
Miskonsepsi Peserta Didik Kelas XI. Journal
of Innovative Science Education. 5 (2). 101 –
110. Retnawati, H. 2016. Analisis Kuantitatif Instrumen
Penelitian (Panduan Peneliti, Mahasiswa,
Dan
Psikometrian). Yogyakarta:
Parama
Publishing. Rusilowti, A. 2015. Pengembangan Tes Diagnostik
Sebagai Alat Evaluasi Kesulitan Belajar
Fisika. Prosiding Seminar Nasional Fisika dan
Pendidikan Fisika (SNFPF). 6 (1). 2302 –
7827. ACKNOWLEDGMENTS Researcher would like to thank SMK N H. Moenadi and SMK N 1 Bawen for granting
permission to conduct research, and for not Rusilowati, A. 2017. Pengembangan Instrumen
Penilaian. Semarang: Unnes Press. 96 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 Suci Widiyana, Ani Rusilowati, AT Sugeng Priyanto/ Journal of Educational Research and Evaluation 8 (2) (2019) 90 - 97 Suwarto. 2013. Pengembangan Tes Diagnostik
dalam Pembelajaran. Yogyakarta: Pustaka
Pelajar. Winarno. 2013. Pembelajaran
Pendidikan
Kewarganegaraan: Isi, Strategi, dan Penilaian. Jakarta: Bumi Aksara. Thiagarajan, S., Semmel, D., & Semmel, M. I. 1974. Instructional
Development
for
Training
Teachers of Exceptional Children. Indiana
University. Wirasini, A. D., Rasyid, M. A., & Winarni. 2017. Pengaruh Penilaian Diagnostik Terhadap
Penguasaan
Kompetensi
Mensintesiskan
Kewenangan
Lembaga
Lembaga
Negara
Menurut UUD Negara Republik Indonesia
Tahun 1945. PKn Progresif. 12(1), 453-465. Tuysuz, C. 2009. Development Of Two-Tier
Diagnostic Instrumen And Assess Student
Misunderstanding In Chemistry. Scientific
Research and Essay. 4(6). 626 – 631. 97
|
https://openalex.org/W1976428633
|
https://www.redalyc.org/pdf/1871/187114368012.pdf
|
English
| null |
A new species of Demidospermus Suriano, 1983 (Monogenea) parasite of gills of Auchenipterus osteomystax (Auchenipteridae), from the upper Paraná river floodplain, Brazil
|
Acta Scientiarum. Biological Sciences
| 2,010
|
cc-by
| 2,142
|
Acta Scientiarum. Biological Sciences
ISSN: 1679-9283
eduem@uem.br
Universidade Estadual de Maringá
Brasil
Castro Tavernari, Fernando de; Massato Takemoto, Ricardo; Figueiredo Lacerda, Ana Carolina; Cezar
Pavanelli, Gilberto
A new species of Demidospermus Suriano, 1983 (Monogenea) parasite of gills of Auchenipterus
osteomystax (Auchenipteridae), from the upper Paraná river floodplain, Brazil
Acta Scientiarum. Biological Sciences, vol. 32, núm. 1, 2010, pp. 79-81
Universidade Estadual de Maringá
.png, Brasil
Available in: http://www.redalyc.org/articulo.oa?id=187114368012 Acta Scientiarum. Biological Sciences
ISSN: 1679-9283
eduem@uem.br
Universidade Estadual de Maringá
Brasil
Castro Tavernari, Fernando de; Massato Takemoto, Ricardo; Figueiredo Lacerda, Ana Carolina; Cezar
Pavanelli, Gilberto
A new species of Demidospermus Suriano, 1983 (Monogenea) parasite of gills of Auchenipterus
osteomystax (Auchenipteridae), from the upper Paraná river floodplain, Brazil
Acta Scientiarum. Biological Sciences, vol. 32, núm. 1, 2010, pp. 79-81
Universidade Estadual de Maringá
.png, Brasil
Available in: http://www.redalyc.org/articulo.oa?id=187114368012 Acta Scientiarum. Biological Sciences
ISSN: 1679-9283
eduem@uem.br
Universidade Estadual de Maringá
Brasil Acta Scientiarum. Biological Sciences
ISSN: 1679-9283
eduem@uem.br
Universidade Estadual de Maringá
Brasil Castro Tavernari, Fernando de; Massato Takemoto, Ricardo; Figueiredo Lacerda, Ana Carolina; Cezar
Pavanelli, Gilberto
A new species of Demidospermus Suriano, 1983 (Monogenea) parasite of gills of Auchenipterus
osteomystax (Auchenipteridae), from the upper Paraná river floodplain, Brazil
Acta Scientiarum. Biological Sciences, vol. 32, núm. 1, 2010, pp. 79-81
Universidade Estadual de Maringá
.png, Brasil Available in: http://www.redalyc.org/articulo.oa?id=187114368012 How to cite
Complete issue
More information about this article
Journal's homepage in redalyc.org
Scientific Information System
Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal
Non-profit academic project, developed under the open access initiative Scientific Information System
Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal
Non-profit academic project, developed under the open access initiative DOI: 10.4025/actascibiolsci.v32i1.3368 Fernando de Castro Tavernari1, Ricardo Massato Takemoto2*, Ana Carolina Figueiredo
Lacerda2 and Gilberto Cezar Pavanelli2 1Programa de Pós-graduação em Zootecnia, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, Brazil. 2Núcleo de Pesquisas em Limnologia, Ictiologia e Aqüicultura, Universidade Estadual de Maringá, Av. Colombo, 5790,
87020-900, Maringá, Paraná, Brazil. *Author for correspondence. E-mail: takemotorm@nupelia.uem.br ABSTRACT. A new species of Demidospermus Suriano, 1983 is described from the gills of
Auchenipterus osteomystax Miranda-Ribeiro, 1918 (Auchenipteridae), collected in the upper
Paraná river floodplain, Brazil. The gills were removed and preserved in 5% formalin. Later
the parasites were removed from the gills with the aid of a stereomicroscope and conserved
in 70% alcohol. Some specimens were stained with Gomori’s trichrome, dehydrated in
absolute alcohol and cleared with faia creosote to observe the internal organs. Other
specimens were mounted in Hoyer’s medium for the study of the sclerotized structures. The present study describes a new monogenetic species, Demidospermus osteomystax n. sp.,
characterized by: tandem gonads; V-shaped haptoral bars with articulation; sinistral, non-
sclerotized vagina; same-size anchors and absence of bulb in the cirrus. Keywords: Auchenipterus osteomystax, Demidospermus, parasite, Monogenea, Paraná river. RESUMO. Uma nova espécie de Demidospermus Suriano, 1983 parasita de
brânquias de Auchenipterus osteomystax da planície de inundação do alto rio Paraná,
Brasil. Uma nova espécie de Demidospermus Suriano, 1983 parasita de brânquias de
Auchenipterus osteomystax Miranda-Ribeiro, 1918 (Auchenipteridae) é descrita. Os peixes
foram coletados na planície de inundação do alto rio Paraná, Brasil. As brânquias foram
removidas e conservadas em formalina 5% e posteriormente os parasitas foram removidos
com o auxílio de um esteromicroscópio e conservados em álcool 70%. Alguns espécimes
foram corados com Tricômio de Gomori, desidratados em álcool absoluto e clarificados
com creosoto de faia para a observação dos órgãos internos. Outros espécimes foram
montados em Hoyer para estudo das estruturas esclerotizadas. O presente estudo descreve
uma nova espécie de monogenético, Demidospermus osteomystax n. sp., caracterizada pela
presença de gônadas em tandem; barras do haptor em forma de V, com articulação; vagina
sinistra, não-esclerotizada; ancoras do mesmo tamanho e ausência do bulbo do cirro. Palavras-chave: Auchenipterus osteomystax, Demidospermus, parasito, Monogenea, rio Paraná. Acta Scientiarum. Biological Sciences Introduction Forty-one specimens of Auchenipterus osteomystax
were collected through gill-nets in the Baía river,
Patos Lagoon, Iguatemi river and Ivinheima river, all
located in the upper Paraná river floodplain,
between March 2004 and March 2005. The gills
were removed and preserved in 5% formalin. Later
the parasites were removed from the gills with the
aid of a stereomicroscope and conserved in 70%
alcohol. Some specimens were stained with
Gomori’s trichrome, dehydrated in absolute alcohol
and cleared with faia creosote to observe the internal
organs. Other specimens were mounted in Hoyer’s
medium for the study of the sclerotized structures Auchenipterus osteomystax Miranda-Ribeiro, 1918
(Auchenipteridae) is a siluriform fish that inhabits
benthopelagic freshwater environments and is
found in the basins of the rivers Paraná, Tocantins
and Amazonas. There are only a few studies about
this species and its helminth parasites. During a survey on parasites of A. osteomystax
from the upper Paraná river floodplain, a new
species of Demidospermus was collected from the
gills. The parasite is described and illustrated. This
is the first record of a monogenean parasitizing the
gills of these hosts. Maringá, v. 32, n. 1, p. 79-81, 2010 Acta Scientiarum. Biological Sciences Tavernari et al. Figure 2. Demidospermus osteomystax n. sp.: A. Copulatory
complex; B. Hook; C. Ventral bar; D. Ventral anchor; E. Dorsal
bar; F. Dorsal anchor. 80 Tavernari et al. Tavernari et al. (EIRAS et al., 2006). Measurements, all in
micrometers, are expressed as the mean, followed by
the range and number of specimens measured in
parenthesis. Illustrations were made with the aid of a
drawing tube and a Nikon YS2 microscope. Holotype and paratypes were deposited in the
Helminthological Collection of ‘Instituto Oswaldo
Cruz’ (CHIOC), Rio de Janeiro State, Brazil. The
ecological terminology follows Bush et al. (1997)
and the terminology of the haptoral sclerites follows
Kritsky and Mizelle (1968) and related papers. Acta Scientiarum. Biological Sciences References Demidospermus was proposed by Suriano (1983) for
D. anus Suriano, 1983 from de gills of Loricaria anus
Valenciennes, 1836 (Loricariidae) in Argentina and is
commonly found parasitizing Neotropical siluriform
fishes (Loricariidae, Pimelodidae and Auchenipteridae)
(KOHN; COHEN, 1998). Gutiérrez and Suriano
(1992) added generic characteristics and Kritsky and
Gutiérrez (1998) proposed an emended diagnosis
which characterizes Demidospermus as species having:
tandem
gonads;
counterclockwise
coiled
male
copulatory organ; sinistral vaginal aperture; U-, W-, or
V-shaped haptoral bars; subspherical eye granules and a
sheath like accessory piece serving as a guide for the
male copulatory organ. Suriano (1983) considered the
presence of encapsulated sperm (sperm packets) within
the testis of adult worms an autapomorphic feature of
the genus. But, according to Kritsky and Gutiérrez
(1998) the sperm packets are not always present or
visible in some specimens of the described species and
they also did not observe them in any of their
specimens. Thus, the authors considered that this
characteristic is not reliable in defining the genus. Species of the genus Demidospermus was recorded
parasitizing another siluriform fish, Iheringichthys
labrosus, from the upper Paraná river floodplain by
França et al. (2003). BUSH, A. O.; LAFFERTY, K. D.; LOTZ, J. M.;
SHOSTAK, A. W. Parasitology meets ecology on its own
terms: Margolis et al. revisited. Journal of Parasitology,
v. 83, n. 4, p. 575-583, 1997. EIRAS, J. C.; TAKEMOTO, R. M.; PAVANELLI, G. C. Métodos de estudo e técnicas laboratoriais em
parasitologia de peixes. Maringá: Eduem, 2006. FRANÇA, J. G.; ISAAC, A.; PAVANELLI, G. C.;
TAKEMOTO, R. M. Dactylogyridae (Monogenea) from
the
gills
of
Iheringicthys
labrosus
(Osteichthyes:
Pimelodidae) from the upper Paraná river floodplain,
Brazil, with the proposal of Pseudovancleaveus n. g. Systematic Parasitology, v. 54, n. 1, p. 25-31, 2003. GUTIÉRREZ, P. A.; SURIANO, D. M. Ancyrocephalids
of the genus Demidospermus Suriano, 1983 (Monogenea)
parasites from siluriform fishes in Argentina, with
descriptions of three new species. Acta Parasitologica,
v. 37, n. 4, p. 169-172, 1992. KOHN, A.; COHEN, S. C. South American Monogenea
– list of species, hosts and geographical distribution. International Journal for Parasitology, v. 28, n. 10,
p. 1517-1554, 1998. KOHN, A.; COHEN, S. C. South American Monogenea
– list of species, hosts and geographical distribution. International Journal for Parasitology, v. 28, n. 10,
p. 1517-1554, 1998. KRITSKY, D. C.; GUTIÉRREZ, P. A. Neotropical
Monogenoidea. 34. Species
of
Demidospermus
(Dactylogyridae, Ancyrocephalinae) from the gills of
pimelodids
(Teleostei,
Siluriformes)
in
Argentina. License information: 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. References Journal
of
the
Helminthological
Society
of
Washington, v. 65, n. 2, p. 147-159, 1998. Demidospermus osteomystax n. sp. is similar to D. anus
Suriano, 1983 in the following characteristics: marginal
hooks of same form and size, dorsal and ventral bars V-
shaped (similar to the dorsal bar of D. anus) and similar
anchors. Demisdospermus osteomystax n. sp. is also similar to
D. mandi França et al., 2003 from the gills of Iheringicththys
labrosus in the following characteristics: similar accessory
piece of the male copulatory organ, ventral and dorsal bars
V-shaped, and accessory piece associated with half of the
male copulatory organ. However, D. osteomystax n. sp. differs from these species by the presence of non-
sclerotized vagina, ventral and dorsal bars with articulation
and absence of bulb in the cirrus. KRITSKY, D. C.; MIZELLE, J. D. Studies on monogenetic
trematodes. XXXV. Some new and previously described
North American species of Gyrodactylus. American Midland
Naturalist, v. 79, n. 1, p. 205-215, 1968. SURIANO, D. M. Demidospermus anus gen. nov. sp. nov. (Monogenea: Ancyrocephalinae) parasita branquial de Loricaria
(L.) anus Valenciennes, 1840 (Pisces: Loricariidae) de la Laguna
de Chascomus-Provincia de Buenos Aires – Republica
Argentina. Neotropica, v. 29, n. 82, p. 111-119, 1983. KRITSKY, D. C.; MIZELLE, J. D. Studies on monogenetic
trematodes. XXXV. Some new and previously described
North American species of Gyrodactylus. American Midland
Naturalist, v. 79, n. 1, p. 205-215, 1968. SURIANO, D. M. Demidospermus anus gen. nov. sp. nov. (Monogenea: Ancyrocephalinae) parasita branquial de Loricaria
(L.) anus Valenciennes, 1840 (Pisces: Loricariidae) de la Laguna
de Chascomus-Provincia de Buenos Aires – Republica
Argentina. Neotropica, v. 29, n. 82, p. 111-119, 1983. Received on May 13, 2008. Accepted on April 20, 2009. New species of Demidospermus Suriano, 1983 81 Type locality: upper Paraná river floodplain, Brazil
(22º50’–22º70’S and 53º15’-53º40’W). for logistic and financial support. F. C. Tavernari was
supported by a Research fellowship from Araucária
Foundation
for
Scientific
and
Technological
Development in Paraná. R. M. Takemoto and G. C. Pavanelli were supported by a Research fellowship
from the National Council for Scientific and
Technological Development (CNPq). A. C. F. Lacerda
was
supported
by
the
Coordination
for
the
Improvement of Higher Education Personnel (Capes). Type locality: upper Paraná river floodplain, Brazil
(22º50’–22º70’S and 53º15’-53º40’W). (
)
Site: Gills. Site: Gills. Infestation: Prevalence 68.3% (28 of 41 examined
fish). Mean intensity: 24.4. Specimens
deposited:
CHIOC
no. 37252a
(holotype); nos 37252b, 37253, 37254 (paratypes). Etymology: The specific epithet refers to the
specific name of the host. Acta Scientiarum. Biological Sciences Results Demidospermus Suriano, 1983 Demidospermus osteomystax n. sp. (Figures 1 and 2) Figure 1. Composite drawing of Demidospermus osteomystax n. sp.,
ventral view. Figure 2. Demidospermus osteomystax n. sp.: A. Copulatory
complex; B. Hook; C. Ventral bar; D. Ventral anchor; E. Dorsal
bar; F. Dorsal anchor. Description [Based upon 15 specimens.] Body
408 (320-540; n = 11) long, fusiform; greatest width
109 (80-190; n = 11) near the level of testis. Head
organs and cephalic lobes present; cephalic glands
posterolateral to pharynx. Eyes formed by dispersed
granules. Pharynx subspherical, 29 (25-34; n = 5)
long, 26 (23-30; n = 5) wide; oesophagus short. Peduncle broad and short; Haptor subhexagonal, 61
(39-74; n = 9) long, 85 (71-108; n = 9) wide. Ventral anchors 25 (23-28, n = 8) long, base 15 (14-
16; n = 8) wide. Dorsal anchors 24 (21-27, n = 8)
long, base 15 (11-16, n = 7) wide. Bars V-shaped;
ventral bar 35 (28-41; n = 9) long, distance between
ends 43 (33-61, n = 9); dorsal bar 39 (33-47, n = 9)
long, distance between ends 41 (30-50, n = 9). Haptor with 7 pairs of hooks, similar in form and
size, 14 (13-15, n = 10) long. Shaft with recurved
point; FH loop about 8/9 shank length. Cirrus 36
(29-48, n = 12) long; accessory piece associated with
half of the copulatory organ, 30 (25-38, n = 12)
long. Gonads tandem; testis posterior to ovary, 41
(33-48, n = 4) long, 27 (20-34, n = 4) wide. Eggs
not observed. Sinistral vaginal aperture; vaginal canal
composed
of
delicated
non-sclerotised
pipe. Vitellaria throughout the trunk, except in the areas
of the reproductive structures. Type host: Auchenipterus osteomystax Miranda-
Ribeiro, 1918. Figure 1. Composite drawing of Demidospermus osteomystax n. sp.,
ventral view. Maringá, v. 32, n. 1, p. 79-81, 2010 Acta Scientiarum. Biological Sciences Received on May 13, 2008.
Accepted on April 20, 2009. Acknowledgements We are thankful to the Nucleus of Research in
Limnology, Ichthyology and Aquaculture (Nupélia) Maringá, v. 32, n. 1, p. 79-81, 2010 Acta Scientiarum. Biological Sciences
|
https://openalex.org/W2899551539
|
https://europepmc.org/articles/pmc6226445?pdf=render
|
English
| null |
Changes in canine serum N-glycosylation as a result of infection with the heartworm parasite Dirofilaria immitis
|
Scientific reports
| 2,018
|
cc-by
| 8,041
|
Changes in canine serum
N-glycosylation as a result of
infection with the heartworm
parasite Dirofilaria immitis
Anna-Janina Behrens1, Rebecca M. Duke1, Laudine M. C. Petralia1, Sylvain Lehoux2,
Clotilde K. S. Carlow1, Christopher H. Taron1 & Jeremy M. Foster1 Received: 13 August 2018
Accepted: 28 October 2018
Published: xx xx xxxx Filariases are diseases caused by infection with filarial nematodes and transmitted by insect vectors. The filarial roundworm Dirofilaria immitis causes heartworm disease in dogs and other carnivores. D. immitis is closely related to Onchocerca volvulus, Wuchereria bancrofti and Brugia malayi, which cause
onchocerciasis (river blindness) and lymphatic filariasis (elephantiasis) in humans and are neglected
tropical diseases. Serum N-glycosylation is very sensitive to both pathological infections and changes
in mammalian biology due to normal aging or lifestyle choices. Here, we report significant changes in
the serum N-glycosylation profiles of dogs infected with D. immitis. Our data derive from analysis of
serum from dogs with established patent infections and from a longitudinal infection study. Overall,
galactosylation and core fucosylation increase, while sialylation decreases in infected dog sera. We
also identify individual glycan structures that change significantly in their relative abundance during
infection. Notably, the abundance of the most dominant N-glycan in canine serum (biantennary,
disialylated A2G2S2) decreases by over 10 percentage points during the first 6 months of infection in
each dog analyzed. This is the first longitudinal study linking changes in mammalian serum N-glycome
to progression of a parasitic infection. Dirofilaria immitis is a filarial roundworm of considerable veterinary importance as the causative agent of heart-
worm disease in domestic dogs (Canis lupus familiaris) and cats (Felis silvestris catus). The parasite affects the
pulmonary arterial system, the lung and the heart of canines and is often fatal1–4. Adult worms are capable of
surviving in the arterial system of dogs for many years during which time they continually release microfilariae
(i.e., L1 larvae) that circulate in peripheral blood vessels. Disease transmission occurs via mosquitos that feed on
microfilaremic blood. Within the mosquito vector, microfilariae mature to infective L3 larvae that subsequently
can be passed on to the next canine host while the mosquito takes its blood meal4,5. In the dogs, these larvae
mature and patent infections (circulating microfilariae) are usually developed by 6–9 months after infection4. it
Dogs can be asymptomatic for many years before signs of heartworm disease develop. Infections can be diag-
nosed by blood tests detecting either microfilariae or adult antigens as well as molecular methods. In clinical
practice nowadays, a combination of antigen and microfilaria testing is recommended for diagnosis6. www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports Received: 13 August 2018
Accepted: 28 October 2018
Published: xx xx xxxx Scientific REPOrTS | (2018) 8:16625 | DOI:10.1038/s41598-018-35038-7 Changes in canine serum
N-glycosylation as a result of
infection with the heartworm
parasite Dirofilaria immitis
Anna-Janina Behrens1, Rebecca M. Duke1, Laudine M. C. Petralia1, Sylvain Lehoux2,
Clotilde K. S. Carlow1, Christopher H. Taron1 & Jeremy M. Foster1 Detection
of circulating antigens is mainly specific for the fecund female adult worm, which makes infection detectable only
about half a year post-infection7,8. However, it is theoretically also possible to detect antibodies raised to parasite
antigens present in earlier (pre-patent) phases of infection9,10.i Glycoproteins, i.e., proteins that are post-translationally modified by the attachment of O- or N-linked glycans,
play important roles in many different biological functions11. Glycans are created by complex, non-template-driven
biosynthetic pathways. As such, glycan structure can be modulated due to changes in gene expression patterns
that occur in response to environmental changes. These changes in glycosylation range from fine-tuning biological
processes to crucial contributions that enable novel biological functions12. Small changes in an N-glycan’s structure
(such as the presence or absence of a core fucose) can have major impacts on the biological role of the protein. For
example, the absence of core fucose on Fc N-glycans on immunoglobulin G (IgG) significantly alters its ability to 1New England Biolabs Inc., Ipswich, Massachusetts, 01938, USA. 2Department of Surgery, Beth Israel Deaconess
Medical Center, Harvard Medical School, Boston, MA, 02115, USA. Correspondence and requests for materials
should be addressed to A.-J.B. (email: annaj.behrens@gmail.com) or J.M.F. (email: foster@neb.com) Scientific REPOrTS | (2018) 8:16625 | DOI:10.1038/s41598-018-35038-7 1 www.nature.com/scientificreports/ elicit effector functions13,14. Serum glycosylation, while strikingly stable within individuals and highly regulated by
hemostasis15, can change considerably with lifestyle, age and pathological conditions16–18. As such, serum glycan
changes have been observed in association with cancer, inflammation, immunological diseases and congenital dis-
eases19–26. Hence, there is a great diagnostic potential for glycobiomarkers, and the N-glycosylation analysis of easily
sourced blood serum can be a valuable tool in the diagnosis of numerous diseases25–32 including infectious diseases
which hitherto have been poorly studied from this perspective. p
y
p
p
Here, we show the impact of parasitic infection with D. immitis on the total canine serum N-glycosylation pro-
file. We observe remarkable changes in the abundances of core fucosylated, galactosylated and sialylated serum
N-glycans when comparing healthy dogs to those that have established patent D. immitis infections. We further
present the detailed analysis of a longitudinal cohort of infected dogs and are thus able to identify temporal glycan
structural changes during infection. Results
Ch
t Characterization of serum N-glycans from healthy and diseased dogs. We have previously
reported the detailed glycosylation analysis of canine serum38. To investigate the impact of filarial infection by
D. immitis on the total N-glycosylation profile of serum, we analyzed serum samples from two different dog
cohorts. In our first study, we analyzed sera from five dogs that had been infected with D. immitis for more than
two years and thus carried a patent (i.e. active production of microfilariae) infection and compared them to sera
from five healthy (control) dogs (Supplementary Table S1). In the second study, we investigated changes in serum
N-glycosylation at initial stages of a D. immitis infection by analyzing a longitudinal serum collection sampled
from four dogs collected over the first 27 weeks of infection (Supplementary Table S2)39. We performed serum
N-glycosylation profiling of PNGase F-released and procainamide-labeled N-glycans by hydrophilic interaction
chromatography-ultraperformance liquid chromatography (HILIC-UPLC) and further analyzed both serum
from infected and uninfected dogs from the patent set by Matrix-assisted laser desorption/ionization time-of-
flight mass spectrometry (MALDI-TOF MS). l
g
p
y
While the patent set was collected in 2015, the longitudinal samples were collected in 1989 and stored at
−80 °C since. Despite the 25-year age difference between the samples, the N-glycosylation profiles of the healthy/
pre-infection serum samples from both cohorts were nearly identical (see Supplementary Fig. S1). There were
only minor differences in the identified N-glycan peaks in the HILIC-UPLC spectra between the two sets (i.e. 42
glycan peaks were identified in total in the longitudinal set, compared to 44 in the patent set), which led to small
differences in the peak numbering (for details see Supplementary Fig. S2 and Table S3). Alteration of serum N-glycosylation in dogs infected with D. immitis. The N-glycosylation profiles
of dogs that carry a patent D. immitis infection differ substantially from healthy dogs (Fig. 1). The most obvious
differences are in the relative abundances of the two dominant glycan structures, the fucosylated biantennary FA2
(Peak No. 5) and the disialylated biantennary A2G2S2 (Peak No. 29; for a description of the glycan nomenclature,
see legend to Supplementary Table S3). While the abundance of FA2 is considerably increased in diseased dogs,
A2G2S2 is decreased. There were also obvious differences in less prominent structures (Fig. 1b). Changes in canine serum
N-glycosylation as a result of
infection with the heartworm
parasite Dirofilaria immitis
Anna-Janina Behrens1, Rebecca M. Duke1, Laudine M. C. Petralia1, Sylvain Lehoux2,
Clotilde K. S. Carlow1, Christopher H. Taron1 & Jeremy M. Foster1 We propose that individual glycan peaks in canine serum N-glycan profiles
as well as more global markers, such as the relative abundance of sialylated glycans, could potentially be consid-
ered as glycobiomarker candidates for D. immitis infection in dogs. We believe that our findings are relevant for
the veterinary field as they suggest potentially new ways of understanding and diagnosing heartworm disease. Further, it is noteworthy that D. immitis is closely related to O. volvulus, W. bancrofti and B. malayi, causative
agents of onchocerciasis and lymphatic filariasis afflicting more than 135 million humans33,34, thus making our
results relevant for a wider filariasis research community. While alterations in IgG N-glycosylation have previ-
ously been associated with leishmaniasis35, asymptomatic filariasis36 and other parasitic infection in developing
countries37 to the best of our knowledge, this is the first report of drastic changes in the mammalian total serum
N-glycosylation profile as a consequence of parasitic infections. Results
Ch
t To investigate
which of the N-glycan peaks significantly change in abundance within the patent set (consisting of 5 healthy and
5 infected dogs), we used linear mixed-effects models for statistical analysis. The volcano plot in Fig. 2a high-
lights the five peaks in the patent set that change significantly (adjusted p-value < 0.05). Among them are the two
major peaks FA2 and A2G2S2, but also less abundant structures like A2 and A2G1. MALDI-TOF MS analysis of
released and permethylated N-glycans from healthy and infected dogs confirms the changes in N-glycosylation
as determined by HILIC-UPLC (Supplementary Fig. S3).i We were further interested in examining whether there are significant changes in serum glycosylation with
regard to broader glycan classes. More precisely, we analyzed the significance of the change in abundance of core
fucosylated, galactosylated (glycans containing at least one terminal galactose), agalactosylated (glycans without any
galactoses) and sialylated glycans based on their sensitivity to α1-2,4,6 Fucosidase, β1-4 Galactosidase and α2-3,6,8
Neuraminidase, respectively. As can be seen in Fig. 2b, agalactosylation, galactosylation and core fucosylation are
all significantly increased in dogs infected with D. immitis, whereas sialylation is decreased. Supplementary Fig. S4
illustrates the chromatographic peaks that were included in the quantification of the four glycans classes. Changes in canine serum N-glycosylation in a longitudinal D. immitis infection set. To investi-
gate when the observed changes in canine serum N-glycosylation arise during the course of a parasitic infection
with D. immitis, we analyzed a longitudinal serum set from four dogs over the first 27 weeks of infection (lon-
gitudinal set). The most noticeable changes arise after about 25 weeks post-infection. The relative abundance of
the main peak (A2G2S2) significantly drops, whereas we see an increase in FA2 (Fig. 3a). In fact, 22 out of 44
chromatographic N-glycan peaks in this longitudinal set change significantly (adjusted p-value < 0.05) 25 weeks
post D. immitis infection (Fig. 4). Similar to what we observed in the patent set, all four glycan classes also show
significant changes after 25 weeks of infection (Fig. 3b). Results
Ch
t Scientific REPOrTS | (2018) 8:16625 | DOI:10.1038/s41598-018-35038-7 2 www.nature.com/scientificreports/ 1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
0
20
40
60
Peak number
Healthy
Disease
2
16
14
10
12
6
4
8
Minutes
Rel. abund. Rel. abund. in %
HILIC-UPLC profile
Quantification
a
b
Mannose, Man
Galactose, Gal
N-Acetylglucosamine, GlcNAc
N-Acetylgalactosamine, GalNAc
Fucose, Fuc
N-Acetylneuraminic acid, Neu5A
N-Glycolylneuraminic acid, Neu5Gc
Figure 1. Serum N-glycosylation profile of dogs with a patent D. immitis infection compared to that of healthy
dogs. (a) Representative HILIC-UPLC profile of enzymatically released and fluorescently labeled serum
N-glycans from dogs carrying a patent D. immitis infection (pink) and of a healthy control sample (green). (b)
Quantification of individual peaks derived from HILIC-UPLC spectra. Shown is mean + s.d of 5 biological
replicates. Same color code as in panel a. See Supplementary Table S3 for peak identifications. Glycan structures
of main peaks are annotated following the nomenclature outlined by the Consortium for Functional Glycomics
(CFG). The inset in b shows the monosaccharide symbols used within this manuscript. 60
Healthy
Disease
2
16
14
10
12
6
4
8
Minutes
Rel. abund. HILIC-UPLC profile
a
b a b 1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
0
20
40
60
Peak number
Minutes
Rel. abund. in %
Quantification
b
Mannose, Man
Galactose, Gal
N-Acetylglucosamine, GlcNAc
N-Acetylgalactosamine, GalNAc
Fucose, Fuc
N-Acetylneuraminic acid, Neu5A
N-Glycolylneuraminic acid, Neu5Gc Peak number Figure 1. Serum N-glycosylation profile of dogs with a patent D. immitis infection compared to that of healthy
dogs. (a) Representative HILIC-UPLC profile of enzymatically released and fluorescently labeled serum
N-glycans from dogs carrying a patent D. immitis infection (pink) and of a healthy control sample (green). (b)
Quantification of individual peaks derived from HILIC-UPLC spectra. Shown is mean + s.d of 5 biological
replicates. Same color code as in panel a. See Supplementary Table S3 for peak identifications. Glycan structures
of main peaks are annotated following the nomenclature outlined by the Consortium for Functional Glycomics
(CFG). Results
Ch
t The inset in b shows the monosaccharide symbols used within this manuscript. Interestingly, the serum N-glycosylation profiles transiently change after about 3 weeks and 9 weeks of infec-
tion, where we see a general decrease in mainly small, agalactosylated glycans as well as galactosylated structures
(Figs 3b and 4). This is somewhat inverted at later timepoints, where, broadly speaking, we see a general increase
in smaller glycans (i.e., agalactosylation and galactosylation) and also in fucosylation. Peak 28, which contains
the biantennary, monosialylated (Neu5Gc) glycan FA2G2SNeu5Gc1, is consistently and significantly decreased in
comparison to healthy dog serum after only 19 weeks of infection (Fig. 4), thus making it a potential biomarker
candidate for early infection. However, we could not identify a similar clear change in the relative abundance of
this particular glycan in dogs with a patent D. immitis infection. The N-glycosylation profile of serum IgG is unaltered. We purified IgG from healthy and infected
dogs (patent set) using Protein G and performed N-glycosylation profiling by HILIC-UPLC. The IgG N-glycan
profiles of healthy and infected dogs look almost identical (Supplementary Fig. S5) and we did not determine any
statistical changes in the abundances of canine IgG glycan structures. However, we further determined the con-
centration of IgG in the serum samples of the patent set using ELISA, and found the average IgG concentration to
be about 1.5 times higher in dogs with a patent infection compared to the healthy controls. Thus, a change in the
relative abundance of serum glycoproteins likely contributes to the observed changes in canine N-glycosylation
upon infection with D. immitis. Discussion Peak 05
eak 03
Peak 08
Peak 32
0.0
2.5
5.0
7.5
10.0
−2
0
2
Log2 fold change
−Log2 (adjusted p−value)
Adj p−value cutoff (0.05)
No change
Decreased
Increased
Agalactosylation
Galactosylation
Core fucosylation
Sialylation
0
20
40
60
80
100
Relative abundance in %
Healthy
Disease
*
*
*
*
a
b
Figure 2. Significant changes of serum N-glycosylation in dogs with a patent D. immitis inf
peaks/classes were tested for significance using linear mixed-effects models. p-values were a
Benjamini and Hochberg method. The analysis is based on 5 biological and 2 technical repli
(healthy and disease; patent set). (a) Volcano Plot comparing serum N-glycan peaks from do
D. immitis to a healthy control group. Illustrated is the log2 fold change in glycan abundance
log2 of adjusted p-values. The horizontal dashed line represents the adjusted p-value cutoff (
above the dashed line are glycan peaks that decrease (red) and increase (blue) significantly. S
Table S4 for quantification data. (b) Significant changes in all analyzed glycan classes in dogs
D. immitis infection. Glycan classes were identified and quantified by exoglycosidase digesti Peak 05
eak 03
Peak 08
Peak 32
0.0
2.5
5.0
7.5
10.0
−2
0
2
Log2 fold change
−Log2 (adjusted p−value)
a Adj p−value cutoff (0.05)
No change
Decreased
Increased Adj p−value cutoff (0.05)
No change
Decreased
Increased
Agalactosylation
Galactosylation
Core fucosylation
Sialylation
0
20
40
60
80
100
Relative abundance in %
Healthy
Disease
*
*
*
*
b b Figure 2. Significant changes of serum N-glycosylation in dogs with a patent D. immitis infection. Glycan
peaks/classes were tested for significance using linear mixed-effects models. p-values were adjusted based on
Benjamini and Hochberg method. The analysis is based on 5 biological and 2 technical replicates per group
(healthy and disease; patent set). (a) Volcano Plot comparing serum N-glycan peaks from dogs infected with
D. immitis to a healthy control group. Illustrated is the log2 fold change in glycan abundance and the negative
log2 of adjusted p-values. The horizontal dashed line represents the adjusted p-value cutoff (0.05). The points
above the dashed line are glycan peaks that decrease (red) and increase (blue) significantly. See Supplementary
Table S4 for quantification data. (b) Significant changes in all analyzed glycan classes in dogs with a patent
D. immitis infection. Glycan classes were identified and quantified by exoglycosidase digestion with α1-2,4,6
Fucosidase, β1-4 Galactosidase or α2-3,6,8 Neuraminidase. See Supplementary Fig. Discussion We observed remarkable changes in the total serum N-glycosylation profiles of dogs infected with D. immitis. The
relative abundance of sialylated N-glycans decreases whereas the level of galactosylation and fucosylation increased. The most obvious and dominant changes occurred as early as 25 weeks post-infection, although we observe some
fluctuation in serum N-glycosylation as early as 3 weeks post-infection. Generally, changes in serum N-glycosylation
can be attributed to either a change in the glycan microheterogeneity of one or more glycoproteins or to a change
in the total abundance of glycoproteins in serum. Among the N-glycan structures that change the most in dogs
infected with D. immitis are FA2 (increase) and A2G2S2 (decrease). FA2 has been shown to predominantly originate
from IgG40,41. While a previous study has reported changes in the IgG sialylation in people infected with a related Scientific REPOrTS | (2018) 8:16625 | DOI:10.1038/s41598-018-35038-7 3 www.nature.com/scientificreports/ Peak 05
eak 03
Peak 08
Peak 32
0.0
2.5
5.0
7.5
10.0
−2
0
2
Log2 fold change
−Log2 (adjusted p−value)
Adj p−value cutoff (0.05)
No change
Decreased
Increased
Agalactosylation
Galactosylation
Core fucosylation
Sialylation
0
20
40
60
80
100
Relative abundance in %
Healthy
Disease
*
*
*
*
a
b
Figure 2. Significant changes of serum N-glycosylation in dogs with a patent D. immitis infection. Glycan
peaks/classes were tested for significance using linear mixed-effects models. p-values were adjusted based on
Benjamini and Hochberg method. The analysis is based on 5 biological and 2 technical replicates per group
(healthy and disease; patent set). (a) Volcano Plot comparing serum N-glycan peaks from dogs infected with
D. immitis to a healthy control group. Illustrated is the log2 fold change in glycan abundance and the negative
log2 of adjusted p-values. The horizontal dashed line represents the adjusted p-value cutoff (0.05). The points
above the dashed line are glycan peaks that decrease (red) and increase (blue) significantly. See Supplementary
Table S4 for quantification data. (b) Significant changes in all analyzed glycan classes in dogs with a patent
D. immitis infection. Glycan classes were identified and quantified by exoglycosidase digestion with α1-2,4,6
Fucosidase, β1-4 Galactosidase or α2-3,6,8 Neuraminidase. See Supplementary Fig. S4 for visualization of
the glycan classes. Bar graphs show mean + s.d. Agalactosylation, adj. p-value = 0.001; galactosylation, adj. p-value = 0.003; core fucosylation, adj. p-value = 0.001; sialylation, adj. p-value = 0.001. Discussion Color Key
Adjusted p−value
−1e−10
−1e−06
−1e−04
−0.001
−0.01
−0.05
1
0.05
0.01
0.001
1e−04
1e−06
1e−10
b
Weeks of infection
0
1
2
3
4
5
8
9
11
13
17
19
21
23
25
27
Agalactosylation
Sialylation
Galactosylation
Fucosylation
Minutes
0 weeks
21 weeks
23 weeks
25 weeks
27 weeks
Weeks post infection
Rel. abund. a
increase
decrease a b 0 Figure 3. Longitudinal serum N-glycosylation profiles of D. immitis infection in dogs. (a) HILIC-UPLC
profiles of enzymatically released and fluorescently labeled serum N-glycans from dog ID 116 (longitudinal
set) from weeks 0, 21, 23, 25 and 27 post-infection with D. immitis. Rel. abund., relative abundance. The glycan
structures of the two dominant peaks are annotated. (b) Heatmap of the changes in the abundance of serum
N-glycan classes in D. immitis infection. Adjusted p-values were determined using linear mixed-effects models. Blue, increase; red, decrease. Glycan classes were identified and quantified by exoglycosidase digestion with α1-
2,4,6 Fucosidase, β1-4 Galactosidase or α2-3,6,8 Neuraminidase. (Supplementary Fig. S3; Table S4). Changes in the abundance of FA2 in blood serum have previously been associated with conditions like liver
fibrosis28, pregnancy in patients with rheumatoid arthritis44 and peritoneal dialysis patients31. Possibly the most
pronounced increases of FA2 in human serum have been reported to correlate with aging in both males and
females17,45. The authors hypothesized that the observed change could possibly be explained by increased activity
of β-galactosidase activity as they also observed a decrease in FA2G2. We, however, did not observe any decrease
in FA2G or FA2G2. On the contrary, corresponding peaks were elevated in the longitudinal set after 25 weeks
(Peak No. 12 and Peak No. 16) and showed no significant change in the patent set. Thus, it is highly unlikely that
the changes observed in our study are age-related or caused by similar effects in enzyme activity. Changes in the abundance of FA2 in blood serum have previously been associated with conditions like liver
fibrosis28, pregnancy in patients with rheumatoid arthritis44 and peritoneal dialysis patients31. Possibly the most
pronounced increases of FA2 in human serum have been reported to correlate with aging in both males and
females17,45. The authors hypothesized that the observed change could possibly be explained by increased activity
of β-galactosidase activity as they also observed a decrease in FA2G2. We, however, did not observe any decrease
in FA2G or FA2G2. Discussion S4 for visualization of
the glycan classes. Bar graphs show mean + s.d. Agalactosylation, adj. p-value = 0.001; galactosylation, adj. p-value = 0.003; core fucosylation, adj. p-value = 0.001; sialylation, adj. p-value = 0.001. filarial nematode, W. bancrofti36, our analysis revealed no change in IgG N-glycan microheterogeneity in dogs with
a patent D. immitis infection. We do, however, see an increased abundance of serum IgG in infected dogs that is
likely responsible for at least part of the change in the relative abundances of serum N-glycans. We hypothesize that
D. immitis may use a long-term polyclonal IgG response as an obfuscation tactic. Along these lines, increased levels
of serum IgG have been previously reported in patients infected with Leishmania donovani42, where changes in IgG
N-glycosylation have been associated with disease severity35. Helminths as such have been shown to modulate and
suppress immune responses by regulating certain types of T cells43. It is highly likely that the observed effects are
caused by multiple serum glycoproteins, but this requires further investigation. Scientific REPOrTS | (2018) 8:16625 | DOI:10.1038/s41598-018-35038-7 4 www.nature.com/scientificreports/ www.nature.com/scientificreports/ Color Key
Adjusted p−value
−1e−10
−1e−06
−1e−04
−0.001
−0.01
−0.05
1
0.05
0.01
0.001
1e−04
1e−06
1e−10
b
Weeks of infection
0
1
2
3
4
5
8
9
11
13
17
19
21
23
25
27
Agalactosylation
Sialylation
Galactosylation
Fucosylation
Minutes
0 weeks
21 weeks
23 weeks
25 weeks
27 weeks
Weeks post infection
Rel. abund. a
increase
decrease
Figure 3. Longitudinal serum N-glycosylation profiles of D. immitis infection in dogs. (a) HILIC-UPLC
profiles of enzymatically released and fluorescently labeled serum N-glycans from dog ID 116 (longitudinal
set) from weeks 0, 21, 23, 25 and 27 post-infection with D. immitis. Rel. abund., relative abundance. The glycan
structures of the two dominant peaks are annotated. (b) Heatmap of the changes in the abundance of serum
N-glycan classes in D. immitis infection. Adjusted p-values were determined using linear mixed-effects models. Blue, increase; red, decrease. Glycan classes were identified and quantified by exoglycosidase digestion with α1-
2,4,6 Fucosidase, β1-4 Galactosidase or α2-3,6,8 Neuraminidase. (Supplementary Fig. S3; Table S4). Discussion While some of the changes Scientific REPOrTS | (2018) 8:16625 | DOI:10.1038/s41598-018-35038-7 5 www.nature.com/scientificreports/ Peak_44
Peak_43
Peak_42
Peak_41
Peak_40
Peak_39
Peak_38
Peak_37
Peak_36
Peak_35
Peak_34
Peak_33
Peak_32
Peak_31
Peak_30
Peak_29
Peak_28
Peak_27
Peak_26
Peak_25
Peak_24
Peak_23
Peak_22
Peak_21
Peak_20
Peak_19
Peak_18
Peak_17
Peak_16
Peak_15
Peak_14
Peak_13
Peak_12
Peak_11
Peak_10
Peak_09
Peak_08
Peak_07
Peak_06
Peak_05
Peak_04
Peak_03
Peak_02
Peak_01
Color Key
Adjusted p−value
−1e−10 −1e−06 −1e−04 −0.001
−0.01 −0.05
1
0.05
0.01
0.001
1e−04
1e−06
1e−10
Weeks of infection
0
1
2
3
4
5
8
9
11
13
17
19
21
23
25
27
decrease
increase
Figure 4. Heatmap of longitudinal canine serum N-glycosylation in D. immitis infection. Serum sample
four dogs were collected over 27 weeks post-infection. Significance was determined using linear mixed-e
models. Blue, increase; red, decrease. See Supplementary Table S3 for peak identifications. See Supplemen
Table S4 for quantification data. Peak_44
Peak_43
Peak_42
Peak_41
Peak_40
Peak_39
Peak_38
Peak_37
Peak_36
Peak_35
Peak_34
Peak_33
Peak_32
Peak_31
Peak_30
Peak_29
Peak_28
Peak_27
Peak_26
Peak_25
Peak_24
Peak_23
Peak_22
Peak_21
Peak_20
Peak_19
Peak_18
Peak_17
Peak_16
Peak_15
Peak_14
Peak_13
Peak_12
Peak_11
Peak_10
Peak_09
Peak_08
Peak_07
Peak_06
Peak_05
Peak_04
Peak_03
Peak_02
Peak_01
Color Key
Adjusted p−value
−1e−10 −1e−06 −1e−04 −0.001
−0.01 −0.05
1
0.05
0.01
0.001
1e−04
1e−06
1e−10
Weeks of infection
0
1
2
3
4
5
8
9
11
13
17
19
21
23
25
27
decrease
increase
Figure 4. Heatmap of longitudinal canine serum N-glycosylation in D. immitis infection. Serum samples from
four dogs were collected over 27 weeks post-infection. Significance was determined using linear mixed-effect
models. Blue, increase; red, decrease. See Supplementary Table S3 for peak identifications. See Supplementary
Table S4 for quantification data. Adjusted p−value
−1e−10 −1e−06 −1e−04 −0.001
−0.01 −0.05
1
0.05
0.01
0.001
1e−04
1e−06
1e−10 Adjusted p−value Figure 4. Heatmap of longitudinal canine serum N-glycosylation in D. immitis infection. Serum samples from
four dogs were collected over 27 weeks post-infection. Significance was determined using linear mixed-effect
models. Blue, increase; red, decrease. See Supplementary Table S3 for peak identifications. See Supplementary
Table S4 for quantification data. in serum N-glycosylation might be transient reflections of canine immune responses to D. Discussion On the contrary, corresponding peaks were elevated in the longitudinal set after 25 weeks
(Peak No. 12 and Peak No. 16) and showed no significant change in the patent set. Thus, it is highly unlikely that
the changes observed in our study are age-related or caused by similar effects in enzyme activity. g
y
g
yf
y
y
In this study, we analyzed two separate sets of canine serum infected with D. immitis; a cohort with a patent
infection and a longitudinal study over the first 27 weeks of infection. We observed a larger number of glycan
structures that showed significant changes after 25 weeks of infection in the longitudinal set (22 peaks) compared
to five peaks in the patent set. Given the time span of about 25 years between the age of the two sources of sera
and the different study designs, particularly the maturity of the heartworm infections, results are only compa-
rable to some degree. Encouragingly, the observed changes in serum N-glycan peak relative abundances upon
infection with D. immitis are broadly the same in both studies (i.e., decrease in sialylation, increase in galacto-
sylation and fucosylation and the larger relative abundance of FA2). Further, all five glycan peaks that showed
significant changes in the patent set after 2.5 years of infection were also significantly altered towards the end of
the longitudinal study (25 weeks post-infection) and thus present potential biomarker candidates. It appears that
serum N-glycosylation is more affected during the initial phase of D. immitis infection, likely reflecting immune
responses as the larvae mature to adulthood, migrate into the heart and the pulmonary arterial system and start
producing microfilariae. More precisely, it has been reported that after about 3 weeks of infection, when we see
the first changes in serum N-glycosylation (Fig. 4), most larvae have migrated from the subcutaneous tissues to
the abdomen4,5. They reach the heart as early as week 10 of infection, which is roughly when we see further dis-
tinct changes in the heatmap in Fig. 4. Dogs usually develop patent infections where they actively produce micro-
filariae 6–9 months post-infection4,5, which coincides with the time point where we observe the beginning of the
most pronounced changes in the serum N-glycosylation profiles (25 weeks; Fig. 4). Discussion immitis infection, it
appears that the quantitatively most significant changes remain present over the longer course of infection as it is
in the case of the patent set.l Given that blood is an easily sampled body fluid and that we observe changes in broad glycan classes one could
imagine potential glycobiomarker candidates for diagnosing or monitoring D. immitis infection. Detection assays
could possibly be based on lectin-based quantification capable of detecting terminal glycan epitopes such as e.g. sialylation or fucosylation. Of course, it needs to be further investigated which (if any) of these serum N-glycan
changes are specific to a canine D. immitis infection and if infected dogs in a more natural infection setting show
equally pronounced glycosylation changes. The dog breed, the presence or absence of microfilariae and the sever-
ity of the disease could very well influence the intensity of glycosylation changes. It also needs to be considered
that the abundance of serum FA2 in dogs could be similarly affected by aging as it is the case in humans17,45.ii f
To the best of our knowledge, this is the first report of significant and drastic serum N-glycosylation changes
during a nematode infection. In the light of the fact that D. immitis is closely related to the human parasites
O. volvulus, W. bancrofti and B. malayi, future studies should investigate if similar drastic changes in serum
N-glycosylation also occur in human nematode infections. Methods Canine serum samples. Canine serum samples originated from beagle dogs and were purchased from TRS
Laboratories Inc (Athens, GA, USA). All animal experiments were approved by the IACUC committee of TRS
Laboratories Inc. and in compliance with the USDA Animal Welfare Act. This study comprises the analysis of sera
originating from two independent canine cohorts that were infected with D. immitis. The first cohort, termed patent Scientific REPOrTS | (2018) 8:16625 | DOI:10.1038/s41598-018-35038-7 6 www.nature.com/scientificreports/ set, contains five healthy (control) dogs and 5 diseased dogs. The 5 diseased dogs were infected via transplantation
of adult worms of one of the D. immitis strains ‘Wildcat’, ‘Pepper’ or ‘Georgia II’ into the jugular vein. Serum sam-
ples were drawn after ~2.5 years of infection. More detailed information on this set can be found in Supplementary
Table S1. The second cohort of serum samples, termed longitudinal set, originated from a previously published
longitudinal study of dogs infected with D. immitis39. In brief, 4 beagle dogs were subcutaneously infected with
L3 larvae at week 0 and week 7. Blood samples were collected for a period of 27 weeks of infection. More detailed
information on this set can be found in Supplementary Table S2. Serum samples were stored at −80 °C. Purification of IgG from canine serum. IgG was purified from canine serum using Protein G magnetic
beads according to the manufacturers’ instructions (New England Biolabs). Determination of IgG concentration. The concentration of IgG in canine serum was determined by an
ELISA assay Kit (Canine IgG ELISA Kit, Abcam) according to the manufacturer’s instructions. N-glycan analysis by HILIC-UPLC. N-glycans were released from serum or IgG using Rapid PNGase F
and fluorescently labeled with procainamide as described previously38. The procainamide labeled N-glycans were
analyzed by HILIC-UPLC with fluorescence and mass detection on a Waters Acquity H-class instrument com-
posed of a binary solvent manager, a sample manager, a fluorescence detector (excitation wavelength 310 nm;
detection wavelength 370 nm) and a QDa mass detector (settings: positive mode; target sampling rate: 10 point/
sec; gain: 1; capillary voltage: 1.5 kV; probe temperature: 600 °C). Glycans were separated using an Acquity BEH
Amide Column (130 Å, 1.7 μm, 2.1 mm × 150 mm; Waters) with 50 mM ammonium formate, pH 4.4 as solvent
A and acetonitrile as solvent B using a linear gradient of 70% to 53% solvent B at 0.56 ml/min for 25 min. Methods Data
acquisition, processing and analysis was performed using Empower 3 software (Waters). Exoglycosidase digestion of released glycans. Digestion of released glycans with a panel of recom-
binant exoglycosidases was performed to quantify the abundance of individual glycan classes (e.g. those car-
rying sialic acids) as well as to confirm glycan structures via sequential digestion as described previously38. In brief, glycans were digested with α2-3,6,8 Neuraminidase, α1-2,4,6 Fucosidase O, β1-4 Galactosidase,
β-N-Acetyl-Glucosaminidase and α1-2,3,6 Mannnosidase (all from New England Biolabs) according to the man-
ufacturer’s instructions. Samples were then analyzed by HILIC-UPLC (see above). Glycan release, permethylation and MALDI-TOF MS analysis. N-glycans were released with
PNGase F, subsequently permethylated and analyzed by MALDI-TOF MS in positive ion mode on an UltraFlex
II MALDI-TOF mass spectrometer (Bruker) as described in detail previously38. Glycan structures were assigned
manually, based on known biosynthesis pathways and with the help of GlycoWorkbench46. Data analysis. Statistical data analysis was performed using R 3.5.0 in an environment of R studio 1.1.447. The impact of D. immitis infection on canine serum glycosylation was explored using linear-mixed effects mod-
els. Peak areas of HILIC-UPLC glycan spectra were quantified using Empower 3 (Waters). The peak areas within
one spectrum were normalized to the same arbitrary total peak area of 100000 among all spectra. The R pack-
age MSstats47 was utilized for data processing (including log transformation) and statistical modeling. MSstats
employs the lm and lmer functionalities in R, but customizes the statistical design i.e. group comparison (patent
set) or time course experiments (longitudinal set) based on the input data. Data Availability y
All data generated and analyzed during this study are included in this published article and its Supplementary
Information files. Scientific REPOrTS | (2018) 8:16625 | DOI:10.1038/s41598-018-35038-7 References References
1. Knight, D. H. Heartworm heart disease. Adv. Vet. Sci. Comp. Med. 21, 107–149 (1977). 1. Knight, D. H. Heartworm heart disease. Adv. Vet. Sci. Comp. Med. 21, 107–149 (1977). g
p
(
)
2. Jackson, R. F. et al. Distribution of heartworms in the right side of the heart and adjacent vessels of the dog. J. Am. Vet. Med. Assoc. 149, 515–518 (1966). g
p
2. Jackson, R. F. et al. Distribution of heartworms in the right side of the heart and adjacent vessels of the dog. J. Am. Vet. Med. Assoc. 149, 515–518 (1966). (
)
3. Knight, D. H. Heartworm infection. Vet. Clin. North Am. Small Anim. Pract. 17, 1463–1518 (1987). 3. K
g t,
. . ea two
ect o . Vet. Clin. North
m. Small
nim. ract. 7,
63
5 8 ( 987). 4. McCall, J. W., Genchi, C., Kramer, L. H., Guerrero, J. & Venco, L. In Advances in Parasitology Vol. 66, 193–285 (Academic Press,
2008).i g
4. McCall, J. W., Genchi, C., Kramer, L. H., Guerrero, J. & Venco, L. In Advances in Parasitology Vol. 66, 193–285 (Acade
2008).i )
5. Kotani, T. & Powers, K. G. Developmental stages of Dirofilaria immitis in the dog. Am. J. Vet. Res. 43, 2199–2206 (1982 p
gi
g
(
6. American Heartworm Society. Prevention, Diagnosis, and Management of Heartworm infection in Dogs (2014).il y
g
g
g
7. Little, S., Saleh, M., Wohltjen, M. & Nagamori, Y. Prime detection of Dirofilaria immitis: understanding the influence of blocked
antigen on heartworm test performance. Parasit. Vectors 11, 186 (2018).i 7. Little, S., Saleh, M., Wohltjen, M. & Nagamori, Y. Prime detection of Dirofilaria immitis: understanding the influence of blocked
antigen on heartworm test performance. Parasit. Vectors 11, 186 (2018).i antigen on heartworm test performance. Parasit. Vectors 11, 186 (2018). 8. Weil, G. J., Malane, M. S., Powers, K. G. & Blair, L. S. Monoclonal antibodies to parasite antigens found in the serum of Dirofilaria
immitis-infected dogs. J. Immunol. 134, 1185–1191 (1985).ii g
p
8. Weil, G. J., Malane, M. S., Powers, K. G. & Blair, L. S. Monoclonal antibodies to parasite antigens found in the serum of Dirofilaria
immitis-infected dogs. J. Immunol. 134, 1185–1191 (1985).ii immitis-infected dogs. J. Immunol. 134, 1185–1191 (1985). y
gy
10. Mejia, J. S., Nkenfou, C., Southworth, M. W., Perler, F. B. & Carlow, C. K. g
p
2. Jackson, R. F. et al. Distribution of heartworms in the right side of the heart and adjacent vessels of the dog. J. Am. Vet. Med. Assoc
149, 515–518 (1966). ,
(
)
3. Knight, D. H. Heartworm infection. Vet. Clin. North Am. Small Anim. Pract. 17, 1463–1518 (1987). References
1. Knight, D. H. Heartworm heart disease. Adv. Vet. Sci. Comp. Med. 21, 107–149 (1977). References Reiding, K. R. et al. Serum Protein N-Glycosylation Changes with Rheumatoid Arthritis Disease Activity during and afte
Pregnancy. Front. Med. 4, 241 (2017). h
l
l
fil
h ft d
h
l
(
) g
y
,
(
)
45. Vanhooren, V. et al. Serum N-glycan profile shift during human ageing. Exp. Gerontol. 45, 738–743 (2010). 45. Vanhooren, V. et al. Serum N-glycan profile shift during human ageing. Exp. Gerontol. 45, 738–743 (2010). 46. Damerell, D. et al. In Glycoinformatics Vol. 1273, Methods in Molecular Biology (eds Lütteke, T. & Frank, M.) Ch. 1, 3–15 (Humana
Press, NY, 2015). g y
pit
g
g
g
p
6. Damerell, D. et al. In Glycoinformatics Vol. 1273, Methods in Molecular Biology (eds Lütteke, T. & Frank, M.) Ch. 1, 3–15 (Humana
Press, NY, 2015). 7 Ch i M
l MS
R
k
f
i i
l
l
i
f
i
i
b
d
i
i 47. Choi, M. et al. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics 30, 2524–2526 (2014). 47. Choi, M. et al. MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experim
Bioinformatics 30, 2524–2526 (2014). Author Contributions A.-J.B., J.M.F., R.M.D., L.M.C.P. and S.L. performed experimental work. A.-J.B., R.M.D. and L.M.C.P., J.M.F. analyzed data. C.K.S.C. provided the longitudinal dog serum set. A.-J.B., C.H.T. and J.M.F. wrote the manuscript. A.-J.B., R.M.D., C.H.T. and J.M.F. designed the study. All authors read and approved the final manuscript. Acknowledgements We thank Dr. Bill Jack and Dr. Tom Evans for critical reading of the manuscript. We thank Dr. Donald Comb and
Mr. James Ellard for their continued support of parasitology and glycobiology research at New England Biolabs. We thank New England Biolabs for financial support. We also gratefully acknowledge the National Center for
Research Resources (a part of the NIH) for support of the National Center for Functional Glycomics (NCFG) at
Beth Israel Deaconess Medical Center (P41GM103694). The content of this work is solely the responsibility of
the authors and does not necessarily represent the official views of the National Center for Research Resources
or the NIH. Mr. James Ellard for their continued support of parasitology and glycobiology research at New England Biolabs. We thank New England Biolabs for financial support. We also gratefully acknowledge the National Center for
Research Resources (a part of the NIH) for support of the National Center for Functional Glycomics (NCFG) at
Beth Israel Deaconess Medical Center (P41GM103694). The content of this work is solely the responsibility of
the authors and does not necessarily represent the official views of the National Center for Research Resources Mr. James Ellard for their continued support of parasitology and glycobiology research at New England Biolabs. We thank New England Biolabs for financial support. We also gratefully acknowledge the National Center for
Research Resources (a part of the NIH) for support of the National Center for Functional Glycomics (NCFG) at J
pp
p
gy
g y
gy
g
We thank New England Biolabs for financial support. We also gratefully acknowledge the National Center for
h
f h
f
f h
l
f
l
l Research Resources (a part of the NIH) for support of the National Center for Functional Glycomics (NCFG) at
Beth Israel Deaconess Medical Center (P41GM103694). The content of this work is solely the responsibility of
the authors and does not necessarily represent the official views of the National Center for Research Resources
or the NIH. References Expression of an Onchocerca volvulus Ov
Dirofilaria immitis: potential in immunodiagnosis of heartworm infection. Parasite Immunol. 16, 297–303 (1994). y
gy
10. Mejia, J. S., Nkenfou, C., Southworth, M. W., Perler, F. B. & Carlow, C. K. Expression of an Onchocerca volvulus Ov33 homolog in
Dirofilaria immitis: potential in immunodiagnosis of heartworm infection Parasite Immunol 16 297–303 (1994) 10. Mejia, J. S., Nkenfou, C., Southworth, M. W., Perler, F. B. & Carlow, C. K. Expression of an Onchocerca volvulus Ov33 homolog in
Dirofilaria immitis: potential in immunodiagnosis of heartworm infection. Parasite Immunol. 16, 297–303 (1994). g
f
y
gy (
)
(
p
g
12. Lauc, G., Kristic, J. & Zoldos, V. Glycans - the third revolution in evolution. Front. Genet. 5, 145 (2014).hf g
f
y
gy (
)
(
p
g
y
)
12. Lauc, G., Kristic, J. & Zoldos, V. Glycans - the third revolution in evolution. Front. Genet. 5, 145 (2014).hf y
13. Baum, L. G. & Cobb, B. A. The direct and indirect effects of glycans on immune function. Glycobiology 2 g y
gf
15. Gornik, O. et al. Stability of N-glycan profiles in human plasma. Glycobiology 19, 1547–1553 (2009). y
g y
pi
p
y
gy
16. Clerc, F. et al. Human plasma protein N-glycosylation. Glycoconj. J. 33, 309–343 (2016).i i
16. Clerc, F. et al. Human plasma protein N-glycosylation. Glycoconj. J. 33, 309–343 (2016). 17 Di
N
t l H
N
l
fil
d
d
d
t A
d A i 7 www.nature.com/scientificreports/ 8. Dall’Olio, F. et al. N-glycomic biomarkers of biological aging and longevity: a link with inflammaging. Ageing Res. Rev. 12, 685–698
(2013). (2013). 19. Azevedo, R., Silva, A. M. N., Reis, C. A., Santos, L. L. & Ferreira, J. A. In silico approaches for unveiling novel glycobiomarkers in
(
) (
)
9. Azevedo, R., Silva, A. M. N., Reis, C. A., Santos, L. L. & Ferreira, J. A. In silico approaches for unveiling novel glycobiomarkers in
cancer. J. Proteomics 171, 95–106 (2018). J
(
)
20. Togayachi, A. et al. Glycobiomarker, fucosylated short-form secretogranin III levels are increased in serum of patients with small cell
lung carcinoma. J. Proteome Res. (2017).f g
1. Seeling, M., Bruckner, C. & Nimmerjahn, F. Differential antibody glycosylation in autoimmunity: sweet biomarker or modulator o
disease activity? Nat. Rev. Rheumatol. 13, 621–630 (2017). y
22. Drabik, A. et al. References IgG1 Fc N-glycan galactosylation as a biomarker for immune activation. Sci. Rep. 6, 28207 (2016). h
l
l
l
fil
f d
l d ff
d
h
l
b l 37. de Jong, S. E. et al. IgG1 Fc N-glycan galactosylation as a biomarker for immune activation. Sci. Rep. 6, 28207 (2016).if g
g
g y
g
y
p
38. Behrens, A.-J. et al. Glycosylation profiling of dog serum reveals differences compared to human serum. Glycobiology 28, 82
(2018). (
)
39. Mejia, J. S. & Carlow, C. K. An analysis of the humoral immune response of dogs following vaccination with irradiated infe
larvae of Dirofilaria immitis Parasite Immunol 16 157 164 (1994) 9. Mejia, J. S. & Carlow, C. K. An analysis of the humoral immune response of dogs following vaccination with irradiated infective
larvae of Dirofilaria immitis. Parasite Immunol. 16, 157–164 (1994). 39. Mejia, J. S. & Carlow, C. K. An analysis of the humoral immune response of dogs following vaccination with irradiated infective
larvae of Dirofilaria immitis. Parasite Immunol. 16, 157–164 (1994). fi
0. Butler, M. et al. Detailed glycan analysis of serum glycoproteins of patients with congenital disorders of glycosylation indicates the
specific defective glycan processing step and provides an insight into pathogenesis. Glycobiology 13, 601–622 (2003). i
40. Butler, M. et al. Detailed glycan analysis of serum glycoprotein i
40. Butler, M. et al. Detailed glycan analysis of serum glycoproteins of patients with congenital disorders of glycosylation indicates the
specific defective glycan processing step and provides an insight into pathogenesis. Glycobiology 13, 601–622 (2003). i
1. Parekh, R. B. et al. Association of rheumatoid arthritis and primary osteoarthritis with changes in the glycosylation pattern of tota
serum IgG. Nature 316, 452–457 (1985). g
(
)
42. Galvao-Castro, B. et al. Polyclonal B cell activation, circulating immune complexes and autoimmunity in human american visceral
leishmaniasis. Clin. Exp. Immunol. 56, 58–66 (1984). g
2. Galvao-Castro, B. et al. Polyclonal B cell activation, circulating immune complexes and autoimmunity in human american viscera
leishmaniasis. Clin. Exp. Immunol. 56, 58–66 (1984). p
3. Rook, G. A. Review series on helminths, immune modulation and the hygiene hypothesis: the broader implications of the hygiene
hypothesis. Immunology 126, 3–11 (2009). yp
gy
,
(
)
44. Reiding, K. R. et al. Serum Protein N-Glycosylation Changes with Rheumatoid Arthritis Disease Activity during and after
Pregnancy. Front. Med. 4, 241 (2017).it yp
gy
4. References Glycosylation Changes in Serum Proteins Identify Patients with Pancreatic Cancer. J. Proteome Res. 16, 1436–1444
(2017).i (
)
3. Miyahara, K. et al. Alteration of N-glycan profiles in patients with chronic hepatitis and hepatocellular carcinoma. Hepatol. Res. 45
986–993 (2014).l (
)
4. Higai, K., Azuma, Y., Aoki, Y. & Matsumoto, K. Altered glycosylation of alpha1-acid glycoprotein in patients with inflammation and
diabetes mellitus. Clin. Chim. Acta 329, 117–125 (2003). 25. Kirwan, A., Utratna, M., O’Dwyer, M. E., Joshi, L. & Kilcoyne, M. Glycosylation-based serum biomarkers for cancer diagnostics and
prognostics. Biomed. Res. Int. 2015, 490531 (2015). p
g
(
)
26. Xia, B. et al. Serum N-glycan and O-glycan analysis by mass spectrometry for diagnosis of congenital disorders of glycosylation. Anal. Biochem. 442, 178–185 (2013).l (
)
27. Gornik, O. & Lauc, G. Glycosylation of serum proteins in inflammatory diseases. Disease Markers 25, 267–278 (2008).i l
28. Vanderschaeghe, D. et al. GlycoFibroTest is a highly performant liver fibrosis biomarker derived from DNA sequencer-based serum
protein glycomics. Mol. Cell Proteomics 8, 986–994 (2009). p
g y
9. Blomme, B. et al. Alterations of serum protein N-glycosylation in two mouse models of chronic liver disease are hepatocyte and no
B cell driven. Am. J. Physiol. Gastrointest. Liver Physiol. 300, 833–842 (2011). y
y
30. Saldova, R. et al. Association of N-glycosylation with breast carcinoma and systemic features using high-resolution quantitative
UPLC. J. Proteome Res. 13, 2314–2327 (2014).fll 31. Ferrantelli, E. et al. Effluent and serum protein N-glycosylation is associated with inflammation and peritoneal membrane transport
characteristics in peritoneal dialysis patients. Sci. Rep. 8, 979 (2018).if p
y
p
p
2. Boeck, C. et al. Alterations of the serum N-glycan profile in female patients with Major Depressive Disorder. J. Affect. Disord. 234
139–147 (2018).ii (
)
33. WHO. Lymphatic filariasis, http://www.who.int/lymphatic_filariasis/epidemiology/en/ (2018). HO. Lymphatic filariasis, http://www.who.int/lymphatic_filariasis/e y p
fi
p
y
pi
p
gy
34. WHO. Onchocerciasis - river blindness - Fact Sheet Nr. 95, http://www.who.int/mediacentre/factsheets/fs095/en/ (2018). ii
34. WHO. Onchocerciasis - river blindness - Fact Sheet Nr. 95, http://www.who.int/mediacentre/fact 35. Gardinassi, L. G. et al. Clinical severity of visceral leishmaniasis is associated with changes in immunoglobulin G Fc N-glycosylation. MBio 5, e01844 (2014). 36. O’Regan, N. L. et al. Filariasis asymptomatically infected donors have lower levels of disialylated IgG compared to endemic n
Parasite Immunol. 36, 713–720 (2014). 37. de Jong, S. E. et al. Scientific REPOrTS | (2018) 8:16625 | DOI:10.1038/s41598-018-35038-7 Additional Information upplementary information accompanies this paper at https://doi.org/10.1038/s41598-018-35038-7. Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-018-35038-7 Competing Interests: The authors declare no competing interests. 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. 8 Scientific REPOrTS | (2018) 8:16625 | DOI:10.1038/s41598-018-35038-7 www.nature.com/scientificreports/ 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 Cre-
ative Commons license, and indicate if changes were made. The images or other third party material in this
article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the
material. If material is not included in the article’s Creative Commons license and your intended use is not per-
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) 2018 Scientific REPOrTS | (2018) 8:16625 | DOI:10.1038/s41598-018-35038-7 9
|
https://openalex.org/W2883292674
|
https://tseg.nl/article/download/8282/8919
|
Dutch
| null |
Studenten strooien hete centen voor het volk. Stedelijke identiteit en de geschiedenis van een omstreden herinnering in Leiden (1841-2016)
|
TSEG/Tijdschrift voor sociale en economische geschiedenis
| 2,018
|
cc-by
| 10,092
|
* We zijn Jaap Moes, Pieter Slaman en Jasper van der Steen zeer erkentelijk voor hun suggesties en com-
mentaar op eerdere versies van dit artikel. Studenten strooien hete centen voor het volk
Stedelijke identiteit en de geschiedenis van een omstreden herinnering in
Leiden (1841-2016)
* Peter Burger & Bart van der Steen Peter Burger & Bart van der Steen tseg 15 (1): 66-88
doi: 10.18352/tseg.1015 tseg 15 (1): 66-88
doi: 10.18352/tseg.1015 1 ‘Échte Leidenaar alleen dankzij de universiteit’, Leidsch Dagblad, 1 oktober 2008.
2 L.D. Frank en H.B. Wiardi Beckman, Geschiedenis van het Leidsche Studentencorps (Leiden 1927);
H.G. van Duyl et al., Gedenkboek van het Leidsche Studentencorps (Leiden 1939); J.P. Naeff et al. (eds.),
Geschiedboek van het Leidsche Studenten Corps (Leiden 1950); P. Bloem et al. (eds.), Mixtamorfose (Lei-
den 1975); S.G. Morsink e.a. (eds.), Geschiedboek van de Leidse Studenten Vereniging Minerva (z.p. 1989);
P. Sigmond en D. Meursink (eds.), Minerva voor het leven (Leiden 2014).
3 R.C.J. van Maanen en J.C.H. Blom (eds.), Leiden. De geschiedenis van een Hollandse stad. Leiden vanaf
1896 (Leiden 2004); C. Smit e.a., Het Leiden boek (Zwolle 2014).
4 De ziel van Leiden (Leiden 2017).
5 P. Burger, De gebraden baby. Sagen en geruchten uit het moderne leven (Amsterdam 1995) 156. Abstract Legend has it that students in the Dutch university town of Leiden used to throw
coins in the street for the less well-off citizens. Picking up the coins, these risked
burning their fingers: the students had heated the coins in a skillet. This story is
told as emblematic for the social and cultural differences dividing labourers and
students, or, more generally, ‘town and gown’. Opinions differ about the veracity of
the story and the time period during which this prank was perpetrated. Our study
of this local legend is based on local newspapers and other digitized sources that
have recently become available, allowing us to trace the story over a time period
that spans the years 1841-2016. The hot coins prank is related to a more benign,
internationally known custom during which both throwers and throwees know
what to expect. In the Netherlands, stories about the prank have become associ-
ated in particular with the town of Leiden, becoming more prominent during the
twentieth century, after the prank itself was no longer performed. We read the hot
coin legend in the context of collective memory and urban identity: over the course
of two centuries, various social groups have used the story as a boundary marker
between in-group and out-group, and more broadly as a means to reflect on the
shifting identity of the town. During the years of urban renewal in the second half
of the twentieth century, Leiden transformed from an old, poor, industrial town into
a modern, affluent urban centre that touts itself as a ‘city of knowledge’. Rhetorically,
the hot coin legend is presented as a test case for social cohesion: did Leiden truly
leave behind its divided history? VOL. 15, NO. 1, 2018 66 STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK In Leiden gaat tot op heden een verhaal rond over een gebruik dat be-
schouwd wordt als sprekend voor de identiteit van de stad: corpsstuden-
ten zouden in het verleden regelmatig gloeiende munten op straat heb-
ben gegooid. Onwetende kinderen en arme Leidenaren zouden daarop,
bij het oprapen van de munten, hun handen hebben gebrand. Abstract Het ver-
haal wordt gezien als kenmerkend voor de grote sociale en culturele ver-
schillen in de stad, die volgens sommigen nog steeds bestaan.j Tijdens een symposium over de identiteit van de stad in 2008 haal-
de de antropologe Rivke Jaffe het verhaal over de gloeiende munten aan
als typerend voor de Leidse identiteit.1 Veel zelfverklaarde ‘echte’ Leide-
naren verwijzen regelmatig naar het gebruik. Toch komt het verhaal niet
voor in de vele geschiedenissen van het studentencorps,2 noch in over-
zichtswerken over de geschiedenis van de stad.3 Ook in de huidige stads-
marketing, die dankbaar gebruik maakt van de roemruchte geschiede-
nis van Leiden als universiteitsstad, is geen plaats voor de hete centen.4 Ondergetekenden hoorden het verhaal over het munten strooien
in het eerste jaar van hun studie (in 1979-1980, respectievelijk 2000-
2001), toen het gebruik al lange tijd tot het verleden behoorde.5 Dit
roept de vraag op: waarom heeft dit verhaal in Leiden, na het uitsterven
van het gebruik, nog zo lang een rol gespeeld in de stad en in discussies
over de stedelijke identiteit? Om deze vraag te beantwoorden, hebben we Leidse kranten door-
zocht op beschrijvingen van en herinneringen aan het munten strooien. Regelmatig komen daarin stadsbewoners aan het woord die de hande-
ling aanhalen, ofwel als persoonlijke herinnering dan wel in meer alge-
mene zin. Doorgaans beschrijven ze niet alleen het gebruik, maar leve-
ren ze ook een duiding, zodat het gerechtvaardigd is om te spreken over
een retorische toop: een welbekende anekdote die feitelijk dient om een
ander punt te ondersteunen. Op het eerste gezicht diende de anekdote
om te reflecteren op de positie van de student in de stad. Afhankelijk van
een positieve of negatieve inschatting daarvan werd de anekdote door Om deze vraag te beantwoorden, hebben we Leidse kranten door-
zocht op beschrijvingen van en herinneringen aan het munten strooien. 67 BURGER & VAN DER STEEN TSEG vertellers als waar of onwaar beschouwd en in een contemporain of ver
verleden geplaatst. Maar de anekdote diende ook om te reflecteren op
de staat van de stad. De anekdote stond daarbij symbool voor Leiden
als oude, arme en verdeelde industriestad en riep de vraag op of Leiden
zijn achtergestelde positie inmiddels overwonnen had. Conceptueel gezien sluit ons artikel aan op discussies over col-
lectief geheugen en stedelijke identiteit. 7 J. Assmann, ‘Communicative and cultural memory’, in: A. Erll en A. Nünning (eds.), A companion to
cultural memory studies. An international and interdisciplinary handbook (Berlijn en New York 2008)
109-118. Zie ook: A. Erll en A. Nünning, A companion to cultural memory studies; J.K. Olick en J. Robbins,
‘Memory studies. From “collective memory” to the historical sociology of mnemonic practices’, Annual
Review of Sociology 24 (1998) 105-140; J.K. Olick, V. Vinitzky-Seroussi en D. Levy, ‘Introduction’, in: J.K.
Olick en J. Robbins, The collective memory reader (New York 2011) 3-62. 6 A. Portelli, The death of Luigi Trastulli and other stories: Form and meaning in oral history (Albany, ny
1991); S. Leydesdorf, Het water en de herinnering. De Zeeuwse Watersnoodramp (1953-1993) (Amster-
dam 1994). 8 P. Pattynama, ‘Cultural memory and Indo-Dutch identity formations’, in: U. Bosma (ed.), Post-Colonial
immigrants and identity formations in the Netherlands (Amsterdam 2012) 175-192.
9 A. Somers en F. van Poppel, ‘Priest, parishioner and posterity. A Dutch urban legend or historical fact?’,
The History of the Family 15 (2010) 174-190. Abstract Uitgangspunt is daarbij dat
conflicten over het eigentijdse zelfbeeld ook de blik op het verle-
den beïnvloeden, waardoor beide veranderlijk zijn en met elkaar ver-
bonden. De geschiedenis van het verhaal over de gloeiende munten
toont dat nog eens extra duidelijk. Het collectieve en veranderlijke
karakter van individuele herinneringen is aangetoond door Oral His-
torians als Portelli en Leydesdorf.6 De laatste liet zien hoe overleven-
den van de Zeeuwse Watersnoodramp van 1953 in de jaren negentig
populaire verhalen vertelden als hun eigen herinnering en gebeurte-
nissen uit de bezettingsjaren verbonden (en vermengden) met herin-
neringen aan de watersnoodramp. Het verband tussen geheugen en geschiedenis is gethematiseerd
door Assmann,7 die een onderscheid maakt tussen cultureel geheu-
gen en communicatief geheugen. De eerste term duidt op het geheel
van historische documenten dat een samenleving bewaart in archie-
ven en bibliotheken, terwijl de laatste term verwijst naar dat deel van
de geschiedenis dat mensen als parate kennis met zich meedragen. Door in kranten en andere publicaties op zoek te gaan naar vertellers
die herinneringen ophalen aan het munten strooien, bevindt ons on-
derzoek zich tussen deze twee velden. Door de opkomst van memory
studies zijn historici zich meer bezig gaan houden met verhalen zoals
het onze, omdat zij een belangrijke bron vormen voor de reconstruc-
tie van het zelfbeeld van mensen en groepen. j Het verband tussen geheugen en geschiedenis is gethematiseerd
door Assmann,7 die een onderscheid maakt tussen cultureel geheu-
gen en communicatief geheugen. De eerste term duidt op het geheel
van historische documenten dat een samenleving bewaart in archie-
ven en bibliotheken, terwijl de laatste term verwijst naar dat deel van
de geschiedenis dat mensen als parate kennis met zich meedragen. Door in kranten en andere publicaties op zoek te gaan naar vertellers
die herinneringen ophalen aan het munten strooien, bevindt ons on- Vaak gaat het daarbij om ‘gekoesterde kwetsuren’, herinneringen
aan al dan niet daadwerkelijk geleden onrecht. Pattynama onder-
zocht de herinnering van Indonesiërs aan borden die tijdens de kolo- 68 VOL. 15, NO. 1, 2018 STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK Illustratie 1 Collage van kran-
tenknipsels (bron: Delpher). Illustratie 1 Collage van kran-
tenknipsels (bron: Delpher). 10 Naast Delpher, Leiden.courant.nu en LexisNexis hebben we vooral gebruik gemaakt van de Digitale
Bibliotheek der Nederlandse Letteren (dbnl), Google Books, studentenalmanakken, blogs en forumdis-
cussies. De drie Leidse dagbladen zijn het Leidsch Dagblad (1860-heden), de Leids(ch)e Courant (1688-
1992) en de Nieuwe Leidsche Courant (1920-1980). Steekproefsgewijs hebben we Google News Archive,
Chronicling America en Proquest Historical Newspapers geraadpleegd. niale periode bij openbare zwembaden stonden met de tekst ‘verboden
voor honden en inlanders’.8 Ondanks uitgebreid onderzoek bestaan er
(nog) geen bewijzen dat deze borden daadwerkelijk naast de zwemba-
den hebben gestaan, maar ze maken desondanks een belangrijk onder-
deel uit van de herinnering van Indonesiërs aan de koloniale periode. Op eenzelfde manier onderzochten Somers en Van Poppel het verhaal
dat priesters vroeger langs de deuren gingen bij katholieke gezinnen om
hen aan te zetten meer kinderen te krijgen.9 In deze twee onderzoeken
ligt de nadruk vooral op het waarheidsgehalte van de verhalen. Wij wil-
len echter onderzoeken hoe het munten strooien zich heeft ontwikkeld
van een algemeen folkloristisch gebruik tot een ‘typisch’ Leidse herinne-
ring. Het verhaal over de gloeiende munten is veel verteld, maar speelt
vrijwel geen rol in de geschiedschrijving over de stad. Deze bijdrage
reageert op deze lacune in de literatuur. Nadat de ontwikkeling van
het gebruik is geschetst, wordt de ontwikkeling van het verhaal gere-
construeerd en vervolgens geanalyseerd hoe verschillende groepen
(corpsstudenten, ‘echte’ Leidenaren en betrokken burgers) zich tot
het verhaal verhielden om te verklaren waarom het nog zo lang een
prominente rol heeft gespeeld in het zelfbeeld van veel Leidenaren. 69 BURGER & VAN DER STEEN TSEG Gedigitaliseerde kranten als historische bron De Leidse dagbladen uit de negentiende en twintigste eeuw bieden een
uitgelezen bron om deze ontwikkeling te reconstrueren. We hebben ons
materiaal aangevuld met andere bronnen, waaronder gedigitaliseerde lan-
delijke en regionale kranten, studentenalmanakken en literaire teksten.10j j
Gedigitaliseerde kranten vormen een seriële bron, die in zijn ge-
heel doorzien en systematisch doorzocht kan worden. Deze bron
leent zich het beste voor het beantwoorden van onze vragen. Inter-
views met Leidenaren geven weliswaar inzicht in hoe individuele
stadsbewoners het gebruik nú herinneren en duiden, maar stellen
ons niet in staat de verandering van deze duiding door de tijd heen te
reconstrueren. Politie- en rechtbankverslagen bieden slechts zeer se-
lectief inzicht in de ontwikkeling van het gebruik, omdat het munten
strooien tot aan het einde van de negentiende eeuw slechts zelden
leidde tot juridisch ingrijpen. We hebben ons dus gewend tot contemporaine verslagen en her-
inneringen, vastgelegd in kranten, vanaf de vroegste vermelding van
het gebruik in 1841 tot op heden. In veel gevallen gaat het om kran-
tenbijdragen waarin redacteurs anekdotes opdissen, persoonlijke
herinneringen delen of interviews afnemen waarin anderen het ge-
bruik noemen. De materiaalverzameling voor dit artikel, afgesloten in mei 2016,
leverde uiteindelijk een corpus op van 162 Nederlandstalige teksten
uit de jaren 1841-2016 (tabel 1). Hiervan gaan er 13 over het strooi-
en van munten buiten Nederland. Van de overige 149 bronnen gaan
er 50 over strooien met gloeiende munten in Leiden (1841-2016); 5
over strooien met onverhitte munten in Leiden (1860-1940); 38 over
gloeiende munten elders in Nederland (1846-2015); en 56 over het
strooien van niet-verhitte munten elders in Nederland (1844-2016)
(tabel 2). Bij de selectie hebben we ernaar gestreefd zo veel mogelijk
verschillende meldingen en meningen over het strooien met verhit-
te en onverhitte munten te vinden. We hebben niet gepoogd om alle
afzonderlijke publicaties hierover op te nemen: krantenartikelen die
in meer kranten werden afgedrukt, zijn slechts een keer opgenomen. 70 VOL. 15, NO. 1, 2018 STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK Wanneer we de meldingen uitsplitsen over decennia (tabel 2),
worden enige trends zichtbaar. In de eerste plaats blijkt dat het
strooien van hete munten ook in andere Nederlandse plaatsen werd
gesitueerd, maar tegelijkertijd disproportioneel vaak geassocieerd
werd met Leiden: meer dan de helft van de berichten over hete mun-
ten (50 van de 88) gaat over de Sleutelstad. Zie voetnoot 10 voor de gebruikte bronnen. 11 M. Broersma, ‘Nooit meer bladeren? Digitale krantenarchieven als bron’, Tijdschrift voor Mediage-
schiedenis 14 (2011) 29-55; M. van den Bos en H. Giffard, ‘The grapevine. Measuring the influence of Gedigitaliseerde kranten als historische bron Bovendien: wanneer be-
richten na 1940 Leiden en munten strooien in een adem noemen,
gaat het altijd om verhitte munten. We zien hier de ontwikkeling van
het verhaal tot een Leidse toop. Tabel 1 Gebruikte Nederlandstalige teksten over het strooien van munten, ver-
deeld naar decennium en herkomst
Decennium
Totaal
Leidse
kranten
Andere
Leidse
bronnen
Andere
Nederlandse
kranten
Andere
Nederlandse
bronnen
1840
4
0
1
1
2
1850
2
0
1
0
1
1860
6
0
1
1
3
1870
5
0
0
1
4
1880
12
2
0
8
2
1890
10
0
0
8
2
1900
5
0
0
4
1
1910
16
1
0
13
2
1920
13
2
0
7
4
1930
20
2
0
15
3
1940
1
1
0
1
0
1950
4
0
1
3
0
1960
7
5
0
1
1
1970
12
4
1
5
2
1980
13
6
2
2
3
1990
10
2
2
5
1
2000
7
3
1
0
3
2010
15
1
3
4
6
Totaal
162
29
13
79
40
Zi
10
d
b
ik
b Tabel 1 Gebruikte Nederlandstalige teksten over het strooien van munten, ver-
deeld naar decennium en herkomst Zie voetnoot 10 voor de gebruikte bronnen. 71 BURGER & VAN DER STEEN TSEG Tabel 2 Verwijzingen naar het strooien van munten in onze bronnen, geordend op
uitvoering en locatie (verhit of niet, gesitueerd in Leiden of elders in het land)
Decennium
Hete munten in
Leiden
Hete munten
elders in
Nederland
Onverhitte
munten in Leiden
Onverhitte
munten elders in
Nederland
1840
1
1
0
2
1850
0
0
0
2
1860
0
0
1
2
1870
0
1
0
4
1880
4
2
0
4
1890
1
0
2
7
1900
0
0
0
4
1910
1
4
0
11
1920
2
4
1
3
1930
1
9
0
9
1940
0
0
1
0
1950
0
1
0
1
1960
5
0
0
2
1970
6
5
0
0
1980
9
1
0
3
1990
5
5
0
0
2000
5
2
0
0
2010
10
3
0
2
Totaal
50
38
5
56
Verwijzingen naar het strooien van munten in het buitenland zijn niet opgenomen. Dutch newspapers on Delpher’, Tijdschrift voor Tijdschriftstudies 38 (2015) 29-41; K. van Krieken, ‘Using
digital archives in quantitative discourse studies. Methodological reflections’, Tijdschrift voor Tijdschrift-
studies 38 (2015) 43-50.
12 B. Zelizer, ‘Why memory’s work on journalism does not reflect journalism’s work on memory’,
Memory Studies 1:1 (2008) 79-87; B. Zelizer en K. Tenenboim-Weinblatt (eds.), Journalism and memory
(Houndmills, Basingstoke 2014).
13 C. Kitch, ‘Placing journalism inside memory – and memory studies’, Memory Studies 1:1 (2008) 311-
320. Gedigitaliseerde kranten als historische bron Zie voetnoot 10 voor de
gebruikte bronnen Tabel 2 Verwijzingen naar het strooien van munten in onze bronnen, geordend op
uitvoering en locatie (verhit of niet, gesitueerd in Leiden of elders in het land)
Decennium
Hete munten in
Leiden
Hete munten
elders in
Nederland
Onverhitte
munten in Leiden
Onverhitte
munten elders in
Nederland
1840
1
1
0
2
1850
0
0
0
2
1860
0
0
1
2
1870
0
1
0
4
1880
4
2
0
4
1890
1
0
2
7
1900
0
0
0
4
1910
1
4
0
11
1920
2
4
1
3
1930
1
9
0
9
1940
0
0
1
0
1950
0
1
0
1
1960
5
0
0
2
1970
6
5
0
0
1980
9
1
0
3
1990
5
5
0
0
2000
5
2
0
0
2010
10
3
0
2
Totaal
50
38
5
56
Verwijzingen naar het strooien van munten in het buitenland zijn niet opgenomen. Zie voetnoot 10 voor de
gebruikte bronnen. Tabel 2 Verwijzingen naar het strooien van munten in onze bronnen, geordend op
uitvoering en locatie (verhit of niet, gesitueerd in Leiden of elders in het land) Verwijzingen naar het strooien van munten in het buitenland zijn niet opgenomen. Zie voetnoot 10 voor de
gebruikte bronnen. Verwijzingen naar het strooien van munten in het buitenland zijn niet opgenomen. Zie voetnoot 10 voor de
gebruikte bronnen. Daarnaast kunnen we drie periodes herkennen waarin het strooien van
munten vaker besproken werd: de laatste twee decennia van de negen-
tiende eeuw, de periode 1910-1940 en de periode 1960-2000. Tegelij-
kertijd zijn de aantallen per decennium zo laag, dat men op moet passen
met al te stellige gevolgtrekkingen. Er zitten enkele methodologische haken en ogen aan gedigitaliseer-
de kranten als historische bron, enerzijds veroorzaakt door de aard van
kranten an sich en anderzijds door de opzet van de digitale archieven.11 72 VOL. 15, NO. 1, 2018 STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK Kranten vormen geen neutrale bron van feitelijke informatie: zowel
hun commerciële als hun wereldbeschouwelijke karakter bepalen de
nieuwsselectie en kleuren de berichtgeving. Bovendien schrijven kran-
ten over incidenten, over gebeurtenissen die ongebruikelijk, schokkend
of controversieel zijn. Het alledaagse speelt in kranten slechts een klei-
ne rol. j Kranten vormen geen neutrale bron van feitelijke informatie: zowel
hun commerciële als hun wereldbeschouwelijke karakter bepalen de
nieuwsselectie en kleuren de berichtgeving. Gedigitaliseerde kranten als historische bron Bovendien schrijven kran-
ten over incidenten, over gebeurtenissen die ongebruikelijk, schokkend
of controversieel zijn. Het alledaagse speelt in kranten slechts een klei-
ne rol. j Nieuws is dan ook niet zozeer een afspiegeling van belangrijke
gebeurtenissen, maar een constructie, die de sociale werkelijkheid
mede schept, door te stipuleren wat belangrijk is. Lokale nieuws-
media rapporteren actuele incidenten – zoals een student die hete
munten naar kinderen gooit – en evalueren ze (‘een rare studenten-
streek’), maar ze leggen ook herinneringen vast van stadsbewoners
en dragen zo bij aan de vorming van het collectieve geheugen van de
stad.12 Aan de ene kant reflecteren kranten het collectieve geheugen,
wanneer zij alom bekende ‘weetjes’ als feiten publiceren. Aan de an-
dere kant sturen ze het collectieve geheugen, omdat mensen voor
hun kennis over hun omgeving voor een groot deel uit deze media
putten.13j Bij het werken met gedigitaliseerde kranten komen er nog een
aantal andere zaken om de hoek kijken. Zoeken op steekwoord kan
tot vertekeningen leiden wanneer men zich te weinig rekenschap
geeft van context en mogelijke betekenisverandering. Daarom is niet
alleen gezocht op gloeiende munten, maar ook op dito centen, dui-
ten en stuivers. Daarbij zijn de munten niet alleen gloeiend, maar ook
heet, verhit, witheet enzovoort. Tegelijkertijd kan zo’n manier van zoe-
ken nog altijd tot vertekeningen leiden, wanneer men zich niet be-
wust is van het feit dat er vaak niet alleen met munten, maar ook met
sigaren, sinaasappels en snoepgoed werd gestrooid (waarvan dikwijls
de spelling varieerde). Het is, kortom, zaak om niet alleen ‘breed’ te
zoeken (middels verschillende zoektermen), maar ook ‘contextueel’
te zoeken (dus niet alleen op munten). 73 14 ‘Drie miljoen nieuwe pagina’s’, Delpher Nieuwsbrief, 13 april 2016. Cijfers over treffers op basis van
zoekactie op 22 april 2016.
15 E. Elzenga, De inhuldigingen. Van Willem tot Beatrix (Amsterdam 2013) 143. BURGER & VAN DER STEEN BURGER & VAN DER STEEN TSEG Ten slotte dekt Delpher, de grootste digitale krantenbank in het
Nederlandse taalgebied, de afgelopen vier eeuwen niet volledig. De
opgenomen kranten zijn niet alleen geselecteerd op basis van oplage
en copyrightkwesties, maar de samenstellers hebben ook gestreefd
naar een zo breed mogelijk palet aan politieke en wereldbeschouwe-
lijke stromingen. Dit roept vragen op over de representativiteit: na-
mens wie sprak een bepaalde krant en welke c.q. hoeveel mensen la-
zen hem? Bovendien groeit Delpher nog altijd, zodat we hier niet te
maken hebben met een duidelijk afgebakend corpus aan bronnen – wat wederom implicaties heeft voor de representativiteit van de
bron. In april 2016 werden aan Delpher ongeveer drie miljoen nieu-
we krantenpagina’s toegevoegd. Hierdoor steeg het aantal – nog niet
op relevantie beoordeelde – treffers voor heete centen, een van onze
zoektermen, van 940 naar 1420.14 Dat laatste speelt bij de Leidse
krantendatabase geen rol, aangezien deze er aanspraak op maakt alle
drie de Leidse dagbladen uit de negentiende en twintigste eeuw vol-
ledig te hebben gedigitaliseerd. – wat wederom implicaties heeft voor de representativiteit van de
bron. In april 2016 werden aan Delpher ongeveer drie miljoen nieu-
we krantenpagina’s toegevoegd. Hierdoor steeg het aantal – nog niet
op relevantie beoordeelde – treffers voor heete centen, een van onze
zoektermen, van 940 naar 1420.14 Dat laatste speelt bij de Leidse
krantendatabase geen rol, aangezien deze er aanspraak op maakt alle
drie de Leidse dagbladen uit de negentiende en twintigste eeuw vol-
ledig te hebben gedigitaliseerd. 16 J. Simpson en S. Roud, Oxford dictionary of English folklore (Oxford 2000) 303. Zie ook: T.W. Carrick,
‘Scraps of English folklore, xviii. Cumberland’, Folklore 40 (1929) 278-290.
17 A. van den Breemer, ‘Townies & Gownies’, de Volkskrant, 15 september 2012. Over Chili: ‘Judaspop-
pen in de fik’, op: http://www.samsam.net/judaspoppen-in-de-fik (opgeroepen 5 december 2016). In de
vs leven herinneringen aan hete munten die met Halloween werden uitgedeeld aan trick-or-treaters:
S. Grider, ‘The razor blades in the apples syndrome’, in: P. Smith (ed.), Perspectives on contemporary le-
gend. Proceedings of the conference on contemporary legend, Sheffield, July 1982 (Sheffield 1984) 128-
140, aldaar 133-134.
18 J. van der Veen, Drentsch mozaïk, 1e stukje (Groningen 1844). Zie ook: J. ter Gouw, De volksvermaken
(Haarlem 1871) 265; ‘Sint Pieter Balslaan’ op: http://www.encyclopediedrenthe.nl/Sint%20Pieter%20
balslaan (13 feb. 2016). Van praktijk tot verhaal Het ‘ware’ verhaal
Hebben Leidse studenten ooit hete munten gegooid naar ‘het volk’? Ja,
dat hebben ze, maar van oorsprong was het gebruik niet typisch Leids
(of zelfs maar Nederlands), noch was het bij uitstek een studenten-
streek. Strooien met hete munten was deel van een oudere en veel bre-
dere folkloristische traditie. Bij bruiloften, meifeesten en intochten wer-
den tot aan het einde van de negentiende eeuw regelmatig hete munten
gestrooid. Voor zover het gebruik Leids en studentikoos was, stierf het
eind negentiende eeuw grotendeels uit, hoewel er incidenten bekend
zijn uit het interbellum en zelfs eenmaal in 1961. Strooien met hete centen was een variatie op het ‘te grabbel’ gooi-
en van muntgeld voor kinderen, armen en onderdanen. Vorsten lie-
ten ter gelegenheid van hun inhuldiging speciale ‘strooipenningen’
slaan, een gebruik dat in Nederland standhield tot het einde van de
negentiende eeuw.15 Het rondstrooien van munten was rond het mid- 74 VOL. 15, NO. 1, 2018 STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK den van de negentiende eeuw tevens een vast onderdeel van fees-
telijkheden, zoals lentefeesten en bruiloften. Maar ook buiten deze
hoogtijdagen om lieten welgestelden kinderen of armen delen in hun
rijkdom door hen een handvol munten toe te werpen. jjj Zowel bij feestelijkheden als bij het ‘alledaagse’ munten strooien
kwam het voor dat de strooiers de munten hadden verhit. In Neder-
land was het gebruik aan het einde van de negentiende eeuw zo be-
kend, dat het aangehaald werd in een lemma van het woordenboek
van Van Dale (1872, ‘omstrooien’): ‘De jongelui hebben gloeiende
centen onder de straatjongens omgestrooid’. Hete munten strooien was geen zuiver Nederlands gebruik, getui-
ge bijvoorbeeld de ‘Rye hot pennies’, die de burgemeester van Rye in
Sussex na zijn verkiezing traditioneel op het stadhuisplein zou heb-
ben gegooid. Deze ‘grabbelfolklore’ is ook in andere Engelse plaatsen
bekend, waarbij vaak plaatselijke ontstaansgeschiedenissen worden
aangehaald – ondanks het feit dat het gebruik wijdverbreid was.16 Zo
zijn er meldingen bekend uit het nabijgelegen Oxford, maar ook uit
Chili en de Verenigde Staten.17j Ook in Nederland zijn er verschillende lokale verhalen bekend
over het munten strooien. Zo kende Sint Pieter te Gees (gemeente
Coevorden) aan het begin van de negentiende eeuw de traditie van
het ‘balslaan’. 19 De getuige was er echter niet van gecharmeerd: ‘Nu, ik ben later nooit weer met soldaten … een her-
berg binnen gegaan’. Zie: ‘Uit den Atjeh-tijd’, Overveluwsch Weekblad/Harderwijkerkrant, 1 juli 1908.
20 ‘Een brief uit Leiden’, Nieuwe Hoornsche Courant, 10 mei 1884. Zie over Leiden als laatste stad met
een Meifeest ook: ‘De meiboom’, De Tijd, 30 april 1899.
21 Noord en Zuid: Akademische mengelingen uitgegeven door het taalminnend studenten-genootschap
[…] te Brussel, met de medewerking van studenten aan de verschillige Hollandsche en Belgische hooge scho-
len. Tweede deel (Brussel 1858) 79.
22 ‘Publieke vermakelijkheden in 1860’, Leidsch Dagblad, 1 maart 1960.
23 Leidsche studenten-almanak voor 1860 (Leiden 1860) 198-199. Van praktijk tot verhaal Een keer per jaar trok de schooljeugd langs de huizen
van jonggehuwden in het dorp, die met centen strooiden: ‘Onder het
grabbelen naar dezelven gebeurt het echter niet zelden, dat deze of
gene volwassene zijne ruwe aardigheden bot viert, door de vrolijk
grabbelende kleinen emmers vol water over het lijf te storten.’18 In andere gevallen kreeg het strooien van centen een grimmiger
karakter, vooral wanneer er onverwachte elementen aan het ‘spel’
werden toegevoegd. Zo beschreef een ooggetuige een gebeurtenis
aan het einde van negentiende eeuw, toen in Harderwijk geleger- 75 BURGER & VAN DER STEEN TSEG de soldaten vanuit een herberg ‘een veertig- of vijftigtal centen’ naar
zo’n vijftig kinderen gooiden, die zich er ‘als honden’ op stortten: ‘Dan
op eens worden van uit de hoogte een paar emmers water leegge-
stort met het gevolg, dat in een oogwenk de bende uiteenstuift.’ ‘Zul-
ke tooneeltjes’ vonden volgens de verteller ‘schier overal’ plaats.19 In
dit geval ging het echter niet om een lokaal gebruik, maar om een dat
met de soldaten meereisde. Het is daarom goed mogelijk dat het wa-
ter een toevoeging was waar de grabbelaars niet op rekenden. j In Leiden werd van oudsher op jaarlijkse vieringen zoals het lente-
feest en het Leids Ontzet (3 oktober) met munten gestrooid. Volgens
de Nieuwe Hoornsche Courant van 1884 werd elk jaar op 30 april de
fontein op de Leidse Vismarkt opnieuw in gebruik genomen met een
ritueel waarbij bewoners van de huizen rondom gloeiende centen uit
het raam gooien voor de ‘lieve jeugd’ bestaande uit ‘straatjongens en
fabriekers’.20jj Rond dezelfde tijd waren ook studenten betrokken bij het mun-
ten strooien. In 1858 trokken Leidse studenten naar het platteland,
waar zij centen naar ‘de boeren en boerinnetjes’ en hun kinderen
strooiden en ‘schaterden’ om het ‘worstelen om den buit’.21 Rond
1860 vond het gebruik ook plaats binnen de muren van de univer-
siteitsstad. De jaarlijkse bijeenkomst van studenten van de sociëtei-
ten Amicitia en Minerva ging standaard gepaard met het strooien
van munten: ‘In den namiddag verzamelt zich dan voor Minerva de
gehele bevolking uit de achterbuurten, om hunne vingers te komen
verschroeijen aan de heete centen, welke dan door de Muzenzonen
met kwistige hand onder hen worden uitgestrooid.’22 Toch leidde het
gebruik toen al tot spanningen. In 1860 werden studenten op straat
door ‘straatjongens’ gevolgd, die bij hen bedelden om centen. 24 ‘Nij kerk’, De Harderwij ker, 27 juli 1895. Van praktijk tot verhaal Toen
deze weigerden, scholden ze de studenten uit voor ‘kale spoelhon-
den’. Een verbolgen student typeerde ‘de Leidsche species van ’t ge-
nus straatjongen’ vervolgens als ‘zeker wel de ellendigste, naarste,
akeligste’ van Nederland.23 VOL. 15, NO. 1, 2018 76 STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK Illustratie 2 ‘Leyden’. De Breestraat bij Minerva. Ca. 1850, door Gerardus Johannes Bos (1825-1898)
(bron: http://www.archiefleiden.nl/home/collecties/beeldmateriaal/). Illustratie 2 ‘Leyden’. De Breestraat bij Minerva. Ca. 1850, door Gerardus Johannes Bos (1825-1898)
(bron: http://www.archiefleiden.nl/home/collecties/beeldmateriaal/). Het gebruik om munten te strooien – ook onverhitte – raakte in
de tweede helft van de negentiende eeuw omstreden. In de lande-
lij ke pers werd het gebruik vaker besproken. Aan het eind van de
eeuw deden zich een aantal noemenswaardige incidenten voor. In
Nij kerk brak een jongen in 1895 zij n been, toen hij viel bij het grab-
belen naar ‘eenige centen’.24 Een jaar later had er een veel tragischer
ongeval plaats in Leiden. Toen de bestuurder van een bierwagen de
Koornbeursbrug wilde afrij den, ‘bemerkte hij aan de Vischmarkt het
stilstaande rij tuig met heeren studenten, rondom waarvan vele men-
schen’. De studenten strooiden munten naar jonge kinderen. De be-
stuurder begon daarop ‘te schreeuwen zoo hard hij kon … doch dit
scheen niet gehoord te worden, althans de lui bleven staan’. De be-
stuurder verloor vervolgens de controle over de wagen en reed een
zevenjarig kind aan, dat hierdoor zwaar gewond raakte. ‘Het kind
werd onmiddellij k naar het politiebureel gedragen, waar het spoe- 24 ‘Nij kerk’, De Harderwij ker, 27 juli 1895. 77 BURGER & VAN DER STEEN TSEG dig overleed’.25 Weer twee jaar later, in 1898 liet koningin Wilhelmi-
na op scholen penningen uitdelen ter ere van haar inhuldiging. Bij
de inhuldiging van Willem iii in Amsterdam in 1849 was er op straat
hard gevochten om gestrooide munten; dat wilde men dit keer voor-
komen.26j Het is aannemelijk dat het gebruik rond de eeuwwisseling is uit-
gedoofd. In 1880 kozen Minervastudenten er tijdens de Diesviering
voor om het gooien van gloeiende munten achterwege te laten; de
‘gebruikelijke warme of gloeiende centen werden nu door sinaasap-
pelen vervangen’.27 In 1914 meldde de Sumatra Post dat het gebruik
in Leiden ‘zijn tijd heeft gehad’.28 In de jaren twintig werd het feno-
meen nog wel genoemd, maar slechts in de verleden tijd. Van praktijk tot verhaal In 1930 stel-
de de Provinciale Overijsselsche en Zwolsche Courant dat het strooien
van verhitte munten in Groningen sinds 1905 niet meer voorkwam.29
Ook vanuit Leiden waren er geen nieuwe berichten over het gebruik
ontvangen: ‘Wij weten niet, of er in Leiden ook nu nog op 3 October
heete centen worden gestrooid.’30 Volgens sommigen leefde het gebruik tot in het interbellum
voort.31 Het is mogelijk dat het in deze periode incidenteel nog voor-
kwam, maar het is zeer onwaarschijnlijk dat het toen nog regelmatig
gebeurde. Opvallend is dan ook dat de variatie in de beschrijving van
het gebruik steeds groter wordt, naarmate het verder in de twintigste
eeuw wordt geplaatst. 25 ‘Leiden, 9 november’, Leidsch Dagblad, 10 november 1896; ‘Gemengd nieuws’, Leidsch Dagblad,
11 november 1896. Volgens de Schoonhovense Courant ging het om een vijfjarig jongetje dat zich niet op
tijd uit de voeten kon maken ‘zoodat de bierwagen over den armen knaap heenging en hem letterlijk de
borstkas verbrijzelde’. De jongen stierf ter plekke. Schoonhovensche Courant, 11 november 1896. 26 P. Jonas, Neêrlands koning in Neêrlands hoofdstad. Eene herinnering aan 11 en 12 mei 1849 (Amster-
dam 1849) 53; D van der Meulen KoningWillem iii 1817-1890 (Amsterdam 2013) 223 25 ‘Leiden, 9 november’, Leidsch Dagblad, 10 november 1896; ‘Gemengd nieuws’, Leidsch Dagblad,
11 november 1896. Volgens de Schoonhovense Courant ging het om een vijfjarig jongetje dat zich niet op
tijd uit de voeten kon maken ‘zoodat de bierwagen over den armen knaap heenging en hem letterlijk de
borstkas verbrijzelde’. De jongen stierf ter plekke. Schoonhovensche Courant, 11 november 1896. 26 P. Jonas, Neêrlands koning in Neêrlands hoofdstad. Eene herinnering aan 11 en 12 mei 1849 (Amster-
dam 1849) 53; D. van der Meulen, Koning Willem iii, 1817-1890 (Amsterdam 2013) 223. 28 ‘Uit de Hofstad’, Sumatra Post, 6 februari 1914.j 28 ‘Uit de Hofstad’, Sumatra Post, 6 februari 1914. 29 ‘Heete centen: Baldigheid vroeger en nu’, Provinciale Overijsselsche en Zwolsche Courant, 5 mei 1930. Zie ook Nieuwsblad van het Noorden, 23 december 1922: ‘Voor omstreeks 130 jaar zag een winkelier dat
eenige dronken heeren zich vermaakten door voor hun clubgebouw eenige gloeiende centen onder een
troep jongens te gooien’. 30 ‘Heete centen. Baldigheid vroeger en nu’, Provinciale Overijsselsche en Zwolsche Courant, 5 mei 1930. 31 ‘Toen de tv kwam, was de gezelligheid voorbij’, Leidsch Dagblad, 7 april 1984. 32 Klikspaan, Studentenschetsen. Studieuitgave, bezorgd door A. Kets e.a. Deel 1: Teksten (Den Haag
2002) 159.
33 Willem Essensteyn. Een aangenaam verhaal van zijne goede daden en gelukkige tevredenheid (Leiden
1845). 33 Willem Essensteyn. Een aangenaam verhaal van zijne goede daden en gelukkige tevredenheid (Leiden
1845). 32 Klikspaan, Studentenschetsen. Studieuitgave, bezorgd door A. Kets e.a. Deel 1: Teksten (Den Haag
2002) 159.j Van praktijk tot verhaal Zie ook: ‘Pleidooi voor
woede’, De Waarheid, 2 oktober 1984; ‘Corpsballen’, Het Vrije Volk, 2 maart 1977. Volgens een verteller
vond het munten strooien zelfs tot in de jaren vijftig plaats: ‘Het volk versus de student’, Mare, 21 septem-
ber 2006. 78 VOL. 15, NO. 1, 2018 34 ‘Feuilleton. Eene variatie op een oud lied’, Het Nieuws van den dag, 5 december 1882.
35 Casacara, ‘Een praatje over Maskerade ii’, Vlissingsche Courant, 5 maart 1885.
36 ‘Onder het zoeklicht’, De Tijd, 29 april 1930.
37 Provinciale Geldersche en Nijmeegsche courant, 3 mei 1930. STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK Het verhaal verteld Al voordat het gebruik van munten strooien door studenten uitstierf,
werd het verhaal erover gebruikt om mensen te typeren, gedrag af te
keuren en bepaalde waarden te huldigen. Het verhaal ontwikkelde zich
tot een retorische toop die regelmatig werd aangehaald in nieuwsbe-
richten, maar ook in persoonlijke verslagen, verhalen en romans. De
oudste en bekendste vermelding stamt uit Studentenschetsen (1841)
van de student-auteur Klikspaan (pseudoniem van Johannes Kneppel-
hout). In dit boek komt de student Flanor voor, van wie wordt gezegd: Flanor was het die op den derden October de meeste en heetste centen uit
het raam gooide op de deftige Leidsche wandelaars, die dan door gretige
kleine straatjongens bestormd en omvergehaald werden en, Gullivers in
handen van Lilliputters, dachten om te komen onder de worsteling welke
om, over en op hen geleverd werd, terwijl de onvermoeibare Studiosus, bij-
gestaan door onvermoeibare vrienden, steeds meer gloeijende centen naar
beneden liet regenen, hetgeen steeds meer gehuil, gevecht, getrap, gekrab
en bloedneuzen onder de lieve Leidsche jeugd te weeg bragt.32 Tussen de types die Klikspaan opvoert, is Flanor de ideale student: de
gulle, brutale gangmaker van de groep. Dat hij de straatjongens laat
vechten om zijn hete centen en zo de ‘deftige Leidsche wandelaars’ te
grazen neemt, is voor de schrijver een voorbeeld van studentikoze le-
venskunst. Dat het gebruik echter – niet alleen de practical joke met hete centen,
ook munten strooien in het algemeen – ook toen al op afkeuring stuitte,
blijkt uit een kinderboek dat nog geen vier jaar later verscheen. In Wil-
lem Essensteyn (1845) geeft een vader zijn drie kinderen elk vijf gulden. Een van de drie, Jan, wisselt de guldens om in kleine munten, die hij op
straat gooit om te zien hoe arme kinderen erom vechten. De vechtpar-
tijen geven Jan veel plezier, maar zijn vader keurt Jans gedrag streng af.33 jj
Deze kritiek neemt toe in de tweede helft van de negentiende eeuw,
maar studenten zelf zagen er lange tijd geen kwaad in. In een feuilleton
uit de jaren 1880 komt een baldadige groep Leidse jongeren voor, onder
wie een jongeheer ‘die het volgend jaar, als het staatsexamen niet weder
ingesteld wordt, hoopt student te worden’. STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK Hij ‘stelt voor, om gloeiende
centen uit te strooien’, maar de rest verkiest het om snoepgoed naar de 79 BURGER & VAN DER STEEN TSEG kinderen te strooien.34 Het gebruik was kennelijk onder de jongeren zijn
aantrekkingskracht aan het verliezen.jj Kritiek werd ook in reactie op daadwerkelijke praktijken geuit. Zo be-
kritiseerde ene ‘Casacara’ in 1885 in een uitgebreid stuk de heer Waring
uit Vlissingen, die zijn meid ‘elken eerste Zaterdag van de maand’ centen
liet strooien voor de armen, die bij het grabbelen leken op ‘een troep kip-
pen’. Het gebruik was volgens Casacara denigrerend en beledigend.35 Na
de eeuwwisseling werd het munten strooien steeds zeldzamer en wan-
neer het gebeurde, leidde dat telkens tot politieoptreden. Hoe minder
het gebruik voorkwam, hoe heviger de reacties in de pers werden. Toen
twee jongemannen in 1930 in Rotterdam gloeiende munten hadden
gestrooid, waarna kinderen brandblaren hadden opgelopen, reageer-
den verschillende journalisten en brievenschrijvers met verontwaardi-
ging. ‘Je zoudt ze ten minste met een paar druppels kokende olie willen
bewerken’, stelde een schrijver.36 Een ander stelde: ‘Wij meenen, dat de
rechter in uitzonderingsgevallen het recht zou moeten hebben om be-
paalden veroordeelden een pak slaag te doen geven.’37 38 ‘Vijf-en-twintig-jarig bestaan van de afdeeling Leiden der sdap’, Leidsch Dagblad, 2 juni 1924.
39 ‘Groot-Nederlandsch Studentencongres’, Nieuwe Leidsche Courant, 22 april 1925. Zie ook: ‘Het tien-
de groot Nederlandsch studentencongres’, Leidsche Courant, 21 april 1925.
40 H. Kramers e.a., Het Leidse Volkshuis: Geschiedenis van een stichting sociaal-kultureel werk (Leiden,
1982); J.P.M. Roozen, ‘Leidse bibliotheken rond de eeuwwisseling’, Leids Jaarboekje (Leiden 1983) 149-
166; W. Otterspeer, Van allegorisch naar echt-historisch en terug. De geschiedenis van de Leidse Studenten
maskerade (Leiden 1980).
41 F. de Raat, ‘Leiden. De ongenadige metamorfose van Leiden’, nrc Handelsblad, 21 december 1996. Jaren twintig: de student als deel van het volk Jaren twintig: de student als deel van het volk In de twintigste eeuw kwam het munten strooien nog maar zelden voor. Des te meer werd er echter over gesproken, waarbij het verhaal telkens
een nieuwe lading kreeg. Als anekdote werd het een middel om te reflec-
teren op de rol van de student in de stad en op de staat van de stad zelf. Dat gebeurde met name in de periode van 1960 tot het begin van de ja-
ren negentig en in mindere mate ook in de jaren twintig. In de jaren twintig haalden zowel Leidse sociaaldemocraten als con-
servatieven het verhaal aan om hun eigen beweging aan te prijzen. Te-
genover de oude verhoudingen, waarin de student tegenover de wer-
kende bevolking stond, plaatsten zij hun eigen beweging, waarin deze
tegenstelling was overwonnen ten bate van een nieuw maatschappij-
beeld, waarin beide groepen harmonieus naast elkaar zouden bestaan. Zo haalden sociaaldemocraten in 1924 het voorbeeld aan van stu-
denten die ‘eertijds’ gloeiend gemaakte centen naar het proletariaat VOL. 15, NO. 1, 2018 80 STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK gooiden, ‘terwijl velen hunner thans welbewust de vaan der bevrijding
volgen’.38 Ook conservatieve studenten spraken in 1925 over het cen-
ten strooien door studenten, om vervolgens te betogen dat de laatsten
inmiddels een deel waren geworden van de natie: ‘Hollanders zijn wer-
kers[,] van den professor, tot den koopman, van den boer tot den wever. [De student] is geen weeldeproduct meer van zijn omgeving, die gloei-
ende centen uit zijn raam strooit en aldus het privilegie van zijn studen-
ten-stand demonstreert.’39 Dat de historische waarheid in deze anekdote ondergeschikt was aan
de boodschap die ermee verteld werd, blijkt uit de terloopse melding
van het gebruik, dat niet verder werd toegelicht. In beide vertogen werd
het centen strooien geplaatst in een onbestemd ‘vroeger’, werd er geen
melding meer gemaakt van het gooien van sinaasappels en sigaren naast
de munten of het gooien van water over de grabbelende kinderen. Uit de
vluchtige vermelding blijkt tevens dat de auteurs ervan uitgingen dat de
lezer het verhaal al kende.jj Tegelijkertijd riepen de stellige beweringen van de sociaaldemocra-
ten en conservatieven ook een spanning op: was de wens hier vader
van de gedachte? Rond de eeuwwisseling was de rol van de student in
de stad een belangrijk thema geweest. 42 ‘Flinke boete voor rare streek’, Leidsche Courant, 24 januari 1961; ‘Rare studentenstreek flink beboet’,
Nieuwe Leidsche Courant, 24 januari 1961; ‘Studentenstreek flink beboet’, Leidsch Dagblad, 25 januari
1961.
43 I. Leermakers, Leidse Stag Drukkerij. Coöperatieve Vereniging ua (Leiden 2015), 16.
44 ‘Feestend Minerva en het klootjesvolk’, Leidsch Dagblad, 3 december 2013. 42 ‘Flinke boete voor rare streek’, Leidsche Courant, 24 januari 1961; ‘Rare studentenstreek flink beboet’,
Nieuwe Leidsche Courant, 24 januari 1961; ‘Studentenstreek flink beboet’, Leidsch Dagblad, 25 januari
1961. Jaren twintig: de student als deel van het volk Via het Toynbeewerk probeer-
den studenten een bijdrage te leveren aan de verheffing van het volk en
in 1905 en 1910 organiseerden zij grote historische optochten door de
stad (maskerades) als geste om hun verbondenheid met de stad te bena-
drukken.40 Na 1910 waren deze inspanningen echter op een lager peil
komen te staan. De economische crisis van de jaren dertig deed de socia-
le tegenstellingen in de stad vervolgens weer toenemen. Volgens de jour-
naliste Friederike de Raat, terugblikkend in 1996, was Leiden lange tijd
een ‘stad met twee gezichten’, waarbij de tweedeling zich ook geogra-
fisch openbaarde: ‘Het noorden en oosten van de binnenstad was over-
wegend eenvoudig en werd grotendeels bewoond door arbeiders en am-
bachtslieden. Het monumentalere zuiden werd gedomineerd door de
universitaire elite rond het Rapenburg. De Rijn vormde de scheiding.’41 81 BURGER & VAN DER STEEN TSEG Pas in de jaren zestig zouden de sociale verhoudingen in Leiden sterk
opgeschud worden, door het opgroeien van de babyboomers, de ster-
ke groei van de studentenpopulatie en het verdwijnen van de industrie. Het gebruik van het hete muntjes strooien was toen al lang verdwenen,
maar het verhaal erover werd juist prominenter. Nadat er in de jaren
veertig en vijftig geen melding werd gemaakt over het strooien van gloei-
ende centen in Leidse kranten, nam het aantal besprekingen in de jaren
zestig, zeventig en tachtig toe. 43 I. Leermakers, Leidse Stag Drukkerij. Coöperatieve Vereniging ua (Leiden 2015), 16. 44 ‘Feestend Minerva en het klootjesvolk’, Leidsch Dagblad, 3 december 2013. Jaren zestig-tachtig: studentenrevolte en stadsvernieuwing J
g
g
g
In de jaren zestig werd het verhaal over de hete munten opnieuw in-
tensief besproken. Daarbij bleek de gespannen verhouding tussen ver-
haal en werkelijkheid. Nadat het strooien van munten in 1960 door de
drie Leidse kranten in algemene zin was aangehaald, besloot een medi-
cijnenstudent in 1961 de proef op de som te wagen. Hij gooide verhit-
te stuivers uit het raam van zijn studentenkamer, waarop kinderen hun
handen brandden. De student werd aangehouden en voor de rechter ge-
daagd, van wie hij een boete van dertig gulden kreeg. De zaak kreeg enige
aandacht in de Leidse pers,42 maar in latere verwijzingen naar het mun-
ten strooien werd nooit meer verwezen naar dit daadwerkelijke incident.j Hoewel het strooien van hete centen dus geen wijdverbreid gebruik
was in Leiden, werd het wel als zodanig aangehaald; als ideale illustra-
tie van een veel breder probleem. Toen de studente Ine Leermakers eind
jaren zestig naar Leiden kwam, ging het verhaal nog altijd rond, met
een duidelijke boodschap: ‘De “corpsballen” waren niet geliefd onder de
Leidse bevolking. Ik had verhalen gehoord [sic], dat ze vanaf hun balkon
gloeiende munten op straat gooiden voor het Leidse volk, dat zich dan
de handen brandde.’43 Volgens sommigen liet het incident zien dat er in
de stedelijke verhoudingen nog weinig veranderd was. Toen het gebouw
van Minerva in 1959 tot de grond toe afbrandde, moest ‘menige voorbij-
ganger … wel gniffelen’, want ‘gewone Leienaars en Minervanen, dat was
water en vuur’.44 Maar het verhaal haakte ook in op ontwikkelingen binnen de Leid-
se studentenbeweging. Deze was halverwege de jaren zestig opgekomen
en had in 1969 haar hoogtepunt bereikt met de bezetting van het Aca- VOL. 15, NO. 1, 2018 VOL. 15, NO. 1, 2018 82 STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK demiegebouw. Toen de regering daarop reageerde met bestuurshervor-
mingen, ontstonden er tegenstellingen onder de studenten: moest men
zich richten op de verdere democratisering van de universiteit of juist de
blik verruimen en zich verbinden met de strijd van de Leidse stadsbevol-
king? 45 S. Slangen, ‘ “Ouwe lullen motten weg”. Studentenprotest, acties en het alternatieve circuit in Leiden
in de late jaren zestig’, in: D. Wintgens Hötte (ed.), De jaren zestig. Actie, kunst en cultuur in Leiden (Leiden
1989) 29-51.
46 W. van der Kooi, ‘Vernieling’, Groene Amsterdammer, 16 februari 1994.
47 J. Bloemkolk, ‘De jongen die stierf onder de roetkap’, Het Parool, 4 december 1998. 45 S. Slangen, ‘ “Ouwe lullen motten weg”. Studentenprotest, acties en het alternatieve circuit in Leiden
in de late jaren zestig’, in: D. Wintgens Hötte (ed.), De jaren zestig. Actie, kunst en cultuur in Leiden (Leiden
1989) 29-51. Jaren zestig-tachtig: studentenrevolte en stadsvernieuwing Het conflict leidde onder andere tot de ondergang van de Algeme-
ne Leidse Studentenvereniging (alsv) en de vorming van een afdeling
van de Kommunistische Eenheidsbeweging Nederland (voorloper van
de sp) in Leiden.45j In het zelfbeeld van maatschappelijk geëngageerde studenten – ook
in andere studentensteden – speelde het verhaal over de munten een
belangrijke rol, zoals bijvoorbeeld blijkt uit een herinnering van de jour-
nalist Walter van der Kooi, die in zijn studententijd het (Amsterdamse)
studentencorps haatte. Hij weigerde in die periode zelfs een glas bier
van een medestudent uit een villa in Amsterdam-Zuid, want: ‘Ik ken-
de het verhaal over, bij wijze van spreken, zijn grootvader die gloeiende
centen uit het raam van de sociëteit gooide waar door kindertjes uit De
Pijp, bij wijze van spreken mijn grootvader, om gevochten werd’.46 Het verhaal paste goed in een populaire redenering, volgens welke
corpsstudenten niet alleen asociaal, maar ook boven de wet verheven
waren. Illustratief daarvoor was niet alleen het verhaal over het munten
gooien, maar ook de zogenaamde roetkap-affaire van 1965; een tragisch
incident bij de ontgroeningen in het Utrechts Studenten Corps (usc),
waarbij een aanstaand lid een roetkap over zijn hoofd geplaatst kreeg
en stikte. De daders werden aangeklaagd, maar kregen uiteindelijk zeer
lage straffen opgelegd. Omdat de autoriteiten in dezelfde periode hard
optraden tegen Provo’s en andere activisten was het oordeel contro-
versieel.47 Terwijl in de praktijk het werpen van munten leidde tot poli-
tie-ingrijpen, speelde de verhevenheid boven de wet toch een belangrij-
ke rol in het verhaal dat erover verteld werd. In de discussies over de rol van de student die in de jaren zestig ge-
voerd werden, liepen lokale en landelijke ontwikkelingen dus door el-
kaar heen. Toch kreeg het verhaal in de periode daarop een sterk lokale
dimensie, omdat de stedelijke verhoudingen in Leiden in de jaren zestig,
zeventig en tachtig stevig op de proef werden gesteld. Leiden was van
oudsher een arme industriestad, die gekenmerkt werd door een scherpe 83 BURGER & VAN DER STEEN TSEG tweedeling tussen de arbeidersbevolking en de ‘universitaire elite’ (stu-
denten en professoren).48j In de jaren zestig golden de lonen in Leiden nog altijd als de laagste
van Nederland, terwijl Het Vaderland de stad uitriep tot ‘tweede lands-
kampioen krotten’.49 Leiden raakte in de daaropvolgende periode in een
crisis. De stedelijke industrie verdween, waardoor de werkloosheid steeg
tot vijftien procent, beduidend hoger dan het landelijk gemiddelde. 48 F. Boersma, ‘Economische en sociale verhoudingen. Breuk met het verleden’, in: Van Maanen, Leiden,
59-99.
49 C. Smit, ‘Rondkomen in Leiden, 1850-2000’, Jaarboek Dirk van Eck (Leiden 2001) 105-152, 124;
Idem, Strijd om kwaliteit. De geschiedenis van de volkshuisvesting in de regio Leiden (Leiden 2006) 127-
130; Idem, ‘Een troosteloze aanblik. Leiden in de jaren zestig’, in: Wintgens Hötte, De jaren zestig, 17-28.
50 Idem, Strijd om kwaliteit, 176-178.
51 Boersma, ‘Economische en sociale verhoudingen’.
52 W. Otterspeer, ‘De Universiteit’, in: Van Maanen, Leiden, 190-205.
53 ‘Wat ik van Leiden vind’, Leidsche Courant, 1 november 1969.
54 R. Kagie, Leiden Noord. Beeld van een wijk (Rijswijk 1981) 6. 48 F. Boersma, ‘Economische en sociale verhoudingen. Breuk met het verleden’, in: Van Maanen, Leiden,
59-99. 55 ‘Leeuw van Njord met pensioen’, Leidsch Dagblad, 5 maart 1980.
56 ‘Minerva tapt uit een ander vaatje’, Leidsche Courant, 1 juli 1989. Zie ook: ‘We willen het lustrum niet
voor onszelf houden’, Leidsch Dagblad, 1 maart 1989.
57 ‘Oeverloos’, De Peueraar, februari 1991; ‘Marsmannetjes’, Leidsch Dagblad, 10 januari 1991.
58 Leidse Studentenbond, Nog meer snikken en glimlachjes … Over de ‘Leidsche Student’ (Leiden 1980) 9.
59 ‘Oeverloos’, De Peueraar, februari 1991; ‘Marsmannetjes’, Leidsch Dagblad, 10 januari 1991. Jaren zestig-tachtig: studentenrevolte en stadsvernieuwing De
stedelijke financiën kwamen in zwaar weer en de stad werd onder cura-
tele gesteld. De stedelijke vernieuwing verliep traag en moeizaam. Een
onderzoeker stelde in 1976: ‘Alle gemeenten hebben problemen, maar
Leiden heeft ze allemaal.’50 Pas in de jaren negentig werd Leiden weder-
om een welvarende stad, vooral door de opkomst van biofarmaceuti-
sche industrie.51 De universiteit werd steeds belangrijker als werkgever
en pijler van de stedelijke economie.52 Terwijl de stad middels een moei-
zaam proces ingrijpend transformeerde, veranderden de rol van de uni-
versiteit en de student in de stad evenzeer. Zowel studenten als ‘gewone’ Leidenaren reflecteerden op deze ont-
wikkelingen. Het verhaal over de gloeiende munten werd daarbij inzet
van een discussie over de positie van de stad en van de student. Zo haal-
de de Zangeres zonder Naam in 1969 het verhaal van de gloeiende mun-
ten aan om het oude Leiden te beschrijven. Zij vervolgde: ‘Als ik Leiden
nu bezoek, vind ik de stad enorm vooruitgegaan, dynamischer, waardi-
ger, kortom een goede stad om in te leven. Veel beter dan in de tijd toen ik
jong was.’53 Deze redenering bleef tot in de jaren tachtig populair. Zo ver-
telde een oudere bewoner van Leiden Noord in 1981 aan Rudie Kagie,
nadat hij over de ‘lamstralen’ had verteld die gloeiende munten uit hun
koetsjes hadden gegooid: ‘Zulke studenten heb je gelukkig niet meer. De
studenten die we nu zien in de wijk zijn aardige jonge mensen. Ze hel-
pen volwassenen met de huiswerkcursus.’54 Weer een andere ‘gewone’
Leidenaar, een trainer bij de studentenroeivereniging Njord, was zo te
spreken over de houding van de studenten dat hij het verhaal geheel in VOL. 15, NO. 1, 2018 84 STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK twijfel trok: ‘Want wie dat praatje ooit in de wereld heeft gebracht …’55 Ook de redeneringen van de corpsstudenten zelf pasten binnen dit
format. In 1989 gaven twee bestuursleden van Minerva ‘volmondig’ toe
dat hun voorgangers gloeiendhete centen van het balkon van de socië-
teit hadden gegooid. Maar, zo stelden ze: ‘Nu is het anders, de studenten
moeten wel degelijk om zich heen kijken en zich aanpassen.’56 In 1991
stelde de voorzitter van Minerva dat het gedaan was met de ‘misstanden
van vroeger’. Jaren zestig-tachtig: studentenrevolte en stadsvernieuwing Inmiddels hadden de corpsstudenten zich ontwikkeld tot
beschaafde en maatschappelijk bewuste burgers: ‘Binnen Minerva is er
nu zelfs een divisie [sic] die zich wijdt aan burgerzaken’.57jj Tegelijkertijd werd deze claim regelmatig ter discussie gesteld. In 1981
haalde de Leidse Studentenbond (lsb) het centen strooien van vroeger
aan, om vervolgens te stellen dat er sindsdien maar weinig veranderd
was. In een brochure werd er een continuïteit geschapen tussen de elitai-
re, reactionaire studentenclubs uit de negentiende eeuw en de corpsstu-
denten uit de jaren zeventig en tachtig. In een van de bijdragen werd een
lange reeks van incidenten opgesomd uit de afgelopen tweehonderd jaar,
waarin Leidse corpsstudenten het de Leidse bevolking zuur hadden ge-
maakt. Een van deze incidenten behelsde het feit ‘dat studenten gloeiend
hete centen naar het volk gooiden op 3 oktober’, wat volgens de auteur
‘waarschijnlijk wel bekend’ was. De opsomming eindigde met een kor-
te uitweiding over incidenten in het jaar 1972, onder de titel ‘nog steeds
dezelfden’.58 Daarmee werd expliciet gemaakt dat volgens de auteur de
houding van de Leidse corpsstudent in tweehonderd jaar ongewijzigd
was gebleven. In 1991 was de positie van de student in de stad zelfs the-
ma van een debatavond in het poppodium en jongerencentrum lvc. Daar
stelde een man uit het publiek over de Minervanen: ‘Bah, jullie zitten op
een ivoren toren en werpen centen naar het volk. Maar we leven in een
verzorgingsstaat en er is dus niemand afhankelijk van liefdadigheid.’59 De discussie in het lvc ging niet over de vraag of studenten wel of
niet met gloeiende munten hadden gestrooid. Het ging om de exempla-
rische waarde van de anekdote: had de corpsstudent zich inmiddels ont-
wikkeld tot een maatschappelijk bewuste burger, of niet? Had de Leid-
se burgerbevolking zich ontworsteld aan onmondigheid en armoede, 85 BURGER & VAN DER STEEN TSEG of niet? Deze twee vragen stonden telkens weer ter discussie wanneer
het verhaal over de gloeiende munten aangehaald werd. Discussies over
de Leidse student raakten zo onlosmakelijk verbonden met discussies
over de staat van de stad. Daarbij gebruikte een groep het voorbeeld van
munten strooien om te laten zien dat de situatie sindsdien sterk verbe-
terd was, terwijl de tweede groep juist benadrukte dat armoede nog al-
tijd een groot probleem was in de stad. Conclusie Het gebruik om (gloeiende) munten te strooien heeft zijn wortels in de
folklore; het was niet typisch Leids en het was geen typische studenten-
streek. Het gebruik wordt in Leiden echter wel zo herinnerd: als teke-
nend voor de Leidse identiteit. Deze specifieke herinnering aan het al-
gemene gebruik heeft zich vooral ontwikkeld in de twintigste eeuw, toen
het strooien van munten als gebruik vrijwel uitgestorven was. Hoe is
deze ontwikkeling te verklaren? g
In de eerste plaats ging de anekdote een centrale rol spelen in dis-
cussies over de rol van de student in de maatschappij. Deze discus-
sies vonden al plaats voor de Tweede Wereldoorlog, maar begonnen
pas echt in de jaren zestig van de vorige eeuw. Zowel voor Leidena-
ren als voor Leidse studenten was het een belangrijk thema en het
verhaal over de gloeiende munten vormde bij discussies een vast re-
ferentiepunt. Toch was deze discussie niet typisch Leids – ze vond
ook plaats in andere studentensteden. Het verhaal werd pas echt een
Leidse toop in de jaren zestig, zeventig en tachtig, omdat het toen een
tweede rol ging vervullen. In deze periode veranderde Leiden van een
arme, industriële, verkrotte en verdeelde stad in een welvarende stad. De overgang was moeizaam en langdurig en ging gepaard met hoge
werkloosheid en sociale spanningen. Stadshistoricus Cor Smit noemt
de jaren zeventig en tachtig daarom een ‘donkere periode in de socia
le geschiedenis van Leiden’.60 Juist in deze periode werd het verhaal
over de munten inzet van discussies over de vraag of Leiden zijn ach-
tergestelde positie aan het overwinnen was of niet. Volgens sommi-
gen toonde het verhaal dat Leiden inmiddels grondig was veranderd,
terwijl anderen juist continuïteit zagen. Toen het overgangsproces
halverwege de jaren negentig was voltooid, begon het verhaal in Lei- In de eerste plaats ging de anekdote een centrale rol spelen in dis-
cussies over de rol van de student in de maatschappij. Deze discus-
sies vonden al plaats voor de Tweede Wereldoorlog, maar begonnen
pas echt in de jaren zestig van de vorige eeuw. Zowel voor Leidena-
ren als voor Leidse studenten was het een belangrijk thema en het
verhaal over de gloeiende munten vormde bij discussies een vast re-
ferentiepunt. Toch was deze discussie niet typisch Leids – ze vond
ook plaats in andere studentensteden. 60 Smit, Strijd om kwaliteit, 176-177. Conclusie Het verhaal werd pas echt een
Leidse toop in de jaren zestig, zeventig en tachtig, omdat het toen een
tweede rol ging vervullen. In deze periode veranderde Leiden van een
arme, industriële, verkrotte en verdeelde stad in een welvarende stad. De overgang was moeizaam en langdurig en ging gepaard met hoge
werkloosheid en sociale spanningen. Stadshistoricus Cor Smit noemt
de jaren zeventig en tachtig daarom een ‘donkere periode in de socia
le geschiedenis van Leiden’.60 Juist in deze periode werd het verhaal
over de munten inzet van discussies over de vraag of Leiden zijn ach-
tergestelde positie aan het overwinnen was of niet. Volgens sommi-
gen toonde het verhaal dat Leiden inmiddels grondig was veranderd,
terwijl anderen juist continuïteit zagen. Toen het overgangsproces
halverwege de jaren negentig was voltooid, begon het verhaal in Lei- VOL. 15, NO. 1, 2018 86 STUDENTEN STROOIEN HETE CENTEN VOOR HET VOLK den aan betekenis en zeggingskracht te verliezen. Desondanks wordt
het gebruik nog veelvuldig aangehaald, niet zozeer in kranten, maar
wel op bijvoorbeeld weblogs.j Ons onderzoek illustreert hoe collectief geheugen en stedelijke
identiteit met elkaar verbonden zijn en elkaar bepalen. Naarmate de
stad verandert, veranderen ook de verhalen over en de herinneringen
aan de stad. In de mate dat kranten informatie geven over informele
stadsverhalen, bieden ze ook de gelegenheid om de verandering van
deze verhalen te reconstrueren en te verklaren. Het gaat in ons on-
derzoek niet zozeer over het waarheidsgehalte van het verhaal, maar
over de veranderende betekenis die het verhaal door de tijd heen
werd toegekend. Kranten bieden de mogelijkheid om de ontwikke-
ling daarvan te onderzoeken, omdat het verhaal daarin vaak wordt
aangehaald: in opmerkingen van journalisten, in interviews met ‘ge-
wone’ Leidenaren en in terugblikken. Het verhaal over de gloeiende
munten laat zien hoe de reflecties op de stedelijke identiteit veran-
derden, omdat verschillende groepen naar het gebruik verwezen en
hier door de tijd heen verschillende betekenissen aan gaven. Ons onderzoek bevat een aantal aanknopingspunten voor verder
onderzoek. In de eerste plaats is het interessant om te weten te ko-
men of het verhaal nu nog leeft onder Leidenaren en Leidse studen-
ten. Middels enquêtes zou zo’n onderzoek kwantitatief opgezet kun-
nen worden. Helaas zijn de mogelijkheden om zulk onderzoek ook
een historische dimensie te geven beperkt. 61 K. Greven, ‘Zo werd een groep dronken psv-supporters wereldnieuws’, nrc Handelsblad, 17 maart
2017. 62 M. Borst, ‘Vindicat staat voor vriendschap, eer en beschaving’, Dagblad van het Noorden, 1 oktober 2016.
63 De ziel van Leiden. Conclusie Een andere mogelijkheid
zou kunnen zijn om te onderzoeken in hoeverre het verhaal over de
gloeiende munten verbonden was met – en versterkt werd door – an-
dere lokale verhalen zoals de anekdote dat de Leidse bevolking – on-
danks de grote studentenpopulatie – gemiddeld het laagste iq had
van Nederland. Dit verhaal deed vooral opgeld in de jaren zeventig en
tachtig en thematiseert op een gelijkaardige manier de positie van de
student in de stad en de al dan niet achtergestelde positie van Leiden.j Het verhaal over gloeiende munten wordt nog altijd verteld. Sterker nog, de praktijk van het munten strooien bestaat nog altijd. In maart 2017 kwamen psv-supporters in het nieuws omdat zij in
Madrid Sinti en Roma naar munten lieten grabbelen.61 Van een ty-
pisch Leids verhaal over het munten strooien is echter geen sprake
meer. Wanneer het gebruik genoemd wordt in verband met studen- BURGER & VAN DER STEEN 87 TSEG ten, vindt dat plaats in een meer algemene context over ontgroe-
ningsexcessen, bijvoorbeeld bij het Groningse Vindicat. Het Dagblad
van het Noorden stelde in dat verband: ‘Verhalen over Vindicaters
die gloeiend hete muntjes wierpen naar de arme burgers op straat
en over piano’s die van het balkon werden gegooid, gaan nog altijd
rond.’62 Onze stelling dat het verhaal sinds de jaren negentig aan zeg-
gingskracht heeft verloren lijkt ook te worden bevestigd door ge-
sprekken met studenten, die het verhaal lang niet altijd kennen. Toch bezit het verhaal over de studenten en hun hete centen nog
steeds een zeker subversief potentieel. Het ontbreekt in de recente
geschiedboeken van het studentencorps en in het stripboek De ziel
van Leiden (2017).63 De Leidse City Marketing roept graag de glorieu-
ze academische geschiedenis van de stad in herinnering, maar gaat
liever voorbij aan de klassentegenstellingen die daar een deel van wa-
ren, inclusief het verhaal over de hete centen. Het verhaal is niet over-
al welkom, omdat het een beeld oproept van een stad waarmee een
steeds kleinere groep zich wil identificeren. 63 De ziel van Leiden. Over de auteurs Peter Burger (1961) is a University Lecturer at the Department of Journal-
ism and New Media at Leiden University. He applies rhetorical perspectives
to journalism, narrative folklore, and social media discourse. Recent publi-
cations include: P. Burger, Monsterlijke verhalen. Misdaadsagen in het nieuws
en op webforums als retorische constructies (Den Haag: Boom Lemma, 2014)
and P. Burger, ‘Komkommers, zeeslangen, canards en faits divers. Nederlandse
kranten (1850-1950) als sagenmedium.’ Volkskunde 3 (2017) 291-318. E-mail: p.burger@hum.leidenuniv.nl Bart van der Steen (1983) is a University Lecturer in modern history at Leiden
University. His research focuses on labour and social movements in Europe
from the late nineteenth century to the present. Recent publications include:
K. Andresen and B. van der Steen, A European Youth Revolt. European Perspec-
tives on Youth Protest and Social Movements in the 1980s (Houndmills: Palgrave
MacMillan, 2016) and B. van der Steen, L. van Hoogenhuijze and A. Katzeff,
The City is Ours. Squatting and Autonomous Movements in Europe, 1980-2014
(Oakland: pm Press, 2014). E-mail: b.s.van.der.steen@hum.leidenuniv.nl 88 VOL. 15, NO. 1, 2018
|
https://openalex.org/W2567485024
|
https://europepmc.org/articles/pmc5155401?pdf=render
|
English
| null |
Alternate-locus aware variant calling in whole genome sequencing
|
Genome medicine
| 2,016
|
cc-by
| 12,222
|
© The Author(s). 2016 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. RESEARCH Open Access Abstract Background: The last two human genome assemblies have extended the previous linear golden-path paradigm of
the human genome to a graph-like model to better represent regions with a high degree of structural variability. The
new model offers opportunities to improve the technical validity of variant calling in whole-genome sequencing (WGS). Methods: We developed an algorithm that analyzes the patterns of variant calls in the 178 structurally variable
regions of the GRCh38 genome assembly, and infers whether a given sample is most likely to contain sequences from
the primary assembly, an alternate locus, or their heterozygous combination at each of these 178 regions. We
investigate 121 in-house WGS datasets that have been aligned to the GRCh37 and GRCh38 assemblies. Results: We show that stretches of sequences that are largely but not entirely identical between the primary
assembly and an alternate locus can result in multiple variant calls against regions of the primary assembly. In WGS
analysis, this results in characteristic and recognizable patterns of variant calls at positions that we term alignable
scaffold-discrepant positions (ASDPs). In 121 in-house genomes, on average 51.8 ± 3.8 of the 178 regions were found
to correspond best to an alternate locus rather than the primary assembly sequence, and filtering these genomes with
our algorithm led to the identification of 7863 variant calls per genome that colocalized with ASDPs. Additionally, we
found that 437 of 791 genome-wide association study hits located within one of the regions corresponded to ASDPs. Conclusions: Our algorithm uses the information contained in the 178 structurally variable regions of the GRCh38
genome assembly to avoid spurious variant calls in cases where samples contain an alternate locus rather than the
corresponding segment of the primary assembly. These results suggest the great potential of fully incorporating the
resources of graph-like genome assemblies into variant calling, but also underscore the importance of developing
computational resources that will allow a full reconstruction of the genotype in personal genomes. Our algorithm is
freely available at https://github.com/charite/asdpex. Keywords: GRCh38, NGS, WGS, Genome sequencing *Correspondence: peter.robinson@jax.org
1Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin,
Augustenburger Platz 1, 13353 Berlin, Germany
2Berlin Brandenburg Center for Regenerative Therapies (BCRT),
Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin,
Germany
Full list of author information is available at the end of the article Alternate-locus aware variant calling in
whole genome sequencing 2, Max Schubach1, Tomasz Zemojtel1, Knut Reinert3, Deanna M. Church4
b
1 2 3 5 6* Jäger et al. Genome Medicine (2016) 8:130
DOI 10.1186/s13073-016-0383-z Jäger et al. Genome Medicine (2016) 8:130
DOI 10.1186/s13073-016-0383-z Alignments of ALT-HAP and REF-HAP sequences Alignments of ALT-HAP and REF-HAP sequences
For each of the 178 alternate-locus-containing regions in
the GRCh38.p2 assembly, we performed pairwise align-
ments between the REF-HAP and each of the alternate
loci at the region. Alignments for each of the alternate
loci in the alts_accessions_GRCh38.p2 and the
various alt_scaffold_placement.txt files were
downloaded from the National Center for Biotechnol-
ogy Information (NCBI) FTP site [10]. The alignments
start with the Gap= flag, followed by several blocks
consisting of a letter (M, I, or D) and a number (length),
where (i) M indicates a matching region between ref
and alt loci, potentially with mismatches but without
gaps; (ii) I indicates an insertion in the alt scaffold (i.e.,
additional sequence information in the alt scaffold);
and (iii) D indicates a deletion in the alt scaffold (e.g.,
Gap = M23343 D19 M5 D24 M4 D11 M88 D1 M54 I1
M59 ...). Manual inspection revealed that parts of
these alignments are often suboptimal in the sense
that potentially alignable regions are split into multiple
small alignment blocks (Additional file 1: Supplemental
Figures S6 and S7). The characterization of variants in an individual
genome is one of the most important tasks in medical
genomics, especially in diagnostic settings or in projects
that aim to identify novel disease-associated genes. Alter-
nate loci for highly variable regions such as the Major
Histocompatibility Complex (MHC) locus may differ at
tens of thousands of positions [5], and thus there is a sub-
stantial potential to improve the accuracy of variant calls
by exploiting the information in the new genome assem-
bly model. In this work, we present an analysis of the
implications of the alternate loci for variant calling. We provide an implementation of the algorithms used
in the work under a Creative Commons CC-BY 4.0 license
at https://github.com/charite/asdpex. Therefore, we used the following strategy to redefine
the sequence alignments for each alignment of an alter-
nate scaffold against the reference. Our method identifies
seed sequences as relatively long M blocks (i.e., matches
or mismatches with no gaps). In many cases, there are
multiple mismatching bases at the very beginning and end
of M blocks, and for this reason we remove 5% but not
more than 50 nt on both ends of the seed. Background subsequent research showed that large-scale structural
variation is more prevalent than previously thought, and
that it is not possible to adequately represent genomic
regions with substantial structural allelic diversity using a
single consensus sequence for the human genome [4]. The initial assembly of the human genome resulted in
a consensus haploid representation of each chromosome
that was the best attainable consensus sequence for the
human genome, the golden path [1–3]. Variants could
then be represented by an annotation to the corre-
sponding position of the golden-path assembly. However, The Genome Reference Consortium (GRC) intro-
duced a new graph-like assembly model with alternative
sequence paths in regions with complex structural vari-
ation in the form of additional locus sequences. While
the previous genome assembly, GRCh37 (also called
hg19), included three regions with nine alternate locus
sequences, the GRCh38 assembly, which was released
in December 2013, has a total of 178 regions with 261 *Correspondence: peter.robinson@jax.org
1Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin,
Augustenburger Platz 1, 13353 Berlin, Germany
2Berlin Brandenburg Center for Regenerative Therapies (BCRT),
Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin,
Germany
Full list of author information is available at the end of the article Page 2 of 15 Page 2 of 15 Jäger et al. Genome Medicine (2016) 8:130 alternate loci. This offers many opportunities to the
genomics and bioinformatics communities to adapt anal-
ysis procedures to a more sophisticated model of the
human genome, but it also presents substantial technical
challenges, since many of the currently used programs for
alignment, variant calling, and analysis expect reads and
features to have a single location within a haploid assem-
bly model [4]. The (SAM) format for sequence alignments
is able to represent reads that align both to chromosomes
of the primary assembly (i.e., chr1-22, chrX, chrY, and
chrMT) and to an alternate locus, whereby the alignment
to the chromosome of the primary assembly is consid-
ered to be the representative alignment, and alignments of
the same read to non-reference chromosomes, called sup-
plementary alignments, are linked to the representative
alignments. However, analogous extensions of the alogous
extensions that would link variants called from the same
reads to multiple loci are not available. regions associated with a total of 261 alternate locus
scaffolds. Alignments of ALT-HAP and REF-HAP sequences For each match
(M) block in the original alignment, we considered the
sequence to be a seed sequence if the trimmed M block
was longer than 50 nt (Additional file 1: Supplemental
Figure S8). Background In our work, we refer to segments of the primary assem-
bly unit that are associated with one or more alternate loci
as REF-HAP sequences, and we refer to the alternate loci
as ALT-HAP sequences. The alternate loci have a num-
ber of different patterns of alignment with the REF-HAP
sequence (Additional file 1: Supplemental Figures S1–S5
and Additional file 1: Supplemental Table S1). Identification of alignable scaffold-discrepant positions We show that stretches of sequences that are largely but
not entirely identical between the primary assembly and
an alternate locus can result in multiple variant calls
against regions of the primary assembly. We will refer
to divergent positions within otherwise similar or identi-
cal stretches of alignment as alignable scaffold-discrepant
positions (ASDPs); the following text will make our defi-
nition more precise. The alignment resulting from the procedure described
in the previous section was taken as the basis for the fol-
lowing algorithm to identify ASDPs. Each position of the
alignment was checked in turn for a mismatch or gap,
and all such positions were recorded in a VCF file. ASDPs
comprise mainly single-nucleotide differences, but inser-
tions and deletions of various sizes are encountered. For
the analysis described in this work, we classified insertion
or deletion (indel) ASDPs into small-indel ASDPs with a
size less than 50 bases or structural variant (SV) ASDPs. This cutoff was chosen since most variant detection tools
(e.g., FreeBayes [13] and GATK [14]) only call indels up to
this size. RV = R△A = (R \ A) ∪(A \ R) = R ∪A \ (R ∩A). RV = R△A = (R \ A) ∪(A \ R) = R ∪A \ (R ∩A). Note that R \ A is the set of non-ASDP variants called
against REF-HAP, and A\R is the set of ASDPs associated
with ALT-HAP not called against REF-HAP (if we assume
that ALT-HAP is truly present, then this could be a false
negative due to a factor such as poor coverage but our
model interprets it as a variant in the REF-HAP sequence). It is easy to see that the number of residual variants is
|RV| = |R| + |A| −2 × |R ∩A|. The assumption of our algorithm is that the haplo-
type associated with the lower number of variants is
more likely to be present. Thus, if |R| >|RV|, REF-HAP
would be associated with more variants than if we assume
the presence of ALT-HAP. Therefore, ASDPex infers that
ALT-HAP is present. The first-pass analysis described above generates a
list of candidate ASDPs (Additional file 1: Supplemental
Figure S10). We chose to restrict the final analysis to
ASDPs that are located within relatively good segments
of the alignment. GRCh38 genome assembly data Prior to the GRCh37 assembly, the human genome ref-
erence sequence was represented as a single consensus
sequence referred to as the golden path [1]. Several chro-
mosomal regions display a sufficiently high degree of
variability that they cannot be adequately represented by
a single sequence [6–8]. For this reason, the GRC began
to provide alternate sequences for selected variant regions
through the inclusion of alternate locus scaffolds (or
alternate loci) starting with the GRCh37 human genome
assembly [9]. Some of the general feature format (GFF) files repre-
senting the alignments contain a second alignment line. In
this case, one finds a large insertion (I) followed by a large
deletion (D) in the main alignment; this represents an
inversion (see Additional file 1: Supplemental Figure S8). To handle this, we split alignments into blocks defined by
the large insertion/deletion boundaries and aligned these
blocks separately. An alternate locus is a sequence that is an alternate
representation of a genomic region in a largely haploid
assembly. Thus, alternate loci are provided for genomic
regions that show substantial variability in the population
and are embedded in an otherwise haploid representa-
tion of the genome. For the analysis described in this
work, the Genome Reference Consortium build 38 patch
2 assembly of the human genome was used (GRCh38.p2). This build has a total of 178 alternate-locus-containing Another relevant issue with the alignments is that they
ignore long stretches with Ns in the alternate scaffold Page 3 of 15 Jäger et al. Genome Medicine (2016) 8:130 is discarded. We will refer to this final list of ASDPs as
high-confidence ASDPs. sequences, that is, N bases are treated as matches (e.g.,
KI270905.1, GL000258.2, and GL383571.1). If the stretch
of N bases was larger than 10 nt, we split the seed into two
separate blocks to either side of the N bases. We note that we use the acronym ASDP to refer to a
divergent position in the alignment between REF-HAP
and ALT-HAP sequences, and not to a called variant;
we will show that many variants called in whole-genome
sequencing (WGS) overlap with ASDPs, and we will refer
to such variants as ASDP-associated variants. The preprocessing steps described above are summa-
rized in Additional file 1: Supplemental Algorithm S1. The
output of the preprocessing consists of a series of seeds of
50 nt or longer in length. ASDPex ASDPex, the ASDP extraction algorithm, is designed to
analyze individual VCF files with the goal of identifying
ASDP-associated variants so that they can be marked or
filtered out of downstream analysis pipelines if desired
(Additional file 1: Supplemental Figure S11). Additionally,
ASDPex calls the most likely combination of haplotypes
for each of the 178 genomic regions. Finally, we note that the alignments between regions and
alternate loci begin with identical anchors, such that the
beginning and end portions of the alignments are identi-
cal. No differences between the two sequences occur in
these regions, and the analysis described in the following
sections was, thus, limited to the portion of the align-
ment between the first and the last difference within each
alignment (Additional file 1: Supplemental Figure S9). For this purpose, ASDPex scans each of the 178 regions
in turn and compares all of the associated alternate loci. For each comparison, all variants called against the ref-
erence haplotype are assigned to the set R. All ASDPs
associated with the alternate locus are assigned to the set
A (many but not necessarily all of these ASDPs can have
corresponding ASDP-associated variants). We define the
set of residual variants RV to be the set of all called vari-
ants that are not ASDP-associated and all ASDPs that are
not called in the sample, which can be expressed as the
symmetric set difference RV = R△A. For this calculation,
we treat an ASDP-associated variant as equivalent to the
corresponding ASDP: GRCh38 genome assembly data The seeds were then used for a
banded chain alignment [11] using the C++ library SeqAn
[12] version 2.0.1. The parameters used for the alignment
were match: 5, mismatch: −2, gapextend: 0, gapopen: −20,
and anchor bands: 10. Results In this work, we explore the implications of the new
graph-like genome assembly model for variant calling in
the context of WGS. In particular, we investigate how
stretches of a sequence that are largely but not entirely
identical between the primary assembly and correspond-
ing alternate loci affect variant calling in short-read (Illu-
mina) WGS. The GRC Human Build 38 patch release
2 genome build (GRCh38.p2) contains a total of 178
genomic regions with one or more alternate loci; in total
there are 261 alternate loci. In most cases (n = 152),
genomic regions had just one alternate locus, but five
regions have five or more alternates: the CYP2D6 region
with five alternate loci, REGION151 and the mucin region
2 with seven each, the MHC region with eight and
the KIR gene family in the leukocyte receptor complex
(LRC) region with 35. The regions range from 33,439 to
5,081,216 nt in length (mean 344,634 nt, median 169,569
nt), with most regions being between 100 and 200 kilo-
bases (Fig. 1, Additional file 1: Supplemental Figures
S1–S5, and Additional file 1: Supplemental Tables S1
and S2). The cumulative length of all of the 178 regions
with alternate loci is 61,896,414 nt, which corresponds to
about 2% of the primary assembly of the GRCh38 human
genome (3,088,269,832 nt). We note that bwa mem aligns reads to the primary
assembly and the alternate loci independently, thus avoid-
ing the potential problem that a read that aligns well to a
sequence in the primary assembly and another sequence
in an alternate locus is given a poor mapping quality. In
this work, we used the bwa mem alignments to the alter-
nate loci for visualization, but we note that ASDPex uses
only variant calls to the primary assembly and, thus, an
alignment performed by any mapper to just the primary
assembly could also be used as input to ASDPex. Finally, samtools [16] was used to sort the alignment and
SAMBLASTER [17] to mark duplicates, which resulted in
the final alignment. This final alignment was then used to
call variants [single nucleotide variants (SNVs) and small
indels] using FreeBayes [13]. There was a mean 37-fold
coverage. Variants were normalized using vcflib vcfallelicprim-
itives (https://github.com/ekg/vcflib–v1.0.0) and vt nor-
malize (https://github.com/atks/vt–v0.57). The 178 regions contain a total of 1120 unique genes,
of which 797 are protein-coding genes. Identification of alignable scaffold-discrepant positions The genome-wide association study GWAS catalog [21]
was downloaded on 1 February 2016. It contained 18,130
unique single nucleotide polymorphisms (SNPs) (GWAS
hits) with chromosomal coordinates that were signifi-
cantly associated with a disease or trait at a p value of less
than 10−5. The genomic feature annotations (e.g., exons and cod-
ing sequence[CDS]) for RefSeq genes [19] and the genome
builds GRCh37.p13 and GRCh38.p2 were downloaded
from the NCBI FTP site. Transcript-based functional an-
notation was performed with Jannovar (version 0.16) [20]. Results Moreover, 106
of these genes are associated with Mendelian diseases
as listed in the Online Mendelian Inheritance in Man
(OMIM) [22] resource. Additionally, 1145 of a total of
23,539 polymorphisms significantly associated with traits
and common complex disease GWAS hits reported in the
GWAS catalog [21] were located in the regions. These Identification of alignable scaffold-discrepant positions Therefore, the final list of ASDPs was
generated by applying the filter that no ASDP can be
located in any 50 base-pair window of the alignment in
which there are more than ten discrepant positions. That
is, the window is advanced one nucleotide at a time, and
if there is any window position at which there are more
than ten discrepant positions, then the candidate ASDP If on the other hand, |RV| ≥|R|, more or equal variants
would be called against ALT-HAP than for REF-HAP, and
ASDPex infers that the alternate locus is not present. If
the algorithm infers that an alternate locus is present, then
it calculates the proportion of variants that correspond
to ASDPs that are also homozygous. If this proportion
is over a threshold (for the analysis presented here, we
chose the threshold to be 90%), then our procedure infers Jäger et al. Genome Medicine (2016) 8:130 Page 4 of 15 Page 4 of 15 Page 4 of 15 that the ALT-HAP is likely to be present in a homozy-
gous state, otherwise it is heterozygous (Additional file 1:
Supplemental Algorithm S2). HLA genes. This assembly is strongly recommended for
GRCh38 mapping by the BWA-kit pipeline. The current
dbSNP release (b146) was downloaded as a VCF file from
the NCBI [10] FTP site for both genome releases. We
adopt dbSNP’s definition of a common polymorphism
as one with a minor allele of frequency ≥1% and for
which two or more founders contribute to that minor
allele frequency. All other polymorphic sites in dbSNP are
considered rare. Finally, if the region R is associated with more than one
alternate locus, then we need to decide which, if any, alter-
nate locus is present. To do so, we calculate the number
of residual variants RV for each alternate locus. The locus
with the smallest value for RV is the best candidate, and
our procedure considers only this locus. We note that our
procedure is a heuristic that considers only variants called
against the canonical chromosomes in a VCF file resulting
from an analysis using the GRCh38 genome assembly. The genomic feature annotations (e.g., exons and cod-
ing sequence[CDS]) for RefSeq genes [19] and the genome
builds GRCh37.p13 and GRCh38.p2 were downloaded
from the NCBI FTP site. Transcript-based functional an-
notation was performed with Jannovar (version 0.16) [20]. Alignment of whole-genome sequencing samples and
variant calling The genome-wide association study GWAS catalog [21]
was downloaded on 1 February 2016. It contained 18,130
unique single nucleotide polymorphisms (SNPs) (GWAS
hits) with chromosomal coordinates that were signifi-
cantly associated with a disease or trait at a p value of less
than 10−5. To validate the ASDPs against real data, we used 121
genomes sequenced on an Illumina HiSeq X-Ten system
(Macrogen, Seoul, Korea). The reads were aligned to the
GRCh37 and GRCh38 genome releases with BWA-MEM
(version 0.7.12-r1039) utilizing bwakit (https://github. com/lh3/bwa/tree/master/bwakit). This tool, which can
be used to align reads to either the GRCh37 or GRCh38
assembly, trims the reads (trimadap), and aligns the
trimmed reads to the reference with BWA-MEM [15]. We
run bwa mem (using the run-bwamem script) as follows:
run-bwamem -sd -t 96 -R <readgroup> -o
<outfile> -H hs38DH.fa sample_R1.fastq.gz
sample_R2.fastq.gz Data sources The hs37d5 reference is assembled from the GRCh37 pri-
mary assembly, the EBV genome and the decoy contigs as
used by 1000 Genome Project [18] phase 3. The hs38DH
reference contains the primary assembly of GRCh38
plus the ALT contigs and additionally decoy contigs and Page 5 of 15 Jäger et al. Genome Medicine (2016) 8:130 Fig. 1 Genomic regions with alternate locus scaffolds (alternate loci). The GRCh38.p2 genome assembly contains 178 genomic regions with one or
more alt loci. The figure was produced using PhenoGram [49] to 661,805 unique REF-HAP positions, since some REF-
HAP regions can be aligned to multiple ALT-HAP loci). We will refer to these positions as ASDPs. represented 353 diseases or traits. Altogether, 104 of the
178 regions contained at least one GWAS hit. Therefore, incorrect calling of variants in these regions
could have implications for the medical interpretation of
genome data. The basic issue is that if a portion of an
ALT-HAP is similar enough to the corresponding region
of REF-HAP, then a read that originates from ALT-HAP
may be falsely aligned to the REF-HAP. If the ALT-HAP
sequence diverges from the REF-HAP sequence at a spe-
cific position, then this might lead to a spurious vari-
ant call at the corresponding position of REF-HAP, even
though the read originates from ALT-HAP. We reasoned that sequence reads corresponding to
ALT-HAP loci are more likely to be aligned to the REF-
HAP sequence if fewer differences between ALT-HAP
and REF-HAP sequences exist. Examination of the align-
ments showed that some regions are identical or nearly
so over up to several thousand nucleotides, while oth-
ers display a greater number of discrepancies (Fig. 2a–d). Each of these discrepancies potentially could lead to a
variant call if an ALT-HAP read is misaligned to REF-
HAP, but the actual likelihood of this occurring depends
on many factors, including the overall degree of similarity
of the REF-HAP and ALT-HAP positions in the corre-
sponding region of the alignment. We, therefore, applied
additional criteria for the goodness of the alignment in
regions surrounding discrepant positions based on align-
ment windows that were allowed to contain up to a certain
number of mismatches or gaps. Data sources We chose a threshold of
1 mismatch per 5 bases (1:5) since the total number of
dbSNP entries that overlap with the discrepant position
is nearly as high as with the 1:4 curve, which, however, is
associated with a much higher overall number of variants
(which we interpret as indicating a lower specificity). We
chose a window size of 50 nt, since there was no substan-
tial increase in the number of total discrepant positions
or positions that overlap with dbSNP entries with larger
window sizes. With these criteria, we identified a total
of 232,333 alignment positions, which we will refer to as
high-confidence ASDPs, and 187,080 of these ASDPs cor-
respond to correspond to SNVs (80.5%), with the remain-
der representing indels ranging in size from 1 to 50 nt and Alignments of primary assembly regions with alternate loci
A comparison of the alignments between REF-HAP and
corresponding ALT-HAP sequences reveals that they con-
tain numerous stretches of alignable sequences that dif-
fer in numerous ways, including SNPs as well as small
and large indels. Manual inspection suggested that the
pairwise alignments between REF-HAP and ALT-HAP
provided by GRC were not optimal in certain regions
(Additional file 1: Supplemental Figures S6 and S7),
and we, therefore, generated pairwise banded chain
alignments between each of the 178 regions and the
corresponding ALT-HAP sequences to refine the align-
ments (Additional file 1: Supplemental Figure S8 and
“Methods”). This resulted in a total of 402 alignment
blocks with a mean length of 248,928 nt (with respect
to the REF-HAP sequence). There were 770,276 single-
or multiple-nucleotide positions in the alignments that
differed between REF-HAP and ALT-HAP, including
768,316 positions with differences less than 50 nt and 1960
structural differences of 50 nt and more (corresponding Page 6 of 15 Jäger et al. Genome Medicine (2016) 8:130 a
b
c
d
e
f
Fig. 2 Frequency of ASDPs. Alignments contain stretches of sequences that are largely but not entirely identical between the primary assembly and
an alternate locus, ranging from regions that are nearly identical to those with a substantial number of differences. ASDPs were defined to be
positions of the alignment that differ between REF-HAP and ALT-HAP and are located in a sliding window in which at most 10 of 50 nucleotides are
discrepant (green check marks). The red crosses show discrepancies that are excluded by this definition. Data sources In a and c, no ASDP was filtered out by the
sliding window whereas in b, stretches of low sequence identity lead to the removal of several positions shown as red crosses. In d, large inserts in
the ALT-HAP lead to a larger number of discrepant positions, which are discarded by the above criteria. e The effects of applying different thresholds
of allowed discrepancies and window sizes to call ASDPs. The dotted lines mark the mismatch frequency (ten mismatches in 50 bases) used in this
work. f Number of ASDPs that overlap with dbSNP variants according to the different thresholds. ASDP alignable scaffold-discrepant position a
b
c
d
e
f
Fig. 2 Frequency of ASDPs. Alignments contain stretches of sequences that are largely but not entirely identical between th
an alternate locus, ranging from regions that are nearly identical to those with a substantial number of differences. ASDPs w
positions of the alignment that differ between REF-HAP and ALT-HAP and are located in a sliding window in which at most
discrepant (green check marks). The red crosses show discrepancies that are excluded by this definition. In a and c, no ASDP w
sliding window whereas in b, stretches of low sequence identity lead to the removal of several positions shown as red cross
the ALT-HAP lead to a larger number of discrepant positions, which are discarded by the above criteria. e The effects of app
of allowed discrepancies and window sizes to call ASDPs. The dotted lines mark the mismatch frequency (ten mismatches in
work. f Number of ASDPs that overlap with dbSNP variants according to the different thresholds. ASDP alignable scaffold-di b d f f e e Fig. 2 Frequency of ASDPs. Alignments contain stretches of sequences that are largely but not entirely identical between the primary assembly and
an alternate locus, ranging from regions that are nearly identical to those with a substantial number of differences. ASDPs were defined to be
positions of the alignment that differ between REF-HAP and ALT-HAP and are located in a sliding window in which at most 10 of 50 nucleotides are
discrepant (green check marks). The red crosses show discrepancies that are excluded by this definition. In a and c, no ASDP was filtered out by the
sliding window whereas in b, stretches of low sequence identity lead to the removal of several positions shown as red crosses. Postprocessing VCF files to infer ASDPs The acronym ASDP refers to a divergent position in the
alignment between REF-HAP and ALT-HAP sequences,
and not to a called variant. We will show that many vari-
ants called in WGS overlap with ASDPs, and we will refer
to such variants as ASDP-associated variants. We restrict
this analysis to the high-confidence ASDPs. Here, we present a heuristic algorithm that infers the pres-
ence of ALT-HAP sequences in WGS data based on the
distribution of ASDP-associated variants in the VCF file
[23]. We chose to use VCF files as input to our algo-
rithm, since VCF files with variants called from exome or
genome sequencing data are commonly used as a stan-
dard format for interpretive software such as Exomiser
[24–26]. We, therefore, developed an algorithm to post-
process VCF files from WGS to identify REF-HAP and
ALT-HAP genotypes and to flag ASDP-associated variant
calls. The algorithm takes as input a VCF file produced
from a variant caller such as the GATK haplotype caller
[14] or FreeBayes [13] that is applied to an alignment
produced by BWA-MEM [15] (see “Methods”). We call
our algorithm ASDPex, because it is designed to extract
ASDP-associated variants from VCF files. There may
be analysis goals for which it would be appropriate to
remove ASDP-associated variants from further analysis. For instance, one might want to remove the 52 vari-
ants called against region 148 (Fig. 3a) and retain only
the single non-ASDP-associated variant called against
KI270808.1. In WGS data, the distribution of ASDP-associated in
the 178 regions can be compared to a fingerprint that
is indicative of the presence of one of the ALT-HAP
sequences, the REF-HAP sequence, or their heterozy-
gous combination. That is, ASDPs are associated with
characteristic patterns of variant calls against the REF-
HAP sequence. Figure 3 shows an example of how ASDPs
affect variant calling in an in-house genome. In Fig. 3a,
multiple homozygous variants called against region 148
on chromosome 7q correspond to ASDPs with a sin-
gle heterozygous non-ASDP-associated variant. Figure 3b
shows the corresponding sub-region of alternate locus
KI270808.1, which is assigned to region 148. Data sources In d, large inserts in
the ALT-HAP lead to a larger number of discrepant positions, which are discarded by the above criteria. e The effects of applying different thresholds
of allowed discrepancies and window sizes to call ASDPs. The dotted lines mark the mismatch frequency (ten mismatches in 50 bases) used in this
work. f Number of ASDPs that overlap with dbSNP variants according to the different thresholds. ASDP alignable scaffold-discrepant position Page 7 of 15 Page 7 of 15 Jäger et al. Genome Medicine (2016) 8:130 about 4% block substitutions (Table 1). The total num-
ber of ASDPs is dependent on the window length and
the number of allowed differences, but was relatively sta-
ble over a range of parameters (Fig. 2e, f). In many cases,
regions associated with multiple loci may have ASDPs
originating from different ALT-HAP loci located at the
same reference position. Such ASDPs may be identical or
involve distinct nucleotide substitutions. All told, 137,156
unique REF-HAP positions, or ∼2.2 variations per kilo-
base of the REF-HAP sequence (61,896,414 bases in the
178 regions), are associated with an ASDP in one or more
ALT-HAP loci. single (heterozygous) non-ASDP variant is called. There-
fore, it is a plausible inference that the sequenced proband
is homozygous for the locus KI270808. Furthermore, the
variants called against the REF-HAP sequence in this
region (region 148) are likely to be spurious in the sense
that the sequenced individual does not have the canonical
chromosome 7p sequence (REF-HAP) in this region, but
instead has KI270808.1 (ALT-HAP). Assuming the variant
call against KI270808.1 is accurate, then the individual has
only this single variant against KI270808.1. Postprocessing VCF files to infer ASDPs Only the Table 1 Distribution of ASDPs
ASDP category
Count
Percentage
SNV
187,080
80.5%
Deletion
15,955
6.9%
Deletion (1 nt)
6,368
2.7%
Deletion (2 nt)
2,413
1.0%
Deletion (3–50 nt)
7,174
3.1%
Insertion
15,286
6.6%
Insertion (1 nt)
6,423
2.8%
Insertion (2 nt)
2,224
1.0%
Insertion (3–50 nt)
6,639
2.9%
Block substitution
14,012
6.0%
Block substitution (2 nt)
11,659
5.0%
Block substitution (3 nt)
1,653
0.7%
Block substitution (4–50 nt)
700
0.3%
A total of 232,333 high-quality ASDPs were characterized by our algorithm of which
80.5% corresponded to SNVs when comparing the alternate locus with the
corresponding primary assembly. About 7% each were deletions and insertions and
6% were block substitutions with equal numbers of nucleotides. ASDP alignable scaffold-discrepant position, SNV single nucleotide variant ASDPex is a heuristic algorithm that compares the dis-
tribution of ASDPs and other variants in the REF-HAP
and ALT-HAP sequences to infer the most likely genotype
of each region (i.e., homozygous REF-HAP, homozygous
ALT-HAP for one of the alternate loci, or heterozygous). ASDPex scans each of the 178 regions (i.e., REF-HAP)
in turn and compares all of the associated alternate loci
(ALT-HAP). ASDPex considers two sets. Let R be the
set of all variants called for the REF-HAP. Note that
these variants may include both ASDP-associated vari-
ants as well as additional variants. Let A be the set of
all ASDPs for the corresponding REF-HAP to ALT-HAP
alignment (Fig. 4). If the sample being sequenced does
not contain the ALT-HAP, then we do not expect the
variants called against REF-HAP to contain many ASDP-
associated variants, and instead interpret all the variants
in the set R as true positives. On the other hand, if the
sample being sequenced does contain the ALT-HAP, then
we expect that many of the variants called against REF-
HAP to be ASDP-associated variants. Our algorithm then Jäger et al. Genome Medicine (2016) 8:130 Page 8 of 15 Fig. 3 Region 148. IGV screenshots [50] are shown with variant calls for in-house sample P. a The presence of numerous ASDP-associated variants as
well as a structural variant associated with the alternate locus KI270808.1 clearly suggest that the sample is homozygous for the KI270808.1 rather
than for the REF-HAP sequence for region 148. Note that most of the variants that correspond to ASDPs are homozygous, suggesting that
KI270808.1 is present in the homozygous state. An additional non-ASDP variant is present. Postprocessing VCF files to infer ASDPs Variants corresponding to 50 of the 52 ASDPs shown are
listed in dbSNP. b The corresponding region on the alternate locus KI270808.1 was alignable well. Only the single non-ASDP-associated variant is
called. IGV shows supplemental reads in blue (i.e., reads that map to the primary assembly as well as to an alternate locus). ASDP alignable
scaffold-discrepant position, SNV single nucleotide variant, SV structural variant, IGV Integrative Genomics Viewer Fig. 3 Region 148. IGV screenshots [50] are shown with variant calls for in-house sample P. a The presence of numerous ASDP-associated variants as
well as a structural variant associated with the alternate locus KI270808.1 clearly suggest that the sample is homozygous for the KI270808.1 rather
than for the REF-HAP sequence for region 148. Note that most of the variants that correspond to ASDPs are homozygous, suggesting that
KI270808.1 is present in the homozygous state. An additional non-ASDP variant is present. Variants corresponding to 50 of the 52 ASDPs shown are
listed in dbSNP. b The corresponding region on the alternate locus KI270808.1 was alignable well. Only the single non-ASDP-associated variant is
called. IGV shows supplemental reads in blue (i.e., reads that map to the primary assembly as well as to an alternate locus). ASDP alignable
scaffold-discrepant position, SNV single nucleotide variant, SV structural variant, IGV Integrative Genomics Viewer Fig. 3 Region 148. IGV screenshots [50] are shown with variant calls for in-house sample P. a The presence of numerous ASDP-associated variants as
well as a structural variant associated with the alternate locus KI270808.1 clearly suggest that the sample is homozygous for the KI270808.1 rather
than for the REF-HAP sequence for region 148. Note that most of the variants that correspond to ASDPs are homozygous, suggesting that
KI270808.1 is present in the homozygous state. An additional non-ASDP variant is present. Variants corresponding to 50 of the 52 ASDPs shown are
listed in dbSNP. b The corresponding region on the alternate locus KI270808.1 was alignable well. Only the single non-ASDP-associated variant is
called. IGV shows supplemental reads in blue (i.e., reads that map to the primary assembly as well as to an alternate locus). ASDP alignable
scaffold-discrepant position, SNV single nucleotide variant, SV structural variant, IGV Integrative Genomics Viewer ALT-HAP if this would reduce the total number of called
variants, i.e., if |RV| < |R| (see Fig. 4 and “Methods”). Postprocessing VCF files to infer ASDPs Genome Medicine (2016) 8:130 If a REF-HAP region is associated with more than one
ALT-HAP, then the ALT-HAP associated with the greatest
reduction in ASDP-associated variants is chosen. Finally,
ASDPex outputs a VCF file in which regions and vari-
ants are correspondingly marked such that they can be
filtered in downstream analysis if desired (see “Methods”
and Additional file 1: Supplemental Figure S11 for details). If a REF-HAP region is associated with more than one
ALT-HAP, then the ALT-HAP associated with the greatest
reduction in ASDP-associated variants is chosen. Finally,
ASDPex outputs a VCF file in which regions and vari-
ants are correspondingly marked such that they can be
filtered in downstream analysis if desired (see “Methods”
and Additional file 1: Supplemental Figure S11 for details). The genotype shown in Fig. 3 was inferred to be
homozygous ALT-HAP by ASDPex. Additional file 1:
Supplemental Figures S12–S22 show additional examples
in which ASDPex inferred an alternate locus to be present
in the homozygous or heterozygous state or inferred
homozygous REF-HAP. 35,171,619 common SNP entries. Of these, 826,612 were
located within the 178 REF-HAP regions. A total of 75,138
of these overlap with an ASDP, including 71,653 unique
REF-HAP variants, which is about 32.3% of all ASDPs
(Additional file 1: Supplemental Table S3). The GWAS Catalog [21] contains 18,130 unique SNPs
(GWAS hits) with chromosomal coordinates which are
significantly associated with a disease or trait at a p
value of less than 10−5. Altogether, 791 GWAS hits are
within the 178 regions associated with alternate locus
regions, and 437 GWAS hits were found to overlap with
ASDPs, 360 of which are located within the MHC region
(Additional file 1: Supplemental Table S4). The genotype shown in Fig. 3 was inferred to be
homozygous ALT-HAP by ASDPex. Additional file 1:
Supplemental Figures S12–S22 show additional examples
in which ASDPex inferred an alternate locus to be present
in the homozygous or heterozygous state or inferred
homozygous REF-HAP. Variant calling on 121 in-house genomes: GRCh37 vs.
GRCh38 The ASDPex algorithm infers whether the canonical chro-
mosome sequence or an ALT-HAP sequence is most likely
given the observed pattern of variants and ASDPs. In addition to the increased numbers of alternate loci in
the GRCh38 build as compared to the GRCh37 build,
there are many other differences, including numerous cor-
rections and the addition of sequences to close many
gaps in the GRCh37 build. We investigated the perfor-
mance of variant calling on 121 in-house genomes that
were processed using BWA-MEM [15] for alignment and
FreeBayes [13] for variant calling. Except for the reference
genome sequence used, all processing steps were identi-
cal (see “Methods” for details). We restricted the analysis
to the chromosomes of the primary assembly except as
noted below. In both cases, the overall quality was good,
with 99.8% of the reads being mapped. Reads that can
be mapped equally well to two or more positions in the
target are referred to as supplementary mapped reads. As expected, a major difference in the alignment was the
presence of a mean of nearly 100 times more supplemen-
tary reads for the GRCh38 alignment than for the GRCh37
alignment. To investigate whether the alternate loci show popula-
tion biases, we used ASDPex to analyze 30 WGS sam-
ples each from four populations from the 1000 Genomes
Project [18]. We observed that several alternate loci
showed a highly specific population bias (Table 2). The
Peruvian population displayed the highest number of
population-specific alternate loci. The lowest mean count
of alternate loci was found in European and African
samples, possibly because these populations have been
extensively studied and are well represented in the cur-
rent genome assembly (Additional file 1: Supplemental
Figure S23). Postprocessing VCF files to infer ASDPs interprets the residual variants (RV), comprising all non-
ASDP-associated variants called against REF-HAP as well
as all ASDPs associated with the ALT-HAP that are not
called against the REF-HAP, as true positives. The set RV
can be calculated as the symmetric difference of the sets
R and A. Our algorithm finally infers the presence of If most of the ASDP-associated variants are called as
homozygous against the REF-HAP (by default 90%), our
heuristic assumes the ALT-HAP is present in a homozy-
gous state, and otherwise it is in a heterozygous state. a
b
Fig. 4 Overview of the ASDPex algorithm. a ASDPex compares the set of all variants called against REF-HAP R with the set of ASDPs associated with
ALT-HAP A. In this example, |A| (the number of ASDPs associated with ALT-HAP) is 6, and |R| (the total number of variants called against
REF-HAP) is 8. ASDPex defines the set of residual variants as the symmetric set difference between R and A, i.e., RV = R△A. Therefore, |RV| = 4,
and because |RV| < |R|, our algorithm infers that ALT-HAP is present. b The pattern of variant calls obtained for ASDPs differs according to
whether the sequenced proband is homozygous for one of the two alternate loci or is heterozygous. Our algorithm exploits this pattern across the
entire length of the alternate locus to infer the most likely genotype. ASDP alignable scaffold-discrepant position f a b Fig. 4 Overview of the ASDPex algorithm. a ASDPex compares the set of all variants called against REF-HAP R with the set of ASDPs associated with
ALT-HAP A. In this example, |A| (the number of ASDPs associated with ALT-HAP) is 6, and |R| (the total number of variants called against
REF-HAP) is 8. ASDPex defines the set of residual variants as the symmetric set difference between R and A, i.e., RV = R△A. Therefore, |RV| = 4,
and because |RV| < |R|, our algorithm infers that ALT-HAP is present. b The pattern of variant calls obtained for ASDPs differs according to
whether the sequenced proband is homozygous for one of the two alternate loci or is heterozygous. Our algorithm exploits this pattern across the
entire length of the alternate locus to infer the most likely genotype. ASDP alignable scaffold-discrepant position Page 9 of 15 Jäger et al. ASDPs in dbSNP We then investigated SNPs and other polymorphisms that
map to the 178 regions in dbSNP [10], which contains Table 2 Population-specific alternate loci
Alternate locus
FIN
LWK
CHB
PEL
chr4_KI270787v1_alt
✓
✓
chr5_GL383531v1_alt
✓
chr5_GL949742v1_alt
✓
chr6_GL383533v1_alt
✓*
chr6_KI270801v1_alt
✓
✓
✓*
chr9_GL383542v1_alt
✓
chr11_JH159136v1_alt
✓
✓*
chr13_KI270839v1_alt
✓
✓
✓*
chr14_KI270844v1_alt
✓
✓
chr15_GL383555v2_alt
✓*
✓
✓*
chr18_GL383570v1_alt
✓
Shown are all the alternate loci that were inferred to be present in at least 90% of
the individuals of a population. Alternate loci present in all investigated individuals
of the population are marked with an asterisk (*)
CHB Asian, Han Chinese in Beijing, China, FIN European, Finnish in Finland, LWK
African, Luhya in Webuye, Kenya, PEL South Americans, Peruvians from Lima, Peru The number of variant calls between the genome
releases and the mean Phred scores were compara-
ble (Table 3). Variants that correspond to ASDPs can
be found in samples with regions that are inferred
to correspond to the primary assembly. However, the
density of ASDPs called against regions of the pri-
mary assembly is substantially and significantly different
according to whether the region was inferred to cor-
respond to the primary assembly or an alternate locus
(Fig. 5). The transition/transversion (Ts/Tv) ratio, a commonly
used quality control parameter for checking overall SNP
quality, is often found to be around 2.0 across the whole
genome [27, 28]. We calculated the Ts/Tv ratio for both
genome releases and found it to be 2.03 for GRCh37 and
1.99 for GRCh38. This difference is related to the sub-
stantially lower Ts/Tv ratio associated with rare variants
(Additional file 1: Supplemental Figure S24). Shown are all the alternate loci that were inferred to be present in at least 90% of
the individuals of a population. Alternate loci present in all investigated individuals
of the population are marked with an asterisk (*)
CHB Asian, Han Chinese in Beijing, China, FIN European, Finnish in Finland, LWK
African, Luhya in Webuye, Kenya, PEL South Americans, Peruvians from Lima, Peru Page 10 of 15 Jäger et al. ASDPs in dbSNP Genome Medicine (2016) 8:130 Table 3 Variant statistics for both genome builds
GRCh37
GRCh38
Chromosome
All
Common
Rare
Phred
All
Common
Rare
Phred
1
344158
299500
44659
503.42
359530
291704
67825
473.83
2
354113
247585
106528
506.54
361469
243400
118069
492.91
3
295447
268021
27426
503.76
301985
263993
37993
492.99
4
319988
290080
29908
515.41
324134
285405
38729
507.33
5
266077
235462
30615
498.58
272482
231747
40734
485.57
6
280789
252705
28084
495.02
279132
246545
32588
487.11
7
249980
220543
29437
488.95
257917
216669
41248
475.69
8
229332
204823
24509
499.70
229541
200845
28696
490.15
9
192615
162202
30413
475.09
200034
159119
40916
466.46
10
217957
194385
23572
508.74
229352
190658
38694
494.18
11
219134
197412
21722
522.84
228324
194132
34192
498.04
12
205085
184477
20608
502.78
212789
175990
36799
483.94
13
166128
151271
14856
530.31
180521
148870
31651
494.65
14
141971
124790
17181
503.15
140443
122524
17919
495.75
15
130324
112085
18239
505.95
131389
109741
21648
493.46
16
134293
116224
18069
487.40
136799
113589
23210
473.36
17
118096
102300
15796
479.64
130637
99074
31563
452.99
18
124509
111958
12552
516.80
132628
110349
22279
485.89
19
98104
84416
13688
456.51
99625
82875
16750
455.35
20
90490
79709
10781
486.09
112562
78562
33999
475.40
21
69511
55211
14300
525.23
73027
53052
19975
513.27
22
59660
50242
9418
455.99
71112
48961
22151
445.27
Total
4307761
4465432
The mean counts of autosomal variants and the median Phred scores per chromosome are shown for GRCh37 and GRCh38. Columns: All: all detected variants; Common: listed in dbSNP common_all_*; Rare: variants that are not common. The mean variant counts for chromosome X were 127,914 (GRCh37) and 132,177 (GRCh38). For chromosome Y, the mean counts could not be estimated since gender
information was not available for all of the 121 in-house genomes. Both genome releases include the identical mitochondrial reference (NC_012920.1) with 27 variants dbSNP, about 13% of all ASDP-associated variants called
per genome were not (Additional file 1: Supplemental
Figure S25). A small number of the ASDP-associated
variants that are not listed in dbSNP were predicted
to have high impact (Additional file 1: Supplemental
Table S5). There was a mean of 24908 ± 380 variants overlap-
ping protein-coding regions (CDS) in the 121 in-house
genomes when analyzed with the GRCh37 genome. Anal-
ysis with the GRCh38 genome revealed slightly more CDS
variants, 26499 ± 421. ASDPs in dbSNP Finally, we investigated the effects of ASDPs on variant
calling in the GRCh38 build. For this analysis, we included
only regions for which the GRCh38 build had at least one
alternate locus. We did not include region 116, because
no alignable sequence in the GRCh37 build was identi-
fied. We applied ASDPex to each of the VCF files resulting
from variant calling in the 121 in-house genomes. Of the
178 regions, 51.8 ± 3.8 (range 38–60) were found to cor-
respond best to an alternate locus rather than the primary
assembly sequence. A mean of 7863 variant calls were
found to be ASDP-associated per genome, or 6.51% of all
variants located in the 178 regions (Table 4). Although
many of these ASDP-associated variants are listed in Discussion Variant calling is required for medical interpretation,
which focuses on sequences that diverge from normal. As
WGS develops into a tool for clinical diagnostics [29–31],
there is a pressing need to improve the technical accu-
racy of sequencing methods and analysis pipelines [32]. Numerous challenges need to be addressed to achieve this
goal, including the low concordance rate of alignment and
variant-calling pipelines [32, 33]. In this work, we have
characterized ASDPs, which correspond to differences in
alignments between sequences that are largely but not Jäger et al. Genome Medicine (2016) 8:130 Page 11 of 15 Fig. 5 Distribution of ASDP-associated variants called against the primary assembly. A significantly and substantially higher number of
ASDP-associated variants are called against the primary assembly according to whether the region is inferred to be REF-HAP or ALT-HAP by the
ASDPex algorithm. The data appear to fall into two well-separated clusters. The figure shows the counts of Ref/Alt ASDP-associated variants per
megabase for seven selected regions for the 121 in-house genomes. *p < 1 × 10−8; **p < 1 × 10−10 (Mann–Whitney test). ASDP alignable
scaffold-discrepant position Fig. 5 Distribution of ASDP-associated variants called against the primary assembly. A significantly and substantially higher number of
ASDP-associated variants are called against the primary assembly according to whether the region is inferred to be REF-HAP or ALT-HAP by the
ASDPex algorithm. The data appear to fall into two well-separated clusters. The figure shows the counts of Ref/Alt ASDP-associated variants per
megabase for seven selected regions for the 121 in-house genomes. *p < 1 × 10−8; **p < 1 × 10−10 (Mann–Whitney test). ASDP alignable
scaffold-discrepant position regions can be compared to a fingerprint that is indica-
tive of the presence of one of the ALT-HAP sequences,
the REF-HAP sequence, or their heterozygous combi-
nation. The distribution of ASDP-associated variants
can be used to infer that variant calls against a struc-
tural variant region of the primary assembly of the
GRCh38 assembly are spurious in the sense that the
sample contains an alternate locus at that segment of the
genome. For instance, in the example shown in Fig. 3,
the variants called against the chromosome sequence
of the primary assembly can be considered to be spu-
rious, since it is much more likely that the sequenced
individual
is
homozygous
for
the
alternate
locus
KI270808.1. entirely identical between the primary assembly and an
alternate locus. Discussion ASDPs are associated with characteristic
patterns of variant calls against the primary assembly and
corresponding alternate loci. The ASDP-associated vari-
ants identified by our analysis can be commonly found in
WGS data (Fig. 3, Additional file 1: Supplemental Figures
S12–S22, and Table 4). Do ASDPs lead to spurious variant calls? Genome Medicine (2016) 8:130 Fig. 6 rs2049805. The GWAS hit rs2049805 corresponds to an ASDP
defined by an alignment between chromosome 1 of the primary
assembly (region MTX1) and the alternate locus GL383519.1, which is
identical over a stretch of 49 nucleotides except for the middle
position. rs2049805 is significantly associated with blood urea
nitrogen levels in east Asian populations [51]. ASDP alignable
scaffold-discrepant position Challenges and opportunities for variant calling with the
GRCh38 genome assembly model Our work has illustrated some of the difficulties that ensue
when calling variants with the GRCh38 genome assem-
bly model. To address these challenges, the community
will need to decide upon the desired output from vari-
ant callers. The current strategy recommended by GATK
is to use BWA-MEM to align reads to both the primary
assembly and the alternate loci followed by variant calling
for the primary assembly and the alternate loci separately
using GATK. Current pipelines do not attempt to disam-
biguate variant calls in regions of the genome associated
with alternate loci. We have presented a downstream tool,
ASDPex, that can process such output with the ambigu-
ities that result from this approach and that would allow
processing of ASDP-associated variants. It is also pos-
sible to imagine that variant calling tools be required
to infer which haplotypes (REF-HAP or ALT-HAP) are
present before calling variants; this process could take
advantage not only of knowledge about structural vari-
ation in the human genome, as ASDPex does, but also
could use information in the alignment (BAM) file itself
to perform variant calling simultaneously with an analy-
sis of reads with supplemental mappings. The community
would need to agree upon the best way of represent-
ing these results in VCF format (see Additional file 1:
Supplemental Figure S11 for the conventions used by
ASDPex). Fig. 6 rs2049805. The GWAS hit rs2049805 corresponds to an ASDP
defined by an alignment between chromosome 1 of the primary
assembly (region MTX1) and the alternate locus GL383519.1, which is
identical over a stretch of 49 nucleotides except for the middle
position. rs2049805 is significantly associated with blood urea
nitrogen levels in east Asian populations [51]. ASDP alignable
scaffold-discrepant position chromosome (Fig. 6). The great majority of GWAS hits
are not themselves disease-causative but rather tag sus-
ceptibility regions (haplotypes that contain one or more
deleterious variants). Do ASDPs lead to spurious variant calls? If, in fact, the alternate loci are asso-
ciated with the trait, rather than a particular haplotype of
the corresponding region of the primary assembly, then
searches for the causative variants associated with GWAS
hits need to take the sequences of the alternate loci into
account. The finding that a single variant colocalizes with an
ASDP is not in itself indicative that the variant is spu-
rious or a false positive. In fact, our results suggest
that the primary assembly may contain polymorphisms
whose alternate alleles correspond to the sequence in an
alternate locus (because we identified ASDP-associated
variants in sequences inferred to be a primary assembly;
see Fig. 6). A limitation of the current study is that we have
not attempted to analyze the frequency of recombina-
tion between REF-HAP and ALT-HAP in the population. Recombination between the different loci at a structurally
variable genomic region may be one reason why ASDP-
associated variants can be found on the background of
haplotypes inferred to be REF-HAP. Our algorithm is
based on the simplifying assumption that the alternate
loci represent complete haplotype blocks. However, link-
age disequilibrium blocks for Europeans are ∼60 kb on
average (and less for African populations) [37]. There-
fore, it is possible that the alternate loci are not always a
valid haplotype observed within the population. The fre-
quency of recombination events between regions of the
primary assembly and the corresponding alternate loci
has yet to be studied in detail. Another limitation of our
analysis is that our definition of ASDPs depends on the
accuracy of the alignment and the parameters used to
define ASDPs. Although the majority of ASDPs identi-
fied by our algorithm were SNVs or small indels (Table 1),
it is possible that more sophisticated methods of iden-
tifying complex rearrangements [38] between REF-HAP
and ALT-HAP sequences may make it possible to identify
corresponding ASDP-associated variants. There are several limitations to the current VCF file for-
mat that make it difficult to represent data fully using
the GRCh38 assembly. The SAM format can represent
supplementary alignments representing reads that map
to an alternate locus in addition to the primary assem-
bly (Additional file 1: Supplemental Figure S26). An
analogous extension to the VCF format does not exist. The current format does not represent the relationship
between alternate alleles and their chromosome locations
(i.e., maintaining the allelic relationships of the alternate
sequences). Do ASDPs lead to spurious variant calls? Variant calling is always contextual, and whether some-
thing is a variant will depend on the reference sequence
used. For instance, over 10,000 sites had a base change
between GRCh37 and GRCh38, so some sites that
were variant in GRCh37 will not be called as variant in
GRCh38. For the most part, these variants are simply
errors in GRCh37, and have been corrected in GRCh38
(including some positions such as chr15:48807637C).1
The ASDP-associated variants characterized in this
work are not false positive in this sense. Instead, the
distribution of ASDP-associated variants in the 178 Accurate calling of variants in these positions will
depend on there being enough sequence context to locate
unambiguously the data upon which the variant call is
made. This may not be possible for technologies such as
Affymetrix SNP-Chips [35, 36] (Fig. 6), which by design
interrogate a stretch of 49 nt. Given the overall similarity
of the REF-HAP and ALT-HAP sequences in the vicin-
ity of many of the ASDPs that overlap with GWAS hits,
it is conceivable that current SNP measurement tech-
nologies such as Affymetrix are identifying sequences on
ALT-HAPs and not (or not just) variants located in the
REF-HAP sequence. Altogether, 139 of the 437 GWAS
hits that overlap with ASDPs are located in regions of the
alignment that are identical in a region of 25 nt up- and
downstream with the exception of the ASDP itself, raising
the question of whether these GWAS hits are actually tag-
ging the presence of an ALT-HAP rather than a polymor-
phism linked to the reported location in the golden-path Table 4 Reduction in called variants by ASDPex
Variant calling pipeline
Total variants
Variants per Mb
GRCh37 canonical
114,023 ± 4,983
2198.3 ± 207.6
GRCh38 canonical
120,807 ± 4,069
1975.2 ± 66.5
The variant counts are shown for 121 in-house whole-genome sequencing samples
in the ALT-LOCI-containing regions. For GRCh37, a liftover of the regions was
performed and region 116 was removed from both datasets, since no alignable
region(s) are present in GRCh37. Since the size of the regions is different in GRCh37
and GRCh38, average variant counts per megabase (Mb) are also shown. On
average, there was a reduction of 7863 ± 2675 (6.5%) variants called using ASDPex
in the ALT-LOCI-containing regions, corresponding to a reduction from 1975.2 ±
66.5 to 1846.7 ± 71.6 variants per Mb Page 12 of 15 Jäger et al. Endnote formats and analysis pipelines to be applied in diagnostic
settings. 1 If
the
wild-type
RefSeq
for
the
FBN1
gene,
NM_000138, is compared to the genomic sequence, a
variant c.1415G>A;p.Tyr472Cys would be called that is
predicted to be pathogenic [34]. The genomic base has
been corrected to a T in GRCh38. Despite the fact that the GRCh38 genome build has
been available for over 18 months, progress in using
GRCh38 in medical interpretation pipelines has been
slow. We suggest that this is a chicken and egg problem. If we want variant callers to be able to use the alternate
loci, we need to be able to express the variants in VCF,
which does not work well with the current specification. Ultimately, new models of representing variation in the
genome may be required [40]. Do ASDPs lead to spurious variant calls? While this is a valid requirement within a spe-
cific assembly unit, it needs to be relaxed when describing
data on the full assembly as a feature can validly be on the
primary assembly as well as an alternate locus. The VCF format can represent hemizygous variants on
the X chromosome in males as 1, although in practice
such variants are often called homozygous (1/1) by vari-
ant callers that are not aware of the sex of the proband. If a
sample was inferred to be heterozygous for REF-HAP and
ALT-HAP, then one potential way of representing vari-
ants called against both haplotypes would be with the 1
notation. It is possible that human genome sequencing will move
towards de novo assembly of genomes as technologies and
bioinformatic analysis strategies mature [39], a step that
would likely require substantial evolution of current file Page 13 of 15 Jäger et al. Genome Medicine (2016) 8:130 Additional file Additional file 1: Online supplemental material. A file with 26 figures, five
tables, and two algorithms. (PDF 24300 kb) Funding Accurate assembly of genomes is essential for the
understanding of genetic variation [39]. The GRCh38
genome assembly was a major step towards develop-
ing a model that can adequately represent the struc-
tural variation in the human population. However, it
is likely that there is a substantially higher number of
regions in the human genome that exhibit a degree of
structural variability that cannot be adequately repre-
sented by a linear genome model. Current work with
long-read technologies and algorithmic advances are
resolving an increasing number of genomic regions,
which may be incorporated into future assemblies of
the human genome [39, 41–47]. As our knowledge
of the human genome and its variation in popula-
tion increases, it seems likely that more sophisticated
graph-based representations of the genome will become
useful [40, 48]. This project was supported by the Bundesministerium für Bildung und
Forschung (projects 0313911 and 01EC1402B). Availability of data and materials We provide an implementation of the algorithms used in the work as well as
an extensive tutorial under a Creative Commons CC-BY 4.0 license at https://
github.com/charite/asdpex. Author details
1 Our results suggest that it could be useful to develop
algorithms that infer the most likely diplotype of each of
the 178 regions associated with alternate loci and instead
realign the original reads with the alternative haplotype
with the primary where indicated, and present the vari-
ant calls accordingly. While this procedure ultimately may
be replaced by full de novo diagnostic genome assembly
or variant calling strategies related to graph-based repre-
sentations, this procedure could be done with the tools
available today. 1Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin,
Augustenburger Platz 1, 13353 Berlin, Germany. 2Berlin Brandenburg Center
for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin,
Augustenburger Platz 1, 13353 Berlin, Germany. 3Institute for Bioinformatics,
Department of Mathematics and Computer Science, Freie Universität Berlin,
Arnimallee 14, 14195 Berlin, Germany. 410x Genomics, 7068 Koll Center
Parkway, Suite 401, 94566 Pleasanton, CA, USA. 5The Jackson Laboratory for
Genomic Medicine, 10 Discovery Drive, 06032 Farmington, CT, USA. 6Institute
for Systems Genomics, University of Connecticut, 06032 Farmington, CT, USA. Received: 8 August 2016 Accepted: 23 November 2016 The pilot project presented in this works suggests the
great potential of fully incorporating the resources of
graph-like genome assemblies into variant calling, but
also underscore the importance of developing computa-
tional resources that will allow full reconstruction of the
genotype in personal genomes. Abbreviations The work presented here is an exploration of the impli-
cations of the new genome build for variant calling in
WGS analysis. We have presented a simple heuristic algo-
rithm designed to search for characteristic distributions
of ASDP-associated variants in VCF files that allow the
presence of alternate loci to be inferred. We have argued
that variants called against the primary assembly may be
spurious in some such cases. ASDP, Alignable scaffold-discrepant position; DNA, Deoxyribonucleic acid;
GFF, General feature format; GRC, Genome Reference Consortium; GWAS,
Genome-wide association study; indel, Insertion or deletion; LRC, Leukocyte
receptor complex; MHC, Major histocompatibility complex; NCBI, National
Center for Biotechnology Information; nt, nucleotides; OMIM, Online
Mendelian Inheritance in Man; SAM, Sequence alignment/map; SNP, Single
nucleotide polymorphism; SNV, Single nucleotide variant; SV, Structural
variant; VCF, Variant calling format; WGS, Whole-genome sequencing Competing interests DMC is an employee of 10x Genomics. The remaining authors declare that
they have no competing interests. Authors’ contributions MJ and PNR conceived the algorithms and analysis strategies. MJ
implemented ASDPex. MJ and PNR prepared the manuscript with critical input
from MS, TZ, KR, and DMC. All authors read and approved the manuscript. 1.
Kent WJ, Haussler D. Assembly of the working draft of the human
genome with gigassembler. Genome Res. 2001;11(9):1541–8.
doi:10.1101/gr.183201. Consent for publication
Not applicable. Consent for publication
Not applicable. References 1. Kent WJ, Haussler D. Assembly of the working draft of the human
genome with gigassembler. Genome Res. 2001;11(9):1541–8. doi:10.1101/gr.183201. 2. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860–921. 2. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860–921. Page 14 of 15 Page 14 of 15 Jäger et al. Genome Medicine (2016) 8:130 3. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The
sequence of the human genome. Science. 2001;291(5507):1304–51. doi:10.1126/science.1058040. 25. Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, et al. Computational evaluation of exome sequence data using human and
model organism phenotypes improves diagnostic efficiency. Genet Med. 2016;18(6):608–17. doi:10.1038/gim.2015.137. 4. Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin
CS, et al. Extending reference assembly models. Genome Biol. 2015;16:13. doi:10.1186/s13059-015-0587-3. 26. Robinson PN, Köhler S, Oellrich A, Wang K, Mungall CJ, Lewis S, et al. Improved exome prioritization of disease genes through cross-species
phenotype comparison. Genome Res. 2014;24(2):340–8. doi:10.1101/gr.160325.113. 5. Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J, et al. Variation analysis and gene annotation of eight MHC haplotypes: the
MHC haplotype project. Immunogenetics. 2008;60(1):1–18. doi:10.1007/s00251-007-0262-2. 27. Bainbridge MN, Wang M, Wu Y, Newsham I, Muzny DM, Jefferies JL,
et al. Targeted enrichment beyond the consensus coding DNA sequence
exome reveals exons with higher variant densities. Genome Biol. 2011;12(7):68. doi:10.1186/gb-2011-12-7-r68. 6. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T,
et al. Mapping and sequencing of structural variation from eight human
genomes. Nature. 2008;453(7191):56–64. doi:10.1038/nature06862. 28. Guo Y, Ye F, Sheng Q, Clark T, Samuels DC. Three-stage quality control
strategies for DNA re-sequencing data. Brief Bioinform. 2014;15(6):879–89. doi:10.1093/bib/bbt069. 7. Zody MC, Jiang Z, Fung HC, Antonacci F, Hillier LW, Cardone MF, et al. Evolutionary toggling of the MAPT 17q21.31 inversion region. Nat Genet. 2008;40(9):1076–83. doi:10.1038/ng.193. 29. Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, et al. Factors influencing success of clinical genome sequencing across a broad
spectrum of disorders. Nat Genet. 2015;47(7):717–26. doi:10.1038/ng.3304. 8. Yuan B, Liu P, Gupta A, Beck CR, Tejomurtula A, Campbell IM, et al. References Comparative genomic analyses of the human NPHP1 locus reveal
complex genomic architecture and its regional evolution in primates. PLoS Genet. 2015;11(12):1005686. doi:10.1371/journal.pgen.1005686. 30. Martin HC, Kim GE, Pagnamenta AT, Murakami Y, Carvill GL, Meyer E,
et al. Clinical whole-genome sequencing in severe early-onset epilepsy
reveals new genes and improves molecular diagnosis. Hum Mol Genet. 2014;23(12):3200–11. doi:10.1093/hmg/ddu030. 9. Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N,
et al. Modernizing reference genome assemblies. PLoS Biol. 2011;9(7):
1001091. doi:10.1371/journal.pbio.1001091. 31. Veltman JA, Lupski JR. From genes to genomes in the clinic. Genome
Med. 2015;7(1):78. doi:10.1186/s13073-015-0200-0. 10. NCBI Resource Coordinators. Database resources of the National Center
for Biotechnology Information. Nucleic Acids Res. 2016;44(D1):7–19. 32. Goldfeder RL, Priest JR, Zook JM, Grove ME, Waggott D, Wheeler MT,
et al. Medical implications of technical accuracy in genome sequencing. Genome Med. 2016;8(1):24. doi:10.1186/s13073-016-0269-0. 11. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, NISC Comparative
Sequencing Program, et al. LAGAN and Multi-LAGAN: efficient tools for
large-scale multiple alignment of genomic DNA. Genome Res. 2003;13(4):
721–31. doi:10.1101/gr.926603. 33. O’Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, et al. Low concordance
of multiple variant-calling pipelines: practical implications for exome and
genome sequencing. Genome Med. 2013;5(3):28. doi:10.1186/gm432. 12. Döring A, Weese D, Rausch T, Reinert K. SeqAn an efficient, generic C++
library for sequence analysis. BMC Bioinform. 2008;9:11. doi:10.1186/1471-2105-9-11. 34. Robinson PN, Booms P, Katzke S, Ladewig M, Neumann L, Palz M, et al. Mutations of fbn1 and genotype-phenotype correlations in Marfan
syndrome and related fibrillinopathies. Hum Mutat. 2002;20(3):153–61. doi:10.1002/humu.10113. 13. Garrison E, Marth G. Haplotype-based variant detection from short-read
sequencing. 2012;1207(3907):. ArXiv 1207.3907. 14. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A,
et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing
next-generation DNA sequencing data. Genome Res. 2010;20(9):
1297–303. doi:10.1101/gr.107524.110. 35. LaFramboise T. Single nucleotide polymorphism arrays: a decade of
biological, computational and technological advances. Nucleic Acids Res. 2009;37(13):4181–93. doi:10.1093/nar/gkp552. g
15. Li H. Aligning sequence reads, clone sequences and assembly contigs
with BWA-MEM. 2013;1303(3997):. ArXiv e-prints 1303.3997. 15. Li H. Aligning sequence reads, clone sequences and assembly contigs
with BWA-MEM. 2013;1303(3997):. ArXiv e-prints 1303.3997. 36. Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR,
Graves PE, et al. Meta-analysis of genome-wide association studies of
asthma in ethnically diverse North American populations. Nat Genet. 2011;43(9):887–92. doi:10.1038/ng.888. 16. References Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The
sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. 37. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, et al. Linkage
disequilibrium in the human genome. Nature. 2001;411(6834):199–204. doi:10.1038/35075590. 17. Faust GG, Hall IM. SAMBLASTER: fast duplicate marking and structural
variant read extraction. Bioinformatics. 2014;30(17):2503–5. doi:10.1093/bioinformatics/btu314. 38. Sun C, Medvedev P. Varmatch: robust matching of small variant datasets
using flexible scoring schemes. bioRxiv. 2016. doi:10.1101/062943. http://
biorxiv.org/content/early/2016/07/08/062943.full.pdf. 18. 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A,
Brooks LD, Durbin RM, et al. A map of human genome variation from
population-scale sequencing. Nature. 2010;467(7319):1061–73. doi:10.1038/nature09534. 39. Chaisson MJP, Wilson RK, Eichler EE. Genetic variation and the de novo
assembly of human genomes. Nat Rev Genet. 2015;16(11):627–40. doi:10.1038/nrg3933. 19. O’Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic
expansion, and functional annotation. Nucleic Acids Res. 2016;44(D1):
733–45. doi:10.1093/nar/gkv1189. 40. Zerbino DR, Ballinger T, Paten B, Hickey G, Haussler D. Representing and
decomposing genomic structural variants as balanced integer flows on
sequence graphs. BMC Bioinformatics. 2016;17(1):400. 41. Huddleston J, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, et al. Reconstructing complex regions of genomes using long-read sequencing
technology. Genome Res. 2014;24(4):688–96. doi:10.1101/gr.168450.113. 20. Jäger M, Wang K, Bauer S, Smedley D, Krawitz P, Robinson PN. Jannovar: a Java library for exome annotation. Hum Mutat. 2014;35(5):
548–55. doi:10.1002/humu.22531. 42. Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, et al. Long-read
sequencing and de novo assembly of a Chinese genome. Nat Commun. 2016;7:12065. doi:10.1038/ncomms12065. 21. Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, et al. The
NHGRI GWAS Catalog, A curated resource of SNP-trait associations. Nucleic Acids Res. 2014;42(Database issue):1001–6. doi:10.1093/nar/gkt1229. 43. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston
J, et al. An integrated map of structural variation in 2,504 human
genomes. Nature. 2015;526(7571):75–81. doi:10.1038/nature15394. 22. Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online
catalog of human genes and genetic disorders. Nucleic Acids Res. 2015;43(Database issue):789–98. doi:10.1093/nar/gku1205. 44. Chaisson MJP, Huddleston J, Dennis MY, Sudmant PH, Malig M,
Hormozdiari F, et al. Resolving the complexity of the human genome
using single-molecule sequencing. Nature. 2015;517(7536):608–11. doi:10.1038/nature13907. 23. Jäger et al. Genome Medicine (2016) 8:130 Jäger et al. Genome Medicine (2016) 8:130 46. Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. Assembling large genomes with single-molecule sequencing and
locality-sensitive hashing. Nat Biotechnol. 2015;33(6):623–30. doi:10.1038/nbt.3238. 47. Miga KH, Newton Y, Jain M, Altemose N, Willard HF, Kent WJ. Centromere reference models for human chromosomes X and Y satellite
arrays. Genome Res. 2014;24(4):697–707. doi:10.1101/gr.159624.113. 48. Computational Pan-Genomics Consortium. Computational
pan-genomics: status, promises and challenges. Brief Bioinform. 2016. [Epub ahead of print] PubMed PMID: 27769991. 49. Wolfe D, Dudek S, Ritchie MD, Pendergrass SA. Visualizing genomic
information across chromosomes with phenogram. BioData Min. 2013;6(1):18. doi:10.1186/1756-0381-6-18. 50. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES,
Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):
24–6. doi:10.1038/nbt.1754. 51. Okada Y, Sim X, Go MJ, Wu JY, Gu D, Takeuchi F, et al. Meta-analysis
identifies multiple loci associated with kidney function-related traits in
East Asian populations. Nat Genet. 2012;44(8):904–9. doi:10.1038/ng.2352. 46. Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. Assembling large genomes with single-molecule sequencing and
locality-sensitive hashing. Nat Biotechnol. 2015;33(6):623–30. doi:10.1038/nbt.3238. 47. Miga KH, Newton Y, Jain M, Altemose N, Willard HF, Kent WJ. Centromere reference models for human chromosomes X and Y satellite
arrays. Genome Res. 2014;24(4):697–707. doi:10.1101/gr.159624.113. 48. Computational Pan-Genomics Consortium. Computational
pan-genomics: status, promises and challenges. Brief Bioinform. 2016. [Epub ahead of print] PubMed PMID: 27769991. 49. Wolfe D, Dudek S, Ritchie MD, Pendergrass SA. Visualizing genomic
information across chromosomes with phenogram. BioData Min. 2013;6(1):18. doi:10.1186/1756-0381-6-18. 50. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES,
Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):
24–6. doi:10.1038/nbt.1754. 50. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES,
Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):
24–6. doi:10.1038/nbt.1754. 51. Okada Y, Sim X, Go MJ, Wu JY, Gu D, Takeuchi F, et al. Meta-analysis
identifies multiple loci associated with kidney function-related traits in
East Asian populations. Nat Genet. 2012;44(8):904–9. doi:10.1038/ng.2352. References Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools,. Bioinformatics. 2011;27(15):2156–8. doi:10.1093/bioinformatics/btr330. 45. Steinberg KM, Schneider VA, Graves-Lindsay TA, Fulton RS, Agarwala R,
Huddleston J, et al. Single haplotype assembly of the human genome
from a hydatidiform mole. Genome Res. 2014;24(12):2066–76. doi:10.1101/gr.180893.114. 24. Smedley D, Jacobsen JOB, Jäger M, Köhler S, Holtgrewe M, Schubach
M, et al. Next-generation diagnostics and disease-gene discovery with the
exomiser. Nat Protoc. 2015;10(12):2004–15. doi:10.1038/nprot.2015.124. Page 15 of 15 Submit your next manuscript to BioMed Central
and we will help you at every step: • We accept pre-submission inquiries
• Our selector tool helps you to find the most relevant journal
• We provide round the clock customer support
• Convenient online submission
• Thorough peer review
• Inclusion in PubMed and all major indexing services
• Maximum visibility for your research
Submit your manuscript at
www.biomedcentral.com/submit
and we will help you at every step:
|
https://openalex.org/W4317940832
|
https://www.researchsquare.com/article/rs-2507401/latest.pdf
|
English
| null |
Targeted-Gene Sequencing and Bioinformatics Analysis of Patients with Gallbladder Neuroendocrine Carcinoma: A Case Report and Literature Review
|
Research Square (Research Square)
| 2,023
|
cc-by
| 5,475
|
Targeted-Gene Sequencing and Bioinformatics
Analysis of Patients with Gallbladder
Neuroendocrine Carcinoma: A Case Report and
Literature Review
Yunchuan Yang
Jinan University
Zhitao Chen
Shulan (Hangzhou) Hospital, Zhejiang Shuren University Shulan International Medical College
Hui Tang
Zhejiang University School of Medicine
Dalong Wan
Zhejiang University School of Medicine
Mulin Liu
(
liumulin66@aliyun.com
)
Jinan University
Case Report
Keywords: gallbladder neuroendocrine carcinoma, targeted-gene sequencing, bioinformatics analysis
Posted Date: January 25th, 2023
DOI: https://doi.org/10.21203/rs.3.rs-2507401/v1
License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full License Case Report Keywords: gallbladder neuroendocrine carcinoma, targeted-gene sequencing, bioinformatics analysis
Posted Date: January 25th, 2023
DOI: https://doi.org/10.21203/rs.3.rs-2507401/v1
License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full License Page 1/20 Page 1/20 Page 1/20 Page 1/20 Abstract Background: Gallbladder Neuroendocrine carcinomas (NEC) is a subtype of gallbladder malignant
tumour that is characterized by low incidence, high malignancy and poor prognosis. To date, the genetic
alterations, mechanistic relationships among mutated genes and signaling pathways of gallbladder NEC
are unclear. Patient and Methods: This paper presents a case of rare primary gallbladder NECin a 73-year-old female
patient. A radical cholecystectomy associated with hepatic hilar lymphadenectomy, resection of
segments IV-B and V of the liver were performed. Targeted-gene sequencing and bioinformatics analysis
tools, including STRING, GeneMANIA, Metascape, TRRUST, Sangerbox, cBioPortal and GSCA, are used to
clarify the biological functions and features of mutated genes in gallbladder NEC. Results: Twelve gene mutations (APC, ARID2, IFNA6, KEAP1, RB1, SMAD4, TP53, BTK, GATA1, GNAS and
PRDM3) were observed, and a tumor mutation burden (TMB) of 9.52 muts/Mb was calculated in the
gallbladder NEC using targeted-gene sequencing. Protein-protein interaction network was constructed,
which showed the significant interactions among twelve mutated genes. In terms of the functions and
pathways of twelve gene mutations based on GO and KEGG, 40 tumor-related results are presented in this
paper. Key regulated factor of Neuroendocrine carcinoma of gallbladder-related genes was established. In
addition, the biological functions and features of gallbladder NEC are further compared with gallbladder
carcinoma. Conclusion: Gallbladder NEC urgently requires standardized and effective treatment protocols. Gallbladder NEC can be compared with other gallbladder carcinoma that have characteristic clinical
phenotype, molecular alterations, functional information and enrichment pathway. Introduction Neuroendocrine carcinoma(NEC) is most common in the digestive and respiratory tracts, such as the
stomach, intestines, pancreas and lung, which account for about 97% of all neuroendocrine
carcinomas[1]. However, the occurrence of gallbladder NEC is quite rare in clinical practice[2]. Due to the
lack of guidelines or consensus on gallbladder NEC, the diagnosis and treatment of gallbladder NEC is
based on the guidelines for gallbladder adenocarcinoma[3]. For patients suitable for radical surgery, the
preferred treatment option is radical surgery with post-operative adjuvant chemotherapy. Close post-
operative follow-up examinations are also essential. Radiotherapy, chemotherapy or participation in
clinical trials are recommended for advanced tumours. Importantly, NEC of the gallbladder, completely
distinct from other types of malignant tumours of the gallbladder, is highly aggressive[4]. However, the
clinicopathological features and genetic and molecular characteristics of gallbladder NEC remain unclear
due to the paucity of research on the disease. Further understanding of gallbladder NEC, particularly the
genetic and genetic features, is urgently required. Comprehensive gene mutation profiling and molecular Page 2/20 analysis may reveal the mechanisms of tumourigenesis and progression, providing important basic
knowledge for future research and clinical diagnosis and treatment. This paper presents a case of NEC of the gallbladder in a 73-year-old woman. In addition to standard
histopathological evaluation, targeted gene sequencing was performed. To date, the mutational
spectrum, key regulated factor, functional relationships and enrichment pathways of mutated genes are
not well studied in NEC of gallbladder. The aim of this article is to describe the clinical features, genetic
characteristics and clinical management of patients with rare gallbladder NEC. In addition, the biological
features of gallbladder NEC are further compared with those of gallbladder adenocarcinoma in the hope
of gaining a better understanding of this disease. Case Report A 73-year-old Chinese female with a week history of upper abdominal discomfort was admitted to our
hospital on December 30, 2019. A week ago, the patient went to the local hospital for examination and
the abdomen ultrasonic scan showed a 7 cm hyperechoic focus with unclear margins and multiple
gallbladder stones with cholecystitis. On admission, edema, anemia, jaundice, hepatomegaly, and
splenomegaly were not noted at that time. The patient reported no discomfort, weight loss, fever, or night
sweats. She had a 5-year history of hypertension and 10-year history of cholelithiasis. The serum levels
of tumor markers, such as carcinoembryonic antigen, carbohydrate antigen 19 − 9, and alpha-fetoprotein
were all within normal limits. AST, ALT, albumin, and bilirubin were also within normal range. Abdominal
contrast-enhanced computed tomography (CT) suggested a 7 cm mass in the segment IVb and V of the
liver, accompanied with localized wall thickening the fundus of the gallbladder that was enhanced from
an early stage with a prolonged contrast effect. Meanwhile, multiple gallbladder stones were also
identified. There were no other findings, such as pancreatic enlargement and bile duct dilatation (Fig. 1). Dynamic contrast enhanced magnetic resonance imaging (MRI) showed a 6.7cm mass with low signal
intensity on T1-weighted imaging, high signal intensity with T2-weighted imaging, and diffusion-weighted
imaging (Fig. 2). Gallbladder carcinoma with peripheral liver invasion and cholelithiasis was considered
firstly. The patient was discussed by our multidisciplinary team (MDT), and a final diagnosis of extensive
gallbladder carcinoma with peripheral liver invasion and cholelithiasis was made. We decided to perform
surgical resection prior to chemotherapy because of concerns about complications developing from
cholelithiasis and patient’s rejection of chemotherapy. A radical cholecystectomy associated with hepatic hilar lymphadenectomy, resection of segments IV-B
and V of the liver were performed. Macroscopic analysis identified a greyish-yellow globular-like lesion
measuring 6×7 cm, at the fundus of the gallbladder, which was almost filled by multiples yellowish
stones (Fig. 3). Detailed postoperative immunohistochemical examination showed that a nest-like pattern
of tumour cells with marked cellular heterogeneity and visible necrosis infiltrated the whole layer of
gallbladder and liver. They were immunohistochemically positive for cytokeratin (CK) 7, CK19, CK(pan),
chromogranin A, synaptophysin, and negative staining for CD56, CK5/6, P40, Hepatocyte. Furthermore, Page 3/20 Page 3/20 the mitotic count was 24 per 10 high-power microscopic fields, and the Ki-67 proliferation index was 70%,
which demonstrated poorly differentiated neuroendocrine carcinoma (Fig. 4). Discussion According to the latest World Health Organization(WHO) nomenclature for neuroendocrine neoplasms in
2019, neuroendocrine neoplasm is used to refer to all tumours of neuroendocrine cell origin, of which
highly differentiated neuroendocrine tumours are named neuroendocrine tumor and poorly differentiated
neuroendocrine tumours are named neuroendocrine carcinoma[5]. Gallbladder NEC is a rare and specific
subtype of gallbladder cancer, accounting for less than 2% of all types of gallbladder cancer[6]. Currently
gallbladder NEC is classified using the same American Joint Committee on Cancer (AJCC) staging
system as gallbladder adenocarcinomas, although it is known that other gastrointestinal and pancreatic
NETs generally have a more indolent clinical course than adenocarcinomas. Some researchers insist tha
NEC is transformed from gallbladder adenocarcinoma and a mutual conversion of NET and
adenocarcinoma in gastrointestinal tract has been proved[7]. Knowledge of the differences and
similarities between gallbladder NEC and gallbladder carcinoma is equally limited. In this study, we
summarize previous articles and use bioinformatics analysis to compare the clinicopathologic and
genetic characteristics of the gallbladder NEC with gallbladder carcinoma. Case Report Tumor DNA from the gallbladder neuroendocrine carcinoma was tested. The panel covered selected
introns of 448 cancer related genes and all exons. Twelve somatic mutations were identified, as
summarised in Table 1. In addition, the tumour mutation burden (TMB) was calculated as the total
number of non-synonymous somatic mutations per megabase (MB) of genome. This patient had a TMB
of 9.52 muts/Mb. Meanwhile, PD-L1 (programmed cell death ligand 1) immunohistochemical assay was
used to predict response to PD-1/PD-L1 inhibitors, showing that PD-L1 was not expressed in gallbladder
neuroendocrine carcinoma. Tumor proportion score (TPS) and combined positivity score (CPS) were
calculated to evaluate the immunohistochemical expression of PD-L1 (Fig. 5). Table 1
The information of Neuroendocrine carcinoma of gallbladder–related mutated genes. Genes
Original name
Cytoband
Exon
count
Variant type
Abundance
variation
APC
APC regulator of WNT
signaling pathway
5q22.2
20
Copy number
variation
CN:1.2
ARID2
AT-rich interaction domain 2
12q12
22
c.3382C > T
(p.Q1128*)
77.3%
IFNA6
interferon alpha 6
9p21.3
1
c.53C > G (p.S18*)
42.8%
KEAP1
kelch like ECH associated
protein 1
19p13.2
7
c.1408C > T
(p.R470C)
87.9%
RB1
RB transcriptional
corepressor 1
13q14.2
27
c.772-776del
(p.N258Efs*11)
76.1%
SMAD4
SMAD family member 4
18q21.2
12
Copy number
variation
CN:1.1
TP53
tumor protein p53
17p13.1
11
Copy number
variation
CN:1.1
c.574C > T
(p.Q192*)
81.3%
BTK
Bruton tyrosine kinase
Xq22.1
21
c.574C > T
(p.D232V)
48.6%
GATA1
GATA binding protein 1
Xp11.23
6
c.173C > A
(p.A58E)
42.5%
GNAS
GNAS complex locus
20q13.32
22
c.1048G > C
(p.E350Q)
42.9%
MECOM
MDS1 and EVI1 complex
locus
3q26.2
24
c.1161G > T
(p.Q387H)
2.4% Page 4/20 The patient recovered smoothly and was discharged on the 8th day after operation. A month after the
discharge, the patient received six cycles of cisplatin (area under the curve of 5 on day 1 repeated every
21 days) and etoposide (80 mg/m2 on days 1 through 3 repeated every 21 days). 2 months later, a
recurrence in the VI segement of liver was detected in the MRI. The patient underwent second-line
chemotherapy with capecitabine and temozolomide orally. (capecitabine 3 tables BID d1-d14,
temozolomide 200mg d10-14, q3w). However, after 1 month, multiple liver recurrences were detected and
she died of progressive disease 15 months after surgery. Genetic Part According to the results of targeted gene sequencing, 12 mutations types that were private to that
specimen (Table 1). To better understand the biologic properties and potential therapeutic targets of this
rare tumor, we utilized these potential oncogenes to further explore the biologic mechanisms of
tumorigenesis based on several bioinformatics databases. Firstly, Protein-protein interaction networks
(PPIs) were analyzed and visualized using the STRING[8] (version: 11.5, https://string-db.org/) database
expansion. The outcome of STRING network consisted of 11 nodes and 14 edges with an average local
clustering coefficient of 0.776 (PPI enrichment p-value < 0.0001) (Fig. 6A). To explore the potential
biological mechanisms, our analysis using GeneMANIA[9] (http://genemania.org/) databases found that
these mutated genes associated with transcription regulator complex, ATPase complex, SWI/SNF
superfamily-type complex, negative regulation of mitotic cell cycle phase transition, negative regulation
of cell cycle phase transition, protein-DNA complex subunit organization, and regulation of
metaphase/anaphase transition of cell cycle (Fig. 6B). In addition, protein-protein interaction enrichment
analysis was performed using Metascape (https://metascape.org/) database (Fig. 6C-6D). Page 5/20 Page 5/20 The transcription factors are important regulators of gene expression and play an important role in the
development of tumors. TRRUST[10] (version 2, https://www.grnpedia.org/trrust/) database was used to
explore the human transcription factors of these mutated genes. YY1, KAT2B, PAX5, DNMT1, EZH2, FOS,
GATA1, SPI1, MYC, E2F1, and TP53 are known to be a pivotal transcription factor related to these
mutated genes (Table 2). Using Sangerbox 3.0 (http://vip.sangerbox.com) database, we analyzed the
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to explore these genes
possible biological functions. In the GO analysis of biological processes (BP), we found that these genes
may take part in regulation of molecular function, regulation of biological quality, and tissue development
(Fig. 7A). In the GO analysis of cellular components (CC), these genes were mainly found to be located in
the nucleoplasm, transcription factor complex, and chromosomal part (Fig. 7B). In GO analysis of the
molecular function (MF), we found that the genes were mainly enriched in identical protein binding,
transcription factor binding, and proximal promoter sequence-specific DNA binding (Fig. 7C). The KEGG
enrichment analysis showed that these genes might be involved in pathways in cancer, hepatocellular
carcinoma, and human papillomavirus infection (Fig. 7D). These results are similar to those of the
Metascape database (Fig. 7E-7F). Page 6/20 Table 2
Key regulated factor of Neuroendocrine carcinoma of gallbladder-related genes. Genetic Part Key TF
Description
Overlapped
genes
P-
value
FDR
1
YY1
YY1 transcription factor
APC, GNAS,
TP53
1.74E-
05
1.32E-
04
2
KAT2B
K(lysine) acetyltransferase 2B
RB1,
SMAD4
2.40E-
05
1.32E-
04
3
PAX5
paired box 5
RB1, TP53
6.45E-
05
2.36E-
04
4
DNMT1
DNA (cytosine-5-)-methyltransferase 1
RB1, TP53
1.42E-
04
3.91E-
04
5
EZH2
enhancer of zeste homolog 2 (Drosophila)
APC, TP53
2.38E-
04
5.24E-
04
6
FOS
FBJ murine osteosarcoma viral oncogene
homolog
SMAD4,
TP53
4.85E-
04
7.61E-
04
7
GATA1
GATA binding protein 1 (globin transcription
factor 1)
GATA1,
GNAS
4.85E-
04
7.61E-
04
8
SPI1
spleen focus forming virus (SFFV) proviral
integration oncogene spi1
BTK, GATA1
5.73E-
04
7.88E-
04
9
MYC
v-myc myelocytomatosis viral oncogene
homolog (avian)
GATA1,
TP53
1.48E-
03
1.81E-
03
10
E2F1
E2F transcription factor 1
RB1, TP53
2.64E-
03
2.90E-
03
11
TP53
tumor protein p53
RB1, TP53
3.92E-
03
3.92E-
03
TF transcription factor; FDR False discovery rate. Table 2 Sakaki et al proposed that gallbladder NECs arise from the metamorphosis of gallbladder
adenocarcinoma[11]. A recent study performed a whole exome sequencing analysis of 151 gallbladder
cancer patients. The results showed that the most common mutated genes in gallbladder cancer included
TP53 (27%), KMT2C (11%), SMAD4 (11%), PER3 (8%), ERBB3 (8%), ARID2 (7%), ARID1A (7%) and ERBB2
(7%), and that the most common mutated signalling pathway was that of the ErbB signalling
pathway[12]. Based on our findings, the mutational profiles of gallbladder NEC are partly the same as
those of gallbladder adenocarcinoma. Therefore, we further analyzed the relationship among them. Tumorigenesis is based on genetic mutations, which make the nucleus become an ideal target for tumor
suppression. The cBioPortal (https://www.cbioportal.org/) database was used to explore the gene
mutation information of these mutated genes in gallbladder carcinoma (MSK, Cancer 2018). As was
shown in Fig. 8A, a high mutation rate of SMAD4 and TP53 was observed in gallbladder carcinoma Page 7/20 Page 7/20 patients. In the 101 sequenced gallbladder carcinoma patients, the genetic alteration were found in 31, 59
gallbladder carcinoma patients and the mutation rate were 31%, 58%, respectively. Meanwhile, we found
that these genes had the highest mutation rate in gallbladder carcinoma (Gene altered in 74.76% of 103
cases), followed by cholangiocarcinomas (Gene altered in 48.92% of 417 cases) and intrahepatic
cholangiocarcinomas (Gene altered in 24.03% of 412 cases) (Fig. 8B). Genetic Part Taken together, these results
introduce these mutated genes may as an important player in gallbladder carcinoma development. KEAP1 is an important tumor suppressor gene. KEAP1 gene mutation reduces the affinity with Nrf2 in the
cytoplasm, resulting in the accumulation of Nrf2 in the nucleus, and then promotes the occurrence and
development of tumors[13]. Importantly, KEAP1 mutations are found in many types of cancer, including
gallbladder cancer[14–16]. Genetic mutations serve as targets in precise therapy for cancer. In present
sample, KEAP1 was the most dominant mutated gene with mutation frequency of 87.9%. To explore
potential drugs based on KEAP1 mutation, the GSCA (http://bioinfo.life.hust.edu.cn/GSCA/), a web server,
was used to explore the drug–gene interactions of mutated genes. As shown in Fig. 8C, the correlation
between KEAP1 expression and the sensitivity of GDSC drugs (top 30) in pan-cancer were displayed. Little is known about the genetic and molecular characteristics of gallbladder NEC, therefore, there is no
clinical application of molecularly targeted therapy for gallbladder NEC[17]. There is an urgent clinical
need to uncover the molecular markers that contribute to their pathological progression and thus develop
new therapeutic modalities. It is reasonable to assume that the gallbladder NEC and the gallbladder
adenocarcinoma. are different diseases but closely conected with each other Thus, treatment strategies
based on gallbladder adenocarcinoma are not fully applicable to gallbladder neuroendocrine tumours. Clinicopathologic Part Almost existing literature on neuroendocrine carcinoma of the gallbladder is limited to case report and
case series. The most common symptoms of gallbladder NEC often manifest as epigastric pain, weight
loss or anorexia. The meidan age of gallbladder NEC is about 60 years. Most patients with
neuroendocrine carcinoma of the gallbladder are female[18]. Gallbladder stones with cholecystitis are
thought to promote the development and progression of the gallbladder neuroendocrine carcinoma. As in
our case, the gallbladder neuroendocrine carcinoma was accompanied by gallbladder stones. Various
imaging modalities are used in the diagnosis of gallbladder NEC, but it is difficult to distinguish it from
other types of gallbladder cancer. Ultrasound is used for the initial screening examination, and further
enhanced CT or MRI is required to assess the staging of the gallbladder tumour. The investigators
considered that most of the gallbladder NEC originated in deep parts of the lamina propria or submucosa
and thus showed on CT and MRI that the mucosal epithelium of the gallbladder surface remained
partially intact with linear enhancement. Similar descriptions have been found in previous studies of NEC
of the gastrointestinal tract[19, 20]. In addition, the size of metastatic lymph nodes in gallbladder NEC
was larger than that of adenocarcinoma[21]. But the preoperative accurate diagnosis of gallbladder NEC
is challenging to the clinician. Page 8/20 The definitive diagnoses of gallbladder NEC require both pathology and immunohistochemistry. Currently,
the most commonly used specific biomarkers available are chromogranin A (CgA), synaptophysin (Syn)
and neuro-specific enolase[22]. In a previous study involving 21 patients with gallbladder NEC, more than
80% of cases showed positive staining for CgA and Syn [23]. In another study, there were 15 patients with
gallbladder NEC. CgA and Syn had positive rates of 92.3% and 100%, respectively[24]. Similarly,
immunohistochemical results of the patients in this study showed chromogranin A and synaptophysin
were positive. Then neuro-specific enolase was not verified in immunohistochemistry. In addition,
previous study has reported that an elevated Ki-67 index and a high mitotic rate may be strongly
associated with poor prognosis[23]. Unfortunately, the cases in this study had high Ki-67 index and
mitotic index. Even with post-operative adjuvant chemotherapy, the tumour recurred quickly and the
patient died 15 months after surgery. There are no guidelines or consensus on the treatment options for NECs of the gallbladder worldwide. Conclusion To sum up, a case of a patient with rare gallbladder NEC is presented and clinicopathologic and genetic
characteristics are discussed based on previous reports. However, the prognosis of gallbladder NEC is
unsatisfactory. Gene sequencing tests may improve clinical management and prognosis of this disease. More cases are needed to investigate the more effective treatment of gallbladder NEC. Clinicopathologic Part Usually, the most consistently practiced treatment for gallbladder NECs is complete resection, which is
extrapolated from gallbladder adenocarcinoma management. Review of published case reports suggests
that the management of gallbladder NETs is highly inconsistent, Early-stage NEC of the gallbladder can
achieve better long-term survival with radical surgery. However, local infiltration and/or distant
metastases have already occurred at the time of detection for gallbladder NEC, which make it unsuitable
for surgical treatment. Chemotherapy is the palliative treatment modality for advanced gallbladder NEC. The effectiveness of chemotherapy for gallbladder NEC is controversial. Wang et al. studied 62 patients
with gallbladder NEC, suggesting that postoperative adjuvant chemotherapy had no significant effect on
overall survival in gallbladder NEC[3]. In addition, a multicenter, large cohort study in China showed no
effect of postoperative platinum-based chemotherapeutic regimens as adjuvant chemotherapy on long-
term survival in gallbladder NEC[18]. However, A Japanese case report exhibited that chemotherapy with
cisplatin and irinotecan combined with radiotherapy can achieve a complete response to an advanced
gallbladder neuroendocrine tumor, with no recurrence after 3 years of follow-up[25]. Ayabe et al
[6]documented and compared the survival of patients undergoing resection for gastrointestinal NETs and
gallbladder adenocarcinoma using the Large National Database. Then they demonstrated that
gallbladder NETs have the worst survival of all gastrointestinal NETs, albeit superior to patients with
gallbladder adenocarcinoma. In general, gallbladder NEC have the similar clinical and imaging features,
but worse prognosis compared with gallbladder cancer. There are no guidelines or consensus on the treatment options for NECs of the gallbladder worldwide. Usually, the most consistently practiced treatment for gallbladder NECs is complete resection, which is
extrapolated from gallbladder adenocarcinoma management. Review of published case reports suggests
that the management of gallbladder NETs is highly inconsistent, Early-stage NEC of the gallbladder can
achieve better long-term survival with radical surgery. However, local infiltration and/or distant Abbreviations Page 9/20 Page 9/20 NEC: Gallbladder Neuroendocrine carcinomas; TMB: tumor mutation burden; CT: computed tomography;
MRI: magnetic resonance imaging; TPS: Tumor proportion score; CPS: combined positivity score; GO:
Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; CgA : chromogranin A ; Syn:
synaptophysin NEC: Gallbladder Neuroendocrine carcinomas; TMB: tumor mutation burden; CT: computed tomography;
MRI: magnetic resonance imaging; TPS: Tumor proportion score; CPS: combined positivity score; GO:
Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; CgA : chromogranin A ; Syn:
synaptophysin Declarations Ethics approval and consent to participate Authors' contributions Yunchuan Yang: Writing – original draft; Writing – review & editing; Methodology. Zhitao Chen: Formal analysis; Methodology; Resources. Hui Tang: Formal analysis; Writing – original draft; Writing. Dalong Wan: Writing – original draft; Writing – review & editing. All authors made substantial contributions to conception and design, acquisition of data, or analysis and
interpretation of data; took part in drafting the article or revising it critically for important intellectual
content; agreed to submit to the current journal; gave final approval of the version to be published; and
agree to be accountable for all aspects of the work Acknowledgements Not applicable Consent for publication We have obtained consent to publish from the patient. We have obtained consent to publish from the patient. Availability of data and materials The datasets used and analysed during the current study are available from the corresponding author on
reasonable request. The authors declare that they have no competing interests. Authors' contributions The authors would like to thank all people involved in this work. 2General Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China;
3Department of Hepatobiliary Surgery Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren 2General Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China; 3Department of Hepatobiliary Surgery, Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren
University Shulan International Medical College, Hangzhou, Zhejiang 310003, China; 4Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine,
Hangzhou, Zhejiang 310003, China; 5Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University
School of Medicine, Hangzhou, Zhejiang 310003, China. Page 10/20 Page 10/20 1. Zhu J, Xiao W, Li Y. Management of Primary Hepatopancreatobiliary and Ampulla Large Cell
Neuroendocrine Carcinoma. 2022, 32:639–645. 1. Zhu J, Xiao W, Li Y. Management of Primary Hepatopancreatobiliary and Ampulla Large Cell
Neuroendocrine Carcinoma. 2022, 32:639–645. 2. Chu H, Zhang C, Shi Y, Wu W, Hu Z, Zhang J, Huang D. Gallbladder neuroendocrine carcinoma: A
single center experience. Med (Baltim). 2020;99:e21912. 3. Wang W, Yang CX. Clinicopathological characteristics and prognostic factors of patients with
primary gallbladder neuroendocrine carcinomas. 2022, 23:166–173. 4. Li M, Liu F, Zhang Y, Wu X, Wu W, Wang XA, Zhao S, Liu S, Liang H, Zhang F, et al. Whole-genome
sequencing reveals the mutational landscape of metastatic small-cell gallbladder neuroendocrine
carcinoma (GB-SCNEC). Cancer Lett. 2017;391:20–7. 5. Nagtegaal ID, Odze RD, Klimstra D, Paradis V, Rugge M, Schirmacher P, Washington KM, Carneiro F,
Cree IA. The 2019 WHO classification of tumours of the digestive system. 2020, 76:182–188. 6. Ayabe RI, Wach M, Ruff S, Martin S, Diggs L, Wiemken T, Hinyard L, Davis JL, Luu C, Hernandez JM. Primary Gallbladder Neuroendocrine Tumors: Insights into a Rare Histology Using a Large National
Database. Ann Surg Oncol. 2019;26:3577–85. 7. Vortmeyer AO, Lubensky IA, Merino MJ, Wang CY, Pham T, Furth EE, Zhuang Z. Concordance of
genetic alterations in poorly differentiated colorectal neuroendocrine carcinomas and associated
adenocarcinomas. J Natl Cancer Inst. 1997;89:1448–53. 8. Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT,
Morris JH, Bork P, et al. STRING v11: protein-protein association networks with increased coverage,
supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47:D607–d613. Page 11/20 Page 11/20 9. Franz M, Rodriguez H, Lopes C, Zuberi K, Montojo J, Bader GD, Morris Q. GeneMANIA update 2018. Nucleic Acids Res. 2018;46:W60–w64. 10. Han H, Cho JW, Lee S, Yun A, Kim H, Bae D, Yang S, Kim CY, Lee M, Kim E, et al. TRRUST v2: an
expanded reference database of human and mouse transcriptional regulatory interactions. Nucleic
Acids Res. 2018;46:D380–d386. 11. Sakaki M, Hirokawa M, Sano T, Horiguchi H, Wakatsuki S, Ogata S. Gallbladder Adenocarcinoma with
Florid Neuroendocrine Cell Nests and Extensive Paneth Cell Metaplasia. Endocr Pathol. 2000;11:365–71. 12. Li M, Liu F, Zhang F, Zhou W, Jiang X, Yang Y, Qu K, Wang Y, Ma Q, Wang T et al. Genomic
ERBB2/ERBB3 mutations promote PD-L1-mediated immune escape in gallbladder cancer: a whole-
exome sequencing analysis. 2019, 68:1024–1033. 13. Yamamoto M, Kensler TW, Motohashi H. The KEAP1-NRF2 System: a Thiol-Based Sensor-Effector
Apparatus for Maintaining Redox Homeostasis. 1. Zhu J, Xiao W, Li Y. Management of Primary Hepatopancreatobiliary and Ampulla Large Cell
Neuroendocrine Carcinoma. 2022, 32:639–645. Physiol Rev. 2018;98:1169–203. 14. Takahashi T, Sonobe M, Menju T, Nakayama E, Mino N, Iwakiri S, Nagai S, Sato K, Miyahara R, Okubo
K, et al. Mutations in Keap1 are a potential prognostic factor in resected non-small cell lung cancer. J
Surg Oncol. 2010;101:500–6. 15. Tian L, Lu Y, Yang T, Deng Z, Xu L, Yao W, Ma C, Li X, Zhang J, Liu Y, Wang J. aPKCι promotes
gallbladder cancer tumorigenesis and gemcitabine resistance by competing with Nrf2 for binding to
Keap1. Redox Biol. 2019;22:101149. 16. Shibata T, Kokubu A, Gotoh M, Ojima H, Ohta T, Yamamoto M, Hirohashi S. Genetic alteration of
Keap1 confers constitutive Nrf2 activation and resistance to chemotherapy in gallbladder cancer. Gastroenterology. 2008;135:1358–68. 1368.e1351-1354. 17. Liu F, Li Y, Ying D, Qiu S, He Y, Li M, Liu Y, Zhang Y, Zhu Q, Hu Y, et al. Whole-exome mutational
landscape of neuroendocrine carcinomas of the gallbladder. Signal Transduct Target Ther. 2021;6:55. 18. Wang Y, Huang B, Fu Q, Wang J, Ye M, Hu M, Qu K, Liu K, Hu X, Wei S, et al. Comprehensive Clinical
Analysis of Gallbladder Neuroendocrine Neoplasms: A Large-Volume Multicenter Study During One
Decade. Ann Surg Oncol. 2022;29:7619–30. 19. Kim SH, Kim SH, Kim MA, Shin CI, Han JK, Choi BI. CT differentiation of poorly-differentiated gastric
neuroendocrine tumours from well-differentiated neuroendocrine tumours and gastric
adenocarcinomas. Eur Radiol. 2015;25:1946–57. 20. Bae JS, Kim SH. Differential and prognostic MRI features of gallbladder neuroendocrine tumors and
adenocarcinomas. 2020, 30:2890–2901. 20. Bae JS, Kim SH. Differential and prognostic MRI features of gallbladder neuroendocrine tumors and
adenocarcinomas. 2020, 30:2890–2901. 21. Faraoun SA, Guerrache Y, Dautry R, Boudiaf M, Dohan A, Barral M, Hoeffel C, Rousset P, Fohlen A,
Soyer P. Computed Tomographic Features of Primary Small Cell Neuroendocrine Tumors of the
Gallbladder. J Comput Assist Tomogr. 2018;42:707–13. 21. Faraoun SA, Guerrache Y, Dautry R, Boudiaf M, Dohan A, Barral M, Hoeffel C, Rousset P, Fohlen A,
Soyer P. Computed Tomographic Features of Primary Small Cell Neuroendocrine Tumors of the
Gallbladder. J Comput Assist Tomogr. 2018;42:707–13. 22. Klimstra DS, Modlin IR, Coppola D, Lloyd RV, Suster S. The pathologic classification of
neuroendocrine tumors: a review of nomenclature, grading, and staging systems. Pancreas. 22. Klimstra DS, Modlin IR, Coppola D, Lloyd RV, Suster S. The pathologic classification of
neuroendocrine tumors: a review of nomenclature, grading, and staging systems. Pancreas. Page 12/20 Page 12/20 2010;39:707–12. 2010;39:707–12. 23. Do MY, Jang SI, Kang HP, Kim EJ. Comparison of the Clinical Features and Outcomes of Gallbladder
Neuroendocrine Carcinoma with Those of Adenocarcinoma: A Propensity Score-Matched Analysis. 2021,13. 24. Yan S, Wang Y. Clinical Analysis of 15 Cases of Gallbladder Neuroendocrine Carcinoma and
Comparison with Gallbladder Adenocarcinoma Using a Propensity Score Matching. 2020, 12:1437–
1446. 24. Yan S, Wang Y. Clinical Analysis of 15 Cases of Gallbladder Neuroendocrine Carcinoma and
Comparison with Gallbladder Adenocarcinoma Using a Propensity Score Matching. 2020, 12:1437–
1446. 25. Takeda Y, Kobayashi N. Case reports: chemoradiotherapy for locally advanced neuroendocrine
carcinoma of the gallbladder. 2022, 15:803–808. 25. Takeda Y, Kobayashi N. Case reports: chemoradiotherapy for locally advanced neuroendocrine
carcinoma of the gallbladder. 2022, 15:803–808. 25. Takeda Y, Kobayashi N. Case reports: chemoradiotherapy for locally advanced neuroendocrine
carcinoma of the gallbladder. 2022, 15:803–808. 23. Do MY, Jang SI, Kang HP, Kim EJ. Comparison of the Clinical Features and Outcomes of Gallbladder
Neuroendocrine Carcinoma with Those of Adenocarcinoma: A Propensity Score-Matched Analysis.
2021,13. Figures Page 13/20 Page 13/20 Page 13/20 Page 13/20 Figure 1 Abdominal contrast-enhanced computed tomography (CT) suggested a 7 cm mass in the segment IVb
and V of the liver, accompanied with localized wall thickening the fundus of the gallbladder that was
enhanced from an early stage with a prolonged contrast effect. (A) Arterial phase showed
inhomogeneous enhancement of the lesion, (B) the portal venous phase showed a mass with a
prolonged contrast effect, (C) in the delay phase, the mass is progressively enhanced, (D) the mass
invades the segment IVb and V of the liver. Figure 2
Preoperative MRI examination of the reported case. (A) The lesion of gallbladder has slightly
hyperintense in T2-weighted imaging, (B) hyperintense in DWI imaging. Figure 2 Preoperative MRI examination of the reported case. (A) The lesion of gallbladder has slightly
hyperintense in T2-weighted imaging, (B) hyperintense in DWI imaging. Preoperative MRI examination of the reported case. (A) The lesion of gallbladder has slightly
hyperintense in T2-weighted imaging, (B) hyperintense in DWI imaging. Page 14/20 Page 14/20 Page 14/20 Figure 3
Details of this patient's surgery. (A) A radical cholecystectomy was performed, (B) the gross tumor
specimen was displayed, (C) macroscopic analysis identified a greyish-yellow globular-like lesion, (D)
multiples yellowish stones were exhibited. Figure 3 Details of this patient's surgery. (A) A radical cholecystectomy was performed, (B) the gross tumor
specimen was displayed, (C) macroscopic analysis identified a greyish-yellow globular-like lesion, (D)
multiples yellowish stones were exhibited. Details of this patient's surgery. (A) A radical cholecystectomy was performed, (B) the gross tumor
specimen was displayed, (C) macroscopic analysis identified a greyish-yellow globular-like lesion, (D)
multiples yellowish stones were exhibited. Page 15/20 Page 15/20 Figure 4
(A) Hematoxylin and eosin (H&E) staining revealed a nest-like pattern of tumour cells with marked cellular
heterogeneity and visible necrosis. (B–D) Immunohistochemical studies show positivity for
chromogranin A, Ki-67 and synaptophysin, respectively. Figure 4 (A) Hematoxylin and eosin (H&E) staining revealed a nest-like pattern of tumour cells with marked cellular
heterogeneity and visible necrosis. (B–D) Immunohistochemical studies show positivity for
chromogranin A, Ki-67 and synaptophysin, respectively. Page 16/20 gure 5
and B) Targeted-gene sequencing showed that PD-L1 was not expressed in gallbladder neuroendocrin
rcinoma. (C and D) Buffer solution and isotype-matched monoclonal antibodies were used for control
aining and to confirm that the specificity of primary antibody binding. (E) Targeted-gene sequencing
owed the quantity of tumor mutation burden (TMB). Figure 5 (A and B) Targeted-gene sequencing showed that PD-L1 was not expressed in gallbladder neuroendocrine
carcinoma. (C and D) Buffer solution and isotype-matched monoclonal antibodies were used for control
staining and to confirm that the specificity of primary antibody binding. (E) Targeted-gene sequencing
showed the quantity of tumor mutation burden (TMB). Page 17/20 Page 17/20 Figure 6
(A and B) Gene–gene interaction network constructed with the 12 mutated genes. (C and D) Protein-
protein interaction enrichment analysis was established with the 12 mutated genes. Figure 6
(A and B) Gene–gene interaction network constructed with the 12 mutated genes. (C and D) Protein-
protein interaction enrichment analysis was established with the 12 mutated genes. Figure 6
(A and B) Gene–gene interaction network constructed with the 12 mutated genes. (C and D) Protein-
protein interaction enrichment analysis was established with the 12 mutated genes. Figure 6 (A and B) Gene–gene interaction network constructed with the 12 mutated genes. (C and D) Protein-
protein interaction enrichment analysis was established with the 12 mutated genes. (A and B) Gene–gene interaction network constructed with the 12 mutated genes. (C and D) Protein-
protein interaction enrichment analysis was established with the 12 mutated genes. Page 18/20 Figure 7
Significantly Enriched GO Terms and KEGG Pathways of Mutated Genes. (A)GO ana Figure 7
Significantly Enriched GO Terms and KEGG Pathways of Mutated Genes. (A)GO analysis of biological
processes (BP), GO analysis of cellular components (CC), (C) GO analysis of the molecular function, (D)
KEGG enrichment analysis. (E and F) Similar results of the Metascape database. Figure 7 Figure 7 Significantly Enriched GO Terms and KEGG Pathways of Mutated Genes. (A)GO analysis of biological
processes (BP), GO analysis of cellular components (CC), (C) GO analysis of the molecular function, (D)
KEGG enrichment analysis. (E and F) Similar results of the Metascape database. Page 19/20 Page 19/20 Page 19/20 Figure 8 Figure 8 (A) Summary of alteration on a query 12 gene mutations by cBioPortal database. (B) Summary of
alterations in 12 gene mutations. (C) the correlation between KEAP1 expression and the sensitivity of
GDSC drugs (top 30) in pan-cancer Page 20/20
|
https://openalex.org/W2767630416
|
https://www.pure.ed.ac.uk/ws/files/187166981/jeb.13206.pdf
|
English
| null |
Testing hypotheses for maternal effects in <i>Daphnia magna</i>
|
Journal of evolutionary biology
| 2,017
|
cc-by
| 7,233
|
General rights
C
i h f
h General rights
Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s)
and / or other copyright owners and it is a condition of accessing these publications that users recognise and
abide by the legal requirements associated with these rights. Testing hypotheses for maternal effects in Daphnia magna Citation for published version:
Coakley, C, Nestoros, E & Little, T 2018, 'Testing hypotheses for maternal effects in Daphnia magna',
Journal of Evolutionary Biology, vol. 31, no. 2, pp. 211-216. https://doi.org/10.1111/jeb.13206 Citation for published version:
Coakley, C, Nestoros, E & Little, T 2018, 'Testing hypotheses for maternal effects in Daphnia magna',
Journal of Evolutionary Biology, vol. 31, no. 2, pp. 211-216. https://doi.org/10.1111/jeb.13206 Citation for published version:
Coakley, C, Nestoros, E & Little, T 2018, 'Testing hypotheses for maternal effects in Daphnia magna',
Journal of Evolutionary Biology, vol. 31, no. 2, pp. 211-216. https://doi.org/10.1111/jeb.13206 Citation for published version: Edinburgh Research Explorer Digital Object Identifier (DOI):
10.1111/jeb.13206 Document Version:
Publisher's PDF, also known as Version of record Published In:
Journal of Evolutionary Biology ª 2 0 1 7 T H E A U T H O R S . J . E V O L . B I O L . 3 1 ( 2 0 1 8 ) 2 1 1 – 2 1 6
211
J O U R N A L O F E V O L U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U T I O N A R Y B I O L O G Y .
T H I S I S A N O P E N A C C E S S A R T I C L E U N D E R T H E T E R M S O F T H E C R E A T I V E C O M M O N S A T T R I B U T I O N L I C E N S E , W H I C H P E R M I T S U S E , D I S T R I B U T I O N A N D
R E P R O D U C T I O N I N A N Y M E D I U M , P R O V I D E D T H E O R I G I N A L W O R K I S P R O P E R L Y C I T E D . Correspondence: C. M. Coakley, Institute of Global Change, School of
GeoSciences, University of Edinburgh, Crew Building, The King’s
Buildings, Alexander Crum Brown Road, Edinburgh EH9 3FF, UK.
Tel.: +44 131 651 7165; E-mail: Christina.coakley@ed.ac.uk Take down policy Take down policy
The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer
content complies with UK legislation. If you believe that the public display of this file breaches copyright please
contact openaccess@ed.ac.uk providing details, and we will remove access to the work immediately and
investigate your claim. Download date: 24. Oct. 2024 Abstract Maternal effects are widely observed, but their adaptive nature remains diffi-
cult to describe and interpret. We investigated adaptive maternal effects in a
clone of the crustacean Daphnia magna, experimentally varying both mater-
nal age and maternal food and subsequently varying food available to off-
spring. We had two main predictions: that offspring in a food environment
matched to their mothers should fare better than offspring in unmatched
environments, and that offspring of older mothers would fare better in low
food environments. We detected numerous maternal effects, for example off-
spring of poorly fed mothers were large, whereas offspring of older mothers
were both large and showed an earlier age at first reproduction. However,
these maternal effects did not clearly translate into the predicted differences
in reproduction. Thus, our predictions about adaptive maternal effects in
response to food variation were not met in this genotype of Daphnia magna. information about the environment, or their condition,
to produce offspring with traits that confer high fitness
in the expected conditions. This predictability, that is
for anticipatory maternal effects (Marshall & Uller,
2007), can take two forms: when there is a positive
environmental correlation across a generation, mothers
prepare their offspring for an environment similar to
their own, while under negative correlations across a
generation, mothers prepare their offspring for the
opposite environment (Kuijper & Hoyle, 2015). Light
sensitivity in plants provides an example of the former:
Campanulastrum americanum from mothers of either
light gap or understory environments do better in that
matched environment (Galloway & Etterson, 2007). Growth rate of Caenorhabditis elegans under normoxic
and anoxic environments is an example of a negative
correlation (Dey et al., 2016). It is often difficult to
determine the adaptive nature of transgenerational
plasticity in matched or unmatched environments due
to the presences of ‘silver spoon’ or carry-over effects
(Engqvist & Reinhold, 2016), which may mask truly
adaptive benefits to offspring of being in a matched
environment. Indeed, outside of a handful of well-
known examples (Galloway & Etterson, 2007; Merrill &
Grindstaff, 2015), adaptive maternal effects have pro-
ven difficult to demonstrate (Uller et al., 2013). Testing hypotheses for maternal effects in Daphnia magna C. M. COAKLEY*
, E. NESTOROS* & T. J. LITTLE†
*Institute of Global Change, School of GeoSciences, University of Edinburgh, Edinburgh, UK
†Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK C. M. COAKLEY*
, E. NESTOROS* & T. J. LITTLE†
*Institute of Global Change, School of GeoSciences, University of Edinburgh, Edinburgh, UK
†Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK Keywords:
fecundity;
matching environments;
maternal age;
maternal effects;
transgenerational. doi: 10.1111/jeb.13206 Introduction not the same 24 mothers that con-
tributed first clutch offspring) G0 mothers, and each of
these G1 offspring was again exposed to one of the two
dietary treatments. Two final offspring were taken from
the fifth clutch of a further 24 (not the same mothers
that contributed first or second clutch offspring) G0
mothers, and each of these G1 offspring was again
exposed to one of the two dietary treatments. In total
then, there were 144 G1 offspring (See Figure 1). offspring of older mothers are larger at birth, mature to
a greater size and show greater early-life reproduction
which
might
trade-off
with
longevity
and
lifetime
reproductive success (Metcalfe & Monaghan, 2001; Pri-
est et al., 2002; Benton et al., 2008; Plaistow et al.,
2015). Similar observations have been made in our
study species, the crustacean Daphnia magna, where we
have observed that increasing maternal age is linked to
increasing size at birth, enhanced parasite resistance
and changes in reproduction (Clark et al., 2017). Varia-
tion in maternal nutrition in D. magna appears to pro-
duce similar phenotypes, as the offspring of dietary
restricted mothers produce relatively large, parasite
resistant
offspring
(Garbutt
&
Little,
2017). These
increases
in
body
size
in
offspring
from
dietary
restricted mothers may be adaptive if these mothers
can expect their offspring to be born into a low food/
high competition environment, and assuming that large
offspring have an advantage in this circumstance. Older
mothers tend to live in more competitive environ-
ments, as might be expected further into the growing
season of seasonal organisms, and here again larger off-
spring could be advantageous. This study explores adaptive maternal-effect hypothe-
ses; specifically, we aimed to determine how both
maternal food and maternal age impact offspring per-
formance in a clone of D. magna. We subjected mothers
to plentiful food or to dietary restriction and took off-
spring from clutch one, two or five (to create different
age classes). These offspring were placed under plentiful
food or dietary restriction, and their reproductive per-
formance measured. Our predictions are as follows: in a
food environment matched to their mothers, offspring
will perform better in their reproduction compared to
those in unmatched environments (in line with antici-
patory maternal effects theory). Our second prediction
is that offspring of older mothers (e.g. individuals from
clutch five) will reproductively out-perform the off-
spring of younger mothers in food-restricted environ-
ments. Introduction The environment, condition or phenotype of a mother
can account for a significant amount of variation in the
traits of her offspring (Wilson et al., 2005). Such mater-
nal effects are known for immunity (Coakley et al.,
2014), variation in feeding rate (Garbutt & Little,
2014), anti-predator behaviour (Agrawal et al., 1999)
and
dispersal
traits
(Dingle,
2014),
among
others. Maternal effects appear to be important across a wide
range of organisms including mammals (Glezen, 2003),
invertebrates (Stjernman & Little, 2011), fish (McGhee
et al., 2012), birds (Boulinier & Staszewski, 2008) and
plants (Vivas et al., 2015). Theoretical studies have
shown the strong potential of maternal effects to alter
population dynamics (Ginzburgh, 1998) and population
genetic structure (Wade, 1998; Wolf et al., 1998), and
so ultimately the evolutionary potential of a population
(Kuijper & Hoyle, 2015). Yet, in most cases, it is
unclear how, or even if, maternal effects are adaptive
(Mousseau & Fox, 1998; Marshall & Uller, 2007). It is hypothesized that maternal effects are a success-
ful adaptive strategy in variable, but predictable envi-
ronments. In
such
cases,
mothers
can
integrate It is well established that older mothers produce off-
spring of different quality to younger mothers (Moorad
&
Nussey,
2016). For
example,
in
some
species, 211 212 COAKLEY ET AL. in a 60-ml jar, were maintained under ad libitum food
conditions (8.75 9 106 Chlorella algae per day) and
standardized to at least three generations (acclimation
generations). Two individuals from the third brood of
each clonal lineage were chosen at random and sub-
jected to either ad libitum food (8.75 9 106 Chlorella
algae per day) or dietary restricted (1.75 9 106 Chlorella
algae per day) environments within 18 hr after birth
(this is the G0 generation), to give a total of 96 individ-
uals. This number of individuals is higher than needed
as
deaths
were
anticipated. Taking
96
individuals
ensured at least 72 lines, which was required for our
study. Again, and throughout, individuals were housed
singly in 60-mL jars, which were stored in climate
chambers at 20°C with 16 h of light and 8 h of dark
per day. Two offspring were taken from the first clutch
of 24 of 72 G0 mothers, and each of these G1 offspring
was exposed to one of the two dietary treatments. Two
offspring were also taken from the second clutch of a
further 24 (i.e. Introduction As we studied both maternal age and dietary
restriction simultaneously, we also explore the interac-
tion effects of these factors. The clutch that an individual came from (first, second
or fifth) was used as a proxy for maternal age and was
considered as an explanatory variable (Figure 1). The
use of clutch as a proxy for age allowed us to compare
a treatment group’s biological age rather than chrono-
logical age. The body size at birth of every G1 individual was
measured, using a camera and IMAGEJ software within
18 h from birth. The later reproductive performance of
these (G1) individuals was measured as age at first
reproduction and number of offspring in the first five
clutches. Statistical analysis Age at first reproduction is a ‘time to event’ variable
and was thus subject to a Cox proportional hazards
analysis. We provide risk ratios and their confidence
limits for the age at first reproduction analysis. The
other response variables, number of offspring born in
the first five clutches and body size at birth, were anal-
ysed with ANOVA, which included all possible interac-
tions between our explanatory variables. A breakdown
of
all
the
models
explored
can
be
found
in
the
Appendix S1. The number of offspring born in the first
five clutches was square-root-transformed to meet the
assumptions of normality. The explanatory variables
were maternal food, maternal age and offspring food
(although not for G1 size at birth, as this would not be ª 2 0 1 7 T H E A U T H O R S . J . E V O L . B I O L . 3 1 ( 2 0 1 8 ) 2 1 1 – 2 1 6
J O U R N A L O F E V O L U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U T I O N A R Y B I O L O G Y Materials and methods This study used a single clone of D. magna collected from
the Kaimes population in the borders of Scotland that
has been the subject of numerous maternal effects inves-
tigations (see (Mitchell & Read, 2005; Stjernman & Little,
2011; Garbutt & Little, 2014; Clark et al., 2017). The par-
ticular clone chosen displays the typical response of this
population to environmental stresses. The use of a single
clone enhances our power to disentangle the studied
effects, as this minimizes variation arising from genetic
difference (Little & Colegrave, 2016). To control the effect of any pre-existing transgenera-
tional effects, 48 replicates, each an individual Daphnia ª 2 0 1 7 T H E A U T H O R S . J . E V O L . B I O L
J O U R N A L O F E V O L U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U 213 Maternal effects in Daphnia magna G0
G1
Acclimation generation
Body size at birth, age at first clutch and number of offspring in first five clutches
LF
HF
LF
HF
Clutch 1
HF
LF
LF
HF
LF
HF
Clutch 2
HF
LF
HF
LF
HF
Clutch 3
HF
LF
LF
12
12
12
12
12
12
12
12
12
12
12
12
24
24
24
24
24
24
Fig. 1 G0 represents the maternal generation for the main analysis. Maternal age is the G0 clutch that G1 was born from (either early –
clutch 1, mid – clutch 2 or later life – clutch 3). G0 individuals were given either ad libitum (HF) or restricted low (LF) food; therefore, the
G0 generation has two treatment types: food and age. The offspring generation (G1) was given HF or LF; measurements were recorded
regarding their body size at birth and reproductive performance (age at first clutch and number of offspring produced). Numbers above
Daphnia indicate sample size at each stage. Materials and methods G0
G1
Acclimation generation
Body size at birth, age at first clutch and number of offspring in first five clutches
LF
HF
LF
HF
Clutch 1
HF
LF
LF
HF
LF
HF
Clutch 2
HF
LF
HF
LF
HF
Clutch 3
HF
LF
LF
12
12
12
12
12
12
12
12
12
12
12
12
24
24
24
24
24
24 Acclimation generation Body size at birth, age at first clutch and number of offspring in first five clutches Body size at birth, age at first clutch and number of offspring in first five clutches Fig. 1 G0 represents the maternal generation for the main analysis. Maternal age is the G0 clutch that G1 was born from (either early –
clutch 1, mid – clutch 2 or later life – clutch 3). G0 individuals were given either ad libitum (HF) or restricted low (LF) food; therefore, the
G0 generation has two treatment types: food and age. The offspring generation (G1) was given HF or LF; measurements were recorded
regarding their body size at birth and reproductive performance (age at first clutch and number of offspring produced). Numbers above
Daphnia indicate sample size at each stage. Fig. 1 G0 represents the maternal generation for the main analysis. Maternal age is the G0 clutch that G1 was born from (either early –
clutch 1, mid – clutch 2 or later life – clutch 3). G0 individuals were given either ad libitum (HF) or restricted low (LF) food; therefore, the
G0 generation has two treatment types: food and age. The offspring generation (G1) was given HF or LF; measurements were recorded
regarding their body size at birth and reproductive performance (age at first clutch and number of offspring produced). Numbers above
Daphnia indicate sample size at each stage. HF
HF
HF
Fig. 2 (A) The effect of mothers (G0) food and age (defined by
clutch) on offspring body size (G1 generation). Error bars represent
one standard error around the mean. LF indicates low maternal
food, and HF indicates high maternal food. HF
HF
HF relevant). For all ANOVA, we provide effect sizes (g2) in
addition to test statistics and P-values. All analyses were
performed using JMP software (Version 12.1.0) with the
default (for ANOVA) implementation of type III sum of
squares. We used a backward elimination process for all
analysis and excluded interactions terms with P > 0.05. Maternal effects on offspring body size G1 body size at birth was influenced by maternal (G0)
food (F1,118 = 27.3, P < 0.0001, g2 = 0.064), maternal
age (F2,118 = 142.7, P < 0.0001, g2 = 0.63) and their
interaction
(F2,118 = 4.6,
P = 0.012,
g2 = 0.016). Offspring body size increased with maternal age, and
offspring of low food mothers were larger in the first
two clutches, but a maternal food effect was not evi-
dent in the oldest mothers (Figure 2). Fig. 2 (A) The effect of mothers (G0) food and age (defined by
clutch) on offspring body size (G1 generation). Error bars represent
one standard error around the mean. LF indicates low maternal
food, and HF indicates high maternal food. ª 2 0 1 7 T H E A U T H O R S . J . E V O L . B I O L . 3 1 ( 2 0 1 8 ) 2 1 1 – 2 1 6
J O U R N A L O F E V O L U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U T I O N A R Y B I O L O G Y Fecundity There was no significant interaction between G0 food and
G1 food on age at first reproduction, nor was there a main
effect of G0 food. G1 age at first reproduction depended on
the food they were given, that is G1 food (X2 = 17.7,
P = < 0.0001), with well-fed Daphnia reproducing earlier. Age at first reproduction also showed a significant rela-
tionship with maternal age (X2 = 21.3, P < 0.0001; Fig-
ure 3), where individuals from older mothers started
reproduction early. Hazard ratios and their confidence
limits for this proportional hazards analysis are shown in
the Figure 3 inset. No significant effect of a maternal age
was noted for the timing of later clutches. Maternal age
did not interact with other factors. The number of offspring in the first five clutches
(Figure 4) was largely explained by G1 food (individuals
under low food produced significantly fewer offspring:
F1,109 = 1740, P < 0.0001, g2 = 0.91), but also maternal
age (F2,109 = 8.67, P = 0.000, g2 = 0.009) and an inter-
action between G1 food and maternal age (F2,109 = 4.6,
P = 0.012, g2 = 0.005; Figure 4). No significant interac-
tion between G0 and G1 food was detected. We also
performed a limited analysis of grandmaternal effects
and present this as Appendix S1. ª 2 0 1 7 T H E A U T H O R S . J . E V O L . B I O L . 3 1 ( 2 0 1 8 ) 2 1 1 – 2 1 6
J O U R N A L O F E V O L U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U T I O N A R Y B I O L O G Y . E V O L . B I O L . Fecundity 3 1 ( 2 0 1 8 ) 2 1 1
2 1 6
N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U T I O N A R Y B I O L O G Y COAKLEY ET AL. 214 Fig. 3 Step series graph of the effects of age on time to age at first
reproduction (G1 generation). Dotted line represents the oldest age
group (clutch 5), solid line represents the middle age group (clutch
2), and the dashed line represents the youngest group (from
clutch 1). found no benefit to being in a food environment
matched to your mother. Our second prediction was
that offspring of older mothers would fare better in low
food environments. We found evidence for maternal
age effects on age at first reproduction, which may be
adaptive. However, this potential adaptive maternal
effect was not specifically in line with our prediction,
which required a significant maternal age by offspring
food interaction to be met. For the other measure of
reproductive performance, the number of offspring pro-
duced in five clutches, we found very weak effect sizes,
with the direction of effects being counter to predic-
tions. Thus, we conclude that there is only weak evi-
dence for adaptive maternal effects in this study. We
also conclude that size at birth, whether determined by
maternal food or maternal age, does not have straight-
forward effects on subsequent reproductive success. Fig. 3 Step series graph of the effects of age on time to age at first
reproduction (G1 generation). Dotted line represents the oldest age
group (clutch 5), solid line represents the middle age group (clutch
2), and the dashed line represents the youngest group (from
clutch 1). Discussion We did not observe maternal food by offspring food
interactions for any traits, and thus, the basic prediction
of adaptive maternal effects theory was not met. More-
over, a large body size as a consequence of low mater-
nal food had no downstream performance advantages
in the Daphnia clone we studied. Food availability fluc-
tuates in the Daphnia environment (Murdoch et al.,
1998; McCauley et al., 1999), and thus, maternal effect
driven by maternal food is a realistic prediction. How-
ever, offspring food clearly, and unsurprisingly, played
the most important role in all traits. This is similar to
the findings of a meta-analysis (exploring both plants
and animals), which revealed subtle effects of matching
environments compared to the direct effects of the focal
environment (Uller et al., 2013). It is possible that low
maternal food is a not a cue for future maternal food,
but is instead a cue for other threats, such as the
increased infection risk associated with crowding (Clark
et al., 2017); see also (LaMontagne & McCauley, 2001). As seen in another study (Beyer & Hambright, 2017)
when making predictions about the adaptive signifi-
cance of maternal effects, it will, in many cases, be dif-
ficult to know exactly what mothers are preparing their
offspring for, and that the basic idea of matching envi-
ronments will often be too simplistic. In this study, we investigated two maternal effects (ma-
ternal age and food) on measures of offspring perfor-
mance
in
a
clone
of
the
fresh
water
crustacean
(Daphnia magna). Our first prediction was that offspring
in a food environment matched to their mothers should
show greater reproductive performance. However, we Fig. 4 Total number of offspring produced by (G1) Daphnia
depending on the food they receive and the age of their mother
(defined by G0 clutch). Error bars represent one standard error
around the mean. LF indicates low food of G1, and HF indicates
high food of G1. ª 2 0 1 7 T H E A U T H O R S . J . E V O L . B I O L . 3 1 ( 2 0 1 8 ) 2 1 1 – 2 1 6
J O U R N A L O F E V O L U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U T I O N A R Y B I O L O G Y Conclusions Although we detected numerous maternal effects, most
notably the large size of offspring from poorly fed or
older mothers and the early age at first reproduction of
offspring born to older mothers, the adaptive nature of
these effects were not clear. Other genotypes, or other
traits, might respond differently to our treatments. At
the same time, the production of larger offspring with
different reproductive features would itself alter the
competitive
environment
(Beckerman
et al.,
2006;
Kindsvater et al., 2011; Prior et al., 2011), a scenario
that could more fully reveal the consequences of mater-
nal effects. Acknowledgments We thank the reviewers for their help improving the
manuscript, Phil Wilson and Jess Clark for their support
and guidance in the laboratory. We are grateful for the
constructive comment on a previous draft of this article
provided by Per Smiseth and Nick Colegrave. This study
was funded by the Natural Environment Research
Council
(NERC)
Research
Experience
Placement
Studentship. Within the Daphnia system, as with low food, older
mothers are established to produce offspring that are less
susceptible to infection (Clark et al., 2017) and thus aged
mothers may be preparing their offspring for a harsh
environment. Presently, this appears to be specific to the
threat of parasitism rather than food stress. Although
there was substantial genetic variation for this maternal
effect in Daphnia, the average effect was for high resis-
tance in offspring from poorly fed mothers (Stjernman &
Little, 2011). Elsewhere, maternal age effects have been
found to impact offspring size in Lemna minor (Barks &
Laird, 2016), offspring development and maturation size
of S. berlesei (Benton et al., 2008) and early-life repro-
duction of Daphnia (Plaistow et al., 2015). It is thus
important to note that there is the potential for maternal
age to be adaptive for traits or environments that we did
not explore. For example, considering competitive abil-
ity, as opposed to the performance proxies we used,
might paint a different picture, as seen in a study using
S. berlesei (Benton et al., 2005). In addition, different
populations will face different environmental pressures,
and the occurrence of adaptive maternal effects could
well
differ
between
populations
(Vijendravarma
&
Kawecki, 2015; Walsh et al., 2016). Maternal age effects Age at first
reproduction is an important component of reproduc-
tive performance (Forslund & P€art, 1995; Kr€uger, 2005)
and should be particularly important for D. magna,
where populations can increase dramatically over a
season, and early reproduction secures resources for
offspring over competitors. However, this timing of
reproduction did not seem to lead to differences in the
total number of offspring produced (Figure 4). Indeed,
effect sizes for the influence of maternal age on number
of offspring were notably small (the significant mater-
nal age by offspring food interaction explained less than
1% of variance). Whereas our study found limited
effects of these traits for a single mother’s reproductive
success, there could be a significant impact on subse-
quent population dynamics. Differences in age at first
reproduction
or
offspring
size,
particularly
for
a
short-lived species such as D. magna, could result in
differences in competitive environments of the next
generation. This in turn could benefit some individuals
more than others (via maternal effects and environ-
mental conditions) for that generation, as seen in a
study
exploring
maternal
effects
and
population
dynamics in Sancassania berlesei (Benton et al., 2005). that then perform poorly (Jann & Ward, 1999). In our
experiment, the age of Daphnia mothers interacted with
maternal
food,
specifically,
maternal
food
effects
appeared dampened in older mothers (Figure 2). Maternal age effects In food-restricted environments, we predicted that the
large offspring of older mothers would show better
reproductive
performance compared
to offspring of
younger mothers. This prediction was not wholly met:
significant maternal age effects on offspring age at first
reproduction were detected, but these were observed in
both offspring food environments. Nonetheless, the
effect
of
maternal
age
on
offspring
age
at
first Fig. 4 Total number of offspring produced by (G1) Daphnia
depending on the food they receive and the age of their mother
(defined by G0 clutch). Error bars represent one standard error
around the mean. LF indicates low food of G1, and HF indicates
high food of G1. ª 2 0 1 7 T H E A U T H O R S . J . E V O L . B I O L . 3 1 ( 2 0 1 8 ) 2 1 1 – 2 1 6
J O U R N A L O F E V O L U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U T I O N A R Y B I O L O G Y ª 2 0 1 7 T H E A U T H O R S . J . E V O L . B I O L
J O U R N A L O F E V O L U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U Maternal effects in Daphnia magna 215 reproduction was substantial (Figure 3). (
)
J O U R N A L O F E V O L U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U ª 2 0 1 7 T H E A U T H O R S . J . E V O L . B I O L . 3 1 ( 2 0 1 8 ) 2 1 1 – 2 1 6
J O U R N A L O F E V O L U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U T I O N A R Y B I O L O G Y ª 2 0 1 7 T H E A U T H O R S . J . E V O L . B I O L . 3 1 ( 2 0 1 8 ) 2 1 1 – 2 1 6
J O U R N A L O F E V O L U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H References evidence for environment matching. Brain Behav. Immun. 45:
71–79. evidence for environment matching. Brain Behav. Immun. 45:
71–79. Coakley, C., Staszewski, V., Herborn, K. & Cunningham, E. 2014. Factors affecting the levels of protection transferred
from mother to offspring following immune challenge. Front. Zool. 11: 46. Metcalfe, N.B. & Monaghan, P. 2001. Compensation for a bad
start: grow now, pay later? Trends Ecol. Evol. 16: 254–260. Dey, S., Proulx, S.R. & Teotonio, H. 2016. Adaptation to Tem-
porally
Fluctuating
Environments
by
the
Evolution
of
Maternal Effects. PLoS Biol. 14: e1002388. Mitchell, S.E. & Read, A.F. 2005. Poor maternal environment
enhances offspring disease resistance in an invertebrate. Proc. R. Soc. B Biol. Sci. 272: 2601–2607. Moorad, J.A. & Nussey, D.H. 2016. Evolution of maternal
effect senescence. Proc. Natl Acad. Sci. 113: 362–367. Dingle, H. 2014. Migration: the Biology of Life on the Move, 2nd
edn. Oxford Univ Press, New York. Mousseau, T.A. & Fox, C.W. 1998. The adaptive significance of
maternal effects. Trends Ecol. Evol. 13: 403–407. Engqvist, L. & Reinhold, K. 2016. Adaptive trans-generational
phenotypic plasticity and the lack of an experimental control
in reciprocal match/mismatch experiments. Methods Ecol. Evol. 7: 1482–1488. Murdoch, W.W., Nisbet, R.M., McCauley, E., deRoos, A.M. &
Gurney, W.S.C. 1998. Plankton abundance and dynamics
across nutrient levels: tests of hypotheses. Ecology 79: 1339–
1356. Forslund,
P. &
P€art,
T. 1995. Age
and
reproduction
in
birds
—
hypotheses
and
tests. Trends
Ecol. Evol. 10:
374–378. Plaistow, S.J., Shirley, C., Collin, H., Cornell, S.J. & Harney,
E.D. 2015. Offspring provisioning explains clone-specific
maternal age effects on life history and life span in the water
flea, Daphnia pulex. Am. Nat. 186: 376–389. Fox, C.W. & Dingle, H. 1994. Dietary Mediation of Maternal
Age Effects on Offspring Performance in a Seed Beetle
(Coleoptera: Bruchidae). Funct. Ecol. 8: 600–606. Priest, N.K., Mackowiak, B. & Promislow, D.E. 2002. The role
of parental age effects on the evolution of aging. Evolution
56: 927–935. Galloway, L.F. & Etterson, J.R. 2007. Transgenerational plastic-
ity is adaptive in the wild. Science 318: 1134–1136. Garbutt, J. S. & Little, T. J. 2014. Maternal food quantity
affects offspring feeding rate in Daphnia magna. Biol. Lett. 10:
20140356. Prior, N.H., Washington, C.N., Housley, J.M., Hall, S.R., Duffy,
M.A. & Caceres, C.E. 2011. Maternal effects and epidemio-
logical traits in a planktonic host–parasite system. Evol. Ecol. Res. 13: 401–413. Garbutt, J.S. & Little, T.J. 2017. Received 24 April 2017; revised 31 October 2017; accepted 1
November 2017 References Bigger is better: changes in
body size explain a maternal effect of food on offspring dis-
ease resistance. Ecol. Evol. 7: 1403–1409. Stjernman, M. & Little, T.J. 2011. Genetic variation for mater-
nal effects on parasite susceptibility. J. Evol. Biol. 24: 2357–
2363. Ginzburgh, L. R. 1998. Inertial growth: population dynamics
based on maternal effects. In: Maternal Effects as Adaptations,
(T. A. Mousseau & C. W. Fox, eds), pp. 42–53. Oxford
University press, Oxford. Uller, T., Nakagawa, S. & English, S. 2013. Weak evidence for
anticipatory parental effects in plants and animals. J. Evol. Biol. 26: 2161–2170. Glezen, W.P. 2003. Effect of maternal antibodies on the infant
immune response. Vaccine 21: 3389–3392. Vijendravarma, R.K. & Kawecki, T.J. 2015. Idiosyncratic evolu-
tion of maternal effects in response to juvenile malnutrition
in Drosophila. J. Evol. Biol. 28: 876–884. Jann, P. & Ward, P.I. 1999. Maternal effects and their conse-
quences for offspring fitness in the Yellow Dung Fly. Funct. Ecol. 13: 51–58. Vivas, M., Kemler, M. & Slippers, B. 2015. Maternal effects on
tree phenotypes: considering the microbiome. Trends Plant
Sci. 20: 541–544. Kindsvater, H.K., Bonsall, M.B. & Alonzo, S.H. 2011. Survival
costs of reproduction predict age-dependent variation in
maternal investment. J. Evol. Biol. 24: 2230–2240. Wade, M.J. 1998. The Evolutionary Genetics of Maternal
Effects. In: Maternal Effects As Adaptations (T.A. Mousseau &
C.W. Fox, eds), pp. 5–21. Oxford University Press, Oxford. Kr€uger, O. 2005. Age at first breeding and fitness in goshawk
Accipiter gentilis. J. Anim. Ecol. 74: 266–273. Kuijper, B. & Hoyle, R.B. 2015. When to rely on maternal
effects and when on phenotypic plasticity? Evolution 69:
950–968. Walsh, M. R., Castoe, T., Holmes, J., Packer, M., Biles, K.,
Walsh, M. et al. 2016. Local adaptation in transgenerational
reesponses to predators. Proc. Biol. Sci. 283: 20152271. LaMontagne, J.M. & McCauley, E. 2001. Maternal effects in
Daphnia: what mothers are telling their offspring and do
they listen? Ecol. Lett. 4: 64–71. Wilson, A.J., Coltman, D.W., Pemberton, J.M., Overall, A.D.J.,
Byrne, K.A. & Kruuk, L.E.B. 2005. Maternal genetic effects
set the potential for evolution in a free-living vertebrate
population. J. Evol. Biol. 18: 405–414. Little, T.J. & Colegrave, N. 2016. Caging and Uncaging Genet-
ics. PLoS Biol. 14: e1002525. Wolf, J.B., Brodie, E.D., Cheverud, J.M., Moore, A.J. & Wade,
M.J. 1998. Evolutionary consequences of indirect genetic
effects. Trends Ecol. Evol. 13: 64–69. Marshall, D. & Uller, T. 2007. References When is a maternal effect adap-
tive? Oikos 116: 1957–1963. McCauley, E., Nisbet, R.M., Murdoch, W.W., de Roos, A.M. &
Gurney, W.S.C. 1999. Large-amplitude cycles of Daphnia
and its algal prey in enriched environments. Nature 402:
653–656. References Agrawal, A.A., Laforsch, C. & Tollrian, R. 1999. Transgenera-
tional induction of defences in animals and plants. Nature
401: 60–63. Barks, P.M. & Laird, R.A. 2016. A multigenerational effect of
parental age on offspring size but not fitness in common
duckweed (Lemna minor). J. Evol. Biol. 29: 748–756. Beckerman, A.P., Benton, T.G., Lapsley, C.T. & Koesters, N. 2006. How effective are maternal effects at having effects? Proc. Biol. Sci. 273: 485–493. Benton, T.G., Plaistow, S.J., Beckerman, A.P., Lapsley, C.T. &
Littlejohns, S. 2005. Changes in maternal investment in eggs
can affect population dynamics. Proc. Biol. Sci. 272: 1351–
1356. Benton, T.G., St Clair, J.J.H. & Plaistow, S.J. 2008. Maternal
effects mediated by maternal age: from life histories to popu-
lation dynamics. J. Anim. Ecol. 77: 1038–1046. Beyer, J. E. & Hambright, K. D. 2017. Maternal effects are no
match for stressful conditions: a test of the maternal match
hypothesis in a common zooplankter. Funct. Ecol. 31: 1933–
1940. Only a handful of studies have explored multiple
maternal effects, as we did. Maternal age and food
effects were explored in seed beetles (Callosobruchus
maculatus) (Fox & Dingle, 1994), but these beetles show
different patterns from those observed presently. For
example, older adult beetles produced small offspring
that
developed
slowly,
the
opposite
of
what
we
observed in D. magna. Older or poorly fed yellow dung
flies (Scathophaga stercoraria) also produce smaller eggs Boulinier, T. & Staszewski, V. 2008. Maternal transfer of anti-
bodies: raising immuno-ecology issues. Trends Ecol. Evol. 23:
282–288. Clark, J., Garbutt, J.S., McNally, L. & Little, T.J. 2017. Disease
spread in age structured populations with maternal age
effects. Ecol. Lett. 20: 445–451. R S . J . E V O L . B I O L . 3 1 ( 2 0 1 8 ) 2 1 1
2 1 6
U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U T I O N A R Y B I O L O G Y 216 216
COAKLEY ET AL. COAKLEY ET AL. ª 2 0 1 7 T H E A U T H O R S . J . E V O L . B I O L . 3 1 ( 2 0 1 8 ) 2 1 1 – 2 1 6
J O U R N A L O F E V O L U T I O N A R Y B I O L O G Y P U B L I S H E D B Y J O H N W I L E Y & S O N S L T D O N B E H A L F O F E U R O P E A N S O C I E T Y F O R E V O L U T I O N A R Y B I O L O G Y Supporting information Additional
Supporting
Information
may
be
found
online in the supporting information tab for this article:
Appendix S1 Maximal models and additional analysis. McGhee, K.E., Pintor, L.M., Suhr, E.L. & Bell, A.M. 2012. Maternal exposure to predation risk decreases offspring
antipredator behaviour and survival in threespined stickle-
back. Funct. Ecol. 26: 932–940. Merrill, L. & Grindstaff, J.L. 2015. Pre and post-natal antigen
exposure can program the stress axis of adult zebra finches:
|
https://openalex.org/W3020258335
|
https://europepmc.org/articles/pmc7215693?pdf=render
|
English
| null |
DFT Study of Molecular and Electronic Structure of Ca(II) and Zn(II) Complexes with Porphyrazine and tetrakis(1,2,5-thiadiazole)porphyrazine
|
International journal of molecular sciences
| 2,020
|
cc-by
| 6,614
|
Received: 20 March 2020; Accepted: 19 April 2020; Published: 22 April 2020 Abstract: Electronic and geometric structures of Ca(II) and Zn(II) complexes with porphyrazine
(Pz) and tetrakis(1,2,5-thiadiazole)porphyrazine (TTDPz) were investigated by density functional
theory (DFT) calculations and compared. The perimeter of the coordination cavity was found to be
practically independent on the nature of a metal and a ligand. According to the results of the natural
bond orbital (NBO) analysis and quantum theory of atoms in molecules (QTAIM) calculations, Ca–N
bonds possess larger ionic contributions as compared to Zn–N. The model electronic absorption
spectra obtained with the use of time-dependent density functional theory (TDDFT) calculations
indicate a strong bathochromic shift (~70 nm) of the Q-band with a change of Pz ligand by TTDPz for
both Ca and Zn complexes. Additionally, CaTTDPz was synthesized and its electronic absorption
spectrum was recorded in pyridine and acetone. Keywords: porphyrazine; 1,2,5-thiadiazole annulated; DFT study; molecular and electronic structure International Journal of
Molecular Sciences International Journal of
Molecular Sciences
Received: 20 March 2020; Accepted: 19 April 2020; Published: 22 April 2020 Int. J. Mol. Sci. 2020, 21, 2923; doi:10.3390/ijms21082923 Arseniy A. Otlyotov, Igor V. Ryzhov, Ilya A. Kuzmin, Yuriy A. Zhabanov *, Maxim S. Mikhailov
and Pavel A. Stuzhin Arseniy A. Otlyotov, Igor V. Ryzhov, Ilya A. Kuzmin, Yuriy A. Zhabanov *, Maxim S. Mikhailo
and Pavel A. Stuzhin Ivanovo State University of Chemistry and Technology, Research Institute of Chemistry of Macrohete
Compounds, 153000 Ivanovo, Russia; otlyotov@isuct.ru (A.A.O.); ryzhoff.ihor@yandex.ru (I.V.R.);
wonderful_37@list.ru (I.A.K.); mihailov_maxim_s@mail.ru (M.S.M.); stuzhin@isuct.ru (P.A.S.)
* Correspondence: zhabanov@isuct.ru; Tel.: +7-4932-35-98-74 Ivanovo State University of Chemistry and Technology, Research Institute of Chemistry of Macroheterocyclic
Compounds, 153000 Ivanovo, Russia; otlyotov@isuct.ru (A.A.O.); ryzhoff.ihor@yandex.ru (I.V.R.);
wonderful_37@list.ru (I.A.K.); mihailov_maxim_s@mail.ru (M.S.M.); stuzhin@isuct.ru (P.A.S.)
* Correspondence: zhabanov@isuct.ru; Tel.: +7-4932-35-98-74 1. Introduction Porphyrins, phthalocyanines and their analogues have found a number of applications, particularly,
due to their intense absorption in the visible region [1–4]. Since the optical properties are governed by
the electronic structure of the macrocycle, thorough theoretical studies by quantum-chemical methods
are usually performed to explain the observed features of the absorption spectra [5–13] and open the
possibilities of their in-silico design in the case of compounds, for which the experimental data are
absent. Such investigations in the case of the complexes with transition metals are often non-trivial
due to the necessity to account for the multireference character of the wavefunction. However, in the
case of the closed-shell species, density functional theory (DFT) can be directly applied to obtain the
qualitative and quantitative information about the ground-state properties. Therefore, a reasonable
first step in the comparative studies of the influences of a transition metal and a ligand on the chemical
bonding and spectral properties is to consider the relatively simple borderline d0 and d10 configurations
(Ca and Zn, respectively) in order to eliminate the multireference effects. p
y
While porphyrins and phthalocyanines have been widely investigated, the information on their
porphyrazine (Pz) analogues is still incomplete. Moreover, in recent years, much attention has
been paid to 1,2,5-thiadiazole-fused porphyrazines possessing especially strongly electron-deficient
macrocycle, and capable of forming layers with strong intermolecular interactions. As a result,
tetrakis(1,2,5-thiadiazole)porphyrazine (TTDPz) and its metal complexes are actively studied for
application in organic electronics, such as n-type semiconductors [14–18]. Therefore, their theoretical Int. J. Mol. Sci. 2020, 21, 2923; doi:10.3390/ijms21082923 www.mdpi.com/journal/ijms 2 of 12
2 of Int. J. Mol. Sci. 2020, 21, 2923
Int. J. Mol. Sci. 2020, 21, x F study is quite important to reveal the influence of 1,2,5-thiadiazole rings on the peculiarities of the
electronic properties of the porphyrazine macrocycle in the metal complexes (Figure 1) with different
contributions of σ- and π-bonding effects in the formation of M-Np bonds [2,3,7,17,19,20]. application in organic electronics, such as n-type semiconductors [14–18]. Therefore, their theoretic
study is quite important to reveal the influence of 1,2,5-thiadiazole rings on the peculiarities of th
electronic properties of the porphyrazine macrocycle in the metal complexes (Figure 1) wi
different contributions of σ and π bonding effects in the formation of M N bonds [2 3 7 17 19 20] (a)
(b)
Figure
1. 1. Introduction Molecular
models
of
M-porphyzarine
(MPz)(a)
and
M-tetrakis(1,2,5-thiadiazole)porphyzarine (MTTDPz) (b) complexes with atom labeling (M = Ca, Zn
Figure 1. Molecular models of M-porphyzarine (MPz) (a) and M-tetrakis(1,2,5-thiadiazole)porphyzarine
(MTTDPz) (b) complexes with atom labeling (M = Ca, Zn). (b) (a) Figure
1. Molecular
models
of
M-porphyzarine
(MPz)(a)
an
M-tetrakis(1,2,5-thiadiazole)porphyzarine (MTTDPz) (b) complexes with atom labeling (M = Ca, Z
Figure 1. Molecular models of M-porphyzarine (MPz) (a) and M-tetrakis(1,2,5-thiadiazole)porphyzarine
(MTTDPz) (b) complexes with atom labeling (M = Ca, Zn). Earlier in our laboratory, the magnesium (II) complexes with tetrakis(1,2,5-chalcogenadiazo
MgTXDPz (X = O, S, Se, Te) were investigated by DFT calculations in order to examine the influen
of a chalcogen atom on their geometry and electronic structure [21]. The theoretical studies of t
molecular structures and electronic spectra of the porphyrazine complexes with the alkaline-ear
metals Be and Mg are described in [13], and for the porphyrazine complexes with alkali metals
[22]. The present contribution aims to determine the nature of the chemical bonding and influence
the metal atom (Ca [d0] and Zn [d10]) and the ligand (Pz and TTDPz) on the electronic absorpti
spectrum. It should be mentioned that the electronic spectrum of ZnPz complex has already be
thoroughly interpreted in [7,11]. We recalculated it using a different theoretical approximation on
for comparison purposes. Besides, in order to complement the comparison, a CaTTDPz complex w
synthesized for the first time and its electronic spectrum was measured. Earlier in our laboratory, the magnesium (II) complexes with tetrakis(1,2,5-chalcogenadiazole)
MgTXDPz (X = O, S, Se, Te) were investigated by DFT calculations in order to examine the influence
of a chalcogen atom on their geometry and electronic structure [21]. The theoretical studies of the
molecular structures and electronic spectra of the porphyrazine complexes with the alkaline-earth
metals Be and Mg are described in [13], and for the porphyrazine complexes with alkali metals in [22]. The present contribution aims to determine the nature of the chemical bonding and influence of the
metal atom (Ca [d0] and Zn [d10]) and the ligand (Pz and TTDPz) on the electronic absorption spectrum. It should be mentioned that the electronic spectrum of ZnPz complex has already been thoroughly
interpreted in [7,11]. We recalculated it using a different theoretical approximation only for comparison
purposes. Besides, in order to complement the comparison, a CaTTDPz complex was synthesized for
the first time and its electronic spectrum was measured. 2.1. Chemical Bonding in MPz and MTTDP
2.1. Chemical Bonding in MPz and MTTDPz g
The closed-shell MPz and MTTDPz complexes with Ca and Zn can be treated usin
single-reference methods. Therefore, DFT was chosen for all calculations. The equilibrium structur
of the complexes ZnPz and ZnTTDPz were determined to possess the planar structures of D
symmetry, while the complexes with Ca(II) exhibit significant doming distortion, and the
structures belong to the C4v point group. The force-field calculations yielded no imagina
frequencies, indicating that the optimized configurations correspond to the minima on the potenti
energy hypersurfaces The calculated molecular parameters are presented in Table 1
The closed-shell MPz and MTTDPz complexes with Ca and Zn can be treated using single-reference
methods. Therefore, DFT was chosen for all calculations. The equilibrium structures of the complexes
ZnPz and ZnTTDPz were determined to possess the planar structures of D4h symmetry, while the
complexes with Ca(II) exhibit significant doming distortion, and their structures belong to the C4v point
group. The force-field calculations yielded no imaginary frequencies, indicating that the optimized
configurations correspond to the minima on the potential energy hypersurfaces. The calculated
molecular parameters are presented in Table 1. energy hypersurfaces. The calculated molecular parameters are presented in Table 1. The results of the natural bond orbital (NBO) analysis of the electron density distribution
demonstrate the different nature of chemical bonding in the MPz and MTTDPz complexes. First,
we find a decrease of the ionic component of M–N bond in the case of the d10 shell of Zn(II), as compared
to the Ca(II) complex with an unoccupied d0 shell. This can be rationalized not only in terms of
the Wiberg bond index Q(M-N), which increases from Ca–N to Zn–N, but also by the comparison Int. J. Mol. Sci. 2020, 21, 2923 3 of 12 of the energies of donor–acceptor interactions (P E(d-a)) between lone pairs on the nitrogen atoms
and 4s-, 3d- and 4p- orbitals of the metal atoms. Another confirmation stems from the values of
the delocalization indices calculated in the framework of the quantum theory of atoms in molecules
(QTAIM) analysis being close to the values of Q(M-N). Table 1. Molecular parameters 1 of M-porphyzarine(MPz) andM-tetrakis(1,2,5-thiadiazole)porphyzarine
(TTDPz) complexes optimized at B3LYP/pcseg-2 level. Table 1. Molecular parameters 1 of M-porphyzarine(MPz) andM-tetrakis(1,2,5-thiadiazole)porphyzarine
(TTDPz) complexes optimized at B3LYP/pcseg-2 level. 2.1. Chemical Bonding in MPz and MTTDP
2.1. Chemical Bonding in MPz and MTTDPz CaPz
CaTTDPz
ZnPz
ZnTTDPz
M-Np
2.276
2.299
1.979
2.025
M-X 2
1.079
1.020
Np-Cα
1.364
1.373
1.363
1.375
Cα-Cβ
1.458
1.462
1.457
1.458
Cα-Nm
1.333
1.322
1.331
1.317
Cβ-Cβ
1.354
1.424
1.457
1.421
Cβ-Nt
1.316
1.316
Nt-S
1.645
1.644
(Np . . . Np)opp
4.008
4.120
3.958
4.049
(Np . . . Np)adj
2.834
2.913
2.799
2.863
∠(Np–M–Np)
123.4
127.3
180.0
180.0
∠(Np–Cα–Nm)
127.6
128.1
127.2
128.0
∠(Cα–Nm–Cα)
124.6
126.7
124.4
125.8
∠(Cα–Np–Cα)
107.7
111.8
108.8
111.7
∠(Nt–S–Nt)
100.2
100.3
1 Bond lengths in Å and bond angles in degrees. 2 X is dummy atom located in center between Np atoms. The complexes of the Pz and TTDPz ligands with Zn(II) are stabilized by strong interactions of
these types: LP(N) →4s(Zn) and LP(N) →4p(Zn) (Figure 2). In the case of the Ca(II) complexes, only
much weaker interactions LP(N) →4s(Ca), LP(N) →3dx2−y2(Ca) and LP(N) →3dyz(Ca) were found
within the NBO scheme (Figure 3). Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW
4 of 13 uch weaker interactions LP(N) →4s(Ca), LP(N) →3dx2−y2(Ca) and LP(N) →3dyz(Ca) were fou
thin the NBO scheme (Figure 3). Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW
4 of
(a)
(b)
Figure 2. Schemes of the dominant donor-acceptor interactions between Zn and Pz ligand: (a) the
result of the orbital interaction of the type LP(N) → 4s(Zn) (E(2) = 54.0 kcal mol−1); (b) the result of the
orbital interaction of the type LP(N) → 4p(Zn) (E(2) = 61.9 kcal mol−1). Only one of the four
corresponding interactions is demonstrated. Figure 2. Schemes of the dominant donor-acceptor interactions between Zn and Pz ligand: (a) the result
of the orbital interaction of the type LP(N) →4s(Zn) (E(2) = 54.0 kcal mol−1); (b) the result of the orbital
interaction of the type LP(N) →4p(Zn) (E(2) = 61.9 kcal mol−1). Only one of the four corresponding
interactions is demonstrated. (a)
(b)
Figure 2. Schemes of the dominant donor-acceptor interactions between Zn and Pz ligand: (a) the
result of the orbital interaction of the type LP(N) → 4s(Zn) (E(2) = 54.0 kcal mol−1); (b) the result of the
orbital interaction of the type LP(N) → 4p(Zn) (E(2) = 61.9 kcal mol−1). Only one of the four
corresponding interactions is demonstrated. Figure 2. 2.1. Chemical Bonding in MPz and MTTDP
2.1. Chemical Bonding in MPz and MTTDPz The
results of the: (a) orbital interaction of the type LP(N) → 4s(Ca) (E(2) = 11.0 kcal mol−1); (b) orbital
interaction of the type LP(N) → 3dx2−y2(Ca) (E(2) = 3.5 kcal mol−1); (c) orbital interaction of the type
LP(N) → 3dyz(Ca) (E(2) = 3.9 kcal mol−1). Figure 3. Schemes of the dominant donor-acceptor interactions between Ca and Pz ligand. The results
of the: (a) orbital interaction of the type LP(N) →4s(Ca) (E(2) = 11.0 kcal mol−1); (b) orbital interaction
of the type LP(N) →3dx2−y2(Ca) (E(2) = 3.5 kcal mol−1); (c) orbital interaction of the type LP(N) →
3dyz(Ca) (E(2) = 3.9 kcal mol−1). In the framework of the QTAIM theory, the existence of a chemical bond indicates the presence
of a bond critical point (BCP) between the corresponding atoms. The nature of the chemical bond can
be determined by the value of the electron density, laplacian ∇2ρ. A positive value of the electron
density laplacian ∇2ρ indicates ionic interaction. However, the values of M-Np bond orders, as well
as the corresponding delocalization indices δ(M|Np) representing the magnitudes of the electron
exchange between the basins of the corresponding atoms, allow to argue that these bonds, along
with an ionic component (Table 2), possess a noticeable covalent component. Interestingly, while the Zn(II) complexes are stable even in concentrated H2SO4 in ambient
conditions [23], the Ca(II) complex with TTDPz macrocycle, first prepared in the present work,
undergoes easy demetalation upon treatment with hot acetic acid, and forms ZnTTDPz upon heating
with the Zn(II) acetate in pyridine. This experimental observation is confirmed theoretically (within
the rigid rotor–harmonic oscillator (RRHO) approximation from the B3LYP/pcseg-2 geometries and
the harmonic frequencies) by the large negative value of the Gibbs free energy (∆rG0(298.15) =
−678 kJ mol−1) of the reaction: CaTTDPz + Zn2+ →Ca2+ + ZnTTDPz. The analogous value for the
reaction CaPz + Zn2+ →Ca2+ + ZnPz is ∆rG0(298.15) = −695 kJ mol−1. Table 2. Selected parameters of MPz and MTTDPz complexes from NBO and quantum theory of
atoms in molecules (QTAIM) calculations. CaPz
ZnPz
CaTTDPz
ZnTTDPz
E(HOMO),eV
−5.73
−5.99
−6.07
−6.19
E(LUMO),eV
−3.10
−3.33
−3.78
−3.91
∆E, eV
2.64
2.66
2.29
2.29
∇2ρ, a.u. 0.219
0.394
0.207
0.339
δ(M|Np)
0.270
0.464
0.262
0.446
In the framework of the QTAIM theory, the existence of a chemical bond indicates the presence of
a bond critical point (BCP) between the corresponding atoms. 2.1. Chemical Bonding in MPz and MTTDP
2.1. Chemical Bonding in MPz and MTTDPz Schemes of the dominant donor-acceptor interactions between Zn and Pz ligand: (a) the result
of the orbital interaction of the type LP(N) →4s(Zn) (E(2) = 54.0 kcal mol−1); (b) the result of the orbital
interaction of the type LP(N) →4p(Zn) (E(2) = 61.9 kcal mol−1). Only one of the four corresponding
interactions is demonstrated. (b) (a) (b) Figure 2. Schemes of the dominant donor-acceptor interactions between Zn and Pz ligand: (a) the
result of the orbital interaction of the type LP(N) → 4s(Zn) (E(2) = 54.0 kcal mol−1); (b) the result of the
orbital interaction of the type LP(N) → 4p(Zn) (E(2) = 61.9 kcal mol−1). Only one of the four
corresponding interactions is demonstrated. Figure 2. Schemes of the dominant donor-acceptor interactions between Zn and Pz ligand: (a) the result
of the orbital interaction of the type LP(N) →4s(Zn) (E(2) = 54.0 kcal mol−1); (b) the result of the orbital
interaction of the type LP(N) →4p(Zn) (E(2) = 61.9 kcal mol−1). Only one of the four corresponding
interactions is demonstrated. Int. J. Mol. Sci. 2020, 21, 2923
orbital interaction
di
i t 4 of 12 nt. J. Mol. Sci. 2020, 21, 2923
4 of 12
orbital interaction of the type LP(N) → 4p(Zn) (E(2) = 61.9 kcal mol−1). Only one of the four
corresponding interactions is demonstrated. (a)
(b)
Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW
5 of 13
(c)
Figure 3. Schemes of the dominant donor-acceptor interactions between Ca and Pz ligand. The
results of the: (a) orbital interaction of the type LP(N) → 4s(Ca) (E(2) = 11.0 kcal mol−1); (b) orbital
interaction of the type LP(N) → 3dx2−y2(Ca) (E(2) = 3.5 kcal mol−1); (c) orbital interaction of the type
LP(N) → 3dyz(Ca) (E(2) = 3.9 kcal mol−1). Figure 3. Schemes of the dominant donor-acceptor interactions between Ca and Pz ligand. The results
of the: (a) orbital interaction of the type LP(N) →4s(Ca) (E(2) = 11.0 kcal mol−1); (b) orbital interaction
of the type LP(N) →3dx2−y2(Ca) (E(2) = 3.5 kcal mol−1); (c) orbital interaction of the type LP(N) →
3dyz(Ca) (E(2) = 3.9 kcal mol−1). p
g
(a)
(b)
Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW
5 of 13 (a)
(b)
J. Mol. Sci. 2020, 21, x FOR PEER REVIEW
(c) (b) (c) Figure 3. Schemes of the dominant donor-acceptor interactions between Ca and Pz ligand. 2.1. Chemical Bonding in MPz and MTTDP
2.1. Chemical Bonding in MPz and MTTDPz The nature of the chemical bond can be
determined by the value of the electron density, laplacian ∇2ρ. A positive value of the electron density
laplacian ∇2ρ indicates ionic interaction. However, the values of M-Np bond orders, as well as the
corresponding delocalization indices δ(M|Np) representing the magnitudes of the electron exchange
between the basins of the corresponding atoms, allow to argue that these bonds, along with an ionic
component (Table 2), possess a noticeable covalent component. 5 of 12 Int. J. Mol. Sci. 2020, 21, 2923 Table 2. Selected parameters of MPz and MTTDPz complexes from NBO and quantum theory of atoms
in molecules (QTAIM) calculations. CaPz
ZnPz
CaTTDPz
ZnTTDPz
E(HOMO),eV
−5.73
−5.99
−6.07
−6.19
E(LUMO),eV
−3.10
−3.33
−3.78
−3.91
∆E, eV
2.64
2.66
2.29
2.29
∇2ρ, a.u. 0.219
0.394
0.207
0.339
δ(M|Np)
0.270
0.464
0.262
0.446
q(M) NPA
1.754
1.198
1.768
1.234
q(Np) NPA
−0.702
−0.633
−0.660
−0.596
configuration
4s0.123d0.14
4s0.363d9.964p0.48
4s0.113d0.13
4s0.353d9.974p0.44
P E(d-a), kcal/mol
18
116
17
103
Q(M-Np)
0.110
0.336
0.104
0.321
r(M-Np)
2.276
1.979
2.299
2.025 The annelated thiadiazole ring in the TTDPz complex also influences the geometry of the
coordination cavity. The electron density is shifted towards electron-withdrawing nitrogen atoms in
the thiadiazole moieties. It in turn leads through the inductive effect to a charge transfer in the row Nt
←Cβ ←Cα. The weakening of the N– Cα bonds results in an increase of the Cα–N–Cα angle and the
elongation of M–N distance in the MTTDPz complexes as compared to their MPz analogues. As it was previously found for the complexes of La and Lu with hemihexaphyrazine [24],
the perimeters of the internal 16-membered macrocycle of all the studied structures (Figure 4) do
practically not depend on the nature of a metal atom, and are equal to 21.55(2) Å. Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW
6 of 13 Figure 4. Internal macrocycle perimeter. Figure 4. Internal macrocycle perimeter. Figure 4. Internal macrocycle perimeter. Figure 4. Internal macrocycle perimeter. 2 2 Mole ula O bital
2.2. Molecular Orbitals 2.2. Molecular Orbitals
The symmetry of the frontier molecular orbitals is similar in the ZnPz and ZnTTDPz complexes,
and is also typical for porphyrzines: the highest occupied molecular orbital (HOMO) is an a1u orbital
and the lowest unoccupied molecular orbitals (LUMOs) are doubly-degenerated eg* orbitals (Figure
5). The LUMOs are localized on the porphyrazine macrocycle. The situation is similar for the calcium
complexes but different in the symmetry of orbitals (for example, the HOMO is an a2 orbital and the
LUMOs are doubly-degenerated e*) due to another symmetry point group
The symmetry of the frontier molecular orbitals is similar in the ZnPz and ZnTTDPz complexes,
and is also typical for porphyrzines: the highest occupied molecular orbital (HOMO) is an a1u orbital
and the lowest unoccupied molecular orbitals (LUMOs) are doubly-degenerated eg* orbitals (Figure 5). The LUMOs are localized on the porphyrazine macrocycle. The situation is similar for the calcium
complexes but different in the symmetry of orbitals (for example, the HOMO is an a2 orbital and the
LUMOs are doubly-degenerated e*) due to another symmetry point group. 6 of 12 Int. J. Mol. Sci. 2020, 21, 2923 Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW
7 of 13
CaPz
CaTTDPz
ZnPz
ZnTTDPz
݁∗
1݁∗
݁
∗
1݁
∗
ܽଶ
3ܽଶ
ܽଵ௨
2ܽଵ௨
2ܽଵ
3ܽଵ
2ܽଶ௨
2ܽଶ௨
1ܽଵ
1ܽଵ
1ܽଶ௨
1ܽଶ௨
Figure 5. Influence of the metal (Ca/Zn) and ligand (Pz/TTDPz) on the molecular orbitals of MPz and
MTTDPz complexes. Figure 5. Influence of the metal (Ca/Zn) and ligand (Pz/TTDPz) on the molecular orbitals of MPz and
MTTDPz complexes. ZnTTDPz CaTTDPz 1݁∗ 1݁
∗ ݁
∗ ݁∗ ܽଶ Figure 5. Influence of the metal (Ca/Zn) and ligand (Pz/TTDPz) on the molecular orbitals of MPz and
MTTDPz complexes. Figure 5. Influence of the metal (Ca/Zn) and ligand (Pz/TTDPz) on the molecular orbitals of MPz and
MTTDPz complexes. The nodes of the HOMO are located on the carbon atoms in the case of Pz complexes and
additionally on the Nt atoms for TTDPz macrocycles. The separation of the HOMO from the other π-MOs
is less pronounced in the case of Pz complexes as compared to their thiadiazole-annelated analogues The HOMO-1 MO in CaPz, the HOMO-2 in CaTTDPz and ZnPz, and the HOMO-4 in ZnTTDPz
are Gouterman type orbitals [25,26] predominantly localized on the nitrogen atoms of the macrocycles,
except for ZnTTDPz. 2 2 Mole ula O bital
2.2. Molecular Orbitals They can be connected with a significant decrease of the energy of this orbital in
the case of ZnTTPz as compared to the other molecules (Figure 6). 7 of 12 7 of 12 Int. J. Mol. Sci. 2020, 21, 2923
I
l
O
-2 -8
-6
-4
-2
2.286
2.634
1a1
1b2
4e
2а1
3b1
5e
3а1
2b2
3а2
1e*
b2*
а1*
2e*
1а1
eb1
b2
2а1
а2
e*
а1*
b1*
2.656
2.286
1a2u
eg
b2u
2a2u
b1g
a1u
eg*
b1u*
a1g
3eu
1a2u 2b2g
2a2u/2b1g
2eg
b2u
2a1u
1eg*
b2u*
a2u*
2eg*
E, eV
CaPz
ZnPz
CaTTDPz
ZnTTDPz
Figure 6. Molecular orbital (MO) level diagram for MPz and MTTDPz complexes (M = Ca, Zn). The
values of highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO)
gaps are given in eV. Figure 6. Molecular orbital (MO) level diagram for MPz and MTTDPz complexes (M = Ca, Zn). The values of highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO)
gaps are given in eV. -8
-6
-4
2.286
2.634
1a1
1b2
4e
2а1
3b1
5e
3а1
2b2
3а2
1e*
b2
1а1
eb1
b2
2а1
а2
e*
2.656
2.286
1a2u
eg
b2u
2a2u
b1g
a1u
eg*
a1g
3eu
1a2u 2b2g
2a2u/2b1g
2eg
b2u
2a1u
1eg*
b2u*
E, eV
Figure 6. Molecular orbital (MO) level diagram for MPz and MTTDPz complexes (M = Ca, Zn). The
values of highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO)
gaps are given in eV. 3. Electonic Absorption Spectra
The comparison of the calculated spectra demonstrates a strong influence of the ligand. F
th Ca and Zn complexes, a strong bathochromic shift (~70 nm) of the Q-band occurs with a chan
Pz ligand by TTDPz (Figure 7). The calculated oscillator strengths (f) for the lowest-allow ZnTTDPz
b ZnPz CaPz -8
-6
1a1
1b2
4e
2а1
3b1
5e
3а1
2b2
3а2
1а1
eb1
b2
2а1
а2
1a2u
eg
b2u
2a2u
b1g
a1u
a1g
3eu
1a2u 2b2g
2a2u/2b1g
2eg
b2u
2a1u
E
1a1
1b2
4e
a1g
3eu
1a2u 2b2g
Molecular orbital (MO) level diagram for MPz and MTTDPz complexes (M = Ca, Zn). T
highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUM
iven in eV. bsorption Spectra Figure 6. Molecular orbital (MO) level diagram for MPz and MTTDPz complexes (M = Ca, Zn). The
values of highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO)
gaps are given in eV. Figure 6. 2 2 Mole ula O bital
2.2. Molecular Orbitals Molecular orbital (MO) level diagram for MPz and MTTDPz complexes (M = Ca, Zn). The values of highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO)
gaps are given in eV. The comparison of the calculated spectra demonstrates a strong influence of the ligand. F
h Ca and Zn complexes, a strong bathochromic shift (~70 nm) of the Q-band occurs with a chan
z ligand by TTDPz (Figure 7). The calculated oscillator strengths (f) for the lowest-allow 2.3. Electonic Absorption Spectra
2.3. Electonic Absorption Spectra
excited states along with their co
The long-wave absorption p
p
The comparison of the calculated spectra demonstrates a strong influence of the ligand. For
both Ca and Zn complexes, a strong bathochromic shift (~70 nm) of the Q-band occurs with a change
of Pz ligand by TTDPz (Figure 7). The calculated oscillator strengths (f) for the lowest-allowed
excited states along with their composition (in terms of one-electron transitions) are given in Table 3. The comparison of the calculated spectra demonstrates a strong influence of the ligand. For both
Ca and Zn complexes, a strong bathochromic shift (~70 nm) of the Q-band occurs with a change of Pz
ligand by TTDPz (Figure 7). The calculated oscillator strengths (f) for the lowest-allowed excited states
along with their composition (in terms of one-electron transitions) are given in Table 3. g
p
(Q
)
p
assigned to the almost pure Goutermantype [25,26] transition ܽଶ→݁
∗ for Ca complexes and ܽଵ௨→
݁
∗ for Zn complexes. The electronic transitions to the higher excited states (the Soret near-UV region
of 300–420 nm) possess larger oscillator strengths and are predominantly composed of transitions
from the filled ܽଵ (Ca complexes) ܽଶ௨ (Zn complexes) type MOs to the LUMOs. The long-wave absorption maxima (Q band) in the spectra of MPz and MTTDPz c
ned to the almost pure Goutermantype [25,26] transition ܽଶ→݁
∗ for Ca complexes and
r Zn complexes. The electronic transitions to the higher excited states (the Soret near-UV
0–420 nm) possess larger oscillator strengths and are predominantly composed of tran
the filled ܽଵ (Ca complexes) ܽଶ௨ (Zn complexes) type MOs to the LUMOs. ZnTTDPz
ZnPz
CaTTDPz
CaPz
0
100
200
300
400
500
600
700
ZnTTDPz
ZnPz
CaTTDPz
CaPz
λ, nm
Figure 7. Calculated TDDFT electronic absorption spectra for MPz and MTTDPz complexes. Figure 7. Calculated TDDFT electronic absorption spectra for MPz and MTTDPz complexes. ZnTTDPz
Figure 7. Calculated TDDFT electronic absorption spectra for MPz and MTTDPz complexes. Figure 7. Calculated TDDFT electronic absorption spectra for MPz and MTTDPz complexes. Int. J. Mol. Sci. 2020, 21, 2923 8 of 12 le 3. Calculated composition of the lowest excited states and corresponding oscillator strengths
z and MTTDPz complexes (M = Ca and Zn). 3. Computational Methods The DFT-based investigation of MPz and MTTDPz included geometry optimizations and
computations of the harmonic vibrations followed by TDDFT calculations of the electronic absorption
spectrum. The number of the calculated excited states was 30. The calculations were performed using
B3LYP functional and pcseg-2 basis set [28] taken from the EMSL BSE library [29,30]. The Firefly QC [31]
package, which is partially-based on the GAMESS(US) [32] source code was used in all the calculations. Optimized Cartesian coordinates of MPz and MTTDPz are available from Supplementary materials. The QTAIM (quantum theory of atoms in molecules) analysis [33] was performed using the
AIMAll [34] software package. Topological parameters of ρ(r) in bond critical points and charges on
atoms are collected in Supplementary materials. The molecular models and orbitals demonstrated in the paper were visualized by means of the
Chemcraft program [35]. Synthesis of CaTTDPz Calcium metal (0.35 g, 8.5 mmol) was refluxed in 50 mL of butanol in a round-bottom flask for 12 h
affording the suspension of Ca(II) butoxide. Further 3,4-dicyano-1,2,5-thiadiazole (1.15 g, 8.5 mmol)
was added and the reaction mass was refluxed with vigorous stirring for 8 h. At the end of the
synthesis, the reaction mixture was poured into a Petri dish and left until the butanol was completely
evaporated. Further, the solid mass was washed with CH2Cl2 to remove the unreacted dinitrile and
low molecular weight reaction intermediates. After drying, the resulting product was poured into a
25% aqueous solution of acetic acid, and at room temperature with continuous stirring it was held
for 1 h to dissolve the calcium butoxide. The solid precipitate was filtered and washed repeatedly
with water and then with acetone and dried to constant weight. The mass of the obtained product
is 0.7 g (yield 45%). Electronic absorption spectra of CaTTDPz in pyridine and acetone are given in
Supplementary materials. 2.3. Electonic Absorption Spectra
2.3. Electonic Absorption Spectra
excited states along with their co
The long-wave absorption State
Composition (%)
λ, nm
f
exp λ, nm
CaPz
1 1E
2a1 →e∗(18)
a2 →e∗(80)
513
0.16
4 1E
1a1 →e∗(33)
2a1 →e∗(53)
a2 →e∗(9)
344
0.21
5 1E
1a1 →e∗(62)
2a1 →e∗(25)
a2 →e∗(9)
308
0.59
10 1E
e →b∗
1 (99)
238
0.06
CaTTDPz
1 1E
3a1 →1e∗(7)
3a2 →1e∗(90)
585
0.27
647 (Py) [this work]
641 (acetone) [this work]
6 1E
3a1 →1e∗(74)
3a2 →1e∗(8)
3a2 →2e∗(8)
322
0.98
16 1E
1b1 →1e∗(9)
5e →a∗
1 (14)
3a1 →2e∗(67)
254
0.28
17 1E
1b1 →1e∗(7)
2b2 →2e∗(77)
251
0.15
18 1E
1a2 →1e∗(6)
1b1 →1e∗(30)
5e →a∗
1 (34)
5e →b∗
2 (5)
3a1 →2e∗(23)
250
0.14
ZnPz
1 1Eu
2a2u →e∗g (17)
a1u →e∗g (82)
505
0.17
584 (Py) [27]
3 1Eu
1a2u →e∗g (50)
b2u →e∗g (6)
2a2u →e∗g (37)
a1u →e∗g (6)
329
0.15
4 1Eu
1a2u →e∗g (44)
2a2u →e∗g (42)
a1u →e∗g (11)
307
0.71
327
5 1Eu
eg →b∗
1u (99)
238
0.06
ZnTTDPz
1 1Eu
2a2u →1e∗g (5)
2a1u →1e∗g (91)
580
0.29
638 (DMSO) [23]
44 (DMF) [8]
4 1Eu
1a2u →1e∗g (44)
2a2u →1e∗g (42)
b2u →1e∗g (11)
334
0.28
400
5 1Eu
1a2u →1e∗g (39)
2a2u →1e∗g (42)
2a1u →1e∗g (7)
2a1u →2e∗g (6)
312
0.81
372
8 1Eu
1a1u →1e∗g (6)
b1u →1e∗g (29)
2eg →b∗
2u (8)
2eg →a∗
2u (52)
252
0.55
320
9 1Eu
2eg →a∗
2u (6)
b2u →2e∗g (86)
246
0.05
12 1Eu
1a1u →1e∗g (52)
1a2u →2e∗g (17)
2a2u →2e∗g (18)
b2u →2e∗g (6)
230
0.10 Int. J. Mol. Sci. 2020, 21, 2923 9 of 12 The long-wave absorption maxima (Q band) in the spectra of MPz and MTTDPz can be assigned
to the almost pure Goutermantype [25,26] transition a2 →e∗
g for Ca complexes and a1u →e∗
g for
Zn complexes. The electronic transitions to the higher excited states (the Soret near-UV region of
300–420 nm) possess larger oscillator strengths and are predominantly composed of transitions from
the filled a1 (Ca complexes) a2u (Zn complexes) type MOs to the LUMOs. 5. Conclusions Funding: This work is supported by the Russian Science Foundation (grant No. 19-73-00256). Abbreviations Pz
Porphyrazine
TTDPz
Tetrakis(1,2,5-thiadiazole) porphyrazine
DFT
Density Functional Theory
TDDFT
Time Dependent Density Functional Theory
NBO
Natural bond orbital
QTAIM
Quantum theory of atoms in molecules Pz
Porphyrazine
TTDPz
Tetrakis(1,2,5-thiadiazole) porphyrazine
DFT
Density Functional Theory
TDDFT
Time Dependent Density Functional Theory
NBO
Natural bond orbital
QTAIM
Quantum theory of atoms in molecules Pz
Porphyrazine
TTDPz
Tetrakis(1,2,5-thiadiazole) porphyrazine
DFT
Density Functional Theory
TDDFT
Time Dependent Density Functional Theory
NBO
Natural bond orbital
QTAIM
Quantum theory of atoms in molecules 5. Conclusions The influence of the nature of the metal (either Ca or Zn) and the ligand (either porphyrazine or
thiadiazole-annelated porphyrazine) on the geometry and electronic structure of the macroheterocyclic
complex was studied with the use of DFT calculations at the B3LYP/pcseg-2 level. The nature of the
chemical bonding is quite different in the case of Zn complexes as compared to the Ca analogues. Overall, all the complexes have a substantial ionic contribution to the M-Np bonding, but a much
larger covalent contribution appears in ZnPz and ZnTTDPz due to the donor-acceptor interactions of
the type LP(N) →4s(Zn) and LP(N) →4p(Zn). The perimeter of the coordination cavity was found to
be practically independent on the nature of a metal and a ligand. The change of Pz ligand by TTDPz causes a strong bathochromic shift (~70 nm) of the Q-band for
both Ca and Zn complexes. As it usually occurs to porphyrazine metal complexes, the Q-band can be
assigned to the almost pure Gouterman type transition. While the complexes of porphyrazine with Mg(II) are easily accessible and well-studied, the Ca(II)
complexes are not known. In this work, we prepared the CaTTDPz complex for the first time and
demonstrated that it possesses high lability. This is explained theoretically by the more ionic nature
of the Np-Ca bonds as compared to the Np-Zn bonds. Unlike the Ca(II) complex, the Zn(II) complex Int. J. Mol. Sci. 2020, 21, 2923 10 of 12 cannot be prepared directly by the template cyclotetramerization of the dinitrile, but instead can be
obtained readily from the Ca(II) complex. cannot be prepared directly by the template cyclotetramerization of the dinitrile, but instead can be
obtained readily from the Ca(II) complex. Supplementary Materials: Supplementary materials can be found at http://www.mdpi.com/1422-0067/21/8/2923/s1. Author Contributions: Conceptualization, P.A.S.; Methodology, Y.A.Z.; Investigation, I.A.K. and M.S.M.;
Resources, Y.A.Z.; Data Curation, I.V.R.; Writing—Original Draft Preparation, A.A.O. All authors have read and
agreed to the published version of the manuscript. di
h
k
d b
h
S
d
(
1
) Author Contributions: Conceptualization, P.A.S.; Methodology, Y.A.Z.; Investigation, I.A.K. and M.S.M.;
Resources, Y.A.Z.; Data Curation, I.V.R.; Writing—Original Draft Preparation, A.A.O. All authors have read and
agreed to the published version of the manuscript. Author Contributions: Conceptualization, P.A.S.; Methodology, Y.A.Z.; Investigation, I.A.K. and M.S.M.;
Resources, Y.A.Z.; Data Curation, I.V.R.; Writing—Original Draft Preparation, A.A.O. All authors have read and
agreed to the published version of the manuscript. References 1. Wöhrle, D.; Schnurpfeil, G.; Makarov, S.G.; Kazarin, A.; Suvorova, O.N. Practical Applications of
Phthalocyanines—From Dyes and Pigments to Materials for Optical, Electronic and Photo-electronic
Devices. Macroheterocycles 2012, 5, 191–202. [CrossRef] 1. Wöhrle, D.; Schnurpfeil, G.; Makarov, S.G.; Kazarin, A.; Suvorova, O.N. Practical Applications of
Phthalocyanines—From Dyes and Pigments to Materials for Optical, Electronic and Photo-electronic
Devices. Macroheterocycles 2012, 5, 191–202. [CrossRef] 2. Donzello, M.P.; Ercolani, C.; Stuzhin, P.A. Novel families of phthalocyanine-like macrocycles-Porphyrazines
with annulated strongly electron-withdrawing 1,2,5-thia/selenodiazole rings. Coord. Chem. Rev. 2006, 250,
1530–1561. [CrossRef] 2. Donzello, M.P.; Ercolani, C.; Stuzhin, P.A. Novel families of phthalocyanine-like macrocycles-Porphyrazines
with annulated strongly electron-withdrawing 1,2,5-thia/selenodiazole rings. Coord. Chem. Rev. 2006, 250,
1530–1561. [CrossRef] 3. Donzello, M.P.; Ercolani, C.; Novakova, V.; Zimcik, P.; Stuzhin, P.A. Tetrapyrazinoporphyrazines and their
metal derivatives. Part I: Synthesis and basic structural information. Coord. Chem. Rev. 2016, 309, 107–179. [CrossRef] 3. Donzello, M.P.; Ercolani, C.; Novakova, V.; Zimcik, P.; Stuzhin, P.A. Tetrapyrazinoporphyrazines and their
metal derivatives. Part I: Synthesis and basic structural information. Coord. Chem. Rev. 2016, 309, 107–179. [CrossRef] 4. Novakova, V.; Donzello, M.P.; Ercolani, C.; Zimcik, P.; Stuzhin, P.A. Tetrapyrazinoporphyrazines and their
metal derivatives. Part II: Electronic structure, electrochemical, spectral, photophysical and other application
related properties. Coord. Chem. Rev. 2018, 361, 1–73. [CrossRef] 5. Zhang, X.; Liu, Z.; Sheng, N.; Jiang, J. Molecular structure, electronic structure and vibrational spectra
of metal-free, N,N′-dideuterio, and magnesium tetrakis(thiadiazole)porphyrazines: Density functional
calculations. J. Mol. Struct. THEOCHEM 2005, 755, 179–186. [CrossRef] 6. Cai, X.; Zhang, Y.; Zhang, X.; Jiang, J. Structures and properties of metal-free and copper tetrakis(thiadiazole)
porphyrazine and metal-free tetrakis(selenodiazole) porphyrazine based on density functional theory
calculations. J. Mol. Struct. THEOCHEM 2007, 812, 63–70. [CrossRef] 7. Donzello,
M.P.;
Ercolani,
C.;
Kadish,
K.M.;
Ricciardi,
G.;
Rosa,
A.;
Stuzhin,
P.A. Tetrakis(thiadiazole)porphyrazines. 5. Electrochemical and DFT/TDDFT studies of the free-base
macrocycle and its MgII ZnII, and CuII complexes. Inorg. Chem. 2007, 46, 4145–4157. [CrossRef] 8. Tverdova, N.V.; Giricheva, N.I.; Savelyev, D.S.; Mikhailov, M.S.; Vogt, N.; Koifman, O.I.; Stuzhin, P.A.;
Girichev, G.V. Molecular structure of tetrakis(1,2,5-thiadiazolo)- porphyrazinatozinc(II) in gaseous phase. Macroheterocycles 2017, 10, 27–30. [CrossRef] 9. Nguyen, K.A.; Pachter, R. Ground state electronic structures and spectra of zinc complexes of porphyrin,
tetraazaporphyrin, tetrabenzoporphyrin, and phthalocyanine: A density functional theory study. J. Chem. Phys. 2001, 114, 10757–10767. [CrossRef] 10. Liao, M.S.; Scheiner, S. Comparative study of metal-porphyrins, -porphyrazines, and -phthalocyanines. J. Comput. Chem. 2002, 23, 1391–1403. [CrossRef] 11. References Baerends, E.J.; Ricciardi, G.; Rosa, A.; Van Gisbergen, S.J.A. A DFT/TDDFT interpretation of the ground and
excited states of porphyrin and porphyrazine complexes. Coord. Chem. Rev. 2002, 230, 5–27. [CrossRef] 11 of 12 Int. J. Mol. Sci. 2020, 21, 2923 12. Rosa, A.; Ricciardi, G.; Baerends, E.J.; Van Gisbergen, S.J.A. The optical spectra of NiP, NiPz, NiTBP, and
NiPc: Electronic effects of meso-tetraaza substitution and tetrabenzo annulation. J. Phys. Chem. A 2001, 105,
3311–3327. [CrossRef] 3. Sliznev, V.V. Theoretical study of structures of alkaline-earth metal (M=Be, Mg) complexes of porph
(MP), porphyrazine (MPz) and phthalocyanine (MPc). Macroheterocycles 2013, 6, 111–122. [CrossRef] 14. Miyoshi, Y.; Kubo, M.; Fujinawa, T.; Suzuki, Y.; Yoshikawa, H.; Awaga, K. Electrochromism and stable n-type
doping of highly oriented thin films of tetrakis(thiadiazole)porphyrazine. Angew. Chem.-Int. Ed. 2007, 46,
5532–5536. [CrossRef] [PubMed] 15. Fujimoto, T.; Miyoshi, Y.; Matsushita, M.M.; Awaga, K. A complementary organic inverter of porphyrazine
thin films: Low-voltage operation using ionic liquid gate dielectrics. Chem. Commun. 2011, 47, 5837–5839. [CrossRef] [PubMed] 16. Miyoshi, Y.; Fujimoto, T.; Yoshikawa, H.; Matsushita, M.M.; Awaga, K.; Yamada, T.; Ito, H. Photoconductivity
and FET performance of an n-type porphyrazine semiconductor, tetrakis(thiadiazole)porphyrazine. Org. Electron. 2011, 12, 239–243. [CrossRef] 17. Miyoshi, Y.; Takahashi, K.; Fujimoto, T.; Yoshikawa, H.; Matsushita, M.M.; Ouchi, Y.; Kepenekian, M.;
Robert, V.; Donzello, M.P.; Ercolani, C.; et al. Crystal structure, spin polarization, solid-state electrochemistry,
and high n-type carrier mobility of a paramagnetic semiconductor: Vanadyl tetrakis(thiadiazole)porphyrazine. Inorg. Chem. 2012, 51, 456–462. [CrossRef] 18. Stuzhin, P.; Mikhailov, M.; Travkin, V.; Gudkov, E.; Pakhomov, G. Multilayer Photovoltaic Structures Based
on Tetrathiadiazoloporphyrazine/Subphthalocyanine Heterojunction. Macroheterocycles 2012, 5, 162–165. [CrossRef] 19. Donzello, M.P.; Agostinetto, R.; Ivanova, S.S.; Fujimori, M.; Suzuki, Y.; Yoshikawa, H.; Shen, J.; Awaga, K.;
Ercolani, C.; Kadish, K.M.; et al. Tetrakis(thiadiazole)porphyrazines. 4. Direct template synthesis, structure,
general physicochemical behavior, and redox properties of Al III, GaIII, and InIII complexes. Inorg. Chem. 2005, 44, 8539–8551. [CrossRef] 20. Pia Donzello, M.; Viola, E.; Giustini, M.; Ercolani, C.; Monacelli, F. Tetrakis(thiadiazole)porphyrazines. 8. Singlet oxygen production, fluorescence response and liposomal incorporation of tetrakis(thiadiazole)
porphyrazine macrocycles [TTDPzM] (M = Mg II(H 2O), Zn II, Al IIICl, Ga IIICl, Cd II, Cu II, 2H I). Dalton Trans. 2012, 41, 6112–6121. [CrossRef] 21. Zhabanov, Y.A.; Tverdova, N.V.; Giricheva, N.I.; Girichev, G.V.; Stuzhin, P.A. DFT Study of molecular and
electronic structure of magnesium (II) tetra(1,2,5-chalcogenadiazolo) porphyrazines, [TXDPzMg] (X = O, S,
Se, Te). J. Porphyr. Phthalocyanines 2017, 21, 439–452. References [CrossRef] 22. Sliznev, V.V.; Girichev, G.V. Theoretical Study of Alkali Metal Complexes of Porphyrin (M2P), Porphyrazine
(M2Pz) and Phthalocyanine (M2Pc), M=Li, Na, K. Macroheterocycles 2011, 4, 8–17. [CrossRef] 23. Bauer, E.M.; Cardarilli, D.; Ercolani, C.; Stuzhin, P.A.; Russo, U. Tetrakis(thiadiazole)porphyrazines. 2. Metal
complexes with Mn(II), Fe(II), Co(II), Ni(II), and Zn(II). Inorg. Chem. 1999, 38, 6114–6120. [CrossRef] 24. Zhabanov, Y.A.; Giricheva, N.I.; Zakharov, A.V.; Islyaikin, M.K. Distinctive features of the structure of
hemihexaphyrazine complexes with Y, La, and Lu according to quantum chemical data. J. Mol. Struct. 2017,
1132, 28–33. [CrossRef] 25. Gouterman, M.; Wagnière, G.H.; Snyder, L.C. Spectra of porphyrins. Part II. Four orbital model. J. Mol. Spectrosc. 1963, 11, 108–127. [CrossRef] 6. Gouterman, M. Spectra of porphyrins. J. Mol. Spectrosc. 1961, 6, 138–163. [CrossRef] 27. Berezin, B.D.; Khelevina, O.G.; Stuzhin, P.A. Kinetics of the formation of metal complexes of unsubstituted
tetraazaporphine (porphyrazine) in pyridine. Russ. J. Phys. Chem. A 1985, 59, 1295–1299. 28. Jensen, F. Unifying general and segmented contracted basis sets. segmented polarization consistent basis
sets. J. Chem. Theory Comput. 2014, 10, 1074–1085. [CrossRef] 29. Pritchard, B.P.; Altarawy, D.; Didier, B.; Gibson, T.D.; Windus, T.L. New Basis Set Exchange: An Open,
Up-to-Date Resource for the Molecular Sciences Community. J. Chem. Inf. Model. 2019, 59, 4814–4820. [CrossRef] 30. Schuchardt, K.L.; Didier, B.T.; Elsethagen, T.; Sun, L.; Gurumoorthi, V.; Chase, J.; Li, J.; Windus, T.L. Basis
set exchange: A community database for computational sciences. J. Chem. Inf. Model. 2007, 47, 1045–1052. [CrossRef] Int. J. Mol. Sci. 2020, 21, 2923 12 of 12 12 of 12 31. Granovsky, A.A. Firefly Version 8. Available online: http://classic.chem.msu.su/gran/firefly/index.html
(accessed on 21 April 2020). 32. Schmidt, M.W.; Baldridge, K.K.; Boatz, J.A.; Elbert, S.T.; Gordon, M.S.; Jensen, J.H.; Koseki, S.; Matsunaga, N.;
Nguyen, K.A.; Su, S.; et al. General atomic and molecular electronic structure system. J. Comput. Chem. 1993,
14, 1347–1363. [CrossRef] 33. Bader, R.F.W. Atoms in Molecules: A Quantum Theory, Oxford University Press; Clarendon Press: Oxford, UK,
1990; ISBN 9780198558651. 34. Some References Related to AIMAll. Available online: http://aim.tkgristmill.com/references.html (accessed
on 13 March 2020). 35. Zhurko, G.A.; Zhurko, D.A. ChemCraft Version 1.6 (build 312); Version 1.6 (build 312) Ed. Available online:
http://www.chemcraftprog.com/index.html (accessed on 21 April 2020). © 2020 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 (http://creativecommons.org/licenses/by/4.0/).
|
https://openalex.org/W3105500644
|
https://www.nature.com/articles/s41467-017-01520-5.pdf
|
English
| null |
Depleted depletion drives polymer swelling in poor solvent mixtures
|
Nature communications
| 2,017
|
cc-by
| 8,712
|
ARTICLE ARTICLE ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 This leads to an effectively reduced repul-
sive interaction around xc = 0.5 because of the reduced number of
solvent particles near the monomer as expected from the varia-
tion of ρtotal with xc. The net result is a swelling of the polymer In this work, we propose a microscopic, generic and thus quite
generally applicable picture of this collapse–swelling–collapse
behavior in poor solvent mixtures. Therefore, we aim to do the
following: (1) devise a thermodynamically consistent generic
(chemically independent) model such that solubility of many
polymers in mixtures of poor solvents, including PMMA in
aqueous alcohol, can be explained within a simplified (universal)
physical concept, (2) develop a microscopic understanding of the
collapse–swelling–collapse
scenario
and
show
that
micro-
scopically this is a second order effect, and (3) investigate if a
polymer in mixed poor solvents can really reach a fully swollen
state characteristic of good solvents. To achieve the above goals,
we combine generic molecular dynamics, all-atom simulations
and analytical theoretical arguments to study polymer behavior in
poor solvent mixtures. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 1.7
Symmetric
Case 1
Case 2
R2
g
1.6
1.5
1.4
1.3
1.2
1.1
1.0
0.0
0.2
0.4
0.6
xc
0.8
1.0
Fig. 1 Polymer conformation and the effect of different mixtures of poor
solvent conditions. Normalized squared radius of gyration R
2
g ¼
R2
g
D
E
= Rg xc ¼ 0
ð
Þ2
D
E
as a function of cosolvent molar concentration xc. Results are shown for the generic simulations and for three different cases. The parameter-specific details of the generic cases are listed in the
Supplementary Table 1. The results are shown for a chain length of Nl = 30,
which corresponds to 30‘p with ‘p being the persistence length. Here
Rg xc ¼ 0
ð
Þ2
D
E
= 2.6 ± 0.4σ2 and R
2
Θ ¼ 2:13 with RΘ ¼ RΘ=Rg xc ¼ 0
ð
Þ is the
normalized Θ—point gyration radius. Here case 2 closely mimics the
conformational behavior of PMMA in aqueous methanol mixture based on
the parameterization presented in the Supplementary Table 1. Lines are
polynomial fits to the data that are drawn to guide the eye 1.7
Symmetric
Case 1
Case 2
R2
g
1.6
1.5
1.4
1.3
1.2
1.1
1.0
0.0
0.2
0.4
0.6
xc
0.8
1.0 T
he understanding of coil-to-globule transition of a mac-
romolecule in solvent mixtures is a fundamental process for
functional soft matter with a huge variety of applications
that goes beyond traditional polymer science1, 2. This reaches from
the responsiveness of hydrogels to external stimuli3, 4 and bio-
medical applications5–8 to the processing of conjugated polymers
for organic electronics9. In this context, it has been commonly
observed that a polymer can collapse in a mixture of two
competing, well miscible good solvents, while the same polymer
remains expanded in these two individual components. This
phenomenon is commonly known as co-non-solvency2, 10–19. However, it has also been observed that a polymer can be
collapsed in two different poor solvents, whereas it is “better”
soluble in their mixtures20–23. Thus far a multitude of specific,
system-dependent explanations hindered the emergence of a clear
physical picture of these two intriguing phenomena. While the
phenomenon of co-non-solvency has been recently brought onto a
firmer ground of a generic explanation2, 18, no equivalent
understanding of the collapse–swelling–collapse behavior has yet
been achieved. T Fig. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 The net result is a swelling of the polymer as a function of cosolvent mole fraction xc from the generic model
and for three different cases described in the Supplementary
Table 1. A closer look at the symmetric case of two almost per-
fectly miscible, but otherwise identical solvents (black Δ) shows
that—while the pure solvent (xc = 0) and the pure cosolvent (xc =
1) are equally poor solvents for the polymer, the same polymer
swells within the intermediate cosolvent compositions, reaching a
maximum swelling of R
2
g by ~20% at around xc = 0.5. How could
this be? Certainly, if both solvent and cosolvent were perfectly
miscible, nothing should happen in this case, as this would be
nothing but identical to a single component solution. Further-
more, given that this is a case of standard poor solvent collapse,
polymer conformations are determined by depletion forces (or
depletion induced attraction)28. When cosolvents are added into
the polymer–solvent system (such as the addition of alcohol in a
PMMA–water system), the addition of cosolvents not only repels
(or depletes) monomers, but also repels solvents and vice versa. In
this context, if we analyze the all-atom system of aqueous alcohol
mixtures, we find that the total number density of the system ρtotal
shows a minimum at 50/50 mixing ratios at constant pressure of
1 atm and temperature of 300 K, see Supplementary Fig. 1. This
suggests that, when alcohol is added in water, the repulsive forces
between the solution components result in a dip in ρtotal, which is
also known from experiments31. In our generic simulations, we
tune
solvent–solvent,
solvent–cosolvent,
cosolvent–cosolvent
interactions, temperature T and pressure P such that we repro-
duce the density dip observed in the all-atom simulations. Fur-
thermore, the system parameters are chosen such that the bulk
solvent–cosolvent solution mixture remains deep in the miscible
state far from phase separation. The representative simulation
snapshot is shown in Fig. 2 for a 50/50 solvent–cosolvent mixture. In the main panel of Fig. 2, we show ρtotal used in our generic
simulations. It can be seen that, in the generic model, we also find
a density dip of about 10% at xc = 0.5, which is consistent with the
all-atom simulations. Depleted depletion drives polymer swelling in poor
solvent mixtures Debashish Mukherji1, Carlos M. Marques
2, Torsten Stuehn1 & Kurt Kremer1 Establishing a link between macromolecular conformation and microscopic interaction is a
key to understand properties of polymer solutions and for designing technologically relevant
“smart” polymers. Here, polymer solvation in solvent mixtures strike as paradoxical phe-
nomena. For example, when adding polymers to a solvent, such that all particle interactions
are repulsive, polymer chains can collapse due to increased monomer–solvent repulsion. This
depletion induced monomer–monomer attraction is well known from colloidal stability. A
typical example is poly(methyl methacrylate) (PMMA) in water or small alcohols. While
polymer collapse in a single poor solvent is well understood, the observed polymer swelling in
mixtures of two repulsive solvents is surprising. By combining simulations and theoretical
concepts known from polymer physics and colloidal science, we unveil the microscopic,
generic origin of this collapse–swelling–collapse behavior. We show that this phenomenon
naturally emerges at constant pressure when an appropriate balance of entropically driven
depletion interactions is achieved. 1 Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany. 2 Institut Charles Sadron, Université de Strasbourg, CNRS, 23 rue du
Loess, 67034 Strasbourg Cedex 2, France. Correspondence and requests for materials should be addressed to D.M. (email: mukherji@mpip-mainz.mpg.de)
or to K.K. (email: kremer@mpip-mainz.mpg.de) NATURE COMMUNICATIONS| 8: 1374
| DOI: 10.1038/s41467-017-01520-5| www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 1 Polymer conformation and the effect of different mixtures of poor
solvent conditions. Normalized squared radius of gyration R
2
g ¼
R2
g
D
E
= Rg xc ¼ 0
ð
Þ2
D
E
as a function of cosolvent molar concentration xc. Results are shown for the generic simulations and for three different cases. The parameter-specific details of the generic cases are listed in the
Supplementary Table 1. The results are shown for a chain length of Nl = 30,
which corresponds to 30‘p with ‘p being the persistence length. Here
Rg xc ¼ 0
ð
Þ2
D
E
= 2.6 ± 0.4σ2 and R
2
Θ ¼ 2:13 with RΘ ¼ RΘ=Rg xc ¼ 0
ð
Þ is the
normalized Θ—point gyration radius. Here case 2 closely mimics the
conformational behavior of PMMA in aqueous methanol mixture based on
the parameterization presented in the Supplementary Table 1. Lines are
polynomial fits to the data that are drawn to guide the eye In a standard poor solvent, starting from a good solvent
condition, an increase of the effective attraction between the
monomers first brings the polymer into Θ—conditions, where the
radius of gyration scales as Rg N1=2
l
with Nl being the chain
length24, 25. Upon further increase of the attraction, a polymer
then collapses into a globular state. The resultant collapsed
globule can be understood by balancing negative second virial
osmotic contributions and three-body repulsions. The effective
attraction between the monomers of a polymer can be viewed as a
depletion induced attraction, a phenomenon well described for
colloidal suspensions26–30 of purely repulsive particles. In this
context, monomer attraction will occur when monomer–solvent
excluded volume interactions become large enough. The resulting
isolated polymer conformation can be well described by the
Porod scaling law of the static structure factor S(q) ∝q−4 fol-
lowing the envelope of the correlation peaks in S(q), presenting a
compact spherical globule. Interestingly, even if a polymer exhi-
bits poor solvent conditions in two different solvents, it can
possibly be somewhat swollen by intermediate mixing ratios of
the
two
poor
solvents. A
system
that
shows
this
collapse–swelling–collapse scenario is poly(methyl methacrylate)
(PMMA) in aqueous alcohol mixtures. More specifically, water
and alcohol are “almost” perfectly miscible and individually poor
solvents for PMMA. However, PMMA shows improved solubility
within intermediate mixing concentrations of aqueous alcohol
and/or other solvent mixtures20–23. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 as a function of cosolvent mole fraction xc from the generic model
and for three different cases described in the Supplementary
Table 1. A closer look at the symmetric case of two almost per-
fectly miscible, but otherwise identical solvents (black Δ) shows
that—while the pure solvent (xc = 0) and the pure cosolvent (xc =
1) are equally poor solvents for the polymer, the same polymer
swells within the intermediate cosolvent compositions, reaching a
maximum swelling of R
2
g by ~20% at around xc = 0.5. How could
this be? Certainly, if both solvent and cosolvent were perfectly
miscible, nothing should happen in this case, as this would be
nothing but identical to a single component solution. Further-
more, given that this is a case of standard poor solvent collapse,
polymer conformations are determined by depletion forces (or
depletion induced attraction)28. When cosolvents are added into
the polymer–solvent system (such as the addition of alcohol in a
PMMA–water system), the addition of cosolvents not only repels
(or depletes) monomers, but also repels solvents and vice versa. In
this context, if we analyze the all-atom system of aqueous alcohol
mixtures, we find that the total number density of the system ρtotal
shows a minimum at 50/50 mixing ratios at constant pressure of
1 atm and temperature of 300 K, see Supplementary Fig. 1. This
suggests that, when alcohol is added in water, the repulsive forces
between the solution components result in a dip in ρtotal, which is
also known from experiments31. In our generic simulations, we
tune
solvent–solvent,
solvent–cosolvent,
cosolvent–cosolvent
interactions, temperature T and pressure P such that we repro-
duce the density dip observed in the all-atom simulations. Fur-
thermore, the system parameters are chosen such that the bulk
solvent–cosolvent solution mixture remains deep in the miscible
state far from phase separation. The representative simulation
snapshot is shown in Fig. 2 for a 50/50 solvent–cosolvent mixture. In the main panel of Fig. 2, we show ρtotal used in our generic
simulations. It can be seen that, in the generic model, we also find
a density dip of about 10% at xc = 0.5, which is consistent with the
all-atom simulations. This leads to an effectively reduced repul-
sive interaction around xc = 0.5 because of the reduced number of
solvent particles near the monomer as expected from the varia-
tion of ρtotal with xc. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 The vertical
arrow indicates the effective Θ—blob size at q = qΘ, estimated using
‘Θblob ¼ 2π=qΘ. Note: to get a better estimate of the cross-over scaling
regime, S(q) is calculated from a simulation of a chain length Nl = 100 chain around xc = 0.5. We coin here the term depleted depletion
for explaining the reduction of depletion forces responsible for
polymer collapse due to mutual solvent–cosolvent exclusion. Notice, however, that this is a common concept in colloidal sci-
ence, where the modifications of the depletion attraction profile
due to depletant-depletant interactions have been extensively
studied28–30. swollen configuration. A quantity that perhaps best characterizes
a polymer conformation is the polymer form factor S(q). In Fig. 3,
we present S(q) for two different values of xc for the system
described by case 1. Part (a) shows S(q) of a fully collapsed chain
in pure solvent (xc = 0) and part (b) presents maximum polymer
swelling (xc = 0.7). For xc = 0.0, the polymer can be well described
by a scaling law known for sphere scattering (Porod scattering),
namely SðqÞ q4 following the envelope of S(q) curve, sug-
gesting a fully collapsed poor solvent conformation. Furthermore,
the data point corresponding to xc = 0.7 shows more interesting
polymer conformations. Within the range 1.5σ−1 < q < 3.0σ−1, an
aparent scaling SðqÞ q2 is observed, which crosses over to
SðqÞ q4 for 0.7σ−1 < q < 1.5σ−1, suggesting that the polymer
remains globally collapsed, consisting of Θ—blobs. The cross-
over point qΘ gives the direct measure of the effective blob size
‘Θblob ¼ 2π=qΘ 4:5σ. The largest blobs are observed when the
polymer is maximally swollen. When the interaction asymmetry between polymer-cosolvent
εpc and polymer–solvent εps is increased (Supplementary Table 1),
where εpc for case 2 < case 1 < symmetric case, not only the
degree of swelling increases, but the swelling region also shifts
between 0.5 < xc < 0.9. This range is found to be in excellent
agreement with the experimental observation of PMMA con-
formations in aqueous alcohol mixtures21, 22. Specifically, our
case 2 closely resembles PMMA in an aqueous methanol mixture. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 Note: to get a better estimate of the cross-over scaling
regime, S(q) is calculated from a simulation of a chain length Nl = 100 0.8
0.6
0.4
xc
0.2
0.0
6.2
total (–3)
6.0
5.8
5.6
5.4
5.2
5.0
1.0 n
c
d
of
y
101 10–1
101
100
q–4
qΘ
q–2
102
a
b
S (q )
101
Simulation
Simulation
[1 + q 2R 2
g/3]–1
Analytical
q–4
100
10–1
10–1
100
q
q
Fig. 3 Single-chain structure factor. Static structure factor S(q) for a chain
of length Nl = 100. a S(q) at xc = 0.0 and (b) xc = 0.7. In a, we also include
the analytical expression for sphere scattering. In b, red and green lines are
power law fits to the data at different length scales. The black line
represents the Guiner region for q→0 (for large length scales). The vertical
arrow indicates the effective Θ—blob size at q = qΘ, estimated using
‘Θblob ¼ 2π=qΘ. Note: to get a better estimate of the cross-over scaling
regime, S(q) is calculated from a simulation of a chain length Nl = 100 101 10–1
101
100
q–4
qΘ
q–2
102
a
b
S (q )
101
Simulation
Simulation
[1 + q 2R 2
g/3]–1
Analytical
q–4
100
10–1
10–1
100
q
q b a Fig. 2 Dependence of bulk solution number density with different Fig. 2 Dependence of bulk solution number density with different
solvent–cosolvent mixing ratios. Main panel presents ρtotal for the generic
model as a function of cosolvent mole fraction xc. The line is drawn based
on Eq. (3), with ρtotal = 1/v. In the inset, we show a simulation snapshot of
the generic system presenting bulk solution for a xc = 0.5 mixture. The
generic parameters for the bulk solution are chosen such that the density
dip observed in generic model closely resembles aqueous methanol
mixture, see Supplementary Fig. 1 Fig. 3 Single-chain structure factor. Static structure factor S(q) for a chain
of length Nl = 100. a S(q) at xc = 0.0 and (b) xc = 0.7. In a, we also include
the analytical expression for sphere scattering. In b, red and green lines are
power law fits to the data at different length scales. The black line
represents the Guiner region for q→0 (for large length scales). NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 0.8
0.6
0.4
xc
0.2
0.0
6.2
total (–3)
6.0
5.8
5.6
5.4
5.2
5.0
1.0
Fig. 2 Dependence of bulk solution number density with different
solvent–cosolvent mixing ratios. Main panel presents ρtotal for the generic
model as a function of cosolvent mole fraction xc. The line is drawn based
on Eq. (3), with ρtotal = 1/v. In the inset, we show a simulation snapshot of
the generic system presenting bulk solution for a xc = 0.5 mixture. The
generic parameters for the bulk solution are chosen such that the density
dip observed in generic model closely resembles aqueous methanol
mixture, see Supplementary Fig. 1
101 10–1
101
100
q–4
qΘ
q–2
102
a
b
S (q )
101
Simulation
Simulation
[1 + q 2R 2
g/3]–1
Analytical
q–4
100
10–1
10–1
100
q
q
Fig. 3 Single-chain structure factor. Static structure factor S(q) for a chain
of length Nl = 100. a S(q) at xc = 0.0 and (b) xc = 0.7. In a, we also include
the analytical expression for sphere scattering. In b, red and green lines are
power law fits to the data at different length scales. The black line
represents the Guiner region for q→0 (for large length scales). The vertical
arrow indicates the effective Θ—blob size at q = qΘ, estimated using
‘Θblob ¼ 2π=qΘ. Note: to get a better estimate of the cross-over scaling
regime S(q) is calculated from a simulation of a chain length Nl = 100 101 10–1
101
100
q–4
qΘ
q–2
102
a
b
S (q )
101
Simulation
Simulation
[1 + q 2R 2
g/3]–1
Analytical
q–4
100
10–1
10–1
100
q
q
Fig. 3 Single-chain structure factor. Static structure factor S(q) for a chain
of length Nl = 100. a S(q) at xc = 0.0 and (b) xc = 0.7. In a, we also include
the analytical expression for sphere scattering. In b, red and green lines are
power law fits to the data at different length scales. The black line
represents the Guiner region for q→0 (for large length scales). The vertical
arrow indicates the effective Θ—blob size at q = qΘ, estimated using
‘Θblob ¼ 2π=qΘ. Results
f Conformation of polymer. Figure 1 summarizes results for the
normalized squared radius of gyration R
2
g ¼
R2
g
D
E
= Rg xc ¼ 0
ð
Þ2
NATURE COMMUNICATIONS| 8: 1374
| DOI: 10.1038/s41467-017-01520-5| www.nature.com/naturecommunications 2 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 Indeed, we tune our monomer–solvent and monomer–cosolvent
interactions in the generic model such that we can reproduce the
correct solvation free energy, as measured by the shift in excess
chemical potential per monomer μp, known from all-atom
simulations of a PMMA system in aqueous methanol mixtures
(Supplementary Fig. 4 and Supplementary Note 2). Furthermore,
because we reproduce μp and ρtotal variation with changing xc in
our generic model as known from all-atom simulations under
ambient condition, T = 0.5ε/kB in the generic model corresponds
to 300 K and P = 16.0ε/σ3 corresponds to 1 atm in all-atom
system. While the swelling around xc 50%, especially for the
symmetric case, is bulk solution number density dependent (at
constant pressure), the shift in the region of maximal swelling is
cosolvent–monomer
interaction
dependent. For
example,
cosolvent–monomer repulsion for symmetric case > case 1 > case
2. This is similar to the PMMA solvation in different aqueous
alcohol mixtures, where the repulsion of methanol–MMA >
ethanol–MMA > propanol–MMA20–23. NATURE COMMUNICATIONS| 8: 1374
| DOI: 10.1038/s41467-017-01520-5| www.nature.com/naturecommunications NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 Therefore, if one would consider exclusively the
solvent–cosolvent system, the natural choice for normalizing free-
energy densities would be the excluded volume of the solvents
that are about eight times smaller than that of Vm, and that would
lead, in those units, to a value of χ? sc χsc=8 0:22. Note also
that standard FH predictions assume that solvent and cosolvent
because of the fixed grid size in the lattice—and also polymer—
are mixed at constant volume, whereas our simulations just as the
experiments are performed at a constant pressure. It should also
be noted that the constant density FH theory put forward in ref.19
requires a strong repulsive interaction parameter between solvent
and cosolvent making χ kBT, but in common mixtures of
water and alcohol χ kBT. Therefore, in the following, we derive
a FH expression for the V values at constant p, which predicts
effective values for χsc dependent on p. The subtle interaction
details seen here are not only restricted to polymer solutions, but
are also important for sequence dependent miscibility of copo-
lymers32, 33. Fv
κBT ¼
vF sðvÞ
κBT þ xcln xc
ð
Þ þ 1 xc
ð
Þln 1 xc
ð
Þ;
þχscðvÞxc 1 xc
ð
Þ;
ð2Þ Fv
κBT ¼
vF sðvÞ
κBT þ xcln xc
ð
Þ þ 1 xc
ð
Þln 1 xc
ð
Þ;
ð2Þ ð2Þ þχscðvÞxc 1 xc
ð
Þ; where F sðvÞ is the volume-dependent free-energy of the pure
(co)solvent systems and where we consider the explicit depen-
dence of χsc on system volume. Note that, since experiments and
simulations are performed at constant number of molecules N ,
the total volume of the system V is simply given by V ¼ N v. For
a given external pressure P, the molar volume v is thus controlled
by, P = Ps(v) −κBTxc(1 −xc)∂χsc(v)/∂v with PsðvÞ ¼ ∂vF s=∂v,
being the pressure of the reference system. If one assumes a small
variation of the molar volume of the solvent–cosolvent mixture
with respect to that of the reference system, one gets v ¼ vo 1 þ ζ xcð1 xcÞ
½
;
ð3Þ ð3Þ where ζ = κBT/v ∂χsc(v)/∂v[∂Ps(v)/∂v]−1 measures the relative
sensitivity of the interaction parameter and reference pressure to
v. In Fig. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 Variation of pressure Ps with change in molar volume v for a bare solvent
system Fig. 4 Variation in monomer excluded volume with changing g
g g
solvent–cosolvent mixing ratios. Normalized excluded volume V ¼ V=Vm
as a function of cosolvent mole fraction xc. The results are shown for two
cases. Lines are fits to the data corresponding to Eq. (1). In the inset, we
present 1=Rg
3 as a function of normalized V. Here, Rg ¼ Rg=Rg xc ¼ 0
ð
Þ is
the normalized gyration radius Rg. The line is a fit based on Eq. (5) Fig. 5 Pressure change in bare solvent with the change in molar volume. Variation of pressure Ps with change in molar volume v for a bare solvent
system identical, but that s−c interactions are distinct from those for s−s,
and c−c. For this case, the total free energy is written as V ¼ 2πR 1 evðrÞ=kBT
r2dr. We use v(r) = −kBT ln[g(r)] as a
guess of the potential of mean force (PMF), which is calculated
from the radial distribution function between non-bonded
monomers g(r). Vm ¼ 2:73σ3 is the bare monomer excluded
volume in the absence of any (co)solvent and corresponds to a
monomer–monomer distance of 0.87σ. Fitting Eq. (1) to the V
data in Fig. 4, we find χps = 1.57, χpc = 1.11, and χsc = 1.74 for case
1 and χps = 1.62, χpc = 0.95, and χsc = 1.74 for case 2. Consistently,
χsc values for both cases are similar and independent of
polymer–solvent interactions. Here, it is important to note that
the V values in Fig. 4 were obtained in simulations that were
performed when the bulk solution density varies over full xc,
keeping pressure invariant. Therefore, the χ values obtained are
not related to constant density case. Furthermore, the value of χsc
obtained here is consistent with the experimental value obtained
in ref.11, but might appear as too strong considering that one is
dealing with well miscible solvents. However, this is simply a
consequence of performing the analysis with free-energy densities
normalized by the monomer volume, a natural choice to inspect
polymer collapsing behavior. Within this normalization, however,
χsc parameter would corresponds to the effective interaction
between two clusters
consisting of solvent and
cosolvent
particles. Discussion
f So far we have discussed that the collapse–swelling–collapse
scenario naturally emerges because of the constant pressure. However, when the number densities for different mixing ratios
are kept fixed (such that the pressure rises within the intermediate
solvent–cosolvent mixing), the collapse–swelling–collapse sce-
nario is not observed. Only when ρtotal is allowed to vary with
changing solvent–cosolvent molar composition (as shown in
Fig. 2), we can observe swelling of a polymer. Therefore, we now
describe the observed collapse–swelling–collapse phenomenon
within the mean-field level by the Flory–Huggins (FH) theory and
its variants. For the case where a polymer with chain length Nl, at
volume fraction ϕp, is dissolved in a mixture of two components s
and c, respectively, FH theory predicts a monomer–monomer
excluded volume of the form24, 25, Single-chain structure factor. A closer look at Fig. 1 shows that
the degree of swelling, within the range 0.5 < xc < 0.9, varies
between 20 and 65% (or 10 and 30% in Rg), depending on the
interaction assymetry. Considering that we are dealing with
combinations of poor solvents, this is a very significant swelling,
making PMMA-based materials permeable to water–alcohol
mixtures. Moreover, analyzing the simulations, it becomes
apparent that the polymer does not necessarily reach a fully V ¼ 1 2 1 xc
ð
Þχps 2xcχpc þ 2xc 1 xc
ð
Þχsc;
ð1Þ ð1Þ where χps and χpc are the Flory–Huggins interaction parameters
between p −s and p −c, respectively. The factor χsc is the para-
meter of s −c interaction. When both solvent and cosolvent are
poor solvents, χps > 1/2 and χpc > 1/2. In our simulations,
V ¼ V=Vm
is
calculated
using
the
expression NATURE COMMUNICATIONS| 8: 1374
| DOI: 10.1038/s41467-017-01520-5| www.nature.com/naturecommunications 3 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 identical but that s−c interactions are distinct from those for s−s
0.0
–0.4
Case 1
Case 2
–0.8
–1.2
–1.6
–2.0
–2.4
0.2
0.4
0.6
xc
0.8
1.0
(1/RΘ)3
(1/Rg)3
1.0
0.8
0.6
0.4
0.2
0.0 0.5 1.0
||
1.5 2.0 2.5
Fig. 4 Variation in monomer excluded volume with changing
solvent–cosolvent mixing ratios. Normalized excluded volume V ¼ V=Vm
as a function of cosolvent mole fraction xc. The results are shown for two
cases. Lines are fits to the data corresponding to Eq. (1). In the inset, we
present 1=Rg
3 as a function of normalized V. Here, Rg ¼ Rg=Rg xc ¼ 0
ð
Þ is
the normalized gyration radius Rg. The line is a fit based on Eq. (5)
1.95
1.92
1.89
1.86
o (3)
1.83
16
Ps (–3)
15
14
13
Fig. 5 Pressure change in bare solvent with the change in molar volume. Variation of pressure Ps with change in molar volume v for a bare solven
system 1.95
1.92
1.89
1.86
o (3)
1.83
16
Ps (–3)
15
14
13
Fig. 5 Pressure change in bare solvent with the change in molar volume. Variation of pressure Ps with change in molar volume v for a bare solvent
system 0.0
–0.4
Case 1
Case 2
–0.8
–1.2
–1.6
–2.0
–2.4
0.2
0.4
0.6
xc
0.8
1.0
(1/RΘ)3
(1/Rg)3
1.0
0.8
0.6
0.4
0.2
0.0 0.5 1.0
||
1.5 2.0 2.5
Fig. 4 Variation in monomer excluded volume with changing
solvent–cosolvent mixing ratios. Normalized excluded volume V ¼ V=Vm
as a function of cosolvent mole fraction xc. The results are shown for two
cases. Lines are fits to the data corresponding to Eq. (1). In the inset, we
present 1=Rg
3 as a function of normalized V. Here, Rg ¼ Rg=Rg xc ¼ 0
ð
Þ is
the normalized gyration radius Rg. The line is a fit based on Eq. (5) 1.95
1.92
1.89
1.86
o (3)
1.83
16
Ps (–3)
15
14
13 0.0
–0.4
Case 1
Case 2
–0.8
–1.2
–1.6
–2.0
–2.4
0.2
0.4
0.6
xc
0.8
1.0
(1/RΘ)3
(1/Rg)3
1.0
0.8
0.6
0.4
0.2
0.0 0.5 1.0
||
1.5 2.0 2.5 1.95
1.92
1.89
1.86
o (3)
1.83
16
Ps (–3)
15
14
13
Fig. 5 Pressure change in bare solvent with the change in molar volume. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 5, we show Ps as a function of v that gives an estimate of
∂Ps(v)/∂v = 20ε/σ6. Equation (3) describes well the observed
density variation of the generic model in Fig. 2 with ζ = 0.26. Note that ρtotal and molar volume v are simply related by ρtotal =
1/v. Also, to first order in (v−vo)/vo, which for our generic model
is of the order of 10%, one gets χscðvÞ ¼ χsc vo
ð
Þ þ v∂χscðvÞ
∂v
xc!0
ζxc 1 xc
ð
Þ:
ð4Þ ð4Þ Since v∂χscðvÞ=∂v ζ, this shows that χsc obtained between
different ensembles is only perturbed to the second order in ζ. This will lead to an effective expression χsc(v) = χsc(vo) −
0.096xc(1 −xc). Furthermore, if we choose xc = 0.5, the above
equation will lead to a ~11% variation in χsc values with respect to
the standard values calculated when ρtotal is kept constant. This
suggests that effective χsc obtained in different ensembles is rather
close. Therefore, showing that, in this system, χsc parameter
relevant to the FH analysis keeps consistent values throughout the
range of compositions. It should also be mentioned that the
variation in χsc is a result of bulk density variation at xc, which is
about 10% (see Fig. 2). Moreover, we find that when the density is
kept constant, there is no variation of polymer conformation over y
In our simulations, we only consider polymer under infinite
dilution ϕp →0 and the large majority of the volume is occupied
by solvent–cosolvent mixture. Therefore, we concentrate our
analysis on the binary mixture. Additionally, we also consider
that the pure reference solvent and cosolvent systems are NATURE COMMUNICATIONS| 8: 1374
| DOI: 10.1038/s41467-017-01520-5| www.nature.com/naturecommunications 4 4 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 full xc range, while pressure of the system goes up with a max-
imum at xc = 0.5. change (i.e., ~10%) in bulk solution density does not significantly
influence the polymer conformation. On the contrary, the
collapse–swelling–collapse behavior, studied here, is due to a
subtle balance of repulsive microscopic interactions and the bulk
solution density. Furthermore, our analysis also suggests that the
collapse–swelling–collapse sequence in poor solvent mixtures is
driven by the mean-field behavior, i.e., contrary to the co-
nonsolvency effect that can not be described by a Flory–Huggins
mean-field picture because of the strong enhancement of the
cosolvent concentration in the vicinity of the polymer chain18. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 Here, the solvent–cosolvent interaction parameter χsc, though
quite small, plays a key role. Our results clarify that although
collapse–swelling–collapse and co-nonsolvency appear as two
symmetric manifestations of polymer solubility, they are in fact
driven by markedly different physical mechanisms. c
Our numerical predictions successfully account for polymer
swelling in solutions of poor solvent mixtures, as the simulations
quantitatively
demonstrate. While
this
fascinating
polymer
behavior is driven by purely repulsive interactions, it also reveals
the subtle balance of depletion forces and bulk solution properties
that enable such a paradoxical phenomenon. Indeed, polymer
collapse in repulsive solvents can be understood by depletion
induced attractions28. The dominant contribution to depletion
induced attraction originates from direct monomer–solvent
repulsion, and is thus proportional to solvent number density
ρtotat dictating the number of depletants. When a few solvent
molecules are replaced by cosolvents, for example, a water by an
alcohol, this preserves the solvent density to the first order. Under
these conditions, one smoothly interpolates between two polymer
collapsed states, without any swelling at intermediate composi-
tions. Here, however, interactions between solvent components
play a delicate role in dictating the depletion forces by bringing in
contributions proportional to second (or to even higher)-order
contributions of ρtotat, see Fig. 2. Interestingly, it is well known
from colloidal sciences that such second order effects may reduce
colloid–colloid attractive forces29, 30. Moreover, these studies in
colloidal systems typically deal with two component systems
where size asymmetry of 10 is needed to observe higher order
effects. In our study, size asymmetry between monomer and
solvent is significantly smaller and second order effects originate
because of the peculiar properties of the solvent–cosolvent mix-
tures. Thus, the polymer case occurs in a different interaction
regime compared to colloidal effect. The solvent–cosolvent
excluded volume is slightly stronger than the corresponding
values for solvent–solvent and cosolvent–cosolvent molecules,
leading to a slightly smaller solution density and a corresponding
diminution of the effective depletion interaction. At intermediate
compositions, where solvent–cosolvent interactions are dominant
in the solution, the effect is the strongest. Therefore, a broad
variety of polymer/solvent systems are expected to display such a
behavior. y
y
p y
In conclusion, we have performed molecular dynamics simu-
lations to unveil the microscopic origin of polymer swelling in
poor solvent mixtures. We propose a unified generic picture of
the polymer collapse–swelling–collapse phenomenon. Methods All generic simulations are based on the “well-known” bead-spring model of
polymers37. In this model, individual monomers of a polymer interact with each
other via a repulsive 6–12 Lennard–Jones (LJ) potential with a cutoff rc = 21/6σ. Additionally, adjacent monomers in a polymer are connected via a finitely
extensible nonlinear elastic potential (FENE). The parameters are chosen such that
a reasonably large time step can be chosen. The results are presented in units of the
LJ interaction energy ε, LJ length unit σ and unit of mass m. This leads to a time
unit of τ = σ(m/ε)1/2. All generic simulations are based on the “well-known” bead-spring model of
polymers37. In this model, individual monomers of a polymer interact with each
other via a repulsive 6–12 Lennard–Jones (LJ) potential with a cutoff rc = 21/6σ. Additionally, adjacent monomers in a polymer are connected via a finitely
extensible nonlinear elastic potential (FENE). The parameters are chosen such that
a reasonably large time step can be chosen. The results are presented in units of the
LJ interaction energy ε, LJ length unit σ and unit of mass m. This leads to a time
unit of τ = σ(m/ε)1/2. R
3
Θ
R
3
g
1 ¼ V
:
ð5Þ ð5Þ In the inset of Fig. 4, we show
1=Rg
3 as a function of V,
where the Rg is taken from Fig. 1a and V is given by the values in
the main panel of Fig. 4. The data are well described by the
theoretical prediction in Eq. (5). Extrapolating the data to V ¼ 0,
we estimate RΘ ¼ 1:46 (or RΘ = 2.34σ), further suggesting that
the polymer remains below Θ—conformation, even when it swells
within intermediate mixing ratios. A bead-spring polymer p is solvated in mixed solutions composed of two
components, solvent s and cosolvent c, respectively. The mole fraction of the
cosolvent component xc is varied from 0 (pure s component) to 1 (pure c com-
ponent). The size of monomers is σp = 1.0σ and sizes of the (co)solvent molecules
are chosen as σs/c = 0.5σ. This specific choice of σs/c is due to the fact that the
monomers are typically twice the size of solvent molecules such as water and
smaller alcohol. NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 This con-
formational change is due to a delicate balance between the
depletion forces and the bulk solution density at constant pres-
sure. Combining the Flory–Huggins type mean-field picture with
molecular dynamics simulations, we show that the polymer
swelling in poor solvents is dictated by reduced depletion forces
that originate from the bulk solution properties. These results
show semi-quantitative agreement of the polymer swelling
behavior in mixtures of two miscible poor solvents such as the
solvation of PMMA in aqueous alcohol mixtures. While the
polymers swell significantly, the mostly swollen polymer structure
still remains below Θ—conformation. Even when we take PMMA
as a test case, there are systems, such as corn starch35 and poly(N-
(6-acetamidopyridin-2-yl)acrylamide)36,
which
also
show
collapse–swelling–collapse
behavior. Interestingly,
the
solvent–cosolvent mixtures in these cases are also aqueous alco-
hol mixtures. Further supporting that the delicate balance
between microscopic repulsion together with density dip of the
bulk solution plays a key role in describing this phenomenon. Being potentially applicable to a large variety of polymers, the
concepts presented here may pave ways towards the functional
design of “smart” polymeric systems for advanced biomedical
purposes. A standard measure of the attractive forces leading to polymer
collapse is provided by the monomer excluded volume V. For
poor solvents, V is negative and the dimensions of the chain can
be understood by balancing the second (negative) virial osmotic
contributions and the three body repulsion24, 25, leading to ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 8. de Beer, S., Kutnyanszky, E., Schön, P. M., Vansco, G. J. & Müser, M. H. Solvent
induced immiscibility of polymer brushes eliminates dissipation channels. Nat. Commun. 5, 3781 (2014). velocity Verlet algorithm with a time step δt = 0.01τ. The simulations were usually
equilibrated for 107 MD time steps. The measurements are typically observed over
another 106 MD steps. During this time, observables such as the gyration radius Rg,
static structure factor S(q), chemical potential of polymer μp, and the polymer
excluded volume V is calculated. The temperature is set to 0.5ε/kBT, which is
employed using a Langevin thermostat with damping constant γ = 1.0τ−1. velocity Verlet algorithm with a time step δt = 0.01τ. The simulations were usually
equilibrated for 107 MD time steps. The measurements are typically observed over
another 106 MD steps. During this time, observables such as the gyration radius Rg,
static structure factor S(q), chemical potential of polymer μp, and the polymer
excluded volume V is calculated. The temperature is set to 0.5ε/kBT, which is
employed using a Langevin thermostat with damping constant γ = 1.0τ−1. 9. Hernandez-Sosa, G. et al. Rheological and drying considerations for uniformly
gravure-printed layers: towards large-area flexible organic light-emitting diodes. Adv. Funct. Mat. 23, 3164 (2013). p y
g
g
p
g
γ
One of the most important aspects of modeling PMMA in aqueous alcohol is to
incorporate bulk solution properties. As mentioned earlier in the main manuscript
text, alcohol and water are poor solvents for PMMA, while it swells in
water–alcohol mixtures. Analyzing the experimental data31 and all-atom simula-
tions of aqueous alcohol mixtures, it has become apparent that the excess volume
of the mixtures increases (or decrease in the total solution number density ρtotal)
from the mean-field values, which follows in a nonlinear dependence with xc
(Supplementary Fig. 1). This deviation is most dominant at intermediate mixing
ratios. In our generic simulation protocol, we choose interaction parameters of the
solution components such that ρtotal of the solution decreases at around 50–50
mixture, while keeping the solution at constant pressure. For this purpose, we
choose εss = εcc = 0.5 and εsc = 2.5, keeping all the interactions repulsive (Supple-
mentary Table 1). It is important to mention that ρtotal = 5.5σ−3 for pure xc = 0 and
xc = 1 solutions. This corresponds to a pressure of p ≈16.0 ± 0.5ε/σ3. ARTICLE Mukherji, D., Marques, C. M., Stuehn, T. & Kremer, K. Co-non-solvency:
Mean-field polymer theory does not describe polymer collapse transition in a
mixture of two competing good solvents. J. Chem. Phys. 142, 114903 (2015). η ¼ Vss þ Vcc 2Vsc:
ð6Þ η ¼ Vss þ Vcc 2Vsc: ð6Þ 19. Dudowicz, J., Freed, K. F. & Douglas, J. F. Communication: cosolvency and
cononsolvency explained in terms of a Flory-Huggins type theory. J. Chem. Phys. 143, 131101 (2015). Here Vij is the excluded volume of the i−j interaction defined a Vij ¼ 2π
Z 1
0
1 evijðrÞ=κBT
h
i
r2dr;
ð7Þ Vij ¼ 2π
Z 1
0
1 evijðrÞ=κBT
h
i
r2dr; y
20. Masegosa, R. M., Prolongo, M. G., Hernandez-Feures, I. & Horta, A. Preferential and total sorption of poly(methyl methacrylate) in the cosolvents
formed by acetonitrile with pentyl acetate and with alcohols (1-butanol, 1-
propanol, and methanol). Macromolecules 17, 1181 (1984). ð7Þ propanol, and methanol). Macromolecules 17, 1181 (1984). where vij is the potential of mean force between i and j components. We find
η ¼ 0:4σ3 for ρtotal = 5.2σ−3, η = −5.5σ3 for ρtotal = 6.4σ−3, and η < −30.0σ3 for
ρtotal = 8.0σ−3. It can be appreciated that η→0 for ρtotal →5.2σ−3, further suggesting
that the bulk solution is stable. 21. Hoogenboom, R., Remzi Becer, C., Guerrero-Sanchez, C., Hoeppener, S. &
Schubert, U. S. Solubility and thermoresponsiveness of PMMA in alcohol-water
solvent mixtures. Aust. J. Chem. 63, 1173 (2010). 22. Lee, S. M. & Bae, Y. C. Enhanced solvation effect of re-collapsing behavior for
cross-linked PMMA particle gel in aqueous alcohol solutions. Polymer= 55,
4684 (2014). The details about generic simulations and all-atom force field parameters are
given in the electronic Supplementary Material. Generic simulations are performed
using the ESPResSo + + molecular dynamics package38, all-atom simulations are
performed using the GROMACS package39, and simulation snapshots are rendered
using VMD40. 23. Yu, Y., Kieviet, B. D., Kutnyanszky, E., Vancso, G. J. & de Beer, S. Cosolvency-
induced switching of the adhesion between Poly(methyl methacrylate) brushes. ACS Macro Lett. 4, 75 (2015). 24. de Gennes, P.-G. Scaling Concepts in Polymer Physics. (Cornell University Press,
London, 1979). Data availability. All presented and analyzed the data is included in both main
text and in the Supplementary Material, including the methods, force fields, and
theory developed. ARTICLE The advan-
tage of this choice of ρtotal is that the solution remains stable over full xc range,
when the ρtotal decreases by ≈10% at xc = 0.5. 10. Wolf, B. A. & Willms, M. M. Measured and calculated solubility of polymers in
mixed solvents: Co-nonsolvency. Makromol. Chem. 179, 2265 (1978). 11. Schild, H. G., Muthukumar, M. & Tirrell, D. A. Cononsolvency in mixed 11. Schild, H. G., Muthukumar, M. & Tirrell, D. A. Cononsolvency in mixed
aqueous solutions of poly(N-isopropylacrylamide). Macromolecules 24, 948
(1991). aqueous solutions of poly(N-isopropylacrylamide). Macromolecules 24, 948
(1991). 12. Zhang, G. & Wu, C. Reentrant coil-to-globule-to-coil transition of a single
linear homopolymer chain in a water/methanol mixture. Phys. Rev. Lett. 86,
822 (2001). 13. Hiroki, A., Maekawa, Y., Yoshida, M., Kubota, K. & Katakai, R. Volume phase
transitions of poly(acryloyl-L-proline methyl ester) gels in response to water-
alcohol composition. Polymer 42, 1863 (2001). y
14. Kiritoshi, K. & Ishihara, K. EMolecular recognition of alcohol by volume phase
transition of cross-linked poly(2-methacryloyloxyethyl phosphorylcholine) gel. Sci. Technol. Adv. Mater. 4, 93 (2003). 15. Lund, R., Willner, L., Stellbrink, J., Radulescu, A. & Richter, D. Role of
interfacial tension for the structure of PEP-PEO polymeric micelles. A
combined SANS and pendant drop tensiometry investigation. Macromolecules
37, 9984 (2004). We also want to mention that even when the parameters are chosen as repulsive
with c−s being more repulsive than c−c and s−s interaction, our bulk solution
remains homogeneous over the full range of mixing ratios. In this context, it is
important to note that the solution phase separation is intimately linked to the
solution density. Within our choice of ρtotal, we do not see any phase separation. In
Supplementary Fig. 2, we show three simulation snapshots for different ρtotal and
for xc = 0.5. It can be appreciated that there is no signature of phase separation
when ρtotal = 5.2σ−3, phase separation can only be seen for ρtotal 6:4σ3. Suggesting
that the bulk solution remains stable. Furthermore, to quantify the possibility of
any phase separation we calculate the quantity η defined as, 16. Heyda, J., Muzdalo, A. & Dzubiella, J. Rationalizing polymer swelling and
collapse under attractive cosolvent conditions. Macromolecules 46, 1231 (2013). kh
l
l b l
l
f 17. Mukherji, D. & Kremer, K. Coil-globule-coil transition of PNIPAm in aqueous
methanol: Coupling all-atom simulations to semi-grand canonical coarse-
grained reservoir. Macromolecules 46, 9158 (2013). 18. Received: 28 February 2017 Accepted: 25 September 2017 27. Phillips, R. et al. Physical Biology of the Cell, 2nd edn (Garland Science 2012). 28. Lekkerkerker, H. N. W. & Tuinier, R. Colloids and the Depletion Interaction. (Clarendon Press, Oxford, 1990). 29. Mao, Y., Cates, M. E. & Lekkerkerker, H. N. W. Depletion stabilization by
semidilute rods. Phys. Rev. Lett. 75, 4548 (1995). ARTICLE Generic simulation scripts will be made available through the
ESPResSo++ webpage http://www.espresso-pp.de/. 25. Des Cloizeaux, J. & Jannink, G. Polymers in Solution: Their Modelling and
Structure. (Clarendon Press, Oxford, 1990). 26. Crocker, J. C., Matteo, J. A., Dinsmore, A. D. & Yodh, A. G. Entropic attraction
and repulsion in binary colloids probed with a line optical tweezer. Phys. Rev. Lett. 82, 4352 (1999). Received: 28 February 2017 Accepted: 25 September 2017 Methods Because s and c are both individually poor solvents for the poly-
mer, p–s and p–c interactions are always repulsive LJ with a cutoff rc = 21/6σij,
where σij is the diameter of p–s and p–c interactions given by the combination rule
σij = (σi + σj)/2. Here we choose, σpp = 1.0σ, σps = 0.75σ, σpc = 0.75σ, σss = 0.50σ, σcc
= 0.50σ, and σsc = 0.50σ. We consider two different cases of solvent qualities that
are dictated by the pairwise ε. A detailed description of ε between the LJ interaction
energies of the individual “pure” poor (co)solvents are presented in Supplementary
Table 1. This collapse–swelling–collapse scenario of PMMA in aqueous
alcohol appears as the opposite effect to that of coil-globule-coil
scenario, e.g., PNIPAm in aqueous alcohol, often referred to as
co-non-solvency2, 11, 12. However, the coil-globule-coil transition
occurs when individually good, but competing, solvents for a
polymer are mixed together and as a result polymer collapses
within the intermediate mixing ratios. Because this is micro-
scopically a good solvent system, it is dictated by the competition
between solvent and cosolvent preferential adsorption with the
polymer2, 34. Typical systems where co-nonsolvency is observed,
require an interaction contrast of about 4kBT17. Therefore, a small We consider a chain of length Nl = 30 solvated in a mixture of 2.0 × 104 solution
particles, in some cases, we also use Nl = 100 solvated in 5.0×104 solution particles. The interactions between different solvent particles are all chosen as repulsive LJ to
mimic depletion effects, as in the case of standard poor solvent collapse. LJ
interaction energies ε are chosen to match the typical thermodynamic condition
known from all-atom simulations. The equations of motion are integrated using a NATURE COMMUNICATIONS| 8: 1374
| DOI: 10.1038/s41467-017-01520-5| www.nature.com/naturecommunications 5 Acknowledgements D.M. thanks Burkhard Dünweg and Vagelis Harmandaris for many stimulating dis-
cussions, Tiago Oliveira for the help to build the all-atom PMMA force field and Björn
Baumeier for suggesting ref.1. in Supplementary Material. C.M.M. acknowledges Max-
Planck Institut für Polymerforschung for hospitality where this work was initiated and
performed. We thank Nancy Carolina Forero-Martinez and Hsiao-Ping Hsu for critical
reading of the manuscript. Reprints and permission information is available online at http://npg.nature.com/
reprintsandpermissions/ Reprints and permission information is available online at http://npg.nature.com/
reprintsandpermissions/ 39. Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E. GROMACS 4: algorithms
for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435 (2008). Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. 40. Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33 (1996). 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 license, and indicate if changes were made. The images or other third party
material in this article are included in the article’s Creative Commons license, unless
indicated otherwise in a credit line to the material. If material is not included in the
article’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. To view a copy of this license, visit http://creativecommons.org/
licenses/by/4.0/. References 30. Mao, Y., Cates, M. E. & Lekkerkerker, H. N. W. Depletion force in colloidal
systems. Physica. A 222, 10 (1995). 1. Cohen-Stuart, M. A. et al. Emerging applications of stimuli-responsive polymer
materials. Nat. Mater. 9, 101 (2010). 31. Perera, A., Sokolic, F., Almasy, L. & Koga, Y. Kirkwood-Buff integrals of
aqueous alcohol binary mixtures. J. Chem. Phys. 124, 124515 (2006). 2. Mukherji, D., Marques, C. M. & Kremer, K. Polymer collapse in miscible good
solvents is a generic phenomenon driven by preferential adsorption. Nat. Commun. 5, 4882 (2014). q
y
y
(
)
32. Balazs, A. C., Sanchez, I. C., Epstein, I. R., Karasz, F. E. & MacKnight, W. J. 32. Balazs, A. C., Sanchez, I. C., Epstein, I. R., Karasz, F. E. & MacKnight, W. J. Effect of sequence distribution on the miscibility of polymer/copolymer blends. Macromolecules 18, 2188 (1985). Effect of sequence distribution on the miscibility of polymer/copolymer blends. Macromolecules 18, 2188 (1985). 3. Chang, D. P., Dolbow, J. E. & Zauscher, S. Switchable friction of stimulus-
responsive hydrogels. Langmuir 23, 250 (2007). 33. Balazs, A. C., Karasz, F. E., MacKnight, W. J., Ueda, H. & Sanchez, I. C. Copolymer/copolymer blends: effect of sequence distribution on miscibility. Macromolecules 18, 2784 (1985). 4. Schmidt, S. et al. Adhesion and mechanical properties of PNIPAM microgel
films and their potential use as switchable cell culture substrates. Adv. Funct. Mater. 20, 3235 (2010). 34. Mukherji, D. et al. Relating side chain organization of PNIPAm with its
conformation in aqueous methanol. Soft Matter 12, 7995 (2016). 5. Vogel, M. J. & Steen, P. H. Capillarity-based switchable adhesion. Proc. Natl
Acad. Sci. USA 107, 3377 (2010). f
35. Galvez, L. O., de Beer, S., van der Meer, D. & Pons, A. Dramatic effect of fluid
chemistry on cornstarch suspensions: linking particle interactions to
macroscopic rheology. Phys. Rev. E 95, 030602 (2017). 6. Lee, H., Lee, B. P. & Messersmith, P. B. A reversible wet/dry adhesive inspired
by mussels and geckos. Nature 448, 338 (2007). 7. Meddahi-Pelle, A. et al. Organ repair, hemostasis, and in vivo bonding of
medical devices by aqueous solutions of nanoparticles. Angew. Chem., Int. Ed. 53, 6369 (2014). p
gy
y
36. Asadujjaman, A., Ahmadi, V., Yalcin, M., ten Brummelhuis, N. & Bertin, A. Thermoresponsive functional polymers based on 2,6-diaminopyridine motif NATURE COMMUNICATIONS| 8: 1374
| DOI: 10.1038/s41467-017-01520-5| www.nature.com/naturecommunications 6 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-01520-5 Competing interests: The authors declare no competing financial interests. 38. Halverson, J. D. et al. ESPResSo++: a modern multiscale simulation package for
soft matter systems. Comp. Phys. Comm. 184, 1129 (2013). Supplementary Information accompanies this paper at doi:10.1038/s41467-017-01520-5. Supplementary Information accompanies this paper at doi:10.1038/s41467-017-01520-5. 37. Kremer, K. & Grest, G. S. Dynamics of entangled linear polymer melts:a
l
l
d
l
h
h
(
) 37. Kremer, K. & Grest, G. S. Dynamics of entangled linear polymer melts:a
moleculardynamics simulation. J. Chem. Phys. 92, 5057 (1990). Competing interests: The authors declare no competing financial interests. Additional information with tunable UCST behaviour in water/alcohol mixtures. Pol. Chem 8, 3140
(2017). with tunable UCST behaviour in water/alcohol mixtures. Pol. Chem 8, 3140
(2017). © The Author(s) 2017 Author contributions D.M., C.M.M. and K.K. designed the research and parameterized the model, D.M. and
T.S. performed the simulations, D.M., C.M.M. and K.K. analyzed the data and for-
mulated the theory and D.M., C.M.M. and K.K. wrote the paper. D.M., C.M.M. and K.K. designed the research and parameterized the model, D.M. and
T.S. performed the simulations, D.M., C.M.M. and K.K. analyzed the data and for-
mulated the theory and D.M., C.M.M. and K.K. wrote the paper. NATURE COMMUNICATIONS| 8: 1374
| DOI: 10.1038/s41467-017-01520-5| www.nature.com/naturecommunications 7 7
|
https://openalex.org/W3107508450
|
https://figshare.com/articles/journal_contribution/Intron-assisted_viroid-based_production_of_insecticidal_circular_double-stranded_RNA_in_i_Escherichia_coli_i_/13620843/1/files/26140434.pdf
|
English
| null |
Intron-assisted, viroid-based production of insecticidal circular double-stranded RNA in<i>Escherichia coli</i>
|
bioRxiv (Cold Spring Harbor Laboratory)
| 2,020
|
cc-by
| 2,788
|
SUPPLEMENTAL DATA Intron-assisted, viroid-based production of insecticidal circular double-
stranded RNA in Escherichia coli SUPPLEMENTAL DATA SUPPLEMENTAL DATA Beltrán Ortoláa, Teresa Corderoa, Xu Hub and José-Antonio Daròsa aInstituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones
Científicas-Universitat Politècnica de Valencia), Valencia, Spain; bCorteva Agriscience,
Johnston, Iowa, USA aInstituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones
Científicas-Universitat Politècnica de Valencia), Valencia, Spain; bCorteva Agriscience,
Johnston, Iowa, USA CONTACT: José-Antonio Daròs, jadaros@ibmcp.upv.es, IBMCP (CSIC-Universitat
Politècnica de Valencia), Avenida de los Naranjos s/n, 46022 Valencia, Spain CONTACT: José-Antonio Daròs, jadaros@ibmcp.upv.es, IBMCP (CSIC-Universitat
Politècnica de Valencia), Avenida de los Naranjos s/n, 46022 Valencia, Spain Supplemental Dataset S1. Nucleotide sequences and elements of plasmids pLELVd,
pLELVd-BZB, pLPP, pLELVd-DvSSJ1, pLELVdPIE-DvSSJ1, pLPIE-DvSSJ1, p15LtRnlSm,
and p15CAT. >pLELVd (2050 bp)
CGATGCTTCTTTGAGCGAACGATCAAAAATAAGTGCCTTCCCATCAAAAAAATATTCTCAACATAAAAAACTTTG
TGTAATACTTGTAACGCTGCCCCATAGGGTGGTGTGTGCCACCCCTGATGAGACCGAAAGGTCGAAATGGGGTTT
CGCCATGGGTCGGGACTTTAAATTCGGAGGATTCGTCCTTTAAACGTTCCTCCAAGAGTCCCTTCCCCAAACCCT
TACTTTGTAAGTGTGGTTCGGCGAATGTACCGTTTCGTCCTTTCGGACTCATCAGGGAAAGTACACACTTTCCGA
CGGTGGGTTCGTCGACACCTCTCCCCCTCCCAGGTACTATCCCCTTTCAAGGATGTGTTCCCTAGGAGGGTGGGT
GTACCTCTTTTGGATTGCTCCGGCCTTCCAGGAGAGATAGAGGACGACCTCTCCCCATAGGGTGGTGTGTGCCAC
CCCTGATGAGACCGAAAGGTCGAAATGGGGGAAATCATCCTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATG
CGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGC
GAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCC
TGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGT
ATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCG
CCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTA
ACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTA
GAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCG
GCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTC
AAGAAGATCCTTTTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAG
TTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATAC
CGCGAGAGCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTG
GTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTA
ATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCA
GCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTC
CTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTA
CTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGC
GGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCA
TCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCA
CTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAA
ATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAA
GCATTTATCAGGGTTATTGTCTCAT In red, E. coli murein lipoprotein promoter. In bold, ELVd cDNA (C327 to G46 of AJ536613),
with the repeated hammerhead ribozyme domain highlighted in yellow, and their self-cleavage
sites underlined. In fuchsia, E. coli ribosomal rrnC terminator. In gray, pUC replication origin. Highlighted in light grey, ampicillin resistance gene (in reverse orientation), with the promoter
highlighted in dark gray). 1 >pLELVd-BZB (2574 bp)
CGATGCTTCTTTGAGCGAACGATCAAAAATAAGTGCCTTCCCATCAAAAAAATATTCTCAACATAAAAAACTTTG
TGTAATACTTGTAACGCTGCCCCATAGGGTGGTGTGTGCCACCCCTGATGAGACCGAAAGGTCGAAATGGGGTTT
CGCCATGGGTCGGGACTTTAAATTCGGAGGATTCGTCCTTTAAACGTTCCTCCAAGAGTCCCTTCCCCAAACCCT
TACTTTGTAAGTGTGGTTCGGCGAATGTACCGTTTCGTCCTTTCGGACTCATCAGGGAAAGTACACACTTTCCGA
CGGTGGGTTCGTCGACACCTCTCCCCCTCCCAGGTACTATCCCCTTGCGTCTTCGCGGGAAAGCGGGCAGTGAGC
GCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGT
TGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTA
ACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCG
AATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAATTCGCCCTATAGT
GAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTT
AATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAA
CAGTTGCGCAGCCTGAATGGCGAATGGGACGCGGGCGGAAGACGCTCAAGGATGTGTTCCCTAGGAGGGTGGGTG
TACCTCTTTTGGATTGCTCCGGCCTTCCAGGAGAGATAGAGGACGACCTCTCCCCATAGGGTGGTGTGTGCCACC
CCTGATGAGACCGAAAGGTCGAAATGGGGGAAATCATCCTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATGC
GTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCG
AAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCT
GCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTA
TCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGC
CTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAA
CAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAG
AAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGG
CAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCA
AGAAGATCCTTTTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGT
TGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACC
GCGAGAGCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGG
TCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAA
TAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAG
CTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCC
TCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTAC
TGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCG
GCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCAT
CATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCAC
TCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAA
TGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAG
CATTTATCAGGGTTATTGTCTCAT In red, E. coli murein lipoprotein promoter. In bold, (C327 to G46 of AJ536613), with the
repeated hammerhead ribozyme domain highlighted in yellow, and their self-cleavage sites
underlined. In blue cDNA coding for LacZ gene inserted between T245 and T246 of ELVd
cDNA. Highlighted in dark blue, recognition sites for type-IIS restriction enzyme BpiI, with
the cleavage sites in underlined bold. In fuchsia, E. coli ribosomal rrnC terminator. In gray,
pUC replication origin. Highlighted in light grey, ampicillin resistance gene (in reverse
orientation), with the promoter highlighted in dark gray). >pLPP (1916 bp) >pLPP (1916 bp)
CGATGCTTCTTTGAGCGAACGATCAAAAATAAGTGCCTTCCCATCAAAAAAATATTCTCAACATAAAAAACTTTG
TGTAATACTTGTAACGCTGGGAGACCGCGGCAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACC
CTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAAT
TCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAATTCGCCCTATAGTGAG
TCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAGGCGGGTCTCGGAAATCATCCTTAGCGAAAGCTAAGGATT
TTTTTTATCTGAAATGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGC
TCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGC
TCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCAT
AGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTT
CAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTG
GCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCT
AACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTT 2 2 GGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGC
AGAAAAAAAGGATCTCAAGAAGATCCTTTTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTA
TTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCC
AGTGCTGCAATGATACCGCGAGAGCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGG
GCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTA
AGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTT
GGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCG
GTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCA
CTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTC
TGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGA
ACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCC
AGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCA
AAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTT
TTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCAT In red, E. coli murein lipoprotein promoter. In bold blue, polylinker with double recognition
sites for the type IIS enzyme BsaI (highlighted in yellow, with the cleavage sites underlined)
separating the polylinker from the plasmid pBSIIKS + (in reverse, in blue italics). In fuchsia,
E. coli ribosomal rrnC terminator. In gray, pUC replication origin. Highlighted in light grey,
ampicillin resistance gene (in reverse orientation), with the promoter highlighted in dark gray). 3 In red, E. coli murein lipoprotein promoter. In bold, (C327 to G46 of AJ536613), with the
repeated hammerhead ribozyme domain highlighted in yellow, and their self-cleavage sites
underlined. Highlighted in green, inverted repeat of an 83 nt fragment of the DvSSJ1 gene
inserted between T245 and T246 of ELVd cDNA. In green, between the two copies of the
DvSSJ1 gene, the cDNA of the group-I Tetrahymena termophila 26S rRNA intron, with the 10
nt of both flanking exons underlined. In fuchsia, E. coli ribosomal rrnC terminator. In gray,
pUC replication origin. Highlighted in light grey, ampicillin resistance gene (in reverse
orientation), with the promoter highlighted in dark gray). In red, E. coli murein lipoprotein promoter. In bold, (C327 to G46 of AJ536613), with the
repeated hammerhead ribozyme domain highlighted in yellow, and their self-cleavage sites
underlined. Highlighted in green, inverted repeat of an 83 nt fragment of the DvSSJ1 gene
inserted between T245 and T246 of ELVd cDNA. In green, between the two copies of the
DvSSJ1 gene, the cDNA of the group-I Tetrahymena termophila 26S rRNA intron, with the 10
nt of both flanking exons underlined. In fuchsia, E. coli ribosomal rrnC terminator. In gray,
pUC replication origin. Highlighted in light grey, ampicillin resistance gene (in reverse
orientation), with the promoter highlighted in dark gray). 4
orientation), with the promoter highlighted in dark gray). >pLELVdPIE-DvSSJ1 (3080 bp)
CGATGCTTCTTTGAGCGAACGATCAAAAATAAGTGCCTTCCCATCAAAAAAATATTCTCAACATAAAAAACTTTG
TGTAATACTTGTAACGCTGCCCCATAGGGTGGTGTGTGCCACCCCTGATGAGACCGAAAGGTCGAAATGGGGTTT
CGCCATGGGTCGGGACTTTAAATTCGGAGGATTCGTCCTTTAAACGTTCCTCCAAGAGTCCCTTCCCCAAACCCT
TACTTTGTAAGTGTGGTTCGGCGAATGTACCGTTTCGTCCTTTCGGACTCATCAGGGAAAGTACACACTTTCCGA
CGGTGGGTTCGTCGACACCTCTCCCCCTCCCAGGTACTATCCCCTTCTTCTGTTGATATGGATGCAGTTCACAGA
CTAAATGTCGGTCGGGGAAGATGTATTCTTCTCATAAGATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGAT
GAAGTGATGCAACACTGGAGCCGCTGGGAACTAATTTGTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGT
AAGGTAGCACCATTGTCCTGAAATTGCTGAAGTTGGTGATCAATTTGATATGTCTCATCTTGTACCGAACCGGAT
ATCAAGGCTACTTCTTATGACTCTCTAAATAGCAATATTTACCTTTGGAGGGAAAAGTTATCAGGCATGCACCTG
GTAGCTAGTCTTTAAACCAATAGATTGCATCGGTTTAAAAGGCAAGACCGTCAAATTGCGGGAAAGGGGTCAACA
GCCGTTCAGTACCAAGTCTCAGGGGAAACTTTGAGATGGCCTTGCAAAGGGTATGGTAATAAGCTGACGGACATG
GTCCTAACCACGCAGCCAAGTCCTAAGTCAACAGATCTTCTGTTGATATGGATGCAGTTCACAGACTAAATGTCG
GTCGGGGAAGATGTATTCTTCTCATAAGATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGATGAAGTGATGC
AACACTGGAGCCGCTGGGAACTAATTTGTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGTAAGGTAGCAA
GAAGTAGCCTTGATATCCGGTTCGGTACAAGATGAGACATATCAAATTGATCACCAACTTCAGCAATTTCAGGAC
AATGGTATGACTCTCTAAATAGCAATATTTACCTTTGGAGGGAAAAGTTATCAGGCATGCACCTGGTAGCTAGTC
TTTAAACCAATAGATTGCATCGGTTTAAAAGGCAAGACCGTCAAATTGCGGGAAAGGGGTCAACAGCCGTTCAGT
ACCAAGTCTCAGGGGAAACTTTGAGATGGCCTTGCAAAGGGTATGGTAATAAGCTGACGGACATGGTCCTAACCA
CGCAGCCAAGTCCTAAGTCAACAGATTCAAGGATGTGTTCCCTAGGAGGGTGGGTGTACCTCTTTTGGATTGCTC
CGGCCTTCCAGGAGAGATAGAGGACGACCTCTCCCCATAGGGTGGTGTGTGCCACCCCTGATGAGACCGAAAGGT
CGAAATGGGGGAAATCATCCTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATGCGTTGCTGGCGTTTTTCCAT
AGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAA
AGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTG
TCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTC
GTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGT
CTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGG
TATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATC
TGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGT
AGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTTTACCAA
TGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTG
TAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAGCCACGCTCACCG
GCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCC
TCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTT
GCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCA
AGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGT
AAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGA
TGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGC
CCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCG
GGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCT
TCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATA
AGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGT
CTCAT
In red, E. coli murein lipoprotein promoter. >pLPP (1916 bp) In bold, (C327 to G46 of AJ536613), with the
repeated hammerhead ribozyme domain highlighted in yellow, and their self-cleavage sites
underlined. In orange, inserted between T245 and T246 of ELVd cDNA, group-I Tetrahymena
termophila 26S rRNA intron with intron-exon permutation between T235 and C236; 10 nt of
both flanking exons underlined. Highlighted in green, inverted repeat of an 83-nt fragment of orientation), with the promoter highlighted in dark gray). >pLELVdPIE-DvSSJ1 (3080 bp)
CGATGCTTCTTTGAGCGAACGATCAAAAATAAGTGCCTTCCCATCAAAAAAATATTCTCAACATAAAAAACTTTG
TGTAATACTTGTAACGCTGCCCCATAGGGTGGTGTGTGCCACCCCTGATGAGACCGAAAGGTCGAAATGGGGTTT
CGCCATGGGTCGGGACTTTAAATTCGGAGGATTCGTCCTTTAAACGTTCCTCCAAGAGTCCCTTCCCCAAACCCT
TACTTTGTAAGTGTGGTTCGGCGAATGTACCGTTTCGTCCTTTCGGACTCATCAGGGAAAGTACACACTTTCCGA
CGGTGGGTTCGTCGACACCTCTCCCCCTCCCAGGTACTATCCCCTTCTTCTGTTGATATGGATGCAGTTCACAGA
CTAAATGTCGGTCGGGGAAGATGTATTCTTCTCATAAGATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGAT
GAAGTGATGCAACACTGGAGCCGCTGGGAACTAATTTGTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGT
AAGGTAGCACCATTGTCCTGAAATTGCTGAAGTTGGTGATCAATTTGATATGTCTCATCTTGTACCGAACCGGAT
ATCAAGGCTACTTCTTATGACTCTCTAAATAGCAATATTTACCTTTGGAGGGAAAAGTTATCAGGCATGCACCTG
GTAGCTAGTCTTTAAACCAATAGATTGCATCGGTTTAAAAGGCAAGACCGTCAAATTGCGGGAAAGGGGTCAACA
GCCGTTCAGTACCAAGTCTCAGGGGAAACTTTGAGATGGCCTTGCAAAGGGTATGGTAATAAGCTGACGGACATG
GTCCTAACCACGCAGCCAAGTCCTAAGTCAACAGATCTTCTGTTGATATGGATGCAGTTCACAGACTAAATGTCG
GTCGGGGAAGATGTATTCTTCTCATAAGATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGATGAAGTGATGC
AACACTGGAGCCGCTGGGAACTAATTTGTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGTAAGGTAGCAA
GAAGTAGCCTTGATATCCGGTTCGGTACAAGATGAGACATATCAAATTGATCACCAACTTCAGCAATTTCAGGAC
AATGGTATGACTCTCTAAATAGCAATATTTACCTTTGGAGGGAAAAGTTATCAGGCATGCACCTGGTAGCTAGTC
TTTAAACCAATAGATTGCATCGGTTTAAAAGGCAAGACCGTCAAATTGCGGGAAAGGGGTCAACAGCCGTTCAGT
ACCAAGTCTCAGGGGAAACTTTGAGATGGCCTTGCAAAGGGTATGGTAATAAGCTGACGGACATGGTCCTAACCA
CGCAGCCAAGTCCTAAGTCAACAGATTCAAGGATGTGTTCCCTAGGAGGGTGGGTGTACCTCTTTTGGATTGCTC
CGGCCTTCCAGGAGAGATAGAGGACGACCTCTCCCCATAGGGTGGTGTGTGCCACCCCTGATGAGACCGAAAGGT
CGAAATGGGGGAAATCATCCTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATGCGTTGCTGGCGTTTTTCCAT
AGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAA
AGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTG
TCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTC
GTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGT
CTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGG
TATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATC
TGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGT
AGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTTTACCAA
TGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTG
TAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAGCCACGCTCACCG
GCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCC
TCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTT
GCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCA
AGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGT
AAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGA
TGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGC
CCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCG
GGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCT
TCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATA
AGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGT
CTCAT
In red, E. coli murein lipoprotein promoter. In bold, (C327 to G46 of AJ536613), with the
repeated hammerhead ribozyme domain highlighted in yellow, and their self-cleavage sites
underlined. In orange, inserted between T245 and T246 of ELVd cDNA, group-I Tetrahymena
termophila 26S rRNA intron with intron-exon permutation between T235 and C236; 10 nt of
both flanking exons underlined. Highlighted in green, inverted repeat of an 83-nt fragment of >pLELVdPIE-DvSSJ1 (3080 bp)
CGATGCTTCTTTGAGCGAACGATCAAAAATAAGTGCCTTCCCATCAAAAAAATATTCTCAACATAAAAAACTTTG
TGTAATACTTGTAACGCTGCCCCATAGGGTGGTGTGTGCCACCCCTGATGAGACCGAAAGGTCGAAATGGGGTTT
CGCCATGGGTCGGGACTTTAAATTCGGAGGATTCGTCCTTTAAACGTTCCTCCAAGAGTCCCTTCCCCAAACCCT
TACTTTGTAAGTGTGGTTCGGCGAATGTACCGTTTCGTCCTTTCGGACTCATCAGGGAAAGTACACACTTTCCGA
CGGTGGGTTCGTCGACACCTCTCCCCCTCCCAGGTACTATCCCCTTCTTCTGTTGATATGGATGCAGTTCACAGA
CTAAATGTCGGTCGGGGAAGATGTATTCTTCTCATAAGATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGAT
GAAGTGATGCAACACTGGAGCCGCTGGGAACTAATTTGTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGT
AAGGTAGCACCATTGTCCTGAAATTGCTGAAGTTGGTGATCAATTTGATATGTCTCATCTTGTACCGAACCGGAT
ATCAAGGCTACTTCTTATGACTCTCTAAATAGCAATATTTACCTTTGGAGGGAAAAGTTATCAGGCATGCACCTG
GTAGCTAGTCTTTAAACCAATAGATTGCATCGGTTTAAAAGGCAAGACCGTCAAATTGCGGGAAAGGGGTCAACA
GCCGTTCAGTACCAAGTCTCAGGGGAAACTTTGAGATGGCCTTGCAAAGGGTATGGTAATAAGCTGACGGACATG
GTCCTAACCACGCAGCCAAGTCCTAAGTCAACAGATCTTCTGTTGATATGGATGCAGTTCACAGACTAAATGTCG
GTCGGGGAAGATGTATTCTTCTCATAAGATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGATGAAGTGATGC
AACACTGGAGCCGCTGGGAACTAATTTGTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGTAAGGTAGCAA
GAAGTAGCCTTGATATCCGGTTCGGTACAAGATGAGACATATCAAATTGATCACCAACTTCAGCAATTTCAGGAC >pLELVdPIE-DvSSJ1 (3080 bp)
CGATGCTTCTTTGAGCGAACGATCAAAAATAAGTGCCTTCCCATCAAAAAAATATTCTCAACATAAAAAACTTTG
TGTAATACTTGTAACGCTGCCCCATAGGGTGGTGTGTGCCACCCCTGATGAGACCGAAAGGTCGAAATGGGGTTT
CGCCATGGGTCGGGACTTTAAATTCGGAGGATTCGTCCTTTAAACGTTCCTCCAAGAGTCCCTTCCCCAAACCCT
TACTTTGTAAGTGTGGTTCGGCGAATGTACCGTTTCGTCCTTTCGGACTCATCAGGGAAAGTACACACTTTCCGA
CGGTGGGTTCGTCGACACCTCTCCCCCTCCCAGGTACTATCCCCTTCTTCTGTTGATATGGATGCAGTTCACAGA
CTAAATGTCGGTCGGGGAAGATGTATTCTTCTCATAAGATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGAT
GAAGTGATGCAACACTGGAGCCGCTGGGAACTAATTTGTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGT >pLELVdPIE-DvSSJ1 (3080 bp)
CGATGCTTCTTTGAGCGAACGATCAAAAATAAGTGCCTTCCCATCAAAAAAATATTCTCAACATAAAAAACTTTG
TGTAATACTTGTAACGCTGCCCCATAGGGTGGTGTGTGCCACCCCTGATGAGACCGAAAGGTCGAAATGGGGTTT
CGCCATGGGTCGGGACTTTAAATTCGGAGGATTCGTCCTTTAAACGTTCCTCCAAGAGTCCCTTCCCCAAACCCT
TACTTTGTAAGTGTGGTTCGGCGAATGTACCGTTTCGTCCTTTCGGACTCATCAGGGAAAGTACACACTTTCCGA
CGGTGGGTTCGTCGACACCTCTCCCCCTCCCAGGTACTATCCCCTTCTTCTGTTGATATGGATGCAGTTCACAGA
CTAAATGTCGGTCGGGGAAGATGTATTCTTCTCATAAGATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGAT
GAAGTGATGCAACACTGGAGCCGCTGGGAACTAATTTGTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGT
AAGGTAGCACCATTGTCCTGAAATTGCTGAAGTTGGTGATCAATTTGATATGTCTCATCTTGTACCGAACCGGAT
ATCAAGGCTACTTCTTATGACTCTCTAAATAGCAATATTTACCTTTGGAGGGAAAAGTTATCAGGCATGCACCTG
GTAGCTAGTCTTTAAACCAATAGATTGCATCGGTTTAAAAGGCAAGACCGTCAAATTGCGGGAAAGGGGTCAACA
GCCGTTCAGTACCAAGTCTCAGGGGAAACTTTGAGATGGCCTTGCAAAGGGTATGGTAATAAGCTGACGGACATG
GTCCTAACCACGCAGCCAAGTCCTAAGTCAACAGATCTTCTGTTGATATGGATGCAGTTCACAGACTAAATGTCG
GTCGGGGAAGATGTATTCTTCTCATAAGATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGATGAAGTGATGC
AACACTGGAGCCGCTGGGAACTAATTTGTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGTAAGGTAGCAA
G
G
GCC
G
CCGG
CGG
C
G
G G C
C
G
C CC
C
C GC
C GG C In red, E. coli murein lipoprotein promoter. In bold, (C327 to G46 of AJ536613), with the
repeated hammerhead ribozyme domain highlighted in yellow, and their self-cleavage sites
underlined. In orange, inserted between T245 and T246 of ELVd cDNA, group-I Tetrahymena
termophila 26S rRNA intron with intron-exon permutation between T235 and C236; 10 nt of
both flanking exons underlined. Highlighted in green, inverted repeat of an 83-nt fragment of In red, E. coli murein lipoprotein promoter. In bold, (C327 to G46 of AJ536613), with the
repeated hammerhead ribozyme domain highlighted in yellow, and their self-cleavage sites
underlined. In orange, inserted between T245 and T246 of ELVd cDNA, group-I Tetrahymena
termophila 26S rRNA intron with intron-exon permutation between T235 and C236; 10 nt of
both flanking exons underlined. Highlighted in green, inverted repeat of an 83-nt fragment of 4 4 the DvSSJ1 gene. >pLPP (1916 bp) In
fuchsia, T7 bacteriophage terminator. In gray, p15A replication origin. Highlighted in light
grey, chloramphenicol resistance gene (in reverse orientation), with the promoter highlighted
in dark gray). >pLPP (1916 bp) In green, non-permutated sequence of the same intron, with the 10 nt of both
flanking exons underlined. In fuchsia, E. coli ribosomal rrnC terminator. In gray, pUC
replication origin. Highlighted in light grey, ampicillin resistance gene (in reverse orientation),
with the promoter highlighted in dark gray). >pLPIE-DvSSJ1 (2694 bp)
CGATGCTTCTTTGAGCGAACGATCAAAAATAAGTGCCTTCCCATCAAAAAAATATTCTCAACATAAAAAACTTTG
TGTAATACTTGTAACGCTGCTTCTGTTGATATGGATGCAGTTCACAGACTAAATGTCGGTCGGGGAAGATGTATT
CTTCTCATAAGATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGATGAAGTGATGCAACACTGGAGCCGCTGG
GAACTAATTTGTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGTAAGGTAGCACCATTGTCCTGAAATTGC
TGAAGTTGGTGATCAATTTGATATGTCTCATCTTGTACCGAACCGGATATCAAGGCTACTTCTTATGACTCTCTA
AATAGCAATATTTACCTTTGGAGGGAAAAGTTATCAGGCATGCACCTGGTAGCTAGTCTTTAAACCAATAGATTG
CATCGGTTTAAAAGGCAAGACCGTCAAATTGCGGGAAAGGGGTCAACAGCCGTTCAGTACCAAGTCTCAGGGGAA
ACTTTGAGATGGCCTTGCAAAGGGTATGGTAATAAGCTGACGGACATGGTCCTAACCACGCAGCCAAGTCCTAAG
TCAACAGATCTTCTGTTGATATGGATGCAGTTCACAGACTAAATGTCGGTCGGGGAAGATGTATTCTTCTCATAA
GATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGATGAAGTGATGCAACACTGGAGCCGCTGGGAACTAATTT
GTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGTAAGGTAGCAAGAAGTAGCCTTGATATCCGGTTCGGTA
CAAGATGAGACATATCAAATTGATCACCAACTTCAGCAATTTCAGGACAATGGTATGACTCTCTAAATAGCAATA
TTTACCTTTGGAGGGAAAAGTTATCAGGCATGCACCTGGTAGCTAGTCTTTAAACCAATAGATTGCATCGGTTTA
AAAGGCAAGACCGTCAAATTGCGGGAAAGGGGTCAACAGCCGTTCAGTACCAAGTCTCAGGGGAAACTTTGAGAT
GGCCTTGCAAAGGGTATGGTAATAAGCTGACGGACATGGTCCTAACCACGCAGCCAAGTCCTAAGTCAACAGATG
AAATCATCCTTAGCGAAAGCTAAGGATTTTTTTTATCTGAAATGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCC
CCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGC
GTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCT
CCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAA
GCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAA
CCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGG
TGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCT
GAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTT
TTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTTTACCAATGCTTAATCAG
TGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTAC
GATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAGCCACGCTCACCGGCTCCAGATTT
ATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTC
TATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTAC
AGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTAC
ATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGC
AGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGT
GACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAAT
ACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACT
CTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTT
TACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACG
GAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCAT >pLPIE-DvSSJ1 (2694 bp)
CGATGCTTCTTTGAGCGAACGATCAAAAATAAGTGCCTTCCCATCAAAAAAATATTCTCAACATAAAAAACTTTG
TGTAATACTTGTAACGCTGCTTCTGTTGATATGGATGCAGTTCACAGACTAAATGTCGGTCGGGGAAGATGTATT
CTTCTCATAAGATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGATGAAGTGATGCAACACTGGAGCCGCTGG
GAACTAATTTGTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGTAAGGTAGCACCATTGTCCTGAAATTGC
TGAAGTTGGTGATCAATTTGATATGTCTCATCTTGTACCGAACCGGATATCAAGGCTACTTCTTATGACTCTCTA
AATAGCAATATTTACCTTTGGAGGGAAAAGTTATCAGGCATGCACCTGGTAGCTAGTCTTTAAACCAATAGATTG
CATCGGTTTAAAAGGCAAGACCGTCAAATTGCGGGAAAGGGGTCAACAGCCGTTCAGTACCAAGTCTCAGGGGAA
ACTTTGAGATGGCCTTGCAAAGGGTATGGTAATAAGCTGACGGACATGGTCCTAACCACGCAGCCAAGTCCTAAG
TCAACAGATCTTCTGTTGATATGGATGCAGTTCACAGACTAAATGTCGGTCGGGGAAGATGTATTCTTCTCATAA
GATATAGTCGGACCTCTCCTTAATGGGAGCTAGCGGATGAAGTGATGCAACACTGGAGCCGCTGGGAACTAATTT
GTATGCGAAAGTATATTGATTAGTTTTGGAGTACTCGTAAGGTAGCAAGAAGTAGCCTTGATATCCGGTTCGGTA
CAAGATGAGACATATCAAATTGATCACCAACTTCAGCAATTTCAGGACAATGGTATGACTCTCTAAATAGCAATA CCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGC
GTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCT
CCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAA
GCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAA
CCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGG
TGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCT
GAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTT
TTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTTTACCAATGCTTAATCAG
TGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTAC
GATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAGCCACGCTCACCGGCTCCAGATTT
ATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTC
TATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTAC
AGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTAC
ATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGC
AGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGT
GACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAAT
ACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACT
CTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTT
TACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACG
GAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCAT In red, E. coli murein lipoprotein promoter. In orange, group-I Tetrahymena termophila 26S
rRNA intron with intron-exon permutation between T235 and C236; 10-nt of both flanking
exons underlined. Highlighted in green, inverted repeat of an 83-nt fragment of the DvSSJ1
gene. In green, non-permutated sequence of the same intron, with the 10 nt of both flanking
exons underlined. In fuchsia, E. coli ribosomal rrnC terminator. In gray, pUC replication origin. Highlighted in light grey, ampicillin resistance gene (in reverse orientation), with the promoter
highlighted in dark gray). >p15LtRnlSm (5415 bp)
CCCGGGGGCGGCGGCCGCCCGCGAAATCGATGCTTCTTTGAGCGAACGATCAAAAATAAGTGCCTTCCCATCAAA
AAAATATTCTCAACATAAAAAACTTTGTGTAATACTTGTAACGCTGGGGAGACCACAACGGTTTCCCTCTAGAAA
TAATTTTGTTTAACTTTAAGAAGGAGATATACCATGTCGGTTTCGCATAGGGTCATTTACTCTTTCACTCATTAC
AAACTCTATAATCTCTCTTCTTCTTTATCATCTTTGCCTTCTAGAATCTTCTTCCCTTTTCAATCTCCTTCCTTT
CACACGTTCTCTTCACTCATGCCCAACAATCAGGAAAGGGGTGGTTATGAAGGAAAAAAATGGCAAGTGAGGCCA
AGTTCCAATAGGGTACCAGGCTCGTCTTCAAATGTGGAACCTGTATCTGCTGCAACTGCTGAAGCCATTACCGAC >p15LtRnlSm (5415 bp)
CCCGGGGGCGGCGGCCGCCCGCGAAATCGATGCTTCTTTGAGCGAACGATCAAAAATAAGTGCCTTCCCATCAAA
AAAATATTCTCAACATAAAAAACTTTGTGTAATACTTGTAACGCTGGGGAGACCACAACGGTTTCCCTCTAGAAA
TAATTTTGTTTAACTTTAAGAAGGAGATATACCATGTCGGTTTCGCATAGGGTCATTTACTCTTTCACTCATTAC
AAACTCTATAATCTCTCTTCTTCTTTATCATCTTTGCCTTCTAGAATCTTCTTCCCTTTTCAATCTCCTTCCTTT
CACACGTTCTCTTCACTCATGCCCAACAATCAGGAAAGGGGTGGTTATGAAGGAAAAAAATGGCAAGTGAGGCCA
AGTTCCAATAGGGTACCAGGCTCGTCTTCAAATGTGGAACCTGTATCTGCTGCAACTGCTGAAGCCATTACCGAC 5 5 CGTCTAAAGTCCGTGGATATTACTGAAAGTGGTGCACAGTCTAGTGTTCCAGTCACATCTCTTCAGTTTGGCAGC
GTTGGATTAGCACCCCAGTCACCTGTGCAACATCAAAAAGTAATCTGGAAACCCAAATCATATGGAACAGTGTCT
GGAGCCCCAGTGGTTGAAGCTGGAAAAACACCAGTTGAACAAAAAAGTGCTCTTTTAAGTAAATTATTCAAGGGT
AATTTATTGGAAAATTTTACTGTAGATAACTCAACATTCTCGAGAGCCCAAGTAAGGGCCACTTTCTACCCAAAA
TTTGAGAATGAGAAATCAGATCAGGAGATCAGGACAAGGATGATAGAGATGGTCTCCAAAGGCTTGGCTATAGTC
GAGGTCACACTTAAGCATTCTGGATCTCTTTTTATGTATGCTGGGCATGAAGGTGGAGCATATGCCAAGAATAGC
TTCGGGAATATCTATACTGCCGTTGGCGTCTTTGTTCTTGGACGGATGTTTCGTGAGGCATGGGGAACTAAAGCA
AGCAAGAAGCAAGCAGAGTTCAATGAGTTTCTTGAGCGCAATCGTATGTGCATATCAATGGAGTTGGTCACGGCA
GTGTTGGGGGACCACGGACAACGCCCACGAGATGATTATGCGGTTGTGACTGCAGTCACGGAGTTGGGAAATGGA
AAACCAACTTTCTATTCAACTCCCGATGTAATTGCTTTTTGCAGGGAATGGCGATTACCAACAAATCATGTATGG
CTGTTCTCAACAAGGAAATCAGTGACTTCCTTCTTTGCTGCGTATGATGCACTTTGCGAGGAAGGTACAGCAACC
ACCGTTTGCGAGGCTCTCAGCGAAGTTGCTGATATTTCTGTACCTGGATCAAAAGACCATATAAAAGTGCAGGGT
GAAATTTTGGAGGGTCTCGTGGCCCGCATCGTAAAACGTGAGAGCTCAGAGCATATGGAGCGGGTTCTGAGAGAT
TTTCCTCCTCCGCCATCAGAGGGTGAGGGTTTGGACCTGGGACCTACGTTACGTGAAATTTGTGCTGCAAACAGA
TCAGAAAAGCAGCAAATAAAGGCACTTCTTCAGAGTGCTGGCACGGCTTTCTGCCCGAATTATTTGGACTGGTTT
GGAGATGAAAACTCTGGTTCACATTCAAGAAATGCTGATCGATCTGTTGTCTCAAAGTTCTTACAATCACATCCT
GCTGATCTTTATACAGGAAAAATACAGGAAATGGTTCGCTTGATGAGGGAAAAGCGCTTTCCTGCTGCTTTCAAG
TGTCATTATAACTTACATAAAATTAATGATGTATCGAGTAACAACCTGCCTTTCAAAATGGTGATCCATGTATAT
AGTGATTCAGGCTTCCGCCGGTACCAGAAAGAGATGAGGCACAAACCAGGACTATGGCCTTTGTATCGAGGCTTT
TTTGTTGACCTGGATTTATTCAAGGTCAATGAGAAGAAAACTGCTGAAATGGCAGGAAGCAACAATCAAATGGTA
AAAAATGTGGAAGAGGACAACAGTTTAGCTGATGAAGATGCAAATCTGATGGTCAAGATGAAATTTCTTACTTAC
AAGTTGAGAACTTTTTTGATCCGTAATGGCTTGTCGACTCTTTTCAAAGAAGGACCTTCTGCGTATAAGTCTTAT
TACCTGAGGCAAATGAAAATTTGGAATACTTCAGCAGCCAAGCAACGAGAACTCAGCAAGATGCTTGATGAATGG
GCAGTATATATACGCAGAAAATATGGGAACAAACCATTGTCATCATCCACATACCTAAGTGAAGCTGAGCCTTTC
CTTGAACAATATGCAAAGCGTAGTCCACAAAATCATGCTTTGATAGGATCTGCTGGAAATTTTGTCAAAGTTGAA
GATTTCATGGCTATTGTTGAAGGAGAAGATGAAGAGGGTGATCTCGAGCCTGCGAAAGATATTGCTCCTTCAAGC
CCTAGTATTTCCACCAGAGACATGGTGGCAAAGAATGAGGGTCTCATTATTTTCTTTCCAGGAATACCAGGTTGT
GCTAAATCTGCACTTTGTAAGGAAATACTGAATGCTCCAGGAGGGCTTGGAGATGATCGACCAGTTAACAGTTTA
ATGGGTGATCTTATTAAAGGTAGATATTGGCAAAAAGTTGCTGATGAACGTCGAAGAAAACCTTACTCGATCATG
CTTGCTGACAAGAATGCACCAAATGAGGAAGTATGGAAACAAATTGAGAACATGTGCCTAAGCACCGGAGCATCT
GCTATTCCAGTTATACCTGATTCAGAAGGAACTGAAACTAATCCATTCTCTATTGATGCACTTGCGGTTTTTATA
TTCCGAGTACTTCACCGTGTCAATCATCCGGGAAATCTTGACAAGTCATCTCCAAATGCTGGATATGTGATGCTT
ATGTTTTATCACCTTTATGATGGAAAGAGCCGTCAGGAGTTCGAGAGTGAGCTTATTGAACGTTTTGGATCGCTT
GTCAGAATTCCTGTACTGAAACCTGAGAGGTCTCCTCTTCCGGATTCTGTGAGGTCTATTATCGAGGAGGGACTC
AGTCTGTACAGACTTCATACAACGAAACATGGAAGATTGGAGTCTACAAAAGGGACATATGTACAAGAGTGGGTT
AAATGGGAGAAGCAATTGAGAGATATTCTACTTGGAAATGCAGACTATCTCAATTCAATACAGGTTCCATTTGAA
TTTGCCGTTAAAGAAGTCCTTGAACAACTGAAAGTTATTGCGAGGGGCGAATATGCAGTGCCTGCTGAGAAGAGG
AAGCTAGGATCCATTGTATTCGCCGCTATCAGCCTGCCAGTTCCAGAAATTCTAGGTCTTCTAAATGATCTAGCA
AAGAAAGATCCAAAGGTTGGCGATTTCATTAAGGACAAGAGCATGGAGAGCAGCATTCAGAAGGCCCATCTTACC
CTGGCTCACAAGAGAAGTCACGGTGTCACTGCAGTTGCCAATTACGGTTCCTTTCTTCATCAAAAGGTGCCAGTA
GACGTGGCTGCTTTGTTGTTCTCCGATAAATTGGCTGCACTAGAAGCTGAGCCTGGCTCTGTTGAAGGTGAAAAG
ATCAATTCTAAAAACTCATGGCCCCATATCACATTATGGTCTGGTGCAGGAGTTGCCGCAAAAGATGCCAATACA
CTACCACAGTTACTTTCCCAAGGGAAGGCTACCCGCATTGATATAAATCCACCGGTCACTATAACTGGCACTCTC
GAATTCTTTCACCACCACCACCACCACTGAGATCCGGCTGCTAACAAAGCCCGAAAGGAAGCTGAGTTGGCTGCT
GCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCTGAAAGGA
GATCTGGCGGGGCCCGCGCTAGCGGAGTGTATACTGGCTTACTATGTTGGCACTGATGAGGGTGTCAGTGAAGTG
CTTCATGTGGCAGGAGAAAAAAGGCTGCACCGGTGCGTCAGCAGAATATGTGATACAGGATATATTCCGCTTCCT
CGCTCACTGACTCGCTACGCTCGGTCGTTCGACTGCGGCGAGCGGAAATGGCTTACGAACGGGGCGGAGATTTCC
TGGAAGATGCCAGGAAGATACTTAACAGGGAAGTGAGAGGGCCGCGGCAAAGCCGTTTTTCCATAGGCTCCGCCC 6 AACGTTTCAGTTTGCTCATGGAAAACGGTGTAACAAGGGTGAACACTATCCCATATCACCAGCTCACCGTCTTTC
ATTGCCATACGGAATTCCGGATGAGCATTCATCAGGCGGGCAAGAATGTGAATAAAGGCCGGATAAAACTTGTGC
TTATTTTTCTTTACGGTCTTTAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTTATAGGTACATTGAGCAACT
GACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTTC
TCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGATAACTCAAAAAATACGCCCGGTAGTGATCTTATTTCATTA
TGGTGAAAGTTGGAA AACGTTTCAGTTTGCTCATGGAAAACGGTGTAACAAGGGTGAACACTATCCCATATCACCAGCTCACCGTCTTTC
ATTGCCATACGGAATTCCGGATGAGCATTCATCAGGCGGGCAAGAATGTGAATAAAGGCCGGATAAAACTTGTGC
TTATTTTTCTTTACGGTCTTTAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTTATAGGTACATTGAGCAACT
GACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTTC
TCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGATAACTCAAAAAATACGCCCGGTAGTGATCTTATTTCATTA
TGGTGAAAGTTGGAA In red, E. coli murein lipoprotein promoter. In bold, chloroplastic isoform of the eggplant tRNA
ligase (JX0225157), with the theoretical amino-terminal transit peptide highlighted in green,
the carboxyl terminal hexahistidine tag in blue and the start and stop codons underlined. In
fuchsia, T7 bacteriophage terminator. In gray, p15A replication origin. Highlighted in light
grey, chloramphenicol resistance gene (in reverse orientation), with the promoter highlighted
in dark gray). In red, E. coli murein lipoprotein promoter. In bold, chloroplastic isoform of the eggplant tRNA
ligase (JX0225157), with the theoretical amino-terminal transit peptide highlighted in green,
the carboxyl terminal hexahistidine tag in blue and the start and stop codons underlined. >p15CAT (1634 bp)
CCCGGGGGCGGCGGCCGC CCCGGGGGCGGCGGCCGCGGCGGACGTCGGCGCCTAAGGGGCGAGATCTGGCGGGGCCCGCGCTAGCGGAGTGTA
TACTGGCTTACTATGTTGGCACTGATGAGGGTGTCAGTGAAGTGCTTCATGTGGCAGGAGAAAAAAGGCTGCACC
GGTGCGTCAGCAGAATATGTGATACAGGATATATTCCGCTTCCTCGCTCACTGACTCGCTACGCTCGGTCGTTCG
ACTGCGGCGAGCGGAAATGGCTTACGAACGGGGCGGAGATTTCCTGGAAGATGCCAGGAAGATACTTAACAGGGA
AGTGAGAGGGCCGCGGCAAAGCCGTTTTTCCATAGGCTCCGCCCCCCTGACAAGCATCACGAAATCTGACGCTCA
AATCAGTGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGCGGCTCCCTCGTGCGCTCT
CCTGTTCCTGCCTTTCGGTTTACCGGTGTCATTCCGCTGTTATGGCCGCGTTTGTCTCATTCCACGCCTGACACT
CAGTTCCGGGTAGGCAGTTCGCTCCAAGCTGGACTGTATGCACGAACCCCCCGTTCAGTCCGACCGCTGCGCCTT
ATCCGGTAACTATCGTCTTGAGTCCAACCCGGAAAGACATGCAAAAGCACCACTGGCAGCAGCCACTGGTAATTG
ATTTAGAGGAGTTAGTCTTGAAGTCATGCGCCGGTTAAGGCTAAACTGAAAGGACAAGTTTTGGTGACTGCGCTC
CTCCAAGCCAGTTACCTCGGTTCAAAGAGTTGGTAGCTCAGAGAACCTTCGAAAAACCGCCCTGCAAGGCGGTTT
TTTCGTTTTCAGAGCAAGAGATTACGCGCAGACCAAAACGATCTCAAGAAGATCATCTTATTAATTACGCCCCGC
CCTGCCACTCATCGCAGTACTGTTGTAATTCATTAAGCATTCTGCCGACATGGAAGCCATCACAGACGGCATGAT
GAACCTGAATCGCCAGCGGCATCAGCACCTTGTCGCCTTGCGTATAATATTTGCCCATGGTGAAAACGGGGGCGA
AGAAGTTGTCCATATTGGCCACGTTTAAATCAAAACTGGTGAAACTCACCCAGGGATTGGCTGAGACGAAAAACA
TATTCTCAATAAACCCTTTAGGGAAATAGGCCAGGTTTTCACCGTAACACGCCACATCTTGCGAATATATGTGTA
GAAACTGCCGGAAATCGTCGTGGTATTCACTCCAGAGCGATGAAAACGTTTCAGTTTGCTCATGGAAAACGGTGT
AACAAGGGTGAACACTATCCCATATCACCAGCTCACCGTCTTTCATTGCCATACGGAATTCCGGATGAGCATTCA
TCAGGCGGGCAAGAATGTGAATAAAGGCCGGATAAAACTTGTGCTTATTTTTCTTTACGGTCTTTAAAAAGGCCG
TAATATCCAGCTGAACGGTCTGGTTATAGGTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGAT
GCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAATC
TCGATAACTCAAAAAATACGCCCGGTAGTGATCTTATTTCATTATGGTGAAAGTTGGAA
In gray p15A replication origin Highlighted in light grey chloramphenicol resistance gene (in In gray, p15A replication origin. Highlighted in light grey, chloramphenicol resistance gene (in
reverse orientation), with the promoter highlighted in dark gray). Highlighted in yellow,
polylinker with recognition sites for NotI (underlined) and BglII (underlined). In gray, p15A replication origin. Highlighted in light grey, chloramphenicol resistance gene (in
reverse orientation), with the promoter highlighted in dark gray). Highlighted in yellow,
polylinker with recognition sites for NotI (underlined) and BglII (underlined). 7 7 Supplemental Figure S1. Construction of expression plasmids to produce DvSSJ1-derived
dsRNA in E. coli. Plasmids purified from independent E. coli clones were separated by
electrophoresis through an agarose gel, which was stained with ethidium bromide. Lane 0, DNA
marker ladder with some of the sizes in bp on the left; lane 1, control plasmid pLELVd
expressing an empty ELVd; lanes 2 to 13, plasmids pLELVd-DvSSJ1 to express the DvSSJ1-
derived dsRNA on an ELVd scaffold obtained from 12 independent E. coli colonies. Supplemental Figure S1. Construction of expression plasmids to produce DvSSJ1-derived
dsRNA in E. coli. Plasmids purified from independent E. coli clones were separated by
electrophoresis through an agarose gel, which was stained with ethidium bromide. Lane 0, DNA
marker ladder with some of the sizes in bp on the left; lane 1, control plasmid pLELVd
expressing an empty ELVd; lanes 2 to 13, plasmids pLELVd-DvSSJ1 to express the DvSSJ1-
derived dsRNA on an ELVd scaffold obtained from 12 independent E. coli colonies. 8 8 Supplemental Figure S2. Effect of exon size in T. thermophila intron processing in the ELVd-
based system to produce dsRNA in E. coli. Aliquots of RNA preparations from E. coli clones
cotransformed with p15LtRnlSm and a series of pLELVd derivatives to produce a 100-bp
dsRNA, in which the exons that flank the T. thermophila intron are increasingly shorter, as
indicated, were separated by denaturing PAGE. The gel was stained with ethidium bromide. Lane 0, RNA marker with sizes (in nt) on the left; lanes 1 to 4, RNAs from constructs with 10,
8, 4 and 2-nt exons, respectively. Orange and black arrows point the positions of the
recombinant ELVd-dsRNA and the spliced introns, respectively. Supplemental Figure S2. Effect of exon size in T. thermophila intron processing in the ELVd-
based system to produce dsRNA in E. coli. Aliquots of RNA preparations from E. coli clones
cotransformed with p15LtRnlSm and a series of pLELVd derivatives to produce a 100-bp
dsRNA, in which the exons that flank the T. thermophila intron are increasingly shorter, as
indicated, were separated by denaturing PAGE. The gel was stained with ethidium bromide. Lane 0, RNA marker with sizes (in nt) on the left; lanes 1 to 4, RNAs from constructs with 10,
8, 4 and 2-nt exons, respectively. Orange and black arrows point the positions of the
recombinant ELVd-dsRNA and the spliced introns, respectively. 9 9 Supplemental Figure S3. 7 Large scale RNA preparations produced in E. coli by means of the
viroid-based system and used in the WCR bioassay. RNAs were separated by denaturing PAGE
and the gels stained with ethidium bromide. (a and b) Lane 0, RNA marker ladder with sizes in
nt on the left. (a) Lanes 1 and 2, large-scale RNA preparations from E. coli transformed with
p15LtRnlSm and pLELVd or pLELVd-DvSSJ1, respectively. (b) Dilution analysis of the ELVd
(lanes 1 to 7) and the ELVd-DvSSJ1 (lanes 8 to 14) RNA preparations. White, orange and black
arrows point to ELVd, ELVd-DvSSJ1 and spliced-intron RNAs, respectively. Supplemental Figure S3. Large scale RNA preparations produced in E. coli by means of the
viroid-based system and used in the WCR bioassay. RNAs were separated by denaturing PAGE
and the gels stained with ethidium bromide. (a and b) Lane 0, RNA marker ladder with sizes in
nt on the left. (a) Lanes 1 and 2, large-scale RNA preparations from E. coli transformed with
p15LtRnlSm and pLELVd or pLELVd-DvSSJ1, respectively. (b) Dilution analysis of the ELVd
(lanes 1 to 7) and the ELVd-DvSSJ1 (lanes 8 to 14) RNA preparations. White, orange and black
arrows point to ELVd, ELVd-DvSSJ1 and spliced-intron RNAs, respectively. 10 plemental Figure S4. Analysis of the recombinant circular dsRNA. RNApreparations from
rent E. coli clones (lanes 1 to 11) co-transformed with p15LtRnlSm and pLELVdPIE-
SJ1 were separated by denaturing PAGE. The gel was (a) stained with ethidium bromide
(b) the RNA transferred to a membrane and hybridized with a 32P-labelled probe to detect
SJ1 RNA. Lane 0, RNA marker with sizes in nt on the left. Blue arrows point to the
mbinant circular dsRNA that exhibits an inverted smile migration across the gel. Supplemental Figure S4. Analysis of the recombinant circular dsRNA. RNApreparations from
different E. coli clones (lanes 1 to 11) co-transformed with p15LtRnlSm and pLELVdPIE-
DvSSJ1 were separated by denaturing PAGE. The gel was (a) stained with ethidium bromide
and (b) the RNA transferred to a membrane and hybridized with a 32P-labelled probe to detect
DvSSJ1 RNA. Lane 0, RNA marker with sizes in nt on the left. Blue arrows point to the
recombinant circular dsRNA that exhibits an inverted smile migration across the gel. 11 Supplemental Figure S5. Effect of the the ELVd scaffold and the tRNA ligase on
accumulation of a recombinant circular dsRNA. RNA preparations from E. 7 coli clones
cotransformed with p15LtRnlSm and a pLELVdPIE-derivative to produce a 100-bp dsRNA or
the empty ligase plasmid (p15CAT) and a pLPIE-derivative (no ELVd scaffold) to produce the
same 100 bp dsRNA were separated by denaturing PAGE. After staining the gels with ethidium
bromide, recombinant circular dsRNA accumulation was quantified (in fluorescence arbitrary
units) using an image analyzer. Normalized average fluorescence is plotted. Error bars represent
standard deviation (n = 5). Supplemental Figure S5. Effect of the the ELVd scaffold and the tRNA ligase on
accumulation of a recombinant circular dsRNA. RNA preparations from E. coli clones
cotransformed with p15LtRnlSm and a pLELVdPIE-derivative to produce a 100-bp dsRNA or
the empty ligase plasmid (p15CAT) and a pLPIE-derivative (no ELVd scaffold) to produce the
same 100 bp dsRNA were separated by denaturing PAGE. After staining the gels with ethidium
bromide, recombinant circular dsRNA accumulation was quantified (in fluorescence arbitrary
units) using an image analyzer. Normalized average fluorescence is plotted. Error bars represent
standard deviation (n = 5). Supplemental Figure S5. Effect of the the ELVd scaffold and the tRNA ligase on
accumulation of a recombinant circular dsRNA. RNA preparations from E. coli clones
cotransformed with p15LtRnlSm and a pLELVdPIE-derivative to produce a 100-bp dsRNA or
the empty ligase plasmid (p15CAT) and a pLPIE-derivative (no ELVd scaffold) to produce the
same 100 bp dsRNA were separated by denaturing PAGE. After staining the gels with ethidium
bromide, recombinant circular dsRNA accumulation was quantified (in fluorescence arbitrary
units) using an image analyzer. Normalized average fluorescence is plotted. Error bars represent
standard deviation (n = 5). 12 Supplemental Table S1. Primers used in the PCR amplifications to build expression plasmid
pLELVd-DvSSJ1, pLELVdPIE-DvSSJ1 and pLPIE-DvSSJ1. Name
Sequence (5’ to 3’)
D2623
ACCATTGTCCTGAAATTGCTGAAGTTGGTGATCAATTTGATATGTCTCA
D2624
AAGAAGTAGCCTTGATATCCGGTTCGGTACAAGATGAGACATATCAAAT
D2625
CCTCTCCCCCTCCCAGGTACTATCCCCTTACCATTGTCCTGAAATTG
D2626
TTTAGAGAGTCATAAGAAGTAGCCTTGATATCCG
D2627
AAGGCTACTTCTTATGACTCTCTAAATAGCAATATTTAC
D2628
AAGGCTACTTCTTGGCTACCTTACGAGTACTCC
D2629
TCGTAAGGTAGCCAAGAAGTAGCCTTGATATCCG
D2630
ACCCACCCTCCTAGGGAACACATCCTTGAACCATTGTCCTGAAATTG
D2936
AAGGGGATAGTACCTGGGAG
D2937
ACCATTGTCCTGAAATTGCTG
D2940
ACCATTGTCCTGAAATTG
D2941
TCAAGGATGTGTTCCCTAG
D3606
CTTCTGTTGATATGGATG
D3285
CAGCGTTACAAGTATTACAC
D3607
GAAATCATCCTTAGCGAAAGC
D3608
ATCTGTTGACTTAGGACTTGGC Supplemental Table S1. Primers used in the PCR amplifications to build expression plasmids
pLELVd-DvSSJ1, pLELVdPIE-DvSSJ1 and pLPIE-DvSSJ1. 13
|
https://openalex.org/W2950615843
|
https://www.frontiersin.org/articles/10.3389/fmicb.2019.01253/pdf
|
English
| null |
An Archaeal Chitinase With a Secondary Capacity for Catalyzing Cellulose and Its Biotechnological Applications in Shell and Straw Degradation
|
Frontiers in microbiology
| 2,019
|
cc-by
| 10,862
|
Keywords: thermostable enzyme, chitinase, cellulose catalysis, yeast expression system, shell and straw
degradation, response surface methodology ORIGINAL RESEARCH
published: 11 June 2019
doi: 10.3389/fmicb.2019.01253 Edited by:
José E. Barboza-Corona,
University of Guanajuato, Mexico Reviewed by:
Dennis Ken Bideshi,
California Baptist University,
United States
Tania Pozzo,
University of California,
United States Numerous thermostable enzymes have been reported from the hyperthermophilic
archaeon Thermococcus kodakarensis KOD1, which made it an attractive resource for
gene cloning. This research reported a glycosyl hydrolase (Tk-ChiA) form T. Kodakarensis
with dual hydrolytic activity due to the presence of three binding domains with affinity
toward chitin and cellulose. The Tk-ChiA gene was cloned and expressed on Pichia
pastoris GS115. The molecular weight of the purified Tk-ChiA is about 130.0 kDa. By
using chitosan, CMC-Na and other polysaccharides as substrates, we confirmed that
Tk-ChiA with dual hydrolysis activity preferably hydrolyzes both chitosan and CMC-Na. Purified Tk-ChiA showed maximal activity for hydrolyzing CMC-Na at temperature 65°C
and pH 7.0. It showed thermal stability on incubation for 4 h at temperatures ranging from
70 to 80°C and remained more than 40% of its maximum activity after pre-incubation at
100°C for 4 h. Particularly, Tk-ChiA is capable of degrading shrimp shell and rice straw
through scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy
(FT-IR) analysis. The main factors affecting shell and straw degradation were determined
to be reaction time and temperature; and both factors were optimized by central composite
design (CCD) of response surface methodology (RSM) to enhance the efficiency of
degradation. Our findings suggest that Tk-ChiA with dual thermostable hydrolytic activities
maybe a promising hydrolase for shell and straw waste treatment, conversion, and utilization. *Correspondence:
Zhengqun Li
lizq13@mails.jlu.edu.cn;
lizhengqun1990@163.com
Shi-Hong Zhang
zhang_sh@jlu.edu.cn †Present address:
Zhengqun Li,
Molecular Biology of Archaea,
Faculty of Biology, University of
Freiburg, Freiburg, Germany Specialty section:
This article was submitted to
Microbiotechnology, Ecotoxicology
and Bioremediation,
a section of the journal
Frontiers in Microbiology Received: 15 February 2019
Accepted: 20 May 2019
Published: 11 June 2019 INTRODUCTION Chen L, Wei Y, Shi M, Li Z and
Zhang S-H (2019) An Archaeal
Chitinase With a Secondary Capacity
for Catalyzing Cellulose and Its
Biotechnological Applications in Shell
and Straw Degradation. F
t Mi
bi l 10 1253 Chitin is an insoluble linear polymer of β-1,4-linked N-acetylglucosamine (GlcNAc) that
is different from cellulose, which consists of non-branched β-1,4-linked glucose. Chitin is
frequently present in the cell walls of fungi, the cuticles of insects (Hanazono et al., 2016),
and the shells of shrimp. However, cellulose is the major polysaccharide of plant cell walls
and is thus the most abundant natural polymer. Cellulose is present in various types of Front. Microbiol. 10:1253. doi: 10.3389/fmicb.2019.01253 June 2019 | Volume 10 | Article 1253 Frontiers in Microbiology | www.frontiersin.org The Applications of Bicatalytic Chitinase Chen et al. show exo-chitinase and endo-chitinase functionality, respectively. In addition, Tk-ChiA has three substrate binding domains,
CBD1, CBD2, and CBD3, which are considered to bind chitin. However, these three domains show sequence similarity with
the cellulose binding domains of various cellulases. CBD1 is
a family V type carbohydrate binding domain that is capable
of cellulose binding (Tomme et al., 1998). CBD2 and CBD3
are classed as family II type carbohydrate binding domains. Binding domains play an important role in determining the
catalysis ability of enzymes (Jendrossek and Handrick, 2002). Strikingly, CBD2 and CBD3 can bind to chitin and cellulose
(Hanazono et al., 2016). However, CBD2 and CBD3 are unable
to bind to xylan and amylopectin. These cellulose binding
domains of Tk-ChiA allow it to perform the secondary function
of catalyzing cellulose degradation. Cellulases hydrolyze the
β-1,4 linkages in cellulose and are the main catalysts involved
in enzymatic hydrolysis. Cellulases function in multi-enzyme
systems
comprising
an
endoglucanase
(EC3.2.1.4),
a
cellobiohydrolase (avicelase, EC3.2.1.91), and a β-d-glucosidase
(EC3.2.1.21), which synergistically hydrolyze cellulose into
monomeric glucose units (Chang et al., 2016). Cellulases are
potentially useful in the biofuel industry because cellulose is
the most abundant energy source on Earth (Zhang and Zhang,
2013). Therefore, a chitinase with the dual capacities for
hydrolyzing chitin and cellulose could be useful for biofuel
industrial applications, but such an enzyme has not been reported. In this study, we purified Tk-ChiA expressed in the Pichia
pastoris system to investigate its secondary ability for cellulose
degradation with a focus on industrial applications. straw and is a valuable natural resource (Li et al., 2018). INTRODUCTION Approximately, 1014–1015 tons of cellulose is produced annually
in the form of raw materials derived from straw, wood,
cotton, reeds, hemp, and mulberry (Bayer et al., 1998; Zarafeta
et al., 2016). In contrast, the annual amount of chitin
production is estimated to be approximately 1010–1011 tons
(Gooday, 1990), which makes it the second most abundant
natural polymer. Chitin and cellulose degradation are excellent
potential sources of biofuel, so industrial utilization of chitin
and cellulose has become a popular area of research aimed
at solving the problems of increasing energy costs, pollution,
and global warming (Wan et al., 2011; Fan et al., 2013). Enzymatic degradation of chitin and cellulose is preferred
over other methods because of its lack of environmental
impact (Zhang et al., 2012). Chitinase [EC3.2.1.14] enzymes have the capacity to hydrolyze
the β-1,4-linkage between GlcNAc molecules in chitin and are
expressed by bacteria, fungi, animals, plants (Adrangi and
Faramarzi, 2013; Hamid et al., 2013), and archaea (Huber et al.,
1995; Tanaka et al., 1999). Chitinases are classified into glycoside
hydrolase family 18 (GH18) and 19 (GH19) in the carbohydrate-
active enzymes (CAZy) database1 based on the amino acid
sequences of their catalytic modules (Henrissat, 1991; Levasseur
et al., 2013). GH18 chitinases always contain one catalytic
domain and several auxiliary domains, including chitin-binding
domains and an N-terminal signal peptide region (Hartl et al.,
2012). Among the domains of GH18 chitinases, the catalytic
domain is most important for chitin hydrolysis and contains
the following highly conserved motif: DXXDXDXE (Henrissat
and Bairoch, 1996). The chitin-binding domains of GH18
chitinases belong to carbohydrate binding module (CBM)
families 5, 12, 14, 18, and 50.h 1http://www.cazy.org/ 2https://tools.thermofisher.com/content/sfs/manuals/pich_man.pdf Frontiers in Microbiology | www.frontiersin.org MATERIALS AND METHODS The ability of chitinases to catalyze chitin degradation
allows the utilization of common sources of chitin, such as
shrimp shell, as energy sources in industrial applications. For the purpose of optimization of industrial processes, it
is necessary to search for chitinases with very high activity
levels under high temperature conditions, which promote
high catalytic rates (Niehaus et al., 1999; Liang et al., 2011;
Frock and Kelly, 2012; Keller et al., 2015). Thermococcus
kodakarensis KOD1 is a hyperthermophilic archaeon with a
fully sequenced genome (Fukui et al., 2005). Over the last
decade, various thermophilic enzymes from T. kodakarensis
KOD1 have been reported, including a lysophospholipase (Cui
et al., 2012), an amylopullulanase (Guan et al., 2013), a
cyclodextrinase (Sun et al., 2015), and proteases (Foophow
et al., 2010; Jia et al., 2015). As a hyperthermophilic anaerobe,
T. kodakarensis KOD1 is a potential thermophilic enzyme
source for industrial applications. Strains, Vectors, and Cultural Media
T. kodakarensis KOD1, which was kindly donated by the Japan
Collection of Microorganisms, RIKEN BioResource Center,
Japan, was used to isolate genomic DNA. T. kodakarensis KOD1
was cultured in 280 Thermococcus medium (Fukui et al., 2005). P. pastoris GS115 and pPIC9K plasmid were used as the host
and expression vector, respectively. The vector pPIC9K2, contains
α-factor signal peptide sequence and a strong promoter
controlling recombinant gene expression, the methanol-inducible
alcohol oxidase gene (AOX1). Cloning, Expression, and Purification of
Tk-ChiA From T. kodakarensis KOD1hi Cloning, Expression, and Purification of
Tk-ChiA From T. kodakarensis KOD1
The gene encoding Tk-ChiA (Tk1765) was amplified via PCR
using DNA as the template (forward primer, 5′-CCG GAA
TTC CAT CAT CAC CAT CAC CAT CTG AAG CTT ACG
TAGA ATT CGA GAG CGT AAG CCT G-3′; reverse primer,
5′-TTG CGG CCG CGC GAA TTA ATT CGC GGC CGC
TCA AAC TGG AAC TGC AA CTG-3′). The endonuclease
sites EcoRI and NotI were introduced as underlined. The PCR
product of Tk1765 was purified with a DNA purification kit T. kodakarensis chitinase Tk-ChiA is encoded by the Tk1765
gene (Tanaka et al., 1999, 2001). Tk-ChiA is a thermostable
enzyme with an optimal temperature of 80°C, which suggests
that it could be useful for chitin degradation in high-temperature
industrial processes. Tk-ChiA consists of two GH18 catalytic
domains, as well as N-terminal and C-terminal domains that June 2019 | Volume 10 | Article 1253 Frontiers in Microbiology | www.frontiersin.org 2 The Applications of Bicatalytic Chitinase Chen et al. (TianGen, Beijing, China). The purified PCR product of Tk1765
and vector pPIC9K was digested with EcoRI and NotI, after
which they were ligated using T4 ligase (Takara, Dalian, China). The correct recombination plasmid pPIC9K-AgCMAase was
linearized using BglII and transformed into P. pastoris GS115
competent cells by electroporation. (TianGen, Beijing, China). The purified PCR product of Tk1765
and vector pPIC9K was digested with EcoRI and NotI, after
which they were ligated using T4 ligase (Takara, Dalian, China). The correct recombination plasmid pPIC9K-AgCMAase was
linearized using BglII and transformed into P. pastoris GS115
competent cells by electroporation. 0.6% (w/v) substrates dissolved in 50 mM citrate-phosphate
buffer (pH 8.0) in a final volume of 0.25 ml, which was
incubated at the optimum reaction temperature for 1 h. The
reaction was stopped by the addition of 0.25 ml DNS. The
treated sample was boiled for 10 min, the color was allowed
to stabilize, and the absorbance was measured at 540 nm. The enzymatic activity was calculated from a calibration
curve constructed using glucose as a standard. One unit of
enzyme activity was defined as the amount of enzyme required
to release 1 mM of reducing sugars from the substrate
per minute. His+ transformants were recovered on MD plates at 30°C
for 3 or 4 days (until single colonies appeared) and placed
into shaking tubes for enzyme production according to the
protocol described in the Pichia manual3. SDS-PAGE and Zymogram Analysishit The purified AgCMCase was visualized after separation by 7%
sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-
PAGE). The protein concentration was measured using a Protein
Assay Kit (Bio-Rad, Hercules, CA, USA). Statistical Experimental Designs p
g
Reaction time (X1), temperature (X2), pH (X3), and enzyme
dosage (X4) were selected as important factors influencing
enzyme activity, and their effects on reducing sugar production
were evaluated using an experiment with a Box-Behnken
factorial design (BBD). All factors were tested at three levels
(Table 1). The results are described using the following equation: 3https://tools.thermofisher.com/content/sfs/manuals/pich_man.pdf Fourier Transform Infrared
Spectroscopy (FT-IR) According to previously described methods (Li et al., 2012;
Li and Yu, 2013a), zymogram analysis was performed by using
a 0.1% CMC-Na (w/v) incorporated into the 7% polyacrylamide
gel. The CMC-Na was pre-mixed with polyacrylamide during
gel preparation. After electrophoresis, the gel was washed 3
times for 30 min in renaturation buffer (50 mM sodium
phosphate buffer, pH 7.0). Then it was left in reaction buffer
containing 50 mM Tris-HCl (pH 7.0) at 65°C for 1 h. The
enzyme band was visualized by staining with 1% (w/v) Congo
red (Lee et al., 2014). The samples of shrimp shell and rice straw were freeze-dried,
smashed into a powder, and mixed with potassium bromide
(1:200). The infrared spectrum of the prepared samples was
recorded by FT-IR (Thermo Nicolet NEXUS 670, USA) between
4,500 and 500 cm−1. Cloning, Expression, and Purification of
Tk-ChiA From T. kodakarensis KOD1hi The recombinant
P. pastoris GS115 containing pPIC9K-Tk1765 was grown at
30°C in 250 ml BMGY medium in a 1-L shaking flask until
the cell density reached an OD600 of 4.0. Cells were collected,
re-suspended in 50 ml BMMY medium with 0.5% (v/v) methanol,
and cultured at 25°C for 3 days with shaking (250 rpm).h The effect of pH on the CMC-Na hydrolysis activity of
purified Tk-ChiA was determined using the DNS method
described above. The reaction was carried out for 30 min at
65°C in buffers with various pH levels (4.0–13.0). The buffers
used in this experiment are shown in Supplementary Table S1. The optimal temperature for CMC-Na degradation by Tk-ChiA
was determined by testing temperatures ranging from 30 to
90°C for 30 min. All assays were performed at the optimal
pH. Thermostability was determined by measuring the residual
enzyme activity level after pre-incubation at 70, 80, 90, and
100°C for varying periods of time without a substrate. After
various time intervals, samples were withdrawn, and the
enzymatic activity of the sample was measured under optimal
reaction conditions. The fermentation broth was centrifuged at 5,000 × g for
10 min and the supernatant was collected. First, the supernatant
was concentrated ∼5-folds using lysis buffer containing 50 mM
Tris-HCl (pH 8.0), 300 mM NaCl, 20 mM 2-mercaptoethanol
by ultrafiltration in a Vivaflow 20 ultrafiltration membrane
(50 kDa cut off; Sartorius Stedim Biotech, Germany). The
concentrated supernantant was loaded onto a Ni2+-NTA column. After washing the column with lysis buffer, a linear gradient
of imidazole (5–500 mM) in the lysis buffer was used to elute
the proteins. Fractions having chitinase and cellulose activity
were pooled and desalted using 0.2 M sodium acetate buffer
(pH 5.0) via dialysis. Scanning Electron Microscopy (SEM)
SEM was conducted at magnification 15,009 for both native
and enzymatic treatment samples (shrimp shell and rice straw)
using a JEOLJSM-7500 scanning electron microscope. June 2019 | Volume 10 | Article 1253 Frontiers in Microbiology | www.frontiersin.org Enzymatic Activity Assayhi The purified enzyme was used to characterize the properties
of Tk-ChiA. The activity of the enzyme was measured using
chitosan, sodium carboxymethyl cellulose (CMC-Na), pullulan,
starch α-glucan from barley and Avicel as substrates. The
enzymatic activity of Tk-ChiA was assessed by the
3,5-dinitrosalicylic acid (DNS, DingGuo, Beijing, China)
method (Miller, 1959) to measure the amount of reducing
sugars released from substrates. The reaction was conducted
in a mixture of appropriately diluted enzyme solution and June 2019 | Volume 10 | Article 1253
TABLE 1 | Experimental design. Levels
Factors
−1
0
1
X1 – time (h)
3
4
5
X2 – temperature (°C)
60
70
80
X3 – pH
7
8
9
X4 – enzyme dosage (ml)
1.5
2
2.5 Frontiers in Microbiology | www.frontiersin.org 3 The Applications of Bicatalytic Chitinase Chen et al. Y
X
X
X
X
X
X
=
+
+
+
+
+
+
b
b
b
b
b
b
b
0
1
1
2
2
3
3
4
4
11
1
2
22
2
2 Y
X
X
X
X
X
X
=
+
+
+
+
+
+
b
b
b
b
b
b
b
0
1
1
2
2
3
3
4
4
11
1
2
22
2
2 A
B
FIGURE 1 | SDS-PAGE (A) and zymogram (B) analysis of Tk-ChiA from
T. kodakarensis KOD1. Lane M, protein marker (GenStar, Beijing); Line 1,
crude extract of P. pastoris GS115 transformed empty plasmid (pPIC9K);
Lane 2, crude protein extract from the supernatant of the recombinant strain
transformed pPIC9K-Tk1765 plasmid; Lane 3, purified recombinant Tk-ChiA. The arrow indicates the position of Tk-ChiA. Statistical Analysis Statistical optimization was performed using Design Expert
(version 7.0, STATEASE Inc., Minneapolis, MN, USA). Data
analyses were carried out by analysis of variance (ANOVA)
using Microsoft EXCEL and GraphPad Prism 5. ANOVA was
used to determine statistically significant differences. All
experiments were performed in triplicate. Central Composite Design (CCD) CCD of response surface methodology (RSM) was used to
optimize the two factors that most significantly influenced
reducing sugar production. Each factor in the design matrix
was tested at five different levels (−1.414, −1, 0, 1, and 1.414). Thirteen runs of two variables for enhancing reducing sugar
production (Y) were conducted in this experimental design. The effects of the selected variables on the response were
calculated by the following second-order model: FIGURE 1 | SDS-PAGE (A) and zymogram (B) analysis of Tk-ChiA from
T. kodakarensis KOD1. Lane M, protein marker (GenStar, Beijing); Line 1,
crude extract of P. pastoris GS115 transformed empty plasmid (pPIC9K);
Lane 2, crude protein extract from the supernatant of the recombinant strain
transformed pPIC9K-Tk1765 plasmid; Lane 3, purified recombinant Tk-ChiA. The arrow indicates the position of Tk-ChiA. FIGURE 1 | SDS-PAGE (A) and zymogram (B) analysis of Tk-ChiA from
T. kodakarensis KOD1. Lane M, protein marker (GenStar, Beijing); Line 1,
crude extract of P. pastoris GS115 transformed empty plasmid (pPIC9K);
Lane 2, crude protein extract from the supernatant of the recombinant strain
transformed pPIC9K-Tk1765 plasmid; Lane 3, purified recombinant Tk-ChiA. The arrow indicates the position of Tk-ChiA. Y
X
X
X
X
X X
=
+
+
+
+
+
b
b
b
b
b
b
0
1
1
2
2
11
1
2
22
2
2
12
1
2
(2) (2) band at approximately 130 kD in the fermentation broth sample,
suggesting that the recombinant Tk-ChiA secreted by P. pastoris
did not need further purification. The mass of the protein
band matched the predicted molecular mass (134.27 kDa) of
Tk-ChiA. The crude Tk-ChiA enzyme was further purified
from the cell-free medium with a single-step process using a
Ni2+-NTA column, which produced a single band in lane 2
of the SDS-PAGE gel (Figure 1). where Y is the dependent variable (reducing sugar production);
β0 is the model constant; β1 and β2 are linear coefficients; β11
and β22 are squared coefficients; β12 is an interaction coefficient. Enzymatic Activity Assayhi A
B Y
X
X
X
X
X
X
X
X
X
=
+
+
+
+
+
+
+
+
+
b
b
b
b
b
b
b
b
b
b
0
1
1
2
2
3
3
4
4
11
1
2
22
2
2
33
3
2
44
4
2
12
1X
X X
X X
X X
X X
X X
2
13
1
3
14
1
4
23
2
3
24
2
4
34
3
4
+
+
+
+
+
b
b
b
b
b
(1) b
b
b
X X
X X
X
23
2
3
24
2
4
34
3
+
+
+
b
b
b
b where Y is the dependent variable (reducing sugar production);
β0 is the model constant; β1, β2, β3, and β4 are linear coefficients;
β11, β22, β33, and β44 are squared coefficients; β12, β13, β14, β23,
β24, and β34 are interaction coefficients. Secondary Cellulose Hydrolytic
Activity of Tk-ChiA Tk-ChiA possesses dual GH18 catalytic domains and triple CBDs
(Figure 2A; Supplementary Figure S1; Tanaka et al., 1999). Based on the sequence aliment of CBD2 and CBD3, they are
classed as family II cellulose binding domains, which include
four strictly conserved tryptophan residues (Din et al., 1994)
and are similar to the Butyrivibrio fibrisolvens H17c endoglucanase
cellulose binding domain (Berger et al., 1989). CBD2 and CBD3
were also expressed and purified independently to investigate
their binding capacity with several substrates (Hanazono et al.,
2016). CBD2 and CBD3 were found to bind to cellulose, suggesting
that Tk-ChiA possesses a secondary cellulose hydrolysis function. Zymographic analysis showed a significant activity band that
corresponded to Tk-ChiA (about 130 kDa) (Figure 1B). Expression and Purification of Tk-ChiA in
the P. pastoris Systemi p
y
Various methods have been tested for the identification of
functional enzyme genes, but expression assays in Escherichia
coli were found to be inefficient due to the formation of
intracellular proteins or inclusion bodies (Bayer et al., 1998;
Chang et al., 2016). P. pastoris is frequently used to express
various heterogeneous proteins, including chitinases, and has
many of the advantages of other expression systems. In addition,
P. pastoris is faster, easier, and less expensive than many other
expression systems. To study the function of Tk-ChiA, a gene
fragment (Tk1765) encoding the enzyme without the signal
peptide was expressed in the P. pastoris system (Figure 1). We selected the positive recombinant strain P. pastoris with
the highest Tk-ChiA activity that was fermented in a 1 L
flask at 30°C for 72 h with 0.5% (v/v) methanol added every
24 h. The yield of crude enzyme product and enzyme activity
reached 0.31 mg/ml and 50.49 U/ml after induction for 72 h,
respectively (Supplementary Table S6). As indicated in lane
1 of the SDS-PAGE gel, there was only one major protein To test the substrate selectivity of Tk-ChiA, various
polysaccharide substrates subjected to degradation, including
chitosan, Sodium carboxymethyl cellulose (CMC-Na), pullulan,
soluble starch, glucan, and Avicel. Corresponding to previous
studies, Tk-ChiA preferably hydrolyzed chitosan, and the chitosan
catalysis activity of Tk-ChiA was scaled to 100%. Strikingly,
Tk-ChiA also had a high level of CMC-Na hydrolysis activity
(approximately 152% compared to chitosan) (Figure 2B). Tk-ChiA
showed nearly no effect on pullulan, soluble starch, and glucan. These results show that Tk-ChiA preferably hydrolyzes the β-1,4-
linkage in chitin and cellulose. However, this enzyme has low
catalysis activity for β-1,3-1,4- linkages, such as that found in
glucan. In addition, Tk-ChiA degraded Avicel, a type of crystalline June 2019 | Volume 10 | Article 1253 Frontiers in Microbiology | www.frontiersin.org 4 The Applications of Bicatalytic Chitinase Chen et al. A
B
FIGURE 2 | Structural features of Tk-ChiA and the hydrolytic activity of the enzyme toward various substrates. (A) Domain architecture of Tk-ChiA. A putative
signal sequence and the enzyme catalytic domains (GH18_ChiA1, 2) are shown in orange and red, respectively. The chitin-binding domain (CBD1) and
chitin/cellulose-binding domains (CBD2, 3) are shown in green and purple, respectively. (B) Hydrolytic activity of Tk-ChiA for chitosan, CMC-Na, pullulan, starch,
glucan and Avicel. The experiment was conducted in triplicate. Expression and Purification of Tk-ChiA in
the P. pastoris Systemi Assays were performed as described in the section “Materials and Methods.” A B
FIGURE 2 | Structural features of Tk-ChiA and the hydrolytic activity of the enzyme toward various substrates. (A) Domain architecture of Tk-ChiA. A putative
signal sequence and the enzyme catalytic domains (GH18_ChiA1, 2) are shown in orange and red, respectively. The chitin-binding domain (CBD1) and
chitin/cellulose-binding domains (CBD2, 3) are shown in green and purple, respectively. (B) Hydrolytic activity of Tk-ChiA for chitosan, CMC-Na, pullulan, starch, B
IGURE 2 | Structural features of Tk-ChiA and the hydrolytic activity of the enzyme toward various substrates. (A) Domain architecture of Tk-ChiA. A putative
gnal sequence and the enzyme catalytic domains (GH18_ChiA1, 2) are shown in orange and red, respectively. The chitin-binding domain (CBD1) and
hiti /
ll l
bi di
d
i
(CBD2 3)
h
i
d
l
ti
l
(B) H d
l ti
ti it
f Tk ChiA f
hit
CMC N
ll l
t
h B B FIGURE 2 | Structural features of Tk-ChiA and the hydrolytic activity of the enzyme toward various substrates. (A) Domain architecture of Tk-ChiA. A putative
signal sequence and the enzyme catalytic domains (GH18_ChiA1, 2) are shown in orange and red, respectively. The chitin-binding domain (CBD1) and
chitin/cellulose-binding domains (CBD2, 3) are shown in green and purple, respectively. (B) Hydrolytic activity of Tk-ChiA for chitosan, CMC-Na, pullulan, starch,
glucan and Avicel. The experiment was conducted in triplicate. Assays were performed as described in the section “Materials and Methods.” The thermal stability of Tk-ChiA was tested by assessing
its activity level under optimal reaction conditions (65°C,
pH 7.0) after pre-incubation of the enzyme at 70–100°C for
4 h. The CMC-Na hydrolysis activity of Tk-ChiA remained
high following exposure to high temperatures (Figure 3C). After pre-incubation at 70°C for 4 h, Tk-ChiA showed nearly
full activity. After pre-incubation at 80°C for 4 h, Tk-ChiA
showed a 30% loss of activity. After pre-incubation at 100°C
for 4 h, Tk-ChiA retained more than 40% of its original activity. These results indicate that Tk-ChiA is a thermostable enzyme
that is capable of hydrolyzing cellulose and thus has potential
industrial applications under high temperature conditions. cellulose (approximately 60% activity compared to chitosan),
indicating that it has dual exo-1,4-β-glucanases and endo-1,4-
β-glucanases functions (Park et al., 2012; Li et al., 2018). Effect of Temperature and pH on Cellulose
Hydrolysis by Tk-ChiA Recombinant full-length Tk-ChiA exhibited maximal cellulose
hydrolysis activity at 65°C when CMC-Na was used as the
substrate (Figure 3A). The activity of purified Tk-ChiA was
detected from 30 to 90°C, and it remained high (>50% of
peak activity) at temperatures ranging from 40 to 70°C
(Figure 3A). Tk-ChiA showed approximately 40% of maximum
cellulose hydrolysis activity at 80°C, which was also found to
be the optimal temperature for chitin degradation (Tanaka
et al., 1999). Therefore, Tk-ChiA can efficiently hydrolyze chitin
and cellulose simultaneously.f Frontiers in Microbiology | www.frontiersin.org The Ability of Tk-ChiA to Degrade Shrimp
Shell and Rice Straw (A) After incubation of Tk-ChiA and shrimp shell at the optimal enzyme reaction conditions (pH 7.0, 65°C) for 5 h, the sample was observed by SEM with
1,000× amplification (right). The control sample was exposed to an equal volume of buffer (left). Scale bar (red), 5 μm. (B) After incubation of Tk-ChiA and rice straw
at the optimal enzyme reaction conditions (pH 7.0, 65°C) for 5 h, the sample was observed by SEM with 1,000× amplification (right). The control sample was
exposed to an equal volume of buffer (left). Scale bar (red), 5 μm. FT-IR spectra of shrimp shell (C) and rice straw (D) with enzymatic treatment (red) and without
enzymatic treatment (green). A
C
B
FIGURE 3 | Characterization of CMC-Na hydrolysis by purified Tk-ChiA. (A) Influence of temperature on Tk-ChiA activity. Enzyme activity levels at various
temperatures were assayed at pH 7.0 for 1 h using CMC-Na as the substrate. Values obtained at 65°C were set as 100%. (B) Effect of pH on Tk-ChiA activity. Enzyme activity levels at various pH values were assayed at 65°C for 1 h using CMC-Na as the substrate. Values obtained at pH 7.0 were set as 100%. (C) Thermostability of Tk-ChiA. Residual activity was assayed using CMC-Na as the substrates after pre-incubation without a substrate at 70°C (circle), 80°C
(square), 90°C (triangle), and 100°C (inverted triangle) for different periods of time. B A
C A
C
B B C C FIGURE 3 | Characterization of CMC-Na hydrolysis by purified Tk-ChiA. (A) Influence of temperature on Tk-ChiA activity. Enzyme activity levels at various
temperatures were assayed at pH 7.0 for 1 h using CMC-Na as the substrate. Values obtained at 65°C were set as 100%. (B) Effect of pH on Tk-ChiA activity. Enzyme activity levels at various pH values were assayed at 65°C for 1 h using CMC-Na as the substrate. Values obtained at pH 7.0 were set as 100%. (C) Thermostability of Tk-ChiA. Residual activity was assayed using CMC-Na as the substrates after pre-incubation without a substrate at 70°C (circle), 80°C
(square), 90°C (triangle), and 100°C (inverted triangle) for different periods of time. A
B
C
D
FIGURE 4 | Scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FT-IR) analysis of shrimp shell and rice straw incubated with
Tk-ChiA. The Ability of Tk-ChiA to Degrade Shrimp
Shell and Rice Straw Tk-ChiA is a thermostable enzyme that can hydrolyze both
chitin (Tanaka et al., 1999) and cellulose (Figure 2B). Therefore,
Tk-ChiA could be suitable for industrial applications such as
shrimp shell and straw degradation. Therefore, we incubated
Tk-ChiA with shrimp shell and rice straw under optimal
reaction conditions and assessed its effects. SEM indicated that
shrimp shell and rice straw incubated with Tk-ChiA were
obviously fractured (Figures 4A,B right) compared to shrimp
shell and rice straw incubated without the enzyme (Figures 4A,B
left). The shrimp shell incubated without Tk-ChiA had a smooth
and rigid microfibrillar crystalline surface and an intact structure. To study the effect of pH on the cellulose degradation activity
of purified Tk-ChiA, the enzyme and CMC-Na were combined
at pH values between 3.0 and 11.0 at the optimal temperature
of 65°C. The purified enzyme showed maximal activity for
hydrolyzing CMC-Na at pH 7.0 and maintained more than
90% of its maximum activity at pH 5.0–8.0 (Figure 3B). Tk-ChiA
showed low activity (40% of peak activity) at pH 11.0. The
remarkable activity level of Tk-ChiA at a relatively wide range
of pH values shows that it is suitable for cellulose degradation
applications in alkaline and acidic environments. June 2019 | Volume 10 | Article 1253 5 Chen et al. The Applications of Bicatalytic Chitinase Frontiers in Microbiology | www.frontiersin.org
6
June 2019 | Volume 10 | Article 1253
A
C
B
FIGURE 3 | Characterization of CMC-Na hydrolysis by purified Tk-ChiA. (A) Influence of temperature on Tk-ChiA activity. Enzyme activity levels at various
temperatures were assayed at pH 7.0 for 1 h using CMC-Na as the substrate. Values obtained at 65°C were set as 100%. (B) Effect of pH on Tk-ChiA activity. Enzyme activity levels at various pH values were assayed at 65°C for 1 h using CMC-Na as the substrate. Values obtained at pH 7.0 were set as 100%. (C) Thermostability of Tk-ChiA. Residual activity was assayed using CMC-Na as the substrates after pre-incubation without a substrate at 70°C (circle), 80°C
(square), 90°C (triangle), and 100°C (inverted triangle) for different periods of time. A
B
C
D
FIGURE 4 | Scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FT-IR) analysis of shrimp shell and rice straw incubated with
Tk-ChiA. The Ability of Tk-ChiA to Degrade Shrimp
Shell and Rice Straw (A) After incubation of Tk-ChiA and shrimp shell at the optimal enzyme reaction conditions (pH 7.0, 65°C) for 5 h, the sample was observed by SEM with
1,000× amplification (right). The control sample was exposed to an equal volume of buffer (left). Scale bar (red), 5 μm. (B) After incubation of Tk-ChiA and rice straw
at the optimal enzyme reaction conditions (pH 7.0, 65°C) for 5 h, the sample was observed by SEM with 1,000× amplification (right). The control sample was
exposed to an equal volume of buffer (left). Scale bar (red), 5 μm. FT-IR spectra of shrimp shell (C) and rice straw (D) with enzymatic treatment (red) and without
enzymatic treatment (green). A C D B B B D B FIGURE 4 | Scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FT-IR) analysis of shrimp shell and rice straw incubated with
Tk-ChiA. (A) After incubation of Tk-ChiA and shrimp shell at the optimal enzyme reaction conditions (pH 7.0, 65°C) for 5 h, the sample was observed by SEM with
1,000× amplification (right). The control sample was exposed to an equal volume of buffer (left). Scale bar (red), 5 μm. (B) After incubation of Tk-ChiA and rice straw
at the optimal enzyme reaction conditions (pH 7.0, 65°C) for 5 h, the sample was observed by SEM with 1,000× amplification (right). The control sample was
exposed to an equal volume of buffer (left). Scale bar (red), 5 μm. FT-IR spectra of shrimp shell (C) and rice straw (D) with enzymatic treatment (red) and without
enzymatic treatment (green). June 2019 | Volume 10 | Article 1253 Frontiers in Microbiology | www.frontiersin.org Frontiers in Microbiology | www.frontiersin.org 6 The Applications of Bicatalytic Chitinase Chen et al. TABLE 2 | Results of the fractional factorial design matrix of rice straw
degradation. The Ability of Tk-ChiA to Degrade Shrimp
Shell and Rice Straw (3) (3) where Y is the yield rate of reducing sugar released from
hydrolysis of rice straw by Tk-ChiA.h y
y
y
The suitability of the model was assessed by calculating
several parameters (p, F-values, R2, lack of fit, and pure error)
as shown in Supplementary Table S2. The R2 of the model
was 0.88, meaning that approximately 88% of the variability
in the response was explained by the model. An R2 between
0.75 and 1 indicates that the model has good accuracy (Moon
et al., 2011). We used p to estimate the significance of the
effect of each factor and the interactions between each
independent variable. Based on the regression analysis
(Supplementary Table S2), the linear coefficients, reaction time
(X1) and temperature (X2) and the quadratic coefficients, X1
2
was extremely significant (p < 0.001) and the interaction between
time and temperature, X1X2, was significant (0.001 < p < 0.05). These results indicate that reaction time and temperature were
the main factors affecting rice straw degradation by Tk-ChiA. In addition, we also analyzed the effects of reaction time
(X1), temperature (X2), pH (X3), and enzyme dosage (X4) on
shrimp shell degradation by Tk-ChiA via orthogonal experimental
designs (Supplementary Table S3). The range analysis indicated The Ability of Tk-ChiA to Degrade Shrimp
Shell and Rice Straw Running
number
X1
X2
X3
X4
Reducing
sugar yield (%)
1
0
0
1
−1
1.71
2
1
−1
0
0
1.28
3
0
0
0
0
1.43
4
−1
−1
0
0
1.23
5
0
0
0
0
1.7
6
0
0
−1
1
1.78
7
0
1
0
−1
1.66
8
1
0
−1
0
1.53
9
0
−1
−1
0
1.62
10
0
−1
1
0
1.33
11
−1
0
−1
0
0.83
12
−1
0
1
0
1.08
13
0
0
0
0
1.74
14
0
0
0
0
1.69
15
0
1
0
1
1.79
16
1
0
0
1
1.81
17
0
0
0
0
1.71
18
0
−1
0
−1
1.09
19
−1
1
0
0
1.13
20
−1
0
0
−1
0.89
21
0
1
1
0
1.75
22
1
1
0
0
1.96
23
0
−1
0
1
1.36
24
1
0
1
0
1.66
25
0
1
−1
0
1.78
26
0
0
1
1
1.76
27
1
0
0
−1
1.47
28
0
0
−1
−1
1.58
29
−1
0
0
1
0.94 TABLE 2 | Results of the fractional factorial design matrix of rice straw
degradation. In contrast, shrimp shell incubated with Tk-ChiA showed
perforations and anomalous morphology (Figure 4A). The
surface of rice straw that was not exposed to Tk-ChiA was
smooth, uniform, and highly ordered. However, the structure
of rice straw treated with Tk-ChiA was uneven, unsmooth,
rough, and rugged (Figure 4B). These results demonstrate that
both shrimp shell and rice straw can be degraded by Tk-ChiA.h p
g
y
The ability of Tk-ChiA to hydrolyze shrimp shell and rice
straw was confirmed by FT-IR analysis. FT-IR spectroscopy
was used to assess changes in the functional groups and
structure of shrimp shell chitin and rice straw cellulose after
Tk-ChiA treatment compared to untreated substrates. The FT-IR
spectra of chitin were characterized by three significant amide
bands at 1,658, 1,546, and 1,315 cm−1, which correspond to
amide Ι (C═O stretching), amide ΙΙ (─NH2 stretching) and
amide ΙΙΙ (C─N stretching), respectively (Liu et al., 2012). The band at 3433 cm−1 corresponded to O─H stretching. The
band located at 1020 cm−1 between 890 and 1,156 cm−1
corresponded to C─O─C stretching of the β-glyosidic bond
in chitin (Povea et al., 2011). These characteristic absorption
peaks diminished after enzymatic treatment (Figure 4C),
indicating that chitin was degraded by Tk-ChiA. Frontiers in Microbiology | www.frontiersin.org The Ability of Tk-ChiA to Degrade Shrimp
Shell and Rice Straw The peak of CH2 stretching located near 2,900 cm−1 and
the peak of ─OH stretching located near 3,400 cm−1 are
distinguishing features of cellulose (Sun et al., 2007) that indicate
its most important functional groups. The peak at 3420 cm−1
that corresponded to the stretching of ─OH groups was
attenuated after Tk-ChiA treatment (Figure 4D), suggesting
that the partial hydrogen bond of cellulose was destroyed. The
peak located at 2917 cm−1 that corresponded to the CH2
stretching decreased in intensity, indicating that the methyl
and methylene groups of cellulose were broken (He et al.,
2008). The peaks located at 900–1,100 cm−1 corresponded to
C─O─C stretching at the β-1,4-glycosidic linkages (Hinterstoisser
et al., 2001; Cao and Tan, 2004; He et al., 2008). The peak
located at 1405 cm−1 was diminished after incubation with
Tk-ChiA (Figure 4D), suggesting that the β-1,4-glycosidic
linkages in rice straw cellulose were hydrolyzed. Y
X
X
X
X
X X
X X
=
+
+
+
+
+
-
+
1 65
0 30
0 18
0 014
0 087
0 19
0 030
0
1
2
3
4
1
2
1
3
. . . . . . . .073
0 065
0 035
0 037
0 31
0 039
0
1
4
2
3
2
4
3
4
1
2
2
2
X X
X X
X X
X X
X
X
+
-
-
-
-
+
. . . . . .015
0 056
3
2
4
2
X
X
- . (3) Y
X
X
X
X
X X
X X
=
+
+
+
+
+
-
+
1 65
0 30
0 18
0 014
0 087
0 19
0 030
0
1
2
3
4
1
2
1
3
. . . . . . . .073
0 065
0 035
0 037
0 31
0 039
0
1
4
2
3
2
4
3
4
1
2
2
2
X X
X X
X X
X X
X
X
+
-
-
-
-
+
. . . . . .015
0 056
3
2
4
2
X
X
- . Optimal Level of Variables for Enhancing
Rice Degradation Reaction time (X1) and temperature (X2) are the main factors
affecting rice straw degradation by Tk-ChiA. These two main
effects (X1 and X2) were further optimized by central composite
design (CCD) of response surface methodology (RSM). The
levels for the variables (time and temperature) are listed in
Table 3, and 13 runs designed via CCD were conducted
(Table 4). The response optimized via CCD was estimated by
the following second-order model: Y
X
X
X X
X
X
=
+
+
-
-
-
1 66
0 19
0 21
0 04
0 057
0 17
1
2
1
2
12
22
. . . . . . (4) (4) FIGURE 5 | Response surface plot of reducing sugar released by rice straw
as a function of time and temperature. where Y is the yield rate of reducing sugar released from rice
straw by Tk-ChiA hydrolysis. The results of the analysis of
variance for the response surface quadratic model are listed
in Supplementary Table S5. The R2 of the model was 0.89,
meaning that approximately 89% of the variability in the
response was explained by the model. The F-value was 11.88,
while the p was 0.0026, suggesting that the test model is a
highly significant model of the reducing sugar yield rate. In addition, the effects of X1, X2, and X22 were significant
based on their p (Supplementary Table S5).h The interactions between X1 and X2 were also plotted on a
response surface diagram (Figure 5), while other factors were
maintained at a moderate (0) level to determine the optimum
levels of X1 and X2 for the maximum response. As shown in
Figure 5, reducing sugar production increased rapidly as the
reaction time increased when the temperature was low, while
it increased only slightly when the temperature was high. This
effect corresponded to a loss of enzyme activity at high
temperatures. However, the reducing sugar yield increased very
rapidly when the temperature range was limited (<0.50 level). Reducing sugar production decreased at a high (>0.50) reaction
temperatures (Figure 5), indicating that the enzyme lost activity
at high temperatures. These findings suggest that the reducing
sugar yield can be maximized by selecting an appropriate reaction
time and temperature. The optimized values for the reaction
time and temperature were determined by the model as follows:
X1 (reaction time) = 5 h, X2 (temperature) = 65.4°C. Reaction Time and Temperature
Are the Main Factors Affecting Reducing
Sugar Production Straw and shell wastes are abundant sources of substrates that
are suitable for degradation by Tk-ChiA to release reducing
sugar. Statistical tests (Mabilia et al., 2010; Zhang and Jia,
2018) were used to study the effects of different reaction
parameters on reducing sugar production. First, three levels
of reaction time (X1), temperature (X2), pH (X3), and enzyme
dosage (X4) were selected (Table 1). To evaluate the effects
of these four factors and identify the main factors influencing
the release of reducing sugar rice straw degradation, a Box–
Behnken factorial design experiment was performed. Twenty-
nine runs were conducted to analyze the effects of the four
variables on rice straw degradation to release reducing sugar. The results of this analysis are shown in Table 2. A model
was obtained by regression analysis as follows: f
In addition, we also analyzed the effects of reaction time
(X1), temperature (X2), pH (X3), and enzyme dosage (X4) on
shrimp shell degradation by Tk-ChiA via orthogonal experimental
designs (Supplementary Table S3). The range analysis indicated June 2019 | Volume 10 | Article 1253 7 Chen et al. The Applications of Bicatalytic Chitinase FIGURE 5 | Response surface plot of reducing sugar released by rice straw
as a function of time and temperature. that reducing sugar production showed large variation under
different levels X1. We further analyzed the F-values and F
critical values to identify the main factors affecting shell
degradation. The F-value of X1 (11.669) is larger than its F
critical value (6.940), suggesting that the effect of X1 is significant
(Supplementary Table S4). Therefore, reaction time was
the most important factor affecting shrimp shell hydrolysis
by Tk-ChiA. Optimal Level of Variables for Enhancing
Rice Degradation The
maximum predicted reducing sugar production (Y) was 1.68%. Frontiers in Microbiology | www frontiersin org
8
TABLE 3 | Range and levels of variables for CCD. Factors
Levels
−1.414
−1
0
1
1.414
X1 – time (h)
2.6
3
4
5
5.4
X2 – temperature (°C)
54
60
70
80
84
TABLE 4 | Experimental design and results of CCD. Running number
X1
X2
Reducing sugar
yield (%)
1
1
1
1.94
2
0
0
1.57
3
−1.414
0
1.32
4
−1
−1
0.88
5
0
0
1.57
6
−1
1
1.53
7
0
0
1.69
8
0
1.414
1.47
9
0
0
1.71
10
1
−1
1.45
11
0
−1.414
1.11
12
1.414
0
1.72
13
0
0
1.74 F
i
i Mi
bi l
|
f
i
i
8
TABLE 3 | Range and levels of variables for CCD. Factors
Levels
−1.414
−1
0
1
1.414
X1 – time (h)
2.6
3
4
5
5.4
X2 – temperature (°C)
54
60
70
80
84
TABLE 4 | Experimental design and results of CCD. Running number
X1
X2
Reducing sugar
yield (%)
1
1
1
1.94
2
0
0
1.57
3
−1.414
0
1.32
4
−1
−1
0.88
5
0
0
1.57
6
−1
1
1.53
7
0
0
1.69
8
0
1.414
1.47
9
0
0
1.71
10
1
−1
1.45
11
0
−1.414
1.11
12
1.414
0
1.72
13
0
0
1.74 TABLE 3 | Range and levels of variables for CCD. Frontiers in Microbiology | www.frontiersin.org DISCUSSION Cellulases for degradation of cellulose have been reported in
all three domains of life including eukaryote, prokaryote and
archaea (Cabrera and Blamey, 2018). However, genes encoding
cellulase are absent in T. kodakarensis, suggesting that
T. kodakarensis cells need other sugars except cellulose degradation
as carbon source to grow (Fukui et al., 2005). Based on the
former researches, there are two hypothesized sugar degradation
pathway of T. kodakarensis: (1) α-amylase (TK1884) (Tachibana June 2019 | Volume 10 | Article 1253 8 The Applications of Bicatalytic Chitinase Chen et al. et al., 1996) and two extracellular pullulanases (Tk0977 and
Tk1774) (Han et al., 2013; Sun et al., 2015) from T. kodakarensis
KOD1 were characterized. These enzymes can cleave α-1,4 and
α-1,6 bonds of α-linked glucans and the hydrolytic products
might be transported by an ABC type transport system and
further enter into the glycolytic pathway. (2) The unique
extracellular chitinase (Tk1765) (Tanaka et al., 1999, 2001; Aslam
et al., 2017), N-acetylchitobiose deacetylase (TK1764) (Tanaka
et al., 2004), exo-β-d-glucosaminidase (TK1754) (Tanaka et al.,
2003), and the glucosamine-6-phosphate deaminase (TK1755)
(Tanaka et al., 2005) were also characterized previously. Tk-CheA
degraded chitin into the disaccharide N-,N = -diacetylchitobiose
(GlcNAc)2 at outside of the cell, and (GlcNAc)2 is then
hypothesized to be transported into cytoplasm of cell by an
ABC type transport system. These enzymes form a novel
chitinolytic pathway for chitin degradation and assimilation
(Aslam et al., 2017). As cellulose is the most abundant polymer
on earth, it is an excellent carbon source for microorganism
growth. Actually, cellulases are frequently present in thermophilic
archaea, such as Pyrococcus (Ando et al., 2002; Nakahira et al.,
2013; Kataoka and Ishikawa, 2014; Kishishita et al., 2015) and
Thermoproteus (Mardanov et al., 2011). Cellulases were also
reported
in
the
thermoacidophilic
archaea
Acidilobus
saccharovorans (Mardanov et al., 2010), Sulfolobus solfataricus
(Huang et al., 2005), and in the haloalkaliphilic archaeon
Haloarcula (Shin et al., 2013; Li and Yu, 2013b). It is a keeping
question why cellulase is absent in T. kodakaraensis. of chitin binding domains (CBD2 and CBD3). The secondary
capacity of Tk-ChiA probably makes T. kodakarensis also utilizing
cellulose as carbon source to compensate for the absence of
cellulase in the species. DISCUSSION The biochemical properties of the
individual catalytic domains (Tk-ChiA1 and Tk-ChiA2)
hydrolyzing chitin were studied in detail and showed that the
amino-terminal domain catalyzes an exo-type cleavage of the
chitin chain, while the carboxy-terminal domain catalyzes an
endo-type cleavage of the chitin chain (Tanaka et al., 2001). The activity of Tk-ChiA1 and Tk-ChiA2 without binding domain
decreased apparently, indicating the important role of binding
domains. We will study the cellulose degradation activity of
each catalytic and binding domain combinations to investigate
how Tk-ChiA catalyzes cellulose in the future. y
The purified Tk-ChiA showed cellulose hydrolysis activity
within a wide range of high temperatures (50–80°C), and its
optimal cellulose catalytic temperature was 65°C (Figure 3A),
which was lower than its optimal chitin catalytic temperature
(80°C). Tk-ChiA showed nearly 100% of its maximum cellulose
hydrolysis activity after pre-incubation at 70°C for 4 h, and
it showed more than 40% of its maximum activity after
pre-incubation at 100°C for 4 h (Figure 3C). The effect of
high temperatures on cellulose hydrolysis by Tk-ChiA is similar
to the effect of high temperatures on chitin degradation by
Tk-ChiA (Tanaka et al., 2001). Industrial enzymatic processes
such as saccharification are generally performed at high
temperatures
for
high
efficiency
(Nigam,
2013). The
thermostability and dual catalytic ability of Tk-ChiA provide
advantages in industrial applications such as shrimp shell and
rice straw degradation. The P. pastoris system was selected to
express Tk-ChiA due to its advantages over other systems. The only major protein band detected in the supernatant of
the fermentation broth of the yeast carrying the Tk-ChiA
expression vector was Tk-ChiA (Figure 1). In addition, the
specific activity of crude enzyme and purified enzyme are
similar, suggesting that this enzyme did not need further
purification. Enzyme purification is expensive, so this finding
also indicates an advantage of Tk-ChiA in industrial applications. y
The chitinase from the hyperthermophilic archaeon
T. kodakarensis KOD1 (Tk-ChiA) is known to be capable of
chitin hydrolysis (Tanaka et al., 1999, 2001; Aslam et al., 2017). Tk-ChiA possesses three binding domains that are considered
to bind to chitin. The identical sequences of Tk-ChiA binding
domains CBD2 and CBD3 are similar to the sequence of family
II cellulose-binding domains (Tanaka et al., 1999) from various
cellulases and chitinases (Tomme et al., 1998). CBD2 and CBD3
are known to be capable of binding chitin and cellulose
(Hanazono et al., 2016). Frontiers in Microbiology | www.frontiersin.org REFERENCES by phosphotungstic acid. Carbohydr. Polym. 94, 1–76. doi: 10.1016/j. carbpol.2013.01.073 by phosphotungstic acid. Carbohydr. Polym. 94, 1–76. doi: 10.1016/j. carbpol.2013.01.073 Adrangi, S., and Faramarzi, M. A. (2013). From bacteria to human: a journey
into the world of chitinases. Biotechnol. Adv. 31, 1786–1795. doi: 10.1016/j. biotechadv.2013.09.012 Foophow, T., Tanaka, S.-I., Koga, Y., Takano, K., and Kanaya, S. (2010). Subtilisin-
like serine protease from hyperthermophilic archaeon Thermococcus
kodakaraensis with N-and C-terminal propeptides. Protein Eng. Des. Sel. 23, 347–355. doi: 10.1093/protein/gzp092 Ando, S., Ishida, H., Kosugi, Y., and Ishikawa, K. (2002). Hyperthermostable
endoglucanase from Pyrococcus horikoshii. Appl. Environ. Microbiol. 68,
430–433. doi: 10.1128/AEM.68.1.430-433.2002 Frock, A. D., and Kelly, R. M. (2012). Extreme thermophiles: moving beyond
single-enzyme biocatalysis. Curr. Opin. Chem. Eng. 1, 363–372. doi: 10.1016/j. coche.2012.07.003 Aslam, M., Horiuchi, A., Simons, J.-R., Jha, S., Yamada, M., Odani, T., et al. (2017). Engineering of a hyperthermophilic archaeon, Thermococcus
kodakarensis, that displays chitin-dependent hydrogen production. Appl. Environ. Microbiol. 83, 00280–00217. doi: 10.1002/mdc3.12530 Fukui, T., Atomi, H., Kanai, T., Matsumi, R., Fujiwara, S., and Imanaka, T. (2005). Complete genome sequence of the hyperthermophilic archaeon
Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res. 15, 352–363. doi: 10.1101/gr.3003105 Bayer, E. A., Shimon, L. J., Shoham, Y., and Lamed, R. (1998). Cellulosomes—
structure and ultrastructure. J. Struct. Biol. 124, 221–234. doi: 10.1006/
jsbi.1998.4065 Gao, J., Bauer, M. W., Shockley, K. R., Pysz, M. A., and Kelly, R. M. (2003). Growth of hyperthermophilic archaeon Pyrococcus furiosus on chitin involves
two family 18 chitinases. Appl. Environ. Microbiol. 69, 3119–3128. doi:
10.1128/AEM.69.6.3119-3128.2003f Berger, E., Jones, W. A., Jones, D. T., and Woods, D. R. (1989). Cloning and
sequencing of an endoglucanase (end1) gene from Butyrivibrio fibrisolvens
H17c. Mol. Gen. Genet. MGG 219, 193–198. doi: 10.1007/BF00261176 Gooday, D. J. (1990). Retinal axons inXenopus laevis recognise differences
between tectal and diencephalic glial cells in vitro. Cell Tissue Res. 259,
595–598. doi: 10.1007/BF01740788 Biswas, A., Saha, B. C., Lawton, J. W., Shogren, R., and Willett, J. (2006). Process for obtaining cellulose acetate from agricultural by-products. Carbohydr. Polym. 64, 134–137. doi: 10.1016/j.carbpol.2005.11.002 Guan, Q., Guo, X., Han, T., Wei, M., Jin, M., Zeng, F., et al. (2013). Cloning,
purification and biochemical characterisation of an organic solvent-, detergent-,
and thermo-stable amylopullulanase from Thermococcus kodakarensis KOD1. Process Biochem. 48, 878–884. doi: 10.1016/j.procbio.2013.04.007 Cabrera, M. Á., and Blamey, J. M. (2018). Biotechnological applications of
archaeal enzymes from extreme environments. Biol. Res. 51:37. No datasets were generated or analyzed for this study. No datasets were generated or analyzed for this study. No datasets were generated or analyzed for this study. FUNDING This work was financially supported by the National Natural
Science Foundation of China (NSFC: 31671972, 31670141) and
a project of the Ministry of Science and Technology of China
(grant no. 2016YFD0300703). ZL was supported by a fellowship
from the China Scholarship Council (CSC). In conclusion, the thermostable enzyme Tk-ChiA has dual
catalytic functions in cellulose and chitin degradation and is
thus suitable for shell and straw degradation in industrial
applications. CCD of RSM is a valuable strategy that can be utilized
to enhance rice straw degradation to release reducing sugar. DISCUSSION Using the optimized reaction parameters
reported here, Tk-ChiA could be utilized for cost-efficient rice
straw degradation in industrial applications. (Table 4, Figure 5). Using the optimized reaction parameters
reported here, Tk-ChiA could be utilized for cost-efficient rice
straw degradation in industrial applications. AUTHOR CONTRIBUTIONS The Supplementary Material for this article can be found online
at: https://www.frontiersin.org/articles/10.3389/fmicb.2019.01253/
full#supplementary-material ZL and S-HZ designed the research. LC and ZL performed
research and interpreted data. MS and YW supported the
experiments. ZL wrote the paper. DISCUSSION However, it is unknown whether
Tk-ChiA catalyzes cellulose degradation. In this study,
we expressed Tk-ChiA in P. pastoris and purified the enzyme. Purified Tk-ChiA was capable of degrading CMC-Na
(Figures 1B, 2B), which corresponded to its ability to bind
cellulose. However, it is unclear why the enzyme, Tk-ChiA,
possesses the capacity to catalyze two different substrates. Shell and straw are abundant wastes. For example, shrimp
shells are discarded as rubbish and large amounts of rice straw
are left on the field and burned off after harvest, causing
environmental problems. However, shrimp shell and rice straw
contain abundant chitin (Zhang et al., 2012) and cellulose (Fan
et al., 2013), respectively, which can serve as low-cost feedstocks
for the production of fuel ethanol (Biswas et al., 2006). Therefore,
nonuse of these wastes results in a loss of a potentially valuable
source of energy (Mishra and Sen, 2011). With recent
developments in fermentation technology, environmentally
friendly processes such as enzymatic chitin and cellulose
degradation have attracted significant interest. Shrimp shell and
rice straw were obviously degraded by Tk-ChiA according to
our SEM and FT-IR analyses (Figure 4). Reaction time and
temperature were determined to be the major factors affecting
degradation of shrimp shell and rice straw by Tk-ChiA to
release reducing sugar (Table 2; Supplementary Tables S2–S4). Therefore, these factors were optimized by CCD of RSM to
maximize the rate of reducing sugar production by Tk-ChiA f
Tk-ChiA is composed of dual catalytic domains on a single
polypeptide. Both catalytic regions were classified in family 18
of glycosyl hydrolases via alignment of amino acid sequence
(Tanaka et al., 1999). In P. furiosus, two chitinases (WP_011012376
and WP_011012377) were found and are homologous to the
first and second catalytic domain of TK-ChiA, respectively (Oku
and Ishikawa, 2006; Kreuzer et al., 2013). These two putative
chitinase genes were expressed in E. coli and products were
clearly identified to show chitinase activity (Gao et al., 2003;
Oku and Ishikawa, 2006). In addition, the blast result of the
sequence of TK-ChiA did not show similarity to catalytic domain
of cellulase (data unshown). However, Tk-ChiA also showed
cellulase activity in our studies. We hypothesized that Tk-ChiA
evolved the secondary catalytic activity relying on its structure Frontiers in Microbiology | www.frontiersin.org June 2019 | Volume 10 | Article 1253 9 The Applications of Bicatalytic Chitinase Chen et al. (Table 4, Figure 5). DATA AVAILABILITY We thank Dr. Tessa Quax for help with English improvement
and valuable advice for this paper. REFERENCES (2013). Overproduction of hyperthermostable β-1, 4-endoglucanase from the archaeon
Pyrococcus horikoshii by tobacco chloroplast engineering. Biosci. Biotechnol. Biochem. 77, 2140–2143. doi: 10.1271/bbb.130413 Keller, M. W., Lipscomb, G. L., Loder, A. J., Schut, G. J., Kelly, R. M., and
Adams, M. W. W. (2015). A hybrid synthetic pathway for butanol production
by a hyperthermophilic microbe. Metab. Eng. 27, 101–106. doi: 10.1016/j. ymben.2014.11.004 Niehaus, F., Bertoldo, C., Kähler, M., and Antranikian, G. (1999). Extremophiles
as a source of novel enzymes for industrial application. Appl. Microbiol. Biotechnol. 51, 711–729. doi: 10.1007/s002530051456 Nigam, P. S. (2013). Microbial enzymes with special characteristics for
biotechnological applications. Biomol. Ther. 3, 597–611. doi: 10.3390/
biom3030597 Kishishita, S., Fujii, T., and Ishikawa, K. (2015). Heterologous expression of
hyperthermophilic cellulases of archaea Pyrococcus sp. by fungus Talaromyces
cellulolyticus. J. Ind. Microbiol. Biotechnol. 42, 137–141. doi: 10.1007/
s10295-014-1532-2 Oku, T., and Ishikawa, K. (2006). Analysis of the hyperthermophilic chitinase
from Pyrococcus furiosus: activity toward crystalline chitin. Biosci. Biotechnol. Biochem. 70, 1696–1701. doi: 10.1271/bbb.60031 Kreuzer, M., Schmutzler, K., Waege, I., Thomm, M., and Hausner, W. (2013). Genetic engineering of Pyrococcus furiosus to use chitin as a carbon source. BMC Biotechnol. 13:9. doi: 10.1186/1472-6750-13-9 Park, I. H., Chang, J., Lee, Y. S., Fang, S. J., and Choi, Y. L. (2012). Gene
cloning of endoglucanase Cel5A from cellulose-degrading Paenibacillus
xylanilyticus KJ-03 and purification and characterization of the recombinant
enzyme. Protein J. 31, 238–245. doi: 10.1007/s10930-012-9396-7 Lee, C.-M., Lee, Y.-S., Seo, S.-H., Yoon, S.-H., Kim, S.-J., Hahn, B.-S., et al. (2014). Screening and characterization of a novel cellulase gene from the
gut microflora of Hermetia illucens using metagenomic library. J. Microbiol. Biotechnol. 24, 1196–1206. doi: 10.4014/jmb.1405.05001 Povea, M. B., Monal, W. A., Cauich-Rodríguez, J. V., Pat, A. M., Rivero, N. B.,
and Covas, C. P. (2011). Interpenetrated chitosan-poly (acrylic acid-co-
acrylamide) hydrogels. Synthesis, characterization and sustained protein
release studies. Mater. Sci. Appl. 2, 509–520. doi: 10.4236/msa.2011.26069 Levasseur, A., Drula, E., Lombard, V., Coutinho, P. M., and Henrissat, B. (2013). Expansion of the enzymatic repertoire of the CAZy database to integrate
auxiliary redox enzymes. Biotechnol. Biofuels 6:41. doi: 10.1186/1754-6834-6-41h Shin, K.-C., Nam, H.-K., and Oh, D.-K. (2013). Hydrolysis of flavanone glycosides
by β-glucosidase from Pyrococcus furiosus and its application to the production
of flavanone aglycones from citrus extracts. J. Agric. Food Chem. 61,
11532–11540. doi: 10.1021/jf403332e Li, Z., Pei, X., Zhang, Z., Wei, Y., Song, Y., Chen, L., et al. (2018). REFERENCES doi: 10.1042/bj2800309i precision of a new passive sampler for the determination of formaldehyde
in the atmosphere. Atmos. Environ. 44, 3942–3951. doi: 10.1016/j. atmosenv.2010.07.013 Henrissat, B., and Bairoch, A. (1996). Updating the sequence-based classification
of glycosyl hydrolases. Biochem. J. 316, 695–696. doi: 10.1042/bj3160695fi Mardanov, A. V., Gumerov, V. M., Beletsky, A. V., Prokofeva, M. I., Bonch-
Osmolovskaya, E. A., Ravin, N. V., et al. (2011). Complete genome sequence
of the thermoacidophilic crenarchaeon Thermoproteus uzoniensis 768-20. Am. Soc. Microbiol. 193, 3156–3157. doi: 10.1128/JB.00409-11 Hinterstoisser, B., Åkerholm, M., and Salmén, L. (2001). Effect of fiber orientation
in dynamic FTIR study on native cellulose. Carbohydr. Res. 334, 27–37. doi: 10.1016/S0008-6215(01)00167-7 Huang, Y., Krauss, G., Cottaz, S., Driguez, H., and Lipps, G. (2005). A highly
acid-stable and thermostable endo-β-glucanase from the thermoacidophilic
archaeon Sulfolobus solfataricus. Biochem. J. 385, 581–588. doi: 10.1042/
BJ20041388 Mardanov, A. V., Svetlitchnyi, V. A., Beletsky, A. V., Prokofeva, M. I., Bonch-
Osmolovskaya, E. A., Ravin, N. V., et al. (2010). The genome sequence
of the crenarchaeon Acidilobus saccharovorans supports a new order,
Acidilobales, and suggests an important ecological role in terrestrial acidic
hot springs. Appl. Environ. Microbiol. 76, 5652–5657. doi: 10.1128/
AEM.00599-10 Huber, R., Stöhr, J., Hohenhaus, S., Rachel, R., Burggraf, S., Jannasch, H. W.,
et al. (1995). Thermococcus chitonophagus sp. nov., a novel, chitin-degrading,
hyperthermophilic archaeum from a deep-sea hydrothermal vent environment. Arch. Microbiol. 164, 255–264. doi: 10.1007/BF02529959 Miller, G. L. (1959). Use of dinitrosaiicyiic acid reagent for determination of
reducing sugar. Anal. Chem. 31, 426–428. doi: 10.1021/ac60147a030 Jendrossek,
D.,
and
Handrick,
R. (2002). Microbial
degradation
of
polyhydroxyalkanoates. Annu. Rev. Microbiol. 56, 403–432. doi: 10.1146/
annurev.micro.56.012302.160838 Mishra,
S.,
and
Sen,
G. (2011). Microwave
initiated
synthesis
of
polymethylmethacrylate grafted guar (GG-g-PMMA), characterizations and
applications. Int. J. Biol. Macromol. 48, 688–694. doi: 10.1016/j. ijbiomac.2011.02.013 Jia, B., Li, Z., Liu, J., Sun, Y., Jia, X., Xuan, Y. H., et al. (2015). A zinc-
dependent protease AMZ-tk from a thermophilic archaeon is a new
member of the archaemetzincin protein family. Front. Microbiol. 6:1380. doi: 10.3389/fmicb.2015.01380 Moon, C., Lee, C. H., Sang, B. I., and Um, Y. (2011). Optimization of medium
compositions favoring butanol and 1,3-propanediol production from glycerol
by Clostridium pasteurianum. Bioresour. Technol. 102, 10561–10568. doi:
10.1016/j.biortech.2011.08.094 Kataoka, M., and Ishikawa, K. (2014). Complete saccharification of β-glucan
using hyperthermophilic endocellulase and β-glucosidase from Pyrococcus
furiosus. Biosci. Biotechnol. Biochem. 78, 1537–1541. doi: 10.1080/
09168451.2014.923300 Nakahira, Y., Ishikawa, K., Tanaka, K., Tozawa, Y., and Shiina, T. REFERENCES The unique
GH5 cellulase member in the extreme halotolerant fungus Aspergillus glaucus
CCHA is an endoglucanase with multiple tolerance to salt, alkali and heat:
prospects for straw degradation applications. Extremophiles 22, 675–685. doi: 10.1007/s00792-018-1028-5i Sun, Y., Lin, L., Pang, C., Deng, H., Peng, H., Li, J., et al. (2007). Hydrolysis
of cotton fiber cellulose in formic acid. Energy Fuel 21, 2386–2389. doi:
10.1021/ef070134z Li, X., Wang, H.-L., Li, T., and Yu, H.-Y. (2012). Purification and characterization
of an organic solvent-tolerant alkaline cellulase from a halophilic isolate of
Thalassobacillus. Biotechnol. Lett. 34,
1531–1536. doi:
10.1007/
s10529-012-0938-z Sun, Y., Lv, X., Li, Z., Wang, J., Jia, B., and Liu, J. (2015). Recombinant
cyclodextrinase
from
Thermococcus
kodakarensis
KOD1:
expression,
purification, and enzymatic characterization. Archaea 2015:397924. doi:
10.1155/2015/397924 Li, X., and Yu, H.-Y. (2013a). Characterization of a halostable endoglucanase
with organic solvent-tolerant property from Haloarcula sp. G10. Int. J. Biol. Macromol. 62, 101–106. doi: 10.1016/j.ijbiomac.2013.08.047 Tachibana, Y., Leclere, M. M., Fujiwara, S., Takagi, M., and Imanaka, T. (1996). Cloning and expression of the α-amylase gene from the hyperthermophilic
archaeon Pyrococcus sp. KOD1, and characterization of the enzyme. J. Ferment. Bioeng. 82, 224–232. doi: 10.1016/0922-338X(96)88812-X Li, X., and Yu, H.-Y. (2013b). Halostable cellulase with organic solvent tolerance
from Haloarcula sp. LLSG7 and its application in bioethanol fermentation
using agricultural wastes. J. Ind. Microbiol. Biotechnol. 40, 1357–1365. doi:
10.1007/s10295-013-1340-0 Tanaka, T., Fujiwara, S., Nishikori, S., Fukui, T., Takagi, M., and Imanaka, T. (1999). A unique chitinase with dual active sites and triple substrate binding
sites from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1. Appl. Environ. Microbiol. 65, 5338–5344. Liang, C., Fioroni, M., Rodriguez-Ropero, F., Xue, Y., Schwaneberg, U., and
Ma, Y. (2011). Directed evolution of a thermophilic endoglucanase (Cel5A)
into highly active Cel5A variants with an expanded temperature profile. J. Biotechnol. 154, 46–53. doi: 10.1016/j.jbiotec.2011.03.025 Tanaka, T., Fukui, T., Atomi, H., and Imanaka, T. (2003). Characterization of
an exo-β-D-glucosaminidase involved in a novel chitinolytic pathway from
the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J. Bacteriol. 185, 5175–5181. doi: 10.1128/JB.185.17.5175-5181.2003 Liu, S., Sun, J., Yu, L., Zhang, C., Bi, J., Zhu, F., et al. (2012). Extraction and
characterization of chitin from the beetle Holotrichia parallela motschulsky. Molecules 17, 4604–4611. doi: 10.3390/molecules17044604 Mabilia, R., Scipioni, C., Vegliò, F., and Tomasi Scianò, M. C. (2010). Fractional
factorial experiments using a test atmosphere to assess the accuracy and Tanaka, T., Fukui, T., Fujiwara, S., Atomi, H., and Imanaka, T. (2004). REFERENCES doi: 10.1186/
s40659-018-0186-3 Cao, Y., and Tan, H. (2004). Structural characterization of cellulose with
enzymatic treatment. J. Mol. Struct. 705, 189–193. doi: 10.1016/j. molstruc.2004.07.010 Hamid, R., Khan, M. A., Ahmad, M., Ahmad, M. M., Abdin, M. Z., Musarrat, J.,
et al. (2013). Chitinases: an update. J. Pharm. Bioallied Sci. 5, 21–29. doi:
10.4103/0975-7406.106559 Chang, C. J., Lee, C. C., Chan, Y. T., Trudeau, D. L., Wu, M. H., Tsai, C. H.,
et al. (2016). Exploring the mechanism responsible for cellulase thermostability
by structure-guided recombination. PLoS One 11:e0147485. doi: 10.1371/
journal.pone.0147485 Han, T., Zeng, F., Li, Z., Liu, L., Wei, M., Guan, Q., et al. (2013). Biochemical
characterization of a recombinant pullulanase from Thermococcus
kodakarensis KOD1. Lett. Appl. Microbiol. 57, 336–343. doi: 10.1111/
lam.12118 Cui, Z., Wang, Y., Pham, B. P., Ping, F., Pan, H., Cheong, G.-W., et al. (2012). High level expression and characterization of a thermostable lysophospholipase
from Thermococcus kodakarensis KOD1. Extremophiles 16, 9–625. doi: 10.1007/
s00792-012-0461-0 Hanazono, Y., Takeda, K., Niwa, S., Hibi, M., Takahashi, N., Kanai, T., et al. (2016). Crystal structures of chitin binding domains of chitinase from
Thermococcus
kodakarensis
KOD1. FEBS
Lett. 590,
298–304. doi:
10.1002/1873-3468.12055 Din, N., Forsythe, I. J., Burtnick, L. D., Gilkes, N. R., Miller, R. C. Jr., Warren,
R. A. J., et al. (1994). The cellulose-binding domain of endoglucanase A
(CenA) from Cellulomonas fimi: evidence for the involvement of tryptophan
residues in binding. Mol. Microbiol. 11, 747–755. doi: 10.1111/j.1365-2958.1994. tb00352.x Hartl, L., Zach, S., and Seidl-Seiboth, V. (2012). Fungal chitinases: diversity,
mechanistic properties and biotechnological potential. Appl. Microbiol. Biotechnol. 93, 533–543. doi: 10.1007/s00253-011-3723-3 He, Y., Pang, Y., Liu, Y., Li, X., and Wang, K. (2008). Physicochemical
characterization of rice straw pretreated with sodium hydroxide in the solid
state for enhancing biogas production. Energy Fuel 22, 2775–2781. doi:
10.1021/ef8000967 Fan, G., Wang, M., Liao, C., Fang, T., Li, J., and Zhou, R. (2013). Isolation
of cellulose from rice straw and its conversion into cellulose acetate catalyzed June 2019 | Volume 10 | Article 1253 Frontiers in Microbiology | www.frontiersin.org 10 The Applications of Bicatalytic Chitinase Chen et al. precision of a new passive sampler for the determination of formaldehyde
in the atmosphere. Atmos. Environ. 44, 3942–3951. doi: 10.1016/j. atmosenv.2010.07.013 Henrissat, B. (1991). A classification of glycosyl hydrolases based on amino
acid sequence similarities. Biochem. J. 280, 309–316. Frontiers in Microbiology | www.frontiersin.org REFERENCES Concerted
action of diacetylchitobiose deacetylase and exo-β-d-glucosaminidase in a Frontiers in Microbiology | www.frontiersin.org Frontiers in Microbiology | www.frontiersin.org June 2019 | Volume 10 | Article 1253 11 Chen et al. The Applications of Bicatalytic Chitinase novel chitinolytic pathway in the hyperthermophilic archaeon Thermococcus
kodakaraensis KOD1. J. Biol. Chem. 279, 30021–30027. doi: 10.1074/jbc. M314187200 Zhang, J., and Jia, B. (2018). Enhanced butanol production using Clostridium
beijerinckii SE-2 from the waste of corn processing. Biomass Bioenergy 115,
260–266. doi: 10.1016/j.biombioe.2018.05.012 Tanaka, T., Fukui, T., and Imanaka, T. (2001). Different cleavage specificities
of the dual catalytic domains in chitinase from the hyperthermophilic
archaeon Thermococcus kodakaraensis KOD1. J. Biol. Chem. 276, 35629–35635. doi: 10.1074/jbc.M105919200 Zhang, H., Jin, Y., Deng, Y., Wang, D., and Zhao, Y. (2012). Production of
chitin from shrimp shell powders using Serratia marcescens B742 and
Lactobacillus plantarum ATCC 8014 successive two-step fermentation. Carbohydr. Res. 362, 13–20. doi: 10.1016/j.carres.2012.09.011 Tanaka, T., Takahashi, F., Fukui, T., Fujiwara, S., Atomi, H., and Imanaka, T. (2005). Characterization of a novel glucosamine-6-phosphate deaminase from
a hyperthermophilic archaeon. J. Bacteriol. 187, 7038–7044. doi: 10.1128/
JB.187.20.7038-7044.2005 Zhang, X., and Zhang, Y. P. (2013). “Cellulases: characteristics, sources, production,
and applications” in Bioprocessing technologies in biorefinery for sustainable
production of fuels, chemicals, and polymers. eds. S. Yang, H. El-Ensashy,
and N. Thongchul (New Jersey: Wiley), 131–146. Tomme, P., Boraston, A., McLean, B., Kormos, J., Creagh, A. L., Sturch, K.,
et al. (1998). Characterization and affinity applications of cellulose-binding
domains1. J. Chromatogr. B Biomed. Sci. Appl. 715, 283–296. doi: 10.1016/
S0378-4347(98)00053-X Conflict of Interest Statement: 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. Wan, C., Zhou, Y., and Li, Y. (2011). Liquid hot water and alkaline pretreatment
of soybean straw for improving cellulose digestibility. Bioresour. Technol. 102, 6254–6259. doi: 10.1016/j.biortech.2011.02.075 Copyright © 2019 Chen, Wei, Shi, Li and Zhang. 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. Zarafeta, D., Kissas, D., Sayer, C., Gudbergsdottir, S. R., Ladoukakis, E., Isupov,
M. Frontiers in Microbiology | www.frontiersin.org June 2019 | Volume 10 | Article 1253 REFERENCES N., et al. (2016). Discovery and characterization of a thermostable and
highly halotolerant GH5 cellulase from an icelandic hot spring isolate. PLoS
One 11:e0146454. doi: 10.1371/journal.pone.0146454 June 2019 | Volume 10 | Article 1253 Frontiers in Microbiology | www.frontiersin.org 12
|
https://openalex.org/W2111274264
|
https://europepmc.org/articles/pmc3926225?pdf=render
|
English
| null |
Spiritual Well-Being and Quality of Life of Iranian Adults with Type 2 Diabetes
|
Evidence-based complementary and alternative medicine
| 2,014
|
cc-by
| 7,358
|
Najmeh Jafari,1,2 Ziba Farajzadegan,2 Amir Loghmani,2
Mansoureh Majlesi,3 and Noushin Jafari4 1 George Washington Institute for Spirituality and Health, School of Medicine and Health Sciences, George
Washington University, Washington, DC 20036, USA 1 George Washington Institute for Spirituality and Health, School of Medicine and Health Sciences, George
Washington University, Washington, DC 20036, USA g
y
g
2 Community Medicine Department, School of Medicine, Isfahan University of Medical Sciences,
Isfahan 81745-313, Iran 2 Community Medicine Department, School of Medicine, Isfahan University of Medical Sciences,
Isfahan 81745-313, Iran 2 Community Medicine Department, School of Medicine, Isfahan University of Medical Sciences,
Isfahan 81745-313, Iran 3 Vice-Chancellery for Treatment, Isfahan University of Medical Sciences (IUMS), Isfahan 81656-47194, Iran
4Anesthesiology Department, School of Medicine, Isfahan University of Medical Sciences,
Isfahan 81745-313, Iran 3 Vice-Chancellery for Treatment, Isfahan University of Medical Sciences (IUMS), Isfahan 81656-47194, Iran
4Anesthesiology Department, School of Medicine, Isfahan University of Medical Sciences,
Isfahan 81745-313, Iran 3 Vice-Chancellery for Treatment, Isfahan University of Medical Sciences (IUMS), Isfahan 81656-47194, Iran
4Anesthesiology Department, School of Medicine, Isfahan University of Medical Sciences,
Isfahan 81745-313, Iran Correspondence should be addressed to Amir Loghmani; a loghmani@resident.mui.ac.ir Correspondence should be addressed to Amir Loghmani; a loghmani@resident.mui.ac.ir Received 6 June 2013; Revised 25 November 2013; Accepted 28 November 2013; Published 29 January 2014 Received 6 June 2013; Revised 25 November 2013; Accepted 28 November 2013; Published 29 January 2014 Academic Editor: Klaus Baumann Copyright © 2014 Najmeh Jafari et al. This is an open access article distributed under the Creative Commons A
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is p Introduction. Diabetes is a major public health problem. Little is known about the spiritual well-being and its relationship with
quality of life (QOL) in Iranian Muslim patients with diabetes. This study investigated the spiritual well-being and QOL of Iranian
adults with type 2 diabetes and the association between spiritual well-being, QOL, and depression. Methods. A cross-sectional
study was done among 203 patients with type 2 diabetes mellitus in Isfahan, Iran. Quality of life and spiritual well-being were
measured using the functional assessment of chronic illness therapy-spiritual well-being (FACIT-Sp). Depression was assessed
using the Patient Health Questionnaire-2 (PHQ-2). Descriptive analysis, Pearson’s correlation, and multiple regression analysis
were performed for statistical assessment. Results. The mean QOL was 61.00 (SD = 9.97) and the mean spiritual well-being was
30.59 (SD = 6.14). Sixty-four percent of our studied population had depressive disorders. Najmeh Jafari,1,2 Ziba Farajzadegan,2 Amir Loghmani,2
Mansoureh Majlesi,3 and Noushin Jafari4 There was a significant positive correlation
between all QOL subscales and meaning, peace, and total spiritual well-being score. Conclusion. The results of this study showed
poor QOL and spiritual well-being and high prevalence of depression in Iranian patients with type 2 diabetes compared to other
studies’ findings especially western studies. This indicates the need for psychosocial and spiritual support in caring for Iranian
patients with diabetes. Hindawi Publishing Corporation
Evidence-Based Complementary and Alternative Medicine
Volume 2014, Article ID 619028, 8 pages
http://dx.doi.org/10.1155/2014/619028 Hindawi Publishing Corporation
Evidence-Based Complementary and Alternative Medicine
Volume 2014, Article ID 619028, 8 pages
http://dx.doi.org/10.1155/2014/619028 Hindawi Publishing Corporation
Evidence-Based Complementary and Alternative Medicine
Volume 2014, Article ID 619028, 8 pages
http://dx.doi.org/10.1155/2014/619028 Research Article
Spiritual Well-Being and Quality of Life of Iranian Adults with
Type 2 Diabetes Najmeh Jafari,1,2 Ziba Farajzadegan,2 Amir Loghmani,2
Mansoureh Majlesi,3 and Noushin Jafari4 1. Introduction psychiatric disorders [4]. Diabetic patients are about twice as
likely as people without the condition to have anxiety, depres-
sion, and serious psychological problems [5–7]. Emotional
distress may influence outcomes in terms of glycemic control,
adherence to medical treatment, cost of care, and mortality
[8]. Diabetes is a serious public health problem with an increasing
incidence in Middle East countries as well as Iran [1]. Five
of the 10 world’s highest national prevalences of diabetes
occur in Middle East countries, that might be expected to
increase in the coming decades [1, 2]. The last nationally
representative report of the burden of diabetes in Iran showed
a high prevalence of diabetes (8.7%) in Iranian population,
which is estimated to rise to 9.8% in upcoming decades [3]. The interface between poor physical health and poor
mental health affects quality of life (QOL) of diabetic patients
[9]. QOL is a broad, multifaceted concept [10]. It incorporates
the individual’s subjective perception of physical, emotional,
cognitive, social, and spiritual domains of an individual’s
life [11]. Several studies indicated that diabetic patients have Diabetes is one of the most psychologically demanding
chronic medical disorders and is often associated with several Evidence-Based Complementary and Alternative Medicine 2 Evidence-Based Complementary and Alternative Medicine 2 reduced QOL compared to general population in the same
age group [12, 13], and their QOL decreases with diseased
progression and complications [14, 15]. illness therapy-spiritual well-Being (FACIT-Sp) scale. This
is a valid and reliable instrument that was developed in
the 1990s to provide an inclusive measure of spirituality in
research and clinical practice [28, 29]. This questionnaire
assesses spirituality well-being as well as QOL regardless of
religious or spiritual tradition [29]. It consists of a core gen-
eral questionnaire for measuring QOL and an additional scale
for measuring spirituality. The core general questionnaire
that measures QOL (FACT-G) is composed of four subscales:
physical well-being (PWB = 7 items), social/family well-being
(SWB = 7-items), emotional wellbeing (EWB = 6 items), and
functional well-being (FWB = 7 items) [30]. The additional
scale for measuring spirituality contains 12 items and three
subdomains (peace, meaning, and faith) [29]. The FACIT-Sp
is self-administered and uses a 5-point Likert-type scale (0 =
not at all; 4 = very much) and the score range of 0–48 [29]. The higher score represents the better spiritual well-being. 1. Introduction To assess the glycemic control of participants we consider
glycosylated hemoglobin HbA1c as a reliable index of long-
term glycemic control in patients with diabetes. An elevated
HbA1c indicates poor long-term glycemic control [34]. In this
study HbA1c level ≤7 was considered as controlled diabetes
and HbA1c level > 7 as uncontrolled diabetes. We evaluated depression using the 2-item patient health
questionnaire depression module, the PHQ-2 [32]. This
tool inquires about the frequency of depressed mood and
anhedonia over the past 2 weeks, scoring each as 0 (not at all)
to 3 (nearly every day); thus, the PHQ-2 score can range from
0 to 6. PHQ-2 cutoff score of ≥3 had the best tradeoff between
sensitivity (79%) and specificity (86%) for any depressive
disorder. This tool appears promising as a brief sensitive and
specific tool for detecting and monitoring of depression [33]. The aims of this study were to describe the spiritual
well-being and QOL of Iranian adults with type 2 diabetes
and to investigate the association between spiritual well-
being, QOL, and depression among Iranian adults with type
2 diabetes. i
To assess the glycemic control of participants we consider
glycosylated hemoglobin HbA1c as a reliable index of long-
term glycemic control in patients with diabetes. An elevated
HbA1c indicates poor long-term glycemic control [34]. In this
study HbA1c level ≤7 was considered as controlled diabetes
and HbA1c level > 7 as uncontrolled diabetes. 2.1. Instruments. To assess the spiritual well-being and QOL
of participants, we used the functional assessment of chronic 1. Introduction All
three scales have high internal consistency (Cronbach’s alpha
for total scale 0.87, for meaning/peace subscale 0.81, for faith
subscale 0.88). This questionnaire is translated and validated
to Persian by authors and we found that the Persian version of
the FACIT-Sp scale is a reliable and valid tool for the clinical
assessment of, and research into, the spiritual well-being of
Muslim Iranians [31]. Among several components of QOL, spirituality receives
more attention in recent years [16]. Spirituality is defined as
“the aspect of humanity that refers to the way individuals
seek and express meaning and purpose and the way they
experience their connectedness to the moment, to self, to
others, to nature, and to the significant or sacred” [17]. There
is a strong association between spirituality and coping with
chronic medical disease [18], willingness to live [19], reducing
anxiety and depression [20], and improving quality of life
[21].h The importance of addressing spirituality in diabetes
management is indicated in several studies. Previous studies
on African American population showed that there is a
positive relationship between spiritual well-being and coping
with diabetes, glycemic control, and self-management. [22–
24]. However, there is minimal information regarding the
spirituality of patients of different cultures such as Iranian
Muslim patients. In two qualitative studies from Iran, the role of spiritual
beliefs in coping with diabetes and patients’ empowerment
is indicated [25, 26]. However, there is still lack of evidence
regarding measuring the spiritual well-being and assessing
its association with QOL using a standard tool. Different
cultural groups and religious affiliations may emphasize
different aspects of their QOL and spiritual well-being [27]. Assessing the local perspectives by international instruments
will provide an opportunity for cross-cultural comparisons
and developing the best interventions based on the needs of
patient with diabetes.h We evaluated depression using the 2-item patient health
questionnaire depression module, the PHQ-2 [32]. This
tool inquires about the frequency of depressed mood and
anhedonia over the past 2 weeks, scoring each as 0 (not at all)
to 3 (nearly every day); thus, the PHQ-2 score can range from
0 to 6. PHQ-2 cutoff score of ≥3 had the best tradeoff between
sensitivity (79%) and specificity (86%) for any depressive
disorder. This tool appears promising as a brief sensitive and
specific tool for detecting and monitoring of depression [33]. 4. Discussion This study was designed to assess spiritual well-being and
QOL together with depression in a population of Iranian
people with type 2 diabetes and to explore their possible
associations. Our studied population had poor spiritual well-
being and quality of life in comparison to the normative data
of the general U.S. population [37] but similar to another
study from Iran in patients with cancer [31]. y
p
In our Muslim population, the highest score of spiritual
well-being was related to faith subdomain of FACIT-Sp12. This coheres with other studies in Muslim population [38,
39]. The “faith” component of FACIT-Sp-12 is most often
associated with religion and religious beliefs [40], but spir-
ituality extends beyond religion and is independent of com-
mitment to a particular religion or doctrine [41]. Spirituality
is experiencing transcendent meaning and purpose in life as
well as sense of connectedness. Several studies indicated the
importance of spirituality in coping with disease, better QOL,
and hopefulness [42–45]. In our study meaning and peace
subscales of FACIT-Sp12 were significantly associated with all
aspects of QOL. In regression analyses, higher meaning and
peace were related to better physical, social, emotional, and
functional well-being as well as total QOL, whereas higher
faith was only associated with physical well-being. These
results are consistent with our study on Iranian patients with
breast cancer, which showed that meaning and peace are
more robust indicators of QOL than faith. This may be due
to negative religious coping (e.g., belief that one’s illness is
God’s punishment or abandonment) in patients with chronic
illnesses [46]. However, this result is not specific to Iranian The mean of fasting blood sugar (FBS) was 163.26 (SD =
62.14). Among our participants, 76 diabetic patients (37.4%)
were in the controlled group (HbA1c ≤7) and 127 (63%) were
in uncontrolled group (HbA1c > 7).hh The mean score of FACT-G was 61.00 (SD = 9.97). The
mean spiritual well-being (FACIT-Sp12) score was 30.59 out
of 48 (SD = 6.14) with the highest mean score in the faith
subscale (mean = 10.78, SD = 2.89) in comparison to the
other subscales. The mean PHQ-2 score was 4.7 (S.D. = 1.5). Considering the cutoff score of ≥3, 63.5% of our studied
population had depressive disorders.i In one-way ANOVA, there was no statistically significant
difference in QOL, spiritual well-being, and depression scales
regarding demographic status (𝑃> 0.05). 2. Materials and Methods 1c
Patients were randomly sampled using IBM SPSS Statis-
tics for Microsoft Windows, Version 21. Demographic infor-
mation (age, marital status, education, and occupation) was
collected through a self-administered questionnaire. Clinical
data including laboratory and concurrent chronic disease
were extracted from medical records. After oral and written
consent, participants were instructed to read the brief direc-
tions at the top of the questionnaire. After confirming the
participants’ correct understanding, they were encouraged to
complete every item in private. A total of 203 participants
completed the FACIT-Sp, PHQ-2, and demographic informa-
tion questionnaire. This was a cross-sectional study, which was conducted in
two diabetes care institutes in Isfahan, Iran, from January
2013 to April 2013. These institutes are main diabetes care
centers located in two different geographic areas of Isfahan
city, covering more than 10,000 diabetes patients with diverse
socioeconomic characteristics. The target population was
patients with type 2 diabetes who had registered in these
institutes and consented to participate. People aged 18 or
above with a definitive diagnosis of type 2 diabetes, as
confirmed by a physician, with or without complication and
the ability to read and write Farsi, were enrolled in the
study. The exclusion criteria was any documented diagnosis
of end-stage renal disease, psychotic disorder, dementia, or
blindness. 2.2. Statistical Analysis. The sample was described using
means and standard deviations for quantitative variables and
relative frequencies and percentages for categorical variables. 𝑡-test analysis was used to compare the mean of FACIT-Sp
and PHQ-2 scores in two groups (controlled diabetes and
uncontrolled group). 2.1. Instruments. To assess the spiritual well-being and QOL
of participants, we used the functional assessment of chronic 3 Evidence-Based Complementary and Alternative Medicine Evidence-Based Complementary and Alternative Medicine Evidence-Based Complementary and Alternative Medicine The bivariate relationship between spiritual well-being,
QOL subscales, depression, and diabetes control (HbA1c) was
assessed by calculating Pearson correlation coefficients. Vari-
ables were selected for inclusion in the multiple regression
model based on theoretical importance as well as significance
in bivariate analyses. Multiple regression analysis was used
to assess the predictor role of the 12-item spiritual well-being
subscale of the FACIT-Sp subdomains (peace, meaning, and
Faith) on determinants of QOL. The FACT-G total scores and
its subdomains (PWB, SWB, EWB, and FWB) considered as
the dependent variables [35] and the independent (predictor)
variables (peace, meaning, and faith, PHQ-2 and HbA1c)
were entered in blocks. 2. Materials and Methods Table 2 lists the bivariate Pearson correlation coefficients
between the QOL, spirituality, and depression measures. There was a statistically significant positive correlation
between all QOL subscales (physical, social, emotional, and
functional well-being) and meaning, peace, and total FACIT-
Sp-12 scores. HbA1c was negatively associated with physi-
cal well-being, emotional well-being, functional well-being,
and peace, otherwise, positively correlated with depression. Depression was also significantly correlated with all QOL and
spiritual well-being subscales and this association was highest
with emotional well-being (𝑟= −0.56, 𝑃< 0.001), physical
well-being (𝑟= −0.52, 𝑃< 0.001), and peace (𝑟= −0.48,
𝑃< 0.001). In regression analyses, after evaluating the correlations
among the independent variables, no multicollinearity prob-
lem was detected. Meaning and peace subscales of FACIT-
Sp12 were significantly associated (𝑃< 0.05) with total QOL. Meaning, peace, faith, and depression were significantly
associated with physical well-being (𝑅2
=
0.37, 𝑃
<
0.005). In each of these analyses, the meaning and peace
subscales were significantly associated with the subdomains
of QOL. The faith subscale, on the other hand, was only
associated with physical well-being and did not provide an
independent contribution to prediction of other domains. Furthermore, HbA1c did not contribute significantly to any
of these outcomes (Table 3). Collinearity diagnostics were performed by means of
the variance inflation factor (VIF) for each independent
variable entered in the regression equations. A VIF > 10
was considered as positive multicollinearity [36]. The level of
significance was set at 𝑃> 0.05, and all tests were two-tailed. Data were analyzed using SPSS (version 21) for Windows. 3. Results Over a six-week-period, 223 patients met the inclusion
criteria and were recruited. Twenty patients were excluded
because of dementia (𝑛= 6), psychotic disorders (𝑛= 3),
and declining to take part (𝑛= 11). The mean age of all
participants was 55.42 (SD = 10.67) with a range of 18–87
years. The majority of participants were female (69.5%) and
married (95.1%). Seventy-two percent of participants were
housewives and 8.4% were retired. Seventy-six percent of
them were educated below high school diploma, 29 patients
received their diploma, and 18 patients had master degree
from the university. No gender differences were detected
regarding education. All patients identified themselves as
Muslim. There was no statistically significant difference
regarding demographic characteristics between patients who
participated and who declined (𝑃> 0.05).h 4. Discussion Among FACIT-
Sp subdomains, the mean of physical well-being, emotional
well-being, functional well-being, and peace scores was
higher in controlled diabetes group in comparison to uncon-
trolled group (𝑃< 0.05). People in uncontrolled group had
higher score in PHQ-2 score of depression (𝑃= 0.047). Table 1 shows participants’ quality of life as well as spiritual
well-being and depression scores in two groups. 4
Evidence-Based Complementary and Alternative Medicine
Table 1: FACT-G, FACIT-Sp12, and PHQ-2 scores of two groups (controlled and uncontrolled diabetic patients). Domains
Group
Mean
Std. deviation
𝑃value
Physical well-being
Controlled
17.61
6.18
0.033
Uncontrolled
15.73
5.99
Social/family well-being
Controlled
16.39
5.18
0.482
Uncontrolled
15.84
5.52
Emotional well-being
Controlled
10.80
5.38
0.045
Uncontrolled
9.27
5.09
Functional well-being
Controlled
19.55
4.24
0.004
Uncontrolled
17.52
5.01
Meaning
Controlled
10.97
3.11
0.214
Uncontrolled
10.44
2.76
Peace
Controlled
10.30
2.49
<0.001
Uncontrolled
8.46
2.68
Faith
Controlled
11.03
2.68
0.339
Uncontrolled
10.63
3.00
FACIT Sp12-score
Controlled
32.31
6.34
0.002
Uncontrolled
29.55
5.79
FACIT Sp-score
Controlled
95.15
13.88
0.005
Uncontrolled
89.45
13.64
PHQ-2 score
Controlled
2.73
1.87
0.047
Uncontrolled
4.22
1.70
HbA1c level ≤7: controlled diabetes (𝑛= 76). HbA1c level > 7: uncontrolled diabetes (𝑛= 127). Table 2: Pearson’s correlation coefficients between FACT-G, FACIT-Sp12, and PHQ-2. Physical
well-being
Social
well-being
Emotional
well-being
Functional
well-being
Peace
Meaning
Faith
Spiritual
well-being
PHQ-2
HbA1c
Physical
well-being
1
0.245∗∗
0.604∗∗
0.381∗∗
0.433∗∗
0.430∗∗
0.476∗∗
0.376∗∗
−0.522∗∗
−0.159∗∗
Social
Well-being
1
0.351∗∗
0.448∗∗
0.475∗∗
0.400∗∗
0.009
0.409∗∗
−0.315∗∗
−0.054
Emotional
well-being
1
0.418∗∗
0.492∗∗
0.558∗∗
0.107
0.534∗∗
−0.565∗∗
−0.141∗
Functional
well-being
1
0.564∗∗
0.601∗∗
0.189∗∗
0.626∗∗
−0.408∗∗
−0.153∗
Meaning
1
0.498∗∗
0.089
0.739∗∗
−0.460∗∗
−0.002
Peace
1
0.237∗∗
0.797∗∗
−0.476∗∗
−0.253∗∗
Faith
1
0.619∗∗
−0.203∗∗
−0.127
Spiritual
well-being
1
−0.511∗∗
−0.213∗∗
PHQ-2
1
0.230∗∗
HbA1c
1
∗∗Correlation is significant at the 0.05 level (2-tailed). ∗Correlation is significant at the 0 05 level (2 tailed) Evidence-Based Complementary and Alternative Medicine 4 Table 1: FACT-G, FACIT-Sp12, and PHQ-2 scores of two groups (controlled and uncontrolled diabetic patients). Domains
Group
Mean
Std. Evidence-Based Complementary and Alternative Medicine Furthermore, psychosocial toll of
living with diabetes and psychiatric disorders such as depres-
sion were shown to be associated with poorer QOL [58].i p
Q
[
]
Depression and diabetes are significantly connected to
each other [59]. In this study, 63.5% of our studied population
had depressive disorders. The prevalence of depression in
our diabetic sample was higher than the range of 2%–9.5%
in Iranian adults [60–62] as well as the rate of 8.3–28.8%
of the diabetic patients in the United States [63]. However,
the estimates of depression prevalence among individuals
with diabetes appear to be higher in developing countries
[64]. In a single point cross-sectional study done in India,
depression was diagnosed in 43.34% [65]. In a study done
in Pakistan, depression was found in 43.5% of patients with
diabetes [66]. In another study from Iran, Khamseh et al. found major depression in 71.8% of a sample of 206 patients
with type 1 and type 2 diabetes [67]. Other reports from
Iran using different tools for depression showed high rates of
depression in people with diabetes [68–70]. The higher co-
incidence of depression in these populations may be due to
the lower socioeconomic status that is a known risk factor
for depression [71]. Furthermore, the high prevalence of
depression in our sample may be due to use of a screening tool
which may detect psychological distress rather than clinical
depression and so may increase rates of disorder [72]. The
results of our study showed that depression is negatively
associated with all aspects of quality of life and spiritual
well-being. In the regression analysis, depression was a
significant predictor of physical and emotional well-being. This coheres with the results of previous studies that showed
a moderate, negative association of depressive symptoms on
physica and mental health [73–75], indicating the importance Diabetes destroys not only the physical well-being of
the patients but also threatens the social, functional, and
emotional well-being of the patients. This condition causes
the patients to ask about themselves, their purpose, and
their meaning in life. Victor Frankl in his famous book
“Man’s search for meaning” states “Human is not destroyed
by suffering; he is destroyed by suffering without meaning”
[52]. Meaning has been assessed in terms of the sense of
purpose in life, productivity, and reason for living [29]. Evidence-Based Complementary and Alternative Medicine 5 Table 3: Association of FACT-G and its subdomains with spiritual well-being, depression, and HbA1c. Predictors
Dependent variables
Physical well-being
Social well-being
Emotional well-being
Functional well-being
FACT-G
𝛽
𝑃
𝛽
𝑃
𝛽
𝑃
𝛽
𝑃
𝛽
𝑃
Meaning
0.182
0.010
0.339
0.000
0.179
0.006
0.347
0.000
0.369
0.000
Peace
0.195
0.007
0.217
0.005
0.321
0.000
0.383
0.000
0.253
0.001
Faith
0.192
0.001
0.087
0.171
0.053
0.335
0.053
0.329
0.111
0.061
PHQ-2
−0.374
0.000
−0.075
0.311
−0.344
0.000
−0.046
0.466
−0.111
0.107
HbA1c
−00.049
00.419
−0.006
0.923
−0.012
0.824
−0.040
0.475
−0.052
0.387
R2
0.374
0.270
0.454
0.461
0.368
F
23.56
14.61
32.76
33.70
22.92
𝛽: standardized beta; 𝑃: 𝑃value; method: enter. The bold 𝑃values show the significant relationships among aspects of spirituality and QOL. Meaning and peace were significantly associated with all aspects
of QOL. Table 3: Association of FACT-G and its subdomains with spiritual well-being, depression, and HbA1c. providing a sense of meaning and concluded that “religious
is beneficial to the degree to which it facilitates the cre-
ation and maintenance of meaning, coherence, and purpose. Conversely, if religious beliefs and practices fail to provide
meaning or provide meaning that is destructive (i.e., God
no longer cares for me), they are ineffectual or detrimental
to well-being” [50]. However, many Islamic scholars believe
that there is no distinction between religion and spiritual
concepts, and spirituality is meaningless without religious
thoughts and performances [51]. Coherent with this, Islamic
clergy men are included in some hospitals in Iran to provide
the religious care to patients. The main aspect of this model of
care is to help patients to do the Islamic rituals appropriately,
which is far away by the spiritual care model that includes
an interdisciplinary management to address all dimensions of
care, including the spiritual, religious, and existential as well
as physical and psychological. A qualitative study on 70 African American women with
type 2 diabetes showed the influence of spirituality in self-
management of people with type 2 diabetes resulted in
diabetes control [56]. In our studied population, individuals in the uncontrolled
group had worse QOL. Diabetes can exert a negative impact
on QOL [12]. Since diabetes is a chronic lifelong disease,
patients with diabetes must deal with their disease all day. Medical therapy, diabetes complications, episodes of hypo-
glycemia, and fear of long term consequences may lead to
reduced quality of life [57]. 4. Discussion deviation
𝑃value
Physical well-being
Controlled
17.61
6.18
0.033
Uncontrolled
15.73
5.99
Social/family well-being
Controlled
16.39
5.18
0.482
Uncontrolled
15.84
5.52
Emotional well-being
Controlled
10.80
5.38
0.045
Uncontrolled
9.27
5.09
Functional well-being
Controlled
19.55
4.24
0.004
Uncontrolled
17.52
5.01
Meaning
Controlled
10.97
3.11
0.214
Uncontrolled
10.44
2.76
Peace
Controlled
10.30
2.49
<0.001
Uncontrolled
8.46
2.68
Faith
Controlled
11.03
2.68
0.339
Uncontrolled
10.63
3.00
FACIT Sp12-score
Controlled
32.31
6.34
0.002
Uncontrolled
29.55
5.79
FACIT Sp-score
Controlled
95.15
13.88
0.005
Uncontrolled
89.45
13.64
PHQ-2 score
Controlled
2.73
1.87
0.047
Uncontrolled
4.22
1.70
HbA1c level ≤7: controlled diabetes (𝑛= 76). HbA1c level > 7: uncontrolled diabetes (𝑛= 127). 1: FACT-G, FACIT-Sp12, and PHQ-2 scores of two groups (controlled and uncontrolled diabetic patients). Table 2: Pearson’s correlation coefficients between FACT-G, FACIT-Sp12, and PHQ-2. Physical
well-being
Social
well-being
Emotional
well-being
Functional
well-being
Peace
Meaning
Faith
Spiritual
well-being
PHQ-2
HbA1c
Physical
well-being
1
0.245∗∗
0.604∗∗
0.381∗∗
0.433∗∗
0.430∗∗
0.476∗∗
0.376∗∗
−0.522∗∗
−0.159∗∗
Social
Well-being
1
0.351∗∗
0.448∗∗
0.475∗∗
0.400∗∗
0.009
0.409∗∗
−0.315∗∗
−0.054
Emotional
well-being
1
0.418∗∗
0.492∗∗
0.558∗∗
0.107
0.534∗∗
−0.565∗∗
−0.141∗
Functional
well-being
1
0.564∗∗
0.601∗∗
0.189∗∗
0.626∗∗
−0.408∗∗
−0.153∗
Meaning
1
0.498∗∗
0.089
0.739∗∗
−0.460∗∗
−0.002
Peace
1
0.237∗∗
0.797∗∗
−0.476∗∗
−0.253∗∗
Faith
1
0.619∗∗
−0.203∗∗
−0.127
Spiritual
well-being
1
−0.511∗∗
−0.213∗∗
PHQ-2
1
0.230∗∗
HbA1c
1
∗∗Correlation is significant at the 0.05 level (2-tailed). ∗Correlation is significant at the 0.05 level (2-tailed). Table 2: Pearson’s correlation coefficients between FACT-G, FACIT-Sp12, and PHQ-2. ∗∗Correlation is significant at the 0.05 level (2-tailed). ∗Correlation is significant at the 0.05 level (2-tailed). [48]. In another study Canada et al. examined the 3-factor
model for FACIT-SP-12 in two hundred and forty females
previously diagnosed with cancer. They found that the peace
factor was only correlated with mental health scores, meaning
it was associated with both physical and mental health scores,
and faith was negatively associated with mental health scores
[49]. Edmondson et al. examined the role of religion in population and is replicated in several international studies. A large Australian study on 449 cancer patients found that
the meaning/peace component being more highly related
to QOL than the faith component [47]. Similarly, in two
longitudinal studies, Yanez et al. showed that meaning and
peace act as a positive resource for cancer survivors, but faith
may serve to facilitate or even hinder positive adjustment Evidence-Based Complementary and Alternative Medicine Evidence-Based Complementary and Alternative Medicine This
sense of meaning helps the patients to cope with their disease,
reframing their lives, having an optimistic look on life and a
“fighting spirit” against their disease [53, 54]. Previous studies
on diabetic patients indicated that higher spiritual well-being
is associated with lower HbA1c and better adjustment to
disease [22]. The findings of this study reflects that the sense
of inner peace and intrinsic strength may guard against
negative feelings and probably result in maintaining higher
self-care behaviors and thus, greater glycemic control in
those with diabetes. This highlights the need for considering
spiritual issues in caring of the diabetic patients [55]. In our study controlled diabetes group (HbA1c level ≤7)
has better QOL and spiritual well-being in comparison to
uncontrolled group (HbA1c level > 7). This is in line with
the results of other studies indicating significant association
of spiritual well-being and diabetes control [22, 23, 43]. Evidence-Based Complementary and Alternative Medicine 6 6 of detecting and managing depressive symptoms in diabetes
care. and 2⋅7 million participants,” The Lancet, vol. 378, no. 9785,
pp. 31–40, 2011. [3] Our study, while having much strength, involved some
limitations that should be mentioned. Our findings cannot
be generalized to the general population of the patients with
diabetes because sicker and older people with type 2 diabetes
did not respond to the survey. Participants were from two
clinics populations, and there was no general population
comparison group to compare. Also, it is important to be
aware that FACIT-Sp is not a diabetes specific tool to assess
the quality of life and spiritual well-being. In this study
we treat the spiritual well-being as the predictor variable. However the developers of this instrument believe that “. . . under certain conditions, spiritual well-being may function
as a process variable or even as a dependent or outcome
variable.” Furthermore we did not assess the religious cop-
ing pattern in our participants. More research, particularly
longitudinal, is warranted to direct the causation between
spiritual well-being, QOL, and depression in diabetic patients
and to examine the feasibility of deriving a spiritual history in
diabetes care. [3] A. Esteghamati, M. M. Gouya, M. Abbasi et al., “Prevalence of
diabetes and impaired fasting glucose in the adult population
of Iran: National survey of risk factors for non-communicable
diseases of Iran,” Diabetes Care, vol. 31, no. 1, pp. 96–98, 2008. [4] M. D. Llorente and V. Evidence-Based Complementary and Alternative Medicine Urrutia, “Diabetes, psychiatric disorders,
and the metabolic effects of antipsychotic medications,” Clinical
Diabetes, vol. 24, no. 1, pp. 18–24, 2006. [5] S. Ali, M. A. Stone, J. L. Peters, M. J. Davies, and K. Khunti,
“The prevalence of co-morbid depression in adults with type
2 diabetes: a systematic review and meta-analysis,” Diabetic
Medicine, vol. 23, no. 11, pp. 1165–1173, 2006. [6] C. Li, L. Barker, E. S. Ford, X. Zhang, T. W. Strine, and A. H. Mokdad, “Diabetes and anxiety in US adults: findings from
the 2006 behavioral risk factor surveillance system,” Diabetic
Medicine, vol. 25, no. 7, pp. 878–881, 2008. [7] C. Li, E. S. Ford, G. Zhao, L. S. Balluz, J. T. Berry, and A. H. Mokdad, “Undertreatment of mental health problems in adults
with diagnosed diabetes and serious psychological distress: the
behavioral risk factor surveillance system, 2007,” Diabetes Care,
vol. 33, no. 5, pp. 1061–1064, 2010. [8] F. Pouwer, “Should we screen for emotional distress in type 2
diabetes mellitus?” Nature Reviews Endocrinology, vol. 5, no. 12,
pp. 665–671, 2009. Despite these limitations, the current study appears to be
unique in that we assessed the QOL, and spiritual well-being
and their association among diabetic patients in an Islamic
context. [9] G. Rodin, “Quality of life in adults with insulin-dependent
diabetes mellitus,” Psychotherapy and Psychosomatics, vol. 54,
no. 2-3, pp. 132–139, 1990. Conflict of Interests [13] W. K. Redekop, M. A. Koopmanschap, R. P. Stolk, G. E. H. M. Rutten, B. H. R. Wolffenbuttel, and L. W. Niessen, “Health-
related quality of life and treatment satisfaction in Dutch
patients with type 2 diabetes,” Diabetes Care, vol. 25, no. 3, pp. 458–463, 2002. The authors declare that there is no conflict of interests
regarding the publication of this paper. Acknowledgments [14] V. Sparring, L. Nystr¨om, R. Wahlstr¨om, P. M. Jonsson, J. ¨Ostman, and K. Burstr¨om, “Diabetes duration and health-
related quality of life in individuals with onset of diabetes in
the age group 15–34 years—a Swedish population-based study
using EQ-5D,” BMC Public Health, vol. 13, article 377, 2013. The authors wish to acknowledge all the patients who so
graciously agreed to participate in this study. Also, the authors
are greatly thankful to Dr. Hoseini of the Parvin Diabetes
Clinic, Mr. Teyfoori of the Isfahan Diabetes Charity Center,
and all staff of these centers for their support throughout the
project. [15] O. Solli, K. Stavem, and I. Kristiansen, “Health-related quality
of life in diabetes: the associations of complications with EQ-
5D scores,” Health and Quality of Life Outcomes, vol. 8, article
18, 2010. [16] T. Borneman, B. Ferrell, and C. M. Puchalski, “Evaluation of
the FICA tool for spiritual assessment,” Journal of Pain and
Symptom Management, vol. 40, no. 2, pp. 163–173, 2010. 5. Conclusion [10] B. K. Haas, “A multidisciplinary concept analysis of quality of
life,” Western Journal of Nursing Research, vol. 21, no. 6, pp. 728–
742, 1999. The results of this study showed poor QOL and spiritual
well-being and high prevalence of depression in Iranian
patients with type 2 diabetes compared to other studies’
findings, especially Western studies. This indicates the need
for psychosocial and spiritual support in caring for Iranian
patients with diabetes. [11] M. A. Verdugo and R. L. Schalock, “Quality of life: from concept
to future applications in the field of intellectual disabilities,”
Journal of Policy and Practice in Intellectual Disabilities, vol. 6,
no. 1, pp. 62–64, 2009. [12] R. R. Rubin and M. Peyrot, “Quality of life and diabetes,”
Diabetes/Metabolism Research and Reviews, vol. 15, no. 3, pp. 205–218, 1999. References [1] J. E. Shaw, R. A. Sicree, and P. Z. Zimmet, “Global estimates of
the prevalence of diabetes for 2010 and 2030,” Diabetes Research
and Clinical Practice, vol. 87, no. 1, pp. 4–14, 2010. [17] C. Puchalski, B. Ferrell, R. Virani et al., “Improving the quality
of spiritual care as a dimension of palliative care: the report of
the consensus conference,” Journal of Palliative Medicine, vol. 12,
no. 10, pp. 885–904, 2009. [2] G. Danaei, M. M. Finucane, Y. Lu et al., “National, regional,
and global trends in fasting plasma glucose and diabetes
prevalence since 1980: systematic analysis of health examination
surveys and epidemiological studies with 370 country-years [18] M. M. Rowe and R. G. Allen, “Spirituality as a means of coping
with chronic illness,” American Journal of Health Studies, vol. 19,
pp. 62–66, 2003. Evidence-Based Complementary and Alternative Medicine Evidence-Based Complementary and Alternative Medicine 7 [19] S. Cotton, C. M. Puchalski, S. N. Sherman et al., “Spirituality and
religion in patients with HIV/AIDS,” Journal of General Internal
Medicine, vol. 24, no. 8, 994 pages, 2009. [35] H. S. Whitford and I. N. Olver, “The multidimensionality of
spiritual wellbeing: peace, meaning, and faith and their associa-
tion with quality of life and coping in oncology,” Psychooncology,
vol. 21, no. 6, pp. 602–610, 2012. [20] K. S. Johnson, J. A. Tulsky, J. C. Hays et al., “Which domains
of spirituality are associated with anxiety and depression in
patients with advanced illness?” Journal of General Internal
Medicine, vol. 26, no. 7, pp. 751–758, 2011. [36] D. G. Kleinbaum, L. L. Kupper, and K. E. Muller, Applied
Regression Analysis and Other Multivariable Methods, Duxbury
Pr, 2007. [37] K. Webster, D. Cella, and K. Yost, “The functional assessment of
chronic illness therapy (FACIT) measurement system: proper-
ties, applications, and interpretation,” Health and Quality of Life
Outcomes, vol. 1, article 79, 2003. [21] R. Sawatzky, P. A. Ratner, and L. Chiu, “A meta-analysis of
the relationship between spirituality and quality of life,” Social
Indicators Research, vol. 72, no. 2, pp. 153–188, 2005. [22] N. Parsian and T. Dunning, “Spirituality and coping in young
adults with diabetes: a cross-sectional study,” European Diabetes
Nursing, vol. 6, no. 3, pp. 100–104, 2009. [38] N. Jafari, A. Zamani, M. Lazenby, Z. Farajzadegan, H. Emami,
and A. References Cella,
“A case for including spirituality in quality of life measurement
in oncology,” Psychooncology, vol. 8, no. 5, pp. 417–428, 1999. [44] C. J. W. Ehman, “Spirituality & health: a select bibliography of
medline-indexed articles published in,” Palliative Medicine, vol. 6, no. 6, pp. 932–933, 2003. [29] J. M. Bredle, J. M. Salsman, S. M. Debb, B. J. Arnold, and D. Cella, “Spiritual well-being as a component of health-related
quality of life: the functional assessment of chronic illness
therapy—spiritual well-being scale (FACIT-Sp),” Religions, vol. 2, pp. 77–94, 2011. [45] D. Baldacchino and P. Draper, “Spiritual coping strategies: a
review of the nursing research literature,” Journal of Advanced
Nursing, vol. 34, no. 6, pp. 833–841, 2001. [46] K. I. Pargament, B. W. Smith, H. G. Koenig, and L. Perez,
“Patterns of positive and negative religious coping with major
life stressors,” Journal for the Scientific Study of Religion, vol. 37,
no. 4, pp. 710–724, 1998. [30] D. F. Cella, D. S. Tulsky, G. Gray et al., “The functional
assessment of cancer therapy scale: development and validation
of the general measure,” Journal of Clinical Oncology, vol. 11, no. 3, pp. 570–579, 1993. [47] H. S. Whitford, I. N. Olver, and M. J. Peterson, “Spirituality as
a core domain in the assessment of quality of life in oncology,”
Psychooncology, vol. 17, no. 11, pp. 1121–1128, 2008. [31] N. Jafari, A. Zamani, M. Lazenby, Z. Farajzadegan, H. Emami,
and A. Loghmani, “Translation and validation of the Persian
version of the functional assessment of chronic illness therapy-
spiritual well-being scale (FACIT-Sp) among Muslim Iranians
in treatment for cancer,” Palliative and Supportive Care, vol. 1,
pp. 1–7, 2012. [48] B. Yanez, D. Edmondson, A. L. Stanton et al., “Facets of
spirituality as predictors of adjustment to cancer: relative
contributions of having faith and finding meaning,” Journal of
Consulting and Clinical Psychology, vol. 77, no. 4, pp. 730–741,
2009. [32] K. Kroenke, R. L. Spitzer, and J. B. W. Williams, “The patient
health questionnaire-2: validity of a two-item depression
screener,” Medical Care, vol. 41, no. 11, pp. 1284–1292, 2003. [49] A. L. Canada, P. E. Murphy, G. Fitchett, A. H. Peterman,
and L. R. Schover, “A 3-factor model for the FACIT-Sp,”
Psychooncology, vol. 17, no. 9, pp. 908–916, 2008. [33] B. L¨owe, K. Kroenke, and K. Gr¨afe, “Detecting and monitoring
depression with a two-item questionnaire (PHQ-2),” Journal of
Psychosomatic Research, vol. 58, no. 2, pp. 163–171, 2005. References Loghmani, “Translation and validation of the Persian
version of the functional assessment of chronic illness therapy-
spiritual well-being scale (FACIT-Sp) among Muslim Iranians
in treatment for cancer,” Palliative and Supportive Care, vol. 11,
no. 1, pp. 29–35, 2013. [23] R. L. Polzer and M. S. Miles, “Spirituality in African Americans
with diabetes: self-management through a relationship with
God,” Qualitative Health Research, vol. 17, no. 2, pp. 176–188,
2007. [39] M. Lazenby, J. Khatib, F. Al-Khair, and M. Neamat, “Psychome-
tric properties of the functional assessment of chronic illness
therapy-spiritual well-being (FACIT-Sp) in an Arabic-speaking,
predominantly Muslim population,” Psychooncology, vol. 22, no. 1, pp. 220–227, 2013. [24] K. Newlin, G. D. Melkus, R. Tappen, D. Chyun, and H. G. Koenig, “Relationships of religion and spirituality to glycemic
control in black women with type 2 diabetes,” Nursing Research,
vol. 57, no. 5, pp. 331–339, 2008. [25] M. H. Maslakpak, F. Ahmadi, and M. Anoosheh, “Spiritual
beliefs and quality of life: a qualitative research about diabetic
adolescent girls’ perception,” Koomesh, vol. 12, no. 2, pp. 144–151,
2010. [40] A. H. Peterman, G. Fitchett, M. J. Brady, L. Hernandez, and D. Cella, “Measuring spiritual well-being in people with cancer:
the functional assessment of chronic illness therapy—spiritual
well-being scale (FACIT-Sp),” Annals of Behavioral Medicine,
vol. 24, no. 1, pp. 49–58, 2002. [26] S. Abdoli, T. Ashktorab, F. Ahmadi, S. Parvizy, and T. Dunning,
“Religion, faith and the empowerment process: stories of
Iranian people with diabetes,” International Journal of Nursing
Practice, vol. 17, no. 3, pp. 289–298, 2011. [41] B. J. Zinnbauer, K. I. Pargament, B. Cole et al., “Religion and
spirituality: unfuzzying the fuzzy,” Journal for the Scientific
Study of Religion, vol. 36, no. 4, pp. 549–564, 1997. [27] N. W. Scott, P. M. Fayers, N. K. Aaronson et al., “The relationship
between overall quality of life and its subdimensions was
influenced by culture: analysis of an international database,”
Journal of Clinical Epidemiology, vol. 61, no. 8, pp. 788–795,
2008. [42] C. M. Puchalski, A Time for Listening and Caring: Spirituality
and the Care of the Chronically Ill and Dying, Oxford University
Press, New York, NY, USA, 2006. [43] N. Unantenne, N. Warren, R. Canaway, and L. Manderson,
“The strength to cope: spirituality and faith in chronic disease,”
Journal of Religion and Health, pp. 1–15, 2011. [28] M. J. Brady, A. H. Peterman, G. Fitchett, M. Mo, and D. Evidence-Based Complementary and Alternative Medicine Evidence-Based Complementary and Alternative Medicine Evidence-Based Complementary and Alternative Medicine 8 8 [51] G. H. Rassool, “The crescent and Islam: Healing, nursing
and the spiritual dimension. Some considerations towards an
understanding of the Islamic perspectives on caring,” Journal of
Advanced Nursing, vol. 32, no. 6, pp. 1476–1484, 2000. [67] M. E. Khamseh, H. R. Baradaran, and H. Rajabali, “Depression
and diabetes in Iranian patients: a comparative study,” Interna-
tional Journal of Psychiatry in Medicine, vol. 37, no. 1, pp. 81–86,
2007. [68] B. Larijani, M. K. S. Bayat, M. K. Gorgani, F. Bandarian,
S. Akhondzadeh, and S. A. Sadjadi, “Association between
depression and diabetes,” German Journal of Psychiatry, vol. 7,
no. 4, pp. 62–65, 2004. [52] V. E. Frankl, Man’s Search for Meaning, Washington Square, New
York, NY, USA, Rev. edition, 1984. [53] C. M. Puchalski, “Spirituality and health: the art of compassion-
ate medicine,” Hospital Physician, vol. 37, pp. 30–36, 2001. [69] A. N. Safa, B. Larijani, B. Shariati, H. Amini, and A. Reza-
gholizadeh, “Depression, quality of life and glycemic control
in patients with diabetes,” Iranian Journal of Diabetes and Lipid
Disorders, vol. 7, no. 2, pp. 195–204, 2007. [54] M. S. Yi, J. M. Mrus, T. J. Wade et al., “Religion, spirituality,
and depressive symptoms in patients with HIV/AIDS,” Journal
of General Internal Medicine, vol. 21, no. 5, pp. S21–S27, 2006. [55] C. P. Lynch, M. A. Hernandez-Tejada, J. L. Strom, and L. E. Egede, “Association between spirituality and depression in
adults with type 2 diabetes,” The Diabetes Educator, vol. 38, no. 3, pp. 427–435, 2012. [70] W. Katon, M. von Korff, P. Ciechanowski et al., “Behavioral and
clinical factors associated with depression among individuals
with diabetes,” Diabetes Care, vol. 27, no. 4, pp. 914–920, 2004. [71] W. W. Eaton, “Epidemiologic evidence for the relation between
socioeconomic status and depression, obesity, and diabetes,”
Journal of Psychosomatic Research, vol. 53, no. 4, pp. 891–895,
2002. [56] C. D. Samuel-Hodge, S. W. Headen, A. H. Skelly et al., “Influ-
ences on day-to-day self-management of type 2 diabetes among
African-American women: spirituality, the multi-caregiver role,
and other social context factors,” Diabetes Care, vol. 23, no. 7, pp. 928–933, 2000. [72] A. K. Ibrahim, S. J. Kelly, C. E. Adams, and C. Glazebrook,
“A systematic review of studies of depression prevalence in
university students,” Journal of Psychiatric Research, vol. 47, no. 3, pp. 391–400, 2013. [57] C. Fidler, T. Evidence-Based Complementary and Alternative Medicine Elmelund Christensen, and S. Gillard, “Hypo-
glycemia: an overview of fear of hypoglycemia, quality-of-life,
and impact on costs,” Journal of Medical Economics, vol. 14, no. 5, pp. 646–655, 2011. [73] N. Webinar, Q. E. Roundtable, and B. W. Part, “Minor depres-
sion and health status among US adults with diabetes mellitus-
page 3,” The American Journal of Managed Care, vol. 13, pp. 65–
72, 2007. [58] M. T. Schram, C. A. Baan, and F. Pouwer, “Depression and
quality of life in patients with diabetes: a systematic review
from the European depression in diabetes (EDID) research
consortium,” Current Diabetes Reviews, vol. 5, no. 2, pp. 112–119,
2009. [74] J. A. H¨anninen, J. K. Takala, and S. M. Kein¨anen-Kiukaanniemi,
“Depression in subjects with type 2 diabetes: predictive factors
and relation to quality of life,” Diabetes Care, vol. 22, no. 6, pp. 997–998, 1999. [59] A. Nouwen, K. Winkley, J. Twisk et al., “Type 2 diabetes mellitus
as a risk factor for the onset of depression: a systematic review
and meta-analysis,” Diabetologia, vol. 53, no. 12, pp. 2480–2486,
2010. [75] M. D. Pawaskar, R. T. Anderson, and R. Balkrishnan, “Self-
reported predictors of depressive symptomatology in an elderly
population with type 2 diabetes mellitus: a prospective cohort
study,” Health and Quality of Life Outcomes, vol. 5, article 50,
2007. [60] M. J. Modabernia, H. S. Tehrani, M. Fallahi, M. Shirazi, and
A. H. Modabbernia, “Prevalence of depressive disorders in
Rasht, Iran: a community based study,” Clinical Practice and
Epidemiology in Mental Health, vol. 4, article 20, 2008. [61] M. R. Mohammadi, H. Ghanizadeh, A. Noorbala, H. Davidian,
A. Malek, and H. R. Naghavi, “Prevalence of mood disorders in
Iran,” Iranian Journal of Psychiatry, vol. 1, pp. 59–64, 2006. [62] M.-R. Mohammadi, H. Davidian, A. A. Noorbala et al., “An
epidemiological survey of psychiatric disorders in Iran,” Clinical
Practice and Epidemiology in Mental Health, vol. 1, article 16,
2005. [63] C. Li, E. S. Ford, T. W. Strine, and A. H. Mokdad, “Prevalence of
depression among U.S. adults with diabetes: findings from the
2006 behavioral risk factor surveillance system,” Diabetes Care,
vol. 31, no. 1, pp. 105–107, 2008. [64] L. E. Egede and C. Ellis, “Diabetes and depression: global
perspectives,” Diabetes Research and Clinical Practice, vol. 87, no. 3, pp. 302–312, 2010. [65] S. Bajaj, S. K. Agarwal, A. Varma, and V. K. References [50] D. Edmondson, C. L. Park, T. O. Blank, J. R. Fenster, and M. A. Mills, “Deconstructing spiritual well-being: existential well-
being and HRQOL in cancer survivors,” Psychooncology, vol. 17,
no. 2, pp. 161–169, 2008. [34] H. F. Burr, “Evaluation of glycosylated hemoglobin in diabetic
patients,” Diabetes, vol. 30, no. 7, pp. 613–617, 1981. Evidence-Based Complementary and Alternative Medicine Singh, “Association
of depression and its relation with complications in newly
diagnosed type 2 diabetes,” Indian Journal of Endocrinology and
Metabolism, vol. 16, article 759, 2012. [66] A. K. Khuwaja, S. Lalani, R. Dhanani, I. S. Azam, G. Rafique, and
F. White, “Anxiety and depression among outpatients with type
2 diabetes: a multi-centre study of prevalence and associated
factors,” Diabetology and Metabolic Syndrome, vol. 2, no. 1,
article 72, 2010.
|
https://openalex.org/W4361986811
|
https://acp.copernicus.org/preprints/acp-2023-38/acp-2023-38.pdf
|
English
| null |
Comment on acp-2023-38
| null | 2,023
|
cc-by
| 22,295
| ERROR: type should be string, got "https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Correspondence to: Christer Johansson (christer.johansson@aces.su.se) \n10 Abstract. As air pollution is regarded as the single largest environmental health risk in Europe it is important that \ncommunication to the public is up-to-date, accurate and provides means to avoid exposure to high air pollution levels. Long- \nas well as short-term exposure to outdoor air pollution is associated with increased risks of mortality and morbidity. Up-to-\ndate information on present and coming days’ air quality help people avoid exposure during episodes with high levels of air \n15 \npollution. Air quality forecasts can be based on deterministic dispersion modelling, but to be accurate this requires detailed \ninformation on future emissions, meteorological conditions and process oriented dispersion modelling. In this paper we apply \ndifferent machine learning (ML) algorithms – Random forest (RF), Extreme Gradient Boosting (XGB) and Long-Short Term \nMemory (LSTM) – to improve 1-, 2- and 3-day deterministic forecasts of PM10, NOx, and O3 at different sites in Greater Abstract. As air pollution is regarded as the single largest environmental health risk in Europe it is important that \ncommunication to the public is up-to-date, accurate and provides means to avoid exposure to high air pollution levels. Long- \nas well as short-term exposure to outdoor air pollution is associated with increased risks of mortality and morbidity. Up-to- as well as short term exposure to outdoor air pollution is associated with increased risks of mortality and morbidity. Up to\ndate information on present and coming days’ air quality help people avoid exposure during episodes with high levels of air \n15 \npollution. Air quality forecasts can be based on deterministic dispersion modelling, but to be accurate this requires detailed \ninformation on future emissions, meteorological conditions and process oriented dispersion modelling. In this paper we apply \ndifferent machine learning (ML) algorithms – Random forest (RF), Extreme Gradient Boosting (XGB) and Long-Short Term \nMemory (LSTM) – to improve 1-, 2- and 3-day deterministic forecasts of PM10, NOx, and O3 at different sites in Greater date information on present and coming days’ air quality help people avoid exposure during episodes with high levels of air \n15 \npollution. Air quality forecasts can be based on deterministic dispersion modelling, but to be accurate this requires detailed \ninformation on future emissions, meteorological conditions and process oriented dispersion modelling. Improving 3-day deterministic air pollution forecasts using machine \nlearning algorithms Christer Johansson1,2, Zhiguo Zhang3, Magnuz Engardt2, Massimo Stafoggia4, Xiaoliang Ma3 \n1Department of Environmental Science, Stockholm University, Stockholm, Sweden \n5 \n2Environment and health administration, SLB-analys, Stockholm, Sweden \n3 KTH Royal Institute of Technology, Dept. of Civil and Architectural Engineering, Stockholm, Sweden \n4 Department of Epidemiology, Lazio Region Health Service, Rome, Italy Christer Johansson1,2, Zhiguo Zhang3, Magnuz Engardt2, Massimo Stafoggia4, Xiaoliang Ma3 \n1Department of Environmental Science, Stockholm University, Stockholm, Sweden \n5 \n2Environment and health administration, SLB-analys, Stockholm, Sweden \n3 KTH Royal Institute of Technology, Dept. of Civil and Architectural Engineering, Stockholm, Sweden \n4 Department of Epidemiology, Lazio Region Health Service, Rome, Italy Correspondence to: Christer Johansson (christer.johansson@aces.su.se) \n10 In this paper we apply \ndifferent machine learning (ML) algorithms – Random forest (RF), Extreme Gradient Boosting (XGB) and Long-Short Term \nMemory (LSTM) – to improve 1-, 2- and 3-day deterministic forecasts of PM10, NOx, and O3 at different sites in Greater Stockholm, Sweden. 20 \nIt is shown that the deterministic forecasts can be significantly improved using the MLs but that the degree of improvement of \nthe deterministic forecasts depends more on pollutant and site than on what machine learning (ML) algorithm is applied. Deterministic forecasts of PM10 is improved by the MLs through the input of lagged measurements and Julian day partly \nreflecting seasonal variations not properly parameterised in the deterministic forecasts. A systematic discrepancy by the Stockholm, Sweden. 20 \nIt is shown that the deterministic forecasts can be significantly improved using the MLs but that the degree of improvement of \nthe deterministic forecasts depends more on pollutant and site than on what machine learning (ML) algorithm is applied. Deterministic forecasts of PM10 is improved by the MLs through the input of lagged measurements and Julian day partly \nreflecting seasonal variations not properly parameterised in the deterministic forecasts. A systematic discrepancy by the deterministic forecasts in the diurnal cycle of NOx is removed by the MLs considering lagged measurements and calendar data \n25 \nlike hour of the day and weekday reflecting the influence of local traffic emissions. For O3 at the urban background site the \nlocal photochemistry not properly accounted for by the relatively coarse Copernicus Atmosphere Monitoring Service ensemble \nmodel (CAMS) used here for forecasting O3, but compensated using the MLs by taking lagged measurements into account. The machine learning models performed similarly well for the sites and pollutants. Performance measures like Pearson \nl ti\nt\n(RMSE)\nb\nl t\nt\n(MAPE)\nd\nb\nl t\n(MAE)\n30 deterministic forecasts in the diurnal cycle of NOx is removed by the MLs considering lagged measurements and calendar data \n25 \nlike hour of the day and weekday reflecting the influence of local traffic emissions. For O3 at the urban background site the \nlocal photochemistry not properly accounted for by the relatively coarse Copernicus Atmosphere Monitoring Service ensemble \nmodel (CAMS) used here for forecasting O3, but compensated using the MLs by taking lagged measurements into account. The machine learning models performed similarly well for the sites and pollutants. Correspondence to: Christer Johansson (christer.johansson@aces.su.se) \n10 Performance measures like Pearson deterministic forecasts in the diurnal cycle of NOx is removed by the MLs considering lagged measurements and calendar data \n25 \nlike hour of the day and weekday reflecting the influence of local traffic emissions. For O3 at the urban background site the \nlocal photochemistry not properly accounted for by the relatively coarse Copernicus Atmosphere Monitoring Service ensemble \nmodel (CAMS) used here for forecasting O3, but compensated using the MLs by taking lagged measurements into account. The machine learning models performed similarly well for the sites and pollutants. Performance measures like Pearson correlation, root mean square error (RMSE), mean absolute percentage error (MAPE) and mean absolute error (MAE), \n30 \ntypically differed less than 30% between ML models. At the urban background site, the deviations between modelled and \nmeasured concentrations (RMSE errors) are smaller than uncertainties in the measurements estimated according to correlation, root mean square error (RMSE), mean absolute percentage error (MAPE) and mean absolute error (MAE), \n30 \ntypically differed less than 30% between ML models. At the urban background site, the deviations between modelled and \nmeasured concentrations (RMSE errors) are smaller than uncertainties in the measurements estimated according to 1 1 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. recommendations by the Forum for Air Quality Modeling (FAIRMODE) in the context of the air quality directives. At the \nstreet canyon sites modelled errors are higher, and similar to measurement uncertainties. Further work is needed to reduce \ndeviations between model results and measurements for short periods with relatively high concentrations (peaks). Such peaks \ncan be due to a combination of non-typical emissions and unfavourable meteorological conditions and may be difficult to \nforecast. We have also shown that deterministic forecasts of NOx at street canyon sites can be improved using MLs even if \n5 \nthey are trained at other sites. For PM10 this was only possible using LSTM. recommendations by the Forum for Air Quality Modeling (FAIRMODE) in the context of the air quality directives. At the \nstreet canyon sites modelled errors are higher, and similar to measurement uncertainties. Further work is needed to reduce \ndeviations between model results and measurements for short periods with relatively high concentrations (peaks). Such peaks \ncan be due to a combination of non-typical emissions and unfavourable meteorological conditions and may be difficult to 5 forecast. Key words: Dispersion modelling, random forest, XGboost, LSTM, neural network, PM10, O3, NOx, GAM Correspondence to: Christer Johansson (christer.johansson@aces.su.se) \n10 We have also shown that deterministic forecasts of NOx at street canyon sites can be improved using MLs even if \n5 \nthey are trained at other sites. For PM10 this was only possible using LSTM. An important aspect to consider when choosing ML is that the decision tree based models (RF and XGB) can provide useful \noutput on the importance of features that is not possible using neural network models like LSTM, and also that training and \noptimisation is more complex with LSTM, which could be important to consider when selecting ML algorithm in an An important aspect to consider when choosing ML is that the decision tree based models (RF and XGB) can provide useful \noutput on the importance of features that is not possible using neural network models like LSTM, and also that training and \noptimisation is more complex with LSTM, which could be important to consider when selecting ML algorithm in an \noperational forecast system. A random forest model is now implemented operationally in the forecasts of air pollution and\n10 An important aspect to consider when choosing ML is that the decision tree based models (RF and XGB) can provide useful \noutput on the importance of features that is not possible using neural network models like LSTM, and also that training and \noptimisation is more complex with LSTM, which could be important to consider when selecting ML algorithm in an operational forecast system. A random forest model is now implemented operationally in the forecasts of air pollution and \n10 \nhealth risks in Stockholm. Development of the tuning process and identification of more efficient predictors may make forecast \nmore accurate. operational forecast system. A random forest model is now implemented operationally in the forecasts of air pollution and \n10 \nhealth risks in Stockholm. Development of the tuning process and identification of more efficient predictors may make forecast \nmore accurate. Key words: Dispersion modelling, random forest, XGboost, LSTM, neural network, PM10, O3, NOx, GAM 15 2 2 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 1 \nIntroduction Studies have used ML to predict both hourly and daily average concentrations \nof particulate matter (PM) as well as gaseous air pollutants using meteorological and traffic data (e.g. Quadeer et al., 2020; Di \net al., 2019; Thongthammachart et al., 2021; Kamińska, 2019; Chuluunsaikhan et al., 2021; Doreswamy et al., 2020; Castelli \net al., 2020; Stafoggia et al., 2020; Stafoggia et al., 2019). In addition, a combination of ML, LUR, dispersion modelling, Application of machine learning models (ML) to predict outdoor air quality is getting more and more popular (Rybarczyk and \n20 \nZalakeviciute, 2018; Iskandaryan et al., 2020). Studies have used ML to predict both hourly and daily average concentrations \nof particulate matter (PM) as well as gaseous air pollutants using meteorological and traffic data (e.g. Quadeer et al., 2020; Di \net al., 2019; Thongthammachart et al., 2021; Kamińska, 2019; Chuluunsaikhan et al., 2021; Doreswamy et al., 2020; Castelli \net al., 2020; Stafoggia et al., 2020; Stafoggia et al., 2019). In addition, a combination of ML, LUR, dispersion modelling, ground-based and satellite measurements have been used to obtain temporally and spatially distributed concentrations (Shtein \n25 \net al., 2020; Staffogia et al., 2019; Brokamp et al., 2017; Di et al., 2019). Although good prediction results have been achieved \nusing machine learning models, the challenges of forecasting air pollution concentrations in a longer-term horizon such as a \nday or even several days have not been investigated and very few studies have combined deterministic models and ML in \nforecasting air pollution levels of a few hours/days in the future. ground-based and satellite measurements have been used to obtain temporally and spatially distributed concentrations (Shtein \n25 \net al., 2020; Staffogia et al., 2019; Brokamp et al., 2017; Di et al., 2019). Although good prediction results have been achieved \nusing machine learning models, the challenges of forecasting air pollution concentrations in a longer-term horizon such as a \nday or even several days have not been investigated and very few studies have combined deterministic models and ML in \nforecasting air pollution levels of a few hours/days in the future. ground-based and satellite measurements have been used to obtain temporally and spatially distributed concentrations (Shtein \n25 \net al., 2020; Staffogia et al., 2019; Brokamp et al., 2017; Di et al., 2019). 1 \nIntroduction CHIMERE, EMEP and \nMATCH are part of the Copernicus Atmosphere Monitoring Service (CAMS, atmosphere.copernicus.eu/) to predict air pollution over Europe (Horàlek et al., 2019). The uncertainties in the output of the deterministic models include uncertainties \n15 \nin the input, such as emissions, model algorithms and parameterisations. In urban areas detailed knowledge of the emissions \nis crucial, and there may be important non-linear relationship between the concentration of contaminants and emission. Another \nmethod widely used to obtain spatio-temporal estimates of air pollutant concentrations without detailed knowledge of \nemissions is Land use regression (Hoek et al., 2008). pollution over Europe (Horàlek et al., 2019). The uncertainties in the output of the deterministic models include uncertainties \n15 \nin the input, such as emissions, model algorithms and parameterisations. In urban areas detailed knowledge of the emissions \nis crucial, and there may be important non-linear relationship between the concentration of contaminants and emission. Another \nmethod widely used to obtain spatio-temporal estimates of air pollutant concentrations without detailed knowledge of \nemissions is Land use regression (Hoek et al., 2008). pollution over Europe (Horàlek et al., 2019). The uncertainties in the output of the deterministic models include uncertainties \n15 \nin the input, such as emissions, model algorithms and parameterisations. In urban areas detailed knowledge of the emissions \nis crucial, and there may be important non-linear relationship between the concentration of contaminants and emission. Another \nmethod widely used to obtain spatio-temporal estimates of air pollutant concentrations without detailed knowledge of \nemissions is Land use regression (Hoek et al., 2008). Application of machine learning models (ML) to predict outdoor air quality is getting more and more popular (Rybarczyk and \n20 \nZalakeviciute, 2018; Iskandaryan et al., 2020). Studies have used ML to predict both hourly and daily average concentrations \nof particulate matter (PM) as well as gaseous air pollutants using meteorological and traffic data (e.g. Quadeer et al., 2020; Di \net al., 2019; Thongthammachart et al., 2021; Kamińska, 2019; Chuluunsaikhan et al., 2021; Doreswamy et al., 2020; Castelli \net al., 2020; Stafoggia et al., 2020; Stafoggia et al., 2019). In addition, a combination of ML, LUR, dispersion modelling, Application of machine learning models (ML) to predict outdoor air quality is getting more and more popular (Rybarczyk and \n20 \nZalakeviciute, 2018; Iskandaryan et al., 2020). 1 \nIntroduction According to the World Health Organisation (WHO) air pollution is one of the leading causes of mortality worldwide and is \nregarded as the single largest environmental health risk (Fuller et al., 2022). Acute effects of air pollution are due to short-term \n(e.g. daily) exposures that can lead to reduced lung function, respiratory infections and aggravated asthma. According to the \n5 According to the World Health Organisation (WHO) air pollution is one of the leading causes of mortality worldwide and is \nregarded as the single largest environmental health risk (Fuller et al., 2022). Acute effects of air pollution are due to short-term According to the World Health Organisation (WHO) air pollution is one of the leading causes of mortality worldwide and is \nregarded as the single largest environmental health risk (Fuller et al., 2022). Acute effects of air pollution are due to short-term \n(e.g. daily) exposures that can lead to reduced lung function, respiratory infections and aggravated asthma. According to the \n5 \nEuropean air quality directive, information on the air quality should be made available to the public. Public information \nregarding the expected health risks associated with current or the next few days concentrations of pollutants can be very \nimportant for sensitive persons when planning their outdoor activities. There are different approaches to obtain information on the spatio-temporal variation of air pollutant concentrations - from There are different approaches to obtain information on the spatio-temporal variation of air pollutant concentrations - from \nsimple statistical models to advanced process-oriented models. Gaussian plume models are widely used in urban areas for \n10 \nestimating impacts on atmospheric concentrations from different emission sources and for health risk assessments (Munir et \nal., 2020; Johansson et al., 2009; Orru et al., 2015; Johansson et al., 2017). Eulerian chemical transport models that describe \nemission, transport, mixing, and chemical transformation of trace gases and aerosols such as e.g. CHIMERE, EMEP and \nMATCH are part of the Copernicus Atmosphere Monitoring Service (CAMS, atmosphere.copernicus.eu/) to predict air simple statistical models to advanced process-oriented models. Gaussian plume models are widely used in urban areas for \n10 \nestimating impacts on atmospheric concentrations from different emission sources and for health risk assessments (Munir et \nal., 2020; Johansson et al., 2009; Orru et al., 2015; Johansson et al., 2017). Eulerian chemical transport models that describe \nemission, transport, mixing, and chemical transformation of trace gases and aerosols such as e.g. 1 \nIntroduction Although good prediction results have been achieved \nusing machine learning models, the challenges of forecasting air pollution concentrations in a longer-term horizon such as a \nday or even several days have not been investigated and very few studies have combined deterministic models and ML in \nforecasting air pollution levels of a few hours/days in the future. In this paper we demonstrate how ML can help improve the accuracy of 1-, 2- and 3-day deterministic forecasts of particulate \n30 \nmatter (PM10, particles with an aerodynamic diameter less than 10 µm), nitrogen oxides (NOx) and ozone (O3) for urban \nbackground and street canyon sites in Stockholm, Sweden. The deterministic forecast utilises the CAMS ensemble model to In this paper we demonstrate how ML can help improve the accuracy of 1-, 2- and 3-day deterministic forecasts of particulate \n30 \nmatter (PM10, particles with an aerodynamic diameter less than 10 µm), nitrogen oxides (NOx) and ozone (O3) for urban \nbackground and street canyon sites in Stockholm, Sweden. The deterministic forecast utilises the CAMS ensemble model to 3 account for non-local sources (long-range transport). A Gaussian model is applied over the urban area of Stockholm accounting \nfor local emissions and a street canyon model (OSPM) to account for the effect of buildings on the dispersion of local traffic \nemissions along the roads in the central area of the city. We compare three different machine learning algorithms; two based \non decision trees (random forest and XG Boost) and one neural network model (LSTM). Important questions addressed are \nalso if there are systematic differences in performance depending on different pollutants and different sites. 5 \nhttps://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. account for non-local sources (long-range transport). A Gaussian model is applied over the urban area of Stockholm accounting \nfor local emissions and a street canyon model (OSPM) to account for the effect of buildings on the dispersion of local traffic \nemissions along the roads in the central area of the city. We compare three different machine learning algorithms; two based \non decision trees (random forest and XG Boost) and one neural network model (LSTM). Important questions addressed are \nalso if there are systematic differences in performance depending on different pollutants and different sites. 5 2.1 \nAir pollution measurements Input data for ML modelling are taken from four monitoring stations in central Stockholm, including one urban background \nsite (Torkel Knutssonsgatan, hereafter called UB or urban) and 3 street canyon sites (Hornsgatan HO, Folkungagatan FO and \nSveavägen SV). They are all located in central Stockholm (Figure 1). Detailed descriptions of measurement methods and sites \n10 \nare provided in Appendix A. Input data for ML modelling are taken from four monitoring stations in central Stockholm, including one urban background \nsite (Torkel Knutssonsgatan, hereafter called UB or urban) and 3 street canyon sites (Hornsgatan HO, Folkungagatan FO and Sveavägen SV). They are all located in central Stockholm (Figure 1). Detailed descriptions of measurement methods and sites \n10 \nare provided in Appendix A. Sveavägen SV). They are all located in central Stockholm (Figure 1). Detailed descriptions of measurement methods and sites \n10 \nare provided in Appendix A. Data from the UB site covers approx. 1000 days (10 April 2019 through 31 December 2021). As the OSPM-model became \noperational at a later date, the street canyon data extends over 500 days (5 August 2020 through 31 December 2021). Two \napproaches were tested to handle missing values. The first approach simply ignores data of the timestamps with missing values, \nwhereas the alternative approach substitutes the missing values with mean values of available data in the neighbourhood. 15 Sveavägen SV). They are all located in central Stockholm (Figure 1). Detailed descriptions of measurement methods and sites \n10 \nare provided in Appendix A. Data from the UB site covers approx. 1000 days (10 April 2019 through 31 December 2021). As the OSPM-model became \noperational at a later date, the street canyon data extends over 500 days (5 August 2020 through 31 December 2021). Two Data from the UB site covers approx. 1000 days (10 April 2019 through 31 December 2021). As the OSPM-model became \noperational at a later date, the street canyon data extends over 500 days (5 August 2020 through 31 December 2021). Two \napproaches were tested to handle missing values. The first approach simply ignores data of the timestamps with missing values, \nwhereas the alternative approach substitutes the missing values with mean values of available data in the neighbourhood. 15 Figure 1. Map of central Stockholm showing locations of the urban background site and the street canyons traffic sites. Base map \ncredits: © OpenStreetMap contributors. Figure 1. 2.1 \nAir pollution measurements Map of central Stockholm showing locations of the urban background site and the street canyons traffic sites. Base map \ncredits: © OpenStreetMap contributors. kholm showing locations of the urban background site and the street canyons traffic sites. Base map \nntributors. 4 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 2.2 \nThe Stockholm air quality forecast system Three different dispersion models are used to forecast concentrations considering emissions and dispersion at European, urban \nand street scale (Figure 2). The CAMS ensemble model, part of the Copernicus program was used to obtain forecasts of long-\nrange transported air pollution from outside of the Greater Stockholm model domain. Previous assessments have found the \n5 \nensemble model to be the more accurate than any individual model part of CAMS (Meteo-France, 2017; Marècal et al., 2015). CAMS regional ensemble forecasts are published once a day and each forecast covers 96 hours (4 days). Forecasted \nconcentrations representative of background air, hour by hour, are extracted from a location outside the greater Stockholm \ndomain. All regional models constituting the CAMS ensemble includes physical and chemical schemes dealing with gas phase chemistry, heterogeneous chemistry, aerosol size distribution, aqueous phase chemistry, dry deposition, sedimentation, mineral \n10 \ndust, sea salt, wet deposition, etc. An evaluation of the CAMS regional ensemble forecast in Stockholm has been performed \nby Säll (2018). The contributions to concentrations due to local emissions in the metropolitan area were performed on a 100 m resolution \nusing a Gaussian dispersion model part of the Airviro system (https://www.airviro.com/airviro/). In this modelling domain 10 (Greater Stockholm, 35 by 35 km) individual buildings and street canyons are not resolved but treated using a roughness \n15 \nparameter (Gidhagen et al., 2005). The Gaussian model is fed with meteorological forecasts from the Swedish Meteorological \nand Hydrological Institute (SMHI). A diagnostic wind model is used to account for influences of variations in topography and \nland-use on the dispersion parameters input to the Gaussian model. For details regarding uncertainties and validation of local \nmodelling see Johansson et al. (2017). (Greater Stockholm, 35 by 35 km) individual buildings and street canyons are not resolved but treated using a roughness \n15 \nparameter (Gidhagen et al., 2005). The Gaussian model is fed with meteorological forecasts from the Swedish Meteorological \nand Hydrological Institute (SMHI). A diagnostic wind model is used to account for influences of variations in topography and \nland-use on the dispersion parameters input to the Gaussian model. For details regarding uncertainties and validation of local \nmodelling see Johansson et al. (2017). Finally, the Operational Street Pollution Model (OSPM, Berkowicz, 2000), driven by forecasted meteorology from SMHI is \n20 \napplied for the street canyon sites. It has been applied earlier at Hornsgatan in Stockholm in a number of modelling studies \n(e.g. 2.2 \nThe Stockholm air quality forecast system The database \nand its applications and comparisons between modelling and measurements are described in SLB (2022). The total emissions from road traffic are based on emission factors for different vehicle types including passenger cars (diesel, gasoline, gas), buses \n10 \n(diesel, ethanol), light duty trucks <3.5 ton (diesel and gasoline) and heavy duty trucks >3.5 ton (diesel). Exhaust emission \nfactors of NOx and particles are based on HBEFA version 3.3 (Keller et al., 2017) depending on vehicles Euro class. The \nemission factors per vehicle category were weighted according to the national Swedish Transport Administration vehicle \nregistry, but the vehicle composition taken from national vehicle registry has been shown to be similar to the local fleet using real world number plate recognition measurements at Hornsgatan in campaigns during 2009 (Burman and Johansson, 2010) \n15 \nand 2017 (Burman et al., 2019). For more details, see also Krecl et al., (2017). Non-exhaust emissions of PM due to wear of \nbrakes, tyres and roads are calculated using the NORTRIP model (Denby et al., 2013) forced by the forecasted meteorology \nfrom SMHI. Information on shares of studded winter tyres is obtained from manual counting every week during the winter at \ndifferent locations in the city centre and along highways outside of the city. Road traffic emissions are calculated for all roads real world number plate recognition measurements at Hornsgatan in campaigns during 2009 (Burman and Johansson, 2010) \n15 \nand 2017 (Burman et al., 2019). For more details, see also Krecl et al., (2017). Non-exhaust emissions of PM due to wear of \nbrakes, tyres and roads are calculated using the NORTRIP model (Denby et al., 2013) forced by the forecasted meteorology \nfrom SMHI. Information on shares of studded winter tyres is obtained from manual counting every week during the winter at \ndifferent locations in the city centre and along highways outside of the city. Road traffic emissions are calculated for all roads with more than 3000 vehicles per day. Other emission sources included in the local emissions database include shipping, \n20 \nprivate and municipal heating (including burning of waste). More information about the Stockholm air quality forecast system \nis provided in Engardt et al. (2021). 2.2 \nThe Stockholm air quality forecast system Krecl et al., 2021; Ottosen et al., 2015). NOx and PM10 are modelled on all scales, whereas O3 is only forecasted by the \nCAMS ensemble model. Finally, the Operational Street Pollution Model (OSPM, Berkowicz, 2000), driven by forecasted meteorology from SMHI is \n20 \napplied for the street canyon sites. It has been applied earlier at Hornsgatan in Stockholm in a number of modelling studies \n(e.g. Krecl et al., 2021; Ottosen et al., 2015). NOx and PM10 are modelled on all scales, whereas O3 is only forecasted by the \nCAMS ensemble model. Finally, the Operational Street Pollution Model (OSPM, Berkowicz, 2000), driven by forecasted meteorology from SMHI is \n20 \napplied for the street canyon sites. It has been applied earlier at Hornsgatan in Stockholm in a number of modelling studies \n(e.g. Krecl et al., 2021; Ottosen et al., 2015). NOx and PM10 are modelled on all scales, whereas O3 is only forecasted by the \nCAMS ensemble model. 5 Figure 2. Illustration of the deterministic modelling from European scale at a resolution of 0.1° by 0.1° (ca 11 km × 6 km), via urban \nscale (100 m resolution over an area of 35 by 35 km) down to the street canyon sites. The CAMS ensemble forecast map example is \ntaken from https://atmosphere.copernicus.eu/ (accessed 1 Feb 2023). The map with the Gaussian model local forecast example is \noutput from the Airviro system (https://www.airviro.com/airviro/, accessed 1 Feb 2023) used in Stockholm. The illustration of a \nstreet canyon site is taken from https://www.wikiwand.com/en/Operational_Street_Pollution_Model (accessed 1 Feb 2023). https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Figure 2. Illustration of the deterministic modelling from European scale at a resolution of 0.1° by 0.1° (ca 11 km × 6 km), via urban \nscale (100 m resolution over an area of 35 by 35 km) down to the street canyon sites. The CAMS ensemble forecast map example is \ntaken from https://atmosphere.copernicus.eu/ (accessed 1 Feb 2023). The map with the Gaussian model local forecast example is \noutput from the Airviro system (https://www.airviro.com/airviro/, accessed 1 Feb 2023) used in Stockholm. The illustration of a \nstreet canyon site is taken from https://www.wikiwand.com/en/Operational_Street_Pollution_Model (accessed 1 Feb 2023). 5 For the urban scale model domain a detailed emission database is used as input for the local dispersion modelling. 2.4 \nMachine learning models As already mentioned in the introduction two decision tree based machine learning models, RF and XGB, and one deep \nlearning model, LSTM are applied. In addition, an ensemble learning approach based on a General Additive Model (GAM), \naggregating the above three learning models, is also applied to further optimise the results. One essential challenge in this study is to forecast hourly concentrations for the coming one day, two days and three days based \n10 \non historical air pollution measurement and other available information as inputs. This indicates that the essential statistical \nprediction involves time series prediction for multiple time steps, for example, 72 time steps for three days prediction. It is \nknown that a sequence-to-sequence time series prediction, implemented using LSTM or other recurrent neural networks, \nprovides a straightforward and rolling-over computational schemes. Nevertheless, training a machine learning model with One essential challenge in this study is to forecast hourly concentrations for the coming one day, two days and three days based \n10 \non historical air pollution measurement and other available information as inputs. This indicates that the essential statistical \nprediction involves time series prediction for multiple time steps, for example, 72 time steps for three days prediction. It is \nknown that a sequence-to-sequence time series prediction, implemented using LSTM or other recurrent neural networks, \nprovides a straightforward and rolling-over computational schemes. Nevertheless, training a machine learning model with p\ng\ng\np\n,\ng\ng\nmultiple outputs requires much more computational effort, but often leads to inferior prediction accuracy compared to \n15 \nrelatively simple models with only a single output dedicated for predicting output of a certain time step. Therefore, this study \nchooses, instead of more complex machine learning structure, multiple single-output machine learning models for forecasting \ndifferent air pollutants for k=1 day, 2 day and 3 day interval: multiple outputs requires much more computational effort, but often leads to inferior prediction accuracy compared to \n15 \nrelatively simple models with only a single output dedicated for predicting output of a certain time step. 2.3 \nMeteorological forecasts 6\nAs an integral part of the Stockholm air quality forecast system, meteorological forecasts for a point in central Stockholm are \n25 \ndownloaded \nevery \nmorning \nfrom \nSMHI \n(https://www.smhi.se/data/oppna-data) \nand \nMET \nNorway \n(https://docs.api.met.no/doc/). The meteorological forecasts extend over 10 days and are a combination of output from a 6\nAs an integral part of the Stockholm air quality forecast system, meteorological forecasts for a point in central Stockholm are \n25 \ndownloaded \nevery \nmorning \nfrom \nSMHI \n(https://www.smhi.se/data/oppna-data) \nand \nMET \nNorway \n(https://docs.api.met.no/doc/). The meteorological forecasts extend over 10 days and are a combination of output from a 6 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. number of regional and global numerical weather prediction models. The combination is based on statistical adjustments as \nwell as manual edits. The meteorology is initially used to drive the models of weather-dependent PM emissions and the urban- \nand street canyon air quality modelling. The forecasted meteorological data are, finally, also used as predictors in the ML \nalgorithms as detailed below. number of regional and global numerical weather prediction models. The combination is based on statistical adjustments as \nwell as manual edits. The meteorology is initially used to drive the models of weather-dependent PM emissions and the urban- \nand street canyon air quality modelling. The forecasted meteorological data are, finally, also used as predictors in the ML \nalgorithms as detailed below. 5 2.4 \nMachine learning models Therefore, this study \nchooses, instead of more complex machine learning structure, multiple single-output machine learning models for forecasting \ndifferent air pollutants for k=1 day, 2 day and 3 day interval: 𝜌̂𝑖,𝑗(𝑑, 𝑡) = mlearn_model (𝜌̃𝑖,𝑗(𝑑−𝑘, 𝑡), 𝜌̅𝑖,𝑗\n𝑆(𝑑−𝑘, 𝑡), 𝜌̌𝑖,𝑗(𝑑, 𝑡), 𝑊(𝑑, 𝑡), 𝐶(𝑑, 𝑡) ) where 𝜌̂𝑖,𝑗(𝑑, 𝑡) is predicted concentration value of the pollutant j for day d and time t at the location i, and 𝜌̃𝑖,𝑗(𝑑, 𝑡) is the \n20 \ncorresponding real measurement; 𝜌̅𝑖,𝑗\n𝑆(𝑑, 𝑡) uses a set S to represent several statistical measures, including maximum, \nminimum, 25% quantile and 75% quantile of the measured concentration data during the past 24 hours until 𝜌̃𝑖,𝑗(𝑑, 𝑡), and the \nmeasurement dataset can be represented by a set, i.e. {𝜌̃𝑖,𝑗(𝑑, 𝑡), 𝜌̃𝑖,𝑗(𝑑, 𝑡−1), 𝜌̃𝑖,𝑗(𝑑, 𝑡−2). . . . }. 𝜌̌𝑖,𝑗(𝑑, 𝑡) is the one day \npredicted concentration value using deterministic physical model. 𝑊(𝑑, 𝑡) represents the weather condition predicted for day d and time t. 25 \nFigure 3 demonstrates the prediction horizon and lagged information horizon for the case of one day prediction. To build \nconsistent statistical machine learning models with a fixed rolling horizon, a new measurement point at current time (d, t) will \nlead to an additional prediction for one day ahead, i.e. the predicted value at (d+1,t). In the case, the measurement statistics \n𝜌̅𝑖,𝑗\n𝑆(𝑑, 𝑡) will be based on one day preceding measurement data of (d, t), leading to a lagged rolling horizon described in the \nfigure. 30 7 7 Figure 3. Illustration of the machine learning modelling framework for one-day prediction based on available datasets. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Figure 3. Illustration of the machine learning modelling framework for one-day prediction b Figure 3. Illustration of the machine learning modelling framework for one-day prediction based on available datasets. This study has applied both LSTM and two conventional supervised learning models, RF and \nlearning cores to carry out supervised learning using the same input and output training dataset This study has applied both LSTM and two conventional supervised learning models, RF and XGB, as the essential machine \nlearning cores to carry out supervised learning using the same input and output training dataset. In fact, an ensemble approach \nbased on all three models is also applied to predict air quality for different days. 2.4 \nMachine learning models The conventional models require nontrivial \n5 \neffort to prepare input feature data as they don’t fit as easily with time series data as RNN. To make a fair comparison with \nboth types of models, LSTM model in this case is only based on the same type of input as other two models. It is well known \nthat LSTM can learn the temporal correlation of different ranges. Nevertheless, this study applies the data to a simple LSTM \nstructure, without taking advantages of its full potential. In principle, the measurement data at (d, t) may provide hourly update based on all three models is also applied to predict air quality for different days. The conventional models require nontrivial \n5 \neffort to prepare input feature data as they don’t fit as easily with time series data as RNN. To make a fair comparison with \nboth types of models, LSTM model in this case is only based on the same type of input as other two models. It is well known \nthat LSTM can learn the temporal correlation of different ranges. Nevertheless, this study applies the data to a simple LSTM \nstructure, without taking advantages of its full potential. In principle, the measurement data at (d, t) may provide hourly update 5 of predicted values within the prediction horizon i.e. from (d,t+1) to (d+1,t). Nevertheless, it is our future work to extend the \n10 \nmodel structure and improve prediction using latest real-time information. In addition to the measured air pollution time series data itself, the forecasted meteorological conditions for the prediction day \nd (or d+1 or d+2) and calendar information such as weekday, hour etc. are also applied as input features. Moreover, the air \npollutant concentrations predicted by the deterministic models is also used as inputs to the MLs. model structure and improve prediction using latest real time information. In addition to the measured air pollution time series data itself, the forecasted meteorological conditions for the prediction day \nd (or d+1 or d+2) and calendar information such as weekday, hour etc. are also applied as input features. Moreover, the air \npollutant concentrations predicted by the deterministic models is also used as inputs to the MLs. Fel! Hittar inte referenskälla. summarizes the methodological framework of machine learning and associated computational \n15 \nexperiments for air pollution prediction. Fel! Hittar inte referenskälla. 2.4 \nMachine learning models summarizes the methodological framework of machine learning and associated computational \n15 \nexperiments for air pollution prediction. Fel! Hittar inte referenskälla. summarizes the methodological framework of machine learning and associated computational \n15 \nexperiments for air pollution prediction. 8 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Th i\ni\nl d\nh d\ni i i f\nf PM\nNO\nd O\nl\nh\nh h d\ni i i f\nb The input includes the deterministic forecasts of PM10, NOx and O3, to evaluate how much the deterministic forecasts can be\nimproved by the ML algorithms. In the computational experiments, data-driven forecasting models are trained for one urban \nbackground site and three street canyon sites separately, and different machine learning models are trained and tested separately\nfor predicting various air pollution concentrations coming 1-day (0 – 24 h), 2-day (25 – 48 h) and 3-day (48 – 72 h) periods. Table 1 presents detailed explanation of the essential input features that are applied in the computational experiments. All \nmachine learning models are implemented in python using existing machine learning libraries including “scikit-learn” and\n“tensorflow” (also implemented using “pytorch”) for conventional machine learning models and deep learnings models\nrespectively. The detailed implementation can be referred to the code provided. The input includes the deterministic forecasts of PM10, NOx and O3, to evaluate how much the deterministic forecasts can be \nimproved by the ML algorithms. In the computational experiments, data-driven forecasting models are trained for one urban \nbackground site and three street canyon sites separately, and different machine learning models are trained and tested separately \n5 \nfor predicting various air pollution concentrations coming 1-day (0 – 24 h), 2-day (25 – 48 h) and 3-day (48 – 72 h) periods. Table 1 presents detailed explanation of the essential input features that are applied in the computational experiments. All \nmachine learning models are implemented in python using existing machine learning libraries including “scikit-learn” and \n“tensorflow” (also implemented using “pytorch”) for conventional machine learning models and deep learnings models \nrespectively. The detailed implementation can be referred to the code provided. 10 background site and three street canyon sites separately, and different machine learning models are trained and tested separately \n5 \nfor predicting various air pollution concentrations coming 1-day (0 – 24 h), 2-day (25 – 48 h) and 3-day (48 – 72 h) periods. 2.4 \nMachine learning models Table 1 presents detailed explanation of the essential input features that are applied in the computational experiments. All \nmachine learning models are implemented in python using existing machine learning libraries including “scikit-learn” and \n“tensorflow” (also implemented using “pytorch”) for conventional machine learning models and deep learnings models \nrespectively. The detailed implementation can be referred to the code provided. 10 9 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Table 1. Measured and forecasted air pollutant concentrations used as input data (features) in the ML modelling of pollutant \nconcentrations at the urban background site (UB) and at the street canyon sites (SC). NOx and PM10 are modelled at both UB and \nSC. Ozone is only modelled at UB. For periodic input data, using sine and cosine values can remove discontinuities and create \nconsistent distance measures, thereby improving model accuracy. Category \nShort \nnames \nDescription \nDeterministic features \nNOx_nday_local \nPM10_nday_local \nn=1, 2, 3 \nDeterministic 1-day, 2-day and 3-day forecast of contributions from \nlocal emissions based on urban scale Gaussian modelling \nNOx_nday_regional \nPM10_nday_regional \nO3_nd_regional \nn=1, 2, 3 \nDeterministic 1-day, 2-day and 3-day forecast of contributions based \nfrom non-local emissions based on CAMS ensemble model (regional \nbackground) \nAutocorrelation features \nNOx_lagXX \nPM10_lagXX \nO3_lagXX \nXX = 24, 48, 72 \nXX hour lagged air pollutant concentrations based on autocorrelation \nand prediction time span. Statistical features \nNOx_Sta_dXX \nPM10_Sta_dXX \nO3_Sta_dXX \nSta=avg., median, min, \nmax, Q1, Q3 \nXX = 24, 48, 72 \nAverage, median, minimum, maximum, quantiles 1 and quantiles 3 of \nlagged air pollutant concentrations in rolling XX hour periods. Time features \nTime \nTime_sin \nTime_cos \nTime= year, julianday, \nmonth, weekday, day, hour \nJulian day of the year (1, 2, 3, … 365), sine and cosine of 2*pi*day/365. Day of the week (1, 2, 3, … 7), sine and cosine of 2*pi*day/7. Hour of the day (0, 1, 2, … 23), sine and cosine of 2*pi*hour/24. Year \nMonth \nDay \nMeteorological features \nwind_direction \nwind_direction_cos \nwind_direction_sin \nWind direction[0, 360) at 10 m in central Stockholm, sine and cosine \nof (2*pi/360)*wind direction \npressure; temperature; \nprecipitation; cloudiness \nPressure (10 m); Temperature (10 m) \nwind_speed \nWind speed (10 m) \nrelative_humidity \nRelative humidity \nboundary_layer_height \nBoundary layer height for central Stockholm 5 2.5 \nStatistical performance indicators Several common performance metrics have been selected for comparing the prediction results of different machine learning \nmodels including Pearson correlation (r) and normalised error measures: mean average error (MAE), mean absolute percentage \nerror (MAPE) and root mean squared error (RMSE). These measures have also been recommended for air quality model \nbenchmarking in the context of the Air Quality Directive 2008/50/EC (AQD) by Janssen and Thunis (2022). 10 Mean absolute error: Mean absolute error: 𝑀𝐴𝐸(𝑦, 𝑦̂) = 1\n𝑛∑ \n𝑛\n𝑖=1\n|𝑦𝑖−𝑦̂𝑖| 𝑀𝐴𝐸(𝑦, 𝑦̂) = 1\n𝑛∑ \n𝑛\n𝑖=1\n|𝑦𝑖−𝑦̂𝑖| 10 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. where 𝑦̂𝑖 is the predicted value of the 𝑖-th sample, and 𝑦𝑖 is the corresponding true value for total 𝑛 samples. q\n𝑅𝑀𝑆𝐸(𝑦, 𝑦̂) = √1\n𝑛∑ \n𝑛\n𝑖=1\n(𝑦𝑖−𝑦̂𝑖)2 MAE and RMSE were normalised by diving by the mean of the measured concentrations, hereafter called nMAE and \n5 \nnRMSE. Mean absolute percentage error: \n𝑛 Mean absolute percentage error: 𝑀𝐴𝑃𝐸(𝑦, 𝑦̂) = 1\n𝑛∑ \n𝑛\n𝑖=1\n|𝑦𝑖−𝑦̂𝑖|\n|𝑦𝑖| 𝑀𝐴𝑃𝐸(𝑦, 𝑦̂) = 1\n𝑛∑ \n𝑛\n𝑖=1\n|𝑦𝑖−𝑦̂𝑖|\n|𝑦𝑖|\n \n0 10 10 Pearson correlation coefficient: Pearson correlation coefficient: r(𝑦, 𝑦̂) =\n∑\n \n𝑛\n𝑖=1 (𝑦𝑖−𝑦𝑖̅)(𝑦̂𝑖−𝑦̂𝑖̅)\n√∑\n \n𝑛\n𝑖=1 (𝑦𝑖−𝑦𝑖̅)2√∑\n \n𝑛\n𝑖=1 (𝑦̂𝑖−𝑦̂𝑖̅)2 r(𝑦, 𝑦̂) =\n∑\n \n𝑛\n𝑖=1 (𝑦𝑖−𝑦𝑖̅)(𝑦̂𝑖−𝑦̂𝑖̅)\n√∑\n \n𝑛\n𝑖=1 (𝑦𝑖−𝑦𝑖̅)2√∑\n \n𝑛\n𝑖=1 (𝑦̂𝑖−𝑦̂𝑖̅)2 The model quality indicator (MQI): In order to properly assess model quality it is necessary to consider measurement uncertainty. In the FAIRMODE community, \n15 \nthe modelling quality indicator (MQI) is used to assess if a model fulfils certain objectives (Janssen and Thunis, 2022). It is \ndefined as the ratio between the model bias at a fixed time (i), quantified by the RMSE, and a quantity proportional to the \nmeasurement uncertainty as: In order to properly assess model quality it is necessary to consider measurement uncertainty. In the FAIRMODE community, \n15 \nthe modelling quality indicator (MQI) is used to assess if a model fulfils certain objectives (Janssen and Thunis, 2022). It is \ndefined as the ratio between the model bias at a fixed time (i), quantified by the RMSE, and a quantity proportional to the \nmeasurement uncertainty as: 𝑀𝑄𝐼(𝑖) = \n√1\n𝑛∑\n \n𝑛\n𝑖=1 (𝑦𝑖−𝑦̂𝑖)2\n𝛽√1\n𝑛∑\n \n𝑛\n𝑖=1 𝑈(𝑦𝑖)2\n= 𝑅𝑀𝑆𝐸\n𝛽𝑅𝑀𝑆𝑈\n \n20 20 20 U(yi) is the expanded 95th percentile measurement uncertainty and β is a coefficient of proportionality (Janssen and Thunis, \n2022). The value of β determines the stringency of the MQI and is set equal to 2, allowing thus deviation between modelled \nand measured concentrations as twice the measurement uncertainty. The uncertainty of the measurements (RMSU) was \ncalculated for the mean of the measurement concentrations as: \n25 𝑈(𝑦𝑖) = 𝑈𝑟(𝑅𝑉)√(1 −∝2)2(𝑦𝑖2) +∝2 𝑅𝑉2 𝑈(𝑦𝑖) = 𝑈𝑟(𝑅𝑉)√(1 −∝2)2(𝑦𝑖2) +∝2 𝑅𝑉2 Here 𝑈𝑟(𝑅𝑉) and ∝ are parameters that depend on pollutant and RV is a reference value, here taken to be 200, 50 and 120 µg \nm-3, corresponding 𝑈𝑟(𝑅𝑉) was 0.24, 0.28 and 0.18 and ∝ was 0.25, 0.20, 0.79 for NO2, PM10 and O3 respectively (Janssen \nand Thunis, 2022). In our case we have calculated NOx, not NO2, but we used the same settings of the parameters for NOx as \nrecommended for NO2. It should be noted that another important source of error when comparing model results with \n30 \nmeasurements is associated with the spatial representativeness of a measurement station for comparison with the model. This Here 𝑈𝑟(𝑅𝑉) and ∝ are parameters that depend on pollutant and RV is a reference value, here taken to be 200, 50 and 120 µg \nm-3, corresponding 𝑈𝑟(𝑅𝑉) was 0.24, 0.28 and 0.18 and ∝ was 0.25, 0.20, 0.79 for NO2, PM10 and O3 respectively (Janssen \nand Thunis, 2022). The model quality indicator (MQI): In our case we have calculated NOx, not NO2, but we used the same settings of the parameters for NOx as \nrecommended for NO2. It should be noted that another important source of error when comparing model results with \n30 \nmeasurements is associated with the spatial representativeness of a measurement station for comparison with the model. This Here 𝑈𝑟(𝑅𝑉) and ∝ are parameters that depend on pollutant and RV is a reference value, here taken to be 200, 50 and 120 µg \nm-3, corresponding 𝑈𝑟(𝑅𝑉) was 0.24, 0.28 and 0.18 and ∝ was 0.25, 0.20, 0.79 for NO2, PM10 and O3 respectively (Janssen \nand Thunis, 2022). In our case we have calculated NOx, not NO2, but we used the same settings of the parameters for NOx as \nrecommended for NO2. It should be noted that another important source of error when comparing model results with \n30 \nmeasurements is associated with the spatial representativeness of a measurement station for comparison with the model. This 11 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. is due to the mismatch between the model grid resolution and the location of the monitoring station. But in this paper we are \nmainly interested in comparing the results of the deterministic model with the results using the different MLs together with the \ndeterministic model output. is due to the mismatch between the model grid resolution and the location of the monitoring station. But in this paper we are \nmainly interested in comparing the results of the deterministic model with the results using the different MLs together with the \ndeterministic model output. 3 \nResults The focus of this paper is to compare the deterministic forecasts of NOx, PM10 and O3 with the forecasts based on the different \n5 \nmachine learners which also include the deterministic forecasts as input variables (features). As described above we have made \ndeterministic and ML forecasts for hourly mean concentrations for the coming 72 hours, based on 1-day, 2-day and 3-day \nmeteorological forecasts for one urban background site (NOx, PM10 and O3) and three street canyon sites (NOx and PM10). We \nalso compare results separately for the urban background site and the street canyon sites. 3.1.1 \nImportance of features - urban background The relative importance of different features depending on model (RF or XGB), pollutant (PM10, NOx, O3) and forecast period \n(1-day, 2-day and 3-day) is shown in plots in Appendix B. It should be noted that the local deterministic models (Gauss and \nOSPM) use the same meteorological data to forecast concentrations, so when the meteorological variables are important features for the MLs, it indicates that the deterministic models don’t capture all processes related to those variables. In summary \n15 \nregarding importance of features for urban background: \nNOx. Lagged 24-hour mean concentrations, calendar data, wind speed and local deterministic forecasts are among the top-10 \nmost important variables using RF and XGB, but it can be noted that the deterministic forecast is not the most important feature \nfor any model. Of the calendar features hour is most important reflecting the importance of regular, diurnal variations in traffic features for the MLs, it indicates that the deterministic models don’t capture all processes related to those variables. In summary \n15 \nregarding importance of features for urban background: \nNOx. Lagged 24-hour mean concentrations, calendar data, wind speed and local deterministic forecasts are among the top-10 regarding importance of features for urban background: \nNOx. Lagged 24-hour mean concentrations, calendar data, wind speed and local deterministic forecasts are among the top-10 \nmost important variables using RF and XGB, but it can be noted that the deterministic forecast is not the most important feature \nfor any model. Of the calendar features hour is most important reflecting the importance of regular, diurnal variations in traffic \nemissions. 20 emissions. 20 \nPM10. The regional deterministic forecast is the most important feature for PM10 forecasts, both for RF and XGB and for all \nforecast days. Also lagged measurements, both average, minimum and maximum concentrations is important. Of the calendar \nfeatures the seasonal variation is reflected in the importance of the Julian day. y\np\ng\np\nregional deterministic forecasts is the dominant feature both for RF and XGB, and for all forecast days. Also lagged measured \n25 \nmaximum concentrations is of some importance. The relative humidity is important, likely reflecting that O3 concentrations \nare typically higher during dry, clear sky conditions, which may not be completely captured by the deterministic forecasts. 12 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 3.1.2 \nComparison between deterministic forecasts and MLs - urban background Figure 4 shows an example of the temporal variations in September 2021 in the forecasts with deterministic modelling and \nGAM in comparison to the observations. Similar plots are also given for individual models in Figure C1. The plots were made \nusing the Openair R package (Carslaw and Ropkins, 2012). For all pollutants the MLs tend to improve the variability in the \nobserved concentrations compared to the deterministic forecasts, but there are significant deviations. For O3 the minimum \n5 \nconcentrations observed is often not forecasted so well and for PM10 the highest concentrations is not captured by the models. concentrations observed is often not forecasted so well and for PM10 the highest concentrations is not captured by the \n \nFigure 4. Temporal variations in hourly mean NOx, PM10 and O3 concentrations at the urban background site during Sep\n2021 based on observations, deterministic forecasts and GAM. Mean of 1-, 2- and 3-day forecasts. Figure 4. Temporal variations in hourly mean NOx, PM10 and O3 concentrations at the urban background site during Septe\n2021 based on observations, deterministic forecasts and GAM. Mean of 1-, 2- and 3-day forecasts. 0 Figure 4. Temporal variations in hourly mean NOx, PM10 and O3 concentrations at the urban background site during September \n2021 based on observations, deterministic forecasts and GAM. Mean of 1-, 2- and 3-day forecasts. 10 10 13 Figure 5 shows example of deviations from observations of forecasted NOx, PM10 and O3 for all models illustrating that during \nsome hours all models systematically show large absolute deviations from the observed mean concentrations. Sometimes the \nhours with large deviation for NOx coincide with deviations for PM10 indicating some specific meteorological situation or \ncommon source that cause this deviation. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Figure 5 shows example of deviations from observations of forecasted NOx, PM10 and O3 for all models illustrating that during \nsome hours all models systematically show large absolute deviations from the observed mean concentrations. Sometimes the \nhours with large deviation for NOx coincide with deviations for PM10 indicating some specific meteorological situation or \ncommon source that cause this deviation. 5 Figure 5. 3.1.2 \nComparison between deterministic forecasts and MLs - urban background Absolute deviations of forecasted NOx, PM10 and O3 concentrations from observed (Obs) concentrations based on mean of \n1-, 2- and 3-day forecasts for September 2021. All data are hourly mean concentrations. Figure 5. Absolute deviations of forecasted NOx, PM10 and O3 concentrations from observed (Obs) concentrations based on mean of \n1-, 2- and 3-day forecasts for September 2021. All data are hourly mean concentrations. Figure C2 shows systematic deviations between the observed mean diurnal variations and the deterministic forecast. This is \nsignificantly improved using the MLs, especially for NOx and O3. For O3 the deterministic forecast systematically \n10 Figure C2 shows systematic deviations between the observed mean diurnal variations and the deterministic forecast. This is \nsignificantly improved using the MLs, especially for NOx and O3. For O3 the deterministic forecast systematically \n0 10 14 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. overestimates the concentrations which is mainly due to the fact that the chemical destruction of O3 in the city centre is not \nproperly accounted for by the regional CAMS model. For NOx the concentrations calculated by the deterministic model are \nsystematically shifted one hour compared to the observed concentration and this is likely associated with errors in \nparameterisation of traffic emissions, which is the most important source of NOx in Stockholm. For PM10 concentrations \nmodelled by the deterministic model are too low during the night compared to observations, but this is corrected using RF and \n5 \nXGB, but not using LSTM. overestimates the concentrations which is mainly due to the fact that the chemical destruction of O3 in the city centre is not \nproperly accounted for by the regional CAMS model. For NOx the concentrations calculated by the deterministic model are \nsystematically shifted one hour compared to the observed concentration and this is likely associated with errors in \nparameterisation of traffic emissions, which is the most important source of NOx in Stockholm. For PM10 concentrations \nmodelled by the deterministic model are too low during the night compared to observations, but this is corrected using RF and \n5 \nXGB, but not using LSTM. As can be seen in Table 2 and Figure 6 most of the statistical performance measures are improved compared to the deterministic \nforecasts of NOx and PM10 using different MLs. For NOx Pearson correlation (r) increases from 0.35-0.39 with deterministic \nforecasts to between 0.49 and 0.70 when MLs are used. 3.1.2 \nComparison between deterministic forecasts and MLs - urban background Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Table 2. Comparison of 1-, 2-, 3-day deterministic and ML forecasts for NOx, PM10 and O3 for the urban background site. r = \nPearson correlation, MAPE = mean absolute percentage error, nRMSE = normalised rootmean square error and nMAE = \nnormalised mean absolute error. All data are based on hourly mean values. NOx \n \nr \nMAPE \nnRMSE \nnMAE \n \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \nDet \n0.39 \n0.38 \n0.35 \n69% \n65% \n67% \n130% \n124% \n116% \n63% \n61% \n61% \nXGB \n0.49 \n0.53 \n0.54 \n42% \n44% \n48% \n118% \n114% \n114% \n44% \n45% \n47% \nRF \n0.54 \n0.57 \n0.60 \n37% \n38% \n37% \n115% \n112% \n111% \n41% \n41% \n41% \nLSTM \n0.70 \n0.69 \n0.66 \n50% \n59% \n54% \n99% \n99% \n101% \n43% \n47% \n46% \nGAM \n0.50 \n0.55 \n0.58 \n37% \n37% \n37% \n117% \n114% \n112% \n42% \n42% \n42% \nPM10 \n \nr \nMAPE \nnRMSE \nnMAE \n \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \nDet \n0.53 \n0.50 \n0.50 \n54% \n56% \n59% \n81% \n85% \n87% \n47% \n48% \n50% \nXGB \n0.71 \n0.65 \n0.56 \n61% \n64% \n69% \n58% \n64% \n69% \n41% \n44% \n47% \nRF \n0.74 \n0.65 \n0.60 \n55% \n74% \n78% \n56% \n63% \n66% \n39% \n45% \n46% \nLSTM \n0.71 \n0.57 \n0.50 \n47% \n54% \n60% \n62% \n73% \n79% \n42% \n49% \n53% \nGAM \n0.73 \n0.64 \n0.59 \n55% \n76% \n80% \n56% \n64% \n67% \n39% \n46% \n47% \nO3 \n \nr \nMAPE \nnRMSE \nnMAE \n \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \nDet \n0.74 \n0.71 \n0.69 \n45% \n49% \n50% \n31% \n32% \n32% \n24% \n25% \n25% \nXGB \n0.75 \n0.71 \n0.67 \n47% \n51% \n53% \n25% \n26% \n27% \n19% \n20% \n21% \nRF \n0.76 \n0.69 \n0.71 \n47% \n54% \n52% \n24% \n26% \n26% \n19% \n21% \n20% \nLSTM \n0.76 \n0.74 \n0.74 \n46% \n47% \n51% \n24% \n25% \n25% \n19% \n20% \n20% \nGAM \n0.75 \n0.66 \n0.69 \n47% \n55% \n52% \n24% \n27% \n27% \n19% \n22% \n21% Table 2. Comparison of 1-, 2-, 3-day deterministic and ML forecasts for NOx, PM10 and O3 for the urban background site. r = \nPearson correlation, MAPE = mean absolute percentage error, nRMSE = normalised rootmean square error and nMAE = \nnormalised mean absolute error. All data are based on hourly mean values. Table 2. Comparison of 1-, 2-, 3-day deterministic and ML forecasts for NOx, PM10 and O3 for the urban background site. 3.1.2 \nComparison between deterministic forecasts and MLs - urban background MAPE, nRMSE and nMAE decreases for all models and all forecast \n10 \ndays. For PM10 Pearson r increases from 0.50-0.53 with deterministic forecasts to between 0.50 and 0.74 when MLs are used. nRMSE and nMAE decreases for forecast days, but for MAPE results are not so consistent – MAPE increases slightly with \nXGB, RF and GAM, while it decrease for 1-day and 2-day forecasts using LSTM. For O3 there are small improvements looking \nat Pearson r and MAPE, nRMSE and nMAE decreases. The Pearson correlation for O3 is already relatively high and errors \nl ti\nl\nll\nith th d t\ni i ti CAMS\nd lli\n15 As can be seen in Table 2 and Figure 6 most of the statistical performance measures are improved compared to the deterministic \nforecasts of NOx and PM10 using different MLs. For NOx Pearson correlation (r) increases from 0.35-0.39 with deterministic \nforecasts to between 0.49 and 0.70 when MLs are used. MAPE, nRMSE and nMAE decreases for all models and all forecast \n10 \ndays. For PM10 Pearson r increases from 0.50-0.53 with deterministic forecasts to between 0.50 and 0.74 when MLs are used. nRMSE and nMAE decreases for forecast days, but for MAPE results are not so consistent – MAPE increases slightly with \nXGB, RF and GAM, while it decrease for 1-day and 2-day forecasts using LSTM. For O3 there are small improvements looking \nat Pearson r and MAPE, nRMSE and nMAE decreases. The Pearson correlation for O3 is already relatively high and errors relatively small with the deterministic CAMS modelling. 15 \nFigure 6 presents mean of 1-day, 2-day and 3-day statistical performances as ratios of ML to deterministic forecasts. This \nshows that NOx is consistently improved using all MLs for all statistical performance indexes, whereas for PM10 and O3 there \nare improvements in nRMSE and nMAE, but MAPE. Overall, the difference in performance between different models is small, \nless than 30%, but larger when comparing different pollutants. y\ng\nFigure 6 presents mean of 1-day, 2-day and 3-day statistical performances as ratios of ML to deterministic forecasts. This \nshows that NOx is consistently improved using all MLs for all statistical performance indexes, whereas for PM10 and O3 there \nare improvements in nRMSE and nMAE, but MAPE. Overall, the difference in performance between different models is small, \nless than 30%, but larger when comparing different pollutants. 15 https://doi.org/10.5194/acp-2023-38\nPreprint. 3.1.2 \nComparison between deterministic forecasts and MLs - urban background r = \nPearson correlation, MAPE = mean absolute percentage error, nRMSE = normalised rootmean square error and nMAE = \nnormalised mean absolute error. All data are based on hourly mean values. 16 os of statistical performances for MLs versus the deterministic hourly forecasts for the urban site. Mean of 1-day, 2-\nforecasts. e 6. Ratios of statistical performances for MLs versus the deterministic hourly forecasts for the urban site. Mean of 1-day, 2 Figure 6. Ratios of statistical performances for MLs versus the deterministic hourly forecasts for the urban site. Mean of 1-day, 2-\nday and 3-day forecasts. For the general public it is important to receive information on future pollution episodes with high concentrations. The plots \nin Figure D1 shows that statistical performances for all models is worse when concentrations higher than when the mean value \n5 \nis analysed. Pearson r is somewhat higher for PM10 and O3, but not when RF and XGB is used for NOx. MAPE is reduced for \nPM10 and NOx but not for O3. The nRMSE is both higher and lower with MLs compared to the deterministic model, while, \nfinally, nMAE is lower for NOx and PM10 using RF and XGB, but not for PM10 using LSTM. g\np\np\np\np\ng\np\nin Figure D1 shows that statistical performances for all models is worse when concentrations higher than when the mean value \n5 \nis analysed. Pearson r is somewhat higher for PM10 and O3, but not when RF and XGB is used for NOx. MAPE is reduced for \nPM10 and NOx but not for O3. The nRMSE is both higher and lower with MLs compared to the deterministic model, while, \nfinally, nMAE is lower for NOx and PM10 using RF and XGB, but not for PM10 using LSTM. 17 17 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. As can be seen in Figure 7 all MQI are below 100% indicating that deviations between model results and measurements are \nsmaller than the estimated uncertainties in the measurements. 3.1.2 \nComparison between deterministic forecasts and MLs - urban background It can also be seen that LSTM is somewhat more efficient in \nreducing MQI, from 68% to 60% for NOx and O3 from 40% to 29%, while RF and XGB provides no improvement for NOx, \nbut both PM10 and O3 shows slightly lower MQI with RF and XGB compared to the deterministic forecast. 5 Figure 7. MQI based on hourly mean concentrations for the whole test period for NOx, PM10 and O3 of the urban site. Mean of 1-, \n2- and 3-day forecasts. Figure 7. MQI based on hourly mean concentrations for the whole test period for NOx, PM10 and O3 of the urban site. Mean of 1-, \n2- and 3-day forecasts. Figure 7. MQI based on hourly mean concentrations for the whole test period for NOx, PM10 and O3 of the urban site. Mean of 1-, \n2- and 3-day forecasts. 3.2.1 \nImportance of features - street canyon sites For the street canyon sites the relative importance of different features is different for PM10 and NOx and also somewhat \ndifferent depending on ML model and street (see figures in Appendix E). There are, however, some typical features that tend \nto be more important. For PM10 Julian day, lagged measurements and deterministic forecasts are mostly among the top 5 most \nimportant features. For NOx deterministic forecasts, hour of the day and weekday are the most important, while lagged \n15 to be more important. For PM10 Julian day, lagged measurements and deterministic forecasts are mostly among the top 5 most \nimportant features. For NOx deterministic forecasts, hour of the day and weekday are the most important, while lagged \n15 \nmeasurements are less useful for the ML models. The importance of calendar data for NOx likely reflects importance of diurnal \nand weekday variations in traffic emissions not correctly captured by the deterministic forecast. Julian day likely reflects \nseasonal variations in non-exhaust emissions of PM10. Even though there are variations it is difficult see any systematic \ndifference in the features between ML for the different street sites. 20 20 3.2.2 \nComparison between deterministic forecasts and MLs - street canyon sites Comparisons between the hourly temporal variations in observations and forecasts of NOx with the GAM model in September \n2022 are shown in Figure 8 and for all models in Appendix F. One can see that the deterministic forecast tend to overestimate \nconcentrations of NOx during daytime especially for Sveavägen and this is corrected when ML modelling is being applied. 18 Corresponding plots for PM10 are shown in Figure 9. In this case the GAM overestimates concentrations on Folkungagatan \nand Hornsgatan during the end of September, but performs well otherwise, whereas the deterministic forecast overestimates \nPM10 on Sveavägen and Hornsgatan during the first half of the month. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Corresponding plots for PM10 are shown in Figure 9. In this case the GAM overestimates concentrations on Folkungagatan \nand Hornsgatan during the end of September, but performs well otherwise, whereas the deterministic forecast overestimates \nPM10 on Sveavägen and Hornsgatan during the first half of the month. Figure 8. Temporal variations in hourly mean NOx concentrations at the street canyon sites during September 2022 based\nobservations (red) and 1-day forecasts based on deterministic modelling (blue) and GAM (green). 5 Figure 8. Temporal variations in hourly mean NOx concentrations at the street canyon sites during September 2022 based on \nobservations (red) and 1-day forecasts based on deterministic modelling (blue) and GAM (green). 19 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Figure 9. Temporal variations in hourly mean PM10 concentrations at the street canyon sites during September 2022 based \nobservations, deterministic modelling and GAM forecasts. Mean of 1-, 2- and 3-day forecasts. Figure 9. Temporal variations in hourly mean PM10 concentrations at the street canyon sites during September 2022 based on \nobservations, deterministic modelling and GAM forecasts. Mean of 1-, 2- and 3-day forecasts. The improvement of the temporal variations of NOx and PM10 is well illustrated by comparing the mean diurnal variations in \n5 \nobservations with deterministic modelling and using the MLs, GAM shown in Figure 10 and all models shown in figures in \nAppendix G. The improvement of the temporal variations of NOx and PM10 is well illustrated by comparing the mean diurnal variations in \n5 \nobservations with deterministic modelling and using the MLs, GAM shown in Figure 10 and all models shown in figures in \nAppendix G. For all street sites, both NOx and PM10 concentrations shows systematic deviations from observations using \ndeterministic modelling, but this is corrected using the MLs, especially for NOx. The tendency that the LSTM model is not as \ngood to capture variations in PM10 at the urban site is also seen here for the street canyon sites. 3.2.2 \nComparison between deterministic forecasts and MLs - street canyon sites For all street sites, both NOx and PM10 concentrations shows systematic deviations from observations using \ndeterministic modelling, but this is corrected using the MLs, especially for NOx. The tendency that the LSTM model is not as \ngood to capture variations in PM10 at the urban site is also seen here for the street canyon sites. The improvement of the temporal variations of NOx and PM10 is well illustrated by comparing the mean diurnal variations in \n5 \nobservations with deterministic modelling and using the MLs, GAM shown in Figure 10 and all models shown in figures in \nAppendix G. For all street sites, both NOx and PM10 concentrations shows systematic deviations from observations using \ndeterministic modelling, but this is corrected using the MLs, especially for NOx. The tendency that the LSTM model is not as \ngood to capture variations in PM10 at the urban site is also seen here for the street canyon sites. 10 20 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Figure 10. Mean diurnal variations in hourly mean observations, deterministic and GAM forecasts of NOx and PM10 for the street \ncanyon sites. Mean of 1-, 2- and 3-day forecasts. Figure 10. Mean diurnal variations in hourly mean observations, deterministic and GAM forecasts of NOx and PM10 for the street \ncanyon sites. Mean of 1-, 2- and 3-day forecasts. 5 For all streets statistical performance of NOx forecasts are improved using the MLs as shown for all forecasts in Table 3. The \nimprovement in terms of Pearson correlation (r), MAPE, nRMSE and nMAE is very similar for the MLs but differ between \nstreets, with forecasts for Hornsgatan showing higher r and lower relative errors compared to the other streets. 0 For all streets statistical performance of NOx forecasts are improved using the MLs as shown for all forecasts in Table 3. The \nimprovement in terms of Pearson correlation (r), MAPE, nRMSE and nMAE is very similar for the MLs but differ between \nstreets, with forecasts for Hornsgatan showing higher r and lower relative errors compared to the other streets. 0 For all streets statistical performance of NOx forecasts are improved using the MLs as shown for all forecasts in Table 3. Figure 11 clearly illustrates the improvements of all statistical performance indexes for NOx at all street canyon sites and for \n5 \nMLs. The errors (MAPE, nRMSE, nMAE) are reduced by between 30% and 60% and the Pearson correlation coefficients \nincrease by between 30% and 50%. 3.2.2 \nComparison between deterministic forecasts and MLs - street canyon sites The \nimprovement in terms of Pearson correlation (r), MAPE, nRMSE and nMAE is very similar for the MLs but differ between \nstreets, with forecasts for Hornsgatan showing higher r and lower relative errors compared to the other streets. 10 21 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Table 3. Comparison of 1-, 2-, 3-day deterministic and ML forecasts for NOx for the street canyon sites. r = Pearson correlation, \nMAPE = mean absolute percentage error, nRMSE = normalised rootmean square error and nMAE = normalised mean absolute \nerror. All data are based on hourly mean values. Folkungagatan \n \nr \nMAPE \nnRMSE \nnMAE \n \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \nDet \n0.48 \n0.49 \n0.47 \n107% \n118% \n120% \n108% \n109% \n106% \n72% \n73% \n73% \nXGB \n0.65 \n0.64 \n0.63 \n67% \n73% \n76% \n74% \n75% \n75% \n47% \n50% \n50% \nRF \n0.66 \n0.65 \n0.65 \n64% \n73% \n81% \n71% \n74% \n77% \n45% \n49% \n53% \nLSTM \n0.64 \n0.61 \n0.62 \n65% \n60% \n79% \n72% \n74% \n74% \n46% \n46% \n50% \nGAM \n0.66 \n0.65 \n0.65 \n65% \n75% \n81% \n73% \n75% \n77% \n46% \n51% \n53% \nSveavägen \n \nr \nMAPE \nnRMSE \nnMAE \n \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \nDet \n0.46 \n0.53 \n0.44 \n159% \n161% \n163% \n137% \n136% \n134% \n99% \n98% \n97% \nXGB \n0.69 \n0.68 \n0.66 \n59% \n57% \n59% \n68% \n69% \n71% \n41% \n41% \n41% \nRF \n0.73 \n0.73 \n0.73 \n51% \n51% \n50% \n65% \n65% \n65% \n37% \n38% \n37% \nLSTM \n0.71 \n0.69 \n0.66 \n58% \n60% \n64% \n68% \n69% \n71% \n41% \n41% \n43% \nGAM \n0.72 \n0.71 \n0.71 \n52% \n51% \n49% \n65% \n67% \n66% \n38% \n39% \n37% \nHornsgatan \n \nr \nMAPE \nnRMSE \nnMAE \n \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \nDet \n0.53 \n0.56 \n0.55 \n80% \n69% \n73% \n82% \n79% \n80% \n55% \n52% \n54% \nXGB \n0.80 \n0.81 \n0.81 \n45% \n45% \n44% \n52% \n51% \n50% \n32% \n32% \n32% \nRF \n0.79 \n0.79 \n0.81 \n42% \n43% \n43% \n52% \n53% \n50% \n31% \n32% \n31% \nLSTM \n0.77 \n0.76 \n0.76 \n48% \n51% \n51% \n57% \n57% \n56% \n36% \n36% \n36% \nGAM \n0.80 \n0.80 \n0.82 \n42% \n43% \n43% \n51% \n51% \n50% \n31% \n32% \n31% \n \nFigure 11 clearly illustrates the improvements of all statistical performance indexes for NOx at all street canyon sites and for \nMLs. The errors (MAPE, nRMSE, nMAE) are reduced by between 30% and 60% and the Pearson correlation coefficients \nincrease by between 30% and 50%. Table 3. 3.2.2 \nComparison between deterministic forecasts and MLs - street canyon sites Comparison of 1-, 2-, 3-day deterministic and ML forecasts for NOx for the street canyon sites. r = Pearson correlation, \nMAPE = mean absolute percentage error, nRMSE = normalised rootmean square error and nMAE = normalised mean absolute \nerror. All data are based on hourly mean values. Figure 11 clearly illustrates the improvements of all statistical performance indexes for NOx at all street canyon sites and for \n5 \nMLs. The errors (MAPE, nRMSE, nMAE) are reduced by between 30% and 60% and the Pearson correlation coefficients \nincrease by between 30% and 50%. 22 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. igure 11. Ratios of statistical performances for MLs versus the deterministic hourly forecasts for NOx at the stree\nMean of 1-day, 2-day and 3-day forecasts. igure 11. Ratios of statistical performances for MLs versus the deterministic hourly forecasts for NOx at the street canyon sites. Mean of 1-day, 2-day and 3-day forecasts. Figure 11. Ratios of statistical performances for MLs versus the deterministic hourly forecasts for NOx at the street canyon sites. Mean of 1-day, 2-day and 3-day forecasts. l performances for MLs versus the deterministic hourly forecasts for NOx at the street canyon sites. ay forecasts. Comparison between the statistical performance measures for MLs and deterministic forecasts for PM10 shows somewhat \n5 \nvariable results depending on statistical measure, street and ML. Person r values increase slightly in most cases and the \nnormalised RMSE and MAE are lower for most MLs and streets, but not always, while MAPE often increase using the MLs \n(Table 4 and Figure 12). Errors measured as nRMSE decrease by between 10% and 30%, whereas errors measured as MAPE \nmostly increase slightly and nMAE is about unchanged. Pearson r increase at Folkungagatan for all MLs (10% - 30%) but \nshow somewhat varying results for Sveavägen and Hornsgatan. 10 23 Table 4. Comparison of 1-, 2-, 3-day deterministic and ML forecasts for PM10 for the street canyon sites. r = Pearson correlation, \nMAPE = mean absolute percentage error, nRMSE = normalised rootmean square error and nMAE = normalised mean absolute \nerror. All data are based on hourly mean values. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Table 4. 3.2.2 \nComparison between deterministic forecasts and MLs - street canyon sites Comparison of 1-, 2-, 3-day deterministic and ML forecasts for PM10 for the street canyon sites. r = Pearson correlation, \nMAPE = mean absolute percentage error, nRMSE = normalised rootmean square error and nMAE = normalised mean absolute \nerror. All data are based on hourly mean values. Folkungagatan \n \nr \nMAPE \nnRMSE \nnMAE \n \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \nDet \n0.32 \n0.30 \n0.34 \n121% \n112% \n119% \n115% \n116% \n115% \n56% \n57% \n56% \nXGB \n0.41 \n0.30 \n0.34 \n122% \n134% \n121% \n85% \n102% \n83% \n52% \n63% \n54% \nRF \n0.36 \n0.39 \n0.41 \n134% \n121% \n129% \n89% \n82% \n75% \n52% \n52% \n49% \nLSTM \n0.47 \n0.43 \n0.34 \n102% \n115% \n141% \n82% \n77% \n83% \n58% \n53% \n58% \nGAM \n0.37 \n0.34 \n0.39 \n132% \n123% \n127% \n88% \n95% \n77% \n52% \n57% \n50% \nSveavägen \n \nr \nMAPE \nnRMSE \nnMAE \n \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \nDet \n0.42 \n0.40 \n0.40 \n98% \n100% \n95% \n92% \n92% \n92% \n55% \n56% \n54% \nXGB \n0.42 \n0.31 \n0.45 \n122% \n124% \n109% \n76% \n92% \n73% \n51% \n58% \n49% \nRF \n0.49 \n0.27 \n0.40 \n113% \n125% \n114% \n67% \n99% \n74% \n45% \n57% \n50% \nLSTM \n0.51 \n0.49 \n0.46 \n90% \n106% \n109% \n67% \n67% \n68% \n47% \n48% \n49% \nGAM \n0.45 \n0.28 \n0.41 \n115% \n121% \n111% \n71% \n93% \n75% \n46% \n56% \n49% \nHornsgatan \n \nr \nMAPE \nnRMSE \nnMAE \n \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \n1-day \n2-day \n3-day \nDet \n0.40 \n0.36 \n0.30 \n81% \n80% \n87% \n113% \n116% \n118% \n59% \n60% \n62% \nXGB \n0.46 \n0.30 \n0.37 \n84% \n103% \n91% \n89% \n110% \n89% \n56% \n67% \n59% \nRF \n0.42 \n0.21 \n0.33 \n85% \n115% \n94% \n91% \n130% \n90% \n57% \n73% \n59% \nLSTM \n0.49 \n0.40 \n0.34 \n77% \n84% \n93% \n82% \n85% \n89% \n56% \n59% \n64% \nGAM \n0.45 \n0.25 \n0.34 \n84% \n107% \n92% \n88% \n114% \n89% \n56% \n68% \n58% Table 4. Comparison of 1-, 2-, 3-day deterministic and ML forecasts for PM10 for the street canyon sites. r = Pearson correlation, \nMAPE = mean absolute percentage error, nRMSE = normalised rootmean square error and nMAE = normalised mean absolute \nerror. All data are based on hourly mean values. 5 24 12. Ratios of statistical performances for MLs versus the deterministic hourly forecasts for PM10 at the street can\nof 1-day, 2-day and 3-day forecasts. e 12. Ratios of statistical performances for MLs versus the deterministic hourly forecasts for PM10 at the street canyon sites. 2. 3.2.2 \nComparison between deterministic forecasts and MLs - street canyon sites Ratios of statistical performances for MLs versus the deterministic hourly forecasts for PM10 at the street canyon sit Figure 12. Ratios of statistical performances for MLs versus the deterministic hourly forecasts for PM10 at the street canyon sites. Mean of 1-day, 2-day and 3-day forecasts. l performances for MLs versus the deterministic hourly forecasts for PM10 at the street canyon sites. ay forecasts. As pointed out before it is important to assess statistical performance measures for periods with high concentrations. Similar \n5 \nto what is seen for the urban site the statistical performances for all models are much worse for the hourly mean concentrations \nthat are higher than the mean values and the pattern is also similar for the different streets. As pointed out before it is important to assess statistical performance measures for periods with high concentrations. Similar \n5 \nto what is seen for the urban site the statistical performances for all models are much worse for the hourly mean concentrations \nthat are higher than the mean values and the pattern is also similar for the different streets. 25 3 2 3\nMQI street canyon sites\nhttps://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 3.2.3 \nMQI street canyon sites Figure 13 illustrates that deviations between model results and measurements compared to the uncertainties of the \nmeasurements for all pollutants and street canyon sites. For NOx relative uncertainties decreases using the MLs compared to \nthe deterministic forecast, while for PM10 results varies, but there is no systematic improvement using MLs compared to the \ndeterministic model. 5 5 dete\nst c\node . 5\n \nFigure 13. MQI for NOx and PM10 forecasts at street canyon sites. Mean values for 1-, 2- and 3-day forecasts. Figure 13. MQI for NOx and PM10 forecasts at street canyon sites. Mean values for 1-, 2- and 3-day forecasts. Figure 13. MQI for NOx and PM10 forecasts at street canyon sites. Mean values for 1-, 2- and 3-day forecasts. 10 26 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 3.3 \nGeneralisation of street canyon modelling Until now, the model performance is evaluated using training and testing data from three single sites respectively. In Stockholm \nas well as in other cities most of the streets do not have any monitoring station. This is of course due to resource constraints \nbut also associated with the fact that the EU Air Quality Directives regulates the number of monitoring sites required in a city \ndepending on the level of air pollution and number of inhabitants. The monitoring stations should provide information for both \n5 \nareas where the highest concentrations of air pollutants occur and other areas that are representative of the exposure of the \ngeneral population. Less resources is required if this information can be achieved by accurate enough modelling. Until now, the model performance is evaluated using training and testing data from three single sites respectively. In Stockholm \nas well as in other cities most of the streets do not have any monitoring station. This is of course due to resource constraints \nbut also associated with the fact that the EU Air Quality Directives regulates the number of monitoring sites required in a city \ndepending on the level of air pollution and number of inhabitants. The monitoring stations should provide information for both \n5 \nareas where the highest concentrations of air pollutants occur and other areas that are representative of the exposure of the \ngeneral population. Less resources is required if this information can be achieved by accurate enough modelling. We therefore analyze the generalization capacities of the models, with the expectation that we can achieve certain prediction \nperformance of one site without having any measurement data. Computational experiments were carried out through cross-\nvalidation, which combines training and testing data coming from different measurement sites. For the street canyon sites, four \n10 \ncombinations of training datasets were applied to evaluate the generalization abilities of different ML models. We therefore analyze the generalization capacities of the models, with the expectation that we can achieve certain prediction \nperformance of one site without having any measurement data. Computational experiments were carried out through cross-\nvalidation, which combines training and testing data coming from different measurement sites. For the street canyon sites, four \n10 \ncombinations of training datasets were applied to evaluate the generalization abilities of different ML models. 3.3 \nGeneralisation of street canyon modelling We therefore analyze the generalization capacities of the models, with the expectation that we can achieve certain prediction \nperformance of one site without having any measurement data. Computational experiments were carried out through cross-\nvalidation, which combines training and testing data coming from different measurement sites. For the street canyon sites, four \n10 \ncombinations of training datasets were applied to evaluate the generalization abilities of different ML models. validation, which combines training and testing data coming from different measurement sites. For the street canyon sites, four \n10 \ncombinations of training datasets were applied to evaluate the generalization abilities of different ML models. Figure 14 shows mean of 1-day, 2-day, and 3-day forecasted NOx concentrations for the three street canyon sites based on \ntraining the models on the other streets. It shows that the forecast is improved compared to the deterministic forecast for g\ny,\ny,\ny\nx\ny\ntraining the models on the other streets. It shows that the forecast is improved compared to the deterministic forecast for \nHornsgatan and Sveavägen, but not so much for Folkungagatan. For Hornsgatan the correlation is 0.55 using the deterministic \n15 \nforecast whereas the MLs gives correlations between 0.61 and 0.67 and all errors decrease slightly using the MLs. For \nSveavägen the correlation is 0.48 using the deterministic forecast whereas the MLs gives correlations between 0.62 and 0.63 \nand here all errors decrease substantially using the MLs. But for Folkungagatan the MLs show different results. Correlations \nare similar or even decreases, whereas errors mostly decreases depending on ML applied. Hornsgatan and Sveavägen, but not so much for Folkungagatan. For Hornsgatan the correlation is 0.55 using the deterministic \n15 \nforecast whereas the MLs gives correlations between 0.61 and 0.67 and all errors decrease slightly using the MLs. For \nSveavägen the correlation is 0.48 using the deterministic forecast whereas the MLs gives correlations between 0.62 and 0.63 \nand here all errors decrease substantially using the MLs. But for Folkungagatan the MLs show different results. Correlations \nare similar or even decreases, whereas errors mostly decreases depending on ML applied. 20 27 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Figure 14. Statistical performances of NOx forecasts for the streets when the MLs are trained using only data from the other streets. Mean of 1-day, 2-day, and 3-day forecasts. Figure 14. 3.3 \nGeneralisation of street canyon modelling Statistical performances of NOx forecasts for the streets when the MLs are trained using only data from the other streets. Mean of 1-day, 2-day, and 3-day forecasts. ances of NOx forecasts for the streets when the MLs are trained using only data from the other streets. day forecasts. Figure 15 shows mean of 1-day, 2-day, and 3-day forecasted PM10 concentrations for the three street canyon sites based on \n5 \ntraining the models on the other streets. It can be seen that it is not possible to find any systematic improvement of the \ndeterministic forecast for the streets using RF and XGB compared to the deterministic forecasts. But with LSTM correlations \nincrease slightly and errors decrease at all streets compared to the deterministic forecasts. Figure 15 shows mean of 1-day, 2-day, and 3-day forecasted PM10 concentrations for the three street canyon sites based on \n5 \ntraining the models on the other streets. It can be seen that it is not possible to find any systematic improvement of the \ndeterministic forecast for the streets using RF and XGB compared to the deterministic forecasts. But with LSTM correlations \nincrease slightly and errors decrease at all streets compared to the deterministic forecasts. 28 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 5. Statistical performances of PM10 forecasts for the streets when the MLs are trained using only data from the other streets. 1-day, 2-day, and 3-day forecasts. Figure 15. Statistical performances of PM10 forecasts for the streets when the MLs are trained using only data from the other streets. Mean of 1-day, 2-day, and 3-day forecasts. 4 \nDiscussion \n5 For PM10 the seasonal variation described \nby Julian day is the most important feature at the street canyon sites, both for RF and XGB. This indicates that the deterministic forecasts is not capable at describing impacts of meteorology and road dust emissions on PM10, even though parameterisations \n10 \nof these processes are included in the deterministic modelling system. The total mass generated by road wear is a key factor \nfor PM10 emissions and these emissions are strongly controlled by surface moisture conditions and this is taken into account \nby the NORTRIP model. But as pointed out by Denby et al (2013b) there are periods where surface wetness is not well \nmodelled and it is not known if this is the result of input data, e.g. precipitation, or of the model formulation itself. forecasts is not capable at describing impacts of meteorology and road dust emissions on PM10, even though parameterisations \n10 \nof these processes are included in the deterministic modelling system. The total mass generated by road wear is a key factor \nfor PM10 emissions and these emissions are strongly controlled by surface moisture conditions and this is taken into account \nby the NORTRIP model. But as pointed out by Denby et al (2013b) there are periods where surface wetness is not well \nmodelled and it is not known if this is the result of input data, e.g. precipitation, or of the model formulation itself. forecasts is not capable at describing impacts of meteorology and road dust emissions on PM10, even though parameterisations \n10 \nof these processes are included in the deterministic modelling system. The total mass generated by road wear is a key factor \nfor PM10 emissions and these emissions are strongly controlled by surface moisture conditions and this is taken into account \nby the NORTRIP model. But as pointed out by Denby et al (2013b) there are periods where surface wetness is not well \nmodelled and it is not known if this is the result of input data, e.g. precipitation, or of the model formulation itself. It is clear that the deterministic forecast of O3 underestimates concentrations at the urban site due to the fact that the local \n15 \nemissions of NOx influencing the photochemistry is not properly considered by the CAMS model, but this is corrected using \nthe MLs. 4 \nDiscussion \n5 Despite this the deterministic forecast is the most important feature for both RF and XGB but also lagged measured \nmean and maximum O3 concentrations improve the deterministic forecasts. Despite the fact that the configurations and traffic situations are quite similar for the street canyon sites the improvements of It is clear that the deterministic forecast of O3 underestimates concentrations at the urban site due to the fact that the local \n15 \nemissions of NOx influencing the photochemistry is not properly considered by the CAMS model, but this is corrected using \nthe MLs. Despite this the deterministic forecast is the most important feature for both RF and XGB but also lagged measured \nmean and maximum O3 concentrations improve the deterministic forecasts. Despite the fact that the configurations and traffic situations are quite similar for the street canyon sites the improvements of It is clear that the deterministic forecast of O3 underestimates concentrations at the urban site due to the fact that the local \n15 \nemissions of NOx influencing the photochemistry is not properly considered by the CAMS model, but this is corrected using \nthe MLs. Despite this the deterministic forecast is the most important feature for both RF and XGB but also lagged measured \nmean and maximum O3 concentrations improve the deterministic forecasts. Despite the fact that the configurations and traffic situations are quite similar for the street canyon sites, the improvements of the deterministic forecasts using ML differs. For NOx forecasts on Hornsgatan are more accurate (lower errors and higher r) \n20 \nthan for the other two sites, while for PM10 there is no obvious difference between the sites. The overall model quality according to the recommendations by the Forum for Air Quality Modeling (FAIRMODE) in the \ncontext of the air quality directives, is improved using the MLs resulting in uncertainties that are significantly smaller than the \nmeasurement uncertainties for all pollutants. But the forecasts of the highest concentrations including episodes with high \nconcentrations is not systematically improved for all pollutants and all statistical performance measures using the MLs\n25 than for the other two sites, while for PM10 there is no obvious difference between the sites. The overall model quality according to the recommendations by the Forum for Air Quality Modeling (FAIRMODE) in the \ncontext of the air quality directives, is improved using the MLs resulting in uncertainties that are significantly smaller than the \nmeasurement uncertainties for all pollutants. 4 \nDiscussion \n5 The performance of the MLs are quite similar for the different sites and forecast days. But there are large differences in \nimprovements for different pollutants. In general, our results indicate that MLs are more effective in improving NOx than PM10 \nand O3. For PM10 the MLs show slight improvement in r but not much improvements in relative errors. This difference in 29 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. improvement is likely associated with the different processes controlling the concentrations, such as different sources: NOx \nconcentrations being mainly due to vehicle exhaust emissions which shows regular variations from one day to the next \ndepending on day of the week and time of day, while PM10 is mainly due to road dust emissions controlled by a combination \nof variations in vehicle volumes and meteorological conditions that affect suspension of coarse particles from street surfaces \n(e g Denby et al., 2013a; Johansson et al., 2007; Krecl et al., 2021). Road dust is accumulated on the road surfaces during wet \n5 \nroad surface conditions and suspended by vehicle induced turbulence during dry conditions (Denby et al 2013a) 5 (e g Denby et al., 2013a; Johansson et al., 2007; Krecl et al., 2021). Road dust is accumulated on the road surfaces during wet \n5 \nroad surface conditions and suspended by vehicle induced turbulence during dry conditions (Denby et al., 2013a). The improvement of the forecasts of NOx with ML is partly driven by the calendar, hour, day of the week and to some degree \nalso Julian day, but different features appear as important for RF compared to XGB. For PM10 the seasonal variation described \nby Julian day is the most important feature at the street canyon sites, both for RF and XGB. This indicates that the deterministic (e g Denby et al., 2013a; Johansson et al., 2007; Krecl et al., 2021). Road dust is accumulated on the road surfaces during wet \n5 \nroad surface conditions and suspended by vehicle induced turbulence during dry conditions (Denby et al., 2013a). The improvement of the forecasts of NOx with ML is partly driven by the calendar, hour, day of the week and to some degree \nalso Julian day, but different features appear as important for RF compared to XGB. 4.1 \nComparison of different MLs This makes it hard to draw general conclusions regarding which model to \nuse. However, we find that other factors may be more important to consider than type of model – such as sources of pollutants and influence of photochemistry, characteristic of the site resulting in different features being of varying importance depending \n15 \non pollutant type of location. In this context RF and XGB can provide useful output on the importance of features that is not \npossible using LSTM. Another more practical aspect to consider when comparing the MLs is the complexity and computer resources required for \ntraining the models. In AQ literature, deep learning models such as standard LSTM and other Recurrent Neural Networks and influence of photochemistry, characteristic of the site resulting in different features being of varying importance depending \n15 \non pollutant type of location. In this context RF and XGB can provide useful output on the importance of features that is not \npossible using LSTM. Another more practical aspect to consider when comparing the MLs is the complexity and computer resources required for \ntraining the models. In AQ literature, deep learning models such as standard LSTM and other Recurrent Neural Networks (RNNs) have been explored for their prediction capacities. However, most of the studies have adopted complex neural network \n20 \nstructures, such as models of multiple outputs that mainly give convenience for data processing and automated feature \nhandling. Nevertheless, training even a simple LSTM model is computationally much more expensive than the two \nconventional machine learning models, i.e. the decision tree based models (RF and XGB) in our case. In fact, we have to resort \nto the high performance machine (The Swedish Berzelius High-performance Computer) to reduce the computational time. For the current practice in our real air quality prediction system, we prefer the two tree-based models over LSTM. But this doesn’t \n25 \ndeny the possibility that well-designed deep learning models may replace the conventional machine learning models being \nadopted in the AQ system in near future, especially when the amount of data increases. 4 \nDiscussion \n5 But the forecasts of the highest concentrations including episodes with high \nconcentrations, is not systematically improved for all pollutants and all statistical performance measures using the MLs. 25 concentrations, is not systematically improved for all pollutants and all statistical performance measures using the MLs. 25 \nWe have shown that the statistical performances of the deterministic forecasts for concentrations of NOx at the street canyon \nsites can be improved using the MLs. But for PM10 only LSTM showed systematic improvements at all sites. So again this \naccentuates the importance of testing the models not only for one pollutant. Further work is needed to improve deterministic \nforecasts of PM10 based on the training of MLs at a few monitoring stations. As discussed above the situation in Stockholm is We have shown that the statistical performances of the deterministic forecasts for concentrations of NOx at the street canyon \nsites can be improved using the MLs. But for PM10 only LSTM showed systematic improvements at all sites. So again this \naccentuates the importance of testing the models not only for one pollutant. Further work is needed to improve deterministic \nforecasts of PM10 based on the training of MLs at a few monitoring stations. As discussed above the situation in Stockholm is \ndifferent from cities in central and southern Europe since the road dust contribution is very large. It might be that results for \n30 \nPM10 is different in other cities, but we have not found any publication on this matter. different from cities in central and southern Europe since the road dust contribution is very large. It might be that results for \n30 \nPM10 is different in other cities, but we have not found any publication on this matter. 30 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 4.1 \nComparison of different MLs Several studies have compared performance of different machine learners for predicting air quality (Zaini et al., 2021). Assessing forecasts of PM10 and PM2.5 concentrations, Czernecki et al. (2021) found that XGB performed the best, followed \nby random forests and an artificial neural network model, while stepwise regression performed the worst in four Polish \nagglomerations. Likewise, Joharestani et al. (2019) found XGB to performed best of three MLs (XGB, RF and a deep learning \n5 \nalgorithm), in predicting PM2.5 in Tehran (Iran). On the contrary, LSTM was shown to outperform XGBoost for forecasting \nhourly PM2.5 concentrations (Qadeer et al., 2020), similar to what was shown by Chuluunsaikhan et al (2021). Cai et al. (2009) \nobtained more accurate predictions of CO concentrations using artificial neural network modelling compared to using multiple \nlinear regression and the deterministic California line source dispersion model. On the other hand Shaban et al. (2015) 10 concluded that a tree based algorithm (M5P) outperformed artificial neural network modelling when comparing forecasts of \n10 \ndifferent pollutants in Qatar. There may be many reasons for the different results presented in the literature, including different \ntypes of input data, different atmospheric conditions and source contributions governing the concentrations. Also different \nstatistical measures of performance has been used. This makes it hard to draw general conclusions regarding which model to \nuse. However, we find that other factors may be more important to consider than type of model – such as sources of pollutants concluded that a tree based algorithm (M5P) outperformed artificial neural network modelling when comparing forecasts of \n10 \ndifferent pollutants in Qatar. There may be many reasons for the different results presented in the literature, including different \ntypes of input data, different atmospheric conditions and source contributions governing the concentrations. Also different \nstatistical measures of performance has been used. This makes it hard to draw general conclusions regarding which model to \nuse. However, we find that other factors may be more important to consider than type of model – such as sources of pollutants concluded that a tree based algorithm (M5P) outperformed artificial neural network modelling when comparing forecasts of \n10 \ndifferent pollutants in Qatar. There may be many reasons for the different results presented in the literature, including different \ntypes of input data, different atmospheric conditions and source contributions governing the concentrations. Also different \nstatistical measures of performance has been used. We have applied different machine learning algorithms to improve 1-, 2- and 3-day deterministic forecasts of NOx, PM10 and \n30 \nO3 concentrations for a number of locations in Stockholm, Sweden. It is shown that degree of improvement of deterministic \nforecasts depend more on pollutant and monitoring site than on what ML algorithm is applied. Deterministic forecasts of NOx 5 \nConclusions We have applied different machine learning algorithms to improve 1-, 2- and 3-day deterministic forecasts of NOx, PM10 and \n30 \nO3 concentrations for a number of locations in Stockholm, Sweden. It is shown that degree of improvement of deterministic \nforecasts depend more on pollutant and monitoring site than on what ML algorithm is applied. Deterministic forecasts of NOx We have applied different machine learning algorithms to improve 1-, 2- and 3-day deterministic forecasts of NOx, PM10 and \n30 \nO3 concentrations for a number of locations in Stockholm, Sweden. It is shown that degree of improvement of deterministic \nforecasts depend more on pollutant and monitoring site than on what ML algorithm is applied. Deterministic forecasts of NOx 31 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. are improved at all sites, using all models. Pearson correlations increase by up to 80% and errors are reduced by up to 60%. For PM10 more variable results are seen likely reflection the more complicated processes controlling the road wear emissions \nwhich constitute a large fraction of PM10. For O3 at the urban background site deviation between deterministically modelled \nabsolute level is correct using the MLs, nRMSE and nMAE is reduced by on average around 20%, but there is almost no \nimprovement in the correlation and MAPE. 5 5 We have shown that it is possible to improve deterministic forecasts of NOx at street canyon sites, based on training MLs at \nother sites. But when tested for PM10 only LSTM showed some improvements of the statistical performances compared to the \ndeterministic forecast of PM10. We have shown that it is possible to improve deterministic forecasts of NOx at street canyon sites, based on training MLs at \nother sites. But when tested for PM10 only LSTM showed some improvements of the statistical performances compared to the \ndeterministic forecast of PM10. A strength of our study is that we compare forecasts based on several pollutants and base A strength of our study is that we compare forecasts based on several pollutants and base our forecasts on a combination of \ndeterministic models (that are based on the underlying physicochemical mechanisms responsible for the emissions and \n10 \ndispersion of the pollutants) and 3 different machine learning algorithms with additional variables such as measurement data, \ncalendar data and meteorological data. 5 \nConclusions And this method is evaluated at different sites and for different pollutants during several \nmonths with different meteorological conditions. deterministic models (that are based on the underlying physicochemical mechanisms responsible for the emissions and \n10 \ndispersion of the pollutants) and 3 different machine learning algorithms with additional variables such as measurement data, \ncalendar data and meteorological data. And this method is evaluated at different sites and for different pollutants during several \nmonths with different meteorological conditions. There is still room for improvements of this work like e g fine tuning of the models, including and excluding features, \nexpanding to other sites and making maps of spatial concentrations over a larger area. 15 There is still room for improvements of this work like e g fine tuning of the models, including and excluding features, \nexpanding to other sites and making maps of spatial concentrations over a larger area. 15 32 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 6 \nAppendix A. Description of measurement methods and sites. All measurement methods are approved for monitoring according to the EU air quality directive for NOx, O3 and PM10. PM10 \nwas measured either using an optical particle counter (Hornsgatan: OPC, Grimm EDM 180-MC) or Tapered Element \nOscillating Microbalance (Sveavägen, Folkungagatan and Urban: TEOM model, 1400AB, Rupprecht & Patashnik, Co). NOx \nwas measured using chemiluminescence (AC32M, Environnement S.A.) and O3 was measured by UV absorption (O342M, \n5 \nEnvironnement S.A.). Table A1. Description of monitoring sites. Site name \nDescription \nTraffic volume \nPhoto \nHornsgatan \nStreet canyon site. Measurements of \nNOx and PM10 on north side of street, \n3 m above ground. Street width 24 m \nand building height 24 m. 23 000 veh/day (4% \nheavy duty vehicles). Vehicle composition \nmeasured during 4 week \ncampaigns using \nautomatic number plate \nrecognition. Sveavägen \nStreet canyon site. Measurements of \nNOx, PM10 on west side of street, 3 m \nabove ground. Street width 33 m and \nbuilding height 24 m. 21 000 veh/day (7% \nheavy duty vehicles). Table A1. Description of monitoring sites. Photo 33 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Folkungagatan \nStreet canyon site. Measurements \nNOx, PM10 on west side of street, 3 m \nabove ground. Street width 24 m and \nbuilding height 24 m. 12 000 veh/day (18% \nheavy duty vehicles). Torkel \nKnutssongatan \nUrban background. Measurements of \nNOx, PM10, ozone and meteorology \non top of a 20 m high building. Ca 13 000 vehicles on \nHornsgatan road 250 m N \nof site. 34 34 7 \nAppendix B Importance of features – urban background \n \n \n \nFigure B1.Most important features for NOx forecasts using XGB and RF at the urban site \n \n \nFigure B2. Most important features for PM10 forecasts using XGB and RF at the urban site. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 7 \nAppendix B Importance of features – urban background \n \n \n \nFigure B1.Most important features for NOx forecasts using XGB and RF at the urban site 7 \nAppendix B Importance of features – urban background 7 \nAppendix B Importance of features – urban background Figure B1.Most important features for NOx forecasts using XGB and RF at the urban site \n \n \nFigure B2. Most important features for PM10 forecasts using XGB and RF at the urban site. 6 \nAppendix A. Description of measurement methods and sites. 5 Figure B1.Most important features for NOx forecasts using XGB and RF at the urban site Figure B1.Most important features for NOx forecasts using XGB and RF at the urban site \n \n \nFigure B2. Most important features for PM10 forecasts using XGB and RF at the urban site. 5 Figure B2. Most important features for PM10 forecasts using XGB and RF at the urban site. 5 35 Figure B3. Most important features for O3 forecasts using XGB and RF at the urban site. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Figure B3. Most important features for O3 forecasts using XGB and RF at the urban site. 36 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 8 \nAppendix C. Temporal variations in hourly mean O3, NOx and PM10 concentrations at the urban background \nFigure C1. Temporal variations of deterministic and ML forecasted NOx, PM10 and O3 concentrations together wit\ncorresponding measured concentrations at the urban background site for September 2021. Mean of 1-, 2- and 3-day forecast 8 \nAppendix C. Temporal variations in hourly mean O3, NOx and PM10 concentrations at the urban background 8 \nAppendix C. Temporal variations in hourly mean O3, NOx and PM10 concentrations at the urban background poral variations in hourly mean O3, NOx and PM10 concentrations at the urban background Figure C1. Temporal variations of deterministic and ML forecasted NOx, PM10 and O3 concentrations together with \ncorresponding measured concentrations at the urban background site for September 2021. Mean of 1-, 2- and 3-day forecasts. Figure C1. Temporal variations of deterministic and ML forecasted NOx, PM10 and O3 concentrations together with \ncorresponding measured concentrations at the urban background site for September 2021. Mean of 1-, 2- and 3-day forecasts. 5 37 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Figure C2. Mean diurnal variations in measured and forecasted concentrations of NOx, PM10 and O3 at the urban site. Mean of \n1-, 2- and 3-day forecasts for August – December 2021. Figure C2. Mean diurnal variations in measured and forecasted concentrations of NOx, PM10 and O3 at the urban site. 6 \nAppendix A. Description of measurement methods and sites. Mean of \n1-, 2- and 3-day forecasts for August – December 2021. 5 5 38 Appendix D. Statistical performance measures for forecasts higher than the hourly mean concentrations at the urban \nit\nhttps://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Appendix D. Statistical performance measures for forecasts higher than the hourly mean concentrations at the urban Appendix D. Statistical performance measures for forecasts higher than the hourly mean concentrations at the urban \nsite. pendix D. Statistical performance measures for forecasts higher than the hourly mean concentrations at the urb\n \nure D1. Statistical performance measures for concentrations of NOx, PM10 and O3 higher than the hourly mean value at t\nan site. Mean of 1-, 2- and 3-day forecasts. Figure D1. Statistical performance measures for concentrations of NOx, PM10 and O3 higher than the hourly mean value at the \nurban site. Mean of 1-, 2- and 3-day forecasts. 5 5 39 9 \nAppendix E. Importance of features – Street canyon sites \n \n \nFigure E1. Most important features (%) for PM10 forecasts using RF and XGB at Folkungagatan. Figure E2. Most important features (%) for PM10 forecasts using RF and XGB at Hornsgatan. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 9 \nAppendix E. Importance of features – Street canyon sites \n \n \nFigure E1. Most important features (%) for PM10 forecasts using RF and XGB at Folkungagatan. 9 \nAppendix E. Importance of features – Street canyon sites 9 \nAppendix E. Importance of features – Street canyon sites \n \n \nFigure E1. Most important features (%) for PM10 forecasts using RF and XGB at Folkungagatan. Figure E1. Most important features (%) for PM10 forecasts using RF and XGB at Folkungagatan. Figure E2. Most important features (%) for PM10 forecasts using RF and XGB at Hornsgatan. 5 Figure E1. Most important features (%) for PM10 forecasts using RF and XGB at Folkungagatan. st important features (%) for PM10 forecasts using RF and XGB at Folkungagatan. Figure E2. Most important features (%) for PM10 forecasts using RF and XGB at Hornsgatan. 5 40 Figure E3. Most important features (%) for PM10 forecasts using RF and XGB at Sveavägen. Figure E4. 6 \nAppendix A. Description of measurement methods and sites. Most important features (%) for NOx forecasts using RF and XGB at Folkungagatan. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Figure E3. Most important features (%) for PM10 forecasts using RF and XGB at Sveavägen. Figure E3. Most important features (%) for PM10 forecasts using RF and XGB at Sveavägen. Figure E3. Most important features (%) for PM10 forecasts using RF and XGB at Sveavägen. Figure E4. Most important features (%) for NOx forecasts using RF and XGB at Folkungagatan. g\np\n(\n)\n10\ng\ng\n \n \nFigure E4. Most important features (%) for NOx forecasts using RF and XGB at Folkungagatan. Figure E4. Most important features (%) for NOx forecasts using RF and XGB at Folkungagatan. Figure E4. Most important features (%) for NOx forecasts using RF and XGB at Folkungagatan. 5 41 Figure E5. Most important features (%) for NOx forecasts using RF and XGB at Sveavägen. Figure E6. Most important features (%) for NOx forecasts using RF and XGB at Hornsgatan. 5 \nhttps://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Figure E5. Most important features (%) for NOx forecasts using RF and XGB at Sveavägen. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Figure E5. Most important features (%) for NOx forecasts using RF and XGB at Sveavägen. Figure E6. Most important features (%) for NOx forecasts using RF and XGB at Hornsgatan. 5 Figure E6. Most important features (%) for NOx forecasts using RF and XGB at Hornsgatan. 5 42 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 10 \nAppendix F. Temporal variations in hourly mean O3, NOx and PM10 concentrations at the street canyon sites \nFigure F1. Temporal variations of hourly deterministic and ML forecasted NOx concentrations together with correspondin\nmeasured concentrations at street canyon sites for September 2021. Mean of 1-, 2- and 3-day forecasts. 10 \nAppendix F. Temporal variations in hourly mean O3, NOx and PM10 concentrations at the street canyon sites 10 \nAppendix F. 6 \nAppendix A. Description of measurement methods and sites. Temporal variations in hourly mean O3, NOx and PM10 concentrations at the street canyon sites emporal variations in hourly mean O3, NOx and PM10 concentrations at the street canyon site Figure F1. Temporal variations of hourly deterministic and ML forecasted NOx concentrations together with corresponding \nmeasured concentrations at street canyon sites for September 2021. Mean of 1-, 2- and 3-day forecasts. 43 Figure F2. Temporal variations of hourly deterministic and ML forecasted PM10 concentrations together with correspondin\nmeasured concentrations at the street canyon sites for September 2021. Mean of 1-, 2- and 3-day forecasts. Figure F2. Temporal variations of hourly deterministic and ML forecasted PM10 concentrations together with corresponding \nmeasured concentrations at the street canyon sites for September 2021. Mean of 1-, 2- and 3-day forecasts. 44 11 \nAppendix G. Mean diurnal variations in hourly mean observations, 1-day, 2-day and 3-day deterministic and ML \nf\nt\nf NO\nd PM\nf\nth\nt\nt\nit\nhttps://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 11 \nAppendix G. Mean diurnal variations in hourly mean observations, 1-day, 2-day and 3-day deterministic and ML \nforecasts of NOx and PM10 for the street canyon sites. Figure G1. Mean diurnal variations in measured and forecasted concentrations of NOx and PM10 at the street canyon sites. Mean of 1-, 2- and 3-day forecasts for August – December 2021.Shaded areas are 95% confidence intervals. Figure G1. Mean diurnal variations in measured and forecasted concentrations of NOx and PM10 at the street canyon sites. Mean of 1-, 2- and 3-day forecasts for August – December 2021.Shaded areas are 95% confidence intervals. 5 45 12 \nAppendix H. Statistical performance measures for forecasted hourly mean concentrations higher than the mean \nvalues at the street canyon sites. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. 12 \nAppendix H. Statistical performance measures for forecasted hourly mean concentrations higher than the mean \nvalues at the street canyon sites. 12 \nAppendix H. Statistical performance measures for forecasted hourly mean concentrations higher than the mean \nvalues at the street canyon sites. stical performance measures for forecasted hourly mean concentrations higher than the mea\n canyon sites. 6 \nAppendix A. Description of measurement methods and sites. 12 \nAppendix H. Statistical performance measures for forecasted hourly mean concentrations higher than the mean \nvalues at the street canyon sites. Figure H1. Statistical performance measures for forecasted NOx and PM10 hourly mean concentrations higher than the mean \nvalues at Hornsgatan. Mean of 1-, 2- and 3-day forecasts. 5 Figure H1. Statistical performance measures for forecasted NOx and PM10 hourly mean concentrations higher than the mean \nvalues at Hornsgatan. Mean of 1-, 2- and 3-day forecasts. 5 46 Figure H2. Statistical performance measures for forecasted NOx and PM10 hourly mean concentrations higher than the mean \nvalues at Folkungagatan. Mean of 1-, 2- and 3-day forecasts. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Figure H2. Statistical performance measures for forecasted NOx and PM10 hourly mean concentrations higher than the mean \nvalues at Folkungagatan. Mean of 1-, 2- and 3-day forecasts. Figure H2. Statistical performance measures for forecasted NOx and PM10 hourly mean concentrations higher than the mean \nvalues at Folkungagatan. Mean of 1-, 2- and 3-day forecasts. 5 5 47 igure H3. Statistical performance measures for forecasted NOx and PM10 hourly mean concentrations higher than the mean \nalues at Sveavägen. Mean of 1-, 2- and 3-day forecasts. ttps://doi.org/10.5194/acp-2023-38\nreprint. Discussion started: 8 February 2023\n⃝Author(s) 2023. CC BY 4.0 License. Figure H3. Statistical performance measures for forecasted NOx and PM10 hourly mean concentrations higher than the mean \nvalues at Sveavägen. Mean of 1-, 2- and 3-day forecasts. Figure H3. Statistical performance measures for forecasted NOx and PM10 hourly mean concentrations higher than the mean \nvalues at Sveavägen. Mean of 1-, 2- and 3-day forecasts. 5 Code/Data availability: Python codes and data are available here: https://zenodo.org/record/7576042#.Y9k3AXbMK71 . References Berkowicz, R.: OSPM - A parameterised street pollution model, Environmental Monitoring and Assessment, 65, 323-331, \n2020. Berkowicz, R.: OSPM - A parameterised street pollution model, Environmental Monitoring and Assessment, 65, 323-331, \n2020. Brokamp, C., Jandarov, R., Rao, M.B., LeMasters, G., Ryan, P.: Exposure assessment models f Brokamp, C., Jandarov, R., Rao, M.B., LeMasters, G., Ryan, P.: Exposure assessment models for elemental components of \nparticulate matter in an urban environment: A comparison of regression and random forest approaches. Atmos. Environ, 151, \n5 \n1–11, 2017. particulate matter in an urban environment: A comparison of regression and random forest approaches. Atmos. Environ, 151, \n5 \n1–11, 2017. Burman, L., Johansson, C.: Emissions and Concentrations of Nitrogen Oxides and Nitrogen Dioxide on Hornsgatan Street, \nEvaluation \nof \nTraffic \nMeasurements \nduring \nAutumn \n2009 \n(In \nSwedish \nOnly). SLB \nReport \n7. https://www.slb.nu/slb/rapporter/pdf8/slb2010_007.pdf, 2010. Burman, L., Johansson, C.: Emissions and Concentrations of Nitrogen Oxides and Nitrogen Dioxide on Hornsgatan Street, \nEvaluation \nof \nTraffic \nMeasurements \nduring \nAutumn \n2009 \n(In \nSwedish \nOnly). SLB \nReport \n7. https://www.slb.nu/slb/rapporter/pdf8/slb2010_007.pdf, 2010. Burman, \nL., \nElmgren, \nM., \nNorman, \nM.: \nFordonsmätningar \npå \nHornsgatan \når \n2017. 10 \nhttps://scholar.google.com/scholar_lookup?title=Fordonsm%C3%A4tningar%20P%C3%A5%20Hornsgatan%20%C3%85r\n%202017&author=L.%20Burman&publication_year=2019, 2019. Cai, M., Yin, Y., Xie, M.: Prediction of hourly air pollutant concentrations near urban arterials using artificial neural network \napproach. Transport Research Part D. 14, 32-41. doi:10.1016/j.trd.2008.10.004, 2009. Burman, \nL., \nElmgren, \nM., \nNorman, \nM.: \nFordonsmätningar \npå \nHornsgatan \når \n2017. 10 \nhttps://scholar.google.com/scholar_lookup?title=Fordonsm%C3%A4tningar%20P%C3%A5%20Hornsgatan%20%C3%85r\n%202017&author=L.%20Burman&publication_year=2019, 2019. %202017&author=L.%20Burman&publication_year=2019, 2019. Cai, M., Yin, Y., Xie, M.: Prediction of hourly air pollutant concentrations near urban arterials using artificial neural network \napproach. Transport Research Part D. 14, 32-41. doi:10.1016/j.trd.2008.10.004, 2009. Cai, M., Yin, Y., Xie, M.: Prediction of hourly air pollutant concentrations near urban arterials using artificial neural network \napproach. Transport Research Part D. 14, 32-41. doi:10.1016/j.trd.2008.10.004, 2009. Cai, M., Yin, Y., Xie, M.: Prediction of hourly air pollutant concentrations near urban arterials using artificial neural network \napproach. Transport Research Part D. 14, 32-41. doi:10.1016/j.trd.2008.10.004, 2009. Carslaw, D.C. and K. Ropkins.: Openair — an R package for air quality data analysis, Environmental Modelling & Software, \n15 \n27-28, 52–61, 2012. Carslaw, D.C. and K. Ropkins.: Openair — an R package for air quality data analysis, Environmental Modelling & Software, \n15 \n27-28, 52–61, 2012. Castelli, M., Clemente, F.M., Popovič, A., Silva, S. and Vanneschi, L.: A Machine Learning Approach to Predict Air Quality \nin California. Hindawi, Complexity, Article ID 8049504, 23 pages, https://doi.org/10.1155/2020/8049504, 2020. Python codes and data are available here: https://zenodo.org/record/7576042#.Y9k3AXbMK71 . Author contribution: ME has been responsible for the deterministic modelling and providing with monitoring data and \nmeteorological forecasts. ZZ and XM has been responsible for the ML modelling and statistical calculations. CJ, XM and ME \ninitiated and planned the project. All authors have contributed to analysing data and writing of the manuscript. 10 Author contribution: ME has been responsible for the deterministic modelling and providing with monitoring data and \nmeteorological forecasts. ZZ and XM has been responsible for the ML modelling and statistical calculations. CJ, XM and ME \ninitiated and planned the project. All authors have contributed to analysing data and writing of the manuscript. 10 Competing interests: The authors declare that they have no conflict of interest. Competing interests: The authors declare that they have no conflict of interest. Acknowledgements: Financial support: The project was funded by ICT – The next generation and Digital future at KTH \nRoyal Institute of Technology (contract VF 2021-0082). 15 Acknowledgements: Financial support: The project was funded by ICT – The next generation and Digital future at KTH \nRoyal Institute of Technology (contract VF 2021-0082). 15 48 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. References Chuluunsaikhan, T., Heak, M., Nasridinov, A., Choi, S.: Comparative Analysis of Predictive Models for Fine Particulate Castelli, M., Clemente, F.M., Popovič, A., Silva, S. and Vanneschi, L.: A Machine Learning Approach to Predict Air Quality \nin California. Hindawi, Complexity, Article ID 8049504, 23 pages, https://doi.org/10.1155/2020/8049504, 2020. Chuluunsaikhan, T., Heak, M., Nasridinov, A., Choi, S.: Comparative Analysis of Predictive Models for Fine Particulate \nMatter in Daejeon, South Korea. Atmosphere, 12, 1295. https://doi.org/10.3390/atmos12101295, 2021. 20 Chuluunsaikhan, T., Heak, M., Nasridinov, A., Choi, S.: Comparative Analysis of Predictive Models for Fine Particulate Matter in Daejeon, South Korea. Atmosphere, 12, 1295. https://doi.org/10.3390/atmos12101295, 2021. 20 \nCzernecki, B., Marosz, M., Jędruszkiewicz, J.: Assessment of Machine Learning Algorithms in Short-term Forecasting of \nPM10 and PM2.5 Concentrations in Selected Polish Agglomerations. Aerosol and Air Quality Research. 21, 200586, \nhttps://doi.org/10.4209/aaqr.200586, 2021. Denby, B. R., Sundvor, I., Johansson, C., Pirjola, L., Ketzel, M., Norman, M., Kupiainen, K., Gustafsson, M., Blomqvist, G., Czernecki, B., Marosz, M., Jędruszkiewicz, J.: Assessment of Machine Learning Algorithms in Short-term Forecasting of \nPM10 and PM2.5 Concentrations in Selected Polish Agglomerations. Aerosol and Air Quality Research. 21, 200586, \nhttps://doi.org/10.4209/aaqr.200586, 2021. https://doi.org/10.4209/aaqr.200586, 2021. Denby, B. R., Sundvor, I., Johansson, C., Pirjola, L., Ketzel, M., Norman, M., Kupiainen, K., Gustafsson, M., Blomqvist, G., Denby, B. R., Sundvor, I., Johansson, C., Pirjola, L., Ketzel, M., Norman, M., Kupiainen, K., Omstedt, G.: A coupled road dust and surface moisture model to predict non-exhaust road traffic induced particle emissions \n25 \n(NORTRIP). Part 1: road dust loading and suspension modelling Atmos. Environ., 77, 283-300, 2013a. Denby, B. R., Sundvor, I., Johansson, C., Pirjola, L., Ketzel, M., Norman, M., Kupiainen, K., Gustafsson, M., Blomqvist, G., \nOmstedt, G.: A coupled road dust and surface moisture model to predict non-exhaust road traffic induced particle emissions \n(NORTRIP). Part 2: surface moisture and salt impact modelling Atmos. Environ., 81, 485-503, 2013b. (NORTRIP). Part 1: road dust loading and suspension modelling Atmos. Environ., 77, 283 300, 2013a. Denby, B. R., Sundvor, I., Johansson, C., Pirjola, L., Ketzel, M., Norman, M., Kupiainen, K., Gustafsson, M., Blomqvist, G., \nOmstedt, G.: A coupled road dust and surface moisture model to predict non-exhaust road traffic induced particle emissions \n(NORTRIP). Part 2: surface moisture and salt impact modelling Atmos. Environ., 81, 485-503, 2013b. Di, Q., Amini, H., Shi, L., Kloog, I., Silvern, R., Kelly, J., Sabath, M.B., Choirat, C., Koutrakis, P., Lyapustin, A., Wang, Y., \n30 \nMickley, L.J., Schwartz. References J.: An ensemble-based model of PM2.5 concentration across the contiguous United States with high \nspatiotemporal resolution. Environment International 130, 104909, 2019. Doreswamy, Harishkumar K S., Yogesh, K.M., Gad, I.: Forecasting Air Pollution Particulate Matter (PM2.5) Using Machine spatiotemporal resolution. Environment International 130, 104909, 2019. Doreswamy, Harishkumar K S., Yogesh, K.M., Gad, I.: Forecasting Air Pollution Particulate Matter (PM2.5) Using Machine \nLearning Regression Models. Procedia Computer Science 171, 2057–2066, 2020. 49 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Engardt, M., Bergström. S. and Johansson, C.: Luften du andas - nu och de kommande dagarna. Utveckling av ett automatiskt \nprognossystem \nför \nluftföroreningar \noch \npollen. SLB \n36:2021, \n33 \npp. (In \nSwedish). https://www.slbanalys.se/slb/rapporter/pdf8/slb2021_036.pdf, 2021. Fuller\nR\nPhilip J Landrigan Kalpana Balakrishnan Glynda Bathan Stephan Bose-O’Reilly\nMichael Brauer\nJack Caravanos, Tom Chiles, Aaron Cohen, Lilian Corra, Maureen Cropper, Greg Ferraro, Jill Hanna, David Hanrahan, Howard \n5 \nHu, David Hunter, Gloria Janata, Rachael Kupka, Bruce Lanphear, Maureen Lichtveld, Keith Martin, Adetoun Mustapha, \nErnesto Sanchez-Triana, Karti Sandilya, Laura Schaefli, Joseph Shaw, Jessica Seddon, William Suk, Martha María Téllez-\nRojo, \nChonghuai \nYan.: \nPollution \nand \nhealth: \na \nprogress \nupdate. Lancet \nPlanet \nHealth, \n6, \ne535–47, \nhttps://doi.org/10.1016/S2542-5196(22)00090-0, 2022. Gidhagen, L., Johansson, C., Langner, J., Foltescu, V. L.: Urban scale modeling of particle number concentration in Stockholm. 10 \nAtmospheric Environment 39, 1711–1725, 2005. Hoek, G., Beelen, R.,, de Hoogh, K., Vienneau, D., Gulliver, J., Fischer, P., Briggs, D.: A review of land-use regression models \nto assess spatial variation of outdoor air pollution. Atmos Environ, 42, 7561-7568, doi:10.1016/j.atmosenv.2008.05.057, 2008. Horálek, J., Hamer, P., Schreiberová, M., Colette, A., Schneider, P., Malherbe, L.: Potential use of CAMS modelling results Gidhagen, L., Johansson, C., Langner, J., Foltescu, V. L.: Urban scale modeling of particle number concentration in Stockholm. 10 \nAtmospheric Environment 39, 1711–1725, 2005. Hoek, G., Beelen, R.,, de Hoogh, K., Vienneau, D., Gulliver, J., Fischer, P., Briggs, D.: A review of land-use regression models \nto assess spatial variation of outdoor air pollution. Atmos Environ, 42, 7561-7568, doi:10.1016/j.atmosenv.2008.05.057, 2008. Horálek, J., Hamer, P., Schreiberová, M., Colette, A., Schneider, P., Malherbe, L.: Potential use of CAMS modelling results \nin air quality mapping under ETC/ATNI. Eionet Report – ETC/ATNI 2019/17, ISBN 978-82-93752-21-9, 2019. 15 Horálek, J., Hamer, P., Schreiberová, M., Colette, A., Schneider, P., Malherbe, L.: Potential u in air quality mapping under ETC/ATNI. Eionet Report – ETC/ATNI 2019/17, ISBN 978-82-93752-21-9, 2019. 15 \nIskandaryan, D., Ramos, F. References and Trilles, S.: Air Quality Prediction in Smart Cities Using Machine Learning Technologies based \non Sensor Data: A Review. Appl. Sci. 2020, 10, 2401, doi: 10.3390/app10072401, 2020. Janssen, S. and Thunis, P.: FAIRMODE Guidance Document on Modelling Quality Objectives and Benchmarking (version \n3.3), EUR 31068 EN, Publications Office of the European Union, Luxembourg, ISBN 978-92-76-52425-0, doi:10.2760/41988, Iskandaryan, D., Ramos, F. and Trilles, S.: Air Quality Prediction in Smart Cities Using Machine Learning Technologies based \non Sensor Data: A Review. Appl. Sci. 2020, 10, 2401, doi: 10.3390/app10072401, 2020. on Sensor Data: A Review. Appl. Sci. 2020, 10, 2401, doi: 10.3390/app10072401, 2020. Janssen, S. and Thunis, P.: FAIRMODE Guidance Document on Modelling Quality Objectives and Benchmarking (version \n3.3), EUR 31068 EN, Publications Office of the European Union, Luxembourg, ISBN 978-92-76-52425-0, doi:10.2760/41988, \nJRC129254, 2022. 20 JRC129254, 2022. 20 \nJohansson, C., Norman, M., Gidhagen, L.: Spatial & temporal variations of PM10 and particle number concentrations in urban \nair. Environ. Monit. Assess. 127, 477–487, 2007. Johansson, C., Burman, L., Forsberg, B.: The effects of congestions tax on air quality and health. Atmos. Environ. 43, 4843-\n4854, 2009. Johansson, C., Norman, M., Gidhagen, L.: Spatial & temporal variations of PM10 and particle number concentrations in urban \nair. Environ. Monit. Assess. 127, 477–487, 2007. Johansson, C., Eneroth, K., Lövenheim, B., Silvergren, S., Burman, L., Bergström, S., Norman, M., Engström Nylén, A., \n25 \nHurkmans, J., Elmgren, M., Brydolf, M., Täppefur, M.: Luftkvalitetsberäkningar för kontroll av miljökvalitetsnormer (with \nsummary in English). SLB 11:2017 ver 2. https://www.slbanalys.se/slb/rapporter/pdf8/slb2017_011.pdf, 2017. Johansson, C. Lövenheim, B.; Schantz, P.; Wahlgren, L.; Almström, P.; Markstedt, A.; Strömgren, M.; Forsberg, B.; Nilsson \nSommar, J.: Impacts on air pollution and health by changing commuting from car to bicycle. Sci. Total Environ. 584-585, 55- Johansson, C. Lövenheim, B.; Schantz, P.; Wahlgren, L.; Almström, P.; Markstedt, A.; Strömgren, M.; Forsberg, B.; Nilsson \nSommar, J.: Impacts on air pollution and health by changing commuting from car to bicycle. Sci. Total Environ. 584-585, 55-\n63, 2017. 30 63, 2017. 30 \nJoharestani, M.Z., Cao, C., Ni, X., Bashir, B. Talebiesfandarani, S.: PM2.5 Prediction Based on Random Forest, XGBoost, \nand Deep Learning Using Multisource Remote Sensing Data. Atmosphere, 10, 373; doi:10.3390/atmos10070373, 2019. Kamińska, J. A.: A random forest partition model for predicting NO2 concentrations from traffic flow and meteorological \nconditions. Science of the Total Environment 651, 475–483, 2019. Kamińska, J. References A.: A random forest partition model for predicting NO2 concentrations from traffic flow and meteorological \nconditions. Science of the Total Environment 651, 475–483, 2019. 50 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Keller, M., Hausberger, S., Matzer, C., Wüthrich, P., Notter, B.: HBEFA 3.3. Update of NOx Emission Factors of Diesel \nPassenger Cars- Background Documentation. https://www.hbefa.net/e/documents/HBEFA33_Documentation_20170425.pdf, \n2017. Krecl, P., Harrison, R.M., Johansson, C., Targino, A.C., Beddows, D.C., Ellermann, T., Lara, C. and Ketzel, M.: Long-term \ntrends in nitrogen oxides concentrations and on-road vehicle emission factors in Copenhagen, London and Stockholm. 5 \nEnvironmental Pollution, 290, 118105, 2021. Krecl, P., Johansson, C., Targino, A.C.,, Ström, J., Burman, L.: Trends in black carbon and size-resolved particle number \nconcentrations and vehicle emission factors under real-world conditions, Atmospheric Environment, 165, 155-168, 2017. Marècal, V., Peuch, V.-H., Andersson, C., Andersson, S., Arteta, J., Beekmann, M., Benedictow, A., Bergström, R., Bessagnet, Krecl, P., Johansson, C., Targino, A.C.,, Ström, J., Burman, L.: Trends in black carbon and size-resolved particle number \nconcentrations and vehicle emission factors under real-world conditions, Atmospheric Environment, 165, 155-168, 2017. B., Cansado, A., Chèroux, F., Colette, A., Coman, A., Curier, R. L., Denier van der Gon, H. A. C., Drouin, A., Elbern, H., \n10 \nEmili, E., Engelen, R. J., Eskes, H. J., Foret, G., Friese, E.,Gauss, M., Giannaros, C., Guth, J., Joly, M., Jaumouillè, E., Josse, \nB., Kadygrov, N., Kaiser, J. W., Krajsek, K., Kuenen, J., Kumar, U., Liora, N., Lopez, E., Malherbe, L., Martinez, I., Melas, \nD., Meleux, F., Menut, L., Moinat, P., Morales, T., Parmentier, J., Piacentini, A., Plu, M., Poupkou, A., Queguiner, S., \nRobertson, L., Rouïl, L., Schaap, M., Segers, A., Sofiev, M., Tarasson, L., Thomas, M., Timmermans, R., Valdebenito, ¡., van Robertson, L., Rouïl, L., Schaap, M., Segers, A., Sofiev, M., Tarasson, L., Thomas, M., Timmerm Velthoven, P., van Versendaal, R.,Vira, J. and Ung, A.: A regional air quality forecasting system over Europe: the MACC-II \n15 \ndaily ensemble production. Geoscientific Model Development, Volume 8, issue 9, 2777–2813, 2015. Meteo-France for Copernicus.: Regional Production, Description of the operational models and of the ENSEMBLE system. Retrieved \n2018-11-20. Available \nat: \nhttps://atmosphere.copernicus.eu/sites/default/files/2018-\n02/CAMS50_factsheet_201610_v2.pdf, 2017. Munir, S., Mayfield, M., Coca, D., Mihaylova, L.S. and Osammor, O.: Analysis of Air Pollution in Urban Areas with Airviro \n20 \nDispersion \nModel—A \nCase \nStudy \nin \nthe \nCity \nof \nSheffield, \nUnited \nKingdom. References Atmosphere \n11, \n285; \ndoi:10.3390/atmos11030285, 2020. Olstrup, H., Johansson, C., Forsberg, B., Åström, C.: Association between Mortality and Short- Term Exposure to Particles, \nOzone and Nitrogen Dioxide in Stockholm, Sweden. Int J Environ Res Public Health, 16, 6, 1028-1042, 2019. Munir, S., Mayfield, M., Coca, D., Mihaylova, L.S. and Osammor, O.: Analysis of Air Pollution in Urban Areas with Airviro \n20 \nDispersion \nModel—A \nCase \nStudy \nin \nthe \nCity \nof \nSheffield, \nUnited \nKingdom. Atmosphere \n11, \n285; \ndoi:10.3390/atmos11030285, 2020. Olstrup, H., Johansson, C., Forsberg, B., Åström, C.: Association between Mortality and Short- Term Exposure to Particles, \nOzone and Nitrogen Dioxide in Stockholm, Sweden. Int J Environ Res Public Health, 16, 6, 1028-1042, 2019. Orru, H. Lövenheim, B. Johansson, C. Forsberg, B.: Estimated health impacts of changes in air pollution exposure associated \n25 \nwith the planned by-pass Förbifart Stockholm. J Expo Sci Environ Epidemiol, 1-8, 2015. Ottosen, T.-B. and Kakosimos, K. E. and Johansson, C. and Hertel, O. and Brandt, J. and Skov, H. and Berkowicz, R. and \nEllermann, T. and Jensen, S. S. and Ketzel, M.: Analysis of the impact of inhomogeneous emissions in the Operational Street \nPollution Model (OSPM). Geoscientific Model Development, 8, 3231—3245, 2015. Orru, H. Lövenheim, B. Johansson, C. Forsberg, B.: Estimated health impacts of changes in air pollution exposure associated \n25 \nwith the planned by-pass Förbifart Stockholm. J Expo Sci Environ Epidemiol, 1-8, 2015. Qadeer, K., Rehman, W.U., Sheri, A.M., Park, I., Kim, H.K. and Jeon, M.: A Long Short-Term Memory (LSTM) Network for \n30 \nHourly Estimation of PM2.5 Concentration in Two Cities of South Korea. Appl. Sci. 2020, 10, 3984, \ndoi:10.3390/app10113984, 2020. Rybarczyk, Y. and Zalakeviciute, R.: Machine Learning Approaches for Outdoor Air Quality Modelling: A Systematic \nReview. Appl. Sci. 2018, 8, 2570, doi:10.3390/app8122570, 2018. Rybarczyk, Y. and Zalakeviciute, R.: Machine Learning Approaches for Outdoor Air Quality Modelling: A Systematic \nReview. Appl. Sci. 2018, 8, 2570, doi:10.3390/app8122570, 2018. 51 https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/acp-2023-38\nPreprint. Discussion started: 8 February 2023\nc⃝Author(s) 2023. CC BY 4.0 License. Säll, B.: Evaluation and validation of Copernicus Atmosphere Monitoring Service regional ensemble forecast of air pollutants \nand birch pollen in the Stockholm region. Master thesis report 30 HP (MO9001). Department of Meteorology, Stockholm \nuniversity, 2018. Säll, B.: Evaluation and validation of Copernicus Atmosphere Monitoring Service regional ensemble forecast of air pollutants \nand birch pollen in the Stockholm region. References Master thesis report 30 HP (MO9001). Department of Meteorology, Stockholm \nuniversity, 2018. Shaban, K., B.,Kadri, A., and Rezk, E.: Urban Air Pollution Monitoring System With Forecasting Models. IEEE sensors \nJournal, 16, 2598-2606, 2016. Journal, 16, 2598-2606, 2016. 5 \nShtein, A., Kloog, I., Schwartz, J., Silibello, C., Michelozzi, P., Gariazzo, C., Viegi, G., Forastiere, F., Karnieli, A., Just, A.C. and Stafoggia, M.: Estimating Daily PM2.5 and PM10 over Italy Using an Ensemble Model. Environmental Science & \nTechnology 54, 120-128 DOI: 10.1021/acs.est.9b04279, 2020. SLB, Methods for calculating air pollution concentrations in relation to the limit values. Report in Swedish with summary in Shtein, A., Kloog, I., Schwartz, J., Silibello, C., Michelozzi, P., Gariazzo, C., Viegi, G., Forastiere, F., Karnieli, A., Just, A.C. and Stafoggia, M.: Estimating Daily PM2.5 and PM10 over Italy Using an Ensemble Model. Environmental Science & \nTechnology 54, 120-128 DOI: 10.1021/acs.est.9b04279, 2020. Technology 54, 120-128 DOI: 10.1021/acs.est.9b04279, 2020. SLB, Methods for calculating air pollution concentrations in relation to the limit values. Report in Swedish with summary in English. Environment and Health Administration of Stockholm, SLB analys, Box 8136, 104 20 Stockholm, Sweden, Report \n10 \nnr. 50:2021. https://www.slbanalys.se/slb/rapporter/pdf8/slb2021_050.pdf, accessed 30 November, 2022. Stafoggia, M., Johansson, C., Glantz, P., Renzi, M., Shtein, A., de Hoogh, K., Kloog, I., Davoli, M., Michelozzi, P., Bellander, \nT.: A Random Forest Approach to Estimate Daily Particulate Matter, Nitrogen Dioxide, and Ozone at Fine Spatial Resolution \nin Sweden. Atmosphere, 11, 239, 1-19, 2020. Stafoggia, M., Bellander, T., Bucci, S., Davoli, M., de Hoogh, K., de Donato, F., Gariazzo, C., Lyapustin, A., Michelozzi, P., \n15 \nRenzi, M., Scortichini, M., Shtein, A., Viegi, G., Kloog, I., Schwartz, J.: Estimation of daily PM10 and PM2.5 concentrations \nin Italy, 2013-2015, using a spatiotemporal land-use random-forest model. Environ. Int., 124, 170−179, 2019. Thongthammachart, T., Araki, S., Shimadera, H., Eto, S., Matsuo, T. and Kondo, A.: An integrated model combining random \nforests and WRF/CMAQ model for high accuracy spatiotemporal PM2.5 predictions in the Kansai region of Japan. Atmospheric Environment 262, 118620, 2021. 20 \nZaini, N., Ean, L.W., Ahmed, A.N., Malek, M.A.: A systematic literature review of deep learning neural network for time \nseries air quality forecasting. Environmental Science and Pollution Research, https://doi.org/10.1007/s11356-021-17442-1, \n2021. 52"
|
https://openalex.org/W2114017212
|
https://infoscience.epfl.ch/record/216707/files/ncomms9900.pdf
|
English
| null |
TRIM33 switches off Ifnb1 gene transcription during the late phase of macrophage activation
|
Nature communications
| 2,015
|
cc-by
| 15,847
|
ARTICLE Received 19 Mar 2015 | Accepted 10 Oct 2015 | Published 23 Nov 2015 Results A rapid early increase of Ifnb1 mRNA
levels was observed in WT and Trim33 / BMDM or PM
activated by LPS (Fig. 1b). Thereafter, Ifnb1 mRNA levels
decreased from 2 h in WT BMDM (or 4 h in WT PM) and
returned to basal levels by 6 h in WT BMDM and PM. In
contrast, although Ifnb1 mRNA levels decreased between 2 and
4 h, Ifnb1 mRNA levels began to rise significantly by 6 h and
remained high 24 h after LPS activation in Trim33 / BMDM
or PM (Fig. 1b). This late sustained expression of Ifnb1 was also
observed when BMDM and PM were stimulated by poly(I:C)
with Ifnb1 mRNA levels being much higher at all late time points
in poly(I:C) treated Trim33 / BMDM compared with WT
(Supplementary Fig. 1b). The increased Ifnb1 mRNA levels in
Trim33 / BMDM activated with LPS correlated with increased
levels of secreted IFN-b (Fig. 1c). Finally, using a sub-optimal
concentration of LPS (0.1 ng ml 1) which did not activate Ifnb1 The tripartite motif (TRIM) protein family is characterized by
a shared N-terminal structure consisting of a RING, two B-box
domains, a coiled-coil domain and, for most of the TRIM family
members, an E3 ubiquitin ligase activity11. TRIM33, together
with TRIM24, TRIM28 and TRIM66, form a sub-family of TRIM
proteins characterized by a C-terminal plant homeodomain
juxtaposed to a bromodomain12. These TRIM proteins do not
directly bind to DNA but can be recruited by DNA-binding
proteins, such as nuclear receptors13, SMAD14, PU.1 or TAL-1
(refs 15,16), to act as transcriptional regulators. in WT BMDM, we showed, in LPS-activated Trim33 /
BMDM, an increased expression of genes whose transcription is
dependent on IFN-b and occurs late during LPS activation
(Fig. 1d). This increased expression was not accounted for by
different responses of WT and Trim33 / BMDM to IFN-b
(Supplementary Fig. 1c) and could be obtained after addition of
IFN-b during the late phases of LPS activation of WT BMDM
(Supplementary Fig. 1d). Altogether, these results show that
TRIM33 deficiency is associated with increased Ifnb1 mRNA level
associated with IFN-b secretion during the late stages of LPS
activation of BMDM. ARTICLE ARTICLE I I
n response to viral or bacterial infections, germ line-encoded
pattern recognition receptors induce type I interferon (IFN-I,
encoded by 14 Ifna and 1 Ifnb genes in mice) gene
transcription in myeloid and non-myeloid cells1. The secreted
type I IFNs act early and transiently during the innate immune
response to prime adaptive immunity and then type I Ifn gene
transcription is shut down2. This transient expression of IFN-I is
physiologically important. Whereas early IFN-I expression is
important to control infection, pathogens that can overcome this
initial control benefit from IFN-I mediated immune system
suppression3,4. and suggested that TRIM33 may regulate myeloid fate and have a
role in macrophages15. Here, we show that TRIM33 deficiency in
macrophages results in sustained expression of Ifnb1 during
the late phases of macrophages activation. Our results indicate
that TRIM33, recruited by PU.1 on a distal regulatory element
of the Ifnb1 gene, regulates Ifnb1 enhanceosome loading and
shuts down Ifnb1 gene transcription during the late stages
of
lipopolysaccharide
(LPS)
activation
of
macrophages
by
preventing recruitment of CBP/p300. NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications
& 2015 Macmillan Publishers Limited. All rights reserved. Results pp
Among type I Ifn genes, Ifnb1 gene regulation has been a
model system to study inducible transcription. After pattern
recognition receptor-mediated activation, a group of transcription
factors,
including
IRF3/IRF7,
NF-kB
and
ATF2/c-jun,
cooperatively binds to a regulatory sequence located between
102 and 47 bp upstream of the Ifnb1 transcriptional start
site (TSS) to form the Ifnb1 enhanceosome. This enhanceosome
recruits CBP/p300 for acetylation of histone H3 and permits
recruitment of chromatin-remodeling complexes for initiation of
transcription5. TRIM33 controls Ifnb1 expression in activated macrophages. Trim33fl/flmice were crossed with mice expressing the Cre
recombinase from the endogenous Lysozyme2 locus (LyzCre) to
generate Trim33 / mice. Trim33 / mice did not display
developmental abnormalities and were healthy. PCR genotyping
of purified haematopoietic cell populations showed deletion
of Trim33 in monocytes, bone-marrow-derived macrophages
(BMDM), peritoneal macrophages (PMs) and neutrophils but not
in myeloid progenitors, nor in B lymphocytes (Fig. 1a, upper
panels and Supplementary Fig. 1a). The deletion of the Trim33
gene allele was associated with a loss of TRIM33 expression in
BMDM (Fig. 1a, lower panel). p
Monocyte/macrophage-specific
regulation
of
Ifnb1
gene
transcription has only been observed in the modulation of the
transcriptional activity of IRF3. In monocytes, a PU.1-binding
site located in the enhanceosome is constitutively bound by a
IRF8/PU.1 myeloid complex that creates a preformed activation
complex. This myeloid complex can recruit IRF3 through direct
IRF3/IRF8 interaction and is involved in the rapid transcription
of Ifnb1 observed in monocytes after pathogenic stimulation6. Conversely, transcriptional regulator MafB can impair the
interactions between IRF3 bound to the enhanceosome and co-
activators, and thus negatively regulates Ifnb1 transcription7. Finally, binding of transcriptional regulator YY1 to different sites
within the enhanceosome has been shown to result in activation
(at the beginning) or repression (at the end) of Ifnb1 gene
transcription in fibroblasts8–10. Altogether, these results point to
the
enhanceosome
as
a
regulator
of
both
initiation
and
termination of the Ifnb1 transcription cycle and of monocyte/
macrophage-specific regulation of Ifnb1 transcription. g
p
The effects of Trim33 deletion on Ifnb1 expression in
macrophages were studied by comparing kinetics of Ifnb1 mRNA
levels in wild-type (WT) or Trim33 / BMDM and PM, upon
TLR4 activation by LPS or upon TLR3 activation by poly(I:C). These two activation protocols mimic bacterial (LPS) or viral
(poly(I:C)) infections. NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications TRIM33 switches off Ifnb1 gene transcription during
the late phase of macrophage activation Federica Ferri1,2,3,4,5,6,*, Aude Parcelier1,2,3,4,5,*, Vanessa Petit1,2,3,4,5, Anne-Sophie Gallouet1,2,3,4,5,
Daniel Lewandowski1,2,3,4,5, Marion Dalloz1,2,3,4,5, Anita van den Heuvel7, Petros Kolovos7, Eric Soler1,2,3,4,7,
Mario Leonardo Squadrito8, Michele De Palma8, Irwin Davidson6, Germain Rousselet1,2,3,4,5
& Paul-Henri Romeo1,2,3,4,5 Despite its importance during viral or bacterial infections, transcriptional regulation of the
interferon-b gene (Ifnb1) in activated macrophages is only partially understood. Here we
report that TRIM33 deficiency results in high, sustained expression of Ifnb1 at late stages of
toll-like receptor-mediated activation in macrophages but not in fibroblasts. In macrophages,
TRIM33 is recruited by PU.1 to a conserved region, the Ifnb1 Control Element (ICE), located
15 kb upstream of the Ifnb1 transcription start site. ICE constitutively interacts with Ifnb1
through a TRIM33-independent chromatin loop. At late phases of lipopolysaccharide
activation of macrophages, TRIM33 is bound to ICE, regulates Ifnb1 enhanceosome loading,
controls Ifnb1 chromatin structure and represses Ifnb1 gene transcription by preventing
recruitment of CBP/p300. These results characterize a previously unknown mechanism of
macrophage-specific regulation of Ifnb1 transcription whereby TRIM33 is critical for Ifnb1 gene
transcription shutdown. 1 CEA/DSV/iRCM/LRTS, 18 route du Panorama, Fontenay-aux-Roses 92265, France. 2 Inserm U967, Fontenay-aux-Roses 92265, France. 3 Universite´
Paris-Diderot, Paris 75013, France. 4 Universite´ Paris-Sud, Orsay 91400, France. 5 Equipe labellise´e Ligue contre le Cancer, 18 route du Panorama, Fontenay-
aux-Roses 92265, France. 6 Department of Functional Genomics and Cancer, Institut de Ge´ne´tique et de Biologie Mole´culaire et Cellulaire, CNRS/INSERM/
ULP, BP 163, Strasbourg, Illkirch Cedex 67404, France. 7 Department of Cell Biology, Erasmus Medical Center, DR Molenwaterplein 50, Rotterdam 3015GE,
The Netherlands. 8 The Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences E´cole Polytechnique Fe´de´rale de Lausanne (EPFL),
Lausanne CH-1015, Switzerland. * These authors contributed equally to this work. Correspondence and requests for materials should be addressed to I.D. (email: irwin@igbmc.fr) or to G.R. (email: germain.rousselet@cea.fr) or to P.-H.R. (email: paul-henri.romeo@cea.fr). 1 NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications URE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www & 2015 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 & 2015 Macmillan Publishers Limited. All rights reserved. Results p
g
A large number of TRIM proteins are innate immune
enhancers and act at multiple levels in signalling pathways,
including production and action of IFN-b to confer antiviral
and antibacterial cytokine production17,18. As for the TRIM33
sub-family, TRIM24 represses the viral-defense IFN response
in
hepatocytes
as
a
consequence
of
repression
of
VL30
transcription13,19. Although these TRIM24 mediated repressions
are potentiated by TRIM33, TRIM33 deficiency alone cannot
elicit the IFN response in hepatocytes13,19. TRIM24 also acts as a
negative regulator of the IFN/signal transducers and activators of
the transcription signalling pathway13,19, and TRIM33 is essential
for cytosolic RNA-induced NLRP3 inflammasome activation20. However, up to now, no TRIM protein has been shown to directly
regulate Ifnb1 gene transcription after recruitment to an Ifnb1
regulatory sequence. To study if TRIM33 deficiency affects the expression of other
Ifn genes, quantitative RT-PCR was performed and showed
similar kinetics of Ifna mRNA levels in WT or Trim33 /
BMDM with no late increased expression of Ifna mRNA levels in
Trim33 / BMDM (Fig. 1e). Finally, highly efficient shRNA-
mediated depletion of TRIM33 in NIH3T3 cells (NIH3T3
TRIM33 ; Supplementary Fig. 1e) did not modify kinetics of
Ifnb1 mRNA levels in response to poly(I:C) (Fig. 1f), indicating
cell-specificity in the regulation of Ifnb1 expression by TRIM33. g
y
We have previously shown that TRIM33 can interact with
PU.1 to repress its transcriptional activity during haematopoiesis Potential direct or indirect roles for TRIM33 in Ifnb1
expression were addressed in ‘rescue’ experiments in which 2 & 2015 Macmillan Publishers Limited. Results All rights reserved ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 a
WT
PM
WT
Trim33–/–
BMDM
WT allele
Excised allele
Trim33 –/– a
b
Ifnb1 mRNA
relative expression
Hours of LPS treatment
BMDM WT
BMDM Trim33 –/–
***
***
***
Ifnb1 mRNA
relative expression
Hours of LPS treatment
PM WT
PM Trim33 –/–
*
**
WT
PM
WT
Trim33–/–
BMDM
WT allele
60,000
60,000
40,000
40,000
20,000
20,000
0
0
6
12
18
24
0
0
6
12
18
24
Excised allele
Trim33 –/– b
Ifnb1 mRNA
relative expression
Hours of LPS treatment
BMDM WT
BMDM Trim33 –/–
***
***
***
Ifnb1 mRNA
relative expression
Hours of LPS treatment
PM WT
PM Trim33 –/–
*
**
60,000
60,000
40,000
40,000
20,000
20,000
0
0
6
12
18
24
0
0
6
12
18
24
ele b a TRIM33
d
e
f
g
Ifnb1 mRNA
relative expression
Hours of LPS treatment
BMDM Trim33 /
***
***
***
Ifnb1 mRNA
relative expression
Hours of LPS treatment
PM Trim33 –/–
*
**
Hours of poly(I:C) treatment
Ifnb1 mRNA
relative expression
NIH3T3 TRIM33+
NIH3T3 TRIM33–
WT
PM
WT
Trim33–/–
BMDM
WT allele
60,000
9,000
60,000
40,000
40,000
20,000
20,000
0
0
6
12
18
24
0
0
6
12
18
24
Excised allele
h
BMDM WT
BMDM Trim33 –/–
Hours of LPS treatment
Ifna mRNA relative
expression
c
BMDM WT
BMDM Trim33 –/–
BMDM
Hours of LPS treatment
Ifnb1 mRNA
relative expression
**
NS
iM WT
iM Trim33 –/–
0
2
12
24
0
250
500
3,000
6,000
Hours of LPS treatment
IFN-β (pg ml–1)
**
**
*
0
2
8
0
2
8
0
2
8
0
2
8
0
2
8
0
50
100
150
200
Hours of LPS treatment
Ifnb1 mRNA
relative expression
**
*
NS
NS
Ifnb1 Isg15 Isg20
Mx1 Rsad2
Ifit1
Ifit3
0
400
300
200
100
0
0
1
2
4
8
1
2
4
8
0
5
10
15
20
25
250
60,000
40,000
20,000
0
0
6
12
18
24
30
36
200
150
100
50
0
0
6
12
18
24
200
350
500
Fold increase of mRNA level
in Trim33-/- vs WT BMDM
**
**
**
**
**
**
**
3 h of LPS activation
24 h of LPS activation
150 kDa
37 kDa
Trim33 –/–
WT
Trim33 –/–
β-Actin
iM Trim33 –/–+ flag-TRIM33
iM Trim33 –/–+ GFP
iM Trim33 –/– + flag-ΔCC
iM Trim33 –/–+ flag-ΔSmad
iM Trim33 –/–+ flag-ΔUb
Figure 1 | TRIM33 regulates Ifnb1 gene expression in activated macrophages. Results (a) Genomic PCR detection of Trim33 in BMDM and PM (top) and western
blot analysis of TRIM33 in BMDM from WTand Trim33 / mice (bottom). (b) Kinetics of Ifnb1 mRNA levels in WTand Trim33 / BMDM (left panel) or
PM (right panel) after activation with LPS. Mean±s.e.m., n ¼ 3 to 6. (c) IFN-b protein levels in supernatants of non-activated and LPS-activated WT and
Trim33 / BMDM. Mean±s.e.m., n ¼ 4. (d) Relative mRNA levels of Ifnb1 and IFN-b target genes in Trim33 / BMDM versus WT BMDM treated with
LPS (0.1 ng ml 1) for 3 or 24 h. Mean±s.e.m., n ¼ 3. (e) Kinetics of Ifna mRNA levels in WT and Trim33 / BMDM activated with LPS. Mean±s.e.m.,
n ¼ 3. (f) Kinetics of Ifnb1 mRNA levels in NIH3T3 cells expressing a shRNA targeting Trim33 (NIH3T3 TRIM33 ) or luciferase (NIH3T3 TRIM33 þ) and
activated with poly(I:C). Mean±s.e.m., n ¼ 3. (g) Kinetics of Ifnb1 mRNA levels in WT and Trim33 / iM treated for the indicated times with LPS. Mean±s.e.m., n ¼ 3. (h) Relative expression of Ifnb1 mRNA 0, 2 and 8 h after LPS treatment of Trim33 / iM transduced with a lentivirus coding for GFP
(iM Trim33 / þ GFP), for full-length flag-TRIM33 and GFP (iM Trim33 / þ flag-TRIM33) or for flag-TRIM33 mutants lacking the coiled-coil domain
(iM Trim33 / þ flag-DCC), the ubiquitin ligase activity (iM Trim33 / þ flag-DUb) or the SMAD-interaction domain (iM Trim33 / þ flag-DSMAD). Mean±s.e.m., n ¼ 5. All qRT-PCR data are normalized to HPRT and, unless otherwise indicated, presented relative to expression of untreated WT cells. *Po0.05; **Po0.01 and ***Po0.001, Mann–Whitney test. Results TRIM33
BMDM
150 kDa
37 kDa
WT
Trim33 –/–
β-Actin 9,000
c
BMDM WT
BMDM Trim33 –/–
0
2
12
24
0
250
500
3,000
6,000
Hours of LPS treatment
IFN-β (pg ml–1)
**
** c d
e
f
Hours of poly(I:C) treatment
Ifnb1 mRNA
relative expression
NIH3T3 TRIM33+
NIH3T3 TRIM33–
BMDM WT
BMDM Trim33 –/–
Hours of LPS treatment
Ifna mRNA relative
expression
Hours of LPS treatment
Ifnb1 Isg15 Isg20
Mx1 Rsad2
Ifit1
Ifit3
0
5
10
15
20
25
250
60,000
40,000
20,000
0
0
6
12
18
24
30
36
200
150
100
50
0
0
6
12
18
24
200
350
500
Fold increase of mRNA level
in Trim33-/- vs WT BMDM
**
**
**
**
**
**
**
3 h of LPS activation
24 h of LPS activation e
f
Hours of poly(I:C) treatment
Ifnb1 mRNA
relative expression
NIH3T3 TRIM33+
NIH3T3 TRIM33–
BMDM WT
BMDM Trim33 –/–
Hours of LPS treatment
Ifna mRNA relative
expression
d2
Ifit1
Ifit3
250
60,000
40,000
20,000
0
0
6
12
18
24
30
36
200
150
100
50
0
0
6
12
18
24
**
**
n
on f
Hours of poly(I:C) treatment
Ifnb1 mRNA
relative expression
NIH3T3 TRIM33+
NIH3T3 TRIM33–
60,000
40,000
20,000
0
0
6
12
18
24
30
36 f f d e e Hours of poly(I:C) treatment p y(
)
h
*
0
2
8
0
2
8
0
2
8
0
2
8
0
2
8
0
50
100
150
200
Hours of LPS treatment
Ifnb1 mRNA
relative expression
**
*
NS
NS
iM Trim33 –/–+ flag-TRIM33
iM Trim33 –/–+ GFP
iM Trim33 –/– + flag-ΔCC
iM Trim33 –/–+ flag-ΔSmad
iM Trim33 –/–+ flag-ΔUb g
Hours of LPS treatment
Ifnb1 mRNA
relative expression
**
NS
iM WT
iM Trim33 –/–
400
300
200
100
0
0
1
2
4
8
1
2
4
8
0 h h g *
0
2
8
0
2
8
0
2
8
0
2
8
0
2
8
0
50
100
150
200
Hours of LPS treatment
Ifnb1 mRNA
relative expression
**
*
NS
NS Hours of LPS treatment Figure 1 | TRIM33 regulates Ifnb1 gene expression in activated macrophages. (a) Genomic PCR detection of Trim33 in BMDM and PM (top) and western
blot analysis of TRIM33 in BMDM from WTand Trim33 / mice (bottom). Results (b) Kinetics of Ifnb1 mRNA levels in WTand Trim33 / BMDM (left panel) or
PM (right panel) after activation with LPS. Mean±s.e.m., n ¼ 3 to 6. (c) IFN-b protein levels in supernatants of non-activated and LPS-activated WT and
Trim33 / BMDM. Mean±s.e.m., n ¼ 4. (d) Relative mRNA levels of Ifnb1 and IFN-b target genes in Trim33 / BMDM versus WT BMDM treated with
LPS (0.1 ng ml 1) for 3 or 24 h. Mean±s.e.m., n ¼ 3. (e) Kinetics of Ifna mRNA levels in WT and Trim33 / BMDM activated with LPS. Mean±s.e.m.,
n ¼ 3. (f) Kinetics of Ifnb1 mRNA levels in NIH3T3 cells expressing a shRNA targeting Trim33 (NIH3T3 TRIM33 ) or luciferase (NIH3T3 TRIM33 þ) and
activated with poly(I:C). Mean±s.e.m., n ¼ 3. (g) Kinetics of Ifnb1 mRNA levels in WT and Trim33 / iM treated for the indicated times with LPS. Mean±s.e.m., n ¼ 3. (h) Relative expression of Ifnb1 mRNA 0, 2 and 8 h after LPS treatment of Trim33 / iM transduced with a lentivirus coding for GFP
(iM Trim33 / þ GFP), for full-length flag-TRIM33 and GFP (iM Trim33 / þ flag-TRIM33) or for flag-TRIM33 mutants lacking the coiled-coil domain
(iM Trim33 / þ flag-DCC), the ubiquitin ligase activity (iM Trim33 / þ flag-DUb) or the SMAD-interaction domain (iM Trim33 / þ flag-DSMAD). Mean±s.e.m., n ¼ 5. All qRT-PCR data are normalized to HPRT and, unless otherwise indicated, presented relative to expression of untreated WT cells. *Po0.05; **Po0.01 and ***Po0.001, Mann–Whitney test. ARTICLE Transcriptional activity
of ICE-reporter (ICE-Ifnb1 Prom-Luc) showed four to tenfold
less activity than the promoter reporter in LPS-activated RAW
264.7
cells
indicating
that
ICE
functions
as
a
cis-acting
transcriptional repressor element in RAW 264.7 cells (Fig. 2e). To determine the TRIM33 protein domains involved in Ifnb1
regulation, mutant flag-TRIM33-IRES-GFP constructs lacking
the coiled-coil domain (flag-DCC), the ubiquitin ligase activity
(flag-DUb) or the Smad-interaction domain (flag-DSmad) were
expressed in Trim33 / iM (Supplementary Fig. 1g). The
flag-DUb and the flag-DSmad rescued normal Ifnb1 expression at
late time points of LPS-activated Trim33 / iM whereas the
flag-DCC did not rescue normal profile of Ifnb1 expression in
activated Trim33 / iM (Fig. 1h). These results indicate that the
Smad-interaction and ubiquitin ligase domains are not necessary
for TRIM33 regulation of Ifnb1 expression and suggest that
TRIM33 is part of a regulatory complex that regulates Ifnb1
transcription. t a sc pt o a
ep esso e e
e t
6 .7 ce s ( g. e). To study the role of ICE in RAW 264.7 and NIH3T3 cells, we
used a CRISPR/Cas9 lentiviral system to deliver Cas9 and gRNA
(Supplementary Fig. 2c). Using this system, we had to screen 200
RAW 264.7 clones to get one RAW 264.7 clone with monoallelic
deletion of ICE (Supplementary Fig. 2d). This low efficiency of
recombination in RAW 264.7 cells does not favour the use of
transient transfection for CRISPR/Cas9-mediated deletion of ICE,
transient transfection efficiency in RAW 264.7 being 15%
compared with 90% using the lentiviral system. RAW 264.7
and
NIH3T3
clones
bearing
this
deletion
on
one
allele
(termed RAW ICE þ / and NIH3T3 ICE þ / , respectively;
Supplementary Fig. 2d) were analysed for Ifnb1 expression after
LPS or poly(I:C) activation. In LPS-activated RAW WT cells,
Ifnb1 mRNA levels increased during the first 4 h and then
gradually decreased (Supplementary Fig. 2e). In contrast, whereas
Ifnb1 mRNA levels increased comparably in RAW ICE þ / cells,
they subsequently remained stable (Fig. 2f and Supplementary
Fig. 2e). In NIH3T3 WT and ICE þ / cells activated with
poly(I:C), kinetics of Ifnb1 mRNA levels were similar (Fig. 2g and
Supplementary Fig. 2f). These results indicate that ICE plays a
role in the negative regulation of Ifnb1 expression at late stages of
LPS activation in RAW cells. ARTICLE p
Altogether, these results reveal a role for TRIM33 in the
regulation of Ifnb1 expression specifically in downregulating its
expression during the late stages of macrophage activation. TRIM33 binds a distal Ifnb1 regulatory element. TRIM33
ChIP-seq data obtained from the RAW 264.7 murine macrophage
cell line or from BMDM treated with LPS for 24 h showed a single
TRIM33 peak at the Ifnb1 locus that overlapped with a PU.1 peak
located 15 kb upstream from the Ifnb1 TSS (Fig. 2a). Interestingly,
no TRIM33 occupancy was observed at the PU.1 peak located just
upstream the Ifnb1 promoter corresponding to the enhanceo-
some-binding sites. We called this 15 kb region the Ifnb1
Control Element (ICE). Recently, the human homologue of ICE,
named L2, has been shown to be a virus-inducible enhancer of
Ifnb1 in non-myeloid cells where it displays promoter and
enhancer activities22. Sequential deletions centered on the PU.1/TRIM33-binding
site of ICE were performed in RAW 264.7 cells using CRISPR/
Cas9 technology (Supplementary Fig. 2g). Of the 96 clones
screened, two carried a biallelic deletion of ICE (Supplementary
Fig. 2d). Two RAW 264.7 clones bearing a 100 or 176 bp deletion
on the two Ifnb1 alleles (termed #34 and #15; Supplementary
Fig. 2g) were analysed for Ifnb1 expression after LPS or poly(I:C)
activation. In the two clones high and sustained Ifnb1 mRNA
levels were found but only after LPS or poly(I:C) activation, with
the highest increase being obtained during the late phase of
activation (Fig. 2h). Constitutive TRIM33 occupancy at ICE was observed in
BMDM although occupancy appeared to increase at late time
points (24 h) following LPS activation (Fig. 2b, left panel). PU.1
binding at the Ifnb1 promoter and at ICE was constitutive and
detected in WT and Trim33 / BMDM (Fig. 2b, middle and
right panels) indicating that PU.1 binding to ICE was not
TRIM33-dependent. Finally, no TRIM33 binding was observed
on the Ifnb1 promoter or ICE in NIH3T3 cells (Fig. 2c),
indicating macrophage specificity of TRIM33 in binding to ICE. To determine if TRIM33-mediated regulation of Ifnb1 in
myeloid cells can be obtained in NIH3T3 by simultaneous
expression of PU.1 and TRIM33, NIH3T3 cells were transduced
with a PU.1 expressing lentivirus (Supplementary Fig. 2a). PU.1
expressing NIH3T3 were then transduced with the lentivirus
that promoted efficient shRNA-mediated depletion of TRIM33
(Supplementary Fig. ARTICLE ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 TRIM33 protein was added back to LPS-activated immortalized
Trim33 / macrophages (iM)21. As anticipated, Trim33 /
iM bore the expected deletion of Trim33 gene and these cells
expressed no TRIM33 protein (Supplementary Fig. 1f). Ifnb1
mRNA levels increased 1 h after LPS activation of WT and
Trim33 / iM and peaked at 2 h with twofold higher observed
expression in WT iM than in Trim33 / iM (Fig. 1g). As
anticipated, Ifnb1 mRNA levels in WT iM then dropped, whereas
in Trim33 / iM, Ifnb1 mRNA levels remained high (Fig. 1g). Thus, LPS activation of Trim33 / iM mimicked the late phase
of the Ifnb1 mRNA kinetics seen in Trim33 / BMDM. To
address
whether
expression
of
ectopic
TRIM33
could
rescue
Ifnb1
downregulation
at
late
time
points,
a
flag-TRIM33-IRES-GFP
(or
GFP
alone)
construct
was
expressed in Trim33 / iM and cells were stimulated with
LPS (Fig. 1h). The full-length exogenous TRIM33 protein
restored Ifnb1 downregulation at late time points of LPS
activation of Trim33 / iM (Fig. 1h) indicating a role for
TRIM33 in the regulation of Ifnb1 gene expression during LPS
activation of macrophage. NIH3T3 PU.1 þTRIM33 responses to poly(I:C) were studied. Whereas TRIM33 deficiency did not modify kinetics of Ifnb1
mRNA levels in response to poly(I:C) in normal NIH3T3 cells
(Fig. 1f), TRIM33 deficiency increased Ifnb1 mRNA levels in
NIH3T3 PU.1 þ cells treated with poly(I:C) but did not result in
sustained expression of Ifnb1 during the late stages of poly(I:C)
activation (Fig. 2d). These results show that TRIM33 can repress
Ifnb1 expression in presence of PU.1 and indicate that additional
factors that are not present in NIH3T3 cells are required for
TRIM33-mediated late downregulation of Ifnb1 expression. To study the effect of ICE on Ifnb1 promoter activity in
myeloid cells, we used RAW 264.7 cells in which LPS regulates
Ifnb1 gene expression (Supplementary Fig. 2b). RAW 264.7 cells
were transfected with luciferase reporter constructs containing a
391 bp fragment of the Ifnb1 promoter preceded by a 408 bp
fragment corresponding to the central region of ICE (ICE-Ifnb1
Prom-Luc) or the fragment containing the Ifnb1 promoter alone
as a control sequence (Ifnb1 Prom-Luc). NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications
& 2015 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications
& 2015 Macmillan Publishers Limited. All rights NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications
& 2015 Macmillan Publishers Limited. All rights reserved. 3 NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 a
b
Hours of LPS treatment
100
80
60
40
20
0
0
2
12
18
24
ChIP PU.1
promoter
Fold enrichment
100
80
60
40
20
0
0
2
12
18
24
ChIP PU.1
ICE
WT
Trim33 –/–
Fold enrichment
Hours of LPS treatment
ChIP TRIM33
ICE
15
10
5
0
0
2 12 24
Fold enrichment
Hours of LPS treatment
h
Hours of LPS treatment
*
*
*
**
**
Fold increase of Ifnb1
mRNA level
Hours of poly(I:C) treatment
*
**
**
**
RAW WT
RAW ICE–/– (#34; Δ100 bp)
RAW ICE–/– (#15; Δ176 bp)
Fold increase of Ifnb1
mRNA level
12
9
6
3
0
0
2
4
8
10
12
12
8
4
0
0
2
4
8
10
16
6
Fold increase of Ifnb1
mRNA level
RAW WT
RAW ICE+/–
NIH3T3 ICE+/–
NIH3T3 WT
*
*
6
4
2
0
0
1
2
3
6
10
24
Fold increase of Ifnb1
mRNA level
5
4
3
2
1
0
5
4
3
2
1
0
TRIM33 IgG
TRIM33 IgG
Fold enrichment
Fold enrichment
c
d
Promoter
ICE
ChIP TRIM33 in NIH3T3
Hours of LPS treatment
Relative luc
*
*
*
Ifnb1 Prom-Luc
ICE-Ifnb1 Prom-Luc
e
0
6
12
18
24
30
320
240
160
80
0
0
2
4
8
0
10,000
20,000
30,000
40,000
NIH3T3 PU.1+ TRIM33+
NIH3T3 PU.1+ TRIM33–
Hours of poly(I:C) treatment
Ifnb1 mRNA
relative expression
*
*
*
f
g
4
2
0
0
2
4
8
10
12
Hours of LPS treatment
Hours of poly(I:C) treatment
PU.1 peaks in BMDM
RAW
50
Ifnb1
Scale
chr4:
88,170,000
10 kb
88,175,000
88,180,000
88,185,000
mm9
88,190,000
RefSeq genes
1
24
1
BMDM
24 h LPS
TRIM33
Enhanceosome
ICE
TRIM33 is bound to a distal Ifnb1 gene regulatory element (ICE) in macrophages. (a) TRIM33 ChIP-seq data in RAW 264.7 cel
for 24 h with LPS showing TRIM33 binding to ICE, located 15 kb upstream the Ifnb1 TSS. Blue boxes indicate PU.1 peaks in BMD
reen boxes indicate positions of ICE and the enhanceosome. (b) ChIP-qPCR data for TRIM33 binding on ICE in WT BMDM (left p
ng on Ifnb1 promoter and on ICE (right panels) in WT and Trim33 / BMDM at indicated time points after LPS activation. Data
t over a negative control region in the b-globin promoter. Mean±s.e.m., n ¼ 3. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 (c) ChIP-qPCR analysis of TRIM33 binding at the I
E in NIH3T3 cells. Mean±s.e.m., n ¼ 3. (d) Kinetics of Ifnb1 mRNA levels in NIH3T3 cells expressing PU.1 and a shRNA targeting Tri
M33 ) or PU.1 and an shRNA targeting luciferase (NIH3T3 PU.1 þ TRIM33 þ) and activated with poly(I:C). Mean±s.e.m., n ¼ 2. ssay in RAW 264.7 cells transfected with reporter constructs containing the Ifnb1 promoter alone (Ifnb1 Prom-luc) or ICE cloned up
oter (ICE-Ifnb1 Prom-Luc) and activated with LPS. Mean±s.e.m., n ¼ 3. (f,g) Fold increase of Ifnb1 mRNA levels in ICE þ / vers
s after LPS activation (f) and in ICE þ / versus WT NIH3T3 cells after poly(I:C) activation (g). Mean±s.e.m., n ¼ 3. (h) Fold inc
CE / versus WT RAW 264.7 cells after LPS (left) or poly(I:C) (right) activation. Mean±s.e.m., n ¼ 3 to 5. Clones carrying diffe
1/TRIM33 site in ICE are indicated in brackets. *Po0.05 and **Po0.01, Mann–Whitney test. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 (a) TRIM33 ChIP-seq d is bound to a distal Ifnb1 gene regulatory element (ICE) in macrophages. (a) TRIM33 ChIP-seq data in RAW 264.7 c Figure 2 | TRIM33 is bound to a distal Ifnb1 gene regulatory element (ICE) in macrophages. (a) TRIM33 ChIP-seq data in RAW 264.7 cells and BMDM
activated for 24 h with LPS showing TRIM33 binding to ICE, located 15 kb upstream the Ifnb1 TSS. Blue boxes indicate PU.1 peaks in BMDM (data from
ref. 43). Green boxes indicate positions of ICE and the enhanceosome. (b) ChIP-qPCR data for TRIM33 binding on ICE in WT BMDM (left panel) and for
PU.1 binding on Ifnb1 promoter and on ICE (right panels) in WT and Trim33 / BMDM at indicated time points after LPS activation. Data represent the
enrichment over a negative control region in the b-globin promoter. Mean±s.e.m., n ¼ 3. (c) ChIP-qPCR analysis of TRIM33 binding at the Ifnb1 promoter
and on ICE in NIH3T3 cells. Mean±s.e.m., n ¼ 3. (d) Kinetics of Ifnb1 mRNA levels in NIH3T3 cells expressing PU.1 and a shRNA targeting Trim33 (NIH3T3
PU.1 þ TRIM33 ) or PU.1 and an shRNA targeting luciferase (NIH3T3 PU.1 þ TRIM33 þ) and activated with poly(I:C). Mean±s.e.m., n ¼ 2. (e) Luciferase
reporter assay in RAW 264.7 cells transfected with reporter constructs containing the Ifnb1 promoter alone (Ifnb1 Prom-luc) or ICE cloned upstream of the
Ifnb1 promoter (ICE-Ifnb1 Prom-Luc) and activated with LPS. Mean±s.e.m., n ¼ 3. (f,g) Fold increase of Ifnb1 mRNA levels in ICE þ / versus WT RAW
264.7 cells after LPS activation (f) and in ICE þ / versus WT NIH3T3 cells after poly(I:C) activation (g). Mean±s.e.m., n ¼ 3. (h) Fold increase of Ifnb1
mRNA in ICE / versus WT RAW 264.7 cells after LPS (left) or poly(I:C) (right) activation. Mean±s.e.m., n ¼ 3 to 5. Clones carrying different deletions
at the PU.1/TRIM33 site in ICE are indicated in brackets. *Po0.05 and **Po0.01, Mann–Whitney test. Figure 2 | TRIM33 is bound to a distal Ifnb1 gene regulatory element (ICE) in macrophages. (a) TRIM33 ChIP-seq data in RAW 264.7 cells and BMDM
activated for 24 h with LPS showing TRIM33 binding to ICE, located 15 kb upstream the Ifnb1 TSS. Blue boxes indicate PU.1 peaks in BMDM (data from
ref. 43). Green boxes indicate positions of ICE and the enhanceosome. ARTICLE 1e) and NIH3T3 PU.1 þTRIM33 þ and Constitutive TRIM33 occupancy at ICE was observed in
BMDM although occupancy appeared to increase at late time
points (24 h) following LPS activation (Fig. 2b, left panel). PU.1
binding at the Ifnb1 promoter and at ICE was constitutive and
detected in WT and Trim33 / BMDM (Fig. 2b, middle and
right panels) indicating that PU.1 binding to ICE was not
TRIM33-dependent. Finally, no TRIM33 binding was observed
on the Ifnb1 promoter or ICE in NIH3T3 cells (Fig. 2c),
indicating macrophage specificity of TRIM33 in binding to ICE. Altogether, these results show that ICE functions as a cis-acting
transcriptional repressor element of the Ifnb1 gene activation in
macrophages and indicate that TRIM33 and PU.1 bound to ICE
may have an important role in Ifnb1 gene transcription shutdown
during the late phase of macrophage activation. g
p
g
p
y
g
To determine if TRIM33-mediated regulation of Ifnb1 in
myeloid cells can be obtained in NIH3T3 by simultaneous
expression of PU.1 and TRIM33, NIH3T3 cells were transduced
with a PU.1 expressing lentivirus (Supplementary Fig. 2a). PU.1
expressing NIH3T3 were then transduced with the lentivirus
that promoted efficient shRNA-mediated depletion of TRIM33
(Supplementary Fig. 1e) and NIH3T3 PU.1 þTRIM33 þ and ICE chromatin structure and interaction with Ifnb1 in BMDM. Comparison of reported human and mouse ICE sequences
showed 70% sequence homology around the TRIM33/PU.1 peak
with consensus binding motifs for AP-1, NF-kB and IRF 4 4 & 2015 Macmillan Publishers Limited. All rights reserve ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 (b) ChIP-qPCR data for TRIM33 binding on ICE in WT BMDM (left panel) and for
PU.1 binding on Ifnb1 promoter and on ICE (right panels) in WT and Trim33 / BMDM at indicated time points after LPS activation. Data represent the
enrichment over a negative control region in the b-globin promoter. Mean±s.e.m., n ¼ 3. (c) ChIP-qPCR analysis of TRIM33 binding at the Ifnb1 promoter
and on ICE in NIH3T3 cells. Mean±s.e.m., n ¼ 3. (d) Kinetics of Ifnb1 mRNA levels in NIH3T3 cells expressing PU.1 and a shRNA targeting Trim33 (NIH3T3
PU.1 þ TRIM33 ) or PU.1 and an shRNA targeting luciferase (NIH3T3 PU.1 þ TRIM33 þ) and activated with poly(I:C). Mean±s.e.m., n ¼ 2. (e) Luciferase
reporter assay in RAW 264.7 cells transfected with reporter constructs containing the Ifnb1 promoter alone (Ifnb1 Prom-luc) or ICE cloned upstream of the
Ifnb1 promoter (ICE-Ifnb1 Prom-Luc) and activated with LPS. Mean±s.e.m., n ¼ 3. (f,g) Fold increase of Ifnb1 mRNA levels in ICE þ / versus WT RAW
264.7 cells after LPS activation (f) and in ICE þ / versus WT NIH3T3 cells after poly(I:C) activation (g). Mean±s.e.m., n ¼ 3. (h) Fold increase of Ifnb1
mRNA in ICE / versus WT RAW 264.7 cells after LPS (left) or poly(I:C) (right) activation. Mean±s.e.m., n ¼ 3 to 5. Clones carrying different deletions
at the PU.1/TRIM33 site in ICE are indicated in brackets. *Po0.05 and **Po0.01, Mann–Whitney test. NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications 5 NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 COMMUNICATIONS | DOI: 10.1038/ncomms9900
A a
PU.1 peaks in BMDM
RAW
50
Ifnb1
Scale
chr4:
88,170,000
10 kb
88,175,000
88,180,000
88,185,000
mm9
88,190,000
RefSeq genes
1
24
1
BMDM
24 h LPS
TRIM33
E h
ICE a
b
Hours of LPS treatment
100
80
60
40
20
0
0
2
12
18
24
ChIP PU.1
promoter
Fold enrichment
100
80
60
40
20
0
0
2
12
18
24
ChIP PU.1
ICE
WT
Trim33 –/–
Fold enrichment
Hours of LPS treatment
ChIP TRIM33
ICE
15
10
5
0
0
2 12 24
Fold enrichment
Hours of LPS treatment
PU.1 peaks in BMDM
RAW
50
Ifnb1
Scale
chr4:
88,170,000
10 kb
88,175,000
88,180,000
88,185,000
mm9
88,190,000
RefSeq genes
1
24
1
BMDM
24 h LPS
TRIM33
Enhanceosome
ICE a 88,190,000 b
ChIP TRIM33
ICE
15
10
5
0
0
2 12 24
Fold enrichment
Hours of LPS treatment b Hours of LPS treatment
100
80
60
40
20
0
0
2
12
18
24
ChIP PU.1
promoter
Fold enrichment
100
80
60
40
20
0
0
2
12
18
24
ChIP PU.1
ICE
WT
Trim33 –/–
Fold enrichment
Hours of LPS treatment
3
24
atment 5
4
3
2
1
0
5
4
3
2
1
0
TRIM33 IgG
TRIM33 IgG
Fold enrichment
Fold enrichment
c
Promoter
ICE
ChIP TRIM33 in NIH3T3 d
0
6
12
18
24
30
0
10,000
20,000
30,000
40,000
NIH3T3 PU.1+ TRIM33+
NIH3T3 PU.1+ TRIM33–
Hours of poly(I:C) treatment
Ifnb1 mRNA
relative expression
*
*
* Hours of LPS treatment
Relative luc
*
*
*
Ifnb1 Prom-Luc
ICE-Ifnb1 Prom-Luc
e
320
240
160
80
0
0
2
4
8 d c e 6
Fold increase of Ifnb1
mRNA level
RAW WT
RAW ICE+/–
*
*
f
4
2
0
0
2
4
8
10
12
Hours of LPS treatment NIH3T3 ICE+/–
NIH3T3 WT
6
4
2
0
0
1
2
3
6
10
24
Fold increase of Ifnb1
mRNA level
g
Hours of poly(I:C) treatment f 1
g h
Hours of LPS treatment
*
*
*
**
**
Fold increase of Ifnb1
mRNA level
Hours of poly(I:C) treatment
*
**
**
**
RAW WT
RAW ICE–/– (#34; Δ100 bp)
RAW ICE–/– (#15; Δ176 bp)
Fold increase of Ifnb1
mRNA level
12
9
6
3
0
0
2
4
8
10
12
12
8
4
0
0
2
4
8
10
16
p y(
) h
Hours of LPS treatment
*
*
*
**
**
Fold increase of Ifnb1
mRNA level
R
R
R
12
9
6
3
0
0
2
4
8
10
12 h Hours of poly(I:C) treatment
*
**
**
**
WT
ICE–/– (#34; Δ100 bp)
ICE–/– (#15; Δ176 bp)
Fold increase of Ifnb1
mRNA level
12
8
4
0
0
2
4
8
10
16 Figure 2 | TRIM33 is bound to a distal Ifnb1 gene regulatory element (ICE) in macrophages. & 2015 Macmillan Publishers Limited. All rights reserved. It then returned to basal levels in WT BMDM, whereas a
5- to 8-fold increase in H3ac was observed after 10 and 24 h in
Trim33 / BMDM (Fig. 4c). H3ac on the Ifnb1 promoter
in LPS-activated Trim33 / iM mimicked that observed in
Trim33 / BMDM (Fig. 4d). Expression of ectopic full-length
flag-TRIM33 in Trim33 / iM led to decreased H3ac on the
Ifnb1 promoter 7 h after LPS stimulation (Fig. 4d), whereas the
flag-DCC that could not rescue normal Ifnb1 expression in
Trim33 / iM (Fig. 1h) did not decrease H3ac on the Ifnb1
promoter 7 h after LPS stimulation (Fig. 4d). These results
indicate a link between TRIM33 and the regulation of H3ac on
the Ifnb1 promoter. Increased H3ac on the Ifnb1 promoter in LPS-activated
Trim33 / BMDM indicated a possible role for TRIM33 in
regulating the equilibrium between recruitment and/or activity
of HAT and histone deacetylases (HDAC). Treatment of
LPS-activated WT BMDM with trichostatine A, an inhibitor of
HDACs, did not result in sustained Ifnb1 expression, whereas it
did alter expression of genes regulated by HDACs (Fig. 4e, left
panel and Supplementary Fig. 4a). Conversely, the increased
H3ac was found to be associated with CBP/p300 HAT binding
on the Ifnb1 promoter 10 and 24 h after LPS activation in
Trim33 / BMDM (Fig. 4e, right panel). As total CBP protein
levels were similar in WT and Trim33 / BMDM (Fig. 4f),
these results indicated that TRIM33 deficiency promotes CBP
recruitment. To determine the importance of CBP/p300 activity
in the phenotype of Trim33 /
BMDM, we used C646,
a
small-molecule
inhibitor
that
efficiently
competes
with
CBP/p300 substrates25. Adding C646 2 h after LPS induction
did not modify Ifnb1 expression in WT BMDM, but reversed the
high sustained Ifnb1 transcription level in Trim33 / BMDMs
at both 10 and 24 h (Fig. 4g). This reversion was associated with
decreased levels of H3ac (Fig. 4h) and reduced Pol II occupancy
within the Ifnb1 promoter region in Trim33 /
BMDM
(Supplementary Fig. 4b). & 2015 Macmillan Publishers Limited. All rights reserved. Then, in WT BMDM, Pol II drops off and Ifnb1 transcription
ceases, whereas in Trim33 /
BMDM, continued Pol II
occupancy and H3K4me3 promote sustained Ifnb1 transcription. Prior to LPS activation, histone H3ac on the Ifnb1 promoter
was similar in WT and Trim33 / BMDM (Fig. 4c). This H3ac
increased at 1 h after LPS activation of WT and Trim33 /
BMDM. It then returned to basal levels in WT BMDM, whereas a
5- to 8-fold increase in H3ac was observed after 10 and 24 h in
Trim33 / BMDM (Fig. 4c). H3ac on the Ifnb1 promoter
in LPS-activated Trim33 / iM mimicked that observed in
Trim33 / BMDM (Fig. 4d). Expression of ectopic full-length
flag-TRIM33 in Trim33 / iM led to decreased H3ac on the
Ifnb1 promoter 7 h after LPS stimulation (Fig. 4d), whereas the
flag-DCC that could not rescue normal Ifnb1 expression in
Trim33 / iM (Fig. 1h) did not decrease H3ac on the Ifnb1
promoter 7 h after LPS stimulation (Fig. 4d). These results
indicate a link between TRIM33 and the regulation of H3ac on
the Ifnb1 promoter. We then determined the effect of TRIM33 deficiency on Ifnb1
transcription and chromatin structure during LPS activation of
BMDM. On the Ifnb1 TSS, low levels of paused Pol II were
observed before LPS stimulation in both WT and Trim33 /
cells (Fig. 4b, upper left panel). In WT BMDM, Pol II occupancy
at TSS and in Ifnb1 30 region increased after 1 h of stimulation
and then was lost at 4 h (Fig. 4b, upper panels). In Trim33 /
BMDM, Pol II occupancy similarly increased after 1 h of
stimulation but its levels were maintained up to 24 h (Fig. 4b,
upper panels). H3K4me3 levels were transiently increased in WT
BMDM after 4 h of LPS stimulation, whereas in Trim33 /
BMDM, persistent and high levels of H3K4me3 were also
observed up to 24 h (Fig. 4b, lower panel and right panel). These
observations suggest that the paused Pol II seen in the absence of
LPS treatment is used for rapid Ifnb1 transcription immediately
following LPS stimulation in WT and Trim33 / BMDM. NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications
& 2015 Macmillan Publishers Limited. All rights reserved. & 2015 Macmillan Publishers Limited. All rights reserved. Then, in WT BMDM, Pol II drops off and Ifnb1 transcription
ceases, whereas in Trim33 /
BMDM, continued Pol II
occupancy and H3K4me3 promote sustained Ifnb1 transcription. g
Analysis of ICE chromatin structure in macrophages showed that
this region is characterized by high levels of H3K4me3 and
H3K27ac modification, flanked by regions enriched for H3K4me1,
all features of transcriptionally active promoters (Supplementary
Fig. 3b,
red
graph,
data
from
ref. 24). These
epigenetic
modifications are present in short-term haematopoietic stem cells
(ST-HSCs) and in myeloid cells, but not in mature erythroid and
lymphoid cells (Supplementary Fig. 3b). We studied the effect of
TRIM33 deficiency on the chromatin structure of ICE in non-
activated and LPS-activated BMDM to ask whether TRIM33 has a
role in histone modification of this region. Before and during LPS
activation of WT and Trim33 /
BMDM, no significant
differences in
H3K4me1 levels
on ICE
could be detected
(Supplementary Fig. 3c). ChIP and ChIP-seq analyses showed a
constitutive
binding
of
RNA
Polymerase
II
(Pol
II)
and
constitutively high levels of H3K4me3 on ICE (Fig. 3b). Prior to
LPS activation, histone H3 acetylation (H3ac) on ICE was similar in
WT and Trim33 / BMDM (Fig. 3c, left panel). During LPS
activation, H3ac on ICE did not change in WT BMDM but was
transiently increased 10 h after LPS activation in Trim33 /
BMDM (Fig. 3c, left panel). This increased H3ac on ICE in
Trim33 / BMDM was associated with transient increase of CBP/
p300 histone H3 acetyl-transferase (HAT) -binding on ICE 10h
after LPS activation (Fig. 3c, right panel). Collectively, database
analyses and our results suggest that, in BMDM, ICE exhibits a
promoter-like chromatin signature established early during myeloid
differentiation. TRIM33 deficiency did not modify ICE chromatin
signature and only led to transient increases of H3ac and CBP/p300
recruitment on ICE whereas a sustained high expression of Ifnb1
was observed in LPS-activated Trim33 / BMDM suggesting that
TRIM33 bound to ICE might act at a distance. Prior to LPS activation, histone H3ac on the Ifnb1 promoter
was similar in WT and Trim33 / BMDM (Fig. 4c). This H3ac
increased at 1 h after LPS activation of WT and Trim33 /
BMDM. NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications & 2015 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 transcription factors (Supplementary Fig. 3a, left panel). Fur-
thermore, c-JUN, the p65 subunit of NF-kB and IRF3, three
transcription factors that form the Ifnb1 enhanceosome and
regulate its transcriptional activity, were also bound to ICE three
hours after LPS activation of BMDM (Supplementary Fig. 3a,
right panel; data from ref. 23). We studied a possible TRIM33
dependency of c-jun and p65 binding to ICE but found that
TRIM33 deficiency did not modify the kinetics of their binding to
ICE (Fig. 3a). transcription factors (Supplementary Fig. 3a, left panel). Fur-
thermore, c-JUN, the p65 subunit of NF-kB and IRF3, three
transcription factors that form the Ifnb1 enhanceosome and
regulate its transcriptional activity, were also bound to ICE three
hours after LPS activation of BMDM (Supplementary Fig. 3a,
right panel; data from ref. 23). We studied a possible TRIM33
dependency of c-jun and p65 binding to ICE but found that
TRIM33 deficiency did not modify the kinetics of their binding to
ICE (Fig. 3a). p65 and c-jun binding to the Ifnb1 promoter was maintained
even 24 h after activation (Fig. 4a). Thus, TRIM33 deficiency
maintains enhanceosome loading by c-jun and p65 during the
late phases of LPS activation. p
We then determined the effect of TRIM33 deficiency on Ifnb1
transcription and chromatin structure during LPS activation of
BMDM. On the Ifnb1 TSS, low levels of paused Pol II were
observed before LPS stimulation in both WT and Trim33 /
cells (Fig. 4b, upper left panel). In WT BMDM, Pol II occupancy
at TSS and in Ifnb1 30 region increased after 1 h of stimulation
and then was lost at 4 h (Fig. 4b, upper panels). In Trim33 /
BMDM, Pol II occupancy similarly increased after 1 h of
stimulation but its levels were maintained up to 24 h (Fig. 4b,
upper panels). H3K4me3 levels were transiently increased in WT
BMDM after 4 h of LPS stimulation, whereas in Trim33 /
BMDM, persistent and high levels of H3K4me3 were also
observed up to 24 h (Fig. 4b, lower panel and right panel). These
observations suggest that the paused Pol II seen in the absence of
LPS treatment is used for rapid Ifnb1 transcription immediately
following LPS stimulation in WT and Trim33 / BMDM. & 2015 Macmillan Publishers Limited. All rights reserved. g
To investigate how TRIM33 bound to ICE, that is located 15 kb
upstream of the Ifnb1 transcription unit, may regulate Ifnb1
transcription, chromosome conformation capture experiments
followed by deep sequencing (3C-seq) were performed in WT
and Trim33 / BMDM before and after LPS activation. ICE
(Fig. 3d, top) and the Ifnb1 gene (Fig. 3d, bottom), including its
promoter, were used as viewpoints. In WT BMDM, both
viewpoints showed a loop between ICE and the Ifnb1 gene
before LPS activation and a twofold stronger interaction 24 h after
LPS activation (Fig. 3d, blue curves). Interestingly, Trim33
deletion did not significantly modify DNA looping in this region,
even after LPS treatment (Fig. 3d, compare red (Trim33 / ) and
blue (WT) curves). These results indicate that ICE interacts with
the Ifnb1 proximal region in a constitutive and TRIM33-
independent manner, but that this interaction is strengthened
following LPS stimulation. TRIM33 represses Ifnb1 by preventing CBP/p300 recruitment. To characterize how TRIM33 might regulate Ifnb1 transcription,
we studied the effect of TRIM33 deficiency on temporal binding
of p65 and c-jun to the enhanceosome as these two factors are
major regulators of its activity. As anticipated, in WT BMDM,
c-jun and p65 were recruited to the Ifnb1 promoter at early times
following LPS activation (1 h), but their binding returned to basal
levels after 24 h (Fig. 4a). In contrast, in the absence of TRIM33, pp
y
g
Altogether, these results show that enhanced CBP/p300
recruitment and activity at late times of activation is required
for sustained Ifnb1 expression in Trim33 / BMDM and that
TRIM33
may regulate Ifnb1
expression
at late times by
preventing the recruitment of CBP/p300. 6 6 NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications
& 2015 Macmillan Publishers Limited. All rights reserved. & 2015 Macmillan Publishers Limited. All rights reserved ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 a
b
c
d
0 h LPS
24 h LPS
WT
Trim33 –/–
EcoRI sites
TRIM33
Ifnb1
Ifna15
Ifna14
Ifnb1
Ifna15
Ifna14
2,500
2,000
1,500
500
0
88,120,000
88,120,000
88,120,000
88,170,000
88,170,000
88,220,000
88,220,000
88,120,000
88,170,000
88,22,0000
88,170,000
88,220,000
1,000
2,500
2,000
1,500
500
0
1,000
1,500
500
0
1,000
1,500
500
0
1,000
EcoRI sites
TRIM33
Ifnb1
ICE
Viewpoint : ICE
r.p.m. per fragment
Viewpoint : Ifnb1
r.p.m. & 2015 Macmillan Publishers Limited. All rights reserved. (d) DNA looping at the Ifnb1 locus was determined by 3C-se
h after LPS activation of WTand Trim33 / BMDM using either ICE (upper panel) or Ifnb1 gene (lower panel) as viewpoints (show
OMMUNICATIONS | DOI: 10.1038/ncomms9900
AR a
0
0
2
4
6
8
1
1
24
24
6
4
2
0
0 1
1
24
24
0
0
Hours of LPS treatment
Hours of LPS treatment
ChIP c-jun
ICE
ChIP p65
ICE
WT
Trim33 –/–
WT
Trim33 –/–
Fold enrichment
Fold enrichment a
0
0
2
4
6
8
1
1
24
24
0
Hours of LPS treatment
ChIP c-jun
ICE
WT
Trim33 –/–
Fold enrichment a ChIP p65
ICE b
0
0
5
10
15
1
4
10
24
Hours of LPS treatment
ChIP RNA POL II
ICE
WT
Trim33 –/–
Fold enrichment b ICE
H3K4me3
WT
Trim33 –/–
4 h
0 h
Scale
chr4:
10 kb
88,185,000
88,180,000
88,190,000
mm9
1
1
1
125
125
125
125
125
1
125
1
1
24 h 0
0
100
200
300
400
500
1
4
10
24
Hours of LPS treatment
ChIP H3K4me3
ICE
WT
Trim33 –/–
Fold enrichment 24
10
1
0
4
0
2
4
6
8
Hours of LPS treatment
ChIP p300
ICE
–
WT
Trim33 –/–
Fold enrichment
** c
24
24
10
1
0
4
0
2
4
6
8
10
4
Hours of LPS treatment
Hours of LPS treatment
1
0
0
20
40
60
80
100
ChIP H3ac
ICE
ChIP p300
ICE
WT
Trim33 –/–
WT
Trim33 –/–
Fold enrichment
Fold enrichment
**
** c
24
10
4
Hours of LPS treatment
1
0
0
20
40
60
80
100
ChIP H3ac
ICE
WT
Trim33 –/
Fold enrichment
** c c d
0 h LPS
EcoRI sites
TRIM33
Ifnb1
Ifna15
Ifna14
2,500
2,000
1,500
500
0
88,120,000
88,120,000
88,170,000
88,22,0000
88,170,000
88,220,000
1,000
1,500
500
0
1,000
E
Viewpoint : ICE
r.p.m. per fragment
Viewpoint : Ifnb1
r.p.m. per fragment
Ifnb1
ICE 24 h LPS
WT
Trim33 –/–
Ifnb1
Ifna15
Ifna14
88,120,000
88,120,000
88,170,000
88,170,000
88,220,000
88,220,000
2,500
2,000
1,500
500
0
1,000
1,500
500
0
1,000
EcoRI sites
TRIM33
Ifnb1
ICE d Figure 3 | ICE chromatin structure and interaction with the Ifnb1 promoter during activation of macrophages. and interaction with the Ifnb1 promoter during activation of macrophages. & 2015 Macmillan Publishers Limited. All rights reserved. per fragment
Ifnb1
ICE
24
24
10
1
0
4
0
2
4
6
8
10
4
Hours of LPS treatment
Hours of LPS treatment
1
0
0
20
40
60
80
100
0
0
0
5
10
15
0
0
2
4
6
8
1
1
24
24
6
4
2
0
0 1
1
24
24
0
0
1
4
10
24
0
100
200
300
400
500
1
4
10
24
Hours of LPS treatment
Hours of LPS treatment
Hours of LPS treatment
Hours of LPS treatment
ChIP H3ac
ICE
ChIP p300
ICE
ChIP H3K4me3
ICE
ChIP RNA POL II
ICE
ChIP c-jun
ICE
ChIP p65
ICE
WT
Trim33 –/–
WT
Trim33 –/–
WT
Trim33 –/–
WT
Trim33 –/–
WT
Trim33 –/–
WT
Trim33 –/–
Fold enrichment
Fold enrichment
Fold enrichment
Fold enrichment
Fold enrichment
Fold enrichment
**
**
ICE
H3K4me3
WT
Trim33 –/–
4 h
0 h
Scale
chr4:
10 kb
88,185,000
88,180,000
88,190,000
mm9
1
1
1
125
125
125
125
125
1
125
1
1
24 h
CE chromatin structure and interaction with the Ifnb1 promoter during activation of macrophages. (a) ChIP-qPCR analysis of c
CE in WT and Trim33 / BMDM treated for the indicated times with LPS. Mean±s.e.m., n ¼ 2 to 4. (b) ChIP-qPCR analysis of
anel) and H3K4me3 (lower left panel) at ICE in WTand Trim33 / BMDM treated for the indicated times with LPS. Mean±s.e.m
) UCSC genome browser images showing H3K4me3 ChIP-seq profiles at ICE in WT and Trim33 / BMDM treated for the ind
PS. (c) ChIP-qPCR analysis of acetylated histone H3 (left panel) and CBP/p300 (right panel) at ICE in WTand Trim33 / BMDM
d times with LPS. Mean±s.e.m., n ¼ 4. **Po0.01, Mann–Whitney test. Discussion Surprisingly, a
**
**
b
**
**
Control
15
10
5
0
0
1
4
10
24
TSA 10 nM
H3K4me3
4 h
0 h
24 h
12 h
Ifnb1
d
c
e
f
LPS (hours)
250 kDa
37 kDa
*
*
5
WT
Trim33 –/–
WT
Trim33 –/–
Trim33 –/–
WT
Trim33 –/–
WT
Trim33 –/–
WT
Trim33 –/–
WT
Trim33 –/–
Trim33 –/–
WT
WT
Scale
chr4:
ChlP p65
promoter
ChlP RNA POL II
promoter
ChlP H3K4me3
promoter
ChlP H3ac
promoter
ChlP p300
promoter
ChlP H3ac
promoter
ChlP RNA POL II
+2.5 kb
ChlP c-jun
promoter
4
*
*
**
**
**
**
iM Trim33 –/– + GFP
iM Trim33 –/– + flag-TRIM33
iM Trim33 –/– + flag-ΔCC
**
**
**
**
3
2
Fold enrichment
Fold enrichment
Fold enrichment
Fold enrichment
Fold enrichment
Fold enrichment
Fold enrichment
Fold enrichment
1
0
40
800
100
7
6
5
4
3
2
1
0
0 7
0 7
0 7
80
60
40
20
0
0
1
4
10
24
600
400
200
0
0
1
4
10
24
15
10
5
0
30
20
10
0
0
1
4
10
24
5
4
3
2
1
0
0
Hours of LPS treatment
Hours of LPS treatment
Hours of LPS treatment
Hours of LPS treatment
Hours of LPS treatment
0
1
4
10
24
Hours of LPS treatment
1 24
0 1 24
0
Hours of LPS treatment
1 24
0 1 24
1,600
Ifnb 1 mRNA
relative expression
1,200
800
200
100
0
0
Hours of LPS treatment
Hours of LPS treatment
4
8
12
190
mm9
2 kb
88,170,000
88,165,000
1
1
1
1
1
190
190
190
190
190
190
190
1
1
1
Ifnb1
β-Actin
CBP
0
4 24
0
4 24 a
*
*
5
WT
Trim33 –/–
WT
Trim33 –/–
ChlP p65
promoter
ChlP c-jun
promoter
4
3
2
Fold enrichment
Fold enrichment
1
0
5
4
3
2
1
0
0
Hours of LPS treatment
1 24
0 1 24
0
Hours of LPS treatment
1 24
0 1 24 a
b
H3K4me3
4 h
0 h
24 h
12 h
Ifnb1
*
*
5
WT
Trim33 –/–
WT
Trim33 –/–
Trim33 –/–
WT
Trim33 –/–
WT
Trim33 –/–
WT
Scale
chr4:
ChlP p65
promoter
ChlP RNA POL II
promoter
ChlP H3K4me3
promoter
ChlP RNA POL II
+2.5 kb
ChlP c-jun
promoter
4
*
*
**
**
**
**
**
**
3
2
Fold enrichment
Fold enrichment
Fold enrichment
Fold enrichment
Fold enrichment
1
0
40
800
600
400
200
0
0
1
4
10
24
15
10
5
0
30
20
10
0
0
1
4
10
24
5
4
3
2
1
0
0
Hours of LPS treatment
Hours of LPS treatment
Hours of LPS treatment
0
1
4
10
24
Hours of LPS treatment
1 24
0 1 24
0
Hours of LPS treatment
1 24
0 1 24
190
mm9
2 kb
88,170,000
88,165,000
1
1
1
1
1
190
190
190
190
190
190
190
1
1
1
Ifnb1 a
*
5
WT
Trim33
ChlP p65
promoter
4
3
2
Fold enrichment
1
0
0
Hours of LPS treatment
1 24
0 1 24 a *
–/–
WT
Trim33 –/–
ChlP c-jun
promoter
Fold enrichment
5
4
3
2
1
0
0
Hours of LPS treatment
1 24
0 1 24 **
**
g
b
**
**
Control
15
10
5
0
0
1
4
10
24
TSA 10 nM
H3K4me3
4 h
0 h
24 h
12 h
Ifnb1
d
c
Ifnb1 mRNA
relative expression
C646
**
**
WT
WT + C646
WT
WT + C646
e
i
f
LPS (hours)
250 kDa
37 kDa
**
**
h
Fibroblast
Activation
ICE
Promoter
Ifnb1
ICE
Promoter
Enhanceosome
Pol II
CBP/p300
ICE
Promoter
Ifnb1
Before
activation
ICE
Promoter
Ifnb1
End of
activation
Macrophage
ICE
Promoter
Ifnb1
Pol II
PU.1
PU.1
ICE
Promoter
Ifnb1
PU.1
PU.1
Pol II
CBP/p300
TRIM33
ICE
Promoter
Ifnb1
ICE
C
Promoter
Enhanceosome
Pol II
PU.1
PU.1
CBP/p300
TRIM33
Trim33 –/–
WT
Trim33 –/–
WT
Trim33 –/–
WT
Trim33 –/–
WT
Trim33 –/–
Trim33
–/– + C646
Trim33
–/– + C646
Trim33
–/–
Trim33
–/–
Trim33 –/–
WT
WT
Scale
chr4:
ChlP RNA POL II
promoter
ChlP H3K4me3
promoter
ChlP H3ac
promoter
ChlP p300
promoter
ChlP H3ac
promoter
ChlP H3ac
promoter
ChlP RNA POL II
+2.5 kb
*
*
**
**
**
**
iM Trim33 –/– + GFP
iM Trim33 –/– + flag-TRIM33
iM Trim33 –/– + flag-ΔCC
**
**
**
**
2
Fold e
Fold enrichment
Fold enrichment
Fold enrichment
Fold enrichment
Fold enrichment
relative to WT 0h
Fold enrichment
Fold enrichment
Fold e
1
0
40
800
100
7
6
5
4
3
2
1
0
0 7
0 7
0 7
80
60
40
20
0
0
1
4
10
24
600
400
200
0
0
1
4
10
24
15
10
5
0
30
20
10
0
0
1
4
10
24
2
1
0
0
Hours of LPS treatment
Hours of LPS treatment
Hours of LPS treatment
Hours of LPS treatment
Hours of LPS treatment
0
1
4
10
24
Hours of LPS treatment
1 24
0 1 24
0
Hours of LPS treatment
1 24
0 1 24
1,600
80,000
60,000
40,000
20,000
0
0
6
12
18
24
Ifnb 1 mRNA
relative expression
1,200
800
200
100
0
0
15
10
5
0
0
4
10
24
Hours of LPS treatment
Hours of LPS treatment
Hours of LPS treatment
Hours of LPS treatment
4
8
12
190
mm9
2 kb
88,170,000
88,165,000
1
1
1
1
1
190
190
190
190
190
190
190
1
1
1
Ifnb1
TRIM33
β-Actin
CBP
0
4 24
0
4 24
NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecomm
& 2015 Macmillan Publishers Limited. Discussion b
H3K4me3
4 h
0 h
24 h
12 h
Ifnb1
Trim33 –/–
WT
Trim33 –/–
WT
Trim33 –/–
WT
Scale
chr4:
ChlP RNA POL II
promoter
ChlP H3K4me3
promoter
ChlP RNA POL II
+2.5 kb
*
*
**
**
**
**
**
**
Fold enrichment
Fold enrichment
Fold enrichment
40
800
600
400
200
0
0
1
4
10
24
15
10
5
0
30
20
10
0
0
1
4
10
24
Hours of LPS treatment
0
1
4
10
24
Hours of LPS treatment
190
mm9
2 kb
88,170,000
88,165,000
1
1
1
1
1
190
190
190
190
190
190
190
1
1
1
Ifnb1 b b
4 h
0 h
Trim33 –/–
WT
Scale
chr4:
ChlP RNA POL II
promoter
ChlP RNA POL II
+2.5 kb
*
*
**
**
**
**
Fold enrichment
Fold enrichment
40
15
10
5
0
30
20
10
0
0
1
4
10
24
Hours of LPS treatment
0
1
4
10
24
Hours of LPS treatment
190
88,165
1
1
1
190
190
190
190
1 H3K4me3
4 h
0 h
24 h
12 h
Ifnb1
Trim33 –/–
WT
Trim33 –/–
WT
Scale
chr4:
190
mm9
2 kb
88,170,000
88,165,000
1
1
1
1
1
190
190
190
190
190
190
190
1
1
1
Ifnb1 d
ChlP H3ac
promoter
**
**
iM Trim33 –/– + GFP
iM Trim33 –/– + flag-TRIM33
iM Trim33 –/– + flag-ΔCC
Fold enrichment
7
6
5
4
3
2
1
0
0 7
0 7
0 7
Hours of LPS treatment **
**
c
Trim33 –/–
WT
ChlP H3ac
promoter
Fold enrichment
100
80
60
40
20
0
0
1
4
10
24
Hours of LPS treatment d c f
LPS (hours)
250 kDa
37 kDa
–
Trim33 –/–
WT
β-Actin
CBP
0
4 24
0
4 24 **
**
15
10
5
0
0
1
4
10
24
Trim33 –/–
WT
ChlP p300
promoter
Fold enrichment
Hours of LPS treatment Control
TSA 10 nM
e
1,600
Ifnb 1 mRNA
relative expression
1,200
800
200
100
0
0
Hours of LPS treatment
4
8
12 f e e i
Fibroblast
Activation
ICE
Promoter
Ifnb1
ICE
Promoter
Enhanceosome
Pol II
CBP/p300
ICE
Promoter
Ifnb1
Before
activation
ICE
Promoter
Ifnb1
End of
activation
Macrophage
ICE
Promoter
Ifnb1
Pol II
PU.1
PU.1
ICE
Promoter
Ifnb1
PU.1
PU.1
Pol II
CBP/p300
TRIM33
ICE
Promoter
Ifnb1
ICE
C
Promoter
Enhanceosome
Pol II
PU.1
PU.1
CBP/p300
TRIM33
TRIM33 WT
WT + C646
**
**
h
Trim33
–/– + C646
Trim33
–/–
ChlP H3ac
promoter
Fold enrichment
relative to WT 0h
15
10
5
0
0
4
10
24
Hours of LPS treatment g
Ifnb1 mRNA
relative expression
C646
**
**
WT
WT + C646
Trim33
–/– + C646
Trim33
–/–
80,000
60,000
40,000
20,000
0
0
6
12
18
24
Hours of LPS treatment i h g NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications
& 2015 Macmillan Publishers Limited. & 2015 Macmillan Publishers Limited. All rights reserved. (a) ChIP-qPCR analysis of c-jun or p65
/ Figure 3 | ICE chromatin structure and interaction with the Ifnb1 promoter during activation of macrophages. (a) ChIP-qPCR analysis of c-jun or p65
binding at ICE in WT and Trim33 / BMDM treated for the indicated times with LPS. Mean±s.e.m., n ¼ 2 to 4. (b) ChIP-qPCR analysis of RNA Pol II
(upper left panel) and H3K4me3 (lower left panel) at ICE in WTand Trim33 / BMDM treated for the indicated times with LPS. Mean±s.e.m., n ¼ 3 to 5. (Right panel) UCSC genome browser images showing H3K4me3 ChIP-seq profiles at ICE in WT and Trim33 / BMDM treated for the indicated
times with LPS. (c) ChIP-qPCR analysis of acetylated histone H3 (left panel) and CBP/p300 (right panel) at ICE in WTand Trim33 / BMDM treated for
the indicated times with LPS. Mean±s.e.m., n ¼ 4. **Po0.01, Mann–Whitney test. (d) DNA looping at the Ifnb1 locus was determined by 3C-seq performed
before or 24 h after LPS activation of WTand Trim33 / BMDM using either ICE (upper panel) or Ifnb1 gene (lower panel) as viewpoints (shown by an eye
and a yellow band). Data represent normalized reads per million (r.p.m.) per restriction fragment. The x axis shows the genomic coordinates of the Ifnb1
locus. The positions of the EcoRI restriction sites and the TRIM33 ChIP-seq profile in BMDM are indicated on the top. 7 ARTICLE Discussion All rights reserved. Discussion despite the importance of IFN-b production by macrophages,
no cis- or trans-acting factor that might confer a myeloid
specificity to Ifnb1 gene transcription has been characterized. The
data presented in this study provide evidence of a previously
unappreciated regulation of Ifnb1 transcription in macrophages Although IFN-a and IFN-b share the same receptor, IFN-b seems
to be the major immune-suppressive IFN26 and macrophage-
restricted synthesis of IFN-b can contribute to protective or
pathological immune responses in the lung27. ARTICLE In contrast, in macrophages, ICE acts as a repressor
of Ifnb1 promoter activity during LPS activation. Furthermore,
the high and sustained expression of Ifnb1 in LPS- or poly(I:C)-
activated RAW cells where both alleles of ICE are deleted using
lentiviral delivery of Cas9 and gRNA indicates that ICE has a
repressor activity when these cells are stimulated. Although the
lentiviral system used might increase the frequency of off-target
effects30,31, the similar results obtained with three different clones
and with different gRNAs make off-target effects less likely. Use
of recombinant Cas9 protein32 or highly efficient transient
transfection of RAW cells will reduce off-target effects and
definitively show that ICE is a unique element that acts as an
enhancer in fibroblasts, but displays promoter marks and acts as a
repressor at late stages of LPS activation of macrophages. These
opposite roles of ICE in fibroblasts and macrophages might be
linked to recruitment of distinct proteins in the two cell types. Indeed, PU.1, which is not expressed in fibroblasts, is bound to
ICE in macrophages and might be involved in the cell-specific
function of ICE. Ectopic PU.1 expression in TRIM33 þ and
TRIM33
NIH3T3
cells
indicates
that
TRIM33-mediated
repression of Ifnb1 is dependent on PU.1 expression. However,
in fibroblasts activated with poly(I:C), PU.1 expression associated
with TRIM33 deficiency does not result in the sustained Ifnb1
expression observed in poly(I:C)-activated Trim33 / BMDM. This result suggests that factors present in BMDM, but not in
fibroblasts, are required for Ifnb1 repression during the late stages
of BMDM activation. Amongst haematopoietic-restricted PU.1
partners, IRF8 and IRF3 that regulate Ifnb1 activation in Two lines of evidence suggest that, during the late stages of LPS
activation of BMDM, TRIM33 represses Ifnb1 expression through
modulation of CBP/p300 recruitment and/or activity at the
Ifnb1 promoter. First, TRIM33 inactivation led to recruitment of
CBP/p300 at the Ifnb1 promoter and enhanced H3ac. Second,
CBP/p300 activity is critical for enhanced Ifnb1 transcription
at late stages as chemical inhibition of CBP/p300 enzymatic
activity could restore the regulated expression of Ifnb1 gene in
Trim33 / macrophages. As CBP/p300 acts as a switch to
initially turn on Ifnb1 gene transcription38, these results indicated
that TRIM33 might turn off Ifnb1 transcription during the
late stages of LPS activation of macrophages by impairing the
CBP/p300 recruitment and activity at the Ifnb1 promoter. ARTICLE ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 through a macrophage-restricted TRIM33 recruitment on a
regulatory sequence, designated as ICE, located 15 kb upstream
from the Ifnb1 TSS. BMDM6,33 are good candidates to cooperate with TRIM33 for
Ifnb1 repression during the late stages of BMDM activation. through a macrophage-restricted TRIM33 recruitment on a
regulatory sequence, designated as ICE, located 15 kb upstream
from the Ifnb1 TSS. f
p
g
g
Several TRIM proteins regulate production and action of
IFN-b during innate immune response. TRIM6 is a positive
regulator of IFN-b and is critical for IFN-b-mediated antiviral
response34, TRIM25 is essential for RIG-I-mediated-type I
IFN induction35, TRIM21 regulates IRF3-dependent IFN-b
expression36 and TRIM56 modulates STING and subsequent
IFN-b induction37. Here, we show the implication of TRIM33 in
the transcriptional regulation of Ifnb1. Interestingly, TRIM33
deficiency did not alter the initial activation of Ifnb1 transcription
after LPS activation of macrophages but impaired repression
of Ifnb1 expression during the late stages of this activation. Together with the continuous binding of TRIM33 on ICE, the
complementation of the Ifnb1 phenotype in macrophages by re-
expression of TRIM33 in Trim33 / immortalized macrophages
suggested a direct role of TRIM33 in Ifnb1 transcription and
indicated that the activity and/or substrate availability of TRIM33
regulated Ifnb1 expression at the end of LPS activation of
macrophages. f
ICE has an open-chromatin structure highly conserved during
myeloid differentiation and characterized by Pol II occupancy
and tri-methylation of H3K4, two features that are not typical
marks of an enhancer or a repressor. In addition to a PU.1-
binding site, ICE contains DNA-binding sites for transcriptional
regulators such as IRF3, c-jun or p65 that are also part of the
enhanceosome. ICE has been recently shown to interact with the
Ifnb1 promoter in human fibroblasts in the absence of any viral
infection22. Here, we show that ICE can also interact with the
Ifnb1 promoter in non-activated macrophages. These combined
findings indicate that ICE/Ifnb1 loop is cell-type independent,
stable and independent of viral or bacterial stimulation. Such
enhancer or repressor loop stability has been described during
development where they are associated with paused polymerase28
and in human fibroblasts where TNF-a-responsive enhancers
contact their target promoters before TNF-a activation29. g
p
Transient transfection in fibroblast cell lines shows that ICE
acts as an enhancer of Ifnb1 promoter activity, but only after viral
infection22. ARTICLE This
TRIM33-dependent recruitment and activity of CBP/p300 could
be direct and/or mediated by trans-acting factors such as p65 that
are, in Trim33 / BMDM, loaded onto the enhanceosome
during the late phases of LPS activation. However, as PU.1 can
interact with CBP/p300 (refs 39,40) and TRIM33, we propose a
model where CBP/p300 and TRIM33 compete for PU.1 binding
during LPS activation of BMDM. During the initial stages of LPS
activation, CBP/p300 recruited by the enhanceosome might
activate Ifnb1 transcription, whereas during the late stages of LPS
activation, TRIM33 might interact with PU.1, impair PU.1/CBP/
p300 interaction and shut down Ifnb1 transcription (Fig. 4i). Numerous studies have shown the complexity of Ifnb1 gene
transcriptional regulation. Our data describe a new regulatory
layer through identification of cis- and trans-acting elements that
regulate Ifnb1 gene transcription at specific steps of macrophage
activation, but not in fibroblasts. These findings not only provide Figure 4 | TRIM33 regulates Ifnb1 gene expression through inhibition of CBP/p300 recruitment. (a) ChIP-qPCR of p65 (left panel) and c-jun (right
panel) at the Ifnb1 promoter in WT and Trim33 / BMDM treated with LPS. Mean±s.e.m., n ¼ 2 to 4. (b, top) ChIP-qPCR of RNA Pol II at the Ifnb1
promoter (left panel) and at a region located þ 2.5 kb from TSS (middle panel) in WTand Trim33 / BMDM treated with LPS. Mean±s.e.m., n ¼ 3 to 5. (Bottom) ChIP-qPCR (left panel) and ChIP-seq (right panel) of H3K4me3 at the Ifnb1 promoter in WT and Trim33 / BMDM treated with LPS. Mean±s.e.m., n ¼ 3. (c) ChIP-qPCR of H3ac at the Ifnb1 promoter in WTand Trim33 / BMDM treated with LPS. Mean±s.e.m., n ¼ 4. (d) ChIP-qPCR of
H3ac at the Ifnb1 promoter in Trim33 / iM expressing GFP (iM Trim33 / þ GFP), full-length flag-TRIM33 and GFP (iM Trim33 / þ flag-TRIM33), or
flag-TRIM33 lacking the coiled-coil domain and GFP (iM Trim33 / þ flag-DCC), and treated for 0 or 7 h with LPS. Mean±s.e.m., n ¼ 3. (e, left) Relative
expression of Ifnb1 mRNA in LPS-activated WT BMDM in presence or absence of Tricostatin A (TSA), added 4 h after LPS stimulation. Mean±s.e.m., n ¼ 3. (Right) ChIP-qPCR of CBP/p300 binding at the Ifnb1 promoter in WT and Trim33 / BMDM treated with LPS. Discussion All rights reserved. 8 Methods
i 3C-seq was performed as previously described41, using EcoRI as first
cutter and DpnII as second cutter. Briefly, cells were fixed with 2% formaldehyde
for 10 min at room temperature, and nuclei were prepared by lysing cells in 10 mM
Tris pH8, 10 mM NaCl, 0.2% NP-40. Nuclei were lyzed in 0.5 ml 1 EcoRI buffer
supplemented with 0.3% SDS for 1 h at 37 C. Triton X-100 was added at 2% final
for another 1 h at 37 C. DNA was then digested with 400 units of EcoRI overnight
at 37 C. Samples were incubated for 25 min at 65 C with 1.6% SDS, diluted to 7 ml
with ligase buffer, supplemented with 1% Triton X-100 and incubated at 37 C for
1 h. Ligation was performed for 4 h at 16 C with 100 u T4 DNA ligase, then 300 mg
proteinase K were added and samples were decrosslinked overnight at 65 C. RNase (300 mg) was added for 45 min at 37 C, and samples were extracted with
phenol/chloroform/isoamyl alcohol (25:24:1; PCI). After precipitation, samples
were digested with DpnII, extracted with PCI and precipitated, and ligated in 15 ml
ligation buffer at 16 C for 4 h before another PCI extraction and precipitation. Samples were amplified by PCR with the primers listed below, and PCR products
were purified on QIAprep columns (Qiagen). The resulting libraries were
sequenced on a Illumina HiSeq 2000 as single-end 100 bp reads. After trimming,
reads were aligned on the mm9 version of the mouse genome using Bowtie. All the clones were verified by sequencing of a 2 kb genomic region containing
the ICE. Protein extraction and western blot. Total proteins from BMDM or iM were
extracted using lysis buffer (50 mM Tris pH8, 300 mM NaCl, 1% Triton X-100,
0.1% sodium dodecyl sulfate, 1 mM EDTA, phosphatase inhibitor cocktail-1 and -2
(Sigma Aldrich) and complete protease inhibitor cocktail (Roche)). Proteins were
separated on 3–8% Tris-Acetate gel or 4–12% Bis Tris gel (Life Technologies),
transferred on a nitrocellulose membrane (Amersham) and blotted with the
indicated antibodies. Following staining with HRP-coupled secondary antibodies,
the proteins were detected with ECL Prime by chemiluminescence (Amersham). Protein extraction and western blot. Methods
i 100 ng ml 1, poly(I:C) at 30 mg ml 1, TSA (Sigma Aldrich) at 10 nM, and C646
(Merck Millipore) at 10 mM. NIH3T3 were transfected with 10 mg ml 1 poly(I:C)
(Sigma Aldrich). Chromatin Immunoprecipitation (ChIP). Cells were fixed with 1% formaldehyde
for 10 min at 37 C, lysed in SDS lysis buffer (50 mM Tris pH8, 10 mM EDTA,
1% SDS, protease inhibitor cocktail (Roche)) and sonicated. Supernatant was
diluted 10 times in IP dilution buffer (16.7 mM Tris pH8, 167 mM NaCl, 1.2 mM
EDTA, 1.1% TritonX-100, 0.01% SDS, protease inhibitor cocktail (Roche)) and
immunoprecipitations were carried out overnight with specific antibodies. Immunoprecipitated chromatin was collected using Protein A Agarose/Salmon
Sperm DNA beads (Millipore) and, after washing and elution, reverse cross-linking
was carried out with 0.2 M NaCl at 65 C overnight. The chromatin was then
digested by 20 mg of Proteinase K (Invitrogen) for 1 h at 45 C and isolated
by phenol–chloroform extraction. PCR reactions were performed using SYBR
Green PCR Master Mix (Applied Biosystems) and specific primers sequences
are listed below. Genomic deletions of ICE with the CRISPR/CAS9 system. Two guides RNA
(gRNA) were designed to delete a 1,361 bp fragment containing the 15 kb region
using the CRISPR Design Tool (http://tools.genome-engineering.org), to minimize
the number of off-target sites. Sequences for gRNA 5A2 and 3A are 50-TTC
TCGTTCATTGTTAGCGA-30 and 50-CTCTAGTTTAGACGTTTAAC-30,
respectively. Singles gRNA were then cloned into the LentiCRISPRv2 (Addgene)
vector, which contains the human CAS9-coding sequence, using BsmBI cloning
sites. Lentivirus were produced and co-transduced into RAW 264.7 and NIH3T3. After puromycin selection (3 mg ml 1, Sigma Aldrich), cells were clonally isolated
by fluorescence-activated cell sorting and individual clones were screened for
deletion by PCR using the following primers: F5-1:50-TGACGACAAATGTGGT
ACTGG-30; F3-1:50-CAGGCGAAAGGGAAACTAAA-30; and R3-1:50-TAGGAG
TGGCAGATGGGAAG-30. For sequencing, 10 ng of purified DNA from ChIP was adapter-ligated, PCR
amplified and sequenced on the Illumina Genome Analyzer IIx as single-end 50
base reads following Illumina’s instructions. Sequence reads were mapped to
reference genome mm9/NCBI37 using Bowtie v0.12.7. Deletions of 100 or 176 bp were carried out using one gRNA guide (50-AAA
CACGTTAGTTGTCAGAC-30) flanking the PU.1/TRIM33 site at the ICE and
cloned into the LentiCRISPRv2 vector as above. After puromycin selection and
clonal isolation, WT and ICE / RAW 264.7 cells were identified by PCR using
the following primers: F: 50-AGCAAAGCCGAAGAAGACAC-30 and R: 50-GGA
AGAGGACGAGAGAACCA-30. 3C-seq. Methods
i iM were activated with LPS
in IMDM supplemented with 2.5% FCS and 1% PS. For cell lines, RAW 264.7 and
NIH3T3 cells were grown in DMEM (Life Technologies) supplemented with 10%
FCS and 1% PS. RAW 264.7 cells were activated with LPS in DMEM supplemented
with 1% FCS. Unless otherwise indicated, LPS (Sigma Aldrich) was used at
100 ng ml 1, poly(I:C) at 30 mg ml 1, TSA (Sigma Aldrich) at 10 nM, and C646
(Merck Millipore) at 10 mM. NIH3T3 were transfected with 10 mg ml 1 poly(I:C)
(Sigma Aldrich). Cell culture. For BMDM generation, mouse bone marrow (BM) was flushed out of
the tibiae, femora and humeri using a syringe with PBS, filtered through a 70-mm
mesh filter (Becton Dickinson) to remove debris and pelleted by centrifugation. Adherent cells were removed by incubating BM cells on culture dishes for 3 h in
IMDM supplemented with 10% foetal calf serum (FCS), 1% penicillin/strepto-
mycin (PS; Life Technologies) and 10 mM thioglycerol (Sigma Aldrich), then
non-adherent cells were cultured for 7 days on culture dishes in the same medium
supplemented with 25 ng ml 1 mouse CSF1 (Miltenyi Biotec). On day 7, BMDM
were activated with LPS or poly(I:C) in IMDM supplemented with 2.5% FCS and
1% PS. For PMs, cells were collected with cold PBS and cultured for 2 h in RPMI
1640 medium (Life Technologies), supplemented with 10% FCS. All adherent cells
expressed F4/80 and were considered as PMs. PM were activated with LPS or
poly(I:C) in RPMI 1640 medium supplemented with 2.5% FCS and 1% PS. WT and
Trim33 / iM were generated as previously described21. Briefly, BM cells isolated
from WT and Trim33 / mice were cultured in IMDM supplemented with 10%
FCS and 50 ng ml 1 mouse CSF1 (Peprotech). After overnight culture, the cells
were transduced with a lentiviral vector expressing the SV40 large Lentiviral vectors for rescue and knockdown. For rescue experiments in
Trim33 / iM, the lentiviral vector was constructed by inserting full-length
flag-TRIM33 from the pSG5-flag-TRIM33 (ref. 15) into the pTRIP/DU3-MND-
IRES-GFP vector, downstream the MND promoter, using the Gateway technology
(Life Technologies). Deletions of the coiled-coil domain (aa 321–457), the ubiquitin
ligase activity (aa 141–145) and the SMAD-interaction (aa 555–876) domain were
generated by PCR. The pTRIP/DU3-MND-GFP was used in control experiments. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 important insights into the cell-specific regulation of Ifnb1 gene
transcription but also extend the role of TRIM proteins as critical
regulators of the innate immune response. Results are presented as the number of reads per million reads per EcoRI fragment,
in the middle of each fragment. Results are presented as the number of reads per million reads per EcoRI fragment,
in the middle of each fragment. Assay for IFN-b. WT and Trim33 / BMDM supernatants were collected
after LPS stimulation. ELISA was performed with LegendMax Mouse IFN-b kit
(Biolegend), according to manufacturer’s instructions. Methods
i Mice. To generate deletion of Trim33 in mature myeloid cells, Trim33fl/fl
C57Bl/6-CD45.2 mice15 were crossed with Lysozyme-Cre C57Bl/6-CD45.2 mice
(strain name: B6.129P2-Lyz2tm1(cre)Ifo/J, The Jackson Laboratory). Male and
female mice of 8–12 months of age were used. Experiments were performed in
compliance with European legislation and with the Ethics Committee of the French
Ministry of Agriculture (Agreement B9203202). Quantitative RT-PCR. Total RNA was extracted with the RNeasy Plus Micro kit
(Qiagen) and reverse transcribed with random primers and Superscript III (Life
Technologies). Quantitative PCR was performed using the Power SYBR green PCR
master mix (Applied Biosystems) in the 7900HT Fast Real-Time or the StepOne
PCR Systems (Applied Biosystems). Primer sequences are listed below. Cell culture. For BMDM generation, mouse bone marrow (BM) was flushed out of
the tibiae, femora and humeri using a syringe with PBS, filtered through a 70-mm
mesh filter (Becton Dickinson) to remove debris and pelleted by centrifugation. Adherent cells were removed by incubating BM cells on culture dishes for 3 h in
IMDM supplemented with 10% foetal calf serum (FCS), 1% penicillin/strepto-
mycin (PS; Life Technologies) and 10 mM thioglycerol (Sigma Aldrich), then
non-adherent cells were cultured for 7 days on culture dishes in the same medium
supplemented with 25 ng ml 1 mouse CSF1 (Miltenyi Biotec). On day 7, BMDM
were activated with LPS or poly(I:C) in IMDM supplemented with 2.5% FCS and
1% PS. For PMs, cells were collected with cold PBS and cultured for 2 h in RPMI
1640 medium (Life Technologies), supplemented with 10% FCS. All adherent cells
expressed F4/80 and were considered as PMs. PM were activated with LPS or
poly(I:C) in RPMI 1640 medium supplemented with 2.5% FCS and 1% PS. WT and
Trim33 / iM were generated as previously described21. Briefly, BM cells isolated
from WT and Trim33 / mice were cultured in IMDM supplemented with 10%
FCS and 50 ng ml 1 mouse CSF1 (Peprotech). After overnight culture, the cells
were transduced with a lentiviral vector expressing the SV40 large
T antigen (SFFV.Tag LV). Cells were then cultured in a chemically defined medium
(SFM-macrophage medium, Life Technologies) supplemented with CSF1
(50 ng ml 1). Single clones were isolated that expressed F4/80, CD11b but not Gr1. The resulting clones, termed iM, were maintained in IMDM supplemented with
20% foetal bovine serum, 1% PS and 50 ng ml 1 CSF1. Methods
i NIH3T3 PU1 þ cells were obtained by transducing a lentiviral vector pTRIP/DU3-
MND-PU.1-IRES-GFP. For TRIM33 knocking-down in NIH3T3 or NIH3T3
PU.1 þ, the sequence of the shRNA targeting mouse Trim33 was obtained
from Sigma Aldrich (50-CCGGCGGACTTAAATCGGTTGTTAACTCGAGTTAA
CAACCGATTTAAGTCCGTTTTTG-30) and cloned in the pSuper vector
(OligoEngine) downstream the H1 promoter. H1-shRNATRIM33 fragment was
then cloned in the pTRIP/DU3-EF1a-GFP, where the GFP coding sequence is
under the control of the EF1a promoter. All the constructs were verified by
sequencing. Lentiviral vector production and cells transduction were carried out as
described42. GFP-positive cells were sorted and used in functional assays. p
g
g
T antigen (SFFV.Tag LV). Cells were then cultured in a chemically defined medium
(SFM-macrophage medium, Life Technologies) supplemented with CSF1
1 p
g
g
pp
(50 ng ml 1). Single clones were isolated that expressed F4/80, CD11b but not Gr1. The resulting clones, termed iM, were maintained in IMDM supplemented with
20% foetal bovine serum, 1% PS and 50 ng ml 1 CSF1. iM were activated with LPS
in IMDM supplemented with 2.5% FCS and 1% PS. For cell lines, RAW 264.7 and
NIH3T3 cells were grown in DMEM (Life Technologies) supplemented with 10%
FCS and 1% PS. RAW 264.7 cells were activated with LPS in DMEM supplemented
with 1% FCS. Unless otherwise indicated, LPS (Sigma Aldrich) was used at
1
1 Luciferase assays. A 391 bp DNA fragment of murine Ifnb1 promoter was
obtained by PCR on genomic DNA and cloned into the pGL3 Basic vector
(Promega) using KpnI and XhoI sites. A 408 bp DNA fragment spanning the
15 kb PU.1/TRIM33-binding site was obtained by PCR of genomic DNA and
cloned upstream of the 391 bp DNA fragment of murine Ifnb1 promoter into the
pGL3 Basic vector. After sequencing of the different constructs, RAW 264.7 cells
were transfected using JetPEI (PolyPlus-transfection) with the indicated constructs
and the TK-renilla reporter vector (Promega), as an internal control for normal-
ization. Twenty-four hours after transfection, cells were activated with LPS
(100 ng ml 1) and luciferase activity was determined using the dual-luciferase
reporter assay (Promega). Firefly luciferase activity was normalized with respect to
renilla luciferase activity. g
100 ng ml 1, poly(I:C) at 30 mg ml 1, TSA (Sigma Aldrich) at 10 nM, and C646
(Merck Millipore) at 10 mM. NIH3T3 were transfected with 10 mg ml 1 poly(I:C)
(Sigma Aldrich). ARTICLE Mean±s.e.m., n ¼ 4. (f) Western blot of
CBP in WT and Trim33 / BMDM treated with LPS. b-actin is shown as control. n ¼ 4 independent experiments. (g) Kinetics of Ifnb1 mRNA levels in
LPS-activated WTand Trim33 / BMDM, in the presence (dotted lines) or absence (continuous lines) of C646. C646 was added 2 h after LPS stimulation
and Ifnb1 mRNA levels were determined. Mean±s.e.m., n ¼ 8. (h) ChIP-qPCR of H3ac at the Ifnb1 promoter in LPS-activated WT and Trim33 / BMDM,
in the presence (hatched columns) or absence (solid columns) of C646. Data are presented relative to H3ac binding in untreated WT BMDM. Mean±s.e.m., n ¼ 2. (i) Schematic representation depicting the role of TRIM33 in the macrophage-restricted Ifnb1 gene transcription shut down. *Po0.05 and **Po0.01, Mann–Whitney test. 9 9 NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications ARTICLE References 31. Wang, X. et al. Unbiased detection of off-target cleavage by CRISPR-Cas9
and TALENs using integrase-defective lentiviral vectors. Nat. Biotechnol. 33,
175–178 (2015). 1. Trinchieri, G. Type I interferon: friend or foe? J. Exp. Med. 207, 2053–2063
(2010). 2. Stetson, D. B. & Medzhitov, R. Type I interferons in host defense. Immunity 25,
373–381 (2006). 32. Kim, S., Kim, D., Cho, S. W., Kim, J. & Kim, J. S. Highly efficient RNA-guided
genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res. 24, 1012–1019 (2014). 3. Teijaro, J. R. et al. Persistent LCMV infection is controlled by blockade of type I
interferon signaling. Science 340, 207–211 (2013). 33. Mancino, A. et al. A dual cis-regulatory code links IRF8 to constitutive and
inducible gene expression in macrophages. Genes Dev. 29, 394–408 (2015). 4. Wilson, E. B. et al. Blockade of chronic type I interferon signaling to control
persistent LCMV infection. Science 340, 202–207 (2013). 34. Rajsbaum, R. et al. Unanchored K48-linked polyubiquitin synthesized by the
E3-ubiquitin ligase TRIM6 stimulates the interferon-IKKepsilon kinase-
mediated antiviral response. Immunity 40, 880–895 (2014). 5. Ford, E. & Thanos, D. The transcriptional code of human IFN-beta gene
expression. Biochim. Biophys. Acta. 1799, 328–336 (2010). p
p y
(
)
6. Li, P. et al. IRF8 and IRF3 cooperatively regulate rapid interferon-beta
induction in human blood monocytes. Blood 117, 2847–2854 (2011). p
p y
6. Li, P. et al. IRF8 and IRF3 cooperatively regulate rapid interferon-beta
i d
ti
i
h
bl
d
t
Bl
d 117 2847 2854 (2011) 35. Inn, K. S. et al. Linear ubiquitin assembly complex negatively regulates RIG-I-
and TRIM25-mediated type I interferon induction. Mol. Cell 41, 354–365 (2011). induction in human blood monocytes. Blood 117, 2847–2854 7. Kim, H. & Seed, B. The transcription factor MafB antagonizes antiviral
responses by blocking recruitment of coactivators to the transcription factor
IRF3. Nat. Immunol. 11, 743–750 (2010). 36. Higgs, R. et al. The E3 ubiquitin ligase Ro52 negatively regulates IFN-beta
production post-pathogen recognition by polyubiquitin-mediated degradation
of IRF3. J. Immunol. 181, 1780–1786 (2008). gg
q
g
g
y
g
production post-pathogen recognition by polyubiquitin-mediated degradation
of IRF3. J. Immunol. 181, 1780–1786 (2008). 8. Siednienko, J. et al. Nuclear factor kappaB subunits RelB and cRel negatively
regulate Toll-like receptor 3-mediated beta-interferon production via induction
of transcriptional repressor protein YY1. J. Biol. Chem. 286, 44750–44763
(2011). 37. Tsuchida, T. et al. References The ubiquitin ligase TRIM56 regulates innate immune
responses to intracellular double-stranded DNA. Immunity 33, 765–776 (2010). 38. Merika, M., Williams, A. J., Chen, G., Collins, T. & Thanos, D. Recruitment of
CBP/p300 by the IFN beta enhanceosome is required for synergistic activation
of transcription. Mol. Cell 1, 277–287 (1998). 9. Josse, T. et al. Association of the interferon-beta gene with pericentromeric
heterochromatin is dynamically regulated during virus infection through a
YY1-dependent mechanism. Nucleic. Acids. Res. 40, 4396–4411 (2012). 39. Yamamoto, H., Kihara-Negishi, F., Yamada, T., Hashimoto, Y. & Oikawa, T. Physical and functional interactions between the transcription factor PU.1 and
the coactivator CBP. Oncogene 18, 1495–1501 (1999). 10. Weill, L., Shestakova, E. & Bonnefoy, E. Transcription factor YY1 binds to the
murine beta interferon promoter and regulates its transcriptional capacity with
a dual activator/repressor role. J. Virol. 77, 2903–2914 (2003). 40. Bai, Y., Srinivasan, L., Perkins, L. & Atchison, M. L. Protein acetylation
regulates both PU.1 transactivation and Ig kappa 3’ enhancer activity. J. Immunol. 175, 5160–5169 (2005). 11. Hatakeyama, S. TRIM proteins and cancer. Nat. Rev. Cancer 11, 792–804
(2011). 41. Stadhouders, R. et al. Multiplexed chromosome conformation capture
sequencing for rapid genome-scale high-resolution detection of long-range
chromatin interactions. Nat. Protoc. 8, 509–524 (2013). 12. Herquel, B., Ouararhni, K. & Davidson, I. The TIF1alpha-related TRIM
cofactors couple chromatin modifications to transcriptional regulation,
signaling and tumor suppression. Transcription 2, 231–236 (2011). 42. Kusy, S. et al. NKX3.1 is a direct TAL1 target gene that mediates proliferation
of TAL1-expressing human T cell acute lymphoblastic leukemia. J. Exp. Med. 207, 2141–2156 (2010). g
g
p
13. Herquel, B. et al. Trim24-repressed VL30 retrotransposons regulate gene
expression by producing noncoding RNA. Nat. Struct. Mol. Biol. 20, 339–346
(2013). 43. Heinz, S. et al. Simple combinations of lineage-determining transcription
factors prime cis-regulatory elements required for macrophage and B cell
identities. Mol. Cell 38, 576–589 (2010). 14. Xi, Q. et al. A poised chromatin platform for TGF-beta access to master
regulators. Cell 147, 1511–1524 (2011). g
15. Kusy, S. et al. Adult hematopoiesis is regulated by TIF1gamma, a repressor of
TAL1 and PU.1 transcriptional activity. Cell Stem Cell 8, 412–425 (2011). ARTICLE ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 c-JUN (sc-1694X, Santa Cruz (1:200)), p65 (sc-372X, Santa Cruz (1:200)), RNA Pol
II (sc-899X, Santa Cruz (1:200)), H3K4me3 (07-473, Millipore (1:500)), PU.1
(sc-352X, Santa Cruz (1:10,000 for western blot; 1:500 for ChIP)), p300 (sc-585X,
Santa Cruz), AcH3 (06-599, Millipore (1:500)), H3K4me1 (ab-8895, Abcam
(1:500)), Flag (M2 monoclonal, Sigma Aldrich (1:1,000)), CBP (A-22, sc-369,
Santa Cruz (1:1,000)), b-actin (A5441, Sigma Aldrich (1:10,000)). 20. Weng, L. et al. The E3 ubiquitin ligase tripartite motif 33 is essential for
cytosolic RNA-induced NLRP3 inflammasome activation. J. Immunol. 193,
3676–3682 (2014). 21. Squadrito, M. L. et al. Endogenous RNAs modulate microRNA sorting to
exosomes and transfer to acceptor cells. Cell Rep. 8, 1432–1446 (2014). 22. Banerjee, A. R., Kim, Y. J. & Kim, T. H. A novel virus-inducible enhancer of the
interferon-beta gene with tightly linked promoter and enhancer activities. Nucleic Acids Res. 42, 12537–12554 (2014). Primer sequences. The following primer sequences were used in quantitative
RT-PCR, ChIP and 3C-seq: Ifnb1 F: 50-CTGGCTTCCATCATGAACAA-30; Ifnb1
R: 50-AGAGGGCTGTGGTGGAGAA-30; Ifna F: 50-GGATGTGACCTTCCTCAG
ACTC-30; Ifna R: 50-ACCTTCTCCTGCGGGAATCCAA-30; Hprt F: 50-GCTGGT
GAAAAGGACCTCT-30; Hprt R: 50-CACAGGACTAGAACACCTGC-30; Ifnb1
promoter F: 50-CCACCTGTTGTTCATGATGG-30; Ifnb1 promoter R: 50-CATT
CTCACTGCAGCCTTTG-30; Ifnb1 ICE F: 50-CCAAGGGTTGCGTAATGAAC-30;
Ifnb1 ICE R: 50-CCCGATCTTCAAATCCAGTC-30; Ifnb1 þ 2,5 kb F: 50-TAGCT
TCCATGCCCAGTTTC-30; Ifnb1 þ 2,5 kb R: 50-CCAAAAGTATGCCCATC
ACC-30; b-globin major promoter F: 50-GAAGCCTGATTCCGTAGAGC-30;
b-globin major promoter R: 50-CAACTGATCCTACCTCACCTTATATGC-30;
ICE EcoRI primer: 50-AATGATACGGCGACCACCGAACACTCTTTCCCTACA
CGACGCTCTTCCGATCT-30 followed by a 4nt tag and 50-GATGGCACACCTT
GAATTC-30; ICE DpnII primer: 50-CAAGCAGAAGACGGCATACGAGACGA
CAAATGTGGTACTG-30; Ifnb1 EcoRI primer: 50-AATGATACGGCGACCACC
GAACACTCTTTCCCTACACGACGCTCTTCCGATCT-30 followed by a 4nt
tag and 50-GGGTGTTCTATTTTATCAATAC-30; Ifnb1 DpnII primer: 50-CAA
GCAGAAGACGGCATACGATTTCTAGAGTTTCCGACTCTG-30. 23. Uhlenhaut, N. H. et al. Insights into negative regulation by the glucocorticoid
receptor from genome-wide profiling of inflammatory cistromes. Mol. Cell 49,
158–171 (2013). 24. Lara-Astiaso, D. et al. Immunogenetics. Chromatin state dynamics during
blood formation. Science 345, 943–949 (2014). 25. Bowers, E. M. et al. Virtual ligand screening of the p300/CBP histone
acetyltransferase: identification of a selective small molecule inhibitor. Chem. Biol. 17, 471–482 (2010). 26. Ng, C. T. et al. Blockade of interferon Beta, but not interferon alpha, signaling
controls persistent viral infection. Cell Host Microbe 17, 653–661 (2015). 27. Hogner, K. et al. Macrophage-expressed IFN-beta contributes to apoptotic
alveolar epithelial cell injury in severe influenza virus pneumonia. PLoS Pathog. 9, e1003188 (2013). 28. Ghavi-Helm, Y. et al. Enhancer loops appear stable during development and
are associated with paused polymerase. Nature 512, 96–100 (2014). 29. Jin, F. et al. ARTICLE A high-resolution map of the three-dimensional chromatin
interactome in human cells. Nature 503, 290–294 (2013). interactome in human cells. Nature 503, 290–294 (2013). 30. Pattanayak, V., Guilinger, J. P. & Liu, D. R. Determining the specificities of
TALENs, Cas9, and other genome-editing enzymes. Methods Enzymol. 546,
47–78 (2014). Acknowledgements 16. Bai, X. et al. TIF1gamma controls erythroid cell fate by regulating transcription
elongation. Cell 142, 133–143 (2010). We are grateful to the staff of the iRCM animal facility for excellent support during the
mouse studies and to N. Dechamps and J. Baijer of the iRCM cytometry platform for
excellent support during FACS experiments. F.F. and A.P. are supported by fellowships
from Dim Stem Pole and La Ligue contre le Cancer. This project was supported by grants to
P.-H.R. from La Ligue contre le Cancer (e´quipe labelise´e), ANR (ANR-12-BSV1-0001-02),
INCA (PL BIO 013031), Inserm, CEA/DSV, Paris-Diderot and Paris-Sud. g
17. Ozato, K., Shin, D. M., Chang, T. H. & Morse, 3rd H. C. TRIM family proteins
and their emerging roles in innate immunity. Nat. Rev. Immunol. 8, 849–860
(2008). 18. McNab, F. W., Rajsbaum, R., Stoye, J. P. & O’Garra, A. Tripartite-motif
proteins and innate immune regulation. Curr. Opin. Immunol. 23, 46–56
(2011). 19. Tisserand, J. et al. Tripartite motif 24 (Trim24/Tif1 alpha) tumor suppressor
protein is a novel negative regulator of interferon (IFN)/signal transducers and
activators of transcription (STAT) signaling pathway acting through retinoic
acid receptor alpha (Rar alpha) inhibition. J. Biol. Chem. 286, 33369–33379
(2011). Methods
i Total proteins from BMDM or iM were
extracted using lysis buffer (50 mM Tris pH8, 300 mM NaCl, 1% Triton X-100,
0.1% sodium dodecyl sulfate, 1 mM EDTA, phosphatase inhibitor cocktail-1 and -2
(Sigma Aldrich) and complete protease inhibitor cocktail (Roche)). Proteins were
separated on 3–8% Tris-Acetate gel or 4–12% Bis Tris gel (Life Technologies),
transferred on a nitrocellulose membrane (Amersham) and blotted with the
indicated antibodies. Following staining with HRP-coupled secondary antibodies,
the proteins were detected with ECL Prime by chemiluminescence (Amersham). Antibodies. The following antibodies were used in western blot and ChIP:
TRIM33 (3E9, Euromedex for WB (1:1,000); A301-059A, Bethyl for ChIP (1:100)), Antibodies. The following antibodies were used in western blot and ChIP:
TRIM33 (3E9, Euromedex for WB (1:1,000); A301-059A, Bethyl for ChIP (1:100)), 10 NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications
& 2015 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications
& 2015 Macmillan Publishers Limited. All rights reserved. & 2015 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9900 design and data analysis for 3C-Seq and wrote the manuscript. M.L.S. and M.D.P. assisted with experimental design for iM production and wrote the manuscript. All
authors approved the final version of the manuscript. Reprints and permission information is available online at http://npg.nature.com/
reprintsandpermissions/ How to cite this article: Ferri, F. et al. TRIM33 switches off Ifnb1 gene transcription
during the late phase of macrophage activation. Nat. Commun. 6:8900
doi: 10.1038/ncomms9900 (2015). Author contributions P.-H.R., F.F., I.D. and G.R. designed the project, analysed data and wrote the manuscript. A.P., V.P., A.-S.G., F.F., G.R., M.D. and D.L. organized, performed and analysed most
experiments and wrote the manuscript. E.S., A.v.d.H. and P.K. assisted with experimental NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications 11 & 2015 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications
& 2015 Macmillan Publishers Limited. All rights reserved. Additional information Accession codes: High throughput sequencing data have been deposited in the Gene
Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo), under accession
codes GSE73322 (3c-seq) and GSE43654 (ChIP-seq). This work is licensed under a Creative Commons Attribution 4.0
International License. The images or other third party material in this
article are included in the article’s Creative Commons license, unless indicated otherwise
in the credit line; if the material is not included under the Creative Commons license,
users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ Supplementary Information accompanies this paper at http://www.nature.com/
naturecommunications Competing financial interests: The authors declare no competing financial interests. 12 NATURE COMMUNICATIONS | 6:8900 | DOI: 10.1038/ncomms9900 | www.nature.com/naturecommunications
& 2015 Macmillan Publishers Limited. All rights reserved.
|
https://openalex.org/W4312435372
|
https://ejournal.mandalanursa.org/index.php/JIME/article/download/83/80
|
Indonesian
| null |
UPAYA MENINGKATKAN MOTIVASI BELAJAR DENGAN MENERAPKAN MODEL READING GUIDE BERBASIS PAIKEM BAGI PESERTA DIDIK KELAS II.B SEMESTER DUA TAHUN 2015/2016 DI SD NEGERI MODEL MATARAM
|
Jurnal Ilmiah Mandala Education
| 2,016
|
cc-by-sa
| 4,663
|
JIME, Vol. 2 No. 2 JIME, Vol. 2 No. 2 ISSN 2442-9511 Oktober 2016 UPAYA MENINGKATKAN MOTIVASI BELAJAR DENGAN MENERAPKAN
MODEL READING GUIDE BERBASIS PAIKEM BAGI PESERTA DIDIK KELAS II.B
SEMESTER DUA TAHUN 2015/2016 DI SD NEGERI MODEL MATARAM Khairul Lutfi, S.Pd
Guru Kelas II.B SD Negeri Model Mataram Abstrak; Penelitian ini bertujuan untuk mengetahui efektifitas penerapan pendekatan Model
Reading Guide Berbasis PAIKEM dalam upaya meningkatkan aktifitas belajar Peserta didik Kelas
II.B SD Negeri Model Mataram. Manfaat penelitian ini adalah sebagai bahan kajian dan bahan
temuan dalam pelaksanaan proses pembelajaran di kelas senyatanya. Bagi guru untuk meningkatkan
kompetensi dalam proses pembelajaran dan bagi peserta didik untuk meningktakan motivasi belajar
yang berdampak meningkatnya hasil belajar peserta didik. Penelitian ini dilaksanakan dua siklus,
masing-masing siklus kegiatannya adalah; perencanaan, pelaksanaan, observasi dan refleksi. Hasil
akhir tindakan pada siklus II menunjukkan bahwa hasil observasi guru memperoleh skor rata-rata
(4,57) dan hasil observasi peserta didik mencapai skor rata-rata (4,32). Sedangkan hasil dari
peningkatan aktifitas belajar peserta didik adalah meningkatnya perolehan hasil belajar peserta
didik mencapai nilai rata-rata (94,05), artinya indikator keberhasilan (> 75,00) telah terlampaui. Karena indikator keberhasilan telah terbukti penelitian dinyatakan berhasil dan dihentikan pada
siklus II. PENDAHULUAN seakan-akan kurang peduli terhadap materi
pelajaran/rasa ingin tahu sangat rendah, 4)
kebanyakan peserta didik berasal dari berbagai
kecamatan di Kota Mataram yang memiliki
karakteristik berbeda-beda sehingga ketika
guru menjelaskan materi pelajaran berprilaku
yang aneh-aneh sesuai dengan pembiasaaan di
kampung halamannya, 5) tingkat kedisiplinan
peserta didik masih sangat rendah, karena usia
kelas II.B adalah usia bermain, sehingga
selama proses pembelajaran terdengar ribut
bahkan ada yang berkelahi, ada yang keluar
masuk kelas tanpa permisi. Proses pembelajaran yang terjadi di
kelas II.B SD Negeri Model Mataram selama
ini kecendrungan masih di dominasi oleh guru
sentris, selama pembelajaran berlangsung guru
aktif
menjelaskan
materi,
membimbing,
mengarahkan, dan sesekali memarahi peserta
didik yang dianggap melanggar tata tertib
selama proses pembelajaran. Peserta didik
duduk manis mendengarkan penjelasan guru,
kesempatan untuk mengemukakan pendapat
sangat terbatas sehingga peserta didik tak
ubahnya seperti kertas kosong yang masih
putih bersih. coretan-coretan pada buku itu
hanya mencatat apa saja yang disuruh oleh
guru kelas. Peserta didik kurang termotivasi
untuk mengikuti pelajaran pelajaran yang
diberikan oleh guru, apalagi merubah pola
pikir peserta didik yang diharapkan mengarah
pada pembelajaran peserta didik aktif sangat
sulit didapatkan. Banyak solusi yang dapat dilakukan
oleh peneliti dalam upaya meningkatkan
motivasi belajar peserta didik kelas II.B SD
Negeri Model Mataram, diantaranya yaitu
dengan
menerapkan
model
pembelajaran
“Reading Guide” berbasis PAIKEM. Model
pembelajaran ini memiliki keunggulan bila
dibandingkan dengan model pembelajaran
yang lain yaitu: 1) peserta didik lebih berperan
aktif, 2) materi dapat diselesaikan dalam kelas,
3) memotivasi peserta didik untuk senang
membaca, 4) membangkitkan minat membaca,
5) mengerti peserta didik yang serius dan tidak
serius, 6) peserta didik dituntut untuk teliti
dalam menjawab soal, 7) guru mudah
mengetahui kelemahan dan kelebihan peserta Jurnal Ilmiah Mandala Education
Rendahnya motivasi belajar peserta
didik kelas II.B SD Negeri Model Mataram
disebabkan karena: 1) kurangnya antusias
peserta didik selama proses pembelajaran yang
cenderung didominasi oleh guru (guru sentris),
2) pemahaman nilai kebersamaan peserta didik
akan pentingnya kebersamaan sesama teman di
kelas kurang dioptimalkan, 3) peserta didik 78 ISSN 2442-9511 JIME, Vol. 2 No. 2 Oktober 2016 terhadap suatu tujuan (goal) atau perangsang
(incentive). Tujuan
adalah
yang
membatasi/menentukan
tingkah
laku
organisme itu (Ngalim Purwanto, 2007 : 61). Dengan demikian motivasi dalam proses
pembelajaran
sangat
dibutuhkan
untuk
terjadinya percepatan dalam mencapai tujuan
pendidikan dan pembelajaran secara khusus. didik
dalam
membaca,
8)
adanya
keseimbangan dalam mengembangkan ranah
kognitif, afektif, dan psikomotorik, dan 9) guru
mudah mengetahui dan memahami peserta
didik yang malas dan yang rajin. PENDAHULUAN Untuk membuktikan dugaan itu maka
perlu diadakan Penelitian Tindakan Kelas
(PTK) dengan judul “Upaya Meningkatak
Motivasi Belajar Dengan Menerapkan model
Reading Guide Berbasis PAIKEM Bagi
Peserta Didik kelas II.B Semester Dua Tahun
2015/2016 di SD Negeri Model Mataram”. Adapun alasan mengambil judul ini adalah 1)
Stategi pembelajaran Reading Guide adalah
strategi pembelajaran dengan menggunakan
bacaan atau teks yang diberikan dan dipandu
untuk dicari kata-kata penting yang terdapat
pada teks atau bacaan tersebut sesuai dengan
topik pembelajaran, 2) pembelajaran PAIKEM
merupakan sebuah strategi yang memiliki 5
(lima)
kriteria
yang
diandalkan
yaitu
pembelajaran yang aktif, inovatif, kreatif,
efektif, dan menyenangkan. Pembelajaran ini
memungkinkan
peserta
didik
untuk
mengerjakan kegiatan yang beragam dalam
rangka
mengembangkan
ketrampilan
dan
pemahamannya, dengan penekanan peserta
didik belajar sambil bekerja, sementara guru
menggunakan berbagai sumber dan alat bantu
ngajar (termasuk pemanfaatan lingkungan)
supaya
pembelajaran
lebih
menarik,
menyenangkan, dan efektif. Penelitian ini
bertujuan
untuk
mengetahui
efektifitas
penerapan model Reading Guide berbasis
PAIKEM dalam upaya meningkatkan motivasi
belajar peserta didik kelas II.B SD Negeri
Model
Mataram
semester
dua
tahun
2015/2016. Belajar dalam arti luas dapat diartikan
sebagai suatu proses yang memungkinkan
timbulnya atau berubahnya suatu tingkah laku
sebagai hasil dari terbentuknya respon utama,
dengan sarat bahwa perubahan atau munculnya
tingkah laku baru itu bukan disebabkan oleh
adanya
kematangan
atau
oleh
adanya
perubahan sementara oleh suatu hal (Nasution,
dkk: 1992: 3). Belajar adalah suatu proses
yamg ditandai dengan adanya perubahan pada
diri seseorang. Perubahan dalam diri seseorang
dapat ditunjukkan dalam berbagai bentuk
seperti
berubahnya
pengetahuannya,
pemahamannya, sikap dan tingkah lakunya,
keterampilan
dan
kemampuannya,
daya
reaksinya, daya penerimaannya dan lain-lain
aspek yang ada pada individu (Sudjana,2002
:280). Pendapat lain mengemukakan bahwa
dua jenis motivasi yaitu sebagai berikut:
“Motivasi primer, adalah motivasi yang
didasarkan atas motif-motif dasar. Motivasi
skunder, adalah yang dipelajari” (Dimyanti
dan Mudjiono, 1999:88). Adanya berbagai
jenis motivasi di atas, memberikan suatu
gambaran tentang motif-motif yang ada pada
setiap
individu. Adapun
motivasi
yang
berkaitan dengan mata pelajaran bahasa arab
adalah motivasi ekstrinsik, dimana motivasi ini
membutuhkan ransangan atau dorongan dari
luar misalnya, media, baik media visual, audio,
maupun audio visual serta buku-buku yang
dapat menimbulkan dan memberikan inspirasi
dan ransangan dalam belajar. Kerangka Teoritis
Motivasi Belajar Definisi Motivasi Belajar Siswa –
Dalam buku psikologi pendidikan Drs. M. Dalyono memaparkan bahwa “motivasi adalah
daya penggerak/pendorong untuk melakukan
sesuatu pekerjaan, yang bisa berasal dari
dalam diri dan juga dari luar” (Dalyono, 2005:
55). Adapun bentuk motivasi yang sering
dilakukan disekolah adalah memberi angka,
hadiah, pujian, gerakan tubuh, memberi tugas,
memberi ulangan, mengetahui hasil, dan
hukuman. (Djmarah dan zain, 2002 : 168). Dalam suatu kegiatan atau pekerjaan
yang dilakukan tidak terlepas adanya fungsi
dan kegunaan. Motivasi dalam belajar yang
merupakan suatu dorongan memiliki fungsi,
yang dikemukakan oleh seorang ahli yaitu: 1) Jurnal Ilmiah Mandala Education
Dalam bukunya Ngalim Purwanto, Sartain
mengatakan bahwa motivasi adalah suatu
pernyataan yang kompleks di dalam suatu
organisme yang mengarahkan tingkah laku 79 79 JIME, Vol. 2 No. 2 ISSN 2442-9511 Oktober 2016 Oktober 2016 Kelebihan dan Kekurangan Metode
Reading Guide. Kelebihan: 1) Peserta didik
lebih
berperan
aktif,
2)
Materi
dapat
diselesaikan dalam kelas, 3) Memotivasi
peserta didik untuk senang membaca, 4)
Membangkitkan minat membaca, 5) Mengerti
peserta didik yang serius dan tidak serius, 6)
Peserta didik dituntun untuk teliti dalam
menjawab soal, 7) Guru mudah mengetahui
kelemahan
dan
kelebihan
siswa
dalam
membaca, 8) Adanya keseimbangan dalam
mengembangkan ranah kognitif, afektif, dan
psikomotorik, 9) Guru mudah mengetahui dan
memahami peserta didik yang malas dan yang
rajin. sedangkan kelemahan adalah: 1) Kurang
efektif dalam membaca karena singkatnya
waktu, 2) Kadang membuat jenuh peserta
didik. Mendorong manusia untuk berbuat atau
bertindak. Motif untuk berfungsi sebagai
penggerak atau sebagai motor penggerak
melepaskan energi, 2) Menentukan arah
perbuatan yaitu petunjuk suatu tujuan yang
hendak
dicapai,
dan
3)
Menyelesaikan
perbuatan
yakni
menentukan
perbuatan-
perbuatan apa yang akan dikerjakan ynag
serasi
guna
mencapai
tujuan
dengan
menyisihkan perbuatan-perbuatan yang tidak
bermanfaat bagi tujuan tersebut. (Purwanto,
2002 : 70). Dalam penelitian ini yang dimaksud
dengan motivasi belajar adalah dorongan batin
dari seorang pelajar untuk berusaha agar
dirinya dapat mengetahui sesuatu berdasarkan
pengalaman belajarnya baik di sekolah, di
keluarga,
maupun
dimasyarakat
(teman
bermain). Adapun jenis motivasi yang diamati
selama proses pembelajaran meliputi: 1)
antusias, 2) bekerjasama, 3) rasa ingin tahu, 4)
berbahasa, 5) disiplin. Dari kelima aspek
motivasi dimaksud selanjutnya akan dijadikan
sebagai obyek Penelitian Tindakan Kelas
(PTK). Kerangka Teoritis
Motivasi Belajar Langkah-langkah Langkah langkah
mengimplementasikan metode Reading Guide:
1) Siapkan bahan ajar yang berupa teks tulis
yang substansinya sesuai dengan materi/tema
yang ditentukan dalam Kompletensi Dasar
(KD), 2) Siapkan kisi-kisi yang berupa tugas
yang
terdiri
dari
beberapa
pertanyaan/pernyataan yang belum lengkap
atau
sempurna
sesuai
dengan
tujuan
pembelajaran yang ingin dicapai sebagaimana
yang
telah
dirumuskan
dalam
Indikator
Pencapaian Kompetensi (IPK), 3) Bagikan
bahan ajar yang berupa teks tulis dan kisi-kisi
yang
berupa
pertanyaan/pernyataan
yang
belum lengkap tersebut kepada para peserta
didik (bisa secara kelompok atau individu), 4)
Mintalah kepada masing-masing kelompok
atau individu untuk membaca dan mempelajari
bahan ajar dan mengisi kisi-kisi tersebut, 5)
Kemudian setelah peserta didik mengerjakan
tugas mintalah kepada mereka baik secara
kelompok ataupun secara individu untuk
mempresentasikan hasil kerjanya masing-
masing, 6) Berikan konfirmasi (klarifikasi)
kepada para peserta didik setelah mereka
selesai mempresentasikan hasil kerjanya. Reading Guide Secara etimologis , Reading Guide
berasal dari bahasa Inggris, yang berarti
Panduan
Membaca. Sedangkan
secara
terminologis Reading Guide adalah merupakan
sebuah metode pembelajaran yang memandu
peserta didik dengan membaca sebuah bahan
bacaan (sebagai panduan) yang disiapkan oleh
guru yang isinya disesuaikan dengan materi
yang akan diajarkan. Di samping itu guru juga
menyiapkan
kisi-kisinya
yang
berupa
pertanyaan-pertanyaan atau bisa juga bagan
atau skema yang dapat dijawab oleh peserta
didik dari bahan bacaan yang telah mereka
baca dan pelajari sebelumnya. Ciri-ciri Metode Pembelajaran Reading
Guide: 1) Adanya bahan bacaan (referensi)
yang isinya sesuai dengan tema yang akan
diajarkan; 2) Adanya tugas yang harus
dikerjakan
peserta
didik
yang
berupa
pernyataan-pernyataan
yang
harus
disempurnakan atau dilengkapi oleh peserta
didik sesuai dengan isi bacaan yang telah
mereka baca, 3) Adanya interaksi persepsional
antar anggota dalam kelompok, jika dilakukan
secara kelompok. Pembelajaran PAIKEM Sebuah proses pembelajaran mutlak
diperlukan
adanya
sebuah
strategi
pembelajaran. Hal ini di maksudkan agar
pembelajaran tidak berlangsung seadanya. Pembelajaran haruslah berlangsung dengan
terencana. Dampak intruksional dan dampak
pengiringnya harus sudah dapat terproyeksikan Jurnal Ilmiah Mandala Education 80 ISSN 2442-9511 JIME, Vol. 2 No. 2 Oktober 2016 sebelumnya. Salah satu pembelajaran yang
belakangan ini mencuat, dan di akui sebagai
strategi pembelajaran yang inovatif serta dapat
menjadi solusi atas kemonotonan pembelajaran
di
kelas
adalah
strategi
pembelajaran
PAIKEM. bermuara
pada
lingkungan. Manfaat
keberhasilan
pembelajaran
akan
terasa
manakala
apa
yang
diperoleh
dari
pembelajaran
dapat
diaplikasikan
dan
diimplementasikan dalam realitas kehidupan. Inilah
salah
satu
sisi
positif
yang
melatarbelakangi
pembelajaran
dengan
pendekatan lingkungan. Pembelajaran PAIKEM adalah sebuah
pembelajaran yang memungkinkan peserta
didik untuk mengerjakan kegiatan yang
beragam
dalam
rangka
mengembangkan
keterampilan dan pemahamannya, dengan
penekanan
peserta
didik
belajar
sambil
bekerja,
sementara
guru
menggunakan
berbagai sumber dan alat bantu belajar
(termasuk pemanfaatan lingkungan), supaya
pembelajaran lebih menarik, menyenangkan
dan efektif. Model
pembelajaran
dengan
pendekatan lingkungan, bukan merupakan
pendekatan
pembelajaran
yang
baru,
melainkan sudah dikenal dan populer, hanya
saja sering terlupakan. Adapun yang dimaksud
dengan pendekatan lingkungan adalah suatu
strategi pembelajaran yang memanfaatkan
lingkungan sebagai sasaran belajar, sumber
belajar, dan sarana belajar. Hal tersebut dapat
dimanfaatkan untuk memecahkan masalah
lingkungan dan untuk menanamkan sikap cinta
lingkungan. Konsep-konsep
sains
dan
lingkungan sekitar siswa dapat dengan mudah
dikuasai siswa melalui pengamatan pada
situasi yang konkret. Dampak positif dari
diterapkannya pendekatan lingkungan yaitu
siswa
dapat
terpacu
sikap
rasa
keingintahuannya tentang sesuatu yang ada di
lingkungannya. Seandainya kita renungi empat
pilar pendidikan yakni learning to know
(belajar untuk mengetahui), learning to be
(belajar untuk menjadi jati dirinya), learning to
do (Belajar untuk mengerjakan sesuatu) dan
learning to life together (belajar untuk bekerja
sama)
dapat
dilaksanakan
melalui
pembelajaran dengan pendekatan lingkungan
yang dikemas sedemikian rupa oleh guru. Pendekatan PAIKEM sebagai sebuah
strategi pembelajaran, memiliki 5 kriteria yang
bisa
dipaparkan
sebagai
berikut
:
1)
Pembelajaran Aktif, 2) Pembelajaran Inovatif ,
3) Pembelajaran Kreatif, 4) Pembelajaran
Efektif, 5) Pembelajaran Menyenangkan. j
y
g
Prinsip-prinsip pembelajaran PAIKEM
antara lain: 1) Mengalami : Peserta didik
terlibat secara aktif baik fisik, mental maupun
emosional. Melalui pengalaman langsung
pembelajaran akan lebih memberi makna
kepada sisa dari pada hanya mendengarkan, 2)
Komunikasi
:
Kegiatan
pembelajaran
memungkinkan terjadinya komunikasi antara
guru dan peserta didik, 3) Interaksi : Kegiatan
pembelajarannya memungkinkan terjadinya
interaksi multi arah, 4) Refleksi : Kegiatan
pembelajarannya memungkinkan peserta didik
memikirkan kembali apa yang telah dilakukan. Tahap Perencanaan (Planning)
Pada tahapan ini guru selaku peneliti
melakukan
kegiatan-kegiatan
sebagai
berikut:
Menyusun
Rencana
Pelaksanaan
Pembelajaran (RPP) dengan skenario
sesuai
dengan
aturan
main
model
pembelajaran
Model
Reading
Guide
berbasis PAIKEM.
Menyiapkan sumber, bahan, dan semua
alat yang digunakan dalam penelitian.
Menyusun/membuat
lembar
observasi
guru dan lembar observasi Peserta didik. Faktor Peserta didik: yaitu peningkatan
motivasi belajar Peserta didik yang terlihat
pada perilaku Peserta didik selama proses
pembelajaran, yang berdampak pada
peningkatan hasil belajar peserta didik
Kelas II.B Semester dua Tahun 2015/2016
di SD Negeri Model Mataram.
Menyusun alat evaluasi.
Menyusun alat evaluasi. Tahap Pelaksanaan (Action) Tahap Pelaksanaan (Action)
Guru
membimbing
peserta
didik
membaca/pengenalan
huruf
dengan
menggunakan alat peraga berupa papan
panel dan potongan huruf. g
Tindakan nyata yang dilakukan oleh
guru
selaku
peneliti
adalah
dengan
menggunakan siklus. Gambaran siklus dalam
penelitian ini adalah sebagai berikut:
Guru meminta semua peserta didik secara
berurutan untuk maju membaca/menempel
huruf di papan. Tahap Refleksi (Reflection) Renungan hasil perolehan data Renungan hasil perolehan data Refleksi Pelaksanaa Pengolahan
dan
analisa
data
hasil
penelitian Mencocokkan hasil analisa data dengan
indikator keberhasilan Rencana perbaikan dan tindak lanjut Rencana perbaikan dan tindak lanjut
SIKLUS II Siklus Tindakan
SIKLUS I Penelitian tindakan kelas (PTK) ini akan
dilaksanakan di kelas II.B SD Negeri Model
Mataram
semester dua Tahun pelajaran
2015/2016, dengan jumlah Peserta didik
berjumlah 20 orang. Faktor
Guru:
yaitu
dengan
mengamati
cara
guru
membuat
Rencana Pelaksanaan Pembelajaran (RPP) dan
pelaksanaannya dalam pembelajaran di kelas
senyatanya dengan menerapkan pendekatan
Model Reading Guide berbasis PAIKEM
dalam upaya meningkatkan motivasi belajar
Peserta didik Kelas II.B SD Negeri Model
Mataram. Tahap Observasi (Observation) g
Perencanaa
n
Pelaksanaa
n
Siklus I
Pengamata
n
Pelaksanaa
n
Siklus II
Refleksi
Pengamata
n
? Refleksi Jurnal Ilmiah Mandala Education
Setiap siklus selama penelitian ini berisi 4
(empat)
tahapan
yaitu:
1)
Perencanaan
(Planning),
2)
Pelaksanaan
(Action),
3)
Perencanaa
n
Pelaksanaa
n
Siklus I
Pengamata
n
Pelaksanaa
n
Siklus II
Refleksi
Pengamata
n
? Refleksi Observasi
guru
:
Dilakukan
oleh
pengawas pembimbing selaku observer
guru
dalam
melaksanakan
proses
pembelajaran di kelas senyatanya. Observasi Peserta didik : Dilaksanakan
oleh guru kelas II.B sekaligus sebagai
peneliti dalam Penelitian Tindakan Kelas
(PTK) pada kegiatan diskusi kelompok. Pembelajaran PAIKEM Proses refleksi sangat perlu dilakukan untuk
mengetahui sejauhmana ketercapaian proses
pembelajaran. Secara garis besar, PAIKEM dapat
digambarkan sebagai berikut: 1) Siswa terlibat
dalam
berbagai
kegiatan
yang
mengembangkan pemahaman dan kemampuan
mereka
dengan
penekanan
pada
belajar
melalui berbuat,
2)
Guru menggunakan
berbagai alat bantu dan berbagai cara dalam
membangkitkan
semangat,
termasuk
menggunakan lingkungan sebagai sumber
belajar
untuk
menjadikan
pembelajaran
menarik, menyenangkan, dan cocok bagi
siswa, 3) Guru mengatur kelas dengan
memajang buku-buku dan bahan belajar yang
lebih menarik dan menyediakan „pojok baca‟,
4) Guru menerapkan cara mengajar yang lebih
kooperatif dan interaktif, termasuk cara belajar
kelompok, 5) Guru mendorong siswa untuk Jurnal Ilmiah Mandala Education
Berlangsungnya proses pembelajaran
tidak terlepas dengan lingkungan sekitar. Sesungguhnya pembelajaran tidak terbatas
pada empat dinding kelas. Pembelajaran
dengan pendekatan lingkungan menghapus
kejenuhan dan menciptakan peserta didik yang
cinta lingkungan. Berdasarkan teori belajar,
melalui pendekatan lingkungan pembelajaran
menjadi bermakna. Sikap verbalisme siswa
terhadap
penguasaan
konsep
dapat
diminimalkan dan pemahaman siswa akan
membekas dalam ingatannya. Buah dari proses
pendidikan dan pembelajaran akhirnya akan 81 JIME, Vol. 2 No. 2 Oktober 2016 ISSN 2442-9511 Observasi (Observation), dan 4) Refleksi
(Reflection). Observasi (Observation), dan 4) Refleksi
(Reflection). Observasi (Observation), dan 4) Refleksi
(Reflection). menemukan caranya sendiri dalam pemecahan
suatu
masalah,
untuk
mengungkapkan
gagasannya, dan melibatkam siswa dalam
menciptakan lingkungan sekolahnya. Tahap Pelaksanaan Pada
tahap
pelaksanaan
proses
pembelajaran
dengan
pendekatan
Model
Reading Guide berbasis PAIKEM ini yang
dilakukan oleh guru adalah 1) tentukan bacaan
yang akan dipelajari, 2) buatlah pertanyaan-
pertanyaan yang akan dijawab peserta didik
atau kisi-kisi dan boleh juga bagan atau skema
yang dapat diisi oleh mereka dari bahan
bacaan yang telah dipilih tadi, 3) bagikan
bahan bacaan dengan pertanyaan atau kisi-kisi
kepada peserta, 4) tugas peserta adalah
mempelajari
bacaan
tersebut
dengan
menggunakan pertanyaan atau kisi-kisi yang
ada. Batasi aktivitas ini sehingga tidak
memakan waktu yang berlebihan, 5) bahas
pertanyaan atau kisi-kisi tersebut dengan
menanyakan jawaban kepada peserta, 6) pada
akhir
pembelajaran,
berilah
ulasan
atau
penjelasan secukupnya, 7) guru melakukan
kesimpulan, klarifikasi, dan tindak lanjut 2. Cara Pengambilan data Observasi guru memperoleh skor rata-
rata sebesar 3,79, observasi peserta didik
memperoleh skor rata-rata sebesar 3,89, dan
hasil tes tertulis peserta didik memperoleh nilai
rata-rata sebesar 71,25. -
Data kegiatan pembelajaran diambil
dari RPP yang dibuat oleh guru dan
lembar observasi pelaksanaan Model
Reading Guide berbasis PAIKEM g
-
Data
kemajuan
motivasi
belajar;
diambil dari lembar observasi selama
proses pembelajaran. HASIL PENELITIAN HASIL PENELITIAN JIME, Vol. 2 No. 2 JIME, Vol. 2 No. 2 Oktober 2016 ISSN 2442-9511 Yang menjadi sumber data dalam
penelitian tindakan kelas (PTK) ini adalah
semua Peserta didik kelas II.B semester dua
tahun 2015/2016 di SD Negeri Model
Mataram. 1. Jenis Data Adapun jenis data yang dikumpulkan
dalam pelaksanaan penelitian tindakan kelas
(PTK) ini meliputi : -
Jenis data yang berasal dari guru selaku
peneliti -
Jenis data yang berasal dari guru selaku
peneliti
1). Data tentang Rencana Pelaksanaan
Pembelajaran (RPP)
2). Data Pelaksanaan Pembelajaran 1). Data tentang Rencana Pelaksanaan
Pembelajaran (RPP)
2). Data Pelaksanaan Pembelajaran 2). Data Pelaksanaan Pembelajaran j
-
Jenis data yang berasal dari Peserta
didik :
1). Data kemajuan motivasi dari
Peserta didik
2). Data
hasil
belajar
Peserta
didik/dampak
dari
peningkatan
motivasi belajar 2). Data
hasil
belajar
Peserta
didik/dampak
dari
peningkatan
motivasi belajar Tahap Refleksi Renungan data hasil perolehan data pada
siklus I -
Data kemajuan hasil belajar; diambil
dari nilai pada saat tes tertulis yang
dilaksanakan
pada
akhir
proses
pembelajaran. Pengolahan data hasil observasi guru,
Peserta didik dan tes tertulis. Mencocokkan hasil yang ada dengan
Indikator keberhasilan. Untuk menganalisis data akan dilakukan
melalui analisis deskriptif kuantitatif melalui
pendataan, analisis dan pembahasan terhadap
data yang diperoleh dengan mencocokkan
tingkat keoptimalan terhadap capaian indikator
keberhasilan yang ada. Merencanakan perbaikan terhadap jenis
tindakan yang menyebabkan belum tuntas
Indikator
keberhasilan. Oleh
karena
Indikator keberhasilan belum terbukti
maka penelitian dilanjutkan ke siklus II. SIKLUS II Pada siklus ini semua kegiatan dan
tahapan selama penelitian adalah sama,
sifatnya mengulang dan memperbaiki terhadap
tindakan
yang
masih
memerlukan
penyempurnaan dan pembenaran sebagaimana
mestinya. Setiap siklus selama penelitian ini berisi 4
(empat)
tahapan
yaitu:
1)
Perencanaan
(Planning),
2)
Pelaksanaan
(Action),
3) Jurnal Ilmiah Mandala Education 82 JIME, Vol. 2 No. 2 p
Tahap Observasi 2. Cara Pengambilan data g
y
g
Tahap Pelaksanaan Tahap Pelaksanaan Secara
umum
tahapan
pelaksanaan
proses pembelajaran pada siklus II ini masih
mengacu
pada
pelaksanaan
proses
pembelajaran sebelumnya. Pemecahan yang
dilakukan pada proses pembelajaran ini
adalah: 1) pelaksanaan proses pembelajaran
lebih
dioptimalkan,
2)
pelaksanaan
pembimbingan
peserta
didik
sekaligus
observasi Peserta didik lebih di efektifkan. Utamanya pengamatan Peserta didik yang
termotivasi, yang kurang motivasi, Peserta
didik yang tidak termotivasi, dengan harapan
proses analisa data lebih signifikan, dan 3)
pelaksanaan tes tertulis yang merupakan
dampak dari peningkatan motivasi belajar
Peserta didik lebih diperketat. Tahap Observasi Observasi guru memperoleh skor rata-
rata sebesar 4,57, observasi peserta didik
memperoleh skor rata-rata sebesar 4,32, dan
hasil tes tertulis peserta didik memperoleh nilai
rata-rata sebesar 94,05. Tahap Observasi Observasi
Guru
:
Observasi
guru
memperoleh skor rata-rata 3,79, sementara
Indikator keberhasilan yang diharapkan (>
4,0), ini artinya kinerja guru dalam
menerapkan pendekatan Model Reading
Guide berbasis PAIKEM masih belum
optimal. Tahap Refleksi Renungan atas perolehan data hasil
observasi guru, observasi Peserta didik,
dan hasil tes tertulis sebagai dampak dari
peningkatan motivasi belajar Peserta didik
di kelas senyatanya. Kegiatan pembelajaran diakhiri dengan
tes tertulis, hal ini dimaksudkan untuk
mengetahui dampak positif dari peningkatan
motivasi belajar Peserta didik kelas II.B SD
Negeri Model Mataram semester dua tahun
2015/2016 dengan penerapan pendekatan
Model Reading Guide berbasis PAIKEM. Asumsi bila motivasi belajar meningkat maka
akan berdampak meningkatnya hasil belajar
Peserta didik. Pengolahan data hasil observasi guru,
observasi Peserta didik dan tes tertulis Mencocokkan
perolehan
data
hasil
tindakan dengan Indikator keberhasilan
yang telah ditetapkan. Guru memberikan hadiah/reward kepada
semua Peserta didik kelas II.B atas
keberhasilannya
dalam
upaya
meningkatkan
motivasi
belajar
yang
berdampak
terhadap
perolehan
hasil
belajar sesuai dengan KKM yang telah
ditetapkan. Tahap Pelaksanaan Dalam
melaksanakan
proses
pembelajaran,
guru
berpedoman
dengan
skenaario yang telaah direncanakan yaitu
penerapan pendekatan Model Reading Guide
berbasis PAIKEM dengan urutan kegiaatan ini
sebagai berikut: 1) tentukan bacaan yang akan
dipelajari, 2) buatlah pertanyaan-pertanyaan
yang akan dijawab peserta didik atau kisi-kisi
dan boleh juga bagan atau skema yang dapat
diisi oleh mereka dari bahan bacaan yang telah
dipilih tadi, 3) bagikan bahan bacaan dengan
pertanyaan atau kisi-kisi kepada peserta, 4)
tugas peserta adalah mempelajari bacaan
tersebut dengan menggunakan pertanyaan atau
kisi-kisi yang ada. Batasi aktivitas ini sehingga
tidak memakan waktu yang berlebihan, 5)
bahas pertanyaan atau kisi-kisi tersebut dengan
menanyakan jawaban kepada peserta, 6) pada
akhir
pembelajaran,
berilah
ulasan
atau
penjelasan secukupnya, 7) guru melakukan
kesimpulan, klarifikasi, dan tindak lanjut. Jurnal Ilmiah Mandala Education Tahap Perencanaan Pada tahapan ini jenis kegiatan yang
dilakukan masih mengacu pada kegiatan siklus
I, bedanya hanya terjadi perbaikan seperlunya
yaitu: 1) penyusunan RPP dengan mengacu
pada pendekatan
Model Reading Guide
berbasis PAIKEM dan penyempurnaan pada
bagian skenario pembelajaran, 2) menyiapkan
alat, sumber, bahan yang diperlukan dalam
proses tindakan dikelas senyatanyan, 3)
menyiapkan lembar observasi guru dan lembar Pada tahapan ini yang telah dilakukan
oleh guru selaku peneliti adalah; 1) menyusun
RPP dengan skenario pembelajaran Model
Reading Guide berbasis PAIKEM, 2) telah
berhasil menyiapkan alat, sumber, bahan yang
diperlukan dalam penelitian, 3) berhasil
menyusun instrument observasi guru dan
instrument observasi Peserta didik, dan 4)
menyusun alat evaluasi. Jurnal Ilmiah Mandala Education 83 ISSN 2442-9511 JIME, Vol. 2 No. 2 Oktober 2016 observasi Peserta didik sebagaimana pada
siklus
I,
4)
menyiapkan
alat
evaluasi
sebagaimana yang telah dibuat pada siklus I. pembelajaran, menyusun instrument observasi
guru maupun instrument observasi Peserta
didik mengalami beberapa kendala, tetapi
setelah berkonsultasi dan meminta petunjuk
kepada pembimbing kendala pun bisa diatas,
dan semua kegiatan bisa berjalan dengan
lancar. p
Tahap Observasi Observasi Guru : Pada siklus II ini hasil
observasi
memperoleh
skor
rata-rata
(4,57) sementara Indikator keberhasilan
yang diharapkan (> 4,0), ini artinya hasil
perolehan
data
telah
mengalami
peningkatan karena Indikator keberhasilan
telah terlampaui Tahap Perencanaan Observasi Peserta didik : Hasil observasi
Peserta didik dalam upaya peningkatan
motivasi belajar Peserta didik kelas II.B
semester dua tahun 2015/2016 di SD Peneliti menyusun RPP dengan skenario
penerapan pendekatan Model Reading Guide
berbasis PAIKEM, menyiapkan alat, sumber,
bahan
yang
diperlukan
dalam
proses Peneliti menyusun RPP dengan skenario
penerapan pendekatan Model Reading Guide
berbasis PAIKEM, menyiapkan alat, sumber,
bahan
yang
diperlukan
dalam
proses 84 Jurnal Ilmiah Mandala Education ISSN 2442-9511 Oktober 2016 JIME, Vol. 2 No. 2 peningkatan motivasi belajar Peserta didik
kelas II.B SD Negeri Model Mataram. Negeri Model Mataram diperoleh skor
rata-rata (3,89). Indikator keberhasilan (>
4,0), berarti perolehan skor rata-rata hasil
observasi Peserta didik dalam upaya
peningkatan
motivasi
belajar
yang
meliputi 5 (lima) aspek motivasi belajar
(antusias, kerjasama, rasa ingin tahu,
berbahasa, dan disiplin) belum mencapai
kriteria yang diharapkan. Negeri Model Mataram diperoleh skor
rata-rata (3,89). Indikator keberhasilan (>
4,0), berarti perolehan skor rata-rata hasil
observasi Peserta didik dalam upaya
peningkatan
motivasi
belajar
yang
meliputi 5 (lima) aspek motivasi belajar
(antusias, kerjasama, rasa ingin tahu,
berbahasa, dan disiplin) belum mencapai
kriteria yang diharapkan. Tahap Pelaksanaan Pada tahap pelaksanaan di siklus II ini
pada
dasarnya
masih
mengacu
pada
pelaksanaan
siklus
I,
yaitu
penerapan
pendekatan Model Reading Guide berbasis
PAIKEM. Bedanya pada siklus ini lebih
dioptimalkan. Dampak dari peningkatan motivasi/belum
meningkatnya motivasi belajar Peserta
didik salah satunya dengan hasil tes
tertulis yang materinya hanya sekitar yang
diajarkan pada saat itu juga, diperoleh
nilai rata-rata (70,15) kategori cukup. Tahap Refleksi Hasil analisa data peningkatan motivasi
belajar pada siklus I ini (3,79) sedangkan yang
diminta dalam Indikator keberhasilan (> 4,0),
ini artinya belum berhasil. Observasi
Peserta
didik
:
Upaya
meningkatkan motivasi belajar Peserta
didik kelas II.B semester dua tahun
2015/2016 di SD Negeri Model Mataram
diperoleh skor rata-rata (4,32), sementara
Indikator
keberhasilan
yang
telah
diharapkan adalah (> 4,0), ini artinya
perolehan skor rata-rata telah melampaui
(0,32) dari Indikator keberhasilan. Sebagai
tolak
ukur
keberhasilan
proses
pembelajaran adalah hasil belajar Peserta
didik meningkat, dari data hasil perolehan
nilai rata-rata tes tertulis adalah (94,05)
sementara pada siklus sebelumnya hanya
(70,15) berarti mengalami peningkaatan
(23,90). Karena Indikator keberhasilan belum
tercapai, penelitian tindakan kelas (PTK)
dilanjutkan ke siklus II dengan harapan
optimalisasi penerapan strategi pembelajaran
dengan pendekatan Model Reading Guide
berbasis
PAIKEM
dapat
meningkatkan
motivasi belajar Peserta didik kelas II.B
semester dua tahun 2015/2016 di SD Negeri
Model Mataram. Jurnal Ilmiah Mandala Education Tahap Perencanaan Peneliti menyusun Rencana Pelaksanaan
Pembelajaran (RPP) dengan memperhatikan
kesalahan-kesalahan pada siklus I. peneliti
lebih memfokuskan tentang Rencana strategi
jitu sehingga proses pembelajaran dengan
pendekatan Model Reading Guide berbasis
PAIKEM
dapat
terelaisasi
dengan baik,
karenanya dalam penyusunan skenario benar-
benar dirinci dari tiap aspek pada proses
pembelajaran dengan model Reading Guide. SIMPULAN DAN SARAN
Simpulan Anonim, 2016, dalam
http://bdkjakarta.kemenag.go.id/index.ph
p?a=artikel&id=843, diambil pada
tanggal 11 Maret 2016, Pukul 12.35 wita Data komulatif dari hasil penelitian
tindakan kelas (PTK) dari siklus I ke Siklus II
adalah sebagai berikut: N
o
Jenis
Kegiatan
Indikator
keberhasil
an
Siklu
s I
Siklu
s II
Keteranga
n
1. Observa
si Guru
> 4,00
3,79
4,57
peningkat
an
(0,78)
2. Observa
si
Peserta
didik
> 4,00
3,89
4,32
peningkat
an
(0,43)
3. Tes
Akhir
> 75,00
70,1
5
94,0
5
peningkat
an
(23,90) Anonim, 2016, dalam
http://azkiyatunnufus.blogspot.co.id/201
1/12/strategi-pembelajaran-paikem.html,
diambil pada tanggal 13 Maret 2016,
pukul 10.55 wita. Arikunto, s. 2009, Penelitian Tindakan Kelas,
Jakarta : Bumi Aksara. Harun Rasyid dan Mansur, 2008, Penilaian
Hasil Belajar, Bandung : CV Wacana
Prima. Penerapan pendekatan Model Reading
Guide Berbasis PAIKEM sangat efektif upaya
untuk meningkatkan motivasi belajar Peserta
didik kelas II.B semester dua tahun 2015/2016
di SD Negeri Model Mataram. Fakta telah
menunjukkan perolehan rata-rata skor motivasi
belajar Peserta didik pada siklus I (3,89),
sedangkan pada siklus II (4,32), hasil belajar
siklus I (70,15) dan Siklus II (94,05) sudah
melampaui
Indikator
keberhasilan
yang
ditetapkan. Penelitian dinyatakan “berhasil”
dan dihentikan pada siklus II. Lukmanul
A,
2008,
Perencanaan
Pembelajaran, Bandung : CV Wacana
Prima. Mukhtar, 2003, Prosedur Penilaian, Jakarta :
Rineka Cipta. Nasution S., 2004, Didaktik Asas-asas
Mengajar, Jakarta: Bumi Aksara. Nurhadi, 2003, Yasin ,B dan Sendule.A, 2003,
Kontekstual dan Penerapannya dalam
KBK,
Malang
:
Unitipetas
Negeri
Malang. Tahap Refleksi Hasil analisa data peningkatan motivasi
belajar Peserta didik pada siklus II adalah
(4,32) sedangkan Indikator keberhasilan (>
4,0). Ini artinya pada siklus II hasilnya telah
melampaui Indikator keberhasilan sebesar
(0,32), sedangkan hasil belajar rata-rata
(94,05) dari indikator keberhasilan > 75,00,
artinya telah melampaui indikator keberhasilan
yang ditentukan. Sebelum
proses
pembelajaran
dilaksanakan, peneliti menyiapkan semua alat,
bahan, dan segala sesuatunya sehingga dalam
pelaksanaan proses pembelajaran berjalan
sesuai
dengan
skenario
yang
telah
direncanakan. Agar proses pembelajaran dapat
teratasi maka peneliti juga menyiapkan lembar
observasi guru dan lembar observasi Peserta
didik
sebagai
tolak
ukur
ketercapaian Karena Indikator keberhasilan telah
terbukti, maka tidak perlu ada upaya perbaikan
dan
penyempurnaan. Pendekatan
Model
Reading Guide berbasis PAIKEM telah
mampu meningkatkan motivasi belajar Peserta
didik
yang
ditandai
dengan
tercapainya Jurnal Ilmiah Mandala Education 85 JIME, Vol. 2 No. 2 Oktober 2016 ISSN 2442-9511 Indikator
keberhasilan
dan
terjadinya
peningkatan
hasil
belajar
Peserta didik. “Penelitian Tindakan Kelas (PTK) dihentikan
pada siklus II dengan hasil memuaskan.” Anonim, 2016, dalam
https://taufikudin.wordpress.com/categor
y/pengertian-motivasi-belajar-siswa-
menurut-para-ahli-definisi/, diambil
pada tanggal 11 Maret 2016, pukul 11.45
wita. SARAN Disarankan kepada guru sejawat untuk
melaksanakan
Penelitian
Tindakan
Kelas
(PTK) dalam upaya untuk meningkatkan
motivasi belajar Peserta didik sesuai dengan
mata pelajaran masing-masing. Disarankan
kepada semua Peserta didik kelas II.B SD
Negeri Model Mataram untuk membiasakan
belajar dengan pendekatan yang kontekstual
utamanya
strategi
yang
mampu
membangkitkan motivasi belajar Peserta didik
yang
dampaknya
hasil
belajar
dapat
ditingkatkan seperti yang diharapkan. Purwanto Ngalim, 2002, Administrasi Dan
Supervisi Pendidikan, Bandung: PT. Remaja Rosdakarya. Robert E Slavin, 2010, Cooperative Learning
Teori, riset dan Praktik, Bandung : Nusa
Media. Sardiman, 2007, Indikator Dan Motivasi
belajar
Mengajar,
Jakarta
:
Raja
Grafindo Perkasa. Supriono, 2009, Cooperative Learning Teori
dan Aplikasi PAIKEM, Yogyakarta :
Pustaka Pelajar. DAFTAR PUSTAKA
A.M. Sardiman, 2005, Interaksi dan Motivasi
Belajar
Mengajar,
Jakarta:
PT
RajaGrafindo Persada. A.M. Sardiman, 2005, Interaksi dan Motivasi
Belajar
Mengajar,
Jakarta:
PT
RajaGrafindo Persada. A.M. Sardiman, 2005, Interaksi dan Motivasi
Belajar
Mengajar,
Jakarta:
PT
RajaGrafindo Persada. Jurnal Ilmiah Mandala Education 86
|
https://openalex.org/W2098968430
|
https://academicjournals.org/journal/JMPR/article-full-text-pdf/0111D4E42665
|
English
| null |
Medico-ethnobotanical investigations in Parbat district of Western Nepal
|
Journal of medicinal plant research
| 2,014
|
cc-by
| 7,718
|
Full Length Research Paper artment of Environmental Science and Engineering, Kathmandu University, P.O. Box No: 6250, Dhulikhel, Kavre
Nepal. 2Department of Biotechnology, Kathmandu University, P.O. Box No: 6250, Dhulikhel, Kavre, Nepal. epa t
e t o
o
e ta Sc e ce a d
g ee
g,
at
a du U
e s ty,
O
o
o 6 50,
u
e ,
a
e
Nepal. 2Department of Biotechnology, Kathmandu University, P.O. Box No: 6250, Dhulikhel, Kavre, Nepal. Accepted 9 December, 2013 The aim of present research was to record the indigenous knowledge on medicinal plants of Parbat
district, Nepal. Field trips were arranged to collect the plants and ethnobotanical information from the
study area during 2011 to 2012. The paper dealt with ethnobotanical plants along with their local names,
parts and ethnomedicinal uses prescribed by ethnic tribes Gurung, Magar and Majhi of the district. A
total of 61 plant species belonging to 59 genera and 43 families had been used by the local tribes for
curing various human diseases. The plant specimens were also collected dried, pressed, mounted on
herbarium sheets and deposited to the Department of Environmental Science and Engineering,
Kathmandu University. The investigation provided immense scope for the active principle analysis and
clinical studies of these ethnomedicinal plants for future drug development. Key words: Ethnobotany, medicinal plants, traditional healers, Gurung, Magar, Majhi. *Corresponding author. b.malla@nins.edu.np. INTRODUCTION In Nepal, there are about 8.4 million indigenous
nationalities of different groups inhabiting various
terrains. These indigenous people possess their own
culture, religious rites and rich traditional medicine
practices. Those ethnic people residing in different
geographical belts of Nepal depends on wild plants to
meet their basic requirements and all the ethnic
communities
have
their
own
pool
of
secret
ethnomedicinal and ethnopharmacological knowledge
about the plants available in their surroundings (Bhattarai
et al., 2006a; Ghimire and Bastakoti, 2009; Joshi et al.,
2011; Kunwar et al., 2009; Manandhar, 2002; Shrestha
and Dhillion, 2003; Acharya and Acharya, 2009;
Bhattarai et al., 2009; Rokaya et al., 2010; Uprety et al.,
2010; Panthi and Chaudhary, 2003) which has been
serving rural people with its superiority. medicines is in rapid decline globally, therefore,
ethnobotanical
exploitation
and
documentation
of
indigenous knowledge about the usefulness of such a
vast pool of genetic resources is deliberately needed
(Bussmann and Sharon, 2006; Behera and Mishra, 2005;
Rajkumar and Shivanna, 2010; Saikia et al., 2006; Rana
et al., 2010). Traditional medicine in Nepal comprises
those practices based on beliefs that were in existence
often for hundreds to thousands of years before the
development and spread of modern medicine, and which
are still in use today (Hamilton and Radford, 2007). Long
ago, there is a common practice of using plants in
traditional medicine in Nepal, because it is not only easily
available, but also affordable to the rural people
(Manandhar, 1998). According to WHO (2001), 80% of
the world population or roughly two thirds of the world’s
population,
rely
almost
exclusively
on
traditional
medicines using natural substances mostly derived from
plants in the treatment of diseases. Approximately 90% of Due to changing life style, extreme secrecy of
traditional healers and negligence of youngsters, the
practice and dependence of ethnic societies in folk *Corresponding author. b.malla@nins.edu.np. J. Med. Plants Res. 96 Fi
1 M
h
i
d Figure 1. Map showing study area. the Nepalese people reside in rural areas where access
to government health care facilities is lacking (Bhattarai,
1998). species for drug development to cure various diseases
(Cox and Balick, 1996; Flaster, 1996). Numerous studies
on ethnomedicinal plants of Nepal have been conducted
in the past by the Nepalese and foreign researcher. In the
present study, some plant species used by three ethnic
groups of Parbat to cure various human diseases are
enumerated. INTRODUCTION As such, the present study was carried out
to fill the gap of knowledge in this field of vital importance. )
Investigation and documenting traditional knowledge
through the ethnobiological approach is important for
highly
valuable
medicinal
plant
conservation
and
sustainable resource use (Gemedo-Dalle et al., 2005). Targeted
based
studies
with
concentration
on
mechanism of action, effective dose and bioavailability
mechanisms need to be conducted in future to explore
medicinal potential of these plants so that the ill ethnic
groups get maximum benefits from traditional medicinal
system. Such scientific investigations are the baseline
information for appropriate use of native medicinal plant MATERIALS AND METHODS This study was undertaken during 2011and 2012 in the different
localities of Parbat to survey the information on ethnomedicinal
uses of plants growing in this region (Figure 1). Regular monthly Malla et al. Malla et al. 97 Herbs 31%
Shrubs 26%
Climbers 5%
Trees 38%
Figure 2. Percentage distribution of plants species according to
habit. used by the three ethnic tribes; Gurung, Magar and Majhi
were arranged alphabetically by genus and species name
(Table 1). A total of 61 plant species belonging to 59
genera in 43 families have been found to be used by the
ethnic tribes for curing various human diseases (Plates 1
and 2). Out of the sixty one plant species, 31% were
herbs, 26% were shrubs, 38% were trees and 5% were
climbers (Figure 2). Herbs 31%
Shrubs 26%
Climbers 5%
Trees 38% Based on the surveyed ethnomedicinal data, a total of
61 plant species belonging to 59 genera under 43
families were used by different ethnic groups, the
Gurung, Magar and Majhi of Parbat district. The present
exploration provides ample information to believe that
traditional medicinal practice of using the native medicinal
plant is shown in the area. The traditional knowledge of
the tribal people of Parbat district has tremendous
ethnobotanical and ethnomedicinal importance. They
commonly use plants and their parts such as roots,
rhizomes, tubers, leaves, stem, wood, bark, flowers,
seeds, and fruits in various purposes in their daily life. Several interesting observations were made during the
course of the survey. Some of the plants used by the
tribe have already been reported to have medicinal
values. Furthermore, the uses of some plants are same
as used by certain other ethnic groups of Nepal (Mahato
and Chaudhary, 2005; Kunwar et al., 2006; Kunwar et al. 2010; Bhattarai et al., 2010). It is evident from the present
study that the tribal communities are dependent on a
variety of plants to meet their requirements and beliefs to
cure various diseases. The different plant parts are used
for medicinal preparation, mode of administration, dosage
and other human consumption. In some cases, the whole
plant parts are utilized only for medicinal purposes. Study
revealed that a total of 47 human diseases are cured
using different plant parts by the tribal people in Parbat
district. Study area Parbat, a hilly district situated in the Dhaulagiri zone of Western
Nepal. It lies between 27° 58' N to 28° 39' N latitudes and 83° 34' E
to 83° 59' E longitudes geographical limits in 536.86 km2 area at
altitudinal variation from 520 to 3309 m. Headquarter of the district
is Kushma. The political boundaries of the district extend in the east
to Syanga and Kaski districts; Baglung, Myagdi and Gulmi districts
in the west; Myagdi and Kaski districts in the north and Syanja and
Gulmi districts in the south (Figure 1). It has sub-tropical, temperate
and sub-alpine monsoon type of climate with maximum temperature
beyond 35°C during summer (May to June) and below 7.0°C during
winter (December to January) and the northern part is moister, due
to high rainfall and southern part is dry due to low rainfall. The
average annual rainfall is 1950 ml. The major caste of the district is
Brahmin (38.48%) followed by Chhetri (16.01%) and other major
tribes inhabiting in this area are Gurung, Magar, Newar, Thakali,
Kumal, Majhi, Bote, Puri, Snayasi, Tolange, Biswakarma, Pariyar,
etc. For the present study only three ethnic groups are investigated,
namely, Gurung, Magar and Majhi. In Parbat district, beside
agriculture, animal husbandry is the main occupation of the tribal
communities due to excess availability of fodders. Goats, cows,
bulls, buffaloes and sheep are the main cattle of the local people in
the district. Geographically, forest is divided into conifer forest
(10.5%), broad leaved forest (69.5%), shrub forest (7%) and mixed
forest (13%). It is traversed by two big rivers Kaligandaki and Modi
as well as other rivulets, streams and streamlets, such as, Lungdi
khola, Panyu khola, Luwa khola, etc. MATERIALS AND METHODS The plant parts are generally used to cure some
important
diseases,
namely,
diarrhoea,
dysentery,
asthma, fever, stomach disorder, cuts and wounds, sore
throat, rheumatism, blood pressure, urinary problems, ear
diseases, headache, cough and cold, hypertension,
venereal disease, scorpion bites, paralysis, blood
pressure, diabetes, eczema, bone fracture, constipation
and piles. The elder ethnic people are more familiar with
the plant species and their use for common ailments, and
the plant remedies being used regularly. Majorities of
young generation do not know many plants and their
medicinal values. Only a few younger ones followed the
medicinal practices and traditional knowledge by the
elders and healers as in the other areas of Nepal (Joshi
and Edington, 1990; Shrestha and Dhillion, 2003; Malla
and Chhetri, 2012). Scientific cultivation, conservation
and sustainable use of plant species by ethnic
communities
would
be
highly
advantageous
for
socioeconomic growth, in conservation of rare and
endangered plant species and the indigenous knowledge
for the future generations. Reported medicinal plants are Figure 2. Percentage distribution of plants species according to
habit. visits were made to eleven different Village Developmental
Committees (VDCs) of Parbat district for collecting ethnomedicinal
information in particular. In this context, herbalist, senior
knowledgeable men and women were interviewed for recording the
ethnobotanical data. Local names and medicinal uses were
documented critically. The herbarium specimens were made
accordingly (Jain and Rao, 1997) and identified with the help of
Flora of Nepal (Hara, 1966). Voucher specimens were deposited at
the Department of Environmental Science and Engineering,
Kathmandu University, Dhulikhel, Nepal. RESULTS AND DISCUSSION The first hand information on the ethnomedicinal plants J. Med. Plants Res. 98 A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
Plate 1. Plants recorded from different areas in Parbat district. (A) Acorus calamus L., (B) Justicia
adhatoda L., (C) Ageratum conyzoides L., (D) Girardinia diversifolia (Link.) Friis, (E) Berberis aristata
DC., (F) Rhus javanica L., (G) Smilax ovalifolia Roxb. Ex. D. Don., (H) Schima wallichii (DC.) Korth., (I)
Diploknema butyracea (Roxb.) Lam, (J) Woodfordia fructicosa (L.) Kurz., (K) Mucuna monosperma
(Roxb.) DC, (L) Jatropha curcas L., (M) Berberis asiatica Roxb. ex DC, (N) Rubus ellipticus Sm., (O)
Reinwardtia indica Dum. H I K
L L O Plate 1. Plants recorded from different areas in Parbat district. (A) Acorus calamus L., (B) Justicia
adhatoda L., (C) Ageratum conyzoides L., (D) Girardinia diversifolia (Link.) Friis, (E) Berberis aristata
DC., (F) Rhus javanica L., (G) Smilax ovalifolia Roxb. Ex. D. Don., (H) Schima wallichii (DC.) Korth., (I)
Diploknema butyracea (Roxb.) Lam, (J) Woodfordia fructicosa (L.) Kurz., (K) Mucuna monosperma
(Roxb.) DC, (L) Jatropha curcas L., (M) Berberis asiatica Roxb. ex DC, (N) Rubus ellipticus Sm., (O)
Reinwardtia indica Dum. Malla et al. 99 A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
Plate 2. Plants recorded from different areas in Parbat district. (A) Gurung healer collecting
Swertia chirayita (Roxb. ex Flem.) Karst., (B) Osbeckia stellata Buch.-Ham., (C) Bauhinia
variegate L., (D) Rubia manjith Roxb. ex Flem., (E) Zanthoxylum armatum DC, (F)
Phyllanthus emblica L., (G) Englehardtia spicata Lesch. ex.Blume, (H) Choerospondias
axillaris (Roxb.) Burt & Hill, (I) A woman with Achyranthes bidentata Blume., (J) Juglans regia
L., (K) Cuscuta reflexa Roxb., (L) Cleistocalyx operculatus Roxb. Murr. & Perry., (M) Grinding
bark of Cleistocalyx operculatus Roxb. Murr. & Perry, (N) Cinnamomum tamala (Buch.-
Ham.) Nees & Eberm., (O) Bombax ceiba L. J J M N Plate 2. Plants recorded from different areas in Parbat district. (A) Gurung healer collecting
Swertia chirayita (Roxb. ex Flem.) Karst., (B) Osbeckia stellata Buch.-Ham., (C) Bauhinia
variegate L., (D) Rubia manjith Roxb. ex Flem., (E) Zanthoxylum armatum DC, (F)
Phyllanthus emblica L., (G) Englehardtia spicata Lesch. ex.Blume, (H) Choerospondias
axillaris (Roxb.) Burt & Hill, (I) A woman with Achyranthes bidentata Blume., (J) Juglans regia
L., (K) Cuscuta reflexa Roxb., (L) Cleistocalyx operculatus Roxb. Murr. & Perry., (M) Grinding
bark of Cleistocalyx operculatus Roxb. Murr. RESULTS AND DISCUSSION & Perry, (N) Cinnamomum tamala (Buch.-
Ham.) Nees & Eberm., (O) Bombax ceiba L. strongly
recommended
for
further
nutritional,
phytochemical and pharmacological studies. nal plants used to treat wide variety of human ailments. According to the tribal communities and their traditional
practices, majority of the ethomedicinal plants are
selected for the treatment of human ailments. The tribal
people used medicinal plants in the treatment of some
very common diseases such as indigestion, diarrhoea
and dysentery, muscular swelling, fever, scabies, ear Conclusion This study showed that the study area has ethnomedici- J. Med. Plants Res. 100 Table 1. Information on ethnomedicinal plants used by ethnic tribes of Parbat district Nepal. S/N
Botanical name/Voucher
number
Family
Local name
Locality
Plant parts used and mode of application
1
Achyranthes bidentata Blume. Malla-0368
Amaranthaceae
Datiwan (N)
Lunkhu Deurali
Root juice is recommended for hypertension and
rheumatism. Paste of root is used for toothache. 2
Acmella calva (Candolle) R.K
Jansen Malla-0386
Asteraceae
Marethi (N)
Bajung
The fruit juice is given for stomach disorder. It is also used
in fish poisoning. 3
Acorus calamus L. Malla-0392
Araceae
Bojho (N, G, M)
Lamtun
Rhizomes are chewed to get relief from sore throat and
voice disorder. Decoction of rhizomes is taken to treat cold,
fever, diarrhoea. Powder of rhizome is put in a cup of tea
for flavor. 4
Ageratum conyzoides L. Malla-
0353
Asterceae
Ganaune jhar (N)
Bhorle
Whole plant juice is applied to blood clotting in fresh cuts
and wounds. 5
Aloe vera (L.) Burm. f. Malla-
0358
Liliaceae
Ghyukumari (N, M),
Chhigu (G)
Sarthan
The gel of leaves is used to relief from burning sensation. Juice is used to treat pain, fever, constipation and jaundice. 6
Amaranthus spinosus L. Malla-0380
Amaranthaceae
Lundekanda (N),
Chikli, Lode (G), Lunde
(M), Gandri (Maj)
Lunkhu Deurali
Root juice is administrated for fever and urinary trouble. A
paste of the root is applied to treat gonorrhea. Fresh leaves
and tender shoots are consumed as a vegetable. 7
Amomum subulatum Roxb. Malla-0403
Zingiberaceae
Alainchi (N)
Simle
Seeds are chewed raw for indigestion and to stop vomiting. Paste of the seed is used as falvour. 8
Artemisia indica Willd. Malla-0435
Asteraceae
Titepati (N),
Chyonre, Pacha (G),
Pati (M)
Phalamkhani
Leaves and young shoots are applied to cure bleeding of
wounds and nose, asthma, fever, headache and diarrhoea. 9
Artocarpus lakoocha Wall. ex
Roxb. Malla-0388
Moraceae
Badahar (N)
Sarthan
Bark juice is applied to cuts and wounds. Ripen fruits are
eaten fresh and immature ones are cooked as a curry. Rhizomes are chewed to get relief from sore throat and
voice disorder. Decoction of rhizomes is taken to treat cold,
fever, diarrhoea. Powder of rhizome is put in a cup of tea
for flavor. Whole plant juice is applied to blood clotting in fresh cuts
and wounds. The gel of leaves is used to relief from burning sensation. Conclusion Juice is used to treat pain, fever, constipation and jaundice. Root juice is administrated for fever and urinary trouble. A
paste of the root is applied to treat gonorrhea. Fresh leaves
and tender shoots are consumed as a vegetable. Seeds are chewed raw for indigestion and to stop vomiting. Paste of the seed is used as falvour. Leaves and young shoots are applied to cure bleeding of
wounds and nose, asthma, fever, headache and diarrhoea. Bark juice is applied to cuts and wounds. Ripen fruits are
eaten fresh and immature ones are cooked as a curry. Malla et al. 101 Table 1. Contd. Barks and leaves are crushed in powder and made juice in
boil water for the treatment of fever, intestinal worms,
ulcers, liver and urinary complaints, cough, headache and
body pain. Flowers are useful for piles and leprosy. Fruits
juice is used for urinary disorder and skin diseases. 10
Azadirachta indica A. Juss. Malla-0431
Meliaceae
Neem (N,G, M)
Kusma
Barks and leaves are crushed in powder a
boil water for the treatment of fever, intest
ulcers, liver and urinary complaints, cough
body pain. Flowers are useful for piles and
juice is used for urinary disorder and skin d
11
Bauhinia variegata L. Malla-
0396
Caesalpiniaceae
Koiralo (N, Maj),
Byahagan, Kurugan
(M)
Kokhe
Bark juice is drunk for tonic and blood puri
is applied to cuts and wounds. Fresh flowe
vegetable and made pickle. 12
Berberis aristata DC. Malla-0410
Berberidaceae
Banchutro (N), Chutro
(G)
Chitre
Root juice is used in fever and dysentery. used for piles, sore throat and skin diseas
are eaten. Barks are also the sources of y
13
B. asiatica Roxb. ex DC. Malla-0426
Berberidaceae
Chutro (N, M), Chotr
(G)
Phalamkhani
Bark juice is used for dysentery and piles. fruits are eaten and also used to distill alco
14
Bombax ceiba L. Malla-0487
Bombacaceae
Simal (N, M, Maj),
Chongonchhi (G)
Simle
Bark juice is useful for diarrhoea, dysenter
tuberculosis. Root juice is used in wounds
good for skin problems. Fruits are also use
gonorrhea and eaten. 15
Cannabis sativa L. Malla-0494
Cannabaceae
Gaanja, Ganja (N,G)
Bhango (M)
Simle
Dried powder of leaves or flowers is drunk
cough, asthma, diarrhoea and dysentery. roasted and pickled. Dried leaves are mixe
and used for smoking. It is also offered to
rituals. 16
Centella asiatica (L.) Urb. Conclusion Malla-0412
Apiaceae
Ghodtapre (N, M),
Jasundo, Topre jhar
(G)
Lunkhu Deurali
Leaves are useful for remedy of skin disea
parts are ground and juice about four teas
day is used to treat fever and indigestion. 17
Cheilanthes dalhousiae Hook
Malla-0434
Pterridaceae
Ranisinka (N, M)
Patichaur
Whole plant juice is used to cure ulcer, sto
Stem is used to thread children’s ear. 10
Azadirachta indica A. Juss. Malla-0431
Meliaceae
Neem (N,G, M)
Kusma
11
Bauhinia variegata L. Malla-
0396
Caesalpiniaceae
Koiralo (N, Maj),
Byahagan, Kurugan
(M)
Kokhe
12
Berberis aristata DC. Malla-0410
Berberidaceae
Banchutro (N), Chutro
(G)
Chitre
13
B. asiatica Roxb. ex DC. Malla-0426
Berberidaceae
Chutro (N, M), Chotr
(G)
Phalamkhani
14
Bombax ceiba L. Malla-0487
Bombacaceae
Simal (N, M, Maj),
Chongonchhi (G)
Simle
15
Cannabis sativa L. Malla-0494
Cannabaceae
Gaanja, Ganja (N,G)
Bhango (M)
Simle
16
Centella asiatica (L.) Urb. Malla-0412
Apiaceae
Ghodtapre (N, M),
Jasundo, Topre jhar
(G)
Lunkhu Deurali
17
Cheilanthes dalhousiae Hook
Malla-0434
Pterridaceae
Ranisinka (N, M)
Patichaur Bark juice is drunk for tonic and blood purifier. Bark paste
is applied to cuts and wounds. Fresh flowers are cooked as
vegetable and made pickle. Root juice is used in fever and dysentery. Bark paste is
used for piles, sore throat and skin disease. The ripen fruits
are eaten. Barks are also the sources of yellow dye. Bark juice is used for dysentery and piles. Fresh and ripe
fruits are eaten and also used to distill alcohol. Bark juice is useful for diarrhoea, dysentery and
tuberculosis. Root juice is used in wounds. Flowers are
good for skin problems. Fruits are also useful in treating
gonorrhea and eaten. Dried powder of leaves or flowers is drunk with milk to cure
cough, asthma, diarrhoea and dysentery. Seeds are
roasted and pickled. Dried leaves are mixed with tobacco
and used for smoking. It is also offered to god Shiva in
rituals. Leaves are useful for remedy of skin diseases. Whole plant
parts are ground and juice about four teaspoons six times a
day is used to treat fever and indigestion. Whole plant juice is used to cure ulcer, stomach ache. Stem is used to thread children’s ear. J. Med. Plants Res. 102 Table 1. Contd. Fruits are eaten fresh or pickled. Farmers normally process
the fruits for their household needs as pickles and chutney,
etc. Conclusion by crushing and boiling the fruits, whereas
entrepreneurs purchase the fruits from growers and
produce varieties of edible pulp cake indigenously called
Titaura items for selling in the market of Nepal. 18
Choerospondias axillaris (Roxb.)
Burt & Hill Malla-0416
Anacardiaceae
Lapsee, Labasi (N),
Khaiya, Kalan (G)
Durlung
Fruits are eaten fresh or pickled. Farmers no
the fruits for their household needs as pickle
etc. by crushing and boiling the fruits, where
entrepreneurs purchase the fruits from growe
produce varieties of edible pulp cake indigen
Titaura items for selling in the market of Nep
19
Cinnamomum tamala (Buch.-
Ham.) Nees & Eberm. Malla-
0377
Lauraceae
Tejpat (N), Lepe (G)
Sarthan
Bark juice is useful for diarrhoea and nausea
used as stimulant in tea and making foods a
also used as spices. 20
Cleistocalyx operculatus Roxb. Murr. & Perry Malla- 0391
Myrtaceae
Kyamuno (N), Kemna
(G), Kyamuna (M)
Sarthan
Bark is crushed and made juice to cure musc
caused by external injury of cattle’s. Barks a
leaves are used to make alcoholic beverage
used to treat throat problems. Fresh ripe fruit
Powder of leaves is smoked in case of cold. 21
Crataeva unilocularis Buch.-
Ham. Malla-0398
Capparidaceae
Sipleegaan (N)
Simle
Leaves paste is used to cure rheumatism. Ba
taken to cure kidney problems. Juice of the y
taken to cure headache. Young twigs are tak
vegetable. 22
Cuscuta reflexa Roxb. Malla-0405
Convolvulaceae
Akasebeli (N), Dyo
dyoali (G)
Phalamkhani
Plant juice doses of about four teaspoons tw
used to treat jaundice and fever. 23
Cynodon dactylon L. Pers. Malla-0375
Poaceae
Dubo (N, M), Nodubo
(G)
Kokhe
Plant juice of about eight teaspoon is used to
indigestion. Paste of the plant is used for the
bleeding from nose and wounds. Leaves are
rituals. 24
Dendrophthoe falcata (L.) f. Etting. Malla-0414
Loranthaceae
Aijeru (N)
Bajung
Bark juice is used for treating asthma, tuberc
menstrual disorders and swelling. Paste of th
applied to set dislocated bones. 25
Diploknema butyracea (Roxb.)
Lam
Malla-0363
Sapotaceae
Chyauree, Chyuri (N,
M),
Sarthan
Ripen fruits are taken as sources of vitamin. about four teaspoon is given to cure indigest
used to make alcoholic beverage. Flowers a
for bees to make honey and leaves are loope 18
Choerospondias axillaris (Roxb.)
Burt & Hill Malla-0416
Anacardiaceae
Lapsee, Labasi (N),
Khaiya, Kalan (G)
Durlung
the fruits
etc. by cr
entrepren
produce v
Titaura ite
19
Cinnamomum tamala (Buch.-
Ham.) Nees & Eberm. Conclusion Malla-
0377
Lauraceae
Tejpat (N), Lepe (G)
Sarthan
Bark juice
used as s
also used
20
Cleistocalyx operculatus Roxb. Murr. & Perry Malla- 0391
Myrtaceae
Kyamuno (N), Kemna
(G), Kyamuna (M)
Sarthan
Bark is cr
caused b
leaves ar
used to tr
Powder o
21
Crataeva unilocularis Buch.-
Ham. Malla-0398
Capparidaceae
Sipleegaan (N)
Simle
Leaves p
taken to c
taken to c
vegetable
22
Cuscuta reflexa Roxb. Malla-0405
Convolvulaceae
Akasebeli (N), Dyo
dyoali (G)
Phalamkhani
Plant juic
used to tr
23
Cynodon dactylon L. Pers. Malla-0375
Poaceae
Dubo (N, M), Nodubo
(G)
Kokhe
Plant juic
indigestio
bleeding
rituals. 24
Dendrophthoe falcata (L.) f. Etting. Malla-0414
Loranthaceae
Aijeru (N)
Bajung
Bark juice
menstrua
applied to
25
Diploknema butyracea (Roxb.)
Lam
Malla-0363
Sapotaceae
Chyauree, Chyuri (N,
M),
Sarthan
Ripen fru
about fou
used to m
for bees t Bark juice is useful for diarrhoea and nausea. Leaves are
used as stimulant in tea and making foods and meat. It is
also used as spices. Bark is crushed and made juice to cure muscular swellings
caused by external injury of cattle’s. Barks and young
leaves are used to make alcoholic beverage. Leaf juice is
used to treat throat problems. Fresh ripe fruits are eaten. Powder of leaves is smoked in case of cold. Leaves paste is used to cure rheumatism. Bark juice is
taken to cure kidney problems. Juice of the young leave is
taken to cure headache. Young twigs are taken as a
vegetable. Plant juice doses of about four teaspoons twice a day is
used to treat jaundice and fever. Plant juice of about eight teaspoon is used to cure
indigestion. Paste of the plant is used for the treatment of
bleeding from nose and wounds. Leaves are used in many
rituals. Bark juice is used for treating asthma, tuberculosis,
menstrual disorders and swelling. Paste of the fruits is
applied to set dislocated bones. Ripen fruits are taken as sources of vitamin. Bark juice
about four teaspoon is given to cure indigestion. Fruits are
used to make alcoholic beverage. Flowers are very useful
for bees to make honey and leaves are looped for fodder. Malla et al. 103 Table 1. Contd. 26
Englehardtia spicata Lesch. Ex
Blume Malla-0365
Juglandaceae
Mahuwa (N)
Bhorle
27
Eupatorium odoratum L. Malla-0361
Asteraceae
Banmara (N), Besi
banmara (M), Thulo
banmara (Maj)
Chitre
28
Euphorbia royleana Boiss. Conclusion It is administered
about two teaspoons three times a day. L
as green compost on the paddy field. Bark juice is given to cure sore throat and bronchitis. Yong
leaves are mixed with sand and ground and added to water
body for fish poisoning. Conclusion Malla-0356
Euphorbiaceae
Siundee (N), Syuri (G),
Dha (M), Kanpate
(Maj)
Chuwa
29
Ficus lacor (Buch.)-Ham. Malla-0354
Moraceae
Kabhro (N), Kapara
(M)
Sarthan
30
Fraxinus floribunda Wall. Malla-0376
Oleaceae
Lankuri (N), Raunle
(G)
Simle
31
Girardinia diversifolia (Link.) Friis
Malla-0433
Urticaceae
Chalne sisno (N)
Chitre
32
Jatropha curcas L. Malla-0401
Euphorbiaceae
Sajiwan (N), Rajani
giri, Sajin (G), Ratyun,
Aren (Maj)
Ranipani
33
Juglans regia L. Malla-0420
Juglandaceae
Okhar (N), Akhor, Katu
(G), Okhar (M)
Lunkhu Deurali
34
Justicia adhatoda L. Malla-0357
Acanthaceae
Asuro (N), Aasuri (G)
Sarthan 26
Englehardtia spicata Lesch. Ex
Blume Malla-0365
Juglandaceae
Mahuwa (N)
Bhorle
Bark juice is given to cure sore throat and
leaves are mixed with sand and ground a
body for fish poisoning. 27
Eupatorium odoratum L. Malla-0361
Asteraceae
Banmara (N), Besi
banmara (M), Thulo
banmara (Maj)
Chitre
Decoction of the plant is used for removin
poisoning. 28
Euphorbia royleana Boiss. Malla-0356
Euphorbiaceae
Siundee (N), Syuri (G),
Dha (M), Kanpate
(Maj)
Chuwa
Leaf latex is used to cure fever, mumps a
warmed over a fire and applied to wounds
toes especially during rainy season while
muddy water. It is also used for fish poiso
29
Ficus lacor (Buch.)-Ham. Malla-0354
Moraceae
Kabhro (N), Kapara
(M)
Sarthan
Bark juice is used to treat ulcers. Seeds a
scabies. Flowers are pickled. Bark gives f
for rope. Plant is looped as fodder. 30
Fraxinus floribunda Wall. Malla-0376
Oleaceae
Lankuri (N), Raunle
(G)
Simle
Stem juice and resin are used to treat sto
sheep and goats. Wood is used to make a
equipments and tools (‘Juwa’ in Nepali). B
for the treatment of broken legs and arms
31
Girardinia diversifolia (Link.) Friis
Malla-0433
Urticaceae
Chalne sisno (N)
Chitre
Juice of the roots can be used for treating
constipation and diabetes, while juice of t
for head ache, fever, joint aches and tube
However, more treatment except boiling. 32
Jatropha curcas L. Malla-0401
Euphorbiaceae
Sajiwan (N), Rajani
giri, Sajin (G), Ratyun,
Aren (Maj)
Ranipani
The plant juice is used in syphilis and pne
are ground and applied in rheumatism an
Young stem is used to wash teeth. 33
Juglans regia L. Malla-0420
Juglandaceae
Okhar (N), Akhor, Katu
(G), Okhar (M)
Lunkhu Deurali
Leaf juice is used as tonic. Bark and fruits
detergent. 34
Justicia adhatoda L. Malla-0357
Acanthaceae
Asuro (N), Aasuri (G)
Sarthan
Leaves are boiled in water, filtered and us
bronchitis and asthma. Decoction of the plant is used for removing lice and fish
poisoning. Decoction of the plant is used for removing lice and fish
poisoning. Leaf latex is used to cure fever, mumps and cuts. Latex is
warmed over a fire and applied to wounds between the
toes especially during rainy season while walking on
muddy water. It is also used for fish poisoning. Bark juice is used to treat ulcers. Seeds are useful in
scabies. Flowers are pickled. Bark gives fiber that is used
for rope. Plant is looped as fodder. Stem juice and resin are used to treat stomach disorder in
sheep and goats. Wood is used to make agricultural
equipments and tools (‘Juwa’ in Nepali). Bark paste is used
for the treatment of broken legs and arms. Juice of the roots can be used for treating gastritis,
constipation and diabetes, while juice of the leaves is used
for head ache, fever, joint aches and tuberculosis. However, more treatment except boiling. Juice of the roots can be used for treating gastritis,
constipation and diabetes, while juice of the leaves is used
for head ache, fever, joint aches and tuberculosis. However, more treatment except boiling. The plant juice is used in syphilis and pneumonia. Roots
are ground and applied in rheumatism and dysentery. Young stem is used to wash teeth. Leaf juice is used as tonic. Bark and fruits are used for
detergent. Leaves are boiled in water, filtered and used to cure cough,
bronchitis and asthma. It is administered to cure fever,
about two teaspoons three times a day. Leaves are used
as green compost on the paddy field. J. Med. Plants Res. 104 Table 1. Contd. The fruits are chewed to cure diarrhoea and toothache. Leaves are used to cure skin diseases. Fruit juice is used
to treat stomach disorder of livestock if they eat poisonous
plants. 35
Lindera neesiana (Wall. ex
Nees) Kurz. Malla-0418
Lauraceae
Siltimur (N, M), Gutum
(G)
Karkineta
36
Macrotyloma uniflorum Lam. Verdc. Malla-0411
Papilionaceae
Gahat (N)
Ranipani
37
Mahonia napaulensis DC
Malla-0421
Berberidaceae
Jamanemandro (N),
Komo (G)
Chitre
38
Mucuna monosperma (Roxb.)
DC
Malla-0351
Leguminosae
Baldhangro (N),
Kaucho (M)
Bhorle
39
Nephrolepsis cordifolia (L) C. Presl. Malla-0417
Neprolepidaceae
Pani amala (N)
Phalamkhani
40
Nicotiana tabacum L. Malla-
0419
Solanaceae
Surtee (N) , Tamahun
(G), Bhusa (M)
Durlung
41
Ocimum sanctum L. Malla-0381
Lamiaceae
Tulsipat (N)
Ranipani
42
Osbeckia stellata Buch.-Ham. Malla-0413
Melastomataceae
Angaru (M), Paglya
jhar (G)
Deupur 35
Lindera neesiana (Wall. ex
Nees) Kurz. Decoction of the plant is used for removing lice and fish
poisoning. 48
Rhus javanica L. Malla-0362
Anacardiaceae
Vakiamilo (N),
Ghursing (G), Muruk
(Mag.)
Bhorle
Fruits are ground to make juice
diarrhoea, blood dysentery and
fruits is applied to treat swelling
chewed in case of stomachache
49
Rubia manjith Roxb. ex Flem. Malla-0402
Rubiacese
Majitho (N), Tiro lahara
(M)
Deupur
Juice of the leaves about 4 teas
given to treat urinary problem a
stem is applied to scorpion bite
reddish dye. 50
Rubus ellipticus Sm. Malla-0374
Rosaceae
Ainselu (N), Melanchi,
Palan (G), Dhewasi
(M), Jyaunsi (Maj)
Chitre
Leaves are ground and taken fo
fresh ripe fruits are eaten and s
51
Sapindus mukorossi Gaertn. Malla-0370
Sapindaceae
Reetha (N), Jharlyang
(M)
Ranipani
Seeds are ground and used as
and hair. The lather of the fruits 43
Oxalis corniculata L. Malla-0390
Oxalidaceae
Chariamilo (N), Chino
(G), Chari amilo (M),
Chariumal (Maj)
Ranipani
44
Phyllanthus emblica L. Malla-0385
Euphorbiaceae
Amala (N, Maj), Kyun,
Titi (G), Aaunlesa (M)
Ranipani
45
Prunus cerasoides D. Don
Malla-0404
Rosaceae
Paiyau (N), Chyarbu
(G), Pange (M)
Deupur
46
Reinwardtia indica Dum. Malla-0366
Linaceae
Pyaulee (N), Gyumi
(G), Gebatisar (M)
Lamtun
57
Rhododendron arboretum Sm. Malla-0432
Ericaceae
Laleegurans (N),
Porota, Pota (G),
Lalisar (M)
Chitre
48
Rhus javanica L. Malla-0362
Anacardiaceae
Vakiamilo (N),
Ghursing (G), Muruk
(Mag.)
Bhorle
49
Rubia manjith Roxb. ex Flem. Malla-0402
Rubiacese
Majitho (N), Tiro lahara
(M)
Deupur
50
Rubus ellipticus Sm. Malla-0374
Rosaceae
Ainselu (N), Melanchi,
Palan (G), Dhewasi
(M), Jyaunsi (Maj)
Chitre
51
Sapindus mukorossi Gaertn. Malla-0370
Sapindaceae
Reetha (N), Jharlyang
(M)
Ranipani Leaves are crushed to make juice to cure stomachic and
fever. Whole plant is used for preparing ‘chutney’. Roasted fruits are eaten to cure diarrhoea, dysentery, sore
throat and prepared pickle. Bark juice is used for bronchitis. Past of root is applied to headache. The juice of the root is
given to treat fever, scabies, wounds and indigestion. Juice of bark is used for treatment of cough, dysentery and
diarrhoea. The petals are eaten raw to get relief from
menstrual disorders and are chewed in case of a fish bone
is stuck in the neck. Petals are used to prepare alcoholic
beverage. Fruits are ground to make juice and used to treat
diarrhoea, blood dysentery and paralysis. A past of the
fruits is applied to treat swelling and wounds. Fruits are
chewed in case of stomachache and as appetizer. Decoction of the plant is used for removing lice and fish
poisoning. Malla-0418
Lauraceae
Siltimur (N, M), Gutum
(G)
Karkineta
36
Macrotyloma uniflorum Lam. Verdc. Malla-0411
Papilionaceae
Gahat (N)
Ranipani
37
Mahonia napaulensis DC
Malla-0421
Berberidaceae
Jamanemandro (N),
Komo (G)
Chitre
38
Mucuna monosperma (Roxb.)
DC
Malla-0351
Leguminosae
Baldhangro (N),
Kaucho (M)
Bhorle
39
Nephrolepsis cordifolia (L) C. Presl. Malla-0417
Neprolepidaceae
Pani amala (N)
Phalamkhani
40
Nicotiana tabacum L. Malla-
0419
Solanaceae
Surtee (N) , Tamahun
(G), Bhusa (M)
Durlung
41
Ocimum sanctum L. Malla-0381
Lamiaceae
Tulsipat (N)
Ranipani
42
Osbeckia stellata Buch.-Ham. Malla-0413
Melastomataceae
Angaru (M), Paglya
jhar (G)
Deupur Seeds are cooked and eaten. Seeds soup is used to treat
menstrual disorders. Soup is also useful for body pain and
used for curing the stone of kidney. The bark juice is taken to cure dysentery, diarrhoea. Ripe
fresh fruits are eaten and pickled. Flowers are used as
ornamental purpose. Bark juice is used for fever and bristle-poisonous. Seeds
are used for detergent. A decoction of the plant is used for cooling cough. Tubers
are eaten fresh for shore throat. Leaf past is used to treat rheumatic swellings, skin
diseases and scorpion sting. Juice of leaves is used to cure
cuts, wounds and removal of cattle lice. The juice of leaves is used to cure fever, stomachic,
bronchitis and earache. Leaves are directly eaten for
gastric disorder. It has also used for spiritual purpose. Juice of the root about 3 teaspoons twice a day is given to
treat diarrhoea and dysentery. A decoction of the plant is
also given to domestic animals when they eat poisonous
plants. Juice of the leaves is applied to treat scabies. Ripe
fruits are eaten fresh. Angaru (M), Paglya
jhar (G)
De Malla et al. 105 Table 1. Contd. Oxalis corniculata L. Malla-0390
Oxalidaceae
Chariamilo (N), Chino
(G), Chari amilo (M),
Chariumal (Maj)
Ranipani
Leaves are crushed to make juice to cure stomachic and
fever. Whole plant is used for preparing ‘chutney’. Phyllanthus emblica L. Malla-0385
Euphorbiaceae
Amala (N, Maj), Kyun,
Titi (G), Aaunlesa (M)
Ranipani
Roasted fruits are eaten to cure diarrhoea, dysentery, sore
throat and prepared pickle. Bark juice is used for bronchitis. Prunus cerasoides D. Don
Malla-0404
Rosaceae
Paiyau (N), Chyarbu
(G), Pange (M)
Deupur
Bark juice is used to cure swelling. Ripe fresh fruits are
eaten. The plant is looped as fodder for livestock
Reinwardtia indica Dum. Decoction of the plant is used for removing lice and fish
poisoning. Malla-0366
Linaceae
Pyaulee (N), Gyumi
(G), Gebatisar (M)
Lamtun
Past of root is applied to headache. The juice of the root is
given to treat fever, scabies, wounds and indigestion. Rhododendron arboretum Sm. Malla-0432
Ericaceae
Laleegurans (N),
Porota, Pota (G),
Lalisar (M)
Chitre
Juice of bark is used for treatment of cough, dysentery and
diarrhoea. The petals are eaten raw to get relief from
menstrual disorders and are chewed in case of a fish bone
is stuck in the neck. Petals are used to prepare alcoholic
beverage. Rhus javanica L. Malla-0362
Anacardiaceae
Vakiamilo (N),
Ghursing (G), Muruk
(Mag.)
Bhorle
Fruits are ground to make juice and used to treat
diarrhoea, blood dysentery and paralysis. A past of the
fruits is applied to treat swelling and wounds. Fruits are
chewed in case of stomachache and as appetizer. Rubia manjith Roxb. ex Flem. Malla-0402
Rubiacese
Majitho (N), Tiro lahara
(M)
Deupur
Juice of the leaves about 4 teaspoons three times a day is
given to treat urinary problem and diabetes. A paste of the
stem is applied to scorpion bites. The root is used for
reddish dye. Rubus ellipticus Sm. Malla-0374
Rosaceae
Ainselu (N), Melanchi,
Palan (G), Dhewasi
(M), Jyaunsi (Maj)
Chitre
Leaves are ground and taken for relief gastric disorder. The
fresh ripe fruits are eaten and sold in the market. Sapindus mukorossi Gaertn. Malla-0370
Sapindaceae
Reetha (N), Jharlyang
(M)
Ranipani
Seeds are ground and used as detergent to washing cloths
and hair. The lather of the fruits is used to treat burns. 43
Oxalis corniculata L. Malla-0390
Oxalidaceae
Chariamilo (N), Chino
(G), Chari amilo (M),
Chariumal (Maj)
Ranipani
Leaves are crushed to make ju
fever. Whole plant is used for p
44
Phyllanthus emblica L. Malla-0385
Euphorbiaceae
Amala (N, Maj), Kyun,
Titi (G), Aaunlesa (M)
Ranipani
Roasted fruits are eaten to cure
throat and prepared pickle. Bar
45
Prunus cerasoides D. Don
Malla-0404
Rosaceae
Paiyau (N), Chyarbu
(G), Pange (M)
Deupur
Bark juice is used to cure swell
eaten. The plant is looped as fo
46
Reinwardtia indica Dum. Malla-0366
Linaceae
Pyaulee (N), Gyumi
(G), Gebatisar (M)
Lamtun
Past of root is applied to heada
given to treat fever, scabies, wo
57
Rhododendron arboretum Sm. Malla-0432
Ericaceae
Laleegurans (N),
Porota, Pota (G),
Lalisar (M)
Chitre
Juice of bark is used for treatme
diarrhoea. The petals are eaten
menstrual disorders and are ch
is stuck in the neck. Petals are
beverage. Decoction of the plant is used for removing lice and fish
poisoning. Juice of the leaves about 4 teaspoons three times a day is
given to treat urinary problem and diabetes. A paste of the
stem is applied to scorpion bites. The root is used for
reddish dye. Leaves are ground and taken for relief gastric disorder. The
fresh ripe fruits are eaten and sold in the market. Seeds are ground and used as detergent to washing cloths
and hair. The lather of the fruits is used to treat burns. J. Med. Plants Res. 106 Table 1. Contd. 52
Sapium insigne (Royal) Benth. Ex Hook. Malla-0352
Euphorbiaceae
Khirro (N), Mibalang
(M), Khirra (Maj)
Lamtun
Milky latex of the plant is used around navel of child to cure
diarrhoea. It is also used to remove worms and germs of
the wounds. Leaves juice is used for fish poison. 53
Schima wallichii (DC.) Korth. Malla-0364
Theaceae
Chilaune (N), Kyosin
(G), Hyansing (M)
Simle
The powder of bark is used to cure cuts and liver flukes in
animals. Young leaves and bark are paste is used for
fishing by local people. Wood is used as timber for
construction. 54
Smilax ovalifolia Roxb.ex.D.Don
Malla-0395
Liliaceae
Kukurdaino (N)
Phalamkhani
Root juice is used to cure venereal disease, rheumatism
and wounds. 55
Swertia chirayita (Roxb. ex
Flem.) Karst. Malla-0408
Gentianaceae
Chiraito (N), Tento
(G), Rauka (M)
Chitre
The leaves juice is excellent drug for fever, skin diseases,
intestinal worms, asthma and diarrhoea. The paste of the
plants is applied to cure eczema. 56
Syzygium cuminii (L.) Skeels. Malla-0372
Myrtaceae
Jamun (N), Jamuna
(G, M), Phandil (Maj)
Bhorle
Bark is crushed and used to cure sore throat, asthma,
dysentery and diarrhoea. The ripen frits are eaten. Timber
is used for home applicants. 57
Terminalia bellirica (Gaertn.)
Roxb. Malla-0359
Combretaceae
Barro (N, G)
Phalamkhani
Roasted seeds are chewed for treating sore throat,
stomach disorders, indigestion, and piles. Leaves are
lopped for palatable fodder. 58
T. chebula Retz. Malla-0383
Combretaceae
Harro (N)
Lunkhu Deurali
Dried bark is chewed to treat inflammation of tonsils. Roasted fruits are used for the remedy of piles and cold. Leaves are looped for fodder. 59
Urtica dioica L. Malla-0378
Urticaceae
Sisnu (N), Polo, Pulu
(G), Dhyo, Hyo (M)
Simle
Root juice is administered for asthma, blood pressure and
sugar. The Magars of Parbat district add sparrow and rat
droppings to paste of the root to treat cuts and wounds. Decoction of the plant is used for removing lice and fish
poisoning. Tender leaves and inflorescences are cooked as
vegetables and taken to lower hypertension. 60
Woodfordia fruticosa (L.) Kurz. Malla-0399
Lythraceae
Dhairo (N), Dhanyar
(G), Dhainra (M),
Dhauli (Maj)
Bhorle
Dried powder of flowers is used to cure dysentery and
diarrhoea. The dried flowers are mixed with ‘Marcha’ yeast
to make alcoholic beverage (Gurung, Magar). Leaves are
lopped as palatable fodder to goats. Milky latex of the plant is used around navel of child to cure
diarrhoea. It is also used to remove worms and germs of
the wounds. Leaves juice is used for fish poison. The powder of bark is used to cure cuts and liver flukes in
animals. Young leaves and bark are paste is used for
fishing by local people. Wood is used as timber for
construction. Root juice is used to cure venereal disease, rheumatism
and wounds. The leaves juice is excellent drug for fever, skin diseases,
intestinal worms, asthma and diarrhoea. The paste of the
plants is applied to cure eczema. Bark is crushed and used to cure sore throat, asthma,
dysentery and diarrhoea. The ripen frits are eaten. Timber
is used for home applicants. Roasted seeds are chewed for treating sore throat,
stomach disorders, indigestion, and piles. Leaves are
lopped for palatable fodder. Dried bark is chewed to treat inflammation of tonsils. Roasted fruits are used for the remedy of piles and cold. Leaves are looped for fodder. Root juice is administered for asthma, blood pressure and
sugar. The Magars of Parbat district add sparrow and rat
droppings to paste of the root to treat cuts and wounds. Tender leaves and inflorescences are cooked as
vegetables and taken to lower hypertension. Dried powder of flowers is used to cure dysentery and
diarrhoea. The dried flowers are mixed with ‘Marcha’ yeast
to make alcoholic beverage (Gurung, Magar). Leaves are
lopped as palatable fodder to goats. Malla et al. 107 Table 1. Contd. The bark is ground and taken for relief fever, cholera and
stomach disorder. Fruits are chewed in toothache and
stomachic. Fruits are widely used for making pickles. Fruits
and thorns are used for fish poisoning (Majhi). Timur (N, M, Maj),
Prumo (G)
Phalamkhani by two village communities in the central Development
Region of Nepal. Econ. Bot. 44:71-83. and biodiversity conservation in the global and Nepalese
contexts. Plant Res. 1:22–31. ache, cuts and wounds, peptic ulcer and
backache. Decoction of the plant is used for removing lice and fish
poisoning. Thus, it is necessary to acquire and
preserves this traditional system of medicine by
proper documentation and identification of plant
species. This traditional knowledge on the
indigenous uses of the medicinal plants could
boost new innovations in the pharmaceutical
industries and have many beneficial applications
such as new medicinal trails for some pernicious
diseases like cancer and AIDS. g
p
Joshi K, Joshi R, Joshi AR (2011). Indigenous knowledge and
uses of medicinal plants in Macchegaun, Nepal. Indian J. Tradit. Know. 10:281–286. Bhattarai S, Chaudhary RP, Taylor RSL (2009). Ethno-
medicinal Plants Used by the People of Nawalparasi district,
Central Nepal. Our Nature 7:82–99. Bhattarai S, Chaudhary RP, Quave CL, Taylor RSL (2010). The use of medicinal plants in the transhimalayan arid zone
of Mustang district, Nepal. J. Ethnobiol. Ethnomed. 6:14. Kunwar RM, Nepal BK, Kshhetri HB, Rai SK, Bussmann RW
(2006). Ethnomedicine in Himalaya: a case study from
Dolpa, Humla, Jumla and Mustang districts of Nepal. J. Ethnobiol. Ethnomed. 2:27. Bussmann RW, Sharon D (2006). Traditional medicinal plant
use in Northern Peru: tracking 2000 years of healing culture. J. Ethnobiol. Ethnomed. 2:47. Kunwar RM, Uprety Y, Burlakoti C, Chaudhary CL, Bussmann
RW (2009). Indigenous Use and Ethnopharmacology of
Medicinal Plants in Far-west Nepal. Ethnobot. Res. Appl. 7:005–028. Cox AP, Balick JM (1996). Ethnobotanical research and
traditional health care in developing countries. Plants,
people and culture New Work: W.H. Freemanand Co. Kunwar RM, Shrestha KP, Bussmann R W (2010). Traditional
herbal medicine in Far-west Nepal: a pharmacological
appraisal. J. Ethnobiol. Ethnomed. 6:35. Flaster T (1995). Ethnobotanical approaches to the discovery
of
bioactive
compounds. Progress
in
new
crops:
Proceedings of the third national symposium. New crops:
New
opportunities,
new
technologies:
Indianapolis
Alexandria: ASHS Press Janick E. pp. 561-656. ACKNOWLEDGEMENT Mahato RB, Chaudhary RP (2005). Ethnomedicinal plants of
palpa district, Nepal. Ethnobotany 17:152-163. The authors express sincere thanks to the tribal
people who extended their valuable help during
the course of investigation. Manandhar NP (1998). Ethnobotanical census on herbal
medicine of Banke district, Nepal. CNAS J. 25(1):57-63. Gemedo-Dalle T, Maass BL, Isselstein J (2005). Plant
biodiversity and ethnobotany of Borana pastoralists in
Southern Oromla, Ethiopia. Econ. Bot. 59:43-65. Manandhar NP (2002). Plants and People of Nepal. Oregon,
USA. Timber Press Portland. Panthi MP, Chaudhary RP (2003). Ethnomedicinal Plant
Resources
of
Arghakhanchi
district,
West
Nepal. Ethnobotany 15:71–86. Ghimire K, Bastakoti RR (2009). Ethnomedicinal knowledge
and healthcare practices among the Tharus of Nawalparasi
district in central Nepal. For. Ecol. Manag. 257:2066–2072. WHO
(2001).
Legal
status
of
traditional
medicine
and
complementary/alternative medicine: A worldwide review. World
Health Organization, Geneva. REFERENCES Hara H (1966). The Flora of Eastern Himalaya. University of
Tokyo, Japan pp. 1-744. Rajkumar N, Shivanna MB (2010). Traditional herbal medicinal
knowledge in Sagar Taluk of Shimoga district, Karnataka,
India. Indian J. Nat. Prod. Res. 1:102–108. Acharya KP, Acharya R (2009). Ethnobotanical study of
medicinal plants used by Tharu community of Parroha VDC,
Rupandehi district, Nepal. Sci. World 7(7):80–84. Hamilton
AC,
Radford
EA
(2007). Identification
and
Conservation of Important Plant Areas for Medicinal Plants
in the Himalaya. Plant life International, Salisbury, United
Kingdom,
and
Ethnobotaniocal
Society
of
Nepal,
Kathmandu, Nepal. Rana MP, Sohel MSI, Akhter S, Islam MJ (2010). Ethno-
medicinal plants use by the Manipuri tribal community in
Bangladesh. J. For. Res. 21:85–92. Behera SK, Mishra MK (2005). Indigenous phytotherapy for
genito-urinary diseases used by the Kandha tribe of Orissa,
India. J. Ethnopharmacol. 102:319–325. Rokaya
MB,
Munzbergovaa
Z,
Timsina
B
(2010). Ethnobotanical study of medicinal plants from the Humla
district of western Nepal. J. Ethnopharmacol. 130:485–504. p
Bhattarai
S,
Chaudhary
RP,
Taylor
RSL
(2006a). Ethnomedicinal plants used by the people of Manang
district, Central Nepal. J. Ethnobiol. Ethnomed. 2:41. Jain SK, Rao RR (1997). A Handbook of Field and Herbarium
Methods. Today & Tomorrow’s Printers and Publishers,
New Delhi, India. p
p
Saikia AP, Ryakala VK, Sharma P, Goswami P, Bora U (2006). Ethnobotany of medicinal plants used by Assamese people p
Bhattarai NK (1998). Traditional Medicine, Medicinal plants Joshi AR, Edington JM (1990). The use of medicinal plants J. Med. Plants Res. 108 for various skin ailments and cosmetics. J. Ethnopharmacol. 106:149–157. for various skin ailments and cosmetics. J. Ethnopharmacol. 106:149–157. WHO
(2001). Legal
status
of
traditional
medicine
and
complementary/alternative medicine: A worldwide review. World
Health Organization, Geneva. Shrestha PM, Dhillion SS (2003). Medicinal plant diversity and use in
the highlands of Dolakha district, Nepal. J. Ethnopharmacol. 86:81–
96. Uprety Y, Asselin H, Boon E K, Yadav S, Shrestha KK (2010). Indigenous use and bio-efficacy of medicinal plants in the Rasuwa
district Central Nepal. J. Ethnobiol. Ethnomed. 6:3.
|
https://openalex.org/W2794528166
|
https://www.scielo.br/j/tla/a/4cSQFGTXnVXVP5rfQN69LSb/?lang=pt&format=pdf
|
Portuguese
| null |
UM ESTUDO SOBRE A FORMAÇÃO DE TRADUTORES E INTÉRPRETES DE LÍNGUAS DE SINAIS
|
Trabalhos em Lingüística Aplicada
| 2,018
|
cc-by
| 9,292
|
http://dx.doi.org/10.1590/010318138651551351951
* Universidade Federal de Goiás (UFG), Goiânia (GO), Brasil. julianagf@ufg.br
** Universitat Autònoma de Barcelona (UAB), Barcelona, Catalunha, Espanha. isabel.galan@uab.cat Um estudo sobre a formação de tradutores
e intérpretes de línguas de sinais
A study on the training of sign language
translators and interpreters Juliana Guimarães Faria*
Anabel Galán-Mañas** RESUMO De acordo com o censo brasileiro de 2010, 5,1% da população possui algum tipo de
deficiência auditiva. Ainda, dados de 2016 mostram que apenas 0,08% dos matriculados
no ensino superior são surdos, surdo-cegos ou deficientes auditivos. A nova Lei de Cotas
n. 13.409/2016, aprovada pelo governo brasileiro, a qual reserva vagas para pessoas com
deficiência nas instituições públicas de educação superior, é uma medida de política
afirmativa que visa incluir os surdos socialmente, sobretudo na educação superior. Como
consequência, existe uma demanda crescente de novos postos de trabalho para tradutores
e intérpretes de língua de sinais. Dada a complexidade das funções estabelecidas na Lei
12.319/2010 e a exigência de profissionais qualificados, justificam-se estudos sobre a
formação de tradutores e intérpretes de língua de sinais no Brasil. O objetivo deste artigo
é apresentar um estudo exploratório que visa traçar uma comparação entre proposta de
formação de tradutores e intérpretes de língua de sinais e línguas orais. A metodologia do
estudo possui uma abordagem qualitativa. Analisam-se dois cursos: um curso que forma
profissionais de línguas orais e outro curso que forma profissionais de língua de sinais,
da Universidade Autônoma de Barcelona, na Espanha, e Universidade Federal de Goiás,
no Brasil, respectivamente. Os elementos analisados são: objetivos de formação, perfil
do egresso e disciplinas do curso no que se refere a temas abordados e tipo de formação
(estudo de língua, prático-operativo ou teórico-conceitual). Os resultados demonstram que
a proposta do curso de formação de tradutores e intérpretes de línguas de sinais ofertado
na UFG possui um viés mais teórico e conceitual se comparado à proposta de formação
de tradutores e intérpretes de línguas orais ofertado na UAB, o qual possui um viés mais
prático, baseado na formação por competências. Palavras-chave: formação; intérpretes; libras. 1. Estes termos são os utilizados no documento do Instituto Nacional de Estudos e Pesquisas
Educacionais Anísio Teixeira (INEP, 2017).
2. Em 2016 haviam 8.048.701 matrículas em cursos superiores no Brasil, conforme dados da Sinopse
Estatística da Educação Superior do Instituto Nacional de Estudos e Pesquisas Educacionais Anísio
Teixeira (INEP) (INEP, 2017). Abstract According to the Brazilian census in 2010, 5.1% of the population has some kind of hearing
impairment. However, only 0.08% of the students enrolled in 2016 in higher education are
deaf, deaf-blind or hearing impaired. Brazilian Law 13409/2016 is an affirmative measure
that aims to socially include the deaf population, especially in higher education reserving Faria & Galán-Mañas Faria & Galán-Mañas student positions for people with disabilities across public institutions of higher education. As a consequence, there is a growing demand for translators and sign language interpreters. Given the complexity of the functions established in the above-mentioned statute and the
requirement of qualified professionals, studies on sign language translator and interpreter
training in Brazil are justified. The purpose of this article is to present an exploratory study
that aims to draw a comparison between translator and interpreter training in sign and oral
languages. The study has a qualitative approach. Two courses are analyzed: one that provides
training for oral language translators and interpreters at the Universitat Autònoma de
Barcelona (UAB) in Spain, and another that trains sign language translators and interpreters
at the Federal University of Goiás in Brazil (UFG). The course components investigated
are: training objectives, graduate profile, and the courses of the curricula on interpreter
training and kind of training (focus on linguistic, operational, or theoretical competence). The results show that the course offered at the UFG has a more theoretical and conceptual
focus compared to the course offered at the UAB, which, in turn, is much more hands-on
and competence based. Keywords: interpreter training; interpreters; sign language. 1. Introdução De acordo com o último censo brasileiro, ainda de 2010, estima-se que 5,1%
da população possui alguma deficiência auditiva, totalizando quase 10 milhões
de pessoas. O mesmo censo mostra que há um milhão de pessoas de até 19 anos
de idade (potenciais candidatos surdos para o ensino superior) com deficiência
auditiva (IBGE, 2010, p. 114). Porém, apesar de aumentar a cada ano, as matrículas
de surdos no ensino superior ainda são tímidas. Em 2011, havia 5.808 matrículas
no ensino superior de alunos surdos, com deficiência auditiva ou surdos-cegos1,
chegando a 8.676 matriculados em 2013. Em 2014 foram 7.066, em 2015 houve
7.110 matriculados e, em 2016, esse numero reduziu para 6.885 (INEP, 2017),
correspondendo a apenas 0,08% do total de matrículas2. Contudo, há uma
expectativa de que esses números aumentem significativamente, visto que, em 2016,
foi aprovada uma nova medida de política afirmativa visando ampliar a quantidade
de estudantes com algum tipo de deficiência na educação superior pública. Trata-
se da Lei 13.409/2016 (BRASIL, 2016), que se refere às cotas para deficientes nas
vagas na educação superior. Políticas afirmativas, como a nova Lei de Cotas citada, podem provocar
uma demanda significativa de Tradutores e Intérpretes de Língua de Sinais (TILS). Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 266 Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais É uma demanda em pleno crescimento, visto que, as pessoas surdas estão tendo
acesso a níveis superiores de educação, e a outros espaços sociais, que não só os
educacionais, demandando mais TILS profissionais. Historicamente, antes de se converter em uma profissão, a função de
intérprete de língua de sinais era exercida por parentes da pessoa surda, que mesmo
não sendo sonantes, conseguiam ser entendidos e se fazer entender de forma
rudimentar (Gambini; Fontana, 2016). Os professores de educação especial
que conheciam a língua de sinais (LS) também se convertiam em intérpretes com
o objetivo de dar uma resposta social a uma necessidade específica (Franchi;
Maragna, 2013). É justamente a partir do momento em que se reconhece o status
linguístico da língua de sinais (LS) que os indivíduos surdos começam a se fortalecer
como comunidade social e a conquistar espaços (Gambini; Fontana, 2016). A profissionalização da tradução e interpretação de LS se remete, dessa forma, às
políticas de inclusão e do desenvolvimento e conquistas sociais das pessoas surdas
em cada país (NAPIER, 2011). 3. Nesse artigo, a palavra Libras possui a inicial em maiúscula por se tratar de um acrônimo pronunciável
de: língua brasileira de sinais. 1. Introdução No Brasil, a tradução e interpretação de LS vem sendo impulsionada por
conquistas sociais e legais, com o reconhecimento da língua brasileira de sinais
(Libras3) de forma oficial, Lei 10.436 de 2002 (BRASIL, 2002). Além desta lei, outros
instrumentos legais foram posteriormente estabelecidos, como a regulamentação da
aplicação da lei de reconhecimento Libras, instituindo mecanismos de formação
de professores de LS e tradutores e intérpretes, bem como direitos educacionais
e de saúde para os surdos (Decreto 5.626/2005 e Lei Brasileira da Inclusão – Lei
13.146/2015) (BRASIL, 2005; 2015). Outro instrumento legal que se refere à área é a regulamentação da
profissão de TILS, descrita na Lei 12.319/2010 (BRASIL, 2010). A formação dos
profissionais TILS no Brasil é mencionada tanto nessa Lei 12.319/2010 quanto no
Decreto 5.626/2005. Embora o Decreto 5.626/2005 determine a formação em
nível superior, em cursos de “Tradução e Interpretação, com habilitação em Libras -
Língua Portuguesa” (art. 17), a Lei 12.319/2010 admite a formação de profissionais
tradutores e intérpretes de Libras em nível médio (art. 4o) (BRASIL, 2005). Segundo esta lei, são atribuições do TILS, no exercício de suas
competências: 1) efetuar comunicação entre surdos e ouvintes, surdos e surdos,
surdos e surdos-cegos, surdos-cegos e ouvintes, por meio da Libras para a língua
oral e vice-versa; 2) interpretar, em língua brasileira de sinais - língua portuguesa,
as atividades didático-pedagógicas e culturais desenvolvidas nas instituições de 3. Nesse artigo, a palavra Libras possui a inicial em maiúscula por se tratar de um acrônimo pronunciável
de: língua brasileira de sinais. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 267 Faria & Galán-Mañas ensino nos níveis fundamental, médio e superior, de forma a viabilizar o acesso aos
conteúdos curriculares; 3) atuar nos processos seletivos para cursos na instituição
de ensino e nos concursos públicos; 4) atuar no apoio à acessibilidade aos serviços
e às atividades-fim das instituições de ensino e repartições públicas; e 5) prestar
seus serviços em depoimentos em juízo, em órgãos administrativos ou policiais. Parece que o nível de exigência destes profissionais justifica que sua formação seja
ministrada por instituições de educação superior e não de nível médio. Da mesma
forma, outra determinação da necessidade de TILS de nível superior é garantida na
Lei Brasileira da Inclusão (Lei 13.146/2015) na qual afirma que para atuar em classes
de educação superior, é exigido profissionais TILS também de nível superior (art. 28, § 2o) (BRASIL, 2015). 6. As sete instituições que oferecem cursos de graduação para formação de tradutores e intérpretes
de Libras no Brasil são: a) Região Sul - Universidade Federal do Rio Grande do Sul (UFRGS) e
Universidade Federal de Santa Catarina (UFSC); b) Região Centro-Oeste - Universidade Federal
de Goiás (UFG); c) Região Sudeste - Universidade Federal de São Carlos (UFSCar), Universidade
Federal do Espírito Santo (UFES) e Universidade Federal do Rio de Janeiro (UFRJ); d) Região
Norte - Universidade Federal de Roraima (UFRR). Não há oferta de curso de graduação para
formação de tradutores e intérpretes de Libras na Região Nordeste. (MEC, 2017). ç
ç
5. Antes do Programa Viver Sem Limites, em 2008 a UFSC iniciou a oferta do curso a distância de
Bacharelado em Letras: Libras que visou a formação de TILS pelo Sistema Universidade Aberta do
Brasil.
6. As sete instituições que oferecem cursos de graduação para formação de tradutores e intérpretes
de Libras no Brasil são: a) Região Sul - Universidade Federal do Rio Grande do Sul (UFRGS) e
Universidade Federal de Santa Catarina (UFSC); b) Região Centro-Oeste - Universidade Federal
de Goiás (UFG); c) Região Sudeste - Universidade Federal de São Carlos (UFSCar), Universidade
Federal do Espírito Santo (UFES) e Universidade Federal do Rio de Janeiro (UFRJ); d) Região
Norte - Universidade Federal de Roraima (UFRR). Não há oferta de curso de graduação para
formação de tradutores e intérpretes de Libras na Região Nordeste. (MEC, 2017). 4. Dentre as instituições federais de educação superior, inclui-se universidades e institutos federais 5. Antes do Programa Viver Sem Limites, em 2008 a UFSC iniciou a oferta do curso a distância de
Bacharelado em Letras: Libras que visou a formação de TILS pelo Sistema Universidade Aberta do
Brasil. 2. A formação superior de tradutores e intérpretes de língua de
sinais no Brasil Após comparação das duas listas, identificou-se
que: a) 15 cursos não possuem nenhuma ligação com a área de tradução e interpretação, visto que
se tratam de cursos de interpretação bíblica, musical, de moda ou textual; b) 35 registros se referem
à tradução e interpretação de outras línguas; c) há 72 cursos de especialização registrados voltados
para formação de tradutores e intérpretes de Libras; e d) 64 cursos se repetiram nas duas listas (dos
quais 63 cursos possuem a Libras como objeto de estudo). Dessa forma, 67,29% dos cursos de
especialização em tradução e interpretação oferecidos no Brasil possuem a Libras como objeto de
estudo. Essa predominância da Libras pode demonstrar certa demanda crescente que o país vive em
busca de formação desses profissionais. Essa realidade implica na necessidade de estudos futuros
sobre a formação de TILS na graduação versus formação na pós-graduação. ç
g
ç
ç
p
g
ç
9. Em 15 de novembro de 2017, a partir do sistema de consulta da Coordenação de Aperfeiçoamento
de Pessoal de Nível Superior (Capes) disponível em <http://www.periodicos.capes.gov.br>,
buscou-se artigos utilizando dois pares de palavras-chave. O primeiro par de palavras-chave foi
Libras e intérpretes e o segundo par de palavras-chave utilizado foi tradutor e língua de sinais. Na primeira busca, encontrou-se 45 registros de artigos. A partir da leitura do título e resumo,
identificou-se que: a) nove artigos se referiam ao tema geral de interpretação e Libras, mas apenas
2 tratavam de formação; b) 24 artigos se referiam a áreas de interface, sobre surdos, sua língua,
educação e saúde; c) 10 artigos não tinham nenhuma ligação com o tema buscado e; d) 2 registros
estavam repetidos. Já na segunda busca, encontrou-se 58 registros de artigos e, também após a
leitura do título e resumo, identificou-se: a) 12 artigos se referiam ao tema geral de tradução e língua
de sinais, mas apenas 3 tratavam de formação; b) a mesma quantidade de 12 artigos encontrados
eram sobre áreas de interface, sobre surdos, sua língua, educação e saúde; c) 33 artigos se referiam a
outros temas que estavam ligados ao tema de interesse ou ao tema de tradução, cujo par linguístico
não tinham nenhuma ligação com a Libras e; d) 1 registro estava repetido. Assim, após as buscas
com dois pares de palavras-chave, identificou-se na primeira busca três artigos que tratavam sobre
formação e na segunda busca identificou-se dois artigos. 2. A formação superior de tradutores e intérpretes de língua de
sinais no Brasil A oferta de cursos superiores para tradutores e intérpretes de Libras no
Brasil se deu, principalmente, a partir da política pública de indução de ações
afirmativas em andamento no Brasil, trazida pelo Decreto 7.612 em 2011 (BRASIL,
2011), com o Programa Viver Sem Limites, o qual financiou instituições federais
de educação superior4 para contratação de novos professores e investimento em
material de consumo e capital (como laboratórios, equipamentos e construção de
novas instalações físicas) visando a abertura de cursos para formar professores de
Libras, tradutores e intérpretes e pedagogos bilíngues para educação de surdos5. No sistema de consulta do Ministério da Educação, dentre as catorze instituições
que oferecem cursos de graduação em tradução e interpretação no Brasil, há sete
com Libras como um dos pares linguísticos de formação6. Antes da oferta desses cursos de graduação, a formação de tradutores e
intérpretes de Libras se situava, na sua maioria, em cursos livres (SANTOS, 2006; Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 268 Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais FERREIRA, 2015), cursos de nível médio ou de capacitação profissional7 (como os
cursos livres oferecidos por Centros de Capacitação de Profissionais da Educação e
de Atendimento às Pessoas com Surdez (CAS), espalhados pelos estados brasileiros
e Associações de Surdos) e em cursos de especialização8. Dessa forma, por ser uma realidade emergente, é natural que essa discussão
sobre a formação superior de TILS também seja recente no Brasil, inclusive
com poucos artigos publicados. Em busca realizada no portal de periódicos da
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Capes), obteve-se
apenas quatro artigos que versam de alguma forma sobre a formação de tradutores e
intérpretes de Libras9 (SANTOS, 2010; STUMPF, QUADROS, 2010; Anater,
Passos, 2010; e MARTINS, NASCIMENTO, 2015). 7. Não há estudos no Brasil que demonstrem a quantidade de cursos de capacitação, atualização e/ou
cursos profissionalizantes para formação de tradutores e intérpretes de Libras. É p
p
ç
p
8. É possível encontrar registros no Ministério da Educação (MEC) sobre os cursos de especialização
lato sensu para formação de tradutores e intérpretes de Libras. Em consulta realizada (MEC, 2017) com
duas palavras-chave (tradução e interpretação) detectou-se 185 registros. Na primeira busca, foram
encontrados 101 registros de cursos. A segunda busca foi feita com a palavra-chave interpretação,
na qual foram encontrados 84 registros de cursos. ç
8. É possível encontrar registros no Ministério da Educação (MEC) sobre os cursos de especialização
lato sensu para formação de tradutores e intérpretes de Libras. Em consulta realizada (MEC, 2017) com
duas palavras-chave (tradução e interpretação) detectou-se 185 registros. Na primeira busca, foram
encontrados 101 registros de cursos. A segunda busca foi feita com a palavra-chave interpretação,
na qual foram encontrados 84 registros de cursos. Após comparação das duas listas, identificou-se
que: a) 15 cursos não possuem nenhuma ligação com a área de tradução e interpretação, visto que
se tratam de cursos de interpretação bíblica, musical, de moda ou textual; b) 35 registros se referem
à tradução e interpretação de outras línguas; c) há 72 cursos de especialização registrados voltados
para formação de tradutores e intérpretes de Libras; e d) 64 cursos se repetiram nas duas listas (dos
quais 63 cursos possuem a Libras como objeto de estudo). Dessa forma, 67,29% dos cursos de
especialização em tradução e interpretação oferecidos no Brasil possuem a Libras como objeto de
estudo. Essa predominância da Libras pode demonstrar certa demanda crescente que o país vive em
busca de formação desses profissionais. Essa realidade implica na necessidade de estudos futuros
sobre a formação de TILS na graduação versus formação na pós-graduação. 7. Não há estudos no Brasil que demonstrem a quantidade de cursos de capacitação, atualização e/ou
cursos profissionalizantes para formação de tradutores e intérpretes de Libras.
É 2. A formação superior de tradutores e intérpretes de língua de
sinais no Brasil Ao compará-los, um artigo estava repetido,
totalizando, portanto, quatro artigos que versam sobre formação de tradutores e intérpretes de
língua de sinais no Brasil. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 269 Faria & Galán-Mañas Santos (2010) estudou tradutores e intérpretes em formação e realizou uma
discussão sobre a identidade desses profissionais. Stumpf e Quadros (2010) fizeram
uma demonstração e discussão sobre as políticas afirmativas que induziram a
evolução das ações e propostas de cursos para formação de TILS no Brasil. E Anater
e Passos (2010) apresentam uma reflexão sobre as diferenças e especificidades
de atuação de tradutores e intérpretes de línguas orais e LS e complementam o
estudo apenas citando alguns cursos de formação disponíveis e como foram se
constituindo mediante as induções provocadas pelas políticas públicas. Sobre a
diferença de atuação dentre tradutores e intérpretes de línguas orais e TILS, as
autoras apresentam quatro dimensões: diferença política, de clientes, de atuação
e de exposição, situando o TILS em um campo mais amplo, com uma língua ainda
estigmatizada e demasiadamente expostos, quando comparados a profissionais
tradutores e intérpretes de línguas orais. O quarto artigo encontrado que versa sobre a formação superior de TILS é o
estudo de Martins e Nascimento (2015). Os autores também realizaram estudo com
estudantes do curso de tradução e interpretação de Libras, como Santos (2010),
e demonstraram que as motivações para o ingresso na profissão não estão mais
exclusivamente ligadas à fatores de afinidade (por exemplo, familiares de surdos),
mas por escolha advinda a partir de uma demanda do mercado profissional. Para os
autores, esse novo perfil de estudante de cursos de formação de TILS significa a
existência de alunos que não possuem nenhum histórico de contato com a Libras e
com a comunidade surda, demandando considerar esse contexto nas propostas de
cursos de formação. No que se refere às pesquisas realizadas em cursos de Mestrado e Doutorado
sobre o tema no Brasil, Santos (2013), em seu estudo de estado da arte em teses
e dissertações, não registra nada específico sobre a formação de tradutores e
intérpretes de Libras em cursos superiores realizados até o ano de 2010. Mas, tão
somente, encontrou pesquisas sobre temas de identidade, trajetória, processos de
tradução e, sobretudo, de temas da tradução e interpretação de língua de sinais
relacionados com a linguística e com a área de educação. 10. As instituições estudadas pela autora foram: UFSC, UFRGS, UFRR, UFES e UFRJ. A UFG e a
UFRGS não participaram da amostra de estudo da autora. 2. A formação superior de tradutores e intérpretes de língua de
sinais no Brasil Após consulta ao Banco de
Teses e Dissertações da Capes (CAPES, 2017), com trabalhos posteriores a 2010,
foi possível encontrar apenas uma dissertação de mestrado (FERREIRA, 2015)
que fez um estudo comparado sobre os currículos de cursos de graduação para
formação de TILS de cinco instituições brasileiras. Demais estudos (por exemplo os
realizados por MELO, 2013 e JORDÃO, 2013) trazem, tão somente, diagnósticos
de formação de profissionais e sua atuação e argumentam e problematizam a
necessidade de formação. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 270 Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais A pesquisa de Ferreira (2015) apresenta uma comparação do currículo dos
cursos superiores de formação de TILS oferecidos por cinco instituições no Brasil10. Na conclusão da autora, os cursos analisados formam profissionais de forma genérica,
ou seja, não há um foco na atuação especializada em áreas, como comunitária ou
interpretação de conferência e, na sua maioria, vinculados fortemente aos cursos de
letras. 3.1 Objetivo O presente estudo visa analisar as aproximações e distanciamentos entre
uma proposta de formação de TILS e uma proposta de formação de tradutores e
intérpretes de línguas orais, focando os seguintes elementos: a) perfil do ingressante;
b) objetivos de formação; c) perfil do egresso; e d) disciplinas dos cursos que se
refere à: temas abordados e formação prático-operativo ou teórico. Busca-se traçar
reflexões e apontamentos que possam contribuir em possíveis propostas futuras
de formação conjunta de profissionais que atuam com línguas orais e de sinais e,
também, identificar aspectos de melhora na formação existente para TILS, sobretudo
no Brasil. Napier (2011) ao analisar os modelos de formação de TILS, ressalta a
necessidade de diálogo entre profissionais de línguas orais e línguas de sinais sob
diferentes aspectos, tanto na formação, quanto na discussão sobre código de ética
e formação bicultural. Dessa forma, esse artigo pode contribuir com a abertura de
possibilidades de diálogos, respeitando as aproximações e distanciamentos de cada
especificidade. 11. O Brasil é fonte de dados: a) por apresentar um cenário de demanda de profissionais TILS, como
apresentado na introdução desse artigo; b) é iniciante na formação superior de TILS e, portanto,
possui pouca experiência; c) Por não ter tradição na formação de TILS, faz-se necessário investir
em pesquisas para o desenvolvimento e melhoria de suas práticas. 3.2 Metodologia Realizou-se um estudo exploratório, com abordagem qualitativa. Este
tipo de abordagem, segundo Guerra (2006), tem como preocupação detectar
lógicas e racionalidades e não comprovar hipóteses definidas a priori. O estudo
exploratório realizou-se a partir da análise de documentos, concretamente, fez-se
uma caracterização descritiva de elementos específicos extraídos dos documentos
analisados das duas instituições selecionadas para o estudo (GIL, 2008). Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 271 Faria & Galán-Mañas Faria & Galán-Mañas Para a comparação da formação entre TILS e tradutores e intérpretes de
línguas de orais (TILO), buscou-se selecionar dois cursos superiores ofertados em
duas instituições diferentes. Selecionaram-se o curso de TILS da Universidade
Federal de Goiás e o curso de TILO da Universitat Autònoma de Barcelona. No que
se refere à língua de sinais, a instituição escolhida deveria se situar no Brasil11,
com cursos recentemente oferecidos. Há sete instituições no país que oferecem
formação superior para TILS, das quais cinco já foram alvo de análise de Ferreira
(2015). Em relação às outras duas instituições que ainda não foram estudadas,
buscamos a que havia iniciado sua formação há mais tempo, ou seja, a Universidade
Federal de Goiás (UFG). No que se refere às línguas orais, buscou-se uma instituição com tradição na
pesquisa da formação de tradutores e intérpretes. A instituição selecionada foi a
Universitat Autònoma de Barcelona (UAB), a qual sedia um dos grupos de pesquisa para a
formação de tradutores e intérpretes considerados de excelência, sendo referência
por seus resultados de pesquisa, suas publicações, a organização de eventos, com
seminários de formação de formadores. Trata-se do Grupo PACTE (Procés d’Adquisició
de la Competència Traductora i Avaluació). O curso da UAB, embora só ofereça formação
de TILO, é uma graduação de quatro anos – à diferença de outros cursos, como o
ofertado pela École supérieure d›interprètes et de traducteurs (ESIT), na França, que é uma
pós-graduação de dois anos – e é um curso baseado na formação por competências. Utilizaram-se dois documentos das instituições selecionadas para o estudo:
a) o projeto do curso de Letras: Tradução e Interpretação em Língua Brasileira
de Sinais/Português, da UFG, no Brasil, iniciado em 2014 (FL/UFG,2014); b) o
projeto do curso de graduação em Tradução e Interpretação da UAB, o primeiro
curso dessa natureza a ser oferecido na Espanha, iniciado em 1972 (FIT/UAB,
2017). 3.2 Metodologia Percebe-se que o primeiro é um curso novo, em pleno início de trabalho, e
o segundo já tem tradição e história. 3.2.1 Quanto aos cursos em análise O curso de Letras: Tradução e Interpretação em Língua Brasileira de Sinais/
Português da UFG forma exclusivamente profissionais para atuarem com os pares
linguísticos de Libras e português. Iniciou sua primeira turma em 2014 e está situado
na Faculdade de Letras da UFG, na região centro-oeste do Brasil. Tem como origem 11. O Brasil é fonte de dados: a) por apresentar um cenário de demanda de profissionais TILS, como
apresentado na introdução desse artigo; b) é iniciante na formação superior de TILS e, portanto,
possui pouca experiência; c) Por não ter tradição na formação de TILS, faz-se necessário investir
em pesquisas para o desenvolvimento e melhoria de suas práticas. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 272 Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais a formação do profissional de Letras, portanto, deve seguir as diretrizes curriculares
brasileiras12 para esse profissional. Isso significa que há uma exigência de conteúdos
mínimos que devem ser contemplados no campo dos estudos linguísticos e literários,
conforme a legislação brasileira. Assim, além de contemplar conteúdos específicos
de tradução e interpretação, da língua de sinais, tem que atender conteúdos do
campo da Letras. Essa característica da formação de TILS vinculada à área de letras na UFG
também se aproxima à que foi detectada por Ferreira (2015) em outras instituições
no país. No Brasil, a vinculação dos estudos da tradução e interpretação com os
estudos linguísticos e literários tem tido uma origem observada não só nos cursos
que tem como um dos pares linguísticos a língua de sinais, como é o caso da UFG e
das instituições estudadas por Ferreira (2015), mas, também, vinculados à formação
de tradutores e intérpretes de línguas orais (PAGANO; VASCONCELOS,
2013). Porém, já se observa um tímido movimento de rompimento em busca de
autonomia do campo de conhecimento, como é o caso do curso de Tradução,
modalidade Bacharelado, do Centro de Ciências Humanas, Letras e Artes, criado na
Universidade Federal da Paraíba que demonstra, em sua proposta, uma autonomia
em relação à quantidade de estudos voltados para o campo da letras e linguística no
seu currículo (UFPB, 2016). No que se refere ao curso de Tradução e Interpretação da UAB, tem sua
origem na Escola Universitária de Tradutores e Intérpretes (EUTI), inaugurada em
1972. Em 1992, a EUTI converteu-se em uma faculdade, de fato a primeira Faculdade
de Tradução e Interpretação (FTI) da Espanha. 12. No Brasil, os cursos de Graduação devem seguir Diretrizes Curriculares Nacionais específicas,
determinadas pelo Conselho Nacional de Educação (CNE), um órgão colegiado do Ministério
da Educação (MEC). Os cursos de Letras, de forma geral, devem seguir normativas específicas:
Parecer CNE/CES 492/2001 e Resolução CNE/CES 18/2002.
13. Na Espanha, os cursos de ensino universitários oficiais devem cumprir com os preceitos
estabelecidos no Real Decreto 1393/2007, de 29 de Outubro. ç
13. Na Espanha, os cursos de ensino universitários oficiais devem cumprir com os preceitos
estabelecidos no Real Decreto 1393/2007, de 29 de Outubro. 3.3.1 Nível linguístico requerido no ingresso O curso da UFG não exige conhecimento pré-linguístico. Não é exigido ao
ingressante o conhecimento da segunda língua, a Libras. Pressupõe-se que, durante
o curso, o estudante se tornará proficiente na Libras. Após a matrícula, é permitido
ao estudante com suficiência na Libras fazer solicitação de dispensa das matérias
correspondentes à aprendizagem de Libras, mediante exames de avaliação em
cada nível oferecido. Pressupõe-se que todos sejam fluentes em língua portuguesa,
porém, é obrigatório a matrícula em disciplinas que ensinam o idioma português. Diferentemente da UFG, na UAB é necessário um conhecimento pré-
linguístico de língua para os ingressantes. Aos ingressantes no curso da UAB, são
exigidos os seguintes níveis de idioma14: • Nível C do Quadro Europeu Comum de Referência para Línguas (MCER)
em espanhol e catalão. Estes dois idiomas são referidos no plano de estudos
como línguas A. Os alunos estrangeiros ou procedentes de outras comunidades
autônomas espanholas em que o catalão não é língua oficial, tem que cursar o
catalão como idioma estrangeiro, para adquirir conhecimentos básicos. • Os alunos que escolhem o inglês como primeira língua estrangeira tem que ter
um nível B2 conforme o marco comum europeu de referência para as línguas, e
B1 os que escolhem francês ou alemão. No plano de estudos, estas três línguas
principais são referidas como línguas B. Para a segunda língua estrangeira, não há necessidade do estudante ter
conhecimento prévio. Esta língua é chamada língua C no plano de estudos e
pode ser: alemão, francês, português, italiano, árabe, russo, chinês, japonês. Há
também a possibilidade de os alunos cursarem uma segunda língua C no último
ano da graduação. Neste caso, os alunos podem escolher quaisquer línguas das
mencionadas ou romeno, coreano ou polonês. 14. É de se destacar que a realidade brasileira e européia são distintas e, por isso, a variedade linguística
da UAB é mais diversificada. 3.2.1 Quanto aos cursos em análise Esta faculdade é independente da
faculdade de Letras, e não faz interface com estudos linguísticos e literários. O atual
curso de graduação em Tradução e Interpretação da UAB13 nasce da necessidade
de adaptar a formação de tradutores e intérpretes aos requerimentos do Espaço
Europeu de Educação Superior. O aluno escolhe duas combinações linguísticas
dentre os idiomas oferecidos: alemão, inglês, francês, português, italiano, árabe,
russo, chinês, japonês, romeno, coreano e, eventualmente, a língua polaca como
línguas estrangeiras, e espanhol e catalão como línguas maternas, garantindo assim o
bilinguismo dos estudantes, já que na Catalunha, o espanhol e o catalão são línguas
oficiais. Todas as opções se tratam de línguas orais. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 273 Faria & Galán-Mañas 3.3.2 Objetivos, competências e habilidades de formação O curso da UFG tem como objetivo uma formação para a análise crítica e
reflexiva sobre as práticas de tradução e interpretação do par linguístico específico
de Libras e português. De acordo com o seu plano de estudo, propõe-se levar 14. É de se destacar que a realidade brasileira e européia são distintas e, por isso, a variedade linguística
da UAB é mais diversificada. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 274 Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais o estudante à capacidade de observar os fenômenos tradutórios e se apropriar
das técnicas e estratégias inerentes à atuação profissional. Ainda, se propõe a
possibilitar que o discente seja capaz de identificar, analisar, descrever e explicar
os problemas com base em teorias da tradução e teorias linguísticas, a partir da
percepção da tradução e interpretação vinculadas a experiências sociais e culturais. Essas características dos objetivos podem ser observadas no trecho a seguir. Pretende-se, assim, levar o discente a observar os fenômenos tradutório, linguístico e cultural,
a refletir sobre eles, a se apropriar de técnicas e estratégias inerentes à atuação do tradutor
e intérprete em Libras/Português. Pretende-se, também, levar o discente a identificar um
problema e analisá-lo, descrevê-lo ou explicá-lo, por meio de elaboração de hipóteses e
fundamentado em pesquisas atualizadas. Para tanto, o discente é apresentado a teorias de
tradução e a teorias linguísticas que possibilitam a busca de conhecimento novo e não a
reprodução do já sabido. (FL/UFG, 2017, p. 10) O objetivo do curso de Tradução e Interpretação da UAB é formar tradutores
e intérpretes capazes de se desenvolver nas principais modalidades de tradução e
interpretação (tradução escrita, tradução audiovisual, localização, tradução à vista,
interpretação bilateral e interpretação consecutiva) tanto em âmbitos tradicionais e
consolidados da prática profissional (tradução especializada e editorial) quanto em
novos contextos (tradução e interpretação em instituições como hospitais, centros
educativos, tribunais, etc.). El objetivo del Grado de Traducción e Interpretación es proporcionar formación en las
modalidades y los ámbitos fundamentales de la traducción y la interpretación, una profesión
que se ejerce en muchos ámbitos y que requiere múltiples habilidades en diferentes
combinaciones lingüísticas. 3.3.2 Objetivos, competências e habilidades de formação Las modalidades fundamentales de la traducción y la interpretación
son la traducción escrita, la traducción audiovisual, la localización, la traducción a vista,
la interpretación bilateral y la interpretación consecutiva tanto en ámbitos tradicionales y
consolidados (traducción especializada y editorial) como en ámbitos más nuevos (traducción
e interpretación en hospitales, centros educativos, juzgados, etc.). (FTI/UAB, 2017, p. 1). Se compararmos os objetivos das duas instituições, observa-se que o
curso da UFG prioriza a análise crítica e reflexiva sobre as práticas de tradução
e interpretação, e não a própria formação para o fazer tradutório e a prática em
tradução e interpretação Libras-português, à diferença do que acontece na UAB,
onde o foco é operativo. As habilidades descritas no plano de estudo do curso da UFG são: domínio
linguístico para comunicação e expressão da Libras e Português; domínio de
conteúdos, métodos e técnicas dos estudos da tradução e interpretação; postura
crítica numa perspectiva teórica das pesquisas na área; conhecimento linguístico;
compreensão histórica, cultural, social e política da comunidade surda, usuária da Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 275 Faria & Galán-Mañas Libras; conhecimento literário; preparação profissional atualizada com as tecnologias
e a ciência; e percepção de diferentes contextos interculturais. Libras; conhecimento literário; preparação profissional atualizada com as tecnologias
e a ciência; e percepção de diferentes contextos interculturais. Na UAB, o curso é organizado em competências básicas, específicas
e transversais, adaptadas da proposta de subcompetências que configuram a
competência tradutória do Grupo PACTE (2001). As competências básicas
descritas no plano de estudo são: demonstrar os conhecimentos das modalidades
fundamentais da tradução e interpretação; aplicar de forma profissional esses
conhecimentos; reunir e interpretar dados sobre modalidades e âmbitos da
tradução e interpretação; transmitir informações, problemas e soluções relativas à
modalidades e âmbitos da tradução e interpretação; e aplicar as competências para
empreender estudos posteriores de especialização. 3.3.2 Objetivos, competências e habilidades de formação As competências específicas são: compreender e elaborar textos orais
e escritos na língua A e na língua estrangeira; aplicar conhecimentos culturais,
temáticos e literários; dominar aspectos relacionados com a evolução histórica,
os fundamentos teóricos e linguísticos da tradução e interpretação; demonstrar
conhecimentos dos agentes e instituições que interferem no processo tradutório;
dominar os princípios metodológicos e os aspectos profissionais; resolver problemas
de tradução de textos não especializados de diferentes âmbitos de especialização,
de tradução à vista, interpretação bilateral e consecutiva; e integrar conhecimentos
e habilidades para a elaboração de trabalhos acadêmicos e profissionais relacionados
à área de tradução e interpretação. No que se refere às competências transversais previstas no plano de estudo
do curso da UAB, detectamos: atuar de forma ética; trabalhar em equipe; elaborar
e gerir projetos; raciocinar criticamente; trabalhar em contextos multiculturais; e
aprender de maneira estratégica, autônoma e contínua. Ao comparar as duas propostas, é possível identificar que o plano de estudo
da UAB está focado à formação por competências e visa profissionais atuantes, com
experiência operativa, à diferença do que prevê o curso da UFG, no qual em seu
documento prevê a reflexão crítica e o conhecimento linguístico e literário. Esta
perspectiva da UAB se aproxima ao que o Grupo PACTE (2001, p. 39) defende
em relação à competência tradutória (CT): “la CT, como todo conocimiento
experto, tiene componentes declarativos y operativos, aunque es un conocimiento
básicamente operativo”. 3.3.3 Perfil do egresso O egresso do curso de Letras: tradução e interpretação em Libras/Português
da UFG será um bacharel da área de Letras com domínio do par linguístico da Libras Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 276 Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais e do português no que se refere à sua estrutura, funcionamento e manifestação
cultural e ainda conhecimento teórico em tradução e linguística. Na citação a seguir,
do projeto do curso da UFG, observamos os grifos no qual destacam a expectativa
de conhecimento teórico. A preocupação com a formação operativa e prática da
tradução e interpretação é citada de forma mais tímida no final da descrição da
expectativa do perfil do egresso. Assim, define-se que os bacharéis em Letras: Tradução e Interpretação em Libras/Português
devem desenvolver em sua formação o domínio da Libras e da Língua Portuguesa, em termos
de estrutura, funcionamento e manifestações culturais, bem como desenvolver a capacidade de
compreensão e expressão em ambas as línguas. Devem ser capazes de refletir teoricamente sobre as questões
de tradução, incluindo aspectos linguísticos, culturais e outros conhecimentos envolvidos, bem como as estratégias de
tradução e interpretação do par linguístico Libras/Português. Esse profissional deve, ainda, ter capacidade de
reflexão crítica sobre temas e questões relativas aos conhecimentos tradutórios, linguísticos e literários. Além disso,
devem saber fazer uso de novas tecnologias e compreender sua formação profissional como
processo contínuo, autônomo e permanente. Prevê-se, sobretudo, a formação de um profissional
crítico, reflexivo e investigativo, preparado para atuar em situações do cotidiano, considerando o eixo epistemológico
do curso: a tradução e a interpretação. Espera-se, também, que o graduando desenvolva competências
em práticas e legislações relacionadas à área (FL/UFG, 2017, p. 17, grifo nosso). Já o plano de estudo do curso de Tradução e Interpretação da UAB oferece
quatro especialidades: 1) tradução especializada (tradução de textos jurídicos,
financeiros, técnicos e científicos), 2) tradução editorial (tradução de textos
literários e não literários, edição e revisão de textos); 3) interpretação (tradução
à vista, interpretação bilateral e consecutiva); e 4) tradução social e institucional
(tradução e interpretação na administração pública como hospitales, centros
educativos, juizados, etc.). Os estudantes podem escolher uma única especialidade
ou combinar disciplinas de duas ou várias especialidades. O egresso também tem
duas combinações linguísticas (elas são obrigatórias) e a possibilidade de uma
terceira. 3.3.3 Perfil do egresso Observa-se mais uma vez, ao comparar as descrições dos dois cursos, que o
viés teórico e conceitual se sobrepõe à formação operativa na proposta de formação
oferecida pela UFG em detrimento de maior foco operativo na formação por
competências proposta na UAB. 3.3.4 Disciplinas dos cursos Para esse item, identificaram-se as disciplinas que configuram os dois cursos. Analisaram-se as ementas do Projeto Pedagógico do curso da UFG (FL/UFG,
2017) e o plano de estudos do curso de Tradução e Interpretação da UAB (FIT/
UAB, 2017). Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 277 Faria & Galán-Mañas Faria & Galán-Mañas Os dois cursos apresentam disciplinas optativas, oferecidas no último ano de
estudo. Esses créditos optativos foram excluídos da análise, visto que é flexível para
cada estudante, a depender das ofertas de disciplinas da instituição (como acontece
na UFG) e de suas escolhas de formação final (como acontece na UAB). Dessa
forma, as demais disciplinas foram distribuídas em três tipos, sendo: disciplinas que
possuem como objetivo a aprendizagem de língua; disciplinas que possuem como
característica a formação prático-operativa da profissão de tradutor e intérprete;
e as disciplinas que possuem como característica principal a formação teórico-
conceitual. O curso da UAB recebe uma quantidade significativa de estudantes em
mobilidade internacional e que não possuem domínio do idioma local (espanhol
e catalão), necessitando de formação complementar com créditos de língua para
estudantes em mobilidade internacional. Esses créditos de língua complementar
(90 horas), para estudantes de mobilidade internacional, foram desconsiderados na
contabilização dentro das três distribuições levantadas. A tabela a seguir demonstra
a divisão das disciplinas. Tabela 01. Distribuição das disciplinas dos cursos da UAB e UFG em três blocos: formação de
línguas, formação prático-operativa, formação teórico-conceitual. Blocos:
UAB
UFG
Formação de línguas
• Idioma B e C para tradutores e
intérpretes 1
• Idioma B e C para tradutores e
intérpretes 2
• Iniciação à tradução B-A
• Idioma B e C para tradutores e
intérpretes 1
• Língua catalã ou espanhola
para tradutores e intérpretes
2 ou Idioma espanhol para
tradutores e intérpretes 2
• Idioma B para tradutores e
intérpretes 3
• Idioma B para tradutores e
intérpretes 4
• Língua portuguesa 1
• Língua portuguesa 2
• Libras básico 1
• Libras básico 2
• Libras intermediário 1
• Libras intermediário 2
• Libras avançado 1
• Libras avançado 2
• Escrita de sinais Tabela 01. Distribuição das disciplinas dos cursos da UAB e UFG em três blocos: formação de
línguas, formação prático-operativa, formação teórico-conceitual. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 3.3.4 Disciplinas dos cursos 2018 278 Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais Formação prático-
operativa
• Iniciação à tradução B-A
• Introdução às tecnologias da
tradução e a interpretação
• Tradução A-A ou Idioma
catalão para tradutores e
intérpretes 2
• Idioma e tradução C1
• Idioma e tradução C2
• Tradução B-A 1
• Tradução B-A 2
• Idioma e tradução C3
• Tradução B-A 3
• Iniciação à tradução
especializada B-A
• Tecnologias da tradução e a
interpretação
• Idioma e tradução C4
• Tradução inversa
• Iniciação à interpretação
• Idioma e tradução C5
• Idioma e tradução C6
• Técnicas de preparação para a
interpretação consecutiva B-A
• Práticas externas
• Idioma C para tradutores e
intérpretes 1
• Idioma C para tradutores e
intérpretes 2
• Documentação aplicada à
tradução e a interpretação
• Terminologia aplicada à
tradução e a interpretação
• Tecnologias na tradução e
interpretação
• Laboratório de tradução e
interpretação
• Laboratório de tradução
• Estágio em tradução
• Estágio em interpretação 1
• Estágio em interpretação 2
• Prática como componente
curricular
Formação teórico-
conceitual
• História da tradução e a
interpretação
• Fundamentos para a mediação
cultural em tradução e
interpretação B
• Teoria da tradução e a
interpretação
• Trabalho de conclusão de
curso
• Fundamentos para a mediação
cultural em tradução e
interpretação C
• Fundamentos para a mediação
cultural em tradução e
interpretação A
*Foco em Letras e Literatura:
• Introdução aos Estudos
Linguísticos
• Estudos Linguísticos 1
• Estudos Linguísticos 2
• Estudos Linguísticos 3
• Princípios de Estudos
Literários Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 279 Faria & Galán-Mañas Formação teórico-
conceitual
*Foco em Estudos da Tradução
e Interpretação:
• Estudos Surdos, Sociedade e
Cultura
• Políticas Linguísticas e
Tradutórias
• Estudos da Tradução e
Interpretação 1
• Estudos da Tradução e
Interpretação 2
• Ética na Tradução e
Interpretação
• Tradução em Diferentes
Contextos
• Interpretação em Diferentes
Contextos
• Introdução à Pesquisa
• Trabalho de Conclusão
de Curso 1 – Tradução e
Interpretação
• Trabalho de Conclusão
de Curso 2 – Tradução e
Interpretação
Fonte: Elaborado pelas autoras a partir dos dados. Fonte: Elaborado pelas autoras a partir dos dados. 15. Sistema Europeu de Transferência e Acumulação de Créditos. Cada ECTS equivale a 25 horas, que
podem ser horas de trabalho presencial ou de trabalho autônomo. 3.3.4 Disciplinas dos cursos Ao analisarmos o número de horas das disciplinas e as agruparmos nos blocos
mencionados acima, identificamos que a UFG possui uma formação em quatro anos
de 2.704 horas presenciais, excluídas as horas de formação optativa (256 horas). Já
o curso da UAB, faz parte do Espaço Europeu de Educação Superior (EEES) e está
organizado em créditos ECTS15. A graduação em Tradução e Interpretação tem
uma presencialidade entre o 20% e 40%, de forma que a carga-horária durante os
quatro anos de formação é de 1.860 horas presenciais, mais 600 horas das disciplinas
optativas. Ao total, portanto, a UFG possui um curso de 2.960 horas e a UAB de
2.460 horas presenciais. A figura a seguir permite observar a comparação da proporcionalidade de
horas de formação presencial divididas dentre os três blocos de distribuição das
disciplinas. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 280 Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais Figura 01. Comparativo da distribuição proporcional das horas de créditos entre UFG e UAB
em três blocos: formação de língua, formação prático-operativa e formação teórico-conceitual. Fonte: Elaborado pelas autoras a partir dos dados. Figura 01. Comparativo da distribuição proporcional das horas de créditos entre UFG e UAB
em três blocos: formação de língua, formação prático-operativa e formação teórico-conceitual. Fonte: Elaborado pelas autoras a partir dos dados. É possível observar, de forma concreta, que, de fato, na UAB o maior foco de
formação está na formação prático-operativa com 60,5% da sua carga-horária (1125
horas). Isso significa que o número de horas presencias que versam sobre o uso
das tecnologias na tradução e interpretação, estudo do idioma aplicado à tradução
e interpretação, prática de tradução especializada, tradução inversa, terminologia
aplicada à tradução e técnicas de preparação para tradução consecutiva. Ao passo
que na UFG, a formação prático-operativa concentra-se apenas em 36% da formação
(848 horas) do currículo, em aulas de laboratório, prática profissional e atividades
de estágios curriculares. 4 Conclusões Esse artigo identifica, a partir de um estudo exploratório comparativo, que a
formação de TILS oferecida por uma instituição brasileira, a UFG, está articulada
com uma forte influência da área de linguística e literatura, se comparada com a
formação oferecida para tradutores de línguas orais na UAB. Estes resultados
coincidem com o estudo de Ferreira (2015), que afirma que os cursos de TILS
no Brasil são genéricos, estão demasiado vinculados aos cursos de Letras e não
oferecem uma especialização em áreas profissionais. Neste sentido, consideramos
necessário maior autonomia dos cursos de formação de TILS – e de tradutores e
intérpretes –, em relação aos cursos de Letras. Além do movimento de busca de autonomia em relação ao predomínio
do campo de letras e da linguística no curso da UFG, são necessários estudos
futuros para avaliar em que medida a proposta desse curso está conseguindo uma
formação prático-operativa suficiente. Um TILS não pode aprender a traduzir e
interpretar estudando teorias de forma predominante, só se aprende traduzindo e
interpretando, ou seja, é preciso dotar os profissionais de uma formação prático-
operativa, em consonância com o que defende o Grupo PACTE (2001). Entre as limitações do estudo queremos mencionar, ainda, que: • trata-se exclusivamente de um estudo exploratório sobre a proposta expressa nos
documentos analisados das duas instituições, sendo preciso ampliá-lo a outras
instituições; • trata-se exclusivamente de um estudo exploratório sobre a proposta expressa nos
documentos analisados das duas instituições, sendo preciso ampliá-lo a outras
instituições; • a estrutura dos dois cursos é diferente: 1) o curso da UFG está definido em
horas, e o da UAB, em ECTS; 2) o curso da UAB tem uma presencialidade de
35%, de forma que aqui só foram comparadas as horas de trabalho presencial,
mas não as horas de trabalho autônomo que deve fazer o aluno, e 3) algumas
disciplinas foram atribuídas ao bloco de formação conceitual, mas de fato são
uma combinação de trabalho teórico-prático, como por exemplo Fundamentos
para a mediação cultural em tradução e interpretação A, da UAB. Como comentado acima (Item 2), as ações afirmativas no Brasil nos últimos
anos tendem a ampliar o número de surdos nos diferentes espaços sociais, sobretudo
na educação básica e superior. Essa realidade, inegavelmente, tem despertado para
novos postos de trabalho e exigência de qualificação profissional de nível superior,
para tradutores e intérpretes de língua de sinais (MARTINS; NASCIMENTO,
2015). 3.3.4 Disciplinas dos cursos A formação em línguas possui certa similitude dentre os
dois cursos, sendo que na UAB, 33,5% das horas são dedicadas à aprendizagem de
língua e na UFG esse percentual é de 28% As disciplinas conceituais da UAB são basicamente duas: História da tradução
e a interpretação e teoria da tradução e a interpretação, embora haja outras disciplinas
que combinam os conteúdos conceituais e práticos, como Fundamentos para a
mediação cultural em tradução e interpretação, e ainda o Trabalho de conclusão
de curso, que pode ser teórico ou prático, à escolha do aluno. Correspondem,
portanto, a 6% da carga-horária (112,5 horas). Porém, no curso da UFG, por ser
uma formação do campo da Letras, os estudos conceituais não são exclusivos da
tradução e interpretação, há um percentual significativo de disciplinas que versam
sobre linguística e literatura. Ao todo, a UFG possui uma carga-horária de 960 horas
de estudos conceituais (36%). trab. ling. aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 281 Faria & Galán-Mañas 4 Conclusões No Brasil, a graduação superior de TILS é uma ação nova, também fruto de
uma política pública (Programa Viver sem Limites), e com pouca tradição. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 282 Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais Devido à novidade deste campo profissional, consideramos de vital
importância conduzir um estudo que analise, por um lado, a atuação profissional
dos TILS no Brasil, e, por outro lado, os egressos dos cursos superiores para
tradutores e intérpretes de Libras no Brasil. Este estudo permitiria conhecer
quais são as competências exigidas pelo mercado de trabalho, as áreas de trabalho
mais demandadas e as principais tarefas desenvolvidas pelos TILS. Os resultados
permitiriam avaliar as propostas de formação existentes no Brasil e inferir se estão
atendendo – ou não – as necessidades do mercado, que são as necessidades da
comunidade surda. Além disso, é de se ressaltar que a permanência, e o sucesso, dos estudantes
surdos nas universidades brasileiras (SANTANA, 2016), e na educação de forma
geral, não pode se garantir simplesmente com a presença de TILS. Existem outras
variáveis às quais não se está dando suficiente importância, como a formação
de professores em metodologias acessíveis, o desenho de materiais didáticos
adequados, dentre outros (SANTANA, 2016). Neste sentido, a formação dos
TILS é fundamental, mas também é necessário que as escolas e as universidades
brasileiras ofereçam formação aos professores, de forma que as práticas de ensino-
aprendizagem sigam os preceitos da igualdade de oportunidades de todos os
estudantes, independentemente de suas necessidades educativas específicas. Referências Bibliográficas ANATER, G. I. P.; PASSOS, G. C. R. dos. (2010). Tradutor e intérprete de língua de sinais:
história, experiências e caminhos de formação. Cadernos de Tradução, Florianópolis, v. 2, n. 26, pp. 207-236. BRASIL. (2002). Lei 10.436, de 24 de abril de 2002. Dispõe sobre a Língua Brasileira de
Sinais – Libras e dá outras providências. Diário Oficial da União, Poder Legislativo,
Brasília, DF, 25 abr. 2002. Seção 1, p. 23. BRASIL. (2005). Decreto 5626, de 22 de dezembro de 2005. Regulamenta a Lei no 10.436, de
24 de abril de 2002, que dispõe sobre a Língua Brasileira de Sinais - Libras, e o art. 18 da Lei no 10.098, de 19 de dezembro de 2000. Diário Oficial da União, Poder
Executivo, Brasília, DF, 23 dez. 2005. Seção 1, p. 28-30. BRASIL. (2010). Lei 12.139, de 01 de setembro de 2010. Regulamenta a profissão de Tradutor
e Intérprete da Língua Brasileira de Sinais – LIBRAS. Diário Oficial da União, Poder
Legislativo, Brasília, DF, 02 set. 2010. Seção 1, p. 1. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018
283 283 Faria & Galán-Mañas BRASIL. (2011). Decreto 7612, de 17 de novembro de 2011. Institui o Plano Nacional dos
Direitos da Pessoa com Deficiência - Plano Viver sem Limite. Diário Oficial da
União, Poder Executivo, Brasília, DF, 18 nov. 2011. Seção 1, p. 12. BRASIL. (2015). Lei 14.146, de 06 de julho de 2015. Institui a Lei Brasileira de Inclusão
da Pessoa com Deficiência (Estatuto da Pessoa com Deficiência). Diário Oficial da
União, Poder Legislativo, Brasília, DF, 07 jul. 2015. Seção 1, p 2. BRASIL. (2016). Lei 13.409, de 28 de dezembro de 2016. Altera a Lei nº 12.711, de 29 de
agosto de 2012, para dispor sobre a reserva de vagas para pessoas com deficiência
nos cursos técnico de nível médio e superior das instituições federais de ensino. Diário Oficial da União, Poder Legislativo, Brasília, DF, 29 dez. 2016. Seção 1, p. 3. CAPES. (2017). Catálogo de teses e dissertações. Disponível em: <http://catalogodeteses.capes. gov.br/catalogo-teses/#!/> Acesso em: 07 dez. 2017. FERREIRA, Daiane. (2015). Estudo comparado de currículos de cursos de formação de tradutores e
intérpretes de Libras-Português no contexto brasileiro. Dissertação de Mestrado em Estudos da
Tradução. Universidade Federal de Santa Catarina, Florianópolis. FTI/UAB. Facultat de Traducció i Interpretació/Universitat Autònoma de Barcelona. (2017). Grau de Traducció i Interpretació (Informació general). Referências Bibliográficas Disponível em: <http://
www.uab.cat/web/estudiar/llistatdegraus/informaciogeneral/x1216708251447. html?param1=1228291018508> Acesso em: 04 out. 2017. FL/UFG. Faculdade de Letras/Universidade Federal de Goiás. (2017). Projeto Pedagógico do
curso de Letras: Tradução e Interpretação em Libras/Português. Goiânia: UFG. Franchi, M.L.; Maragna, S. (2013): La figura dell’interprete . In: Franchi, M.L.;
Maragna, S. (orgs.): Manuale dell’Interprete della Lingua dei Segni Italiana. Un percorso
formativo con strumenti multimediali per l’apprendimento. Milano: Franco Angeli. Gambini, D.; Fontana, S. (2016). La lengua de signos: aspectos traslativos y
sociolinguísticos desde un observatorio italiano. Revista Española de Discapacidad, Madri/
ES, v. 4, n. 1, p. 155-175. GIL, Antônio Carlos. (2008). Métodos e técnicas de pesquisa social. 6. ed. São Paulo: Atlas GUERRA, I. C. (2006). Pesquisa qualitativa e análise de conteúdo: sentido e formas de uso. 2 ed. Estoril: Princípia Editora. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 284 Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais IBGE. Instituto Brasileiro de Geografia e Estatística. (2010). Censo demográfico 2010:
características gerais da população, religião e pessoas com deficiência. Rio de Janeiro:
IBGE. Disponível em <http://biblioteca.ibge.gov.br/visualizacao/periodicos/94/
cd_2010_religiao_deficiencia.pdf>. Acesso em 20 ago. 2013. INEP. Instituto Nacional de Estudos e Pesquisas Educacionais Anísio Teixeira. (2017). Sinopse Estatística da Educação Superior. Brasília: INEP. Disponível em <http://portal. inep.gov.br/web/guest/sinopses-estatisticas-da-educacao-superior>. Acesso em 06
dez. 2017. JORDÃO, U. V. (2013). O que dizem os intérpretes de Libras do sudeste goiano sobre formação e atuação. Dissertação de Mestrado em Educação Especial. Universidade Federal de São
Carlos, São Carlos/SP. MARTINS, V. R. de O.; NASCIMENTO, V. (2015). Da formação comunitária à formação
universitária (e vice e versa): novo perfil dos tradutores e intérpretes de língua de
sinais no contexto brasileiro. Cadernos de Tradução. v. 35, n. 2, pp. 78-112. MEC. (2017). Cadastro e-MEC de Instituições e Cursos de Educação Superior. Disponível em <http://
emec.mec.gov.br>. Acesso em 06 dez. 2017. MELO, A. V. S. de. (2013). Formação e atuação do tradutor e intérprete em sala de aula. Dissertação
de Mestrado em Educação. Universidade Tiradentes, Aracaju. NAPIER, J. (2011). Signed Language Interpreting. In: Windle, K.; Malmkjaer, K. (orgs.). The Oxford Handbook of Translation Studies. Oxford: Oxford University Press,
pp. 353-372. PAGANO, A.; VASCONCELOS, M. L. (2013). Estudos de tradução no Brasil: reflexões
sobre teses e dissertações elaboradas por pesquisadores brasileiros nas décadas de
1980 e 1990. DELTA. vol.19, n. esp., pp.1-25. Disponível em: <http://www.scielo. br/scielo.php?script=sci_arttext&pid=S010244502003000300003&lng=en&nrm
=iso&tlng=pt> Acesso em: 10 nov. 2017. PACTE. (2001). La competencia traductora y su adquisición. Quaderns - Revista de traducció,
Barcelona, v. 1, n. 6, pp. 39-45. Disponível em: <http://www.raco.cat/index.php/
QuadernsTraduccio/article/view/25279/25114> Acesso em 19 set 2017. Santana, A.P. (2016). A inclusão do surdo no ensino superior no Brasil. Journal of Research
in Special Educational Needs, v. 16, n. s1, pp. 85–88. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 285 Faria & Galán-Mañas SANTOS, S. A. (2006). Intérpretes de língua de sinais: Um estudo sobre as identidades. Dissertação de Mestrado em Educação. Universidade Federal de Santa Catarina,
Florianópolis. SANTOS, S. A. dos. (2010). Tradução e interpretação de língua de sinais: deslocamentos
nos processos de formação. Cadernos de Tradução, v. 2, n. 26, pp. 145-164. STUMPF, M.; QUADROS, R. M. de. (2010). Tradução e interpretação da Língua Brasileira
de Sinais: Formação e Pesquisa. Cadernos de Tradução. v. 2, n. 26, pp. 165-205. UFPB. Trab. Ling. Aplic., Campinas, n(57.1): 265-286, jan./abr. 2018 Recebido: 26/01/2018
Aceito: 19/02/2018 Um estudo sobre a formação de tradutores e intérpretes de línguas de sinais Universidade Federal da Paraíba. (2016). Resolução 40/2016. Aprova o Projeto Político-
Pedagógico do Curso de Graduação em Tradução, modalidade Bacharelado, do
Centro de Ciências Humanas Letras e Artes, Campus I, desta Universidade. João
Pessoa: UFPB. Disponível em <http://www.cchla.ufpb.br/ctrad/wp-content/
uploads/2017/05/RES-CONSEPE-40-2016-Novo-PPC-Traducao.pdf> Acesso em
07 dez. 2017. Recebido: 26/01/2018
Aceito: 19/02/2018 286
|
https://openalex.org/W4293348769
|
https://ris.utwente.nl/ws/files/275928033/acsanm.1c03322.pdf
|
English
| null |
Controlled Nanoconfinement of Polyimide Networks in Mesoporous γ-Alumina Membranes for Molecular Separation of Organic Dyes
|
HAL (Le Centre pour la Communication Scientifique Directe)
| 2,022
|
cc-by
| 11,671
|
Downloaded via UNIV TWENTE on January 25, 2022 at 12:55:53 (UTC).
See https://pubs.acs.org/sharingguidelines for options on how to legitimately share published articles. ABSTRACT: Polyimide networks are key in the development of stable, resilient, and
efficient membranes for separation applications under demanding conditions. To this aim,
the controlled design of the network’s nanostructure and its properties are needed. However,
such control remains a challenge with currently available synthesis methods. Here, we present
a simple nanofabrication approach that allows the controlled nanoconfinement, growth, and
covalent attachment of polyimide (PI) networks inside the mesopores of γ-alumina layers. The attachment of the PI network on the γ-alumina layer was initiated via different
prefunctionalization steps that play a pivotal role in inducing the in situ polymerization
reaction at the pore entrance and/or at the inner pore surface. The nanoconfinement was found to be limited to the 1.5 μm-thick γ-
alumina supporting layer at maximum, and the resulting hybrid PI/ceramic membranes showed stable performance in a variety of
solvents. These PI/ceramic membranes were found to be very efficient in the challenging separation of small organic dye molecules
such as Rhodamine B (479 g mol−1) from toxic solvents such as dimethylformamide or dioxane. Therefore, this technique opens up
possibilities for a multitude of separations. Moreover, the PI synthesis approach can be applied to other applications that also rely on
porosity and stability control, such as for advanced insulation and anticorrosion. KEYWORDS: polyimide, nanoconfinement, mesoporous γ-alumina membranes, solvent-resistant nanofiltration,
organically modified membranes, surface-induced in situ polymerization applications are called solvent-tolerant nanofiltration (STNF)
membranes.2,4
The most common materials used to prepare STNF
membranes are polymers, such as polyamide−imides,5
polydimethylsiloxanes,6 etc. These polymeric membranes
have generally shown high permeability and stable rejection
with polar organic solvents such as alcohols or tetrahydrofuran. However, the performance of these membranes is unsat-
isfactory in the presence of apolar solvents, mainly due to the
degradation of the supporting layer.4 As a result, the
permeability often becomes lower and the rejection becomes
unpredictable. Hence, such behavior hinders the implementa-
tion of this membrane technology in water/solvent streams. The combination of a chemically inert porous ceramic support
functionalized with polyimides (PI) can overcome the
instability issue of the support. PI are among the most resilient
polymeric membrane-based materials used nowadays. PI are
polymers characterized by a stable imide ring as a repetitive
Received:
October 11, 2021
Accepted:
December 1, 2021
Published: December 10, 2021
4035
https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 © 2021 The Authors. Published by
American Chemical Society www.acsanm.org Controlled Nanoconfinement of Polyimide Networks in Mesoporous
γ‑Alumina Membranes for the Molecular Separation of Organic Dyes Controlled Nanoconfinement of Polyimide Networks in Mesoporous
γ‑Alumina Membranes for the Molecular Separation of Organic Dyes Nikos Kyriakou, Louis Winnubst,* Martin Drobek, Sissi de Beer, Arian Nijmeijer,
and Marie-Alix Pizzoccaro-Zilamy* Read Online Article Recommendations *
sı
Supporting Information www.acsanm.org Supporting Information Metrics & More ACS Applied Nano Materials www.acsanm.org Scheme 1. Schematic Illustration of the Two Fabrication Routes, A and B, Used for the Controlled Nanoconfinement of the PI
Network in a Tortuous but Defined, Rigid Mesoporous γ-Alumina Layer Matrixa Scheme 1. Schematic Illustration of the Two Fabrication Routes, A and B, Used for the Controlled Nanoconfinement of the PI
Network in a Tortuous but Defined, Rigid Mesoporous γ-Alumina Layer Matrixa ,
,
Network in a Tortuous but Defined, Rigid Mesoporous γ-Alumina Layer Matrixa
aBoth routes originate from prefunctionalized supports with APTES molecules (dark orange arrows) grafted at the top surface of the support. In
route A, a direct growth of the PI takes place between PMDA (blue diamond), MA (red triple arrow), and the superficial amino functionality,
leading to the formation of the PI network at the top surface and pore entrance. In route B, an additional prefunctionalization of the APTES
modified support (top and pore surface) is conducted only with PMDA (blue diamond). Via this route, the subsequent PI network formation is
also extended (favored) inside the γ-alumina mesopores. aBoth routes originate from prefunctionalized supports with APTES molecules (dark orange arrows) grafted at the top surface of the support. In
route A, a direct growth of the PI takes place between PMDA (blue diamond), MA (red triple arrow), and the superficial amino functionality,
leading to the formation of the PI network at the top surface and pore entrance. In route B, an additional prefunctionalization of the APTES
modified support (top and pore surface) is conducted only with PMDA (blue diamond). Via this route, the subsequent PI network formation is
also extended (favored) inside the γ-alumina mesopores. associated with material stability and processability.11 For
example, Kuttiani Ali et al.12 developed hydrophilic nano-
composite membranes for ultrafiltration by adding silica
nanoparticles prefunctionalized with deep-eutectic solvents
into a polyimide solution prior to casting. The membranes
containing 2 wt % of nanoparticles presented the best
mechanical properties and phenol retention under a wide pH
range. Moreover, recently, Wei et al.13 prepared an ultrathin
polyimide/silica nanofiltration membrane by in situ hydrolysis
and condensation of tetraethoxysilane. The resulting mem-
brane presented improved hydrophilicity, mechanical strength,
and thermal stability compared to the pure PI-NF membrane. By using a similar approach, Qiang et al.14 formed a resistant
STNF membrane. https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 ■INTRODUCTION applications are called solvent-tolerant nanofiltration (STNF)
membranes.2,4 Industry relies heavily on separation methods, from the
purification of primary materials to the isolation of polymers,
pharmaceuticals, and many other products.1 Conventional
separation methods, such as distillation, are principally
thermally driven. As a result, they can be costly, energy-
intensive, and inefficient in separating thermally sensitive
intermediates or products.1−3 As an alternative, nanofiltration
membrane-based separation technologies are increasingly
implemented in industry either in combination with distillation
or extraction as hybrid processes or by totally replacing these
conventional methods. The term “nanofiltration” (NF) refers
to a pressure-driven membrane-based separation process in
which particles and dissolved molecules smaller than 2 nm are
rejected. By replacing the high energy-demanding thermally
driven separation methods (e.g., distillation) with low energy-
demanding pressure-driven NF membranes, one can get more
energy-efficient and environmentally friendly processes.1−3
Nevertheless, current membrane materials, which are often
polymeric, are not always compatible with industrial streams,
particularly mixtures of water and organic solvents, causing
membrane failure due to degradation or dissolution of the
material itself. Therefore, when designing a membrane for
complex applications, one should consider not only the
mixture of solutes but also the nature of the solvents involved. Nowadays, membranes developed for such challenging The most common materials used to prepare STNF
membranes are polymers, such as polyamide−imides,5
polydimethylsiloxanes,6 etc. These polymeric membranes
have generally shown high permeability and stable rejection
with polar organic solvents such as alcohols or tetrahydrofuran. However, the performance of these membranes is unsat-
isfactory in the presence of apolar solvents, mainly due to the
degradation of the supporting layer.4 As a result, the
permeability often becomes lower and the rejection becomes
unpredictable. Hence, such behavior hinders the implementa-
tion of this membrane technology in water/solvent streams. The combination of a chemically inert porous ceramic support
functionalized with polyimides (PI) can overcome the
instability issue of the support. PI are among the most resilient
polymeric membrane-based materials used nowadays. PI are
polymers characterized by a stable imide ring as a repetitive Received:
October 11, 2021
Accepted:
December 1, 2021
Published: December 10, 2021
5
https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 Received:
October 11, 2021
Accepted:
December 1, 2021
Published: December 10, 2021 © 2021 The Authors. Published by
American Chemical Society © 2021 The Authors. Published by
American Chemical Society https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. ■INTRODUCTION 2021, 4, 14035−14046 14035 ACS Applied Nano Materials ■RESULTS AND DISCUSSION Synthesis and Characterization of the Prefunctional-
ized γ-Alumina Layer and Polyimide Membranes. Our
strategy to prefunctionalize supports and subsequently form
polyimide (PI)-based membranes is presented in Scheme 1. The PI-nanoconfined membranes were prepared by the
prefunctionalization of the mesoporous γ-alumina layer with
3-aminopropyl trimethoxysilane (APTES). A reliable vapor-
phase grafting procedure has been developed by our research
group to covalently attach APTES molecules at the pore
surface of the γ-alumina layer. Indeed, carefully selecting the
grafting conditions and a suitable pore filling agent can lead to
a homogeneous monolayer of APTES molecules without the
problem of homocondensation reactions occurring between
the alkoxysilane linking group.24 The primary amine group of
APTES can react via a condensation reaction with the
dianhydride precursor of the PI network during the subsequent
polyimidization reaction between pyromellitic dianhydride
(PMDA) and melamine (MA). This reaction should lead to
the covalent attachment of the polyimide network exclusively
on the top surface and pore entrance of the mesoporous γ-
alumina layer (Scheme 1, route A). Here, we employed a pore-
blocking agent, allowing us to graft only the top surface and
pore entrance of the γ-alumina layer. Hence, we assume that
the rapid PI network formation from the functionalized pore
entrance will limit the diffusion of monomers as well as any PI
oligomer units formed in the bulk solution into the pristine
pores. In this way, a PI concentration gradient is induced along
the mesoporous layer with the highest concentration close to
the pore entrance. To allow for the PI network formation to
also occur inside the mesopores of the support, samples were
modified in solution with only PMDA before the in situ
polycondensation (Scheme 1, route B). Here, PMDA can react
not only with the amino group of the grafted APTES molecules In fact, it has been shown that grafting-to and grafting-from
reactions can be applied to modify dense substrates28 as well as
the pore entrance and inner pore surface of γ-alumina
mesoporous layers.4,24−27 Sun et al.28 used the grafting-from
method to grow polyglycidyl methacrylate brushes from the
surface (−induced) of silicon wafers. These brushes were
utilized as an adhesive interlayer for chemically attaching a
polyimide film on silicon wafers. As a result, improved friction
and wear resistance was observed compared to the polyimide
films on bare silicon wafers. ACS Applied Nano Materials www.acsanm.org Article as indicated in Scheme 1. Our strategy is to use two different
precursors that promote the confinement of the PI network in
the ceramic support. The first precursor, bearing an amino
functional group, is located at the top surface and pore
entrance, while the second one, consisting of an anhydride
functional group, is present on both the surface and within the
mesopores of the γ-alumina layer. Indeed, the above functional
groups induce a surface polyimidization reaction that controls
the location of the network formation either at the pore
entrance or inside the γ-alumina layer. Furthermore, we show
that by increasing the reaction time from 1 to 5 days, the
membrane performance was significantly improved due to the
increase in concentration of the polyimide network into/on the
mesoporous layer. To demonstrate the successful growth and
confinement of the polymer inside the mesoporous layer, a
combination of different surface and pore characterization
techniques were employed. In addition, the nanoconfined PI-
based membranes were tested in different model mixtures
where its potential as a solvent-resistant nanofiltration (NF)
membrane was demonstrated. The concept described in this
work illustrates how a cross-linked polyimide can grow in a
nanoconfined space, such as the tortuous but defined
mesopores of our alumina membranes. This can be achieved
by simply controlling the grafting of the initiator for the
surface-induced in situ polymerization from the alumina
support. This approach can be expanded in other fields
where controlled nanoconfinement of a cross-linked crystalline
polymer is desired for different applications. Following this latter strategy, Isaacson et al.16,17 nano-
confined a PI network in a mesoporous tortuous organosilica
matrix. The preparation procedure involved infiltrating
polyamic acid oligomers into the porous matrix and
subsequent cross-linking of the polymer units. As a result,
the composite film/layer prepared showed enhanced resistance
to fracture compared to the pristine mesoporous support due
to a so-called confinement-induced molecular bridging
mechanism. Such confined polyimide systems could be used
as a thermal barrier coating for high-temperature operations
(at least up to 350 °C) and superior lightweight materials for
aerospace applications. However, the possibility to use this
confined PI network as a separation layer is unknown. ACS Applied Nano Materials Despite the promising performances, the
potential leaching of nanoparticles is not negligible and can
lead to potential human and environmental exposure.15 Thus
far, many researchers have focused on introducing inorganic
nanoparticles into the PI matrix. The opposite approach in
which PI networks are confined in an inorganic matrix could
also be employed. unit that exhibits good mechanical properties, chemical solvent
resistance, heat resistance, and electrical properties.7 Polyimides are prepared by the polycondensation reaction
between (di)anhydrides and (di or tri)amines at temperatures
between 180 and 300 °C. Due to their high thermal (>400 °C)
and chemical resistance, polyimides are extensively used as
membrane materials for applications in gas separation, solvent
filtration, and many others.8 Commercial PI membranes such
as PuraMem were found to be well adapted for specific STNF
applications in solvents such as toluene and heptane but only
in operating conditions up to 50 °C.9 To prevent dissolution
and to increase the hydrophilicity (imide group to amic acid)
of the PI membrane material in polar aprotic or chlorinated
solvents, it has been reported that additional cross-linking steps
are often needed.8 Even though amic acids are more
hydrophilic than imides, they nevertheless are less chemically
stable.10 Therefore, in membrane technology, it is crucial to
combine a high stable material such as polyimides, which are
also potentially processable to membranes. Therefore, different
approaches were explored to overcome the problems 14036 ACS Applied Nano Materials p
y
Studies have shown that the nanoconfinement of a
crystallized polymer within nanoporous anodic aluminum
oxide (AAO) templates is a suitable approach to prepare
innovative systems for biosensing as well as optical and
electrical-related applications.18 When a polymer is confined
within a micrometer-thick rigid AAO template comprising of
vertically oriented large pores (10−100 nm) that are not
tortuous, the crystallization behavior experiences dramatic
changes as the pore size is reduced. This approach allows
modulation of the polymer nanostructures for specific
applications but is not suitable for practical separation
applications in industry due to the limited surface area of the
AAO supports when dealing with cubic meters of water and
their fragility when exposed to harsh conditions.19 In contrast
to previous studies done on AAO supports or mesoporous
organosilica layers, we looked at defined and rigid mesoporous
ceramic membranes with relatively low tortuosity. Alumina (γ-
or α-phase) membranes are commercially predominant in the
market and are available in the shape of discs and tubes.20,21
Compared to AAO templates, mesoporous γ-Al2O3 mem-
branes are supported on millimeter-thick α-alumina supports
and commercialized in the form of modules, making them
suitable for real separations under demanding conditions (high
pressure and temperature).22,23 However, due to their
relatively large pores (∼5 nm), they are not selective in the
nanofiltration range. Nevertheless, the γ-alumina surface is rich
in free hydroxyl groups that can be used to modify the pore
entrance and inner pore surface by covalently attaching
molecules, oligomers, and polymer brushes to prepare hybrid
membranes.4,24−27 ■RESULTS AND DISCUSSION https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 ■RESULTS AND DISCUSSION However, the possibility of
simultaneous pore confinement and covalent attachment of a
cross-linked PI network onto the ceramic support has not been
demonstrated yet. Furthermore, the growth of a crystalline
polymer in one step from the surface of a ceramic support as
well as the applicability of such material under membrane
conditions is still not shown in the literature. In this work, we have initiated for the first time the in situ
polymerization reaction of a PI network directly from an
inorganic surface and controlled the nanoconfinement inside
rigid and well-defined, tortuous γ-alumina mesoporous layers 14037 https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 Figure 1. (a) FTIR spectra of the prefunctionalized samples (A, red and B, orange) and comparison with the pristine γ-alumina layer (γ-Al2O3) in
the interval between 1000 and 4000 cm−1. (b) Oxygen permeance as a function of the relative cyclohexane vapor pressure for the pristine γ-alumina
layer, sample A, and sample B. The oxygen flux is measured only through active pores in the range of 2−50 nm. Using the Kelvin equation, the pore
diameter distribution can be estimated for the pristine γ-alumina layer and sample A as shown in Figure S19. However, the pore diameter of sample
B is below the molecular size of cyclohexane (condensable liquid). Thus, pore size distribution cannot be estimated in this way. ACS Applied Nano Materials
www.acsanm.org
Article ACS Applied Nano Materials www.acsanm.org Figure 1. (a) FTIR spectra of the prefunctionalized samples (A, red and B, orange) and comparison with the pristine γ-alumina layer (γ-Al2O3) in
the interval between 1000 and 4000 cm−1. (b) Oxygen permeance as a function of the relative cyclohexane vapor pressure for the pristine γ-alumina
layer, sample A, and sample B. The oxygen flux is measured only through active pores in the range of 2−50 nm. Using the Kelvin equation, the pore
diameter distribution can be estimated for the pristine γ-alumina layer and sample A as shown in Figure S19. However, the pore diameter of sample
B is below the molecular size of cyclohexane (condensable liquid). Thus, pore size distribution cannot be estimated in this way. Figure 2. (a) FTIR analysis of the PI-nanoconfined samples. The complete spectra between 4000 and 400 cm−1 are provided in the SI. (b) Water
contact angles of the PI-nanoconfined samples. (c) AFM micrographs of the top surface of the PI-nanoconfined samples and the pristine γ-alumina
layer. https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 ■RESULTS AND DISCUSSION The bands at 1565 and
1453 cm−1 are attributed to the stretching vibration of the
triazine ring and appear in all membranes.34 The band at 1660
cm−1 could indicate the presence of amic acid on the γ-alumina
layer. However, no other absorption bands confirm the
presence of amide. To get a better insight into this observation,
the powders (I-1 and I-5) collected from the reaction mixture
were used to indirectly gain information on the nature of the
material, confined in the mesopores (Figures S13 and S14). The FTIR spectra of the powders, formed in the bulk solution
during in situ polymerization of membrane samples, clearly
show the formation of an amino-terminated imide network. Hence, in situ polymerization seems to promote imide
formation for both 1 and 5 days of reaction time without
any indications of amic acid presence. Finally, the band
between 1390 and 1360 cm−1 is ascribed to the absorption of
the C−N−C group.35−37 Thus, leading to the conclusion that
the FTIR analysis strongly suggests the presence of a polyimide
network in the γ-alumina layer. absorption bands detected. Instead of attributing each
vibration band, only the most important ones are discussed
here. The formation of the imide functional group and
attachment of PMDA is confirmed first by the vibration bands
at 1787 and 1727 cm−1, which is ascribed to the CO bond,
and the band at 1365 cm−1, which is related to CNC
bond. In addition, the anhydride group is also apparent at 1856
cm−1, which suggests either the partial reaction of PMDA with
the amino-functionalized support (A) and/or the presence of
unreacted and physically adsorbed PMDA on the ceramic
support. The band at 2460 cm−1 attributed to the carboxylate
groups (COO−)32 in the sample is due to the formation of an
amic acid group or PMDA grafting at the pore surface.29,32 g
p
g
g
p
Cyclohexane permporometry was used to study the effect of
prefunctionalization on the pore size distribution of the
support. This dynamic characterization technique allows
measuring the pore diameter of active pores present in the
prefunctionalized γ-alumina layer. The stepwise analysis will
enable one to follow the change in pore diameter starting from
the pristine γ-alumina layer and moving toward the function-
alized samples (A and B in Figure 1b). ■RESULTS AND DISCUSSION The pristine γ-alumina
layer exhibits a mean pore diameter of ∼5.5 nm, and the
support prefunctionalized with APTES (sample A) shows no
pore size diminution. This last result differs from published
reports where a pore shrinkage of 0.5 nm was observed and no
glycerol or other pore-blocking agents were used.33 This means
that glycerol, used as the pore-blocking agent, has allowed us
to control the grafting reaction and to functionalize only the
top surface of the γ-alumina layer. However, subsequent
functionalization with PMDA (sample B) resulted in a
significant reduction of the pore diameter. Compared to
pristine γ-alumina and sample A, the oxygen permeation curve
of sample B presented in Figure 1b suggests that the pore
opening occurs at low cyclohexane relative pressures during
the desorption step (∼0.1 instead of 0.4P/P0). Considering the
data acquired via cyclohexane permporometry, we cannot
determine the exact pore diameter since the Kelvin equation is
not valid since no clear transition point is obtained for this
sample. Nevertheless, knowing the limit of the measurement,
which corresponds to the molecular diameter of cyclohexane
(∼0.5 nm), one can assume that the pore diameter of the
sample B must be lower than 1 nm. Overall, the cyclohexane
permporometry results indicate the presence of PMDA in the
pores of the γ-alumina layer, which can be physically or
chemically adsorbed at the pore entrance and inner pore
surface. The high crystallinity of aromatic polyimides has been
demonstrated in the literature by powder X-ray diffraction
(XRD) analysis.7 In our work, no diffraction peaks
corresponding to crystalline aromatic polyimides could be
detected in the membrane samples (Figure S15). The XRD
pattern obtained revealed the presence of the highly intense
diffraction peaks of the α-alumina macroporous support, which
can be explained by the X-rays’ penetration depth (being more
than 3 μm in the XRD configuration used). The absence of
diffraction peaks correlated with the γ-alumina phase where the
polyimide network is confined can be explained by the
nanosized nature of this layer. Kim and Nam38 described a
decrease in the diffraction peaks of the α-alumina phase when
different polyimide/α-alumina film composites were prepared
using an amorphous polymer. Interestingly, the diffraction
peaks of the α-alumina phase were identical with our pristine
support, thus suggesting either small amounts or even the
absence of the PI network in the α-alumina pores. ■RESULTS AND DISCUSSION The line represents the averaged roughness profile of each sample. (d) Oxygen permeation as a function of cyclohexane partial pressure of the
PI-nanoconfined membranes. Figure 2. (a) FTIR analysis of the PI-nanoconfined samples. The complete spectra between 4000 and 400 cm−1 are provided in the SI. (b) Water
contact angles of the PI-nanoconfined samples. (c) AFM micrographs of the top surface of the PI-nanoconfined samples and the pristine γ-alumina
layer. The line represents the averaged roughness profile of each sample. (d) Oxygen permeation as a function of cyclohexane partial pressure of the
PI-nanoconfined membranes. between 1180 and 970 cm−1, which is associated with the
formation of the AlOSi bond and confirms the grafting of
the APTES at the top surface and pore entrance. This finding
is further confirmed by the presence of the asymmetric and
symmetric stretching vibration bands at 2927 and 2886 cm−1,
which can be attributed to the alkyl groups (−CH2−) of the
grafted APTES molecules. In addition, the sharp vibration
band at 2974 cm−1 (Figure S4) attributed to the linking
function (CH3CH2OSi) is not present in the spectrum of
sample A, suggesting complete hydrolysis of the functional
group during the grafting reaction and thus confirming the
formation of the desired SiOAl bond again.24 In
comparison with sample A, the interpretation of the FTIR
spectrum of sample B is more difficult due to the number of but also with free hydroxyl groups at the inner pore surface of
γ-alumina layer.29 Thus, the PI network formation takes place
uniformly from the whole surface, including the pore entrance
and pore surface, of the mesoporous γ-alumina layer. Fourier transform infrared (FTIR) analysis was employed to
demonstrate the prefunctionalization of the mesoporous γ-
alumina layer. The spectra of the pristine γ-alumina layer and
the layers prefunctionalized respectively with APTES (sample
A) and APTES + PMDA (sample B) are shown in Figure 1a. The FTIR spectrum of the pristine mesoporous layer shows a
broad band centered at 3420 cm−1, which can be attributed to
the stretching vibration of adsorbed water and surface hydroxyl
groups.30,31 Functionalization of the γ-alumina layer with
APTES results in the appearance of primarily a broad band 14038 https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 ACS Applied Nano Materials Article www.acsanm.org longer reaction times for both routes. https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 ■RESULTS AND DISCUSSION Li et al.35
described the preparation of a PI powder between PMDA and
MA below 200 °C leading to a relatively amorphous material
(two broad peaks between 10 and 50°), whereas at 200 °C or
above,40 a semicrystalline structure was observed. Thus, the
powder XRD results provided here confirm that the
organization of the material depends both on the temperature
of the polycondensation reaction and the reaction times. However, when the PI powder was treated at 300 °C for
several hours, a new diffraction peak at 44° was observed,
which is possibly related to the degradation by-products. Thermal treatment of the PI powders at 400 °C resulted in an
almost complete loss of crystallinity and increase in intensity of
the diffraction peak at 44° (Figure S17). The observed thermal
degradation evidenced by powder XRD is also corroborated by
the thermogravimetric analysis (TGA) provided in Figure S18. A small weight loss for both I-1 and I-5, 2.2 and 1.4%,
respectively, occurred upon heating from room temperature to
300 °C. However, above 300 °C, a significant weight loss
occurs, particularly for sample I-1. Thus, we can assume that
the PI network remains stable at temperatures below 300 °C,
which is ideal for membrane applications. membrane separation performance. Therefore, it is crucial to
look closer at the PI network inside the support and well
describe the nanoconfinement effect. PI Network Nanoconfinement Characteristics. A series
of analytical techniques were employed to investigate the
influence of the supports’ prefunctionalization on the extent of
the PI nanoconfinement. First, water contact angle analysis was
done on the PI-nanoconfined samples and the pristine support
to evaluate (indirectly) the polymerization effect on the
support surface properties. The results are given in Figure 2b. Compared to the pristine layer, which presents a water contact
angle of 14° (disappearing in 6−7 s) characterizing a porous
hydrophilic surface, the PI-nanoconfined samples show an
increased water contact angle (40−65°). This observation
suggests that the membrane surface is still hydrophilic (water
contact angles < 90°) but certainly less hydrophilic than the
pristine support. Interestingly, different water contact angles
were obtained for the samples prepared via routes A and B,
respectively, 63° (±16°) and 54° (±5°) for the same reaction
time (1 day). ■RESULTS AND DISCUSSION To shed
more light into the confined network’s nature, XRD analysis
was conducted on the powder extracted from the bulk solution
at the end of the synthesis of the membranes. The powder
XRD patterns between 5 and 50° 2θ are provided in Figure
S16 for the powder samples obtained after 1 or 5 days of
reaction time (denoted as I-1 and I-5). The analysis revealed
the formation of polycrystalline materials with an amorphous
background observed in small proportion. The comparison of
the diffractograms between samples I-1 and I-5 shows a clear
relationship between increasing reaction time and improved
crystallinity evidenced by the narrowing of the diffraction
peaks and a decrease in the baseline broadening. These results
are corroborated by the scanning electron microscopy (SEM)
analysis of the powders (Figure S20), which also shows
changes in morphology as a function of reaction time. The
sample I-1 appeared to consist of a mixture of platelet
crystallites of several micrometer wide, cauliflower-like
aggregates and clustered (random) spherical porous phases
(ranging from nanometers to micrometers in diameter). Increasing reaction time led to the growth of a fascinating
morphology consisting of defined flower-shaped crystallites, as
observed with sample I-5, decorated with smaller crystallites. Similar results were obtained by Baumgartner et al.,7,39 who
observed an “amorphous” baseline while analyzing the
produced polyimide crystalline samples under hydrothermal
conditions using p-phenylenediamine and PMDA as mono- As explained before, the attachment, growth, and molecular
confinement of the PI network in the γ-alumina layer was
performed via two different approaches; first, by the direct
formation of the PI network from the prefunctionalized surface
of sample A, where the functional groups were at the top
surface and pore entrance of the γ-alumina layer, and second,
from sample B, where the functional groups were located at the
top and pore surface of the γ-alumina layer. FTIR analysis was
performed on the nanoconfined PI membranes to assess the
spectroscopic characteristics of the network formed after in situ
polymerization. Figure 2a displays the spectra of the four PI-
nanoconfined membrane samples (A-1/5 and B-1/5). All
samples exhibit similar spectroscopic characteristics with minor
differences in the intensity of certain bands for the two
different reaction times (1 and 5 days) and both reaction
routes. The two bands at ∼1780 and ∼1720 cm−1 are ascribed
to the CO bond of the imide and are more intense with 14039 ACS Applied Nano Materials www.acsanm.org Figure 3. https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 ■RESULTS AND DISCUSSION (a) Images of the PI-nanoconfined membranes (left) accompanied with HR-SEM micrographs of the top surfaces (middle) and the cross
sections (right). (b) Evolution of the carbon/aluminum ratio (wt % by EDS) along the membrane cross section. The dashed white line denotes the
limit between the γ-alumina layer (left) and the α-alumina support (right). Figure 3. (a) Images of the PI-nanoconfined membranes (left) accompanied with HR-SEM micrographs of the top surfaces (middle) and the cross
sections (right). (b) Evolution of the carbon/aluminum ratio (wt % by EDS) along the membrane cross section. The dashed white line denotes the
limit between the γ-alumina layer (left) and the α-alumina support (right). mers. Comparison with published records of polyimide
powders prepared using the same precursors (PMDA and
MA) but under different experimental conditions (temperature
and solvent) shows different crystal structures. Li et al.35
described the preparation of a PI powder between PMDA and
MA below 200 °C leading to a relatively amorphous material
(two broad peaks between 10 and 50°), whereas at 200 °C or
above,40 a semicrystalline structure was observed. Thus, the
powder XRD results provided here confirm that the
organization of the material depends both on the temperature
of the polycondensation reaction and the reaction times. However, when the PI powder was treated at 300 °C for
several hours, a new diffraction peak at 44° was observed,
which is possibly related to the degradation by-products. Thermal treatment of the PI powders at 400 °C resulted in an
almost complete loss of crystallinity and increase in intensity of
the diffraction peak at 44° (Figure S17). The observed thermal
degradation evidenced by powder XRD is also corroborated by
the thermogravimetric analysis (TGA) provided in Figure S18. A small weight loss for both I-1 and I-5, 2.2 and 1.4%,
respectively, occurred upon heating from room temperature to
300 °C. However, above 300 °C, a significant weight loss
occurs, particularly for sample I-1. Thus, we can assume that
the PI network remains stable at temperatures below 300 °C,
which is ideal for membrane applications. mers. Comparison with published records of polyimide
powders prepared using the same precursors (PMDA and
MA) but under different experimental conditions (temperature
and solvent) shows different crystal structures. ACS Applied Nano Materials However, the pore sizes are significantly affected,
indicating either an ultrathin top layer or a confined polymer in
the mesoporous layer. To better understand this finding and to
observe the PI network on the γ-alumina layer directly, we
proceeded with HR-SEM analyses of the studied membrane
samples. In conclusion, by combining the knowledge gained from
HR-SEM and EDS, we can assure that the functionalization of
the support promotes the growth of the PI network during
polymerization. Based on these results, a membrane formation
mechanism was drawn (Scheme 1). The membranes prepared
via route A, thanks to the presence of the amino group
(APTES) at the top surface of the support, exhibit a higher
concentration of PI near the pore entrance. Alternatively, with
route B, a homogeneous polymer distribution is observed
throughout the γ-alumina layer, which is attributed to the
functionalization of the inner pore surface with anhydride
functional groups (PMDA). These differences in membrane
architecture can significantly affect their membrane perform-
ance due to an increase in the thickness of the separating layer,
as schematically shown in Scheme 1. Additionally, longer
reaction times lead to higher concentrations of polymer inside
the γ-alumina layer, which could potentially promote
formation of smaller pore diameters and, thus, better
separation performance. To confirm our interpretation from
the HR-SEM and EDS analysis, a series of membrane
separation tests have been performed with model aqueous
solutions described hereafter. The top surface and cross-sectional high-resolution SEM
pictures of the PI-nanoconfined membranes are given in Figure
3a, together with photographs of the membrane samples. Compared to the pristine γ-alumina layer, which is naturally
white (Figure S21), the PI-nanoconfined membrane samples
appear to be substantially covered by the polymeric network as
denoted by brownish coloration, which is typical for a
polyimide material. The comparison of the top-surface
micrographs of membrane samples prepared by the two
fabrication routes (A and B) does not show any significant
differences at first glance. One day of reaction leads to the
formation of small particles with a sheet-like structure visible
on both A-1 and B-1 samples. Increasing the reaction time to 5
days leads to the disappearance of the sheet structure,
suggesting the formation of a thin homogeneous layer. From
the SEM analysis of PI powders (Figure S20), we observed
that the 5 day long reaction yields a clear platelet-like structure,
whereas the 1 day reaction results in a mixture of aggregates
and crystallites. ACS Applied Nano Materials Article www.acsanm.org to affect the surface roughness (∼3 nm). Samples reacted for 5
days show only a slight increase in surface roughness, with the
A-5 samples exhibiting larger differences in height on the
surface (∼4 nm) compared to B-5 samples (∼3 nm) as shown
in Figure 2c. The empirical information gained from water
contact angle and AFM analyses postulates a fundamental
difference between the two routes, which becomes more
prevalent after longer reaction times. The influence of reaction
conditions on the pore diameter of the PI-nanoconfined
membranes was investigated by means of cyclohexane
permporometry. The results are provided in Figure 2d. During
the analysis, no oxygen permeation was measured at low
cyclohexane partial pressures (<0.55), which indicates the
presence of micropores (pore diameter < 1.5 nm) or even of a
dense sample. This suggests a pore diameter shrinkage of more
than 4 nm. Indeed, the permporometry analysis demonstrates
that the presence of the PI network affects the pore size of the
mesoporous γ-alumina layer. finding thus strongly indicates that longer reaction times of
polymerization on prefunctionalized γ-alumina layers pro-
moted the nanoconfinement of the PI network in the 5 nm
pores of the γ-alumina layer. Evidently, the difference between
the membranes A-1 and B-1 suggests that the choice of
prefunctionalization can affect the extent of the PI nano-
confinement in the γ-alumina layer. In complement, energy-dispersive X-ray spectroscopy (EDS)
analysis can offer qualitative elemental information over a
membrane’s cross section (Figure 3b). By measuring the ratio
of carbon over aluminum along the cross section of the
different membrane samples, one can define the influence of
the preparation route and, indirectly, the prefunctionalization
steps on the nanoconfinement of the PI network. Overall, the
EDS analysis reveals that organic (polymeric) material resides
in the γ-alumina layer. In route A, the network accumulates
near the pore entrance, whereas in route B (samples B-1 and B-
5), a spread distribution of the PI network inside the γ-alumina
layer is observed. These results clearly indicate a link between
the prefunctionalization step and the nanoconfinement of PI
networks inside the γ-alumina layer. On the other hand, the
reaction time merely affects the concentration of the polymeric
network. All the results described above showed that the polymer
network changes the morphology of the surface only in a subtle
manner. https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 ■RESULTS AND DISCUSSION Nevertheless, with the increase of the reaction
time, a rise of 11° was measured for the samples prepared via
route B, while a decrease of 19° was measured for the samples
made via route A. As for porous hydrophilic surfaces, accurate
estimation of a descending water contact angle is challenging. Still, the difference observed between the two routes can be
inherent to the prefunctionalization step. It must be noted that the confinement of a polyimide
network in the γ-alumina layer should lead to an enhancement
of the physicochemical stability of the polyimide network as
shown by Isaacson et al.17 Based on the powders’ crystallinity
and morphology, one can assume that the PI membrane
samples exhibit similar structural characteristics as the
polyimide powders. If our assumptions are confirmed, it
would mean that by simply varying the reaction time, we can
engineer the membrane’s micropores and thus enhance the Further investigation and comparison of the PI-nano-
confined membrane surface morphology with that of the γ-
alumina layer was conducted by atomic force microscopy
(AFM) analysis, and the results are shown in Figure 2c. From
the average roughness profiles, it is apparent that the surface
morphology of the PI-nanoconfined membranes changes with
increasing reaction time. Compared with the pristine γ-alumina
layer, polymerization for 1 day, for both routes, does not seem 14040 14040 ACS Applied Nano Materials ACS Applied Nano Materials (b) Retention of Brilliant Yellow
(BY) and Rhodamine B in water for PI-nanoconfined membranes and
the pristine layer (γ-Al2O3). Each test was repeated three times (the
presented permeation and retention are averages, and the errors refer
to the standard deviation from the average value of three samples). (c) Performance of A-5 and B-5 samples in different solvents. (d) RB
retention in different solvents for A-5 and B-5 samples. (a) Water permeability of the PI-nanoconfined membrane of the polymeric network in the tortuous mesopores, there are
still many open pores that are either smaller than the
Rhodamine B molecule (sieving effect) or are small and
charged (Donnan effect) and thus have a direct influence on
the separation performance of the membranes. In 1,4-dioxane, a different mechanism is probably at play. The solubility of RB in 1,4-dioxane is significantly lower than
in ethanol, DMF, or water. In this regard, the solvent is
expected to have a much higher preference to the polymer (PI)
than to the solute, leading to high retentions observed
experimentally for the studied systems. These tests suggest
that the PI network confined in the γ-alumina layer could be
slightly charged since RB retentions are the best in water and
DMF, where the zwitterionic form is dominant. The charge
could originate either from the presence of primary terminal
amines, which is also suggested from the FTIR analysis, or the
monomer ratio used during membrane preparation. As such,
we propose that by adjusting the in situ polymerization
conditions, such as monomer ratio, one can tune the final
membrane properties. p
p
The water permeability results, on the other hand, suggest a
clear difference between routes A and B, particularly for
samples treated for 5 days. It is evidenced from the increase in
RB retention for sample A-5 compared to A-1 that for route A,
the polymer amount in the γ-alumina pores is increasing and,
hence, the pores are shrunk significantly. However, since the
water permeability for A-5 remains comparable to that of A-1,
this can be regarded as an indication that the polymer
concentration is only increasing at the pore entrance, leading
to thin selective barriers. For sample B-5, the RB retention is
also increasing compared to B-1; here, however, decreasing
permeability is suggesting a thicker selective barrier. ACS Applied Nano Materials From the HR-SEM analysis of the top surface
of both A-1 and B-1 samples, one can observe similar sheet-like
structures. This indicates that the PI networks that are growing
on the surface of the γ-alumina layer and those growing in the
bulk solution exhibit similar characteristics. Hence, we expect
that the PI network growth, induced from the ceramic surface,
will have a similar morphology with smaller particles mainly
when infiltrated in the pores. Finally, it is expected that such
platelet-like particles should ensure good coverage of the
support surface, as seen on the micrographs of both A-5 and B-
5 samples. PI-Nanoconfined Membrane Performance. The PI-
nanoconfined membranes were tested first in aqueous
solutions of Brilliant Yellow (BY, 625 g mol−1) or Rhodamine
B (RB, 479 g mol−1) and compared with the pristine γ-alumina
layer. The retention and water permeability results are
summarized in Figure 4. All four PI-nanoconfined membranes
show retentions above 90% of BY (627 g mol−1) in water,
which is a significant increase compared to the pristine γ-
alumina layer (76%). However, with Rhodamine B (RB, 479 g
mol−1), the retentions for the A-1 and B-1 samples were
between 70 and 80%. With increasing the polyimidization
reaction time, the membranes (A-5 and B-5) show RB
retentions well over 90%. This can be attributed to the
increasing PI concentration in the pores of the γ-alumina layer. Compared with the pristine γ-alumina layer (14% retention for
RB), the separation performance of the PI-nanoconfined
membranes thus displays a significant improvement. These
results also suggest that, despite this increase in concentration In comparison, the HR-SEM cross-sectional analysis of the
membranes shows a clear difference between the two synthesis
routes after 1 day of reaction. For the A-1 sample, the PI
network seems to be located at the γ-alumina layer top surface. In contrast, for the B-1 sample, infiltration of the PI network in
the γ-alumina layer could be observed. The samples A-5 and B-
5, after 5 days of reaction time, also present extended
infiltration of the PI network in the γ-alumina layer. This 14041 https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 Figure 4. (a) Water permeability of the PI-nanoconfined membranes
and the pristine layer (γ-Al2O3). (b) Retention of Brilliant Yellow
(BY) and Rhodamine B in water for PI-nanoconfined membranes and
the pristine layer (γ-Al2O3). ACS Applied Nano Materials Each test was repeated three times (the
presented permeation and retention are averages, and the errors refer
to the standard deviation from the average value of three samples). (c) Performance of A-5 and B-5 samples in different solvents. (d) RB
retention in different solvents for A-5 and B-5 samples. ACS Applied Nano Materials ACS Applied Nano Materials Article www.acsanm.org Sample A-5 was also tested for 5 days in RB/water solution
to assess the stability of the PI-nanoconfined ceramic
membranes. The results are provided in Figure S27. As
shown, the RB retention remains stable at approximately 98−
99%. Furthermore, the water flux increases slightly after the
first day (from 8 to 10 L m−2 h−1) but remains relatively stable
in the following 4 days. Therefore, this preliminary result
shows that the method used to prepare the PI-nanoconfined
membranes results in relatively stable membranes. The two membranes showing the best rejection, the B-5 and
A-5 samples, were subsequently tested in different solvents
containing RB. The results for the solvent permeability and RB
retention in solvents are accordingly given in Figure 4c,d. Three different organic solvents were selected based on their
polarity: ethanol, DMF, and 1,4-dioxane with polarity values of
0.654, 0.386, and 0.164, respectively. Indeed, by testing the
membranes in different liquid media, we gain more insight into
the membrane layer’s properties. As shown in Figure 4c, the
membranes perform well in all solvents. Only in ethanol the
retention performance of the PI-nanoconfined membranes
lower than 90% (79% for B-5 and 83% for A-5). The results
can be attributed to the nature and solubility of RB in different
solvents. According to Hinckley et al.,41 RB in a solution can
be present in two forms, the lactone (L) and the zwitterionic
(Z) form, which are in equilibrium, and the most dominant
form depends on the solvent. Hinckley et al.41 showed that the
ratio zwitterionic:lactone (charged:neutral) in water (Z:L =
4.4) and formamide (Z:L = 7.67) is higher than in ethanol
(Z:L = 2.4). Since ethanol favors the neutral form of RB
compared to water and DMF, we expect that the zwitterion
rejection might be related to ionic repulsions between the
membrane and the solute, thus leading to slightly lower
rejections in ethanol. Figure 4. (a) Water permeability of the PI-nanoconfined membranes
and the pristine layer (γ-Al2O3). https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 ■METHODS Materials. Solvents ethanol (technical grade > 95%), anisole
(>99%, Merck, NL), N-methyl-2-pyrrolidone (NMP) (>99%,
anhydrous, Merck, NL), mesitylene (>99%, Acros Organics, NL),
isoquinoline (95%, TCI, Europe), acetone (technical grade, >95%),
1,4-dioxane (anhydrous, Sigma Aldrich, NL), dimethylformamide
(>99%, Sigma Aldrich, NL), and ethanol (analytical grade, Merck,
NL) were used as received. Water was purified through a Milli-Q
Reference Water Purification System. Glycerol (anhydrous, Merck,
NL), 3-aminopropyl triethoxysilane (>98%, Sigma Aldrich, NL),
pyromellitic dianhydride (PMDA) (97%, Sigma Aldrich, NL),
melamine (MA) (99%, Sigma Aldrich, NL), Brilliant Yellow (70%,
Sigma Aldrich, NL), and Rhodamine B (>99%, Merck, NL) were used
as received. The chemical structures and abbreviations can be found
in Figure S1 of the Supporting Information. Materials. Solvents ethanol (technical grade > 95%), anisole
(>99%, Merck, NL), N-methyl-2-pyrrolidone (NMP) (>99%,
anhydrous, Merck, NL), mesitylene (>99%, Acros Organics, NL),
isoquinoline (95%, TCI, Europe), acetone (technical grade, >95%),
1,4-dioxane (anhydrous, Sigma Aldrich, NL), dimethylformamide
(>99%, Sigma Aldrich, NL), and ethanol (analytical grade, Merck,
NL) were used as received. Water was purified through a Milli-Q
Reference Water Purification System. Glycerol (anhydrous, Merck,
NL), 3-aminopropyl triethoxysilane (>98%, Sigma Aldrich, NL),
pyromellitic dianhydride (PMDA) (97%, Sigma Aldrich, NL),
melamine (MA) (99%, Sigma Aldrich, NL), Brilliant Yellow (70%,
Sigma Aldrich, NL), and Rhodamine B (>99%, Merck, NL) were used
as received. The chemical structures and abbreviations can be found
in Figure S1 of the Supporting Information. g
pp
g
Support Fabrication. The α-alumina (α-Al2O3 > 99%) flat-sheet
substrates (disc: diameter, 21 mm; thickness, 2 mm; pore diameter,
80 nm) with one polished side were purchased from Pervatech B.V.,
the Netherlands. The polished side was dip-coated with a boehmite
sol (prepared in-house) and subsequently calcined at 650 °C for 3 h
to form a γ-alumina layer of 1.5 μm in total thickness and 5.5 nm in
mean pore diameter. Further details for the fabrication of the γ-
alumina layer can be found elsewhere.23,49 The calcined supports were
washed by immersion in a 2:1 v/v water/ethanol solution for at least 8
h at room temperature and then dried overnight in a vacuum oven at
50 °C. Figure 5. ■CONCLUSIONS In this work, PI networks were confined in mesoporous
inorganic layers by top or inner pore surface-induced
polyimidization. By prefunctionalizing the top surface of the
support, the polymeric network was confined at the top and
entrance of the pores. Inner pore surface functionalization led
to a homogeneous polymer distribution throughout the
functionalized ceramic layer. The two monomers employed,
MA and PMDA, allowed the formation of a cross-linked and,
thus, chemically resistant PI network inside the top layer of the
ceramic support. By tuning the reaction time, we showed that
the nanoconfinement of the polymer could also be effectively
tuned. All these membranes were scrutinized through a series
of characterization techniques, including SEM, FTIR, and pore
diameter measurements, to demonstrate the influence of the
applied methodology on their structure and final physico-
chemical properties. The as-prepared PI-nanoconfined mem-
branes showed attractive separation performance with good
retention of Rhodamine B (479 g mol−1) in water and different
organic solvents. At this moment, we do not foresee how to
measure the resulting molecular weight of these nanoconfined
PI networks, that we expect to be very small. This will be the
object. pp
g
Prefunctionalization of the γ-Alumina Layer’s Inner Pore
Surface. Under an inert atmosphere in a 50 mL reaction vessel
charged with 40 mg (0.18 mmol) of PMDA, 20 mL of mesitylene was
added and stirred for 1−2 min. A sample was then immersed in the
solution, and the mixture was heated to 160 °C overnight. The
mixture was cooled to room temperature, and the sample was washed
with n-methyl-2-pyrrolidone (NMP) and acetone in a sonicated bath
for 30 min. Finally, the sample (denoted as B) was dried in a vacuum
oven at 50 °C overnight. g
Pore Surface-Induced Polyimidization Reaction. In a 50 mL
reaction vessel, 530 mg (2.43 mmol) of PMDA and 260 mg (2.06
mmol) MA were added. Under an inert atmosphere, 9 mL of
anhydrous NMP, 9 mL of mesitylene, and 0.9 mL of isoquinoline
were added in the reaction vessel and stirred for a few minutes. Afterward, the prefunctionalized sample (A or B) was added in the
mixture and was heated to 200 °C for either 1 or 5 days. After the
reaction was completed, the dark brown mixture was cooled to room
temperature, and the membrane was removed from the solution and
washed with 20 mL of NMP in a sonicated bath for 1 h. ACS Applied Nano Materials These
preliminary results indicate that the polymer concentration is
increasing with increasing reaction time (A-5 and B-5), but the
location where the polymer concentration is increased depends
on the prefunctionalization of the support. This means that for
route A, the polymer grows only at the top surface and pore
entrance, influencing positively the retention of the membrane
but evidently leaving the water permeability unaffected. On the
other hand, for route B, the polymer grows in the whole or part
of the γ-alumina layer, as also indicated by EDS analysis. Hence, from this series of water permeation tests accompanied
with permporometry, HR-SEM, and EDS analyses, we have
clearly evidenced that in the synthesis of PI-nanoconfined
membranes, the prefunctionalization step controls the extent of
polymerization inside the mesoporous support. To conclude, a comparison between different membranes
from the literature with the A-5 membrane samples is shown in
Figure 5. Evidently, A-5 is a potentially interesting membrane
with permeabilities in different solvents between 1 and 1.6 L
m−2 h−1 bar−1 and retentions in the NF range (479 g mol−1). However, since the water permeability of the pristine γ-alumina
supported on α-alumina (4−5 L m−2 h−1 bar−1) is relatively
low, we expect that utilizing supports with a thinner
intermediate layer, for example, of nanometer thickness, as
well as an α-alumina support with a larger pore diameter and
higher porosity can potentially improve the membrane
performance even further. 14042 Figure 5. Comparison of the best-performing membrane from this
work (A-5) with other membranes reported in the literature (solvents
and Mw of dyes studied are given in brackets).24,42−44 Membrane A-5
was tested in different solvents including water, IPA, EtOH, DMF,
and dioxane with RB (479 Da) as solute to ensure a good comparison
with the literature. The membranes used in this figure are similar in
terms of the support or the membrane layer used. ACS Applied Nano Materials ACS Applied Nano Materials Article Article www.acsanm.org ACS Applied Nano Materials ■METHODS Comparison of the best-performing membrane from this
work (A-5) with other membranes reported in the literature (solvents
and Mw of dyes studied are given in brackets).24,42−44 Membrane A-5
was tested in different solvents including water, IPA, EtOH, DMF,
and dioxane with RB (479 Da) as solute to ensure a good comparison
with the literature. The membranes used in this figure are similar in
terms of the support or the membrane layer used. Prefunctionalization of the Top Surface and Pore Entrance. The γ-alumina layer was first filled with 1−2 mL of glycerol by
rubbing the viscous liquid onto the surface and letting it soak for >10
min. The top surface of the substrate was dabbed clean with a fiberless
tissue. Then, 21 μL of 3-aminopropyl trimethoxysilane (APTES) was
dissolved in anisole (anhydrous) and transferred into a reaction vessel
with the glycerol-filled γ-alumina layer suspended above the solution. The solution was heated to 105 °C for 3 h in a sealed vessel. After
grafting, the functionalized porous support was washed with 20 mL of
anisole for 1 h and 20 mL of water for 20 min under sonication and
dried overnight at 50 °C under vacuum. Amino-functionalized
supports, obtained at this stage, were denoted as A. https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 ■CONCLUSIONS Then, the
membrane was immersed in 20 mL of fresh NMP and left for 3 days
at room temperature to remove unreacted monomers or ungrafted
polymer. Finally, the membrane was sonicated in 20 mL of acetone
and dried in a vacuum oven at 50 °C overnight. Membrane samples
prepared via route A (Scheme 1) are denoted as A-1 and A-5 (or A-1/
5) respectively for 1 and 5 days of reaction. Samples prepared via
route B (Scheme 1) are denoted as B-1 and B-5 (or B-1/5). The principal asset of the work presented here relies on a
demonstration of a method allowing control of the polymer-
ization of a cross-linked polymer inside the confined space of
the 5.5 nm pores of the γ-alumina layer for the preparation of
hybrid NF membranes. This work is a forerunner for confining
polymers in nanoporous substrates and regulating the location
of the polymer growth. We assume that this method can be
used to grow polymers with even higher chemical resistance,
such as polybenzimidazoles, by using a similar preparation
method as for polyimides. Furthermore, this method can be
advantageously used as a tool in other fields to confine cross-
linked polymers with low processability inside rigid supports to
form, for example, low-density, high-strength, and thermally
conductive nanocomposites for microelectronic insulation45−47
or anticorrosion coatings.48 After the preparation of each membrane, the remaining reaction
solution was collected and filtered under vacuum to yield a dark
brown powder. These powders were then washed with 50 mL of
NMP and 50 mL of acetone. Finally, the powders were dried in a
vacuum oven at 50 °C overnight. Powder samples collected from the 14043 ACS Applied Nano Materials www.acsanm.org Article solution are denoted as I-1 and I-5. Detailed information on the
spectroscopic characterization of the PI powders can be found in the
SI samples; X-ray diffraction analysis data; cyclohexane
pore radius measurement of grafted samples; high-
resolution SEM images of the pristine support; EDS raw
data of synthesized membrane samples (PDF) Material Characterization. Fourier transform infrared spectros-
copy (FTIR) measurements on both membrane and powder samples
were done using a PerkinElmer UATR Spectrum Two. Wavenumbers
between 4000 and 550 cm−1 were scanned in reflectance mode at a
resolution of 4 cm−1 for a minimum of 16 scans. ■CONCLUSIONS Powder X-ray
diffraction (XRD) patterns were recorded using a PANanalytical
X’Pert PRO diffractometer at the wavelength of Cu Kα (λ = 1.5405 Å)
(X-ray power: 40 kV, 40 mA) in Bragg−Brentano scanning mode. The program scanned angles (2θ) from 5 to 55° with a 0.026° step
and a step time of 158 s. Scanning electron microscopy (SEM) images
of powder and membrane samples and energy-dispersive X-ray
spectroscopy (EDS) were obtained using a JEOL JSM-6010LA
scanning electron microscope using an accelerating voltage of 5 kV. SEM samples were sputtered with 5 nm of palladium/platinum layer
to avoid sample charging. High-resolution scanning electron
microscopy (HR-SEM) micrographs of membrane samples were
obtained with a Hitachi S-4800 field-emission scanning electron
microscope (Japan) using an accelerating voltage of 2 kV. Samples
were metallized with platinum to favor charge release. The change in
the pore diameter of the membrane samples was determined by
permporometry using cyclohexane as condensable vapor. The
experimental procedure is described in detail elsewhere.49 Water
contact angles were measured using the sessile drop method with 2
μL drops of Milli-Q water. Atomic force microscopy (AFM) imaging
was carried out in intermittent-contact mode in air with AFM
instrument Bruker Dimension ICON. The average roughness profile
of the samples was determined by imaging 1 μm2 of each sample. ■ACKNOWLEDGMENTS Özlem Kap from the Physic of Complex Fluids is acknowl-
edged for the AFM analysis. Bernard Fraisse from the Institut
Charles Gerhardt, Montpellier, France, and Karin Nieuwen-
huijzen from the Inorganic Material Science group at the
University of Twente are acknowledged for XRD and capillary
measurements, respectively. Our special thanks go also to
Didier Cot from Institut Européen des Membranes in
Montpellier, France, for the SEM observations of the
membrane samples. Author Contributions N.K. designed and performed the experiments and wrote part
of the paper. M.-A.P.-Z. supervised the project, helped with
understanding the results, and wrote part of the paper. M.D. provided important feedback on the manuscript and the
figures. S.d.B. provided feedback on the manuscript and
figures. A.N. is head of the group and provided important
feedback on the work. L.W. supervised the whole project with
weekly feedback and provided detailed scientific input during
the progress of the project. =
−
R
c
c
1
/
p
f =
−
R
c
c
1
/
p
f
(1) (1) where cp and cf are the permeate and feed solute concentrations,
respectively. Retention samples were obtained at recoveries between
35 and 50%. The dye adsorption during retention measurements was
calculated with the equation Corresponding Authors Louis Winnubst −Inorganic Membranes, MESA+ Institute for
Nanotechnology, University of Twente, 7500 AE Enschede,
The Netherlands;
orcid.org/0000-0003-0362-1585;
Email: a.j.a.winnubst@utwente.nl Marie-Alix Pizzoccaro-Zilamy −Inorganic Membranes,
MESA+ Institute for Nanotechnology, University of Twente,
7500 AE Enschede, The Netherlands;
orcid.org/0000-
0003-2496-099X; Email: m.d.pizzoccaro@utwente.nl Notes The authors declare no competing financial interest. Complete contact information is available at:
https://pubs.acs.org/10.1021/acsanm.1c03322 Complete contact information is available at:
https://pubs.acs.org/10.1021/acsanm.1c03322 Authors Nikos Kyriakou −Inorganic Membranes, MESA+ Institute for
Nanotechnology, University of Twente, 7500 AE Enschede,
The Netherlands Martin Drobek −Institut Européen des Membranes,
UMR5635, CNRS-UM-ENSCM, Université de Montpellier
(CC047), 34095 Montpellier, France Sissi de Beer −Sustainable Polymer Chemistry Group,
Department of Molecules and Materials, MESA+ Institute for
Nanotechnology, University of Twente, 7500 AE Enschede,
The Netherlands;
orcid.org/0000-0002-7208-6814 Membrane Performance. Permeability and retention data were
collected with a custom-made, dead-end filtration setup connected via
a pressure regulator valve to a nitrogen tank for pressurizing the
solutions. Permeability (L m−2 h−1 bar−1) is expressed as the flux (L
h−1) of water or a solvent across a membrane per unit of driving force
per square meter of exposed membrane area (2.4 cm2). Flux data were
collected by weighing the mass of the permeate at four-time intervals,
while permeability was determined from flux data at three applied
transmembrane pressures between 8 and 20 bar by taking the slope of
a linear fit of the collected flux data. All slopes were found to be linear
unless otherwise noted. Retentions (R) of Brilliant Yellow (BY, Mw =
624.55 g mol−1, 50 ppm) and Rhodamine B (RB, Mw = 479.02 g
mol−1, 50 ppm) were calculated with the equation Arian Nijmeijer −Inorganic Membranes, MESA+ Institute for
Nanotechnology, University of Twente, 7500 AE Enschede,
The Netherlands (2) where MAds is the amount of dye adsorbed on each membrane, Mf is
the total amount of dye used at the beginning of each separation test
(feed solution), MR is the amount of dye in the retentate, and Mp is
the amount of dye in the permeate. In all cases, the dye concentration
of BY and RB was increased in the retentate to account for limited
adsorption of 2−3% for the PI-nanoconfined ceramic membranes. Solute concentrations of BY and RB were calculated from
PerkinElmer λ12 UV−Vis spectrophotometer results at the character-
istic wavelengths of 401.5 (BY), 543 (RB/water), 554 (RB/water and
RB/1,4-dioxane), and 560 (RB/DMF) nm. Funding =
−
+
M
M
M
M
Ads
f
R
p
(2) This work is part of the research program entitled “Solvent
Tolerant Nanofiltration and reverse osmosis membranes for
the purification of industrial aqueous streams” (STNF), which
is taking place within the framework of the Institute for
Sustainable Process Technology (ISPT, project no. BL-20-12). Notes (2) https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 ■REFERENCES Stöber-Solution Pore-Growth Approach. ACS Appl. Mater. Interfaces
2019, 11, 18528−18539. (1) Sholl, D. S.; Lively, R. P. Seven Chemical Separations to Change
the World. Nature 2016, 532, 435−437. (20) Home - inopor −the cutting edge of nano-filtrationhttps://
www.inopor.com/en/ (accessed Nov 19, 2021). (2) Marchetti, P.; Solomon, M. F. J.; Szekely, G.; Livingston, A. G. Molecular Separation with Organic Solvent Nanofiltration: A Critical
Review. Chem. Rev. 2014, 114, 10735−10806. p
(21) Pervaporation Membranes by Pervatechhttps://pervaporation-
membranes.com/(accessed Nov 19, 2021). (22) Abedini, S.; Parvin, N.; Ashtari, P.; Jazi, F. S. Microstructure,
Strength and CO2 Separation Characteristics of α-Alumina Supported
γ-Alumina Thin Film Membrane. Adv. Appl. Ceram. 2013, 112, 17−
22. ,
,
(3) Vandezande, P.; Gevers, L. E. M.; Vankelecom, I. F. J. Solvent Resistant Nanofiltration: Separating on a Molecular Level. Chem. Soc. Rev. 2008, 37, 365−405. (4) Merlet, R. B.; Pizzoccaro-Zilamy, M. A.; Nijmeijer, A.; Winnubst,
L. Hybrid Ceramic Membranes for Organic Solvent Nanofiltration:
State-of-the-Art and Challenges. J. Membr. Sci. 2020, 117839. (23) Uhlhorn, R. J. R.; Veld, M. H. B. J. H. I.; Keizer, K.; Burggraaf,
A. J. Synthesis of Ceramic Membranes. J. Mater. Sci. 1992, 27, 527−
537. (5) Volkov, A. V.; Parashchuk, V. V.; Stamatialis, D. F.; Khotimsky,
V. S.; Volkov, V. V.; Wessling, M. High Permeable PTMSP/PAN
Composite Membranes for Solvent Nanofiltration. J. Memb. Sci. 2009,
333, 88−93. (24) Kyriakou, N.; Merlet, R. B.; Willott, J. D.; Nijmeijer, A.;
Winnubst, L.; Pizzoccaro-Zilamy, M.-A. New Method toward a
Robust Covalently Attached Cross-Linked Nanofiltration Membrane. ACS Appl. Mater. Interfaces 2020, 12, 47948−47956. (6) Darvishmanesh, S.; Van der Bruggen, B. Mass Transport through
Nanostructured Membranes: Towards a Predictive Tool. Membranes
2016, 6, 49. (25) Kyriakou, N.; Pizzoccaro-Zilamy, M.-A.; Nijmeijer, A.; Luiten-
Olieman, M.; Winnubst, L. Hydrolytic Stability of PEG-Grafted γ-
Alumina Membranes: Alkoxysilane vs Phosphonic Acid Linking
Groups. Microporous Mesoporous Mater. 2020, 307, 110516. (7) Baumgartner, B.; Puchberger, M.; Unterlass, M. M. Towards a
General Understanding of Hydrothermal Polymerization of Poly-
imides. Polym. Chem. 2015, 6, 5773−5781. p
p
p
(26) Tanardi, C. R.; Pinheiro, A. F. M.; Nijmeijer, A.; Winnubst, L. (26) Tanardi, C. R.; Pinheiro, A. F. M.; Nijmeijer, A.; Winnubst, L. PDMS Grafting of Mesoporous γ-Alumina Membranes for Nano-
filtration of Organic Solvents. J. Memb. Sci. 2014, 469, 471−477. (8) Vanherck, K.; Koeckelberghs, G.; Vankelecom, I. F. J. Crosslinking Polyimides for Membrane Applications: A Review. Prog. Polym. Sci. 2013, 38, 874−896. ■REFERENCES J.; Lin, L.; Deng, X.; Zheng, T.; Wang, Q.;
Gao, Y.; Zhang, Y. Bioinspired: A 3D Vertical Silicon Sponge-Inspired
Construction of Organic-Inorganic Loose Mass Transfer Nano-
channels for Enhancing Properties of Polyimide Nanofiltration
Membranes. Sep. Purif. Technol. 2021, 259, 118038. (14) Qiang, R.; Wei, C. J.; Lin, L.; Deng, X.; Zheng, T.; Wang, Q.;
Gao, Y.; Zhang, Y. Bioinspired: A 3D Vertical Silicon Sponge-Inspired (32) Tena, A.; Marcos-Fernández, A.; Lozano, A. E.; de la Campa, J. G.; de Abajo, J.; Palacio, L.; Prádanos, P.; Hernández, A. Thermally
Treated Copoly(Ether-Imide)s Made from Bpda and Alifatic plus
Aromatic Diamines. GAS Separation Properties with Different
Aromatic Diamimes. J. Memb. Sci. 2012, 387-388, 54−65. g
p
p
g
p
Construction of Organic-Inorganic Loose Mass Transfer Nano-
channels for Enhancing Properties of Polyimide Nanofiltration
Membranes. Sep. Purif. Technol. 2021, 259, 118038. p
f
(15) Mueller, N. C.; Van der Bruggen, B.; Keuter, V.; Luis, P.; Melin,
T.; Pronk, W.; Reisewitz, R.; Rickerby, D.; Rios, G. M.; Wennekes,
W
Nowack B Nanofiltration and Nanostructured Membranes (15) Mueller, N. C.; Van der Bruggen, B.; Keuter, V.; Luis, P.; Melin,
T.; Pronk, W.; Reisewitz, R.; Rickerby, D.; Rios, G. M.; Wennekes,
W.; Nowack, B. Nanofiltration and Nanostructured Membranes
Should They Be Considered Nanotechnology or Not? J. Hazard. (15) Mueller, N. C.; Van der Bruggen, B.; Keuter, V.; Luis, P.; Melin,
T.; Pronk, W.; Reisewitz, R.; Rickerby, D.; Rios, G. M.; Wennekes,
W.; Nowack, B. Nanofiltration and Nanostructured Membranes (33) Pinheiro, A. F. M.; Hoogendoorn, D.; Nijmeijer, A.; Winnubst,
L. Development of a PDMS-Grafted Alumina Membrane and Its
Evaluation as Solvent Resistant Nanofiltration Membrane. J. Memb. Sci. 2014, 463, 24−32. Should They Be Considered Nanotechnology or Not? J. Hazard. Mater. 2012, 211-212, 275−280. (16) Isaacson, S. G.; Lionti, K.; Volksen, W.; Magbitang, T. P.;
Matsuda, Y.; Dauskardt, R. H.; Dubois, G. Fundamental Limits of
Material Toughening in Molecularly Confined Polymers. Nat. Mater. 2016, 15, 294−298. (34) Mircescu, N. E.; Oltean, M.; Chis, V.; Leopold, N. FTIR, FT-
Raman, SERS and DFT Study on Melamine. Vib. Spectrosc. 2012, 62,
165−171. (35) Li, Z.; Zhou, J.; Xu, R.; Liu, S.; Wang, Y.; Li, P.; Wu, W.; Wu,
M. Synthesis of Three Dimensional Extended Conjugated Polyimide
and Application as Sodium-Ion Battery Anode. Chem. Eng. J. 2016,
287, 516−522. (17) Isaacson, S. G.; Fostvedt, J. I.; Koerner, H.; Baur, J. W.; Lionti,
K.; Volksen, W.; Dubois, G.; Dauskardt, R. H. ACS Applied Nano Materials ACS Applied Nano Materials Article Article www.acsanm.org ■REFERENCES (27) Merlet, R.; Winnubst, L.; Nijmeijer, A.; Amirilargani, M.;
Sudhölter, E. J. R.; Smet, L. C. P. M. d.; Cob, S. S.; Vandezande, P.;
Dorbec, M.; Sluijter, S.; Veen, H. v.; VanDelft, Y.; Wienk, I.; Cuperus,
P.; Behera, S.; Hartanto, Y.; Vankelecom, I. F. J.; Wit, P. d. Comparing
the Performance of Organic Solvent Nanofiltration Membranes in
Non-Polar Solvents. Chemie Ing. Tech. 2021, 93, 1389−1395. g
y
(9) Product overview - PuraMem® Membranes for organic solvent
nanofiltration (OSN) - Evonik Industries https://www.membrane-
separation.com/en/organic-solvent-nanofiltration-with-puramem-
duramem/product-overview (accessed Jun 9, 2021). duramem/product-overview (accessed Jun 9, 2021). (
) (10) Cai, D.; Su, J.; Huang, M.; Liu, Y.; Wang, J.; Dai, L. Synthesis,
Characterization and Hydrolytic Stability of Poly (Amic Acid)
Ammonium Salt. Polym. Degrad. Stab. 2011, 96, 2174−2180. g
(28) Sun, C.; Zhou, F.; Shi, L.; Yu, B.; Gao, P.; Zhang, J.; Liu, W. Tribological Properties of Chemically Bonded Polyimide Films on
Silicon with Polyglycidyl Methacrylate Brush as Adhesive Layer. Appl. Surf. Sci. 2006, 253, 1729−1735. y
g
(11) Morikawa, A.; Iyoku, Y.; Kakimoto, M.-A.; Imai, Y. Preparation
of a New Class of Polyimide-Silica Hybrid Films by Sol-Gel Process. Polym. J. 1992, 24, 107. (29) Amirilargani, M.; Merlet, R. B.; Chu, L.; Nijmeijer, A.;
Winnubst, L.; de Smet, L. C. P. M.; Sudhölter, E. J. R. Molecular
Separation Using Poly (Styrene-Co-Maleic Anhydride) Grafted to γ-
Alumina: Surface versus Pore Modification. J. Memb. Sci. 2019, 582,
298−306. (12) Kuttiani Ali, J.; Maher Chabib, C.; Abi Jaoude, M.; Alhseinat,
E.; Teotia, S.; Patole, S.; Hussain Anjum, D.; Qattan, I. Enhanced
Removal of Aqueous Phenol with Polyimide Ultrafiltration Mem-
branes Embedded with Deep Eutectic Solvent-Coated Nanosilica. Chem. Eng. J. 2021, 408, 128017. (30) Coates, J. Interpretation of Infrared Spectra, A Practical
Approach. In Encyclopedia of Analytical Chemistry; John Wiley & Sons,
Ltd:
Chichester,
UK,
2006. doi:
DOI:
10.1002/
9780470027318.a5606. g
(13) Wei, C.; Qiang, R.; Lin, L.; Gao, Y.; Ma, S.; Zhang, X.; Huang,
X. Combing Three-Dimensional Water Channels and Ultra-Thin Skin
Layer Enable High Flux and Stability of Loose Polyimide/SiO2
Nanofiltration Membranes at Low Operating Pressure via One Step
in-Situ Modification. J. Memb. Sci. 2021, 623, 118944. (31) Merlet, R. B.; Amirilargani, M.; de Smet, L. C. P. M.; Sudhölter,
E. J. R.; Nijmeijer, A.; Winnubst, L. Growing to Shrink: Nano-
Tunable Polystyrene Brushes inside 5 Nm Mesopores. J. Memb. Sci. 2019, 572, 632−640. (14) Qiang, R.; Wei, C. *
sı Supporting Information * Supporting Information
The Supporting Information is available free of charge at
https://pubs.acs.org/doi/10.1021/acsanm.1c03322. Chemical structures of compounds used; complete FTIR
spectra of the starting compounds and synthesized 14044 https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 ■REFERENCES Synthesis of Polyimides
in Molecular-Scale Confinement for Low-Density Hybrid Nano-
composites. Nano Lett. 2017, 17, 7040−7044. (36) Wang, Y.; Gao, Q.; You, Q.; Liao, G.; Xia, H.; Wang, D. Porous
Polyimide Framework: A Novel Versatile Adsorbent for Highly
Efficient Removals of Azo Dye and Antibiotic. React. Funct. Polym. 2016, 103, 9−16. p
(18) Liu, G.; Müller, A. J.; Wang, D. Confined Crystallization of
Polymers within Nanopores. Acc. Chem. Res. 2021, 54, 3028−3038. (19) Pizzoccaro-Zilamy, M.-A.; Huiskes, C.; Keim, E. G.; Sluijter, S. N.; van Veen, H.; Nijmeijer, A.; Winnubst, L.; Luiten-Olieman, M. W. (37) Sadhasivam, B.; Muthusamy, S. Synthesis and Characterization
of Optically Active Polyimides and Their Octa(Aminophenyl)- J. New Generation of Mesoporous Silica Membranes Prepared by a 14045 https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046 ACS Applied Nano Materials www.acsanm.org Silsesquioxane Nanocomposites. High Perform. Polym. 2016, 28, 547−
561. (38) Kim, H.-J.; Nam, S.-M. High Loading of Nanostructured
Ceramics in Polymer Composite Thick Films by Aerosol Deposition. Nanoscale Res. Lett. 2012, 7, 1. (39) Baumgartner, B.; Bojdys, M. J.; Unterlass, M. M. Geomimetics
for Green Polymer Synthesis: Highly Ordered Polyimides via
Hydrothermal Techniques †. Polym. Chem. 2014, 5, 3771−3776. (40) Duan, H.; Lyu, P.; Liu, J.; Zhao, Y.; Xu, Y. Semiconducting
Crystalline Two-Dimensional Polyimide Nanosheets with Superior
Sodium Storage Properties. ACS Nano 2019, 13, 2473−2480. (41) Hinckley, D. A.; Seybold, P. G.; Borris, D. P. Solvatochromism
and Thermochromism of Rhodamine Solutions. Spectrochim. Acta,
Part A 1986, 42, 747−754. (42) Tanardi, C. R.; Catana, R.; Barboiu, M.; Ayral, A.; Vankelecom,
I. F. J.; Nijmeijer, A.; Winnubst, L. Polyethyleneglycol Grafting of Y-
Alumina Membranes for Solvent Resistant Nanofiltration. Microporous
Mesoporous Mater. 2016, 229, 106−116. (43) Tanardi, C. R.; Nijmeijer, A.; Winnubst, L. Coupled-PDMS
Grafted Mesoporous γ-Alumina Membranes for Solvent Nano-
filtration. Sep. Purif. Technol. 2016, 169, 223−229. (44) Li, X.; Vandezande, P.; Vankelecom, I. F. J. Polypyrrole
Modified Solvent Resistant Nanofiltration Membranes. J. Memb. Sci. 2008, 320, 143−150. (45) Zhou, Y.; Chen, Y.; Wang, H.; Wong, C. P. Creation of a
Multilayer Aluminum Coating Structure Nanoparticle Polyimide
Filler for Electronic Applications. Mater. Lett. 2014, 119, 64−67. (46) Zhou, Y.; Bai, Y.; Yu, K.; Kang, Y.; Wang, H. Excellent Thermal
Conductivity and Dielectric Properties of Polyimide Composites
Filled with Silica Coated Self-Passivated Aluminum Fibers and
Nanoparticles. Appl. Phys. Lett. 2013, 102, 252903. (47) Li, X.; Dong, G.; Liu, Z.; Zhang, X. ■REFERENCES Polyimide Aerogel Fibers
with Superior Flame Resistance, Strength, Hydrophobicity, and
Flexibility Made via a Universal Sol−Gel Confined Transition
Strategy. ACS Nano 2021, 15, 4759. (48) Hicyilmaz, A. S.; Bedeloglu, A. C. Applications of Polyimide
Coatings: A Review. SN Appl. Sci. 2021, 3, 363. (49) Cuperus, F. P.; Bargeman, D.; Smolders, C. A. Permporometry:
The Determination of the Size Distribution of Active Pores in UF
Membranes. J. Memb. Sci. 1992, 71, 57−67. https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046
4046 14046 https://doi.org/10.1021/acsanm.1c03322
ACS Appl. Nano Mater. 2021, 4, 14035−14046
|
https://openalex.org/W4366339229
|
https://essd.copernicus.org/preprints/essd-2022-439/essd-2022-439.pdf
|
English
| null |
Reply on RC1
| null | 2,023
|
cc-by
| 15,916
|
The UKSCAPE-G2G river flow and soil moisture datasets:
1
Grid-to-Grid model estimates for the UK for historical and
2
potential future climates
3 Alison L Kay, Victoria A Bell, Helen N Davies, Rosanna A Lane, Alison C
4 UK Centre for Ecology & Hydrology, Wallingford, UK, OX10 8BB
6 Correspondence to: A.L. Kay (alkay@ceh.ac.uk)
7 Abstract
8 Appropriate adaptation planning is contingent upon information about the potential
9
future impacts of climate change, and hydrological impact assessments are of
10
particular importance. The UKSCAPE-G2G datasets were produced, as part of the
11
NERC UK-SCAPE programme, to contribute to this information requirement. They
12
use the Grid-to-Grid (G2G) national-scale hydrological model configured for both
13
Great Britain and Northern Ireland (and the parts of the Republic of Ireland that drain
14
to rivers in NI). Six separate datasets are provided, for two sets of driving data —
15
one observation-based (1980–2011) and one climate projection-based (1980–2080)
16
— for both river flows and soil moisture on 1 km x 1 km grids across GB and NI. The
17
river flow datasets include grids of monthly mean flow, annual maxima of daily mean
18
flow, and annual minima of 7-day mean flow (m3s-1). The soil moisture datasets are
19
grids of monthly mean soil moisture content (m water / m soil), which should be
20
interpreted as depth-integrated values for the whole soil column. The climate
21
projection-based datasets are produced using data from the 12-member 12km
22
regional climate model ensemble of the latest UK climate projections (UKCP18),
23
which uses RCP8.5 emissions. The production of the datasets is described, along
24
with details of the file format, and how the data should be used. Example maps are
25
provided, as well as simple UK-wide analyses of the various outputs. These suggest
26
potential future decreases in summer flows, annual minimum 7-day flows, and
27
summer/autumn soil moisture, along with possible future increases in winter flows
28
and annual maximum flows. References are given for published papers providing
29
more detailed spatial analyses, and some further potential uses of the data are
30
suggested. 31 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. Keywords
32 Climate change; hydrological impacts; rainfall-runoff; UK Climate Projections 2018;
33
UKCP18
34 Climate change; hydrological impacts; rainfall-runoff; UK Climate Projections 2018;
33
UKCP18
34 1 Introduction
35 Information on the potential future impacts of climate change is crucial to enable
36
appropriate adaptation planning, and impacts on the hydrological cycle and river
37
flows are one of the main ways by which climate change will affect both society and
38
the natural environment. UK-SCAPE (UK Status, Change And Projections of the
39
Environment; ukscape.ceh.ac.uk) is a five-year programme funded by the Natural
40
Environment Research Council (NERC) as part of a National Capability Science
41
Single Centre award, and the main aim of Work Package 2.2 of UK-SCAPE is to
42 Information on the potential future impacts of climate change is crucial to enable
36
appropriate adaptation planning, and impacts on the hydrological cycle and river
37
flows are one of the main ways by which climate change will affect both society and
38
the natural environment. UK-SCAPE (UK Status, Change And Projections of the
39
Environment; ukscape.ceh.ac.uk) is a five-year programme funded by the Natural
40
Environment Research Council (NERC) as part of a National Capability Science
41
Single Centre award, and the main aim of Work Package 2.2 of UK-SCAPE is to
42 1 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. deliver data and analyses showing how future climate change could influence water
43
quantity. The hydrological datasets presented here were produced as part of UK-
44
SCAPE WP2.2. 45
The datasets consist of 1 km x 1 km gridded outputs from a national-scale
46
hydrological model (Grid-to-Grid), and include both river flows and soil moisture, for
47
Great Britain (GB) and Northern Ireland (NI). The model has been driven with
48
observation-based data, and with an ensemble of Regional Climate Model (RCM)
49
data from the latest climate projections for the UK (UKCP18; Lowe et al. 2018). A
50
summary of the six available datasets, including references, is provided in Table 1. 51
The datasets have been used within UK-SCAPE WP2.2 to support analyses of
52
potential future changes in river flows and soil moisture (Kay 2021, Lane & Kay
53
2021, Kay et al. 2021a, Kay et al. 2022a), but could also be used to support other
54
hydrological research and wider studies such as ecological and agricultural
55
modelling. 1 Introduction
35 56
Section 2 describes how the datasets were produced, including the hydrological
57
model and the driving data applied. Section 3 presents some high level analyses of
58
the datasets, and describes the results of more detailed analyses presented in other
59
published papers. Section 4 discusses potential uses and caveats, with conclusions
60
in Section 5. 61
62
Table 1 Summary of the six UKSCAPE-G2G datasets. 63
Observation-driven
River flow
GB:
https://doi.org/10.5285/2f835517-253e-4697-b774-ab6ff2c0d3da
(Kay et al. 2021c)
NI:
https://doi.org/10.5285/f5fc1041-e284-4763-b8b7-8643c319b2d0
(Kay et al. 2021d)
Soil moisture
GB
and
NI:
https://doi.org/10.5285/c9a85f7c-45e2-4201-af82-
4c833b3f2c5f (Kay et al. 2021e)
Climate projection-driven
River flow
GB: https://doi.org/10.5285/18be3704-0a6d-4917-aa2e-bf38927321c5
(Kay et al. 2022b)
NI:
https://doi.org/10.5285/76057b0a-b18f-496f-891c-d5b22bd0b291
(Kay et al. 2022c)
Soil moisture
GB
and
NI:
https://doi.org/10.5285/f7142ced-f6ff-486b-af33-
44fb8f763cde (Kay et al. 2022d) Table 1 Summary of the six UKSCAPE-G2G datasets. 63
Observation-driven
River flow
GB:
https://doi.org/10.5285/2f835517-253e-4697-b774-ab6ff2c0d3da
(Kay et al. 2021c)
NI:
https://doi.org/10.5285/f5fc1041-e284-4763-b8b7-8643c319b2d0
(Kay et al. 2021d)
Soil moisture
GB
and
NI:
https://doi.org/10.5285/c9a85f7c-45e2-4201-af82-
4c833b3f2c5f (Kay et al. 2021e)
Climate projection-driven
River flow
GB: https://doi.org/10.5285/18be3704-0a6d-4917-aa2e-bf38927321c5
(Kay et al. 2022b)
NI:
https://doi.org/10.5285/76057b0a-b18f-496f-891c-d5b22bd0b291
(Kay et al. 2022c)
Soil moisture
GB
and
NI:
https://doi.org/10.5285/f7142ced-f6ff-486b-af33-
44fb8f763cde (Kay et al. 2022d) 64 2.2 Observation-based driving data
91 Gridded time-series of precipitation and potential evaporation (PE) are required to
92
drive the G2G, plus temperature for the snow module. The observation-based driving
93
data are applied as follows:
94 Daily 1km grids of precipitation (CEH-GEAR; Tanguy et al. 2016) are divided
95
equally over each model time-step within a day. For use in NI they are first re-
96
projected from the Irish national grid to the GB national grid. 97 Monthly 40km grids of PE for short grass (MORECS; Hough and Jones 1997) are
98
copied down to the 1km grid, then divided equally over each model time-step
99
within a month. For use in NI they are first re-projected from the Irish national grid
100
to the GB national grid. The data do not cover all the required parts of the UK, so
101
have been extended where necessary (i.e. some coastal areas and some parts of
102
the RoI that drain into NI) by copying from the nearest cell with data. 103 Daily 1km grids of min and max temperature (Met Office 2019) are interpolated
104
through the day using a sine curve (Kay and Crooks 2014). The data do not
105
cover the required parts of the RoI, so have been infilled from the nearest cell
106
with data, using a lapse rate with elevation data (Morris and Flavin 1990). 107 2 Data production methods
65 While the effect of urban/suburban land-cover on runoff
82
is accounted for, the effect of lake/reservoir storage and regulation is generally
83
neglected at the national scale; lake grid-cells are treated as though they were rivers. 84
This has a minimal effect across most of GB; the largest lake in Scotland, Loch
85
Lomond, has an area of ~71km2, and the largest lake in England, Windermere, has
86
an area of ~15km2. But in NI the dominant presence of Lough Neagh (~390km2)
87
limits model performance downstream (the Lower Bann river; Kay et al. 2021a), and
88
Lough Erne in the south-west of NI is also relatively large (Upper and Lower Lough
89
Erne have a combined area of ~144km2). 90 2 Data production methods
65 2.1 The hydrological model
66
The Grid-to-Grid (G2G) is a national-scale grid-based hydrological model which
67
typically operates on a 1km x 1km grid at a 15-minute time-step (Bell et al. 2009),
68
with an optional snow module (Bell et al. 2016). It was originally configured to cover
69
Great Britain (GB), on a spatial domain aligned with the GB national grid, but more
70
recently a version was configured to cover Northern Ireland (NI) and areas in the
71
Republic of Ireland (RoI) that drain into NI, also on a domain aligned with the GB
72
national grid (Kay et al. 2021a). The G2G is configured using spatial datasets (e.g. 73
soil types, land-cover, flow directions), in preference to parameter identification via
74 2.1 The hydrological model
66
The Grid-to-Grid (G2G) is a national-scale grid-based hydrological model which
67
typically operates on a 1km x 1km grid at a 15-minute time-step (Bell et al. 2009),
68
with an optional snow module (Bell et al. 2016). It was originally configured to cover
69
Great Britain (GB), on a spatial domain aligned with the GB national grid, but more
70
recently a version was configured to cover Northern Ireland (NI) and areas in the
71
Republic of Ireland (RoI) that drain into NI, also on a domain aligned with the GB
72
national grid (Kay et al. 2021a). The G2G is configured using spatial datasets (e.g. 73
soil types, land-cover, flow directions), in preference to parameter identification via
74 2 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. calibration; where model parameters are required (such as the wave speeds used in
75
lateral routing) nationally-applicable values are applied (Bell et al. 2009). 76 p
q
(
p
lateral routing) nationally-applicable values are applied (Bell et al. 2009). 76
G2G has been shown to perform well for a wide range of catchments across GB and
77
NI, including for the modelling of high flows / floods and low flows / droughts (Bell et
78
al. 2009, 2016; Rudd et al. 2017; Formetta et al. 2018; Kay et al. 2021a,b). This is
79
particularly the case for catchments with more natural flow regimes, as the model
80
does not routinely account for artificial influences like abstractions/discharges
81
(Rameshwaran et al. 2022). The climate projection data are applied as follows:
120 2.3 Climate projection-based driving data
108 The file naming convention is
163
described in Table 2 for the observation-based datasets and Table 3 for the climate
164
projection-based datasets. 165 Daily 12km grids of PE are not directly available from the UKCP18 Regional
128
projections. Instead they are calculated from other meteorological variables in a
129
way which closely replicates MORECS (as in Robinson et al. (2021, 2022), but
130
using the bias-adjusted precipitation in the interception component). PE is only
131
estimated for 12km ‘land’ RCM boxes; where PE is required for boxes classed as
132
‘sea’ in the RCM, it is copied from the nearest 12km ‘land’ box. The method also
133
includes increased stomatal resistance under future higher atmospheric CO2
134
concentrations (Rudd and Kay 2016, Guillod et al. 2018). The 12km PE are
135
copied down to the 1km grid, then divided equally over each model time-step
136
within a month (as for observed data). 137 Daily 12km grids of min and max temperature are directly available from the
138
UKCP18 Regional projections. These are downscaled to 1km using a lapse rate
139
with elevation data, and interpolated through the day using a sine curve (as for
140
observed data). 141 Daily 12km grids of min and max temperature are directly available from the
138
UKCP18 Regional projections. These are downscaled to 1km using a lapse rate
139
with elevation data, and interpolated through the day using a sine curve (as for
140
observed data). 141 Daily 12km grids of min and max temperature are directly available from the
138
UKCP18 Regional projections. These are downscaled to 1km using a lapse rate
139
with elevation data, and interpolated through the day using a sine curve (as for
140
observed data). 141 2.4 Hydrological model runs and outputs
142 annual maxima (AMAX) of daily mean river flow (m3s-1), for water years
149 monthly mean soil moisture content (m water / m soil). 153 2.3 Climate projection-based driving data
108 The climate change simulations use data from the UKCP18 Regional projections
109
(Met Office Hadley Centre 2018). These comprise a 12-member perturbed
110
parameter ensemble (PPE) of the Hadley Centre ~12km Regional Climate Model
111
(RCM) nested in an equivalent PPE of their ~60km Global Climate model (GCM)
112
(Murphy et al. 2018). Ensemble member 01 represents the standard
113
parameterisation, with members 02-15 representing a range of credible variations in
114
parameters (note that there are no RCM equivalents for GCM PPE members 02, 03
115
and 14). The data cover Dec 1980–Nov 2080 under RCP8.5 emissions (Riahi et al. 116
2011), and have a 360-day year (twelve 30-day months). The data are available re-
117
projected from the native climate model grid onto a 12km grid aligned with the GB
118
national grid – the latter are used here. 119 The climate change simulations use data from the UKCP18 Regional projections
109
(Met Office Hadley Centre 2018). These comprise a 12-member perturbed
110
parameter ensemble (PPE) of the Hadley Centre ~12km Regional Climate Model
111
(RCM) nested in an equivalent PPE of their ~60km Global Climate model (GCM)
112
(Murphy et al. 2018). Ensemble member 01 represents the standard
113
parameterisation, with members 02-15 representing a range of credible variations in
114
parameters (note that there are no RCM equivalents for GCM PPE members 02, 03
115
and 14). The data cover Dec 1980–Nov 2080 under RCP8.5 emissions (Riahi et al. 116
2011), and have a 360-day year (twelve 30-day months). The data are available re-
117
projected from the native climate model grid onto a 12km grid aligned with the GB
118
national grid – the latter are used here. 119 The climate projection data are applied as follows:
120 3 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. Daily 12km grids of precipitation are directly available from the UKCP18 Regional
121
projections. These are first adjusted for bias using 12km grids of monthly
122
correction factors derived by comparing baseline values against CEH-GEAR data
123
averaged up to the 12km resolution (Kay 2021, Kay et al. 2021a). They are then
124
spatially downscaled to 1km using patterns of average annual rainfall (1961–
125
1990; Bell et al. 2007), and divided equally over each model time-step within a
126
day (as for observed data). 2.3 Climate projection-based driving data
108 127
Daily 12km grids of PE are not directly available from the UKCP18 Regional
128
projections. Instead they are calculated from other meteorological variables in a
129
way which closely replicates MORECS (as in Robinson et al. (2021, 2022), but
130
using the bias-adjusted precipitation in the interception component). PE is only
131
estimated for 12km ‘land’ RCM boxes; where PE is required for boxes classed as
132
‘sea’ in the RCM, it is copied from the nearest 12km ‘land’ box. The method also
133
includes increased stomatal resistance under future higher atmospheric CO2
134
concentrations (Rudd and Kay 2016, Guillod et al. 2018). The 12km PE are
135
copied down to the 1km grid, then divided equally over each model time-step
136
within a month (as for observed data). 137
Daily 12km grids of min and max temperature are directly available from the
138
UKCP18 Regional projections. These are downscaled to 1km using a lapse rate
139
with elevation data, and interpolated through the day using a sine curve (as for
140
observed data). 141
2.4 Hydrological model runs and outputs
142
The observation-based simulation (hereafter ‘SIMOBS’) is initialised using a states
143
file saved at the end of a prior observation-based run (Jan 1970–Nov 1980). The
144
same state initialisation file is used for each RCM-based simulation (hereafter
145
‘SIMRCM’). 146
Model outputs consist of 1km x 1km gridded time-series of
147
monthly mean river flow (m3s-1);
148
annual maxima (AMAX) of daily mean river flow (m3s-1), for water years
149
(October–September);
150
annual minima (AMIN) of 7-day mean river flow (m3s-1), for years spanning
151
December–November; and
152
monthly mean soil moisture content (m water / m soil). 153
The flow variables are provided for all non-sea and non-tidal 1km cells with a
154
catchment drainage area of at least 50km2, while the soil moisture is provided for all
155
non-sea 1km cells. G2G soil moisture estimates are provided as monthly averages
156
of daily mean soil moisture in the unsaturated zone, which can be interpreted as
157
volumetric soil moisture content, θ, where 0 ≤ θ ≤ 1. In G2G soil depth can vary from
158
a few centimetres to several metres, and soil moisture estimates should be
159
interpreted as depth-integrated values for the whole soil column. 2.3 Climate projection-based driving data
108 160
2.5 Format of the gridded datasets
161
The 1km x 1km gridded data are provided as a NetCDF4 file for each variable,
162
following UKCEH gridded dataset conventions. The file naming convention is
163
described in Table 2 for the observation-based datasets and Table 3 for the climate
164
projection-based datasets. 165 Daily 12km grids of precipitation are directly available from the UKCP18 Regional
121
projections. These are first adjusted for bias using 12km grids of monthly
122
correction factors derived by comparing baseline values against CEH-GEAR data
123
averaged up to the 12km resolution (Kay 2021, Kay et al. 2021a). They are then
124
spatially downscaled to 1km using patterns of average annual rainfall (1961–
125
1990; Bell et al. 2007), and divided equally over each model time-step within a
126
day (as for observed data). 127
Daily 12km grids of PE are not directly available from the UKCP18 Regional
128
projections. Instead they are calculated from other meteorological variables in a
129
way which closely replicates MORECS (as in Robinson et al. (2021, 2022), but
130
using the bias-adjusted precipitation in the interception component). PE is only
131
estimated for 12km ‘land’ RCM boxes; where PE is required for boxes classed as
132
‘sea’ in the RCM, it is copied from the nearest 12km ‘land’ box. The method also
133
includes increased stomatal resistance under future higher atmospheric CO2
134
concentrations (Rudd and Kay 2016, Guillod et al. 2018). The 12km PE are
135
copied down to the 1km grid, then divided equally over each model time-step
136
within a month (as for observed data). 137
Daily 12km grids of min and max temperature are directly available from the
138
UKCP18 Regional projections. These are downscaled to 1km using a lapse rate
139
with elevation data, and interpolated through the day using a sine curve (as for
140
observed data). 141
2.4 Hydrological model runs and outputs
142
The observation-based simulation (hereafter ‘SIMOBS’) is initialised using a states
143
file saved at the end of a prior observation-based run (Jan 1970–Nov 1980). The
144
same state initialisation file is used for each RCM-based simulation (hereafter
145
‘SIMRCM’). 2.3 Climate projection-based driving data
108 146
Model outputs consist of 1km x 1km gridded time-series of
147
monthly mean river flow (m3s-1);
148
annual maxima (AMAX) of daily mean river flow (m3s-1), for water years
149
(October–September);
150
annual minima (AMIN) of 7-day mean river flow (m3s-1), for years spanning
151
December–November; and
152
monthly mean soil moisture content (m water / m soil). 153
The flow variables are provided for all non-sea and non-tidal 1km cells with a
154
catchment drainage area of at least 50km2, while the soil moisture is provided for all
155
non-sea 1km cells. G2G soil moisture estimates are provided as monthly averages
156
of daily mean soil moisture in the unsaturated zone, which can be interpreted as
157
volumetric soil moisture content, θ, where 0 ≤ θ ≤ 1. In G2G soil depth can vary from
158
a few centimetres to several metres, and soil moisture estimates should be
159
interpreted as depth-integrated values for the whole soil column. 160
2.5 Format of the gridded datasets
161
The 1km x 1km gridded data are provided as a NetCDF4 file for each variable,
162
following UKCEH gridded dataset conventions. The file naming convention is
163
described in Table 2 for the observation-based datasets and Table 3 for the climate
164
projection-based datasets. 165 Daily 12km grids of precipitation are directly available from the UKCP18 Regional
121
projections. These are first adjusted for bias using 12km grids of monthly
122
correction factors derived by comparing baseline values against CEH-GEAR data
123
averaged up to the 12km resolution (Kay 2021, Kay et al. 2021a). They are then
124
spatially downscaled to 1km using patterns of average annual rainfall (1961–
125
1990; Bell et al. 2007), and divided equally over each model time-step within a
126
day (as for observed data). 127 y
g
p
p
y
g
projections. These are first adjusted for bias using 12km grids of monthly
122
correction factors derived by comparing baseline values against CEH-GEAR data
123
averaged up to the 12km resolution (Kay 2021, Kay et al. 2021a). They are then
124
spatially downscaled to 1km using patterns of average annual rainfall (1961–
125
1990; Bell et al. 2007), and divided equally over each model time-step within a
126
day (as for observed data). 127
Daily 12km grids of PE are not directly available from the UKCP18 Regional
128
projections. 2.3 Climate projection-based driving data
108 Instead they are calculated from other meteorological variables in a
129
way which closely replicates MORECS (as in Robinson et al. (2021, 2022), but
130
using the bias-adjusted precipitation in the interception component). PE is only
131
estimated for 12km ‘land’ RCM boxes; where PE is required for boxes classed as
132
‘sea’ in the RCM, it is copied from the nearest 12km ‘land’ box. The method also
133
includes increased stomatal resistance under future higher atmospheric CO2
134
concentrations (Rudd and Kay 2016, Guillod et al. 2018). The 12km PE are
135
copied down to the 1km grid, then divided equally over each model time-step
136
within a month (as for observed data). 137
Daily 12km grids of min and max temperature are directly available from the
138
UKCP18 Regional projections. These are downscaled to 1km using a lapse rate
139
with elevation data, and interpolated through the day using a sine curve (as for
140
observed data). 141
2.4 Hydrological model runs and outputs
142
The observation-based simulation (hereafter ‘SIMOBS’) is initialised using a states
143
file saved at the end of a prior observation-based run (Jan 1970–Nov 1980). The
144
same state initialisation file is used for each RCM-based simulation (hereafter
145
‘SIMRCM’). 146
Model outputs consist of 1km x 1km gridded time-series of
147
monthly mean river flow (m3s-1);
148
annual maxima (AMAX) of daily mean river flow (m3s-1), for water years
149
(October–September);
150
annual minima (AMIN) of 7-day mean river flow (m3s-1), for years spanning
151
December–November; and
152
monthly mean soil moisture content (m water / m soil). 153
The flow variables are provided for all non-sea and non-tidal 1km cells with a
154
catchment drainage area of at least 50km2, while the soil moisture is provided for all
155
non-sea 1km cells. G2G soil moisture estimates are provided as monthly averages
156
of daily mean soil moisture in the unsaturated zone, which can be interpreted as
157
volumetric soil moisture content, θ, where 0 ≤ θ ≤ 1. In G2G soil depth can vary from
158
a few centimetres to several metres, and soil moisture estimates should be
159
interpreted as depth-integrated values for the whole soil column. 160
2.5 Format of the gridded datasets
161
The 1km x 1km gridded data are provided as a NetCDF4 file for each variable,
162
following UKCEH gridded dataset conventions. 2.5 Format of the gridded datasets
161 The 1km x 1km gridded data are provided as a NetCDF4 file for each variable,
162
following UKCEH gridded dataset conventions The file naming convention is
163 The 1km x 1km gridded data are provided as a NetCDF4 file for each variable,
2
following UKCEH gridded dataset conventions. The file naming convention is
3 The 1km x 1km gridded data are provided as a NetCDF4 file for each variable,
162
following UKCEH gridded dataset conventions. The file naming convention is
163
described in Table 2 for the observation-based datasets and Table 3 for the climate
164
projection-based datasets. 165 described in Table 2 for the observation-based datasets and Table 3 for the climate
164
projection-based datasets. 165 4 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. 166
Table 2 The file naming convention for the observation-based datasets. 167
Data
Names of NetCDF files
Years
available
monthly mean river flow
G2G_GB_mmflow_obs_1980_2011.nc
G2G_NI_mmflow_obs_1980_2011.nc
Dec 1980–
Nov 2011
annual maxima of daily
mean river flow
G2G_GB_amaxflow_obs_1980_2011.nc
G2G_NI_amaxflow_obs_1980_2011.nc
Oct 1981–
Sep 2011
annual minima of 7-day
mean river flow
G2G_GB_aminflow_obs_1980_2011.nc
G2G_NI_aminflow_obs_1980_2011.nc
Dec 1980–
Nov 2011
monthly mean soil
moisture content
G2G_GB_mmsoil_obs_1980_2011.nc
G2G_NI_mmsoil_obs_1980_2011.nc
Dec 1980–
Nov 2011 Table 2 The file naming convention for the observation-based datasets. 167 moisture content
G2G_NI_mmsoil_obs_1980_2011.nc
Nov 2011
168
Table 3 The file naming convention for the climate projection-based datasets. 169
Data
Names of NetCDF files
Years
available
monthly mean river
flow
G2G_GB_mmflow_UKCP18RCM_ensnum_1980_2080.nc
G2G_NI_mmflow_UKCP18RCM_ensnum_1980_2080.nc
Dec 1980–
Nov 2080
annual maxima of daily
mean river flow, and
dates of occurrence
G2G_GB_amaxflow_UKCP18RCM_ensnum_1980_2080.nc
G2G_NI_amaxflow_UKCP18RCM_ensnum_1980_2080.nc
Oct 1981–
Sep 2080
annual minima of 7-day
mean river flow, and
dates of occurrence
G2G_GB_aminflow_UKCP18RCM_ensnum_1980_2080.nc
G2G_NI_aminflow_UKCP18RCM_ensnum_1980_2080.nc
Dec 1980–
Nov 2080
monthly mean soil
moisture content
G2G_GB_mmsoil_UKCP18RCM_ensnum_1980_2080.nc
G2G_NI_mmsoil_UKCP18RCM_ensnum_1980_2080.nc
Dec 1980–
Nov 2080
ensnum is the number of the ensemble member (01, 04, 05, 06, 07, 08, 09, 10, 11, 12, 13, 15)
170
For the observation-based datasets, the time stamp in the NetCDF files is “days
171
since 1900-01-01”, and the monthly mean river flows and monthly mean soil
172
moisture are nominally assigned to the first day of the month. The annual
173
maximum/minimum flow values are nominally assigned to the start year of the 12-
174
month period over which they are calculated, e.g. the annual maximum flow
175
assigned to 1981 is for 1/10/1981–30/9/1982 (water years), while the annual
176
minimum flow assigned to 1981 is for 1/12/1981–30/11/1982 (Dec–Nov years). 2.5 Format of the gridded datasets
161 The
195
catchment area grids are mapped in Figure 1, while the majority lake cells and
196
gauging station locations are mapped in Figure 2 (note that although GB and NI are
197
mapped together, the data for GB and NI are provided separately). At the gauging
198
station locations the G2G flow estimates can be compared to observed river flows. 199
200
Table 5 The additional data files for GB and NI. 201
Data
File names
Description
Catchment
area grid
UKSCAPE_G2G_GB_CatchmentAreaGrid.nc
UKSCAPE_G2G_NI_CatchmentAreaGrid.nc
Digitally-derived catchment area
(km2) draining to every 1km x 1km
grid box. Majority
lake cells
grid
UKSCAPE_G2G_GB_SoilMoisture_LakeGrid.nc
UKSCAPE_G2G_NI_SoilMoisture_LakeGrid.nc
Cells with greater than 85% of area
covered by water (according to
25m data from Land Cover Map
2015, Rowland et al. 2017). These
grids can be applied to exclude use
of soil moisture data in majority
lake cells. 1=land, 2=lake, and -9999=sea. UKSCAPE_G2G_NI_LakeGrid.nc
As above but cells with greater
than 70% of area covered by water,
plus some manual additions of cells
for Lough Erne to avoid more than
one change from river to lake to
river for each flow pathway. This
grid can be applied to exclude use
of river flow data in lake cells in NI. Gauging
station
location
grid
UKSCAPE_G2G_GB_NRFAStationIDGrid.nc
UKSCAPE_G2G_NI_NRFAStationIDGrid.nc
Best locations corresponding to
1038 gauging stations in GB and
43 gauging stations in NI,
referenced by NRFA station
number (nrfa.ceh.ac.uk). NRFA
station number at gauging station
locations, 0=land, and -9999=sea. Gauging
station info
UKSCAPE_GB_NRFAStationIDs.csv
UKSCAPE_NI_NRFAStationIDs.csv
Information on stations included in
location grids. Information for 18
additional stations is included in the
GB file; these are each located in
the same 1km cell as one of the
stations in the grid (as detailed in
the comments column of the csv
file). Table 4 Summary of domain sizes and extents, including the OSGB co-ordinates for
190
the lower left and upper right corners (m). 191
GB
NI
Domain size
700 km × 1000 km
187 km × 170 km
Lower left corner
(0,0)
(-7000,440000)
Upper right corner
(700000,1000000)
(180000,610000) Table 4 Summary of domain sizes and extents, including the OSGB co-ordinates for
190
the lower left and upper right corners (m). 191 200
Table 5 The additional data files for GB and NI. 201
Data
File names
Description
Catchment
area grid
UKSCAPE_G2G_GB_CatchmentAreaGrid.nc
UKSCAPE_G2G_NI_CatchmentAreaGrid.nc
Digitally-derived catchment area
(km2) draining to every 1km x 1km
grid box. 2.5 Format of the gridded datasets
161 The
177
‘time_bnds’ variable gives the start and end dates of the time period over which the
178
annual maximum or minimum flow are extracted. 179
For the climate projection-based datasets, the data have 30-day months due to the
180
“360_day” calendar of the Hadley Centre climate model. The files are otherwise as
181
above, except that the dates of occurrence of the annual maximum and minimum
182
flows are also provided, as additional variables in the ‘amaxflow’ and ‘aminflow’
183
NetCDF files respectively. 184
Table 4 summarises the spatial domains covered by the GB and NI datasets. River
185
flows are only provided for non-sea and non-tidal river cells with a catchment area of
186
at least 50km2, and set to missing elsewhere. Soil moisture estimates are provided
187
for all non-sea cells, and set to missing elsewhere. 188
189 168
Table 3 The file naming convention for the climate projection-based datasets. 169
Data
Names of NetCDF files
Years
available
monthly mean river
flow
G2G_GB_mmflow_UKCP18RCM_ensnum_1980_2080.nc
G2G_NI_mmflow_UKCP18RCM_ensnum_1980_2080.nc
Dec 1980–
Nov 2080
annual maxima of daily
mean river flow, and
dates of occurrence
G2G_GB_amaxflow_UKCP18RCM_ensnum_1980_2080.nc
G2G_NI_amaxflow_UKCP18RCM_ensnum_1980_2080.nc
Oct 1981–
Sep 2080
annual minima of 7-day
mean river flow, and
dates of occurrence
G2G_GB_aminflow_UKCP18RCM_ensnum_1980_2080.nc
G2G_NI_aminflow_UKCP18RCM_ensnum_1980_2080.nc
Dec 1980–
Nov 2080
monthly mean soil
moisture content
G2G_GB_mmsoil_UKCP18RCM_ensnum_1980_2080.nc
G2G_NI_mmsoil_UKCP18RCM_ensnum_1980_2080.nc
Dec 1980–
Nov 2080
ensnum is the number of the ensemble member (01, 04, 05, 06, 07, 08, 09, 10, 11, 12, 13, 15)
170 For the climate projection-based datasets, the data have 30-day months due to the
“360_day” calendar of the Hadley Centre climate model. The files are otherwise as
above, except that the dates of occurrence of the annual maximum and minimum
flows are also provided, as additional variables in the ‘amaxflow’ and ‘aminflow’
NetCDF files respectively. 189 5 5 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. Table 4 Summary of domain sizes and extents, including the OSGB co-ordinates for
190
the lower left and upper right corners (m). 191
GB
NI
Domain size
700 km × 1000 km
187 km × 170 km
Lower left corner
(0,0)
(-7000,440000)
Upper right corner
(700000,1000000)
(180000,610000)
192
To aid use of the datasets, further data files are provided for both GB and NI,
193
including catchment area grids, grids identifying majority lake cells, and grids
194
identifying the approximate locations of river flow gauging stations (Table 5). 2.5 Format of the gridded datasets
161 Majority
lake cells
grid
UKSCAPE_G2G_GB_SoilMoisture_LakeGrid.nc
UKSCAPE_G2G_NI_SoilMoisture_LakeGrid.nc
Cells with greater than 85% of area
covered by water (according to
25m data from Land Cover Map
2015, Rowland et al. 2017). These
grids can be applied to exclude use
of soil moisture data in majority
lake cells. 1=land, 2=lake, and -9999=sea. UKSCAPE_G2G_NI_LakeGrid.nc
As above but cells with greater
than 70% of area covered by water,
plus some manual additions of cells
for Lough Erne to avoid more than
one change from river to lake to
river for each flow pathway. This
grid can be applied to exclude use
of river flow data in lake cells in NI. Gauging
station
location
grid
UKSCAPE_G2G_GB_NRFAStationIDGrid.nc
UKSCAPE_G2G_NI_NRFAStationIDGrid.nc
Best locations corresponding to
1038 gauging stations in GB and
43 gauging stations in NI,
referenced by NRFA station
number (nrfa.ceh.ac.uk). NRFA
station number at gauging station
locations, 0=land, and -9999=sea. Gauging
station info
UKSCAPE_GB_NRFAStationIDs.csv
UKSCAPE_NI_NRFAStationIDs.csv
Information on stations included in
location grids. Information for 18
additional stations is included in the
GB file; these are each located in
the same 1km cell as one of the
stations in the grid (as detailed in
the comments column of the csv
file). Cells with greater than 85% of area
covered by water (according to
25m data from Land Cover Map
2015, Rowland et al. 2017). These
grids can be applied to exclude use
of soil moisture data in majority
lake cells. 1=land, 2=lake, and -9999=sea. As above but cells with greater
than 70% of area covered by water,
plus some manual additions of cells
for Lough Erne to avoid more than
one change from river to lake to
river for each flow pathway. This
grid can be applied to exclude use
of river flow data in lake cells in NI. Best locations corresponding to
1038 gauging stations in GB and
43 gauging stations in NI,
referenced by NRFA station
number (nrfa.ceh.ac.uk). NRFA
station number at gauging station
locations, 0=land, and -9999=sea. Information on stations included in
location grids. Information for 18
additional stations is included in the
GB file; these are each located in
the same 1km cell as one of the
stations in the grid (as detailed in
the comments column of the csv
file). UKSCAPE_G2G_NI_LakeGrid.nc Gauging
station info
UKSCAPE_GB_NRFAStationIDs.csv
UKSCAPE_NI_NRFAStationIDs.csv 202 6 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. g
(
211 2.6 How to use the datasets
212 Comparison of climate projection-based simulations to the
246
observation-based simulation will indicate how both natural variability and
247
(remaining) biases in the climate projection data affect the hydrological model
248
simulations for the baseline period, while comparison to observed data themselves
249
will be additionally affected by the accuracy of the G2G model. 250
The climate projection-based datasets for baseline and future periods can be
251
compared statistically, to investigate the potential impacts of climate change on river
252
flows (e.g. Kay 2021, Lane & Kay 2021, Kay et al.2021a) and soil moisture (e.g. Kay
253
et al. 2022a). Analyses should use the full ensemble; each member should be
254
considered as a different but plausible realisation. Comparison between periods
255
should use the same ensemble member for each period, not a baseline from one
256
member and a future from another member. 257 Users should be aware that the effect of water bodies such as lakes and reservoirs is
232
not accounted for within the model; any impact of lake storage and regulation on
233
downstream river flows has been neglected, and lake grid-cells are treated as
234
though they were rivers. The data files thus include ‘river flows’ and ‘soil moisture’ for
235
1km cells located within lakes. Additional files identify majority lake cells in GB and
236
NI, so that these can be excluded from analyses if desired (see Table 5). 237 For historical periods, the climate projection-based river flow and soil moisture
238
datasets can be compared to the observation-based datasets, or to observed data. 239
However, comparisons in either case should only be made statistically (over multi-
240
decadal periods), not directly (time point by time point), as there will be no
241
equivalence between observed weather features and those in the RCM PPE at the
242
same date. An example of such a comparison is presented in Supp. Fig. 4 of Kay et
243
al. 2021a, where mean monthly flows, flood frequency curves and low flow frequency
244
curves are compared for the baseline SIMRCM ensemble and SIMOBS, for 8
245
catchments in NI. 2.6 How to use the datasets
212 2.6 How to use the datasets
212
River flows from the observation-based simulation can be compared to observed
213
(gauged) river flows (for example from the National River Flow Archive, NRFA;
214
nrfa.ceh.ac.uk), and to facilitate such comparisons files identifying gauging station
215
locations on the 1km G2G model grid for GB and NI are provided (see Table 5). 216
However, it should be borne in mind that G2G provides natural flow estimates, so
217
comparisons in catchments affected by artificial influences like abstractions and
218
discharges may not be as good as those in catchments with relatively natural flow
219
regimes (Rameshwaran et al. 2022). Also, although the gauging station locations
220
have been identified as the G2G cell closest in terms of geographical location and
221
catchment area, and checks have been undertaken to ensure that the G2G flows are
222
for the correct river rather than a nearby river with a similar catchment area, in some
223
cases the derived catchment area draining to the 1km x 1km cell will be different to
224
the “observed” NRFA catchment area. This problem can particularly affect smaller
225
catchments, for which discretisation to a 1km x 1km grid can lead to proportionally
226
larger errors, although flow data provided here are in any case limited to catchments
227
with drainage areas of at least 50km2. The catchment area grids (Table 5) can be
228
used to check the drainage area of gauged catchments, and could also be used to
229
identify the most appropriate 1km x 1km cell corresponding to any particular
230
ungauged catchment of interest. 231 2.6 How to use the datasets
212
River flows from the observation-based simulation can be compared to observed
213
(gauged) river flows (for example from the National River Flow Archive, NRFA;
214
nrfa.ceh.ac.uk), and to facilitate such comparisons files identifying gauging station
215
locations on the 1km G2G model grid for GB and NI are provided (see Table 5). 216
However, it should be borne in mind that G2G provides natural flow estimates, so
217
comparisons in catchments affected by artificial influences like abstractions and
218
discharges may not be as good as those in catchments with relatively natural flow
219
regimes (Rameshwaran et al. 2022). 2.6 How to use the datasets
212 Also, although the gauging station locations
220
have been identified as the G2G cell closest in terms of geographical location and
221
catchment area, and checks have been undertaken to ensure that the G2G flows are
222
for the correct river rather than a nearby river with a similar catchment area, in some
223
cases the derived catchment area draining to the 1km x 1km cell will be different to
224
the “observed” NRFA catchment area. This problem can particularly affect smaller
225
catchments, for which discretisation to a 1km x 1km grid can lead to proportionally
226
larger errors, although flow data provided here are in any case limited to catchments
227
with drainage areas of at least 50km2. The catchment area grids (Table 5) can be
228
used to check the drainage area of gauged catchments, and could also be used to
229
identify the most appropriate 1km x 1km cell corresponding to any particular
230
ungauged catchment of interest. 231
Users should be aware that the effect of water bodies such as lakes and reservoirs is
232
not accounted for within the model; any impact of lake storage and regulation on
233
downstream river flows has been neglected, and lake grid-cells are treated as
234
though they were rivers. The data files thus include ‘river flows’ and ‘soil moisture’ for
235
1km cells located within lakes. Additional files identify majority lake cells in GB and
236
NI, so that these can be excluded from analyses if desired (see Table 5). 237
For historical periods, the climate projection-based river flow and soil moisture
238
datasets can be compared to the observation-based datasets, or to observed data. 239
However, comparisons in either case should only be made statistically (over multi-
240
decadal periods), not directly (time point by time point), as there will be no
241
equivalence between observed weather features and those in the RCM PPE at the
242
same date. An example of such a comparison is presented in Supp. Fig. 4 of Kay et
243
al. 2021a, where mean monthly flows, flood frequency curves and low flow frequency
244
curves are compared for the baseline SIMRCM ensemble and SIMOBS, for 8
245
catchments in NI. 2.5 Format of the gridded datasets
161 203 203
204
Figure 1 Map showing the catchment area grids for GB and NI (see Table 5). 205
206 0
Figure 1 Map showing the catchment area grids for GB and NI (see Table 5). 205 7 7 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. 207 208
Figure 2 Map showing the majority lake cells and gauging station locations for GB
209
and NI (see Table 5), along with the main rivers (catchment area ≥ 50km2; blue lines). 210
211 208
Figure 2 Map showing the majority lake cells and gauging station locations for GB
209
and NI (see Table 5), along with the main rivers (catchment area ≥50km2; blue lines). 210 208
Figure 2 Map showing the majority lake cells and gauging station locations for GB
209
and NI (see Table 5), along with the main rivers (catchment area ≥ 50km2; blue lines). 210 208
Figure 2 Map showing the majority lake cells and gauging station locations for GB
209
and NI (see Table 5), along with the main rivers (catchment area ≥ 50km2; blue lines). 210 8 8 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. 2.6 How to use the datasets
212 Comparison of climate projection-based simulations to the
246
observation-based simulation will indicate how both natural variability and
247
(remaining) biases in the climate projection data affect the hydrological model
248
simulations for the baseline period, while comparison to observed data themselves
249
will be additionally affected by the accuracy of the G2G model. 250 The climate projection-based datasets for baseline and future periods can be
251
compared statistically, to investigate the potential impacts of climate change on river
252
flows (e.g. Kay 2021, Lane & Kay 2021, Kay et al.2021a) and soil moisture (e.g. Kay
253
et al. 2022a). Analyses should use the full ensemble; each member should be
254
considered as a different but plausible realisation. Comparison between periods
255
should use the same ensemble member for each period, not a baseline from one
256
member and a future from another member. 257 The observation-based datasets for GB can be considered updates to MaRIUS-
258
G2G-MORECS-monthly flow and soil moisture data (Bell et al. 2018a). The main
259 The observation-based datasets for GB can be considered updates to MaRIUS-
258
G2G-MORECS-monthly flow and soil moisture data (Bell et al. 2018a). The main
259 9 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. differences are the shorter simulation period here (Dec 1980–Nov 2011 vs 1960–
260
2015 or 1891–2015), the inclusion here of the optional snow module, some changes
261
to the land-sea mask, some changes related to infilling of missing soil type data, and
262
minor changes to the discretised river flow network to improve the G2G model
263
catchment areas (thus the additional spatial datasets provided here may differ in
264
places to those provided with the MaRIUS dataset). 265
The climate projection-based datasets for GB are analogous to the MaRIUS-G2G-
266
WAH2-monthly flow and soil moisture data (Bell et al. 2018b), which were driven by
267
weather@home climate model data (Guillod et al. 2017). The main differences, as
268
well as the factors listed above for the observation-based datasets, are the climate
269
model version, the smaller ensemble size here (12 members vs 100 members), and
270
the provision here of transient rather than time-slice data (Dec 1980–Nov 2080 vs
271
1900–2006, 2020–2049 and 2070–2099). 2.6 How to use the datasets
212 272
3 Results
273
3.1 Monthly mean river flows
274
Maps of example monthly mean river flows across GB and NI from SIMOBS and two
275
SIMRCM ensemble members (Figure 3) illustrate the accumulation of water as it
276
flows downstream, with typically higher flows for downstream locations with larger
277
catchment areas. The example maps also show the generally lower flows in summer
278
(July) compared to winter (January). Note that, although GB and NI are mapped
279
together, the data for GB and NI are provided separately. 280 differences are the shorter simulation period here (Dec 1980–Nov 2011 vs 1960–
260
2015 or 1891–2015), the inclusion here of the optional snow module, some changes
261
to the land-sea mask, some changes related to infilling of missing soil type data, and
262
minor changes to the discretised river flow network to improve the G2G model
263
catchment areas (thus the additional spatial datasets provided here may differ in
264
places to those provided with the MaRIUS dataset). 265
The climate projection-based datasets for GB are analogous to the MaRIUS-G2G-
266
WAH2-monthly flow and soil moisture data (Bell et al. 2018b), which were driven by
267
weather@home climate model data (Guillod et al. 2017). The main differences, as
268
well as the factors listed above for the observation-based datasets, are the climate
269
model version, the smaller ensemble size here (12 members vs 100 members), and
270
the provision here of transient rather than time-slice data (Dec 1980–Nov 2080 vs
271
1900–2006, 2020–2049 and 2070–2099). 272
3 Results
273
3.1 Monthly mean river flows
274
Maps of example monthly mean river flows across GB and NI from SIMOBS and two
275
SIMRCM ensemble members (Figure 3) illustrate the accumulation of water as it
276
flows downstream, with typically higher flows for downstream locations with larger
277
catchment areas. The example maps also show the generally lower flows in summer
278
(July) compared to winter (January). Note that, although GB and NI are mapped
279
together, the data for GB and NI are provided separately. 2.6 How to use the datasets
212 280 differences are the shorter simulation period here (Dec 1980–Nov 2011 vs 1960–
260
2015 or 1891–2015), the inclusion here of the optional snow module, some changes
261
to the land-sea mask, some changes related to infilling of missing soil type data, and
262
minor changes to the discretised river flow network to improve the G2G model
263
catchment areas (thus the additional spatial datasets provided here may differ in
264
places to those provided with the MaRIUS dataset). 265 The climate projection-based datasets for GB are analogous to the MaRIUS-G2G-
266
WAH2-monthly flow and soil moisture data (Bell et al. 2018b), which were driven by
267
weather@home climate model data (Guillod et al. 2017). The main differences, as
268
well as the factors listed above for the observation-based datasets, are the climate
269
model version, the smaller ensemble size here (12 members vs 100 members), and
270
the provision here of transient rather than time-slice data (Dec 1980–Nov 2080 vs
271
1900–2006, 2020–2049 and 2070–2099). 272 Maps of example monthly mean river flows across GB and NI from SIMOBS and two
275
SIMRCM ensemble members (Figure 3) illustrate the accumulation of water as it
276
flows downstream, with typically higher flows for downstream locations with larger
277
catchment areas. The example maps also show the generally lower flows in summer
278
(July) compared to winter (January). Note that, although GB and NI are mapped
279
together, the data for GB and NI are provided separately. 280 10 281
Figure 3 Maps of monthly mean river flows (m3s-1) for January and July 1982, from
282
SIMOBS (left) and two SIMRCM ensemble members (01 – centre, and 15 – right). Also
283
shown are Lough Neagh and Lough Erne in NI (bright blue shading). 284
285
Time-series plots of UK-mean annual mean river flows from SIMOBS and the
286
SIMRCM ensemble show good correspondence (Figure 4). There is a relatively
287
small but highly statistically significant decrease in the SIMRCM ensemble mean
288
flow over Dec 1980–Nov 2080 (-0.695 m3s-1 / 100 years) (Figure 4). Six of the 12
289
individual ensemble members show decreases significant at the 10% level, while
290
four show non-significant decreases and two show non-significant increases. 2.6 How to use the datasets
212 Plots of
291
the monthly climatology of UK-mean river flows for the first and last 30 years (Dec
292
1980–Nov 2010 and Dec 2050–Nov 2080) show a clear reduction in flows during
293
summer and early autumn, but a possible increase in winter (Figure 4). 294 Figure 3 Maps of monthly mean river flows (m3s-1) for January and July 1982, from
2
SIMOBS (left) and two SIMRCM ensemble members (01 – centre, and 15 – right). Also
3
shown are Lough Neagh and Lough Erne in NI (bright blue shading). 4 Figure 3 Maps of monthly mean river flows (m3s-1) for January and July 1982, from
SIMOBS (left) and two SIMRCM ensemble members (01 – centre, and 15 – right). Also
shown are Lough Neagh and Lough Erne in NI (bright blue shading). Figure 3 Maps of monthly mean river flows (m3s-1) for January and July 1982, from
282
SIMOBS (left) and two SIMRCM ensemble members (01 – centre, and 15 – right). Also
283
shown are Lough Neagh and Lough Erne in NI (bright blue shading). 284
285
Time-series plots of UK-mean annual mean river flows from SIMOBS and the
286
SIMRCM ensemble show good correspondence (Figure 4). There is a relatively
287
small but highly statistically significant decrease in the SIMRCM ensemble mean
288
flow over Dec 1980–Nov 2080 (-0.695 m3s-1 / 100 years) (Figure 4). Six of the 12
289
individual ensemble members show decreases significant at the 10% level, while
290 Time-series plots of UK-mean annual mean river flows from SIMOBS and the
286
SIMRCM ensemble show good correspondence (Figure 4). There is a relatively
287
small but highly statistically significant decrease in the SIMRCM ensemble mean
288
flow over Dec 1980–Nov 2080 (-0.695 m3s-1 / 100 years) (Figure 4). Six of the 12
289
individual ensemble members show decreases significant at the 10% level, while
290
four show non-significant decreases and two show non-significant increases. Plots of
291
the monthly climatology of UK-mean river flows for the first and last 30 years (Dec
292
1980–Nov 2010 and Dec 2050–Nov 2080) show a clear reduction in flows during
293
summer and early autumn, but a possible increase in winter (Figure 4). 294
295 Time-series plots of UK-mean annual mean river flows from SIMOBS and the
286
SIMRCM ensemble show good correspondence (Figure 4). 2.6 How to use the datasets
212 300
301 296 Figure 4 Time-series of UK-mean annual mean river flows (top), and the baseline (Dec
297
1980–Nov 2010) and future (Dec 2050–Nov 2080) monthly climatology of UK-mean
298
river flows (bottom), for SIMOBS and the SIMRCM ensemble. The shading in the
299
bottom plot shows the SIMRCM ensemble range for each period. 300
301
Kay (2021) used the GB SIMRCM monthly mean river flow data to investigate
302
potential future changes in seasonal mean flows, for two future time-slices (2020–
303
2050 and 2050–2080). This suggested large decreases in summer mean flows
304
everywhere, but possible increases in winter mean flows, especially in the north and
305
west. A similar analysis using the NI SIMRCM monthly mean river flow data (Kay et
306
al. 2021a) suggested decreases in spring–autumn mean flows, especially in
307
summer, but possible increases in winter mean flows. 308
3.2 Extreme river flows
309
Maps of example GB and NI AMAX of daily mean river flows and AMIN of 7-day
310
mean river flows from SIMOBS and two SIMRCM ensemble members (Figure 5)
311
show less spatial variation than those of monthly mean river flows (when plotted on
312
the same scale). Note that, although GB and NI are mapped together, the data for
313
GB and NI are provided separately. 314
315 Figure 4 Time-series of UK-mean annual mean river flows (top), and the baseline (Dec
1980–Nov 2010) and future (Dec 2050–Nov 2080) monthly climatology of UK-mean
river flows (bottom), for SIMOBS and the SIMRCM ensemble. The shading in the
bottom plot shows the SIMRCM ensemble range for each period. Figure 4 Time-series of UK-mean annual mean river flows (top), and the baseline (Dec
297
1980–Nov 2010) and future (Dec 2050–Nov 2080) monthly climatology of UK-mean
298
river flows (bottom), for SIMOBS and the SIMRCM ensemble. The shading in the
299
bottom plot shows the SIMRCM ensemble range for each period. 300
301
Kay (2021) used the GB SIMRCM monthly mean river flow data to investigate
302
potential future changes in seasonal mean flows, for two future time-slices (2020–
303
2050 and 2050–2080). 2.6 How to use the datasets
212 There is a relatively
287
small but highly statistically significant decrease in the SIMRCM ensemble mean
288
flow over Dec 1980–Nov 2080 (-0.695 m3s-1 / 100 years) (Figure 4). Six of the 12
289
individual ensemble members show decreases significant at the 10% level, while
290
four show non-significant decreases and two show non-significant increases. Plots of
291
the monthly climatology of UK-mean river flows for the first and last 30 years (Dec
292
1980–Nov 2010 and Dec 2050–Nov 2080) show a clear reduction in flows during
293
summer and early autumn, but a possible increase in winter (Figure 4). 294
295 11 296
Figure 4 Time-series of UK-mean annual mean river flows (top), and the baseline (Dec
297
1980–Nov 2010) and future (Dec 2050–Nov 2080) monthly climatology of UK-mean
298
river flows (bottom), for SIMOBS and the SIMRCM ensemble. The shading in the
299
bottom plot shows the SIMRCM ensemble range for each period. 300
301
Kay (2021) used the GB SIMRCM monthly mean river flow data to investigate
302
potential future changes in seasonal mean flows, for two future time-slices (2020–
303
2050 and 2050–2080). This suggested large decreases in summer mean flows
304
everywhere, but possible increases in winter mean flows, especially in the north and
305
west. A similar analysis using the NI SIMRCM monthly mean river flow data (Kay et
306
al. 2021a) suggested decreases in spring–autumn mean flows, especially in
307
summer, but possible increases in winter mean flows. 308
3.2 Extreme river flows
309
Maps of example GB and NI AMAX of daily mean river flows and AMIN of 7-day
310
mean river flows from SIMOBS and two SIMRCM ensemble members (Figure 5)
311
show less spatial variation than those of monthly mean river flows (when plotted on
312
the same scale). Note that, although GB and NI are mapped together, the data for
313 296
Figure 4 Time-series of UK-mean annual mean river flows (top), and the baseline (Dec
297
1980–Nov 2010) and future (Dec 2050–Nov 2080) monthly climatology of UK-mean
298
river flows (bottom), for SIMOBS and the SIMRCM ensemble. The shading in the
299
bottom plot shows the SIMRCM ensemble range for each period. 2.6 How to use the datasets
212 This suggested large decreases in summer mean flows
304
everywhere, but possible increases in winter mean flows, especially in the north and
305 Figure 4 Time-series of UK-mean annual mean river flows (top), and the baseline (Dec
297
1980–Nov 2010) and future (Dec 2050–Nov 2080) monthly climatology of UK-mean
298
river flows (bottom), for SIMOBS and the SIMRCM ensemble. The shading in the
299
bottom plot shows the SIMRCM ensemble range for each period. 300
301
Kay (2021) used the GB SIMRCM monthly mean river flow data to investigate
302 1980–Nov 2010) and future (Dec 2050–Nov 2080) monthly climatology of UK-mean
298
river flows (bottom), for SIMOBS and the SIMRCM ensemble. The shading in the
299
bottom plot shows the SIMRCM ensemble range for each period. 300
301
Kay (2021) used the GB SIMRCM monthly mean river flow data to investigate
302
potential future changes in seasonal mean flows, for two future time-slices (2020–
303
2050 and 2050–2080). This suggested large decreases in summer mean flows
304
everywhere, but possible increases in winter mean flows, especially in the north and
305
west. A similar analysis using the NI SIMRCM monthly mean river flow data (Kay et
306
al. 2021a) suggested decreases in spring–autumn mean flows, especially in
307
summer, but possible increases in winter mean flows. 308 Kay (2021) used the GB SIMRCM monthly mean river flow data to investigate
302
potential future changes in seasonal mean flows, for two future time-slices (2020–
303
2050 and 2050–2080). This suggested large decreases in summer mean flows
304
everywhere, but possible increases in winter mean flows, especially in the north and
305
west. A similar analysis using the NI SIMRCM monthly mean river flow data (Kay et
306
al. 2021a) suggested decreases in spring–autumn mean flows, especially in
307
summer, but possible increases in winter mean flows. 308 315 12 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. 316
Figure 5 Maps of AMAX of daily mean river flows for Oct 1982–Sep 1983 (m3s-1; top)
317
and AMIN of 7-day mean river flows for Dec 1982–Nov 1983 (m3s-1; bottom), from
318
SIMOBS (left) and two SIMRCM ensemble members (01 – centre, and 15 – right). Also
319
shown are Lough Neagh and Lough Erne in NI (bright blue shading). 2.6 How to use the datasets
212 320
321
Time-series plots of UK-mean AMAX and AMIN river flows from SIMOBS and the
322
SIMRCM ensemble show good correspondence (Figure 6). The SIMRCM ensemble
323
mean AMAX flows show a highly statistically significant increase over Oct 1981–Sep
324
2080 (8.51 m3s-1 / 100 years) (Figure 6). Nine of the 12 individual ensemble
325
members show increases in AMAX flows significant at the 10% level, while one
326
shows non-significant increases and two show non-significant decreases. The
327
SIMRCM ensemble mean AMIN flows show a highly statistically significant decrease
328
over Dec 1980–Nov 2080 (-0.670 m3s-1 / 100 years) (Figure 6), and all 12 individual
329
ensemble members show decreases significant at the 10% level. 330
331 316
Figure 5 Maps of AMAX of daily mean river flows for Oct 1982–Sep 1983 (m3s-1; top)
317
and AMIN of 7-day mean river flows for Dec 1982–Nov 1983 (m3s-1; bottom), from
318
SIMOBS (left) and two SIMRCM ensemble members (01 – centre, and 15 – right). Also
319
shown are Lough Neagh and Lough Erne in NI (bright blue shading). 320
321
Time-series plots of UK-mean AMAX and AMIN river flows from SIMOBS and the
322
SIMRCM ensemble show good correspondence (Figure 6). The SIMRCM ensemble
323
mean AMAX flows show a highly statistically significant increase over Oct 1981–Sep
324
2080 (8.51 m3s-1 / 100 years) (Figure 6). Nine of the 12 individual ensemble
325
members show increases in AMAX flows significant at the 10% level, while one
326
shows non-significant increases and two show non-significant decreases. The
327
SIMRCM ensemble mean AMIN flows show a highly statistically significant decrease
328
over Dec 1980–Nov 2080 (-0.670 m3s-1 / 100 years) (Figure 6), and all 12 individual
329
ensemble members show decreases significant at the 10% level. 330
331 Figure 5 Maps of AMAX of daily mean river flows for Oct 1982–Sep 1983 (m3s-1; top)
and AMIN of 7-day mean river flows for Dec 1982–Nov 1983 (m3s-1; bottom), from
SIMOBS (left) and two SIMRCM ensemble members (01 – centre, and 15 – right). Also
shown are Lough Neagh and Lough Erne in NI (bright blue shading). Figure 5 Maps of AMAX of daily mean river flows for Oct 1982–Sep 1983 (m3s-1; top)
317
and AMIN of 7-day mean river flows for Dec 1982–Nov 1983 (m3s-1; bottom), from
318
SIMOBS (left) and two SIMRCM ensemble members (01 – centre, and 15 – right). 2.6 How to use the datasets
212 Also
319
shown are Lough Neagh and Lough Erne in NI (bright blue shading). 320
321
Ti
i
l t
f UK
AMAX
d AMIN i
fl
f
SIMOBS
d th
322 Time-series plots of UK-mean AMAX and AMIN river flows from SIMOBS and the
322
SIMRCM ensemble show good correspondence (Figure 6). The SIMRCM ensemble
323
mean AMAX flows show a highly statistically significant increase over Oct 1981–Sep
324
2080 (8.51 m3s-1 / 100 years) (Figure 6). Nine of the 12 individual ensemble
325
members show increases in AMAX flows significant at the 10% level, while one
326
shows non-significant increases and two show non-significant decreases. The
327
SIMRCM ensemble mean AMIN flows show a highly statistically significant decrease
328
over Dec 1980–Nov 2080 (-0.670 m3s-1 / 100 years) (Figure 6), and all 12 individual
329
ensemble members show decreases significant at the 10% level. 330
331 331 13 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. 332
Figure 6 Time-series of UK-mean AMAX of daily mean river flows (top) and AMIN of 7-
333
day mean river flows (bottom), for SIMOBS and the SIMRCM ensemble. 334
335
Lane & Kay (2021) used the GB SIMRCM AMAX and AMIN river flow data to
336
investigate potential future changes in high/low flows by 2050–2080. All ensemble
337 Figure 6 Time-series of UK-mean AMAX of daily mean river flows (top) and AMIN of 7-
day mean river flows (bottom), for SIMOBS and the SIMRCM ensemble. Figure 6 Time-series of UK-mean AMAX of daily mean river flows (top) and AMIN of 7-
333
day mean river flows (bottom), for SIMOBS and the SIMRCM ensemble. 334
335
Lane & Kay (2021) used the GB SIMRCM AMAX and AMIN river flow data to
336
investigate potential future changes in high/low flows by 2050–2080. All ensemble
337
members showed large reductions in 10-year return period low flows. The direction
338
of change for 10-year return period high flows was more uncertain, but increases of
339
over 9% were possible in most areas. Simultaneous worsening of both high and low
340
flow extremes was projected in the west. A similar analysis using the NI SIMRCM
341
AMAX and AMIN flow data (Kay et al. 2.6 How to use the datasets
212 2021a) suggested large reductions in 10-year
342
return period low flows everywhere, and large increases in 10-year return period high
343
flows for some locations and ensemble members. Analyses of the GB and NI dates
344
of occurrence of SIMRCM AMAX and AMIN showed few significant changes in
345
timing (Lane & Kay 2021, Kay et al. 2021a). 346
347
3.3 Soil moisture
348
Maps of example GB and NI monthly mean soil moisture content from SIMOBS and
349
two SIMRCM ensemble members (Figure 7) show the spatial variation, which is
350
generally related to the variation in soil types. The example maps also show the
351 Figure 6 Time-series of UK-mean AMAX of daily mean river flows (top) and AMIN of 7-
333
day mean river flows (bottom), for SIMOBS and the SIMRCM ensemble. 334
335
Lane & Kay (2021) used the GB SIMRCM AMAX and AMIN river flow data to
336
investigate potential future changes in high/low flows by 2050–2080. All ensemble
337
members showed large reductions in 10-year return period low flows. The direction
338
of change for 10-year return period high flows was more uncertain, but increases of
339 Lane & Kay (2021) used the GB SIMRCM AMAX and AMIN river flow data to
336
investigate potential future changes in high/low flows by 2050–2080. All ensemble
337
members showed large reductions in 10-year return period low flows. The direction
338
of change for 10-year return period high flows was more uncertain, but increases of
339
over 9% were possible in most areas. Simultaneous worsening of both high and low
340
flow extremes was projected in the west. A similar analysis using the NI SIMRCM
341
AMAX and AMIN flow data (Kay et al. 2021a) suggested large reductions in 10-year
342
return period low flows everywhere, and large increases in 10-year return period high
343
flows for some locations and ensemble members. Analyses of the GB and NI dates
344
of occurrence of SIMRCM AMAX and AMIN showed few significant changes in
345
timing (Lane & Kay 2021, Kay et al. 2021a). 346 14 although GB and NI are mapped together, the data for GB and NI are provided
354
separately.
355 separately. 355
356
357
Figure 7 Maps of monthly mean soil moisture content (m water / m soil) for January
358
and July 1982, from SIMOBS (left) and two SIMRCM ensemble members (01 – centre,
359
and 15 – right). 360 356 356
357
Figure 7 Maps of monthly mean soil moisture content (m water / m soil) for January
358
and July 1982, from SIMOBS (left) and two SIMRCM ensemble members (01 – centre,
359
and 15 – right). 360 Figure 7 Maps of monthly mean soil moisture content (m water / m soil) for January
and July 1982, from SIMOBS (left) and two SIMRCM ensemble members (01 – centre,
and 15 – right). Figure 7 Maps of monthly mean soil moisture content (m water / m soil) for January
358
and July 1982, from SIMOBS (left) and two SIMRCM ensemble members (01 – centre,
359
and 15 – right). 360
361
Time-series plots of UK-mean annual mean soil moisture content from SIMOBS and
362
the SIMRCM ensemble show good correspondence (Figure 8). The SIMRCM
363
ensemble mean soil moisture content shows a highly statistically significant
364
decrease over Dec 1980–Nov 2080 (-0.035 / 100 years) (Figure 8), and all 12
365
individual ensemble members show decreases significant at the 10% level. Plots of
366
the monthly climatology of UK-mean soil moisture content for the first and last 30
367
years (Dec 1980–Nov 2010 and Dec 2050–Nov 2080) show a clear reduction in
368
summer and autumn (Figure 8). 369
370 Time-series plots of UK-mean annual mean soil moisture content from SIMOBS and
362
the SIMRCM ensemble show good correspondence (Figure 8). The SIMRCM
363
ensemble mean soil moisture content shows a highly statistically significant
364
decrease over Dec 1980–Nov 2080 (-0.035 / 100 years) (Figure 8), and all 12
365
individual ensemble members show decreases significant at the 10% level. Plots of
366
the monthly climatology of UK-mean soil moisture content for the first and last 30
367
years (Dec 1980–Nov 2010 and Dec 2050–Nov 2080) show a clear reduction in
368
summer and autumn (Figure 8). 369
370 15 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. although GB and NI are mapped together, the data for GB and NI are provided
354
separately.
355 426
5 Conclusions
427
The datasets presented here provide consistent spatial simulations of river flows and
428
soil moisture for the whole of the UK, driven by both observed data and by an
429
ensemble of regional climate model data from the latest UK climate projections,
430
UKCP18. These enable direct studies of historical and potential future river flows and
431
soil moisture, but they can also be used to provide inputs for further studies, for
432
example to simulate water quality (e.g. Hutchins et al. 2016), crop yields (e.g. Cai et
433
al. 2009), irrigated agriculture economic risk (Salmoral et al. 2019), or ecological
434
impacts (e.g. Bussi et al. 2016). 435
An online (anonymous) stakeholder survey was carried out for UK-SCAPE WP2.2 in
436
late 2021 (Kay et al. 2022e). This asked a set of questions divided into three broad
437
classes; ‘job role and level of experience’, ‘data of interest’, and ‘data format/access
438
preferences’. The responses on ‘data of interest’ showed that there is a lot of interest
439
in water quantity, including both river flows and soil moisture, and a lot of interest in
440 2021, Lane & Kay 2021, Kay et al. 2021a, Kay et al. 2022a). These changes are
394
consistent with the climate projections, which give wetter winters and drier and hotter
395
summers (Murphy et al. Fig. 5.2), and increased summer PE (Robinson et al. 2022). 396
A study of trends in historical gauged flows from the UK Benchmark Network
397
(Harrigan et al. 2017) shows a tendency for an increase in winter mean flows and
398
high flow indices over the past 50 years, although with significant natural decadal
399
variability (clear so-called flood-rich and flood-poor periods). The datasets here
400
suggest that this overall trend could continue into the future, and they could
401
potentially be used to further investigate natural variability. The analysis of Harrigan
402
et al. (2017) shows less consistent changes in summer mean flows or low flow
403
indices, with catchments in the south/east often showing decreases, but catchments
404
in the north/west typically showing increases. The datasets here suggest that more
405
consistent decreases could be seen everywhere in future. 406 However, the fact that the UKCP18 Regional climate projections applied here only
407
use one GCM/RCM needs to be borne in mind. although GB and NI are mapped together, the data for GB and NI are provided
354
separately.
355 Other climate models tend to give
408
smaller decreases (or increases) in summer precipitation than the UKCP18 Regional
409
projections (Murphy et al. 2018 Fig. 5.2), so are likely to give lower reductions in
410
summer flows and soil moisture. Similarly, other climate models give a wider range
411
of changes in winter precipitation than the UKCP18 Regional projections (Murphy et
412
al. 2018 Fig. 5.2), so could give larger or smaller increases in winter flows. In
413
addition, the use of a high emissions scenario (RCP8.5) for the UKCP18 Regional
414
projections is likely to lead to more extreme changes than would occur for lower
415
emissions (e.g. Arnell et al. 2014). 416 Further sources of uncertainty in the datasets include the calculation of future PE. 417
The RCM PE used here includes the effect of stomatal closure under higher CO2
418
concentrations but does not include a potential leaf area increase due to carbon
419
fertilisation (Rudd and Kay 2016; Robinson et al.2022). Potential future changes in
420
land cover are also excluded, as are any artificial influences on river flows. Also, only
421
one hydrological model has been applied; a catchment-based dataset of simulated
422
river flows from the ‘Enhanced future FLows and Groundwater’ (eFlaG) project
423
(Hannaford et al. 2022b) uses similar driving data from the UKCP18 Regional
424
projections for three hydrological models (including G2G), so could be used to look
425
at potential uncertainty from hydrological model structure (Hannaford et al. 2022a). 426 although GB and NI are mapped together, the data for GB and NI are provided
354
separately.
355 2 371
Figure 8 Time-series of UK-mean annual mean soil moisture content (m water / m soil;
372
top), and the baseline (Dec 1980–Nov 2010) and future (Dec 2050–Nov 2080) monthly
373
climatology of UK-mean soil moisture content (m water / m soil; bottom), for SIMOBS
374
and the SIMRCM ensemble. The shading in the bottom plot shows the SIMRCM
375
ensemble range for each period. 376
377 Figure 8 Time-series of UK-mean annual mean soil moisture content (m water / m soil;
top), and the baseline (Dec 1980–Nov 2010) and future (Dec 2050–Nov 2080) monthly
climatology of UK-mean soil moisture content (m water / m soil; bottom), for SIMOBS
and the SIMRCM ensemble. The shading in the bottom plot shows the SIMRCM
ensemble range for each period. Kay et al. (2022a) used the GB and NI SIMRCM monthly mean soil moisture data to
378
investigate potential future changes in occurrence of indicative soil moisture
379
extremes and changes in typical wetting and drying dates of soils by 2050–2080
380
across the UK. This also suggested large increases in the spatial occurrence of low
381
soil moisture levels, and later soil wetting dates. Changes to soil drying dates were
382
less apparent. 383 Ensemble data from the historical period of the climate projection-driven datasets
385
show good correspondence with the observation-driven datasets, for both river flows
386
and soil moisture. More detailed performance analyses are provided elsewhere (Kay
387
2021, Lane & Kay 2021, Kay et al. 2021a, Kay et al. 2022a). 388
The climate projection-driven river flow and soil moisture datasets suggest potential
389
future decreases in summer flows, annual minimum 7-day flows, and
390
summer/autumn soil moisture, along with possible future increases in winter flows
391
d
l
i
fl
M
d t il d
l
t d
l
h
ill
t
t
392 16 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. 2021, Lane & Kay 2021, Kay et al. 2021a, Kay et al. 2022a). These changes are
394
consistent with the climate projections, which give wetter winters and drier and hotter
395
summers (Murphy et al. Fig. 5.2), and increased summer PE (Robinson et al. 2022). 396
A study of trends in historical gauged flows from the UK Benchmark Network
397
(Harrigan et al. although GB and NI are mapped together, the data for GB and NI are provided
354
separately.
355 2017) shows a tendency for an increase in winter mean flows and
398
high flow indices over the past 50 years, although with significant natural decadal
399
variability (clear so-called flood-rich and flood-poor periods). The datasets here
400
suggest that this overall trend could continue into the future, and they could
401
potentially be used to further investigate natural variability. The analysis of Harrigan
402
et al. (2017) shows less consistent changes in summer mean flows or low flow
403
indices, with catchments in the south/east often showing decreases, but catchments
404
in the north/west typically showing increases. The datasets here suggest that more
405
consistent decreases could be seen everywhere in future. 406
However, the fact that the UKCP18 Regional climate projections applied here only
407
use one GCM/RCM needs to be borne in mind. Other climate models tend to give
408
smaller decreases (or increases) in summer precipitation than the UKCP18 Regional
409
projections (Murphy et al. 2018 Fig. 5.2), so are likely to give lower reductions in
410
summer flows and soil moisture. Similarly, other climate models give a wider range
411
of changes in winter precipitation than the UKCP18 Regional projections (Murphy et
412
al. 2018 Fig. 5.2), so could give larger or smaller increases in winter flows. In
413
addition, the use of a high emissions scenario (RCP8.5) for the UKCP18 Regional
414
projections is likely to lead to more extreme changes than would occur for lower
415
emissions (e.g. Arnell et al. 2014). 416
Further sources of uncertainty in the datasets include the calculation of future PE. 417
The RCM PE used here includes the effect of stomatal closure under higher CO2
418
concentrations but does not include a potential leaf area increase due to carbon
419
fertilisation (Rudd and Kay 2016; Robinson et al.2022). Potential future changes in
420
land cover are also excluded, as are any artificial influences on river flows. Also, only
421
one hydrological model has been applied; a catchment-based dataset of simulated
422
river flows from the ‘Enhanced future FLows and Groundwater’ (eFlaG) project
423
(Hannaford et al. 2022b) uses similar driving data from the UKCP18 Regional
424
projections for three hydrological models (including G2G), so could be used to look
425
at potential uncertainty from hydrological model structure (Hannaford et al. 2022a). 5 Conclusions
427 A large proportion of respondents were also happy downloading the full
446
dataset as NetCDF files from the EIDC. The datasets described here thus provide for
447
a significant stakeholder demand, although there is always more that could be done. 448
Further developments could include a web-tool allowing interactive data exploration
449
and plotting. 450 potential future changes in river flows, although slightly less so for changes in soil
441
moisture. Furthermore, the responses on ‘data format/access preferences’ showed
442
that the greatest 1st preference was for grids covering sub-regions or the whole
443
country, although perhaps unsurprising this varied by job role (Academic,
444
Government/Regulator, Practitioner/ Consultant), which likely influences how data
445
are used. A large proportion of respondents were also happy downloading the full
446
dataset as NetCDF files from the EIDC. The datasets described here thus provide for
447
a significant stakeholder demand, although there is always more that could be done. 448
Further developments could include a web-tool allowing interactive data exploration
449
and plotting. 450 Further developments could include a web-tool allowing interactive data exploration
449
and plotting. 450 Data Availability
456 The six datasets described in this manuscript are available from the Environmental
457
Information Data Centre (EIDC); see Table 1. 458 The six datasets described in this manuscript are available from the Environmental
7
Information Data Centre (EIDC); see Table 1. 8 p
Information Data Centre (EIDC); see Table 1. 458 Acknowledgements
451 This work was supported by the Natural Environment Research Council award
452 This work was supported by the Natural Environment Research Council award
2
number NE/R016429/1 as part of the UK-SCAPE programme delivering National
3 pp
y
number NE/R016429/1 as part of the UK-SCAPE programme delivering National
453 number NE/R016429/1 as part of the UK-SCAPE programme delivering National
453
Capability. Thanks to Emma Robinson (UKCEH) for work on the estimation of PE
454
from climate model data. 455 p
p
g
g
Capability. Thanks to Emma Robinson (UKCEH) for work on the estimation of PE
454
f
li
t
d l d t
455 p
p
g
g
Capability. Thanks to Emma Robinson (UKCEH) for work on the estimation of PE
454
from climate model data. 455 from climate model data. 455 5 Conclusions
427 The datasets presented here provide consistent spatial simulations of river flows and
428
soil moisture for the whole of the UK, driven by both observed data and by an
429
ensemble of regional climate model data from the latest UK climate projections,
430
UKCP18. These enable direct studies of historical and potential future river flows and
431
soil moisture, but they can also be used to provide inputs for further studies, for
432
example to simulate water quality (e.g. Hutchins et al. 2016), crop yields (e.g. Cai et
433
al. 2009), irrigated agriculture economic risk (Salmoral et al. 2019), or ecological
434
impacts (e.g. Bussi et al. 2016). 435 An online (anonymous) stakeholder survey was carried out for UK-SCAPE WP2.2 in
436
late 2021 (Kay et al. 2022e). This asked a set of questions divided into three broad
437
classes; ‘job role and level of experience’, ‘data of interest’, and ‘data format/access
438
preferences’. The responses on ‘data of interest’ showed that there is a lot of interest
439
in water quantity, including both river flows and soil moisture, and a lot of interest in
440 17 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. potential future changes in river flows, although slightly less so for changes in soil
441
moisture. Furthermore, the responses on ‘data format/access preferences’ showed
442
that the greatest 1st preference was for grids covering sub-regions or the whole
443
country, although perhaps unsurprising this varied by job role (Academic,
444
Government/Regulator, Practitioner/ Consultant), which likely influences how data
445
are used. A large proportion of respondents were also happy downloading the full
446
dataset as NetCDF files from the EIDC. The datasets described here thus provide for
447
a significant stakeholder demand, although there is always more that could be done. 448
Further developments could include a web-tool allowing interactive data exploration
449
and plotting. 450 potential future changes in river flows, although slightly less so for changes in soil
441
moisture. Furthermore, the responses on ‘data format/access preferences’ showed
442
that the greatest 1st preference was for grids covering sub-regions or the whole
443
country, although perhaps unsurprising this varied by job role (Academic,
444
Government/Regulator, Practitioner/ Consultant), which likely influences how data
445
are used. References
459 Arnell NW, Charlton MB, Lowe JA (2014). The effect of climate policy on the impacts
460
of climate change on river flows in the UK. J Hydrol, 510, 424-435. 461 Bell VA, Kay AL, Davies HN, Jones RG (2016). An assessment of the possible
462
impacts of climate change on snow and peak river flows across Britain. Clim
463
Change, 136(3), 539–553. 464 Bell VA, Kay AL et al. (2007). Development of a high resolution grid-based river flow
465
model for use with regional climate model output. Hydrol Earth Syst Sci, 11, 532–
466
549. 467 Bell VA, Kay AL et al. (2009). Use of soil data in a grid-based hydrological model to
468
estimate spatial variation in changing flood risk across the UK. J Hydrol, 377, 335–
469
350. 470 Bell VA, Rudd AC, Kay AL, Davies HN (2018a). Grid-to-Grid model estimates of
471
monthly mean flow and soil moisture for Great Britain (1960 to 2015): observed
472
driving data [MaRIUS-G2G-MORECS-monthly]. NERC Environmental Information
473
Data Centre. doi:10.5285/e911196a-b371-47b1-968c-661eb600d83b
474 Bell VA, Rudd AC, Kay AL, Davies HN (2018a). Grid-to-Grid model estimates of
471
monthly mean flow and soil moisture for Great Britain (1960 to 2015): observed
472
driving data [MaRIUS-G2G-MORECS-monthly]. NERC Environmental Information
473 Bell VA, Rudd AC, Kay AL, Davies HN (2018a). Grid-to-Grid model estimates of
471
monthly mean flow and soil moisture for Great Britain (1960 to 2015): observed
472
d i i
d t
[M RIUS G2G MORECS
thl ] NERC E
i
t l I f
ti
473 Bell VA, Rudd AC, Kay AL, Davies HN (2018a). Grid to Grid model estimates of
471
monthly mean flow and soil moisture for Great Britain (1960 to 2015): observed
472 Bell VA, Rudd AC, Kay AL, Davies HN (2018b). Grid-to-Grid model estimates of
475
monthly mean flow and soil moisture for Great Britain: weather@home2 (climate
476
model) driving data [MaRIUS-G2G-WAH2-monthly]. NERC Environmental
477
Information Data Centre. doi:10.5285/3b90962e-6fc8-4251-853e-b9683e37f790
478 Bell VA, Rudd AC, Kay AL, Davies HN (2018b). Grid-to-Grid model estimates of
475
monthly mean flow and soil moisture for Great Britain: weather@home2 (climate
476
model) driving data [MaRIUS-G2G-WAH2-monthly] NERC Environmental
477 Bussi G Whitehead PG Bowes MJ et al (2016) Impacts of climate change land
479 Bussi G, Whitehead PG, Bowes MJ et al. (2016). References
459 Managing the Risks, Impacts and
490
Uncertainties of drought and water Scarcity (MaRIUS) project: Large set of potential
491 Uncertainties of drought and water Scarcity (MaRIUS) project: Large set of potential
1
past and future climate time series for the UK from the weather@home2 model. 2 Uncertainties of drought and water Scarcity (MaRIUS) project: Large set of potential
491
past and future climate time series for the UK from the weather@home2 model. 492
Centre for Environmental Data Analysis. 493 g
y (
) p
j
g
p
past and future climate time series for the UK from the weather@home2 model. 492 p
Centre for Environmental Data Analysis. 493 Centre for Environmental Data Analysis. 493 Centre for Environmental Data Analysis. 493 y
doi:10.5285/0cea8d7aca57427fae92241348ae9b03. 494 Hannaford J, Mackay JD, Ascot M et al. (2022a). eFLaG: enhanced future FLows
495 Hannaford J, Mackay JD, Ascot M et al. (2022a). eFLaG: enhanced future FLows
495
and Groundwater. A national dataset of hydrological projections based on UKCP18. 496
Earth Syst Sci Data Discuss, doi:10.5194/essd-2022-40. 497 and Groundwater. A national dataset of hydrological projections based on UKCP18. 496
Earth Syst Sci Data Discuss, doi:10.5194/essd-2022-40. 497 Hannaford J, Mackay J, Ascot M, et al. (2022b). Hydrological projections for the UK,
498
based on UK Climate Projections 2018 (UKCP18) data, from the Enhanced Future
499
Flows and Groundwater (eFLaG) project. NERC EDS Environmental Information
500
Data Centre. doi:10.5285/1bb90673-ad37-4679-90b9-0126109639a9
501 based on UK Climate Projections 2018 (UKCP18) data, from the Enhanced Future
499
Flows and Groundwater (eFLaG) project. NERC EDS Environmental Information
500
Data Centre. doi:10.5285/1bb90673-ad37-4679-90b9-0126109639a9
501 Harrigan S, Hannaford J et al. (2018). Designation and trend analysis of the updated
502
UK Benchmark Network of river flow stations: the UKBN2 dataset. Hydrology
503
Research, 49, 552–567. 504 Harrigan S, Hannaford J et al. (2018). Designation and trend analysis of the updated
502
UK Benchmark Network of river flow stations: the UKBN2 dataset. Hydrology
503
Research 49 552 567
504 Harrigan S, Hannaford J et al. (2018). Designation and trend analysis of the updated
502
UK Benchmark Network of river flow stations: the UKBN2 dataset. Hydrology
503 Hough M, Jones RJA (1997). The United Kingdom Meteorological Office rainfall and
505
evaporation calculation system: MORECS version 2.0– an overview. Hydrol Earth
506
Syst Sci, 1(2), 227–239. 507 Hutchins MG, Williams RJ, Prudhomme C et al. (2016). References
459 Impacts of climate change, land-
479 ,
,
(
)
p
g ,
use change and phosphorus reduction on phytoplankton in the River Thames (UK),
480 ,
,
(
)
p
g ,
use change and phosphorus reduction on phytoplankton in the River Thames (UK),
480
Sci Total Environ, 572, 1507-1519. 481 g
p
p
p y
p
(
)
Sci Total Environ, 572, 1507-1519. 481 Sci Total Environ, 572, 1507-1519. 481 18 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. Cai X, Wang D, Laurent R (2009). Impact of Climate Change on Crop Yield: A Case
482
Study of Rainfed Corn in Central Illinois. J Appl Meteorol Climatol, 4(9), 1868–1881. 483 Cai X, Wang D, Laurent R (2009). Impact of Climate Change on Crop Yield: A Case
482
St d
f R i f d C
i
C
t
l Illi
i
J A
l M t
l Cli
t l 4(9) 1868 1881
483 Cai X, Wang D, Laurent R (2009). Impact of Climate Change on Crop Yield: A Case
482
Study of Rainfed Corn in Central Illinois. J Appl Meteorol Climatol, 4(9), 1868–1881. 483 Formetta, G., Prosdocimi, I., Stewart, E., Bell, V. (2018). Estimating the index flood
484
with continuous hydrological models: an application in Great Britain. Hydrol Res, 49,
485
123–133. 486 Guillod BP, Jones RG, Dadson SJ et al. (2018). A large set of potential past, present
487
and future hydro-meteorological time series for the UK. Hydrol. Earth Syst. Sci.,
488
22(1), 611–634. 489 Guillod BP, Jones RG, Kay AL et al. (2017). Managing the Risks, Impacts and
490
Uncertainties of drought and water Scarcity (MaRIUS) project: Large set of potential
491 Guillod BP, Jones RG, Kay AL et al. (2017). Managing the Risks, Impacts and
490
Uncertainties of drought and water Scarcity (MaRIUS) project: Large set of potential
491
past and future climate time series for the UK from the weather@home2 model
492 Guillod BP, Jones RG, Kay AL et al. (2017). Managing the Risks, Impacts and
490 Guillod BP, Jones RG, Kay AL et al. (2017). References
459 Projections of future
508
deterioration in UK river quality are hampered by climatic uncertainty under extreme
509
conditions, Hydrological Sciences Journal, 61:16, 2818-2833. 510 Kay AL (2021). Simulation of river flow in Britain under climate change: baseline
511
performance and future seasonal changes. Hydrol Process. 35(4), e14137, doi:
512
10.1002/hyp.14137
513 Kay AL, Crooks SM (2014). An investigation of the effect of transient climate change
514
on snowmelt, flood frequency and timing in northern Britain. International Journal of
515
Climatology, 34(12), 3368–3381. 516 Kay AL, Davies HN, Lane RA, Rudd AC, Bell VA (2021a). Grid-based simulation of
517
river flows in Northern Ireland: model performance and future flow changes. Journal
518
of Hydrology: Regional Studies, 38, 100967. 519 Kay AL, Griffin A, Rudd AC, Chapman RM, Bell VA, Arnell NW (2021b). Climate
520
change effects on indicators of high and low river flow across Great Britain. 521
Advances in Water Resources, 151, 103909. 522 Kay AL, Lane RA, Bell VA (2022a). Grid-based simulation of soil moisture in the UK:
523
future changes in extremes and wetting and drying dates. Environmental Research
524
Letters, 17(7), 074029. 525 19 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. Kay AL, Rudd AC, Davies HN, Lane RA, Bell VA (2021c). Grid-to-Grid model
526
estimates of river flow for Great Britain driven by observed data (1980 to 2011). 527
NERC Environmental Information Data Centre. doi:10.5285/2f835517-253e-4697-
528
b774-ab6ff2c0d3da. 529 Kay AL, Rudd AC, Davies HN, Lane RA, Bell VA (2021d). Grid-to-Grid model
530
estimates of river flow for Northern Ireland driven by observed data (1980 to 2011). 531
NERC Environmental Information Data Centre. doi:10.5285/f5fc1041-e284-4763-
532
b8b7-8643c319b2d0. 533 Kay AL, Rudd AC, Davies HN, Lane RA, Bell VA (2021e). Grid-to-Grid model
534
estimates of soil moisture for Great Britain and Northern Ireland driven by observed
535
data (1980 to 2011). NERC Environmental Information Data Centre. 536
doi:10.5285/c9a85f7c-45e2-4201-af82-4c833b3f2c5f. 537 estimates of soil moisture for Great Britain and Northern Ireland driven
535
data (1980 to 2011). NERC Environmental Information Data Centre. 536
doi:10.5285/c9a85f7c-45e2-4201-af82-4c833b3f2c5f. 537 Kay AL, Rudd AC, Davies HN, Lane RA, Bell VA (2022b). Grid-to-Grid model
538
estimates of river flow for Great Britain driven by UK Climate Projections 2018
539
(UKCP18) Regional (12km) data (1980 to 2080) v2. NERC Environmental
540
Information Data Centre. doi:10.5285/18be3704-0a6d-4917-aa2e-bf38927321c5. 541 Kay AL, Rudd AC, Davies HN, Lane RA, Bell VA (2022c). References
459 Grid-to-Grid model
542
estimates of river flow for Northern Ireland driven by UK Climate Projections 2018
543
(UKCP18) Regional (12km) data (1980 to 2080) v2. NERC Environmental
544
Information Data Centre. doi:10.5285/76057b0a-b18f-496f-891c-d5b22bd0b291. 545 Kay AL, Rudd AC, Davies HN, Lane RA, Bell VA (2022d). Grid-to-Grid model
546
estimates of soil moisture for Great Britain and Northern Ireland driven by UK
547 Kay AL, Rudd AC, Davies HN, Lane RA, Bell VA (2022d). Grid-to-Grid model
546
estimates of soil moisture for Great Britain and Northern Ireland driven by UK
547
Climate Projections 2018 (UKCP18) Regional (12km) data (1980 to 2080). NERC
548
Environmental Information Data Centre. doi:10.5285/f7142ced-f6ff-486b-af33-
549
44fb8f763cde. 550 Climate Projections 2018 (UKCP18) Regional (12km) data (1980 to 2080). NERC
548
Environmental Information Data Centre. doi:10.5285/f7142ced-f6ff-486b-af33-
549
44fb8f763cde. 550 Kay AL, Spencer M, Bell VA (2022e). UK-SCAPE WP2.2: Water Futures. 551
Stakeholder questionnaire results. Wallingford, UK Centre for Ecology & Hydrology,
552
14pp. nora.nerc.ac.uk/id/eprint/531705/
553 Lane RA, Kay AL (2021). Climate change impact on the magnitude and timing of
554
hydrological extremes across Great Britain. Frontiers in Water, 3:684982,
555
doi:10.3389/frwa.2021.684982. 556 Lowe JA, Bernie D, Bett P et al. (2018). UKCP18 Science Overview report. Exeter,
557
UK: Met Office Hadley Centre. 558 Lowe JA, Bernie D, Bett P et al. (2018). UKCP18 Science Overview report. Exeter,
557
UK: Met Office Hadley Centre. 558 Met Office Hadley Centre (2018). UKCP18 Regional Projections on a 12km grid over
559
the UK for 1980-2080. CEDA, September 2019. 560
catalogue.ceda.ac.uk/uuid/589211abeb844070a95d061c8cc7f604. 561 Met Office Hadley Centre (2018). UKCP18 Regional Projections on a 12km grid ove
559 Met Office Hadley Centre (2018). UKCP18 Regional Projections on a 12km grid over
559
the UK for 1980-2080. CEDA, September 2019. 560 Met Office Hadley Centre (2018). UKCP18 Regional Projections on a 12km grid over
559
the UK for 1980-2080. CEDA, September 2019. 560 Met Office, Hollis D, McCarthy M et al. (2019). HadUK-Grid Gridded Climate
562
Observations on a 1km grid over the UK v1 0 0 0 (1862 2017) Centre for
563 Met Office, Hollis D, McCarthy M et al. (2019). HadUK-Grid Gridded Climate
562 Met Office, Hollis D, McCarthy M et al. (2019). HadUK-Grid Gridded Climate
562
Observations on a 1km grid over the UK, v1.0.0.0 (1862-2017). Centre for
563
Environmental Data Analysis, 14 November 2019. 564 Observations on a 1km grid over the UK, v1.0.0.0 (1862-2017). Centr
563
Environmental Data Analysis, 14 November 2019. References
459 564 g
,
(
Environmental Data Analysis, 14 November 2019. 564 Environmental Data Analysis, 14 November 2019. 564 doi:10.5285/2a62652a4fe6412693123dd6328f6dc8. 565 Morris DG, Flavin RW (1990). A digital terrain model for hydrology. In: Proceedings
566
of the 4th International Symposium on Spatial Data Handling, Zurich, Switzerland,
567
23–27 July 1990, 250–262. 568 Morris DG, Flavin RW (1990). A digital terrain model for hydrology. In: Proceedings
566
of the 4th International Symposium on Spatial Data Handling, Zurich, Switzerland,
567 Morris DG, Flavin RW (1990). A digital terrain model for hydrology. In: Proceedings
566 Murphy, J.M., Harris, G.R., Sexton, D.M.H. et al. (2018). UKCP18 Land Projections:
569
Science Report. Met Office Hadley Centre, Exeter, UK. 570 Murphy, J.M., Harris, G.R., Sexton, D.M.H. et al. (2018). UKCP18 Land Projections:
569
Science Report. Met Office Hadley Centre, Exeter, UK. 570 20 https://doi.org/10.5194/essd-2022-439
Preprint. Discussion started: 26 January 2023
c⃝Author(s) 2023. CC BY 4.0 License. Rameshwaran P, Bell VA, Brown MJ, Davies HN, Kay AL, Rudd AC, Sefton C
571
(2022). Use of abstraction and discharge data to improve the performance of a
572
national-scale hydrological model. Water Resources Research, 5(1),
573
e2021WR029787. 574 Riahi K, Krey V et al. (2011). RCP-8.5: exploring the consequence of high emission
575
trajectories. Clim Change, 109, 33–57. 576 Robinson EL, Kay AL, Brown M, Chapman R, Bell V, Blyth EM (2021). Potential
577
evapotranspiration derived from the UK Climate Projections 2018 Regional Climate
578 Robinson EL, Kay AL, Brown M, Chapman R, Bell V, Blyth EM (2021). Potential
577
evapotranspiration derived from the UK Climate Projections 2018 Regional Climate
578
Model ensemble 1980-2080 (Hydro-PE UKCP18 RCM). NERC Environmental
579
Information Data Centre. doi:10.5285/eb5d9dc4-13bb-44c7-9bf8-c5980fcf52a4. 580 evapotranspiration derived from the UK Climate Projections 2018 Regional Climate
578
Model ensemble 1980-2080 (Hydro-PE UKCP18 RCM). NERC Environmental
579
Information Data Centre. doi:10.5285/eb5d9dc4-13bb-44c7-9bf8-c5980fcf52a4. 580 Robinson EL, Kay AL, Brown M, Chapman R, Bell V, Blyth E (2022). Hydro-PE:
581
gridded datasets of historical and future Penman-Monteith potential evaporation for
582
the United Kingdom. Earth Syst. Sci. Data Discuss., doi:10.5194/essd-2022-288. 583 Rowland CS, Morton RD, Carrasco L et al. (2017) Land Cover Map 2015 (25m
584
raster, N. Ireland). NERC EIDC, doi:10.5285/47f053a0-e34f-4534-a843-
585
76f0a0998a2f. 586 raster, N. Ireland). NERC EIDC, doi:10.5285/47f053a0-e34f-4534-a843-
585
76f0a0998a2f. 586 Rudd AC, Bell VA, Kay AL (2017). National-scale analysis of simulated hydrological
587
droughts (1891-2015). J Hydrol, 550, 368-385. 588 Rudd AC, Kay AL (2016). References
459 Use of very high resolution climate model data for
589
hydrological modelling: estimation of potential evaporation. Hydrology Research,
590
47(3), 660–670, doi:10.2166/nh.2015.028. 591 Salmoral, G., Rey, D. Rudd, A., de Margon, P., Holman I. (2019). A Probabilistic Ris
592 Salmoral, G., Rey, D. Rudd, A., de Margon, P., Holman I. (2019). A Probabilistic Risk
2
Assessment of the National Economic Impacts of Regulatory Drought Management
3 Salmoral, G., Rey, D. Rudd, A., de Margon, P., Holman I. (2019). A Probabilistic Risk
592
Assessment of the National Economic Impacts of Regulatory Drought Management
593
on Irrigated Agriculture. Earth’s Future, 7(2), 178-196. 594 Tanguy M, Dixon H et al. (2016). Gridded estimates of daily and monthly areal
595
rainfall for the United Kingdom (1890-2015) [CEH-GEAR]. NERC EIDC. 596
doi:10 5285/33604ea0-c238-4488-813d-0ad9ab7c51ca
597 Tanguy M, Dixon H et al. (2016). Gridded estimates of daily and monthly areal
595
i f ll f
th
U it d Ki
d
(1890 2015) [CEH GEAR] NERC EIDC
596 g y
(
)
y
y
rainfall for the United Kingdom (1890-2015) [CEH-GEAR]. NERC EIDC. 596 21
|
https://openalex.org/W4304187573
|
https://ora.ox.ac.uk/objects/uuid:4040c644-1979-4790-9b2f-9eb38a0aae60/files/rm326m2417
|
English
| null |
Managing clustering effects and learning effects in the design and analysis of randomised surgical trials: a review of existing guidance
|
Trials
| 2,022
|
cc-by
| 6,545
|
Managing clustering effects and learning
effects in the design and analysis of randomised
surgical trials: a review of existing guidance zabeth J. Conroy1,2* , Jane M. Blazeby3 , Girvan Burnside1 , Jonathan A. Cook2 and Car Abstract Background: The complexities associated with delivering randomised surgical trials, such as clustering effects, by
centre or surgeon, and surgical learning, are well known. Despite this, approaches used to manage these complexi-
ties, and opinions on these, vary. Guidance documents have been developed to support clinical trial design and
reporting. This work aimed to identify and examine existing guidance and consider its relevance to clustering effects
and learning curves within surgical trials. Methods: A review of existing guidelines, developed to inform the design and analysis of randomised controlled
trials, is undertaken. Guidelines were identified using an electronic search, within the Equator Network, and by a
targeted search of those endorsed by leading UK funding bodies, regulators, and medical journals. Eligible documents
were compared against pre-specified key criteria to identify gaps or inconsistencies in recommendations. Results: Twenty-eight documents were eligible (12 Equator Network; 16 targeted search). Twice the number of guid-
ance documents targeted design (n/N=20/28, 71%) than analysis (n/N=10/28, 36%). Managing clustering by centre
through design was well documented. Clustering by surgeon had less coverage and contained some inconsistencies. Managing the surgical learning curve, or changes in delivery over time, through design was contained within several
documents (n/N=8/28, 29%), of which one provided guidance on reporting this and restricted to early phase stud-
ies only. Methods to analyse clustering effects and learning were provided in five and four documents respectively
(N=28). Conclusions: To our knowledge, this is the first review as to the extent to which existing guidance for designing
and analysing randomised surgical trials covers the management of clustering, by centre or surgeon, and the surgi-
cal learning curve. Twice the number of identified documents targeted design aspects than analysis. Most notably,
no single document exists for use when designing these studies, which may lead to inconsistencies in practice. The
development of a single document, with agreed principles to guide trial design and analysis across a range of realistic
clinical scenarios, is needed. Keywords: Trials, Clinical trial, Randomised controlled trial, Complex intervention, Surgical intervention, Trial design,
Trial analysis, Summary, Review, Clustering, Learning Background Randomised controlled trials (RCTs) are recognised
as providing the highest level of evidence, second only
to systematic reviews of such trials [1]. There are many
practical and methodological difficulties that a medical
researcher must overcome to deliver successful RCT. In © 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
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://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. *Correspondence: elizabeth.conroy@ndorms.ox.ac.uk 2 Oxford Clinical Trials Research Unit, Centre for Statistics in Medicine, Nuffield
Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences,
University of Oxford, Windmill Road, Oxford OX3 7LD, UK
Full list of author information is available at the end of the article Conroy et al. Trials (2022) 23:869
https://doi.org/10.1186/s13063-022-06743-6 Open Access © 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
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://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Conroy et al. Trials (2022) 23:869 Page 2 of 8 trials with a surgical intervention, these difficulties are
often magnified [2–5]. Surgical interventions, delivered
as an intervention or as a setting, consist of many inter-
acting components — such as the procedure itself, sur-
geon expertise, and pre- or postoperative care [4]. Because of the nature of the search, full texts of iden-
tified guidelines were obtained to determine eligibility. Documents that provided guidance such that RCTs and
statistical aspects were covered within their scope were
included and reasons for exclusion were recorded. Patient outcomes often depend on the treatment pro-
vider delivering the intervention. Due to the nature of
surgical interventions, RCTs within this field can be vul-
nerable to criticism if concerns over variability in treat-
ment delivery are raised. Variability can arise between
intervention providers (clustering) or due to change in
delivery over time, often as a result of increased experi-
ence (learning) [6–8]. Therefore, when designing these
trials, it is important to consider the homogeneity of the
treatment effect and therefore the potential existence and
impact of both clustering and learning, by centre and sur-
geon. This should be done as early as possible during trial
design to avoid issues arising that violate the validity of
the trial results [9].hf Key criteria relevant to the design and analysis of surgi-
cal trials, or trials of complex interventions, were iden-
tified a priori (see Table 1). Identifying eligible documents The search within the EQUATOR website identified 80
documents: 36 (45%) were identified using the search
term ‘statistic’ and 44 (55%) using the search term ‘sur-
gery’. The search was conducted on 21 October 2021. Figure 1 presents the flowchart of eligibility, with rea-
sons for exclusion where necessary. An additional 16
documents were manually identified from the tar-
geted search (funders: 2; regulators: 6; journals: 8, see
Supplementary Material 1 and Fig. 1). There were no
duplicates between the two searches leaving a total
of 28 eligible documents for review. Supplementary
Material 1 provides the list of included documents. Details as to the background and justification for the
documents included as part of the targeted search are
provided in Supplementary Material 2. The importance of managing these effects within these
trials is well known, but the methods used to do so in
practice, and opinions on these, vary [10–12]. Guid-
ance documents exist to support clinical trial design and
reporting, but the majority target generic aspects of clini-
cal trials and originate specifically from medicinal trials. Therefore, whilst their relevance to all trials is indisput-
able, the extent to which they cover clustering and learn-
ing may be limited.h The aim of this review is to identify and examine exist-
ing guidance and consider its relevance to clustering
effects and learning curves within surgical trials. Methodsh This work sought to include guidance documents devel-
oped to inform the design and analysis of randomised
controlled trials (RCTs). Guidelines for inclusion in this
review were identified by undertaking: Summary of identified guidance Seven of the 28 eligible documents (25%) were developed
specifically for surgery. Of those that were not (n=21), • An electronic search within the Equator Network
(http://www.equator-network.org), an online library
containing a comprehensive searchable database of
reporting guidelines, using each of the search terms
‘surgery’ and ‘statistic’. Documents that provided
guidance specific to non-randomised studies, aspects
of trial methodology or medical specialties that were
not applicable, or focussed on applicable medical
specialties, such as surgery, with no statistical scope
were excluded. Table 1 Key criteria to be considered within design and analysis Eligible documents were
compared against these to identify gaps or inconsisten-
cies in recommendations. Guidelines for reporting the
aspects of design and analysis were also assessed against
these criteria. Specific methods within the guidelines
related to analysing clustering or learning, at the centre
or treatment provider level, were also collected. Docu-
ments were examined using NVivo qualitative data analy-
sis software [13]. Design
• The appropriate trial design, such as an expertise-based design
• Delivery of the intervention in terms of:
◦ The health professionals delivering treatment
◦ The extent to which treatments are to be standardised
◦ The potential for change in delivery over time
• Adjusting the sample size
• Balancing treatment within centres and treatment providers
Analysis
• When the randomisation has been stratified
• When analysing the primary outcome, such as adjustment
• When there are multiple centres and/or treatment providers Design • A targeted search of guidelines endorsed by leading
UK funding bodies, regulators, and medical journals
such that they covered aspects of trial design, analy-
sis, and reporting. Analysis Conroy et al. Trials (2022) 23:869 Page 3 of 8 Fig. 1 Flowchart of identification of guidelines Fig. 1 Flowchart of identification of guidelines two were written for complex interventions, two for
devices, and the remaining 17 for general medicine. of inter-rater reliability, between individual centres and
surgeons, can provide an understanding of any impact
due to expertise. This type of analysis can be useful when
considering rolling out the interventions into routine
healthcare, see the ‘Analysing a trial with clustering and
learning’ section [15]. Designing a trial with clustering and learning
Choosing a trial design Eleven out of 28 documents (39%) provided guidance
relating to trial design. See D1 in Supplementary Table 1. In cluster randomised trials, groups of patients are the
unit of randomisation. These designs are less common
and are generally less efficient than individually ran-
domised studies. They require more surgeons and intro-
duce the potential for the treatment comparison to be
confounded by the delivery, despite inflating the sample
size to account for the intraclass correlation coefficient
(ICC) [3, 4, 17]. The options of trial design depend on the unit of ran-
domisation and the intervention of interest. The key
aspects of relevant designs are briefly summarised here. Many design options, and associated limitations, were
discussed and no single document provided a single com-
prehensive summary. In individually randomised trials, patients are the unit
of randomisation [3]. When conducting these trials in
surgery, differential expertise between the treatments
being investigated can raise issues that can be alleviated
by defining eligibility criteria for centres and surgeons,
such as years in practice or the number of interven-
tions performed previously [14, 15]. However, applying
criteria that are too strict may reduce the generalis-
ability of trial results [16]. Instead, a statistical analysis Expertise-based designs are a half-way house between
individual and cluster randomised trials. Patients are
individually randomised to surgeon, who treats all
patients with a single intervention. This can be the sur-
geon’s preferred technique or an unavoidable feature in
trials comparing interventions delivered by different
specialties [4, 14]. This design has the same limitations
as cluster trials, and when a surgeon is only performing Conroy et al. Trials (2022) 23:869 Page 4 of 8 prepare investigators and standardise performance were
suggested by one document [24]. their preferred technique, shared waiting lists [4] and
understanding how the treatment can be rolled out into
routine healthcare can be a challenge. Resultantly, this
design is relatively uncommon [10, 11]. Monitoring treatment adherence was an important
aspect across documents [5, 9, 14, 24, 25]. Suggested
methods included reviewing case report forms, vide-
otapes, and audiotapes, extending to decertifying and
excluding surgeons not submitting a videotape rated
acceptable by an independent committee [14]. Tracker designs, proposed by Ergina et al., where new
or evolving interventions can theoretically be developed
within a single randomised study, and the incremental
changes to the intervention tracked within the analysis,
would be very challenging in practice [4]. Considering who will deliver the interventionh Thirteen out of 28 documents (46%) discussed the impor-
tance of deciding who will deliver the intervention. See
D2 in Supplementary Table 1. Some variation in delivery, in part, will depend on the
skill and training of those delivering the intervention [4,
14, 18]. As such, the selection of centres and treatment
providers was a critical element of design discussed by a
number of guidance documents [9, 17, 19, 20]. Any eligi-
bility criteria for participating centres and treatment pro-
viders, and a description such as the degree to which they
are typical, should be reported [14, 16, 21]. Anticipating changes over time Eight out of 28 documents (29%) discussed considering
changes in the delivery of the intervention over time. See
D4 in Supplementary Table 1. Delivery may still vary irrespective of training, expe-
rience, and other steps to enforce standardisation. The
amount of variation will depend on the stage and tech-
nicality of intervention development [3, 5, 14, 26]. An
important aspect of surgical evaluation across the guide-
lines was that delivery may change over time for prag-
matic reasons, changes in external factors, or as a result
of expertise developing during the study [3–5]. Two guidelines suggested criteria by which recruiting
centres should be chosen, such as caseload for the proce-
dure under investigation and ensuring sufficient numbers
of the target population [14, 20]. No guidelines provided advice on selecting treatment
providers. Treatment providers could be a limited group
or all professionals offering the intervention [22]. If it is a
limited group, guidance on selecting centres, and report-
ing requirements, may be looked upon as a proxy for tri-
alists when deciding how to select treatment providers,
for example caseload and ensuring specific qualifications
[14, 20, 21].h Expertise can develop over a very long time and so
requiring a set expertise level can slow the delivery of
surgical trials [4]. Some guidelines discussed evaluating
the learning curve within the trial [5] and highlighted this
was particularly important in earlier phase trials [26]. In
trials comparing more established techniques, the statis-
tical advantages and gain in ‘internal validity’ need to be
considered against the loss of generalisability or ‘external
validity’ of applying too much emphasis on the learning
curve [3]. The results of the main trial should report on the num-
ber of centres and treatment providers performing each
intervention [21]. Designing a trial with clustering and learning
Choosing a trial design Reporting in-depth details of the intervention, and
comparator, was required by a number of documents. Aspects required included technical procedures; full
details on preoperative, intraoperative, and postoperative
care; and the extent to which delivery was permitted to
vary between participants, treatment providers, and cen-
tres [14, 16, 25]. Ensuring that the intervention is standardised Reporting learning curve assessment results was
required by one document but this was limited to early
phase studies [26]. Fifteen out of 28 documents (54%) discussed the impor-
tance of standardising the intervention. See D3 in Sup-
plementary Table 1. When analysing the primary outcome Two out of 28 documents (18%) provided guidance on
adjusting the primary outcome analysis. See A2 in Sup-
plementary Table 1. Unexplained differences between treatments, for exam-
ple between adjusted and unadjusted analyses, can jeop-
ardise the trial results [27]. For this reason, when the
primary outcome is expected to be influenced by centre
or treatment provider, an adjustment should be planned. When the potential value of an adjustment is in doubt,
such as little existing prior knowledge, the primary analy-
sis should be an unadjusted analysis, supported by an
adjusted analysis [9, 27]. In general, larger datasets gener-
ally support more factors than smaller ones and results
based on simpler models are generally numerically stable,
the assumptions underpinning the statistical model eas-
ier to validate and improve generalisability [27]. Estimating the sample size Variation in delivery can be reduced by standardising
all, or aspects of, the intervention of interest. Limiting
variation in treatment delivery may be more desirable
in an efficacy trial than a pragmatic, effectiveness study
[3, 5]. In pragmatic trials, standardisation might con-
sist of simply informing treatment providers to perform
the treatment as usual [14]. Regardless of the stage, trial
delivery should be similar at all centres [9] and designed
such that a clear description of the procedures per-
formed can be provided [16, 23]. Investigator meetings to Eight out of 28 documents (29%) discussed sample size. See D5 in Supplementary Table 1. A number of guidance documents highlighted the
impact of failing to reduce variation within trial arms by
standardising the intervention on the sample size and
power calculation, where typical estimates assume that
differences between the treatments across centres, or
treatment provider, are unbiased estimates of the same
quantity [3, 9]. In the presence of multilevel data struc-
tures, where variability in individual-level outcomes can Conroy et al. Trials (2022) 23:869 Conroy et al. Trials (2022) 23:869 Page 5 of 8 also include treatment provider in surgical trials, but no
guidance specifically made this point. reflect higher-level processes, calculations are more com-
plicated [7, 9, 18]. To avoid associated imprecision in
results, the sample size should adjust for any clustering
effects as estimated by the intraclass correlation coeffi-
cient (ICC) and this should be reported in the main result
paper [14, 21]. Conversely, two documents that discussed
sample size did not comment on adjusting for clusters
[15, 20]. Analysing multi‑centre trials Balance can be achieved by stratifying the randomisa-
tion and stratifying by centre was a common topic, par-
ticularly when centre is expected to be confounded with
other prognostic factors [9, 20, 27]. When there are too
few patients per centre, stratifying by a larger unit, such
as country or region, may be warranted [27]. Despite
stratifying by treatment provider not being specifically
addressed within the documents, in some circumstances,
it may be desirable to stratify for more than just both
centre and treatment provider, or treatment provider
alone, where numbers allow [27]. The use of more than
two stratification factors is rarely necessary [9]. Six out of 28 documents (21%) provided guidance on
analysing multi-centre trials. See A3 in Supplementary
Table 1. Investigations into the heterogeneity of the main treat-
ment effect across centre and/or treatment provider were
covered by a number of documents [5, 9, 14, 25, 26]. Fur-
thermore, the main trial publication should report meth-
ods to adjust for, and results into, clustering by centre or
treatment provider [14, 21]. These investigations are crit-
ical when a positive treatment effect is found and there
are appreciable numbers of subjects per centre [9]. In the
simplest multi-centre trial, a single investigator recruits
and is responsible for all patients within a single hospi-
tal, such that the centre is identified uniquely by hospi-
tal. When the definition of a centre is ambiguous, such as
a single investigator recruits from several hospitals or a
clinical team recruits from numerous clinics, the proto-
col should provide a definition [9, 25]. Analysing a trial with clustering and learning
When the randomisation was stratified Two out of 28 documents (18%) provided guidance on
adjusting the analysis following stratification. See A1 in
Supplementary Table 1. Stratifying randomisation and subsequently adjusting
the analysis are complementary methods of accounting
for prognostic factors, unless the stratification factor was
chosen for administrative reasons only [9, 27]. i
Quantitative approaches may comprise a graphical
display of the results of individual centres, such as forest
plots, or analytical methods, such as a significance test
although this generally has low power [9]. One stated that
investigations use a model which allows for centre differ-
ences but no interaction terms [9]. Fixed or mixed effects
models can be used, although mixed models are especially
relevant when there is a large number of centres [9, 25]. Two documents discussed the issue of adjusting for
too many, or too small, strata in the analysis, for which
there is no best solution [9, 27]. When included in the
randomisation scheme, ignoring centres or adjusting for
a large number of small centres might lead to unreliable
estimates of the treatment effect and p-values [27]. At
best, using an unadjusted analysis should be supported
by sensitivity analyses that indicate trial conclusions are
not affected because of this [27]. As above, the statistical
justifications for including centre could be considered to Ensuring balance of treatment within centre and treatment
provider Six out of 28 documents (21%) discussed ensuring that
treatment allocations are equally distributed within cen-
tre. See D6 in Supplementary Table 1. Balancing treatment groups with respect to prognos-
tic factors enhances trial credibility [20, 27]. Ensuring
balancing of patients within centre was highlighted as
important within many of the guidance documents [9,
20, 27], and similar reasoning would lead surgical trial-
ists to extend this to treatment provider which was not
discussed within any document. Methods for investigating the learning curve Four out of 28 documents (14%) provided guidance on
analysing the learning curve within centre and/or treat-
ment provider. See A4 in Supplementary Table 1. Conroy et al. Trials (2022) 23:869 Conroy et al. Trials (2022) 23:869 Page 6 of 8 Clustering, at the centre level, was well covered within
the design, analysis, and reporting guidance. However,
there were inconsistencies with regard to the treatment
provider coverage. For example, reporting required that
the eligibility of the treatment provider be covered, yet no
guidance on the design or analysis covered this [14, 21]. However, this may be due to the original guidance largely
not being written specifically for surgery, or indeed com-
plex interventions, where these effects may be more
prominent [10, 11]. The role of the centre within conven-
tional drug trials could be extended to provide guidance
on the role of the treatment provider in surgery trials [3,
9, 20]. Methods to monitor the quality of delivery of the
trial intervention through study conduct have been con-
sidered, recommending that stablished protocols that
determine prohibited, mandated, and flexible interven-
tion components and monitoring adherence are devel-
oped [28]. Yet a specific guidance document that covers
the design and analysis of randomised surgical trials, or
intervention trials, could address the discrepancies iden-
tified within this review to improve the quality of under-
standing and awareness of these issues [10–12]. Reporting of continuous quality control measures can
be useful for all phases of the trial, particularly early
phase surgical trials [5, 26]. Time series and longitudinal
models or multilevel models can be used to analyse long
and short sequences of data respectively [3, 18]. Simpler
exploratory methods such as cusum plots enable centres
or surgeons to be compared against themselves which
can be preferable to surgeons [5, 26]. Method for investigating clustering Five out of 28 documents (18%) provided guidance on
investigating clustering due to centre and/or treatment
provider. See A5 in Supplementary Table 1. Hierarchically structured data, such as patients within
surgeon, can be analysed using multilevel models or gen-
eralised estimating equations (GEEs) [3, 21]. Multilevel
models are subject-specific models whereas GEEs are
population average. For multilevel models, fixed, random,
or mixed effects can be specified to account for clustering
[21] and different types of these models allow for flexible
data structures [18].f For ordinary linear models, the treatment effect esti-
mate is likely to be similar but not necessarily iden-
tical for adjusted and unadjusted models. Adjusted
analyses are more efficient, and so a less significant result
for unadjusted should not be a concern. For generalised
linear or non-linear models, adjusted and unadjusted
treatment effects may not have the same interpretation
and may provide different results [27]. A number of guidance documents acknowledged the
importance of the surgical learning curve, or delivery
changing over time, within design and analysis, particu-
larly in early phase surgical trials or when the interven-
tions differ in their technicality [3–5, 14, 26]. Yet there
was little coverage within reporting standards to reflect
this, with the surgical learning curve analysis only neces-
sary in the early phase, and not necessarily randomised,
trials [26] and broader RCT reporting guidelines only
requiring differential expertise be addressed in the dis-
cussion [14]. Lack of clear standards, and guidance that
is too broad in scope, may lead to reporting how delivery
of intervention changes over time, despite its importance,
being generally under-recognised in the literature [10,
11]. Supplementary Information analysis of the trial. Being able to explore effects will be par-
ticularly beneficial if concerns of learning or clustering are
raised, or more generally will allow better understanding to
contextualise study findings to ultimately support the roll-
out of the interventions into routine practice. The online version contains supplementary material available at https://doi.
org/10.1186/s13063-022-06743-6. The online version contains supplementary material available at https://doi.
org/10.1186/s13063-022-06743-6. Additional file 1: Supplementary Material 1. List of eligible guidance
documents. Supplementary Material 2. Additional information on docu-
ments obtained by the targeted search. Supplementary Table 1. Key
criteria coverage across documents summary. Additional file 1: Supplementary Material 1. List of eligible guidance
documents. Supplementary Material 2. Additional information on docu-
ments obtained by the targeted search. Supplementary Table 1. Key
criteria coverage across documents summary. When reading this review, it is important to consider
its limitations. First, country-specific guidance beyond
the UK, such as US Food and Drug Administration,
was not included. However, international documents
that are applicable to other countries, including the UK,
were obtained, such as ICH which are followed globally
and EMA which are adopted within Europe. Second,
only four guidance documents, developed by the same
research group, were written specifically for surgery and
not written specifically for RCTs, which may explain the
lack of specific coverage of the surgeon in the wider set
[4, 5, 26, 32]. Third, very little of the guidance documents
covered statistical aspects, leaving a trialist to extend the
centre-drug connection to surgeon-intervention using
existing guidelines [9, 27]. The development of a statis-
tical guidance document that covers randomised surgi-
cal trials in more depth would help trialists, in particular
statisticians, and the IDEAL framework provide a good
basis for this development to be integrated [4, 5, 26, 32]. Abbreviations
GEE: Generalised estimating equation; ICC: Intraclass correlation coefficient;
RCT: Randomised controlled trial. Conclusionshi This is the first review, to our knowledge, to explore the
coverage of guidance for managing clustering effects and
the surgical learning curve within the design and analy-
sis of randomised surgical trials. Twice the number of
identified documents target design aspects than analysis. Furthermore, no single and complete guidance document
exists that covers aspects of learning and clustering leav-
ing trialists to have to access multiple documents to gain
full understanding of these considerations. Competing interests CG, JAC, and JMB co-authored some of the guidance documents included
within this review. The authors declare that they have no other competing
interests. Existing documents should therefore be extended to
incorporate statistical guidance on the management of
clustering and learning. The IDEAL framework aligns
perfectly with the focus of this work as it is developed
specifically for surgical trials and is already widely used
by surgical trialists [5]. Future work should address
integrating these statistical themes into this framework
as a priority. This would encourage better consistency
between trialists, improve awareness of these methodo-
logical challenges, and support the use of optimal meth-
ods within the surgical field. Availability of data and materials Datasets used and/or analysed during the current study, which are not already
included in this published article, are available from the corresponding author
on reasonable request. Author details 1 Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK. 2 Oxford Clinical Trials Research Unit, Centre for Statistics in Medicine, Nuffield
Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences,
University of Oxford, Windmill Road, Oxford OX3 7LD, UK. 3 Centre for Surgical
Research, Bristol Biomedical Research Centre, Population Health Sciences,
University of Bristol, Bristol, UK. Received: 28 February 2022 Accepted: 13 September 2022 Declarations Ethics approval and consent to participate
Not applicable. Authors’ contributions EJC participated in the study design, developed the data extraction form,
drafted the manuscript, and extracted and analysed the data. CG partici-
pated in the study design, developed the data extraction form, and drafted
the manuscript. GB, JMB, and JAC participated in the study design and
contributed to manuscript development. The authors read and approved
the final manuscript. Funding This research was funded by National Institute for Health Research (NIHR)
Doctoral Fellowship Programme (DRF-2015-08-082). EJC is funded through
this fellowship programme. Department of Health disclaimer
f The views expressed are those of the authors and not necessarily of the
National Health Service, the National Institute for Health Research (NIHR), or
the Department of Health and Social Care. Discussion Trialists should consider the impact of clustering and
learning when designing and analysing randomised sur-
gical trials. Considerations should be incorporated into
reporting to aid the interpretation and applicability of
trial results. This investigation is the first review as to the
extent that existing guidance within the UK covers these
important effects. Existing guidance documents are iden-
tified and summarised, with a focus on aspects relating to
clustering effects and the learning curve and their appli-
cation to surgical trials. Not all documents were written
specifically for surgery, yet all contain aspects that can
be applied to surgery, for example, the role of the cen-
tre in the delivery of treatments in drug trials has some
commonalities to the role of the surgeon in delivering a
surgical trial. Twice the number of identified documents
targeted design aspects than analysis. Whilst a good anal-
ysis cannot rescue a poor design, and this may have led
to a larger focus on the design on guidance for trialists,
there is a notable dearth of analysis guidance available
that requires addressing. In addition, there is also scope
for guidance on study conduct. When designing and analysing a randomised surgical
trial, there can be a view that clustering and learning are less
pronounced or irrelevant in more pragmatic large-scale tri-
als where the interventions are stabilised and in widespread
use. Measures to reduce variation in treatment effects are
often introduced into the trial design by defining a mini-
mum level of expertise or providing training for treatment
providers [12]. However, despite measures being taken,
variation in delivery may remain, and the need to account
for the breadth of the setting, learning curve, and experi-
ence of surgeons is an area for improvement in more prag-
matic RCTs [29–31]. Trialists should therefore be aware
of the potential for clustering and learning and routinely
consider their impact at the trial outset. Early and careful
consideration will improve data collection to ensure that, if
required, investigation can be integrated into the planned Conroy et al. Trials (2022) 23:869 Page 7 of 8 Consent for publication Consent for publication
Not applicable. 2.
Cook JA. The challenges faced in the design, conduct and analysis of
surgical randomised controlled trials. Trials. 2009;10:9. https://doi.org/10.
1186/1745-6215-10-9. 1.
Evans D. Hierarchy of evidence: a framework for ranking evidence evalu-
ating healthcare interventions. J Clin Nurs. 2003;12(1):77–84.
2.
Cook JA. The challenges faced in the design, conduct and analysis of
surgical randomised controlled trials. Trials. 2009;10:9. https://doi.org/10.
1186/1745-6215-10-9. Abbreviations
GEE G
li
d 1. Evans D. Hierarchy of evidence: a framework for ranking evidence evalu-
ating healthcare interventions. J Clin Nurs. 2003;12(1):77–84. 2. Cook JA. The challenges faced in the design, conduct and analysis of
surgical randomised controlled trials. Trials. 2009;10:9. https://doi.org/10.
1186/1745-6215-10-9. Conroy et al. Trials (2022) 23:869 Conroy et al. Trials (2022) 23:869 Page 8 of 8 3. Craig P, Dieppe P, Macintyre S, Michie S, Nazareth I, Petticrew M. Developing and evaluating complex interventions2019. Available from:
https://mrc.ukri.org/documents/pdf/complex-interventions-guidance/;
Accessed 30 Nov 2021. ema.europa.eu/en/documents/scientific-guideline/ich-e-8-general-consi
derations-clinical-trials-step-5_en.pdf. Accessed 3 Aug 2022. ema.europa.eu/en/documents/scientific-guideline/ich-e-8-general-consi
derations-clinical-trials-step-5_en.pdf. Accessed 3 Aug 2022. 25. 25. Group IEW. ICH harmonised tripartite guideline: structure and content
of clinical study reports E3 ICH harmonisation for better health web site:
International Conference on Harmonisation of Technical Requirements
for Registration of Pharmaceuticals for Human Use; 1995. Available from:
https://database.ich.org/sites/default/files/E3_Guideline.pdf. Accessed 3
Aug 2022. 4. Ergina PL, Cook JA, Blazeby JM, Boutron I, Clavien PA, Reeves BC, et al. Challenges in evaluating surgical innovation. Lancet. 2009;374:1097–104. 5. McCulloch P, Altman DG, Campbell B, Flum DR, Glasziou P, Marshall J, et al. No surgical innovation without evaluation: the IDEAL recommendations. Lancet. 2009;374:1105–12. 26. Bilbro NA, Hirst A, Paez A, Vasey B, Pufulete M, Sedrakyan A, et al. The
IDEAL reporting guidelines: a Delphi consensus statement stage specific
recommendations for reporting the evaluation of surgical innovation. Ann Surg. 2021;273(1):82–5. 6. Cook JA, Bruckner T, MacLennan GS, Seller CM. Clustering in surgical tri-
als–database of intracluster correlations. Trials. 2012;13:2. 7. Cook JA, Ramsay CR, Fayers P. Statistical evaluation of learning curve
effects in surgical trials. Clin Trials. 2004;1:421–7. 27. Committee for Medicinal Products for Human Use (CHMP). Guideline on
adjustment for baseline covariates in clinical trials European Medicines
Agency Science Medicines Health web site: European Medicines Agency;
2015. Available from: https://www.ema.europa.eu/en/documents/scien
tific-guideline/guideline-adjustment-baseline-covariates-clinical-trials_
en.pdf. Accessed 30 Nov 2021. f
8. Lee KJ, Thompson SG. Clustering by health professional in individually
randomised trials. BMJ. 2005;330:142. f
8. Lee KJ, Thompson SG. Clustering by health professional in individually
randomised trials. BMJ. 2005;330:142. 9. ICH Harmonised Tripartite Guideline. Statistical principles for clinical trials. International Conference on Harmonisation E9 Expert Working Group. Stat Med. 1999;18(15):1905-42. 28. Blencowe NS, Mills N, Cook JA, Donovan JL, Rogers CA, Whiting P, et al. Standardizing and monitoring the delivery of surgical interventions in
randomized clinical trials. Br J Surg. 2016;103(10):1377–84. 10. Conroy EJ, Rosala-Hallas A, Blazeby JM, Burnside G, Cook JA, Gamble C. Abbreviations
GEE G
li
d Randomized trials involving surgery did not routinely report considera-
tions of learning and clustering effects. J Clin Epidemiol. 2019a;107:27–35. 29. Hyman WA. Medical device and diagnostic industry online, FDA flirts with
the learning curve. 2019. Available from: https://www.mddionline.com/
regulatory-quality/fda-flirts-learning-curve. 11. Conroy EJ, Rosala-Hallas A, Blazeby JM, Burnside G, Cook JA, Gamble C. Funders improved the management of learning and clustering effects
through design and analysis of randomized trials involving surgery. J Clin
Epidemiol. 2019b;113:28–35. l
30. Ritchey ME. Chapter 25 - Special considerations of interventions: Medi-
cal devices. In: Girman CJ, Ritchey ME, editors. Pragmatic Randomized
Clinical Trials. Academic Press; 2021. p. 387–95. https://doi.org/10.1016/
B978-0-12-817663-4.00032-5. 12. Conroy EJ, Blazeby JM, Burnside G, Cook JA, Gamble C. Managing
clustering effects and learning effects in the design and analysis of
multicentre randomised trials: a survey to establish current practice. Trials. 2020;21(1):433. 31. Shaw W, Semb G. The Scandcleft randomised trials of primary surgery
for unilateral cleft lip and palate: 11. What next? J Plast Surg. Hand Surg. 2017;51(1):88–93. 13. QSR International Pty Ltd. NVivo (Version 12). 2018. https://www.qsrin
ternational.com/nvivo-qualitative-data-analysis-software/home. 14. Boutron I, Moher D, Altman DG, Schulz KF, Ravaud P, Grp C. Extend-
ing the CONSORT statement to randomized trials of nonpharma-
cologic treatment: explanation and elaboration. Ann Intern Med. 2008;148(4):295–309. 32. Barkun JS, Aronson JK, Feldman LS, Maddern GJ, Strasberg SM, Bal-
liol C, et al. Evaluation and stages of surgical innovations. Lancet. 2009;374(9695):1089–96. 15. National Institute for Health Research. Planning a Randomised Controlled
Trial (RTC) – points to consider 2016. Available from: https://www.ct-toolk
it.ac.uk/routemap/trial-planning-and-design/downloads/planning-a-
randomised-controlled-trial.pdf/. Accessed 30 Nov 2021. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations. Springer Nature remains neutral with regard to jurisdictional claims in pub-
lished maps and institutional affiliations. 16. Zwarenstein M, Treweek S, Gagnier JJ, Altman DG, Tunis S, Haynes B,
et al. Improving the reporting of pragmatic trials: an extension of the
CONSORT statement. Brit Med J. 2008;337:a2390. 17. Campbell MK, Piaggio G, Elbourne DR, Altman DG, Group C. Consort 2010
statement: extension to cluster randomised trials. BMJ. 2012;345:e5661. 18. Jackson DL. Reporting results of latent growth modeling and multilevel
modeling analyses: some recommendations for rehabilitation psychol-
ogy. Rehabil Psychol. 2010;55(3):272–85. 18. Jackson DL. Reporting results of latent growth modeling and multilevel
modeling analyses: some recommendations for rehabilitation psychol-
ogy. Rehabil Psychol. 2010;55(3):272–85. 19. Group IEW. ICH harmonised tripartite guideline: guideline for good
clinical practice E6(R2) ICH Harmonisation for better health web site:
International Conference on Harmonisation of Technical Requirements
for Registration of Pharmaceuticals for Human Use; 2016 Available from:
https://database.ich.org/sites/default/files/E6_R2_Addendum.pdf. Accessed 3 Aug 2022. 19. Group IEW. ICH harmonised tripartite guideline: guideline for good
clinical practice E6(R2) ICH Harmonisation for better health web site:
International Conference on Harmonisation of Technical Requirements
for Registration of Pharmaceuticals for Human Use; 2016 Available from:
https://database.ich.org/sites/default/files/E6_R2_Addendum.pdf. Accessed 3 Aug 2022. 20. Medicines & Healthcare products Regulatory Agency. Clinical investiga-
tions of medical devices – statistical considerations 2021. Available from:
https://assets.publishing.service.gov.uk/government/uploads/system/
uploads/attachment_data/file/989415/Statistical_considerations_clini
cal_investigations_-_May_2021.pdf. Accessed 30 Nov 2021. •
fast, convenient online submission
•
thorough peer review by experienced researchers in your field
•
rapid publication on acceptance
•
support for research data, including large and complex data types
•
gold Open Access which fosters wider collaboration and increased citations
maximum visibility for your research: over 100M website views per year
•
At BMC, research is always in progress. Learn more biomedcentral.com/submissions
Ready to submit your research
Ready to submit your research ? Choose BMC and benefit from:
? Choose BMC and benefit from: •
fast, convenient online submission
•
thorough peer review by experienced researchers in your field
•
rapid publication on acceptance
•
support for research data, including large and complex data types
•
gold Open Access which fosters wider collaboration and increased citations
maximum visibility for your research: over 100M website views per year
•
At BMC, research is always in progress. Learn more biomedcentral.com/submissions
Ready to submit your research
Ready to submit your research ? Publisher’s Note Choose BMC and benefit from:
? Choose BMC and benefit from: •
fast, convenient online submission
•
thorough peer review by experienced researchers in your field
•
rapid publication on acceptance
•
support for research data, including large and complex data types
•
gold Open Access which fosters wider collaboration and increased citations
maximum visibility for your research: over 100M website views per year
•
At BMC, research is always in progress. Learn more biomedcentral.com/submissions
Ready to submit your research
Ready to submit your research ? Choose BMC and benefit from:
? Choose BMC and benefit from: 21. Boutron I, Altman DG, Moher D, Schulz KF, Ravaud P, Group CN. CONSORT
statement for randomized trials of nonpharmacologic treatments: a 2017
update and a CONSORT extension for nonpharmacologic trial abstracts. Ann Intern Med. 2017;167(1):40–7. 22. Elias KM, Stone AB, McGinigle K, Tankou JI, Scott MJ, Fawcett WJ, et al. The Reporting on ERAS Compliance, Outcomes, and Elements Research
(RECOvER) checklist: a joint statement by the ERAS(I) and ERI(R) USA
societies. World J Surg. 2019;43(1):1–8. 23. Vanhie A, Meuleman C, Tomassetti C, Timmerman D, D’Hoore A, Wolthuis
A, et al. Consensus on recording deep endometriosis surgery: the
CORDES statement. Hum Reprod. 2016;31(6):1219–23. 24. ICH Expert Working Group. ICH harmonised tripartite guidelines: general
considerations for clinical trials E8. 1998. Available from: https://www. 24. ICH Expert Working Group. ICH harmonised tripartite guidelines: general
considerations for clinical trials E8. 1998. Available from: https://www.
|
https://openalex.org/W2149470396
|
https://europepmc.org/articles/pmc2671603?pdf=render
|
English
| null |
Use of Self-Selected Postures to Regulate Multi-Joint Stiffness During Unconstrained Tasks
|
PloS one
| 2,009
|
cc-by
| 10,926
|
Use of Self-Selected Postures to Regulate Multi-Joint
Stiffness During Unconstrained Tasks 1 Sensory Motor Performance Program, Rehabilitation Institute of Chicago, Chicago, Illinois, United States of America, 2 Department of Biomedical Engineering,
Northwestern University, Evanston, Illinois, United States of America, 3 Department of Mechanical Engineering, National Chiao Tung University, Hsinchu, Taiwan, 4 Brain
Research Center, National Chiao Tung University, Hsinchu, Taiwan, 5 Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, Illinois,
United States of America Abstract Gribble, The University of Western Ontario, Canada
Received January 12, 2009; Accepted April 1, 2009; Published May 1, 2009
Copyright: 2009 Trumbower et al This is an open access article distributed under the terms of the Creative Commons Attribution License which permits utky MA, Yang B-S, Perreault EJ (2009) Use of Self-Selected Postures to Regulate Multi-Joint Stiffness During Unconstrained
doi:10.1371/journal.pone.0005411 Received January 12, 2009; Accepted April 1, 2009; Published May 1, 2009 Copyright: 2009 Trumbower 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. supported by NIH grants K25 HD044720 and NS053813. The funders had no role in study design, data collection and analysis, decision to
f the manuscript. Funding: This work was supported by NIH grants K25 HD044720 and NS053813. The funders had no role in study design, data collecti
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 exist. * E-mail: e-perreault@northwestern.edu * E-mail: e-perreault@northwestern.edu . These authors contributed equally to this work. . These authors contributed equally to this work. orientation of maximal stiffness [2,4]. At a fixed posture, stiffness
can be regulated through changes in muscle activation. These
changes in activation can occur via feedforward changes in co-
contraction [5,6] or through changes in the sensitivity of reflex
feedback [7–10]. Numerous studies have focused on how changes
in muscle activation can lead to task-appropriate changes in limb
stiffness, increasing limb stability and endpoint accuracy during
both reaching and postural tasks [9,11–14]. However, Milner
suggested that these changes and their corresponding functional
consequences can be small relative to those associated with
changes in limb posture [15]. Because most studies examining the
control of limb stiffness have constrained limb posture, it is unclear
if posture selection is a critical component of endpoint stiffness
regulation during more natural tasks in which the kinematic
redundancies of the arm can be exploited to change posture
without altering endpoint location. PLoS ONE | www.plosone.org Abstract Background: The human motor system is highly redundant, having more kinematic degrees of freedom than necessary to
complete a given task. Understanding how kinematic redundancies are utilized in different tasks remains a fundamental
question in motor control. One possibility is that they can be used to tune the mechanical properties of a limb to the
specific requirements of a task. For example, many tasks such as tool usage compromise arm stability along specific
directions. These tasks only can be completed if the nervous system adapts the mechanical properties of the arm such that
the arm, coupled to the tool, remains stable. The purpose of this study was to determine if posture selection is a critical
component of endpoint stiffness regulation during unconstrained tasks. Methodology/Principal Findings: Three-dimensional (3D) estimates of endpoint stiffness were used to quantify limb
mechanics. Most previous studies examining endpoint stiffness adaptation were completed in 2D using constrained
postures to maintain a non-redundant mapping between joint angles and hand location. Our hypothesis was that during
unconstrained conditions, subjects would select arm postures that matched endpoint stiffness to the functional
requirements of the task. The hypothesis was tested during endpoint tracking tasks in which subjects interacted with
unstable haptic environments, simulated using a 3D robotic manipulator. We found that arm posture had a significant effect
on endpoint tracking accuracy and that subjects selected postures that improved tracking performance. For environments
in which arm posture had a large effect on tracking accuracy, the self-selected postures oriented the direction of maximal
endpoint stiffness towards the direction of the unstable haptic environment. Conclusions/Significance: These results demonstrate how changes in arm posture can have a dramatic effect on task
performance and suggest that postural selection is a fundamental mechanism by which kinematic redundancies can be
exploited to regulate arm stiffness in unconstrained tasks. Citation: Trumbower RD, Krutky MA, Yang B-S, Perreault EJ (2009) Use of Self-Selected Postures to Regulate Multi-Joint Stiffness During Unconstrained
Tasks. PLoS ONE 4(5): e5411. doi:10.1371/journal.pone.0005411
Editor: Paul L. Introduction Many functional tasks, such as the use of hand tools, compromise
the stability of the arm in a specific direction [1]. For example, use of
a screwdriver compromises limb stability in directions orthogonal to
the long axis of the tool, toward which it tends to topple when
exerting forces against the head of a screw. This task only can be
performed if the nervous system adapts the mechanical properties of
the arm such that the arm, coupled to the tool, remains stable. One
way to quantify arm stability during such postural tasks is through
estimates of endpoint stiffness, which characterizes the static
mechanics of the limb as seen at the point of contact with the
environment [2]. Hogan [3] first proposed that endpoint stiffness
may be regulated specifically to compensate for such instabilities. There are a number of ways by which endpoint stiffness can be
regulated. Changes in limb posture have a profound effect on the PLoS ONE | www.plosone.org May 2009 | Volume 4 | Issue 5 | e5411 May 2009 | Volume 4 | Issue 5 | e5411 1 Postural Control of Stiffness limb for estimating endpoint stiffness in the second set of
experiments. The robot was instrumented to measure endpoint
displacements and forces, both which were recorded at 1.25 kHz. During the second set of experiments, endpoint displacement was
redundantly measured using an optical motion analysis system
[Optotrak 3020; Northern Digital, Waterloo, Ontario] with an
accuracy of 0.1 mm. The optical tracking data were used to
correct for small errors in the endpoint displacement measures
obtained from the robot, due to compliance between the robot’s
end effector and its displacement sensors. The Optotrak tracks the
motion of infrared LEDs, which were mounted on a rigid body
attached to a wrist cast and used to monitor endpoint location. All
optical data were collected at 250 Hz and later interpolated to
1.25 kHz to match the sampling rate of the robotic system. Data
acquisition was synchronized between the two systems through the
use of a common clock and trigger. The purpose of this study was to determine if posture selection is
a critical component of endpoint stiffness regulation during
unconstrained tasks. Our hypothesis was that subjects would
select arm postures that matched endpoint stiffness to the
functional requirements of the task. Introduction The hypothesis was tested
during endpoint tracking tasks in which subjects interacted with
unstable haptic environments, simulated using a three degrees of
freedom (3DOF) robotic manipulator. The study had three specific
goals. The first was to quantify how arm posture influenced
tracking performance during interactions with unstable environ-
ments. The second was to determine if subjects self-selected similar
postures when interacting with the same haptic environment. The
third goal was to determine if the self-selected postures oriented
the direction of maximal endpoint stiffness in a manner that would
best compensate for the unstable nature of the haptic environ-
ment. Our results demonstrate how changes in arm posture can
have a dramatic effect on task performance and suggest that
postural selection is a fundamental mechanism by which arm
stiffness is controlled in unconstrained tasks. Protocols Endpoint tracking. The purpose of the first experiment was
to quantify the influence of prescribed and self-selected arm
postures on the ability to control hand position during interactions
with unstable environments. We attempted to have subjects
interact with the simulated environments under functionally
relevant conditions by removing all physical restraints between
the subject and the robot and by having subjects support the
weight of their arm in all tasks. Subjects stood upright with the feet
side-by-side during these experiments, with the shoulders parallel
to the Y-axis (Figure 1). They interacted with the robot by
grasping a plastic sphere attached to the endpoint. The center of
the sphere was defined as the endpoint of the arm. The shoulder
and elbow were unconstrained in these first experiments, requiring
subjects to support the weight of the arm against gravity. The only
postural constraint was that the hand always was positioned in the
sagittal plane at the height of the sternum, so as to restrict the
experimental degrees of freedom to a manageable number. Subjects Nine subjects, 24 to 40 years of age (7 males and 2 females),
participated in this study. Subjects had no history of neurological
or orthopedic impairments of the upper limbs. Data were collected
in two separate experimental sessions. All subjects participated in
the first experiment and five subjects returned to the laboratory for
the second. The haptic environment simulated in these experiments was
primarily a ‘‘negative-stiffness’’ spring, acting along a line in 3D
space. These environments were oriented into and away from the
body in the sagittal plane (6X; Figure 1A), in the medial-lateral
direction (6Y; Figure 1B), or in the vertical direction (6Z;
Figure 1C). As subjects moved the position of their hand away (x,
y, or z) from the neutral position (xo, yo, or zo), the robot pushed
the hand further with a force (F) proportional to the distance Ethics Statement The protocol was approved by the Institutional Review Board
of Northwestern University’s Office for the Protection of Research
Subjects (IRB#1322-001). All subjects gave written, informed
consent and were free to withdraw at any time. Equipment Subjects interacted with a 3DOF robotic manipulator [Haptic-
Master; FCS Control Systems, The Netherlands; Figure 1A–1C]
during both experiments. The robot uses an admittance control
algorithm, allowing it to simulate a range of haptic environments
[16]. It was used to simulate unstable haptic environments during
the first set of experiments and as a position servo to perturb the Figure 1. Experimental setup for tracking task. Subjects stood upright and used the arm to interact with unstable haptic environments
oriented along the X (A), Y (B) or Z (C) measurement axes. During target tracking, movements were constrained to lie along these axes by 50 kN/m Figure 1. Experimental setup for tracking task. Subjects stood upright and used the arm to interact with unstable haptic environments
oriented along the X (A), Y (B) or Z (C) measurement axes. During target tracking, movements were constrained to lie along these axes by 50 kN/m
virtual walls. doi:10.1371/journal.pone.0005411.g001 May 2009 | Volume 4 | Issue 5 | e5411 PLoS ONE | www.plosone.org PLoS ONE | www.plosone.org 2 Postural Control of Stiffness prescribed postures were chosen to examine the effect of hand
position and shoulder abduction, the two unconstrained degrees of
freedom, on tracking performance. For the prescribed postures the
hand was located directly in front of the sternum at a distance of
either 1/3 or 5/6 the length of the arm, and the shoulder was
abducted to either ,20u or ,80u. The lesser angle was chosen to
position the arm close to the trunk, while avoiding any contact; the
greater angle was chosen as required to keep the forearm
horizontal. In both cases, the available angles were limited by
the constraint of keeping the hand in front of the sternum. Hand
location was set with a resolution of 1 cm, as measured using a
tape measure. Shoulder angles were set manually with a
goniometer and then remeasured prior to the start of each
experiment. The actual abduction angles were 2162u and 7163u. For the self-selected posture, subjects had their choice of hand
location and shoulder abduction angle, with only two restrictions:
(1) the hand was restricted to be in front of the sternum and (2) the
arm was not allowed to touch the trunk or be lifted above the
horizontal plane. The maintenance of consistent arm postures was
monitored visually during the experiment by observing the height
of the elbow relative to the starting position. Equipment Two consecutive endpoint tracking trials were repeated at
each of the four prescribed postures, followed by two trials at the
self-selected posture. Subjects were allowed as much time as
needed to choose a self-selected posture, but once the posture
was selected it was kept constant throughout the course of the
data collection trials. Allowing subjects to stand during these
tracking experiments made it easy for them to manipulate the
available degrees of freedom and choose an appropriate self-
selected posture. For each environment with which subjects
interacted
(X,
Y,
and
Z),
all
five
postures
were
tested
consecutively before subjects interacted with a new environment. A total of 30 trials were performed (5 postures62 trials63
environments). The sequential orders of the prescribed postures
and the haptic environments were randomized across subjects. A
minimum of a two minute rest period was provided between
successive trials to prevent fatigue. Endpoint stiffness. The purpose of the second experiment
was to quantify the orientation of maximal endpoint stiffness at the
self-selected postures chosen during interactions with each of the
three unstable environments (X, Y, and Z). For this purpose the
robot was configured as a stiff position servo and used to apply 3D,
stochastic perturbations to the endpoint of the arm. The
perturbations were similar to those we have used previously
[17,18], having a standard deviation of 3.0 mm and frequency
spectrum that was flat up to 5 Hz, beyond which it decayed at a
rate of 40 dB/decade. Subjects were rigidly attached to the robot
using a custom-fitted fiberglass cast. The cast extended ,1/3 of
the distance from the wrist to the elbow, fixing the wrist in the
neutral position. The cast was mounted to a low mass, custom
gimbal attached to the end of the manipulator, allowing the
application of pure endpoint forces and no moments to the arm. The gimbal was instrumented with potentiometers that were used
to provide subjects with visual feedback of arm posture so that a
fixed posture could be maintained throughout each trial. The
gimbal’s center was positioned along the axis of the forearm, under
the middle metacarpophalangeal joint, which we defined as the
endpoint of the limb for these experiments. Subjects were seated
during these experiments and harnessed at the shoulders and waist
to an immobile chair. Equipment Trials in which elbow
height changed by more than 62 cm were repeated. Table 1. Haptic environments used during endpoint tracking. Subject
Strength of Unstable Haptic Environment (N/m)
X
Y
Z
1*
2500
2500
2500
2*
2500
2500
2500
3*
2500
2500
2500
4
2500
2500
2500
5
2500
2500
2500
6*
2300
2300
2300
7*
2500
2400
2300
8
2500
2500
2500
*denotes that subject participated in endpoint stiffness experiment. doi:10.1371/journal.pone.0005411.t001 Table 1. Haptic environments used during endpoint tracking. Subject
Strength of Unstable Haptic Environment (N/m)
X
Y
Z
1*
2500
2500
2500
2*
2500
2500
2500
3*
2500
2500
2500
4
2500
2500
2500
5
2500
2500
2500
6*
2300
2300
2300
7*
2500
2400
2300
8
2500
2500
2500
*denotes that subject participated in endpoint stiffness experiment. doi:10.1371/journal.pone.0005411.t001 *denotes that subject participated in endpoint stiffness experiment. doi:10.1371/journal.pone.0005411.t001 *denotes that subject participated in endpoint stiffness experiment. doi:10.1371/journal.pone.0005411.t001 between the hand and the neutral point, according to the
equations displayed in Figure 1. The strength of the unstable
haptic environments was 2500 N/m for all subjects except two
who could not maintain endpoint stability when interacting with
an environment of this strength (Table 1). For directions
orthogonal to the line of instability, the haptic environment was
programmed to be rigid, having a stiffness of 50 kN/m. The
haptic environment had a simulated mass of 5.0 kg and was
critically damped in all directions; virtual stops were located at a
distance of 6100 mm from the neutral position to ensure the
safety of subjects. The negative stiffness values used in these
experiments were greater than those reported in previous similar
experiments [15], as was needed to challenge the subjects’ ability
to
maintain
stable
endpoint
positions. Two
factors
likely
contributed to this need. The first is that subjects were required
to support the weight of their limb during our experiments. The
increased muscle activation associated with this task would
increase endpoint stiffness beyond that in the supported conditions
reported previously. The second factor is our use of an admittance
controller. This controller required the simulated haptic environ-
ment to have mass as well as stiffness. These simulated inertial
properties provided some resistance transient perturbations of
posture, and also may have contributed to the increased negative
stiffness required in these experiments. PLoS ONE | www.plosone.org Equipment We chose to restrain subjects at the trunk
and shoulders so that estimates of endpoint stiffness would
characterize only the mechanical properties of the arm, not the
net mechanical properties of the arm coupled to the unconstrained The subjects’ task was to track specified endpoint target
locations while interacting with the unstable haptic environ-
ments. The target was randomly positioned in one of three
locations (210 mm, 0 mm, and +10 mm) relative to the neutral
point of the haptic environment. The target was held at each
location for four seconds before it appeared at the next location. Each trial contained 19 target jumps, lasting for a total of 76 s. Subjects received visual feedback of endpoint and target location
and were instructed to move to each target as rapidly and
accurately as possible. Subjects were instructed to support the
weight of their limb during these experiments and not to rely on
the rigid walls orthogonal to the haptic instabilities. Visual
feedback of endpoint forces was not provided during the tracking
experiments, but a subsequent analysis indicated that subjects
supported
approximately
85%
or
their
arm
mass
during
tracking. The average forces exerted against the X, Y and Z
constraints were 1.360.2 N, 0.060.0 N and 21.860.3 N,
respectively (mean6SE). To test the influence of arm posture on the ability to control the
endpoint location, subjects performed the tracking task at four
prescribed arm postures, then at one self-selected posture. The PLoS ONE | www.plosone.org May 2009 | Volume 4 | Issue 5 | e5411 3 Postural Control of Stiffness shoulder girdle and trunk [19,20] since we only manipulated arm
postures in these experiments. ally observed immediately following perturbation onset. Four trials
were conducted for each combination of posture and endpoint
force, resulting in a total of 48 trials for each subject (3 self-selected
postures64 forces64 repetitions). The subjects’ task was to maintain a fixed arm posture while
exerting a constant endpoint force, but not reacting to the
perturbation. The endpoint force targets were 65 N or 610 N. These magnitudes were chosen to be similar to those encountered
during the endpoint tracking tasks. The direction of the target
forces was matched to the orientation of the haptic environment
for which each posture was selected. Equipment For example, target forces
were in the X direction when the subject was positioned in the
posture they selected to interact with the environment unstable
along the X direction. Real-time visual feedback of the 3D
endpoint force was displayed to the subject (Figure 2B). The angle
of shoulder elevation, which was the only unconstrained degree of
freedom, also was displayed. During each trial (Figure 2C and 2D),
subjects first supported the arm’s weight against gravity for 2 s,
after which a visual cue corresponding to the target force was
presented. Once the target force was reached and held steady
(within 61 N) for 0.7 s, the robot applied a stochastic perturbation
that lasted for 60 s. Only the final 55 s of each trial were analyzed,
to avoid the small non-stationary corrective movements occasion- We were interested in determining how well the self-selected
postures aligned the direction of maximal endpoint stiffness with
the orientation of the unstable haptic environments. To interpret
our results, we needed also to quantify the range of endpoint
stiffness orientations that could be achieved by moving the arm
throughout the range of postures allowed in these experiments. This was accomplished by estimating endpoint stiffness from two
subjects at 9 prescribed postures spanning the allowable range. These corresponded to all combinations of three hand positions
and three shoulder abduction angles: the hand positions were (1)
as near and (2) as far as possible from the sternum, and (3)
midway in between; the shoulder abduction angles were (1) full
abduction (,80u, keeping the forearm horizontal), (2) the arm
nearly touching the trunk (,20u), and (3) midway between
(,45u). Stiffness was estimated while subjects applied 610 N in
the X, Y, and Z directions at each posture. All other aspects of
this experiment were identical to those described above. Figure 2. Stiffness estimation experiments. (A) Subjects were seated and strapped to a rigid chair in all stiffness estimation experiments. (B
Visual feedback of the three-dimensional target endpoint force and measured endpoint force was provided to the subject, as was the orientation o
the arm. Arm orientation was displayed by the angle of a bar attached to the endpoint force cursor. (C) Endpoint displacements in the X, Y, and Z
directions are shown for a typical stiffness estimation experiment. (D) The corresponding endpoint forces. In this trial, the subject was instructed to
generate 10 N in the +X direction. Analysis The influence of posture on
tracking was assessed using linear mixed-effects model computed
in R [21]. The independent factors in this analysis were hand
position and shoulder abduction angle; subjects were treated as a
random
factor. All
confidence
intervals
are
reported
as
mean6standard error. Figure 3. Refined estimate of endpoint displacement. An
instrumental variable (IV) technique was used to increase the accuracy
of the measured endpoint displacement. The figure shows typical data
measured along the X axis. The displacement measured by the robot
sensors is shown by the black dashed line; it differs from the true
displacement due to compliance in the robot transmission. A noisy, but
more accurate estimate was obtained using optical tracking (thick gray
line). The combined estimate, obtained using instrumental variables, is
shown by the solid black line. doi:10.1371/journal.pone.0005411.g003 Figure 3. Refined estimate of endpoint displacement. An
instrumental variable (IV) technique was used to increase the accuracy
of the measured endpoint displacement. The figure shows typical data
measured along the X axis. The displacement measured by the robot
sensors is shown by the black dashed line; it differs from the true
displacement due to compliance in the robot transmission. A noisy, but
more accurate estimate was obtained using optical tracking (thick gray
line). The combined estimate, obtained using instrumental variables, is
shown by the solid black line. doi:10.1371/journal.pone.0005411.g003 compensate for any transmission compliance (Figure 3). This led to
a small (1.360.3%), but significant (paired t-test; t = 4.79;
P,0.001), improvement in the ability to estimate the force
response to the applied perturbations. The use of this technique
also reduces the possibility for bias errors associated with noise on
the input [25]. Because this study was concerned with postural control, we
chose to focus on the static component of endpoint impedance,
endpoint elasticity or stiffness. The dynamics equations describing
impedance can be expressed in the frequency domain by Eq. 1,
where f is frequency, Fx(f), Fy(f), Fz(f) are the Fourier transforms of
the endpoint forces along each measurement axis, X(f), Y(f), and
Z(f) are the Fourier transforms of the endpoint displacements, and
Hij(f) are the nine transfer functions relating displacements in the
direction j to forces in the direction i. These transfer functions were
estimated nonparametrically [23], and then parameterized by
fitting a second order model with inertial, viscous, and elastic
parameters. Equipment Data from the first 2 seconds of each trial were used to record baseline values (‘a’). Afterwards, a visual cue
instructed the subject to generate an endpoint force to match the target force. Once the target force was held steady, a stochastic perturbation wa
applied (‘b’), lasting for 60 s. doi:10.1371/journal.pone.0005411.g002 Figure 2. Stiffness estimation experiments. (A) Subjects were seated and strapped to a rigid chair in all stiffness estimation experiments. (B)
Visual feedback of the three-dimensional target endpoint force and measured endpoint force was provided to the subject, as was the orientation of
the arm. Arm orientation was displayed by the angle of a bar attached to the endpoint force cursor. (C) Endpoint displacements in the X, Y, and Z
directions are shown for a typical stiffness estimation experiment. (D) The corresponding endpoint forces. In this trial, the subject was instructed to
generate 10 N in the +X direction. Data from the first 2 seconds of each trial were used to record baseline values (‘a’). Afterwards, a visual cue
instructed the subject to generate an endpoint force to match the target force. Once the target force was held steady, a stochastic perturbation was
applied (‘b’), lasting for 60 s. doi:10.1371/journal.pone.0005411.g002 May 2009 | Volume 4 | Issue 5 | e5411 PLoS ONE | www.plosone.org 4 Postural Control of Stiffness Figure 3. Refined estimate of endpoint displacement. An
instrumental variable (IV) technique was used to increase the accuracy
of the measured endpoint displacement. The figure shows typical data
measured along the X axis. The displacement measured by the robot
sensors is shown by the black dashed line; it differs from the true
displacement due to compliance in the robot transmission. A noisy, but
more accurate estimate was obtained using optical tracking (thick gray
line). The combined estimate, obtained using instrumental variables, is
shown by the solid black line. doi:10.1371/journal.pone.0005411.g003
Postural Control of Stiffness We also ran a control experiment to determine the influence of
pronation/supination on the orientation of maximal endpoint
stiffness. It was difficult to accurately measure pronation/
supination angles during the self-selected tracking experiments,
and we were concerned that differences in pronation/supination
between the tracking and stiffness experiments could have altered
our results. Equipment Therefore, we quantified the influence of pronation/
supination in two subjects by estimating endpoint stiffness with the
forearm supinated to 45u, pronated to 45u, and in the neutral
position for a single arm posture (elbow flexed to 90u; shoulder
elevated to 70u). Target forces were 10 N along the X and Y axes. All other aspects of this control experiment were identical to those
described above. Analysis These fits were conducted over the frequency range of
0–10 Hz using least squares optimization, as we have described
previously [18,23]. This resulted in 363 matrices characterizing
the endpoint inertia (I), viscosity (B) and stiffness (K). Endpoint
stiffness
experiments. Endpoint
impedance
completely
describes
the
dynamic
relationship
between
displacements applied to the hand and the forces generated in
response. Endpoint stiffness is the static component of impedance
and can be obtained from these more general estimates. Endpoint
impedance was calculated from the endpoint position and force
data collected during the stochastic perturbation experiments
using nonparametric system identification techniques we have
described previously [23]. Force data were utilized as recorded by
the robot. The redundant displacements measured with the
motion analysis system were used to account for compliance
between the robot’s displacement sensors and endpoint. To
enhance the resolution of the optically recorded displacement
data, we used an instrumental variables technique [24] to predict
the
optically
measured
endpoint
displacements
from
the
displacements estimated from the robot sensors. This technique
could be used because the displacements estimated from the robot
sensors were correlated with those measured by the motion
analysis system, but not with the noise in the motion analysis data,
which arose mainly from quantization errors. The resulting
displacement data had reduced noise but were corrected to Fx f
ð Þ
Fy f
ð Þ
Fz f
ð Þ
2
64
3
75~t
Hxx f
ð Þ
Hxy f
ð Þ
Hxz f
ð Þ
Hyx f
ð Þ
Hyy f
ð Þ
Hyz f
ð Þ
Hzx f
ð Þ
Hzy f
ð Þ
Hzz f
ð Þ
s
X f
ð Þ
Y f
ð Þ
Z f
ð Þ
2
64
3
75
ð1Þ ð1Þ Three measurements were used to evaluate the quality of the
estimated impedance models. First, we evaluated the nonpara-
metric fit for each trial using the multiple correlation coefficient,
R2, to characterize the relationship between the predicted and
measured endpoint forces. Next, multiple coherence was used to
determine the range of frequencies for which the linear transfer
functions were appropriate [25]. Finally, we quantified how well
the predicted endpoint force, obtained using the estimated I, B,
and K parameters, approximated the actual force, again using R2. Endpoint stiffness can be described graphically using an
ellipsoid [2]. Analysis y
Endpoint tracking experiments. We hypothesized that
arm posture would significantly affect each subject’s ability to
accurately control hand position during interactions with unstable
environments. This was tested by quantifying the error with which
subjects tracked the endpoint target, then comparing this error
across the tested postures. Tracking error for each trial (TERR) was
quantified using the root mean square (RMS). Since our goal was
to evaluate the ability to hold the hand at each of the stationary
targets, not the ability to move between targets, only the final 3 s
of the 4 s hold phases were used for the analysis. To facilitate
comparing data across subjects and conditions, tracking errors at
the 4 prescribed postures were normalized by the error at the self-
selected posture for each environment. The influence of posture on
tracking was assessed using linear mixed-effects model computed
in R [21]. The independent factors in this analysis were hand
position and shoulder abduction angle; subjects were treated as a
random
factor. All
confidence
intervals
are
reported
as
mean6standard error. A secondary goal of the tracking experiment was to determine if
subjects self-selected postures with similar hand positions and
shoulder abduction angles when interacting with the same haptic
environment. This was examined by plotting the relationship
between the selected shoulder abduction angles and hand positions
for each self-selected postures. Statistical comparisons of the
postures selected for each haptic environment were obtained using
a jackknife analysis [22] to account for potentially non-gaussian
distributions. Significance levels of 0.05 were used for these
numerically evaluated tests. Endpoint tracking experiments. We hypothesized that
arm posture would significantly affect each subject’s ability to
accurately control hand position during interactions with unstable
environments. This was tested by quantifying the error with which
subjects tracked the endpoint target, then comparing this error
across the tested postures. Tracking error for each trial (TERR) was
quantified using the root mean square (RMS). Since our goal was
to evaluate the ability to hold the hand at each of the stationary
targets, not the ability to move between targets, only the final 3 s
of the 4 s hold phases were used for the analysis. To facilitate
comparing data across subjects and conditions, tracking errors at
the 4 prescribed postures were normalized by the error at the self-
selected posture for each environment. Effect of Posture on Tracking Performance Arm posture had a strong influence on tracking error. This can
be seen in Figure 4A, which displays typical endpoint position data
for tracking performed during interactions with the Y instability. A
single trial is shown for each prescribed posture. Trials in which
endpoint position (thin black lines) closely follows the target (thick
gray lines) correspond to trials with low error. For example, across
the prescribed postures tracking error was lowest with the hand at
1/3 arm length from the sternum and the shoulder abducted to
90u (elbow high). Even lower tracking errors were recorded at the
self-selected posture (Figure 4B), which for this subject and task
corresponded to a normalized hand distance of ,30% arm length
from the sternum to the hand and a shoulder abduction angle of
71u. The tracking results for this subject are summarized in
Figure 4C, which displays the average tracking error for each trial
displayed in Figure 4A and 4B. Figure 5. Group data for the endpoint tracking task. All data
have been normalized to the tracking errors recorded at the self-
selected posture; a normalized value of 1.0 is indicated by the dashed
line. Characters depict the prescribed postures during interactions with
each of the haptic environments. Tracking errors significantly greater
than those measured at the self-selected posture are indicated by an *
(p,0.05). doi 10 1371/jo rnal pone 0005411 g005 Across all subjects, tracking errors were lowest at the self-
selected postures. This can be seen from the group data presented
in Figure 5. In this figure, the tracking errors from each subject are
normalized by those recorded at the self-selected posture for each environment. Across all conditions, the normalized tracking errors
are never significantly less than 1, indicating that the greatest
tracking accuracy was achieved at the self-selected postures. Figure 4. Endpoint tracking data collected during individual
trials from a single subject. Data were collected during interactions
with the Y instability. Black and gray lines correspond to the actual and
target positions, respectively. (A) Data collected at the four prescribed
postures, as indicated by the characters shown in each row and column. ‘Elbow low’ and ‘elbow high’ correspond to 25u and 90u of shoulder
abduction, respectively. ‘1/3’ and ‘5/6’ correspond to hand position at 1/
3 and 5/6 arm length from the sternum, respectively. (B) Endpoint
tracking data from the same subject at the self-selected posture. Effect of Posture on Tracking Performance (C)
RMS tracking error for each of the trials presented in Figure 3A and 3B. Labels correspond to ‘hand position (1/3 or 5/6 arm length) +elbow
height (Low or High)’ or the self-selected posture (‘SS’). doi:10.1371/journal.pone.0005411.g004 The influence of arm posture on tracking accuracy varied with
the directional characteristics of the environment. Posture had the
greatest influence on tracking accuracy during interactions with
the Z instability. The effects of both hand position and shoulder
abduction
were
significant
(tposition = 4.82,
pposition,0.001;
tshoulder = 3.73, pshoulder,0.001), but the interaction term was not
(tinteraction = 1.47; pinteraction = 0.15). For the range of postures
tested, changes in hand distance had a slightly larger effect
(1.7260.36) than changes in shoulder angle (1.2460.33), although
these differences did not reach statistical significance. Finally, all
prescribed postures had a tracking error that was significantly
greater than that at the self-selected posture (all t.3.44; all
p,0.004), except for the posture corresponding to the hand held
at 1/3 arm length from the body and the shoulder abducted to
25u. A similar but less dramatic influence of arm posture was
observed during interactions with the Y instability. Again, changes
in both hand position and shoulder abduction had significant
effects
on
tracking
accuracy
(tposition = 7.52,
pposition,0.001;
tshoulder = 2.67, pshoulder = 0.01), while the interaction term was
insignificant (tinteraction = 0.18; pinteraction = 0.86). Changes between
the prescribed hand positions had a significantly larger effect
(0.8160.11) than that due to changes between the prescribed
shoulder abduction angles (0.2760.10) during interactions with
the Y instability. The only prescribed posture that did not have
significantly greater tracking errors than the self-selected postures
was with the shoulder abducted to 90u and the hand at 1/3 arm
length from the sternum; all others had larger tracking error (all
t.3.04; all p,0.007) than the self-selected posture. Figure 4. Endpoint tracking data collected during individual
trials from a single subject. Data were collected during interactions
with the Y instability. Black and gray lines correspond to the actual and
target positions, respectively. (A) Data collected at the four prescribed
postures, as indicated by the characters shown in each row and column. ‘Elbow low’ and ‘elbow high’ correspond to 25u and 90u of shoulder
abduction, respectively. ‘1/3’ and ‘5/6’ correspond to hand position at 1/
3 and 5/6 arm length from the sternum, respectively. (B) Endpoint
tracking data from the same subject at the self-selected posture. Analysis The long axis of the ellipsoid describes the direction PL PLoS ONE | www.plosone.org May 2009 | Volume 4 | Issue 5 | e5411 5 Postural Control of Stiffness Figure 5. Group data for the endpoint tracking task. All data
have been normalized to the tracking errors recorded at the self-
selected posture; a normalized value of 1.0 is indicated by the dashed
line. Characters depict the prescribed postures during interactions with
each of the haptic environments. Tracking errors significantly greater
than those measured at the self-selected posture are indicated by an *
(p,0.05). doi:10.1371/journal.pone.0005411.g005 in which the arm is most resistant to postural disturbances. The
principal axes of the stiffness ellipsoid were calculated using
singular value decomposition, as described by Gomi and Osu [26]. Self-Selected Postures At each posture, stiffness was estimated as subjects exerted 4
levels of voluntary force. The results from all force levels at a given
posture were averaged to provide a single estimate of stiffness
orientation. This was possible because the small bias forces used in
this study did not cause consistent changes in the orientation of
maximal endpoint stiffness. This was assessed using an ANOVA to
compare the influence of endpoint force on the estimated
orientation of maximal endpoint stiffness. Separate ANOVAs
were performed for each posture. In all cases, the influence of
force was not significant (all p. = 0.30). It is important to note that
the endpoint force targets along each of the measurement axes
contributed to only a fraction of the muscle activity required to
complete the postural tasks in this study. Subjects also were
required to support the weight of their limb in all experiments and
the muscle activity required to accomplish that goal likely
dominated the measured endpoint stiffness. When subjects do
not support the weight of their limb, it is well documented that
small changes in endpoint force can have significant effects on the
orientation of maximal endpoint stiffness [17,26,27]. The self-selected postures were different during interactions
with each haptic environment. This can be seen in Figure 6, which
summarizes the postures selected by all subjects. Shoulder
abduction was larger during interactions with the Y-instability
relative to that during interactions with the other two haptic
environments. Hand distance from the sternum was greatest
during interactions with the X-instability. No other comparisons
reached statistical significance at the level of p,0.05. Subjects tended to self-select similar postures when interacting
with environments in which posture had a large effect on tracking
accuracy. This can be seen by the variability of the self-selected
postures for each of the haptic environments. Shoulder angle had
the most dramatic effect on tracking accuracy during interactions
with the Z instability and the variance of the self-selected postures
was lowest during interactions with this haptic environment
(p,0.05). There also was a tendency for reduced variability of the
self-selected hand positions during interactions with the Z and Y
instabilities, although this did not reach statistical significance
when compared to the large variability observed during interac-
tions with the X instability. Stiffness Although there was variability in the self-selected postures, the
90% confidence ellipsoids of the postures selected for each haptic
environment each encompass one of the prescribed postures used
during the tracking experiments. These are the same prescribed
postures for which the tracking error was not significantly different
than that at the self-selected posture (Figure 5). The self-selected postures for each environment tended to orient
the direction of maximal stiffness toward the direction of the
environmental instability. This can be seen in Figure 8, which
displays typical endpoint stiffness ellipsoids overlaid on characters
that depict the posture selected by this subject. For example,
during interactions with the Y instability this subject positioned the
forearm in the horizontal plane and the hand close to the sternum. At this posture, maximal stiffness was oriented primarily in the
horizontal plane, rotated toward the Y axis (Figure 8, middle row). For interactions with the Z instability, the shoulder abduction The self-selected postures for each environment tended to orient
the direction of maximal stiffness toward the direction of the
environmental instability. This can be seen in Figure 8, which
displays typical endpoint stiffness ellipsoids overlaid on characters
that depict the posture selected by this subject. For example,
during interactions with the Y instability this subject positioned the
forearm in the horizontal plane and the hand close to the sternum. Effect of Posture on Tracking Performance (C)
RMS tracking error for each of the trials presented in Figure 3A and 3B. Labels correspond to ‘hand position (1/3 or 5/6 arm length) +elbow
height (Low or High)’ or the self-selected posture (‘SS’). doi:10.1371/journal.pone.0005411.g004 The least dramatic effect of posture on tracking accuracy occurred
for interactions with the X instability. The influence of shoulder
abduction on the observed tracking errors was small but significant
(tshoulder = 2.46, pshoulder = 0.017), but the influence of hand position
did not reach significance (tposition= 1.82, pposition= 0.074); the
interaction term also did not reach significance (tinteraction= 0.64, May 2009 | Volume 4 | Issue 5 | e5411 PLoS ONE | www.plosone.org 6 Postural Control of Stiffness pinteraction = 0.52). There was no significant difference between
the influence of shoulder abduction (0.2060.08) and hand
position (0.1760.09). Even with these small posture-dependent
changes in tracking accuracy, tracking performance at most
prescribed postures was significantly worse than that at the self-
selected posture. The two were statistically indistinguishable only
for the prescribed posture corresponding to the hand at 5/6 arm
length from the sternum and the shoulder abducted to 25u
(t = 0.86, p = 0.404). Tracking accuracy was worse at all other
prescribed postures (all t.3.18; all p,0.006). transfer functions. Across all subjects and bias forces, the average
R2 value for force data predicted by these transfer functions was
92.661.1%. Additionally, the multiple coherence functions for
each output approached 1.0 between ,2–10 Hz. (Figure 7B). This
result was consistent across subjects and indicated that for these
frequencies the recorded endpoint forces were well described using
a linear model. Finally, these nonparametric transfer functions
(Figure 7A; black lines) were well characterized by second-order
models (Figure 7A; gray lines) over the range of 0–10 Hz. These
parametric models described 71.462.0% of the data variance over
this frequency range. Controlling for Forearm Rotation angle was small, which had the effect of rotating the direction of
maximal stiffness vertically, toward the Z axis (Figure 8; third row). This subject extended the arm during interactions with the X
instability, which tended to orient the direction of maximal
stiffness towards the X axis (Figure 8; top row). Rotation of the forearm did not influence estimates of maximal
stiffness orientation. Since the forearm postures selected during the
tracking experiments did not necessarily match those during the
estimation of arm stiffness, we performed a control experiment to
determine the influence of forearm rotation on endpoint stiffness
orientation. Posture dependent changes in stiffness were examined
using a linear mixed-effects model to examine changes in stiffness
orientation. The independent factors were forearm posture and
the level of voluntary force; subjects were treated as a random
factor, and the dependent factors were the angles of the stiffness
orientation vector projected into the XY and YZ planes. For both
projections, the influence of posture was small. The largest change
in
stiffness
orientations
between
the
tested
postures
was
1.9761.33u, which was between the most supinated and pronated
positions, This effect did not reach statistical significance (t = 1.47,
p = 0.15) and was small relative to the changes due to variations in
hand distance and shoulder abduction angle (Figure 9). These results were consistent across the group of subjects tested. This was examined by calculating the angles between the major
axis of the estimated stiffness ellipsoids and the vector describing
the X, Y and Z axes, along which the three unstable environments
were aligned (Figure 9). For each self-selected posture, the
corresponding orientation of maximal endpoint stiffness was most
closely aligned with the orientation of the environmental instability
with which the subject was interacting (paired t-test; all * in
Figure 9 denote p,0.001). The direction of maximal endpoint stiffness for each self-
selected posture was never perfectly aligned with the direction of
the environmental instability. Such an alignment was not possible
given the experimental constraint of keeping the hand in front of
the sternum. The available range of stiffness orientations was
measured in two subjects, as described previously. The limits of
this range across both subjects are indicated by the dashed lines in
Figure 9. Note that the range of available stiffness orientations was
consistent across both subjects. Controlling for Forearm Rotation Across all postures, the average
difference in the orientation of maximal endpoint stiffness between
subjects was only 461u. Estimates of Endpoint Stiffness Linear, nonparametric transfer functions were appropriate for
characterizing the 3D impedance of the human arm. Figure 7A
illustrates the magnitude portion of typical endpoint impedance Figure 6. Self-selected postures during interactions with each of the haptic environments. Postures were chosen during interactions with
unstable environments aligned to the X (A), Y (B) and Z (C) axes. Each filled circle corresponds to the posture chosen by a single subject. Dashed lines
correspond to 90% confidence interval ellipses, computed from the covariance between shoulder angle and hand position [45]. The characters are
placed at locations along horizontal and vertical axes corresponding to the posture that they depict. doi:10.1371/journal.pone.0005411.g006 Figure 6. Self-selected postures during interactions with each of the haptic environments. Postures were chosen during interactions with
unstable environments aligned to the X (A), Y (B) and Z (C) axes. Each filled circle corresponds to the posture chosen by a single subject. Dashed lines
correspond to 90% confidence interval ellipses, computed from the covariance between shoulder angle and hand position [45]. The characters are
placed at locations along horizontal and vertical axes corresponding to the posture that they depict. doi:10.1371/journal.pone.0005411.g006 PLoS ONE | www.plosone.org May 2009 | Volume 4 | Issue 5 | e5411 PLoS ONE | www.plosone.org 7 7 Postural Control of Stiffness Figure 7. Nonparametric estimates of endpoint impedance for a single experimental condition. The subject’s posture placed the hand at
190 mm in front of the sternum and had the shoulder abducted to 14u. (A) Nonparametric transfer functions (gray lines) and the corresponding
second-order fits (black lines). (B) Multiple coherence functions for forces along each of the three measurement axes. Horizontal dashed lines (1.0)
correspond to perfect coherence. doi:10.1371/journal.pone.0005411.g007 Figure 7. Nonparametric estimates of endpoint impedance for a single experimental condition. The subject’s postur
190 mm in front of the sternum and had the shoulder abducted to 14u. (A) Nonparametric transfer functions (gray lines) and Figure 7. Nonparametric estimates of endpoint impedance for a single experimental condition. The subject’s posture placed the hand at
190 mm in front of the sternum and had the shoulder abducted to 14u. (A) Nonparametric transfer functions (gray lines) and the corresponding
second-order fits (black lines). (B) Multiple coherence functions for forces along each of the three measurement axes. Horizontal dashed lines (1.0)
correspond to perfect coherence. doi:10.1371/journal.pone.0005411.g007 PLoS ONE | www.plosone.org Discussion The purpose of this study was to determine how subjects
compensate for environmental instabilities during tasks in which
they are free to select from a range of available arm postures. First,
we tested the influence of different prescribed postures on the PLoS ONE | www.plosone.org May 2009 | Volume 4 | Issue 5 | e5411 May 2009 | Volume 4 | Issue 5 | e5411 PLoS ONE | www.plosone.org 8 Figure 9. Orientation of maximal endpoint stiffness for each
self-selected posture. Each bar corresponds to the orientation of
maximal endpoint stiffness relative to the orientation of the X, Y, and Z
axes. The dark gray bars correspond to postures selected during
interactions with the haptic environment that was unstable in the X
direction; the light gray bars correspond to postures selected during
interactions with the haptic environment that was unstable in the Y
direction; the white bars correspond to postures selected during
interactions with the haptic environment that was unstable in the Z
direction; The asterisks above the bars correspond to significant
differences between stiffness orientations across the self-selected
postures (p,0.01; paired t-test). Bars are mean6standard error. The
horizontal dashed lines denote the range of possible stiffness
orientations. doi:10.1371/journal.pone.0005411.g009
Postural Control of Stiffness Postural Control of Stiffness Postural Control of Stiffness Figure 8. Endpoint stiffness ellipsoids from a typical subject. Two views are shown for the self-selected postures used for each haptic
environment. At each posture, stiffness was estimated as the subject
applied a +10 N force along the direction of the haptic instability. doi:10.1371/journal.pone.0005411.g008 Figure 9. Orientation of maximal endpoint stiffness for each
self-selected posture. Each bar corresponds to the orientation of
maximal endpoint stiffness relative to the orientation of the X, Y, and Z
axes. The dark gray bars correspond to postures selected during
interactions with the haptic environment that was unstable in the X
direction; the light gray bars correspond to postures selected during
interactions with the haptic environment that was unstable in the Y
direction; the white bars correspond to postures selected during
interactions with the haptic environment that was unstable in the Z
direction; The asterisks above the bars correspond to significant
differences between stiffness orientations across the self-selected
postures (p,0.01; paired t-test). Bars are mean6standard error. The
horizontal dashed lines denote the range of possible stiffness
orientations. Discussion doi:10 1371/journal pone 0005411 g009 doi:10.1371/journal.pone.0005411.g009 doi:10.1371/journal.pone.0005411.g009 stronger influence on the ability to maintain stable endpoint
postures than changes in voluntary co-contraction. Our results are
similar. In addition, we extended Milner’s findings to 3D and
demonstrated that when the limb is unconstrained, subjects self-
select postures that increase limb stability and the corresponding
ability to maintain steady hand positions in the presence of
destabilizing environmental loads. Figure 8. Endpoint stiffness ellipsoids from a typical subject. Two views are shown for the self-selected postures used for each haptic
environment. At each posture, stiffness was estimated as the subject
applied a +10 N force along the direction of the haptic instability. doi:10.1371/journal.pone.0005411.g008 ability to maintain endpoint position within directionally unstable
environments. This performance was then tested against that
obtained
at
the
self-selected
postures. Importantly,
posture
significantly influenced performance, and performance was always
best at the self-selected posture. When posture had a large
influence on performance, subjects self-selected similar postures
that tended to orient the direction of maximal endpoint stiffness
toward the direction of the environmental instability. Limb
mechanics, which were quantified using estimates of endpoint
stiffness, can be regulated using a variety of motor behaviors. Our
results suggest that when the arm is unconstrained, posture
selection is a fundamental means by which these mechanics are
regulated. Regulation of Limb Mechanics In addition to improving tracking performance, the self-selected
postures tended to orient the direction of maximal stiffness toward
the direction of the environmental instability. These results
support the idea that endpoint stiffness is regulated to counteract
environmental instabilities and improve task performance [1,3,28]
and that this regulation can occur, at least partly, through
voluntary changes in limb posture. Additional motor behaviors
also may have been used to improve performance during the
tracking tasks. The most obvious is voluntary co-contraction,
which can be used to increase limb stiffness and to provide stability
during
interactions
with
destabilizing
environments
[6,29]. However, co-contraction is metabolically costly, and it has been
suggested that humans tend to use the minimal amount of co-
contraction necessary to maintain limb stability [30]. It is likely
that subjects in the present study also attempted to minimize co-
contraction, and that this minimization was done by selecting a
limb posture that matched the intrinsic mechanical properties of
the arm to the functional requirements of the task. By relying more
heavily on postural shifts than voluntary co-contraction, it may be
possible to decrease energy expenditure. This notion is consistent
with studies suggesting that the central nervous system attempts to
minimize energy expenditure during unconstrained tasks [31,32]. PLoS ONE | www.plosone.org Influence of Posture on Tracking Performance Posture had a strong influence on the ability to maintain stable
endpoint locations in our experiments. The present results are
consistent with those reported by Milner [15], who examined the
influence of arm posture on the ability to maintain endpoint
location during interactions with unstable loads oriented within
the horizontal plane. In his studies, subjects attempted to hold the
hand at the equilibrium position of the unstable environments
using two prescribed postures. During interactions with an
environment that was unstable in the medial-lateral direction,
task performance was greatly increased when the hand was held
near the trunk, relative to when it was held away from the body. Also, during interactions with loads in the anterior-posterior
direction, task performance was only slightly affected by posture. In both cases, it appeared likely that postural changes had a Increased stretch reflex sensitivity also may have influenced
tracking performance during interactions with the unstable loads. Stretch sensitive reflexes are known to modulate with changes in
the mechanical properties of the environment [7,8,10] and can
substantially alter the mechanical properties of a limb [33–36]. PLoS ONE | www.plosone.org May 2009 | Volume 4 | Issue 5 | e5411 9 Postural Control of Stiffness Furthermore, it has been suggested that adaptation of reflex gains
can provide a means for maintaining limb stability while
minimizing energy expenditure [37,38]. Such an optimization
may have occurred in these experiments, but if so, it was done in
concert with the observed postural shifts. Furthermore, it has been suggested that adaptation of reflex gains
can provide a means for maintaining limb stability while
minimizing energy expenditure [37,38]. Such an optimization
may have occurred in these experiments, but if so, it was done in
concert with the observed postural shifts. interacting with the Z instability, both hand location and shoulder
abduction had large effects on the ability to maintain stable hand
positions. All subjects performing this task selected consistent hand
and shoulder postures that enhanced tracking performance. In
contrast, hand position had the largest influence on tracking ability
when interacting with the Y instability, and this is the degree of
freedom that was most consistently selected by the subjects. Much
more variability was seen in the shoulder angles selected by all. Posture had the least influence on tracking when subjects
interacted with the X instability. Influence of Posture on Tracking Performance Correspondingly, the self-selected
postures were most variable across both degrees of freedom when
subjects interacted with this environment. These posture selection
results are consistent with the concept of controlling degrees of
freedom most relevant to task performance [43,44]. We have described our results primarily in the context of
endpoint stiffness. However, posture also has a strong effect on the
inertial and viscous properties of the arm [2,18,39], and any of
these posture dependent changes in arm mechanics and use may
have influenced tracking performance. We have focused on
endpoint stiffness because we examined the performance of a
postural task and because the task involved interactions with
negative stiffness fields. Nevertheless, contributions from other
components of limb impedance would still support our conclusion
that when the limb is unconstrained, subjects self-select arm
postures that match the mechanical properties of the arm to the
mechanical constraints of the task. Task performance was not greatly affected by arm posture when
subjects interacted with the X instability. This is somewhat
counterintuitive since it is well documented that arm stiffness can
be dramatically increased along this direction by reaching outward
from the body [2,17,26]. These changes in arm stiffness, which
would have occurred for the most extended prescribed postures,
had little effect on tracking performance. This most likely is due to
the fact that endpoint stiffness in these tasks was limited more by
the trunk than by the arm [19]. Due to the fact that subject were
required to have a side-by-side stance for these experiments, trunk
compliance likely would have been lowest in the X direction and
therefore would have had the greatest influence on the mechanical
properties of the endpoint for tasks in which this direction was
most relevant. Though we were most interested in the relationship
between arm mechanics and task performance, this result
emphasizes that during natural tasks the mechanics and posture
of the entire body can contribute to the endpoint mechanics of the
arm. The force manipulability [40] of a limb changes with posture in
a manner that is similar to endpoint stiffness, and it is possible that
subjects chose postures that were optimal for generating forces
required to maintain the endpoint at the target locations. While
our current data do not allow us to definitively rule out this
possibility, we consider it to be unlikely that postures were selected
to optimize only force manipulability. Acknowledgments The authors would like to thank Bob Kirsch, who provided constructive
suggestions during the early stages of this study. They also would like to
thank Timothy Haswell for his technical assistance and Eileen Krepkovich
for her assistance with manuscript preparation. Influence of Posture on Tracking Performance The maximum forces due to
the environmental instability at each of these targets was only 5 N,
which is small relative to the maximum forces that could be
generated and, more importantly, small relative to the equivalent
endpoint force required to support the weight of the limb during
these tasks. The equivalent endpoint force required to oppose
gravity would be approximately 15 N in the vertical direction for a
typical 70 kg subject [41]. Therefore, during interactions with all
environments, the largest component of the endpoint force, and
the associated muscle activity required to complete the task, was in
the vertical direction. Nevertheless, there were substantial changes
in the self-selected postures during interactions with each of the
haptic environments. Only during interactions with the Z
instability would these postures have resulted in near-optimal
force manipulability [42]. This is the one condition in which the
endpoint force required for the task was co-aligned with the haptic
instability. Consistency of Self-Selected Postures Conceived and designed the experiments: EJP. Performed the experiments:
RDT MAK BSY. Analyzed the data: RDT MAK BSY. Wrote the paper:
RDT MAK. Conceived and designed the experiments: EJP. Performed the experiments:
RDT MAK BSY. Analyzed the data: RDT MAK BSY. Wrote the paper:
RDT MAK. Conceived and designed the experiments: EJP. Performed the experiments:
RDT MAK BSY. Analyzed the data: RDT MAK BSY. Wrote the paper:
RDT MAK. Consistent postures were selected only when arm posture had a
substantial effect on task performance. For example, when References 1. Rancourt D, Hogan N (2001) Stability in force-production tasks. J Mot Behav
33: 193–204. 1. Rancourt D, Hogan N (2001) Stability in force-production tasks. J Mot Behav
33: 193–204. 10. Perreault EJ, Chen K, Trumbower RD, Lewis G (2008) Interactions with
compliant loads alter stretch reflex gains but not intermuscular coordination. J Neurophysiol 99: 2101–2113. 2. Mussa-Ivaldi FA, Hogan N, Bizzi E (1985) Neural, mechanical, and geometric
factors subserving arm posture in humans. The Journal of Neuroscience 5:
2732–2743. 2. Mussa-Ivaldi FA, Hogan N, Bizzi E (1985) Neural, mechanical, and geometric
factors subserving arm posture in humans. The Journal of Neuroscience 5:
2732–2743. 11. Gribble PL, Mullin LI, Cothros N, Mattar A (2003) Role of cocontraction in
arm movement accuracy. J Neurophysiol 89: 2396–2405. 12. Darainy M, Malfait N, Gribble PL, Towhidkhah F, Ostry DJ (2004) Learning to
control arm stiffness under static conditions. J Neurophysiol 92: 3344–3350. 3. Hogan N (1985) The mechanics of multi-joint posture and movement control. Biological Cybernetics 52: 315–331. 13. Franklin DW, Burdet E, Osu R, Kawato M, Milner TE (2003) Functional
significance of stiffness in adaptation of multijoint arm movements to stable and
unstable dynamics. Exp Brain Res 151: 145–157. 4. Flash T, Mussa-Ivaldi FA (1990) Human arm stiffness characteristics during the
maintenance of posture. Experimental Brain Research 82: 315–326. 5. Kearney RE, Weiss PL, Morier R (1990) System identification of human ankle
dynamics: intersubject variability and intrasubject reliability. Clinical Biome-
chanics 5: 205–207. 14. Franklin DW, Liaw G, Milner TE, Osu R, Burdet E, et al. (2007) Endpoint
stiffness of the arm is directionally tuned to instability in the environment. J Neurosci 27: 7705–7716. 6. Milner TE (2002) Adaptation to destabilizing dynamics by means of muscle
cocontraction. Exp Brain Res 143: 406–416. 15. Milner TE (2002) Contribution of geometry and joint stiffness to mechanical
stability of the human arm. Exp Brain Res 143: 515–519. 7. Dietz V, Discher M, Trippel M (1994) Task-dependent modulation of short- and
long-latency electromyographic responses in upper limb muscles. Electroence-
phalogr Clin Neurophysiol 93: 49–56. 16. Van der Linde RQ, Lammertse P, Frederiksen E, Ruiter B (2002) The
HapticMaster, a new high-performance haptic interface. Edinburgh. pp 1–5. 8. Doemges F, Rack PM (1992) Task-dependent changes in the response of human
wrist joints to mechanical disturbance. J Physiol 447: 575–585. 8. Doemges F, Rack PM (1992) Task-dependent changes in the response of human
wrist joints to mechanical disturbance. 4. Flash T, Mussa-Ivaldi FA (1990) Human arm stiffness characteristics during the
maintenance of posture. Experimental Brain Research 82: 315–326. References J Physiol 447: 575–585. 17. Perreault EJ, Kirsch RF, Crago PE (2001) Effects of voluntary force
generation on the elastic components of endpoint stiffness. Exp Brain Res
141: 312–323. 9. Kimura T, Haggard P, Gomi H (2006) Transcranial magnetic stimulation over
sensorimotor cortex disrupts anticipatory reflex gain modulation for skilled
action. J Neurosci 26: 9272–9281. 9. Kimura T, Haggard P, Gomi H (2006) Transcranial magnetic stimulation over
sensorimotor cortex disrupts anticipatory reflex gain modulation for skilled
action. J Neurosci 26: 9272–9281. 18. Perreault EJ, Kirsch RF, Crago PE (2004) Multijoint dynamics and postural
stability of the human arm. Exp Brain Res 157: 507–517. PLoS ONE | www.plosone.org May 2009 | Volume 4 | Issue 5 | e5411 10 Postural Control of Stiffness 19. Perreault EJ, Kirsch RF, Crago PE (2000) Effects of shoulder stability on
endpoint stiffness. IEEE Engineering in Medicine and Biology 19: 53–58. spatial and temporal motor plans simplifies movement dynamics. J Neurosci 27:
13045–13064. spatial and temporal motor plans simplifies movement dynamics. J Neurosci 27:
13045–13064. p
g
g
gy
. Rancourt D, Hogan N (2001) Dynamics of pushing. J Mot Behav 3 33. Kearney RE, Stein RB, Parameswaran L (1997) Identification of intrinsic and
reflex contributions to human ankle stiffness dynamics. IEEE Transactions on
Biomedical Engineering 44: 493–504. 21. R Development Core Team (2008) R: A Language and Environment for
Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. 3-900051-07-0 3-900051-07-0. 34. Mirbagheri MM, Barbeau H, Kearney RE (2000) Intrinsic and reflex
contributions to human ankle stiffness: variation with activation level and
position. Exp Brain Res 135: 423–436. 22. Politis DN (1998) Computer-intensive methods in statistical analysis. Ieee Signal
Processing Magazine 15: 39–55. 23. Perreault EJ, Kirsch RF, Acosta AM (1999) Multiple-input, multiple-output
system identification for the characterization of limb stiffness dynamics. Biological Cybernetics 80: 327–337. 35. Sinkjaer T, Toft E, Andreassen S, Hornemann BC (1988) Muscle stiffness in
human ankle dorsiflexors: intrinsic and reflex components. Journal of
Neurophysiology 60: 1110–1121. g
y
24. Ljung L (1999) System Identification Theory for the User. Kailath T, ed. Upper
Saddle River, NJ: Prentice-Hall. p y
gy
36. Allum JHJ, Mauritz K-H, Vogele H (1982) The mechanical effectiveness of short
latency reflexes in human triceps surae muscles revealed by ischaemia and
vibration. Experimental Brain Research 48: 153–156. 25. Bendat JS, Piersol AG (2000) Random Data: Analysis & Measurement
Procedures. New York: Wiley-Interscience. 37. de Vlugt E, Schouten AC, van der Helm FC (2002) Adaptation of reflexive
feedback during arm posture to different environments. Biol Cybern 87: 10–26. 26. Gomi H, Osu R (1998) Task-dependent viscoelasticity of human multijoint arm
and its spatial characteristics for interaction with environments. J Neurosci 18:
8965–8978. 38. Schouten AC, de Vlugt E, van der Helm FC, Brouwn GG (2001) Optimal
posture control of a musculo-skeletal arm model. Biol Cybern 84: 143–152. 27. Franklin DW, Milner TE (2003) Adaptive control of stiffness to stabilize hand
position with large loads. Exp Brain Res 152: 211–220. 39. Tsuji T, Morasso PG, Goto K, Ito K (1995) Hand impedance 39. Tsuji T, Morasso PG, Goto K, Ito K (1995) Hand impedance characteristics
during maintained posture. Biological Cybernetics 72: 475–485. Postural Control of Stiffness during maintained posture. Biological Cybernetics 72: 475–48 p
g
p
28. Burdet E, Osu R, Franklin DW, Milner TE, Kawato M (2001) The central
nervous system stabilizes unstable dynamics by learning optimal impedance. Nature 414: 446–449. 40. Sciavicco L, Siciliano B (2000) Modelling and control of robot manipulators. New York: Springer. 41. Winter DA (2005) Biomechanics and Motor Control of Human Movement. Hoboken: John Wiley & Sons, Inc. 29. Milner TE, Cloutier C (1993) Compensation for mechanically unstable loading
in voluntary wrist movement. Exp Brain Res 94: 522–532. 42. Lenarcic J (1999) Basic kinematic characteristics of humanoid manipulators. Laboratory Robotics and Automation 11: 227–278. 30. Franklin DW, So U, Kawato M, Milner TE (2004) Impedance control balances
stability with metabolically costly muscle activation. J Neurophysiol 92:
3097–3105. y
43. Scholz JP, Schoner G (1999) The uncontrolled manifold conce 43. Scholz JP, Schoner G (1999) The uncontrolled manifold concept: identifying
control variables for a functional task. Exp Brain Res 126: 289–306. control variables for a functional task. Exp Brain Res 126: 289–3 31. Soechting JF, Buneo CA, Herrmann U, Flanders M (1995) Moving effortlessly in
three dimensions: does Donder’s law apply? The Journal of Neuroscience 15:
6271–6280. 44. Cohen RG, Sternad D (2009) Variability in motor learning: relocating,
channeling and reducing noise. Exp Brain Res 193: 69–83. channeling and reducing noise. Exp Brain Res 193: 69–83. 32. Biess A, Liebermann DG, Flash T (2007) A computational model for redundant
human three-dimensional pointing movements: integration of independent 45. Press W, Flannery BP, Teukolsky SA, Vetterling WT (1992) Numerical Recipes
in C. New York: Cambridge University Press. PLoS ONE | www.plosone.org May 2009 | Volume 4 | Issue 5 | e5411 11
|
https://openalex.org/W4288287669
|
https://zenodo.org/records/3268688/files/IRJAES-V4N2P673Y19.pdf
|
English
| null |
The Relationship between Vital Statistics with Pregnant Body Weight of Etawah Cross Bred Goat in Malang District, Indonesia
|
Zenodo (CERN European Organization for Nuclear Research)
| 2,019
|
cc-by
| 3,265
|
The Relationship between Vital Statistics with
Pregnant Body Weight of Etawah Cross Bred Goat in
Malang District, Indonesia Rifa’i1, Puguh Surjowardojo2, dan Tri Eko Susilorini2
1Student in Animal Science Master Study Program Animal Science Faculty, Brawijaya University
2Lecture of Animal Production Animal Science Faculty, Brawijaya University
Veteran Street (65145) Malang City, East Java
Email address: rifai01 askaf @ gmail. com Abstract— The research uses a case study in the Technical
Implementation Unit of Breeding and Forage Livestock Feed (UPT
PT and HMT) Singosari, Malang Regency as a place for the
maintenance of old pregnant Etawah Cross Bred goats. The purpose
of this research was to determine the relationship between chest
circumference, height, and length of the body of the old pregnant
Etawah Cross Bred Goat. The material used in the research was 85
old pregnant Etawah Cross Bred goats. The closeness value of the
correlation between body weight and height, body length is 0.46 and
0.42. The highest correlation value is between chest circumference
and body weight 0.73 (P <0.01). The vital statistical determination
coefficient with body weight is 53% chest circumference, 21% height,
and 17% body length. Correlation and regression analysis is used to
estimate the relationship between these traits. This research
concluded that body weight had a strong correlation with chest
circumference (0.73), and the correlation was strong enough at
height and body length, respectively 0.46 and 0.42. The productivity of Etawah Cross Bred goats is influenced
by two main factors, namely genetic and environmental. Genetic factors determine production capabilities, while
environmental factors to support livestock to be able to
produce according to their abilities. Environmental factors
include feed, maintenance, and climate. Genetics and the
environment have an important role because superior genetics
without the support of good maintenance, feed and feeding is
not maximal. Conversely, livestock has given good feed but
livestock do not have superior genetics, the production will
not be optimal. p
Body weight has an important role in the pattern of good
maintenance because knowing the body weight of goats can
facilitate the administration of drug doses, determining the
amount of feeding. Goat weight can be known in two ways,
namely by weighing and estimating. Both of these techniques
each have their advantages and limitations. The weighing
method is the most accurate but has obstacles, including the
limitations of tools and labor and can cause stress on goats. International Research Journal of Advanced Engineering and Science
ISSN (Online): 2455-9024 International Research Journal of Advanced Engineering and Science
ISSN (O l The Relationship between Vital Statistics with
Pregnant Body Weight of Etawah Cross Bred Goat in
Malang District, Indonesia The second goat weight measurement method is estimating
through linear regression analysis between vital livestock
statistics such as chest circumference, body length, height, and
body weight. The ideal body weight for pregnant goats has an
important role, so it is necessary to do research on vital
statistic relationships with the weight of old pregnant Etawah
Cross Bred goats. Keywords— Etawah Cross Bred Goat, Old Pregnant, Body Weight,
Chest Size, High and Long Body. Keywords— Etawah Cross Bred Goat, Old Pregnant, Body Weight,
Chest Size, High and Long Body. I.
INTRODUCTION Etawah Cross Bred goat in Indonesia is one type of goat that is
widely maintained because it is profitable for farmers,
including rapid breeding, capital needed is relatively small,
cages and maintenance are relatively easy, and can be used as
savings for livestock farming communities. Sumartono,
Hartutik, Nuryadi, and Suyadi (2016) Indonesian local goat
Etawah Cross Bred types that have good development and
prospects to support the economy of local livestock farmers. Rifa’i, Puguh Surjowardojo, and dan Tri Eko Susilorini, “The Relationship between Vital Statistics with Pregnant Body Weight of Etawah
Cross Bred Goat in Malang District, Indonesia,” International Research Journal of Advanced Engineering and Science, Volume 4, Issue 3,
pp. 13-16, 2019. A. The Relationship between Vital Statistics with the Body
Weight of Old Pregnant Etawah Cross Bred goats A. The Relationship between Vital Statistics with the Body
Weight of Old Pregnant Etawah Cross Bred goats The magnitude of the influence of vital statistical measures
on the body weight of old pregnant Etawah Cross Bred goats
can be seen from the coefficient of determination with the
following formula:
2
2 The correlation value between vital statistics (X) with
body weight (Y) old pregnant Etawah Cross Bred goats can be
seen in Table I. R2 = r2 x 100% TABLE I. The correlation value between vital statistics with body weight old pregnant Etawah Cross Bred goats
Variable
N
r
R2
t count
t table
0,05
0,01
Chest circumference
85
0,73
53%
7,144
1,9882
2,6349
Body height
85
0,46
21%
1,301
1,9882
2,6349
Body length
85
0,42
17%
0,277
1,9882
2,6349
Note: N= number of samples; r = correlation coefficient; R2 = coefficient of determination The The results of this research indicate that overall the
relationship between vital statistics (chest circumference,
height and body length) with the body weight of old pregnant
Etawah Cross Bred goats had a positive relationship. Correlation coefficient values of chest circumference, height
and body length respectively are 0.73; 046; 042. Criteria for
correlation coefficient values are used to help conclude about
the closeness between variables one with other variables. Correlation coefficient value criteria based on Victori,
Purbowati, and Lestari (2016) can be seen in Table II. comes from the chest to the hips when Etawah Cross Bred goats
in the old pregnant phase increase fetal growth, placental
development and udder glands, overall affecting the parent
body weight. So that the older the Etawah Cross Bred goat the
greater the size of the chest circumference, the body weight
gets heavier because it is followed by the greater the size of
the mother's abdominal circumference. Dalton (1984) in Tama
(2016) adds that in ruminants, the gastrointestinal tract in the
abdomen accounts for 10-25% of the body weight. y
g
Height with body weight has a correlation value of 0.46
which is lower when compared to the correlation value
between chest circumference and body weight which is 0.73. The size of the animal's body is influenced by the growth of
the leg bones. International Research Journal of Advanced Engineering and Science
ISSN (O l ISSN (Online): 2455-9024 ISSN (Online): 2455-9024 This research uses primary data obtained through direct
observation. Primary data retrieval is done by direct
observation (observation) regarding the identification of vital
livestock statistics and weighing body weight, while sampling
is done by purposive sampling. Regression analysis was used to determine the relationship
of vital statistics (chest circumference, body length, height) to
the body weight of old Etawah Cross Bred pregnant goats using
the following equation: Y = a + bX Y = Body weight Y = Body weight Y = Body weight b = regression coefficient b = regression coefficient p
g
y Percentage of deviation estimates of animal body weight
through the regression equation can be known by using the
following calculations: Note: g
% deviation g
% deviation % deviation r : Correlation X : Vital statistics (chest circumference, body length, height) X : Vital statistics (chest circumference, body length, height) B. Data Analysis X = vital statistics (chest circumference, body length, height)
a = constants X = vital statistics (chest circumference, body length, height)
a = constants The data obtained were analyzed using correlation analysis
and simple linear regression analysis. A. Research Material and Method y
Vital statistics of Etawah Cross Bred include chest
circumference, body length, and height. These vital statistics
can be used as indicators of livestock growth, such as
estimating animal body weight. The physical characteristics of
Etawah Cross Bred goats are almost the same as Ettawah
goats, which are long-eared and hanging, convex face profile,
short horned and have white and black feathers. Etawah Cross
Bred goats are classified as dual-purpose livestock (Zuriati,
Maheswari, and Susanty, 2011). Susilorini, Sawitri, and
Muharlien (2008) characteristics of Etawah Cross Bred goats
are long hanging ears with black or red and white feathers and
having a male body weight of around 40-45 kg and female
body weight of around 32 kg. Superior livestock Etawah
Cross Bred goats that can adapt to climate conditions in
Indonesia. The research uses a case study in the Technical
Implementation Unit of Breeding and Forage Livestock Feed
(UPT PT and HMT) Singosari, Malang Regency as a place for
the maintenance of old pregnant Etawah Cross Bred goats. The
material used in the research was 85 pregnant Etawah Cross
Bred old goats, consisting of 2 pregnant Etawah Cross Bred old
goats Permanent Incisors (I1), 15 pregnant Etawah Cross Bred
old goats Permanent Incisors (I2), 42 pregnant Etawah Cross
Bred old goats Permanent Incisors (I3), 26 pregnant Etawah
Cross Bred old goats Permanent Incisors (I4). Equipment used
by measuring ruler with an accuracy of 1 mm, measuring tape
with an accuracy of 1 mm, and digital weighing capacity of
2000 Kg with an accuracy of 0.5 kg. 13 Rifa’i, Puguh Surjowardojo, and dan Tri Eko Susilorini, “The Relationship between Vital Statistics with Pregnant Body Weight of Etawah
Cross Bred Goat in Malang District, Indonesia,” International Research Journal of Advanced Engineering and Science, Volume 4, Issue 3,
pp. 13-16, 2019. Rifa’i, Puguh Surjowardojo, and dan Tri Eko Susilorini, “The Relationship between Vital Statistics with Pregnant Body Weight of Etawah
Cross Bred Goat in Malang District, Indonesia,” International Research Journal of Advanced Engineering and Science, Volume 4, Issue 3,
pp. 13-16, 2019. III. RESULTS AND DISCUSSION n : Number of samples International Research Journal of Advanced Engineering and Science
ISSN (Online): 2455-9024 0, 4 ± 0.1 cm, the average growth 0, 4 ± 0.1 cm, the average growth of the fetus until the age of 30 days of pregnancy is 0.19 ±
0.1 cm per day. Sufficiently high deviations in the chest circumference
regression equation indicate that the chest circumference
regression equation is not strong enough to predict the body
weight of the old pregnant Etawah Cross Bred goat. This is
because the old pregnant Etawah Cross Bred goat has increased
diameter in the abdomen because of the development of the
fetus, placenta and udder glands. So to find out the body
weight of Etawah Cross Bred pregnant goats is better and more
accurate by doing the direct weighing The results of this pregnant Etawah Cross Bred goat have
the lowest correlation coefficient value of 0.42, when
compared to the correlation coefficient values of chest
circumference and height of 0.73 and 0,46, respectively. The
correlation coefficient of 0.42 can prove that the relationship
between body length and body weight in old pregnant Etawah
Cross Bred goats is quite strong. Victori et al. (2016) based on
the correlation coefficient value criteria that the value of r =
0.40-0.599 was stated to have a fairly strong level of
relationship. IV.
CONCLUSION The results of this study indicate that the vital statistical
measure of old pregnant Etawah Cross Bred which includes
chest circumference, height and body length has a strong
closeness, especially between chest circumference and body
weight, whereas between body height and length with body
weight has a fairly close relationship which is shown from the
correlation coefficients sequentially, are 0.73, 0.46 and 0.42. B. Estimation of the Body Weight of Old Pregnant Etawah
Cross Bred Goats Rifa’i, Puguh Surjowardojo, and dan Tri Eko Susilorini, “The Relationship between Vital Statistics with Pregnant Body Weight of Etawah
Cross Bred Goat in Malang District, Indonesia,” International Research Journal of Advanced Engineering and Science, Volume 4, Issue 3,
pp. 13-16, 2019. V.
SUGGESTION The results of this research obtained a regression equation
of the size of the chest circumference, height and length of the
body with body weight, and Levels of deviation estimating the
body weight of old pregnant Etawah Cross Bred goats can be
seen in Table III. Further research is needed with the uniform age of Etawah
Cross Bred goats. A. The Relationship between Vital Statistics with the Body
Weight of Old Pregnant Etawah Cross Bred goats This low correlation value for height is due to
muscle tissue that is attached to the foot area less than the
amount of muscle tissue in the chest area and along with the
constituent bones of the body length. Sutiyono, Nurul and
Endang (2006) height is influenced by the constituent bones of
the forefoot and is not directly related to the abdominal space,
where the forefoot bone functions only to support the The
correlation coefficient between chest circumference and body
weight has the strongest relationship compared to height and
body length, which is equal to 0.73. The results of the
correlation coefficient of 0.73 are still smaller than those of
Afolayan, Adeyinka, and Lakpini (2006) in Yakansa sheep;
Basbeth, Dilaga, and Purnomoadi (2015) in young male
Jawarandu goats; Melawa (2009) in Donggala sheep who
reported that the chest circumference had the highest and very
strong correlation coefficient of 0.94; 0.93 and 0.91. This is TABLE II. Criteria for correlation coefficient values(r)
Correlation coefficient interval
Relationship level TABLE II. Criteria for correlation coefficient values(r)
Correlation coefficient interval
Relationship level
0,00-0,199
Very low
0,20-0,399
Low
0,40-0,599
Strong Enough
0,60-0,799
Strong
0,80-1,00
Very Strong The correlation coefficient between chest circumference
and body weight has the strongest relationship compared to
height and body length, which is equal to 0.73. The results of
the correlation coefficient of 0.73 are still smaller than those
of Afolayan, Adeyinka, and Lakpini (2006) in Yakansa sheep;
Basbeth, Dilaga, and Purnomoadi (2015) in young male
Jawarandu goats; Melawa (2009) in Donggala sheep who
reported that the chest circumference had the highest and very
strong correlation coefficient of 0.94; 0.93 and 0.91. This is
presumably because the chest circumference is directly related
to the chest and abdominal space where most body weight 14 International Research Journal of Advanced Engineering and Science
ISSN (Online): 2455-9024 ISSN (Online): 2455-9024 weight of 0, 77 kg. The regression line equation is vital
statistics for body length (X) with body weight (Y) Y = -13.94
+ 0.51 X, meaning that every 1 cm increase in body length of
Etawah Cross Bred goat increases the body weight of 0.51 kg. presumably because the chest circumference is directly related
to the chest and abdominal space where most body weight
comes from the chest to the hips when Etawah Cross Bred goats
in the old pregnant phase increase fetal growth, placental
development and udder glands, overall affecting the parent
body weight. So that the older the Etawah Cross Bred goat the
greater the size of the chest circumference, the body weight
gets heavier because it is followed by the greater the size of
the mother's abdominal circumference. Dalton (1984) in Tama
(2016) adds that in ruminants, the gastrointestinal tract in the
abdomen accounts for 10-25% of the body weight. Estimation of body weight of old pregnant Etawah Cross
Bred goats using regression of chest circumference, height and
body length has a deviation value of 48%, 48%, and 20%
respectively. The value of this large deviation is thought to be
the factor of the weight of the old pregnant mother body is
influenced by the development of the fetus, placenta and udder
glands. Santosa, Amrozi, Purwantara, and Herdis (2016) the
growing age of fetuses will increase in diameter and will
affect maternal weight, fetal goat nuts at the age of 20 days of
pregnancy have a diameter of 1.2 ± 0.1 cm, age 22 days fetus
0 4 ± 0 1 cm the average growth y
g
Height with body weight has a correlation value of 0.46
which is lower when compared to the correlation value
between chest circumference and body weight which is 0.73. The size of the animal's body is influenced by the growth of
the leg bones. This low correlation value for height is due to
muscle tissue that is attached to the foot area less than the
amount of muscle tissue in the chest area and along with the
constituent bones of the body length. Sutiyono, Nurul and
Endang (2006) height is influenced by the constituent bones of
the forefoot and is not directly related to the abdominal space,
where the forefoot bone functions only to support the motion
activity of livestock. [11] Zuriati Y., R.R.A. Maheswari dan H. Susanty. 2011. The characteristics
of quality of fresh and yogurt milk from three dairy goats in supporting
food security and food diversification programs. National seminar on
animal husbanry and veterinary technology 2011. [10] Victori, A., E. Purbowati dan C. M. S. Lestari. 2016. Relationship
between body measurements and body weight of male Etawah Breeders
in Klaten Regency. Journal of Animal Sciences. 26 (1): 23-28.
http://jiip.ub.ac.id gy
[8] Sumartono, Hartutik, Nuryadi, and Suyadi. 2016. Productivity Index of
Etawah Crossbred Goats at Different Altitude in Lumajang District, East
Java Province, Indonesia. IOSR Journal of Agriculture and Veterinary
Science. 9 (4) : 24-30. [9] Tama, W. A., M. Nasich dan S. Wahyuningsih. 2016. The relationship
between chest circumference, length and height with male Senduro goat
body weight in Senduro Subdistrict, Lumajang district. Journal of
Animal Sciences. 26 (1): 37-42 Rifa’i, Puguh Surjowardojo, and dan Tri Eko Susilorini, “The Relationship between Vital Statistics with Pregnant Body Weight of Etawah
Cross Bred Goat in Malang District, Indonesia,” International Research Journal of Advanced Engineering and Science, Volume 4, Issue 3,
pp. 13-16, 2019. REFERENCES [1] Afolayan, R. A. I. A., Adeyinka and C. A. M. Lakpini. 2006. The
estimation of live weight from body measurements in Yankasa sheep. Czech J. Anim. Sci. 51 (8): 343-348 TABLE III. Estimating body weight through regression equations and
estimation deviations
No
Estimating variable
Equations / formulas
Deviation
1
Chest Circular regression equation
Y = -35,29+1,02 X
48%
2
Height regression equation
Y = -8,57+0,77 X
48%
3
Body length regression equation
Y = -13,94+0,51 X
20% TABLE III. Estimating body weight through regression equations and
estimation deviations [2] Basbeth, A. H. W. S., Dilaga dan A. Purnomoadi. 2015. The relationship
between body measurements of body weight of young male jawarandu
goats in Kendal district, Central Java. Animal Agriculture Journal. 4(1):
35-40 [3] Dalton, D. C. 1984. An introduction to practical animal breeding. Granada Publishing, Ltd. London Based on Table 3, it can be seen that the results of
statistical analysis show that the relationship between vital
chest circumference statistics (X) with body weight (Y) has a
regression line equation Y = -35.29 + 1.02X, meaning that
each 1 cm increase in Etawah Cross Bred chest circumference
than there is an increase in the body weight of 1.02 kg. Furthermore, the relationship between vital height (X)
statistics and body weight (Y) has a regression line equation Y
= -8.57 + 0.77X, meaning that every 1 cm increase in Etawah
Cross Bred goat height then an increase in the parent body [4] Melawa, A. 2009.Examination of body weight based on chest
circumference and body length of donggala sheep. Agroland journal. 16
(1): 91-97 ( )
[5] Santosa, Amrozi, B. Purwantara, dan Herdis. 2016. Early pregnancy
sonogram on Kacang (Capra hircus) goats. Veterinary Science Journal. 34(2):188-193 [6] Susilorini, T. E. Sawitri, M. E dan Muharlien. 2008. Cultivation of 22
Potential Livestock. Penebar Swadaya. Jakarta. [7] Sutiyono, B., J. W. Nurul dan P. Endang. 2006. Study of the
performance of Etawah Cross Bred goat parents based on the number of
children born in Banyuringin Village, Singorojo District, Kendal 15 Regency. National Seminar on Animal Husbandry and Veterinary
Technology. International Research Journal of Advanced Engineering and Science
ISSN (Online): 2455-9024 16 Rifa’i, Puguh Surjowardojo, and dan Tri Eko Susilorini, “The Relationship between Vital Statistics with Pregnant Body Weight of Etawah
Cross Bred Goat in Malang District, Indonesia,” International Research Journal of Advanced Engineering and Science, Volume 4, Issue 3,
pp. 13-16, 2019.
|
https://openalex.org/W4200493207
|
https://www.nature.com/articles/s41598-021-03671-4.pdf
|
English
| null |
Author Correction: Atmosphere similarity patterns in boreal summer show an increase of persistent weather conditions connected to hydro-climatic risks
|
Scientific reports
| 2,021
|
cc-by
| 233
|
www.nature.com/scientificreports www.nature.com/scientificreports www.nature.com/scientificreports © The Author(s) 2021 Author Correction: Atmosphere
similarity patterns in boreal
summer show an increase
of persistent weather conditions
connected to hydro‑climatic risks
Peter Hoffmann Jascha Lehmann Bijan Fallah & Fred F Hattermann
OPEN Peter Hoffmann, Jascha Lehmann, Bijan Fallah & Fred F. Hattermann Correction to: Scientific Reports https://doi.org/10.1038/s41598-021-01808-z, published online 24 November
2021 The original version of this Article contained an error in the spelling of the author Bijan Fallah which was
incorrectly given as Bijan H. Fallah. The original Article and accompanying Supplementary Information file
have been corrected. 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 Author(s) 2021 | https://doi.org/10.1038/s41598-021-03671-4 Scientific Reports | (2021) 11:24242
|
https://openalex.org/W2169483374
|
https://europepmc.org/articles/pmc2288597?pdf=render
|
English
| null |
Principles of cartilage tissue engineering in TMJ reconstruction
|
Head & face medicine
| 2,008
|
cc-by
| 6,738
|
BioMed Central BioMed Central BioMed Central Published: 25 February 2008 Head & Face Medicine 2008, 4:3
doi:10.1186/1746-160X-4-3 This article is available from: http://www.head-face-med.com/content/4/1/3 © 2008 Naujoks et al; licensee BioMed Central Ltd. j
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 Diseases and defects of the temporomandibular joint (TMJ), compromising the cartilaginous layer
of the condyle, impose a significant treatment challenge. Different regeneration approaches,
especially surgical interventions at the TMJ's cartilage surface, are established treatment methods
in maxillofacial surgery but fail to induce a regeneration ad integrum. Cartilage tissue engineering, in
contrast, is a newly introduced treatment option in cartilage reconstruction strategies aimed to
heal cartilaginous defects. Because cartilage has a limited capacity for intrinsic repair, and even
minor lesions or injuries may lead to progressive damage, biological oriented approaches have
gained special interest in cartilage therapy. Cell based cartilage regeneration is suggested to
improve cartilage repair or reconstruction therapies. Autologous cell implantation, for example, is
the first step as a clinically used cell based regeneration option. More advanced or complex
therapeutical options (extracorporeal cartilage engineering, genetic engineering, both under
evaluation in pre-clinical investigations) have not reached the level of clinical trials but may be
approached in the near future. In order to understand cartilage tissue engineering as a new
treatment option, an overview of the biological, engineering, and clinical challenges as well as the
inherent constraints of the different treatment modalities are given in this paper. Head & Face Medicine Open Access Principles of cartilage tissue engineering in TMJ reconstruction
Christian Naujoks*1, Ulrich Meyer1, Hans-Peter Wiesmann2, Janine Jäsche-
Meyer3, Ariane Hohoff3, Rita Depprich1 and Jörg Handschel1 ddress: 1Clinic for Maxillofacial and Plastic Facial Surgery, Westdeutsche Kieferklinik, University of Düsseldorf, Germ
Maxillofacial Surgery, University of Münster, Germany and 3Clinic for Orthodontics, University of Münster, Germany Email: Christian Naujoks* - christian.naujoks@med.uni-duesseldorf.de; Ulrich Meyer - ulrich.meyer@med.uni-duesseldorf.de; Hans-
Peter Wiesmann - wiesmap@uni-muenster.de; Janine Jäsche-Meyer - jajamey@uni-muenster.de; Ariane Hohoff - hohoffa@uni-muenster.de;
Rita Depprich - depprich@med-uni-duesseldorf.de; Jörg Handschel - handschel@med.uni-duesseldorf.de * Corresponding author Received: 11 July 2007
Accepted: 25 February 2008 Page 1 of 7
(page number not for citation purposes) Cartilage histology The three types of cartilage (hyaline cartilage, elastic carti-
lage, and fibrocartilage) are present in adults. The type of
cartilage differs in the various locations of the body (at the
articular surface of bones, in the trachea, bronchi, nose,
ears, larynx, and in intervertebral disks). The cartilage of
the condylar head is fibroelastic [11]. The histology of the
condyle mirrors the functional needs of mandibular
movement [12]. The cartilage cap of the joint contains
cells, fibers, and amorphous ground substance. It is dom-
inated by the acellular elements and is devoid of blood
vessels and nerves. Cartilage is occupied by an extensive
extracellular matrix that is synthesised by chondrocytes. A
chondrocyte always generates from a mesenchymal cell,
the prechondrogenic cell or chondrocyte precursor cell,
which is – due to lack of specific markers – only defined
by the expectation that its daughter cell will be a differen-
tiated chondrocyte (for review see Behonick and Werb
[13]). Chondrocyte precursor cells are of general fibrob-
lastic appearance and synthesises – like fibroblasts – type
I and III collagen, fibronectin, and noncartilage-type pro-
teoglycans [14]. Stem cells with chondrogenic potential
persist throughout adult life and can be induced to differ-
entiate into chondrocytes during fracture callus forma-
tion, osteophyte formation, or as ectopic cartilage. As articular cartilage has, in contrast to bone, only a lim-
ited capacity to regenerate itself, regeneration supporting
therapies are of high relevance when this tissue is involved
in the destruction process [5]. It is well known that lesions
which are confined to the articular cartilage alone have lit-
tle or no capacity to heal. In general, the patients become
symptomatic and a significant progression to osteoarthri-
tis is possible [6]. Those lesions that penetrate the
subchondral bone have a limited repair capacity because
they have access to the bone marrow space and chondro-
progenitor cells. The regeneration and repair of lesions in
the condylar head depend therefore on the extent of
destruction and, when being severe, impose a significant
problem in maxillofacial practice. That is why new thera-
peutic strategies focus on cartilage tissue engineering strat-
egies to regenerate or reconstruct condylar cartilage [4,7]. As an unimpaired biomechanical function of articular car-
tilage containing joints is dependant on the anatomical
integrity of the joint [8], custom made engineered struc-
tures are of importance [9]. Introduction turbances in the cartilage layer are often associated with
severe functional disturbances and a subsequent progres-
sion of cartilage degeneration or inflammation. Diseased
or lost TMJ structures are most common as sequelae of
trauma, degeneration, infection, or autoimmune disease. The treatment of TMJ defects is complex and based mainly
on the underlying cause of defect generation [2]. Indica-
tions for a surgical management can be devided in relative
and absolute indications. Due to the multitude of patho-
genic disturbances and based on the extent of TMJ struc-
ture involvement attempts to heal TMJ lesions span the Skeletal defects in the adults craniofacial skeleton com-
promises mainly bony structures, whereas chondral or
osteochondral defects are less common, but when present
are accompanied by a significant morbidity. Articular car-
tilage tissue is present in the adult patient in the temporo-
mandibular joint (TMJ). Despite this relative minor
prevalence of cartilage defects towards bony destructions,
defects of the TMJ plays an important clinical role in max-
illofacial surgery [1]. The consequences oft TMJ tissue
alteration may be pain and functional impairments. Dis- Page 1 of 7
(page number not for citation purposes) Page 1 of 7
(page number not for citation purposes) http://www.head-face-med.com/content/4/1/3 http://www.head-face-med.com/content/4/1/3 Head & Face Medicine 2008, 4:3 whole range between symptomatic measures and exten-
sive surgical interventions. Absolute indications are com-
monly reserved for more severe alterations of the TMJ disc
or the condyle. Whereas interventions at the base of the
skull are seldom performed, repair of the disc or the con-
dyle is a matter of special interest in maxillofacial surgery. The spectrum of surgical procedures for the treatment of
temporomandibular joint disorders is wide and ranges
from simple arthrocentesis and lavage to more complex
open joint surgical procedures. The most invasive proce-
dure is the resection and reconstruction of the TMJ. Autol-
ogous cartilage-bone grafts, e.g. from the rib, and
alloplastic materials like a patient-fitted prostheses can be
used for the reconstruction of the joint. The issue on engi-
neering the TMJ disc, reviewed extensively by Allan and
Athanasiou [3], is from a structural and biological aspect
distinct from those at the cartilage containing condylar
head [4]. cartilage engineering it is important to give a brief intro-
duction in cartilage histology and cartilage regeneration
and to consider the common repair procedures, before the
field of cartilage tissue engineering in the narrower sense
is discussed in detail. Page 2 of 7
(page number not for citation purposes) Surgical repair strategies In maxillofacial surgery, there are two general goals for
cartilage reconstruction. The first is the immediate need
for clinical pain relief and restoration of joint function. The second goal is to prevent or at least delay the onset of
subsequent joint alterations. From a practical perspective,
the current objective of articular cartilage repair is to avoid
the development of a deformed joint surface [30]. Besides
non-surgical therapies that are based on the administra-
tion of drugs (non-steroidal antiphlogistics, steroids) and
biologicals (hyaluronan), surgical options play a signifi-
cant role aimed to gain pain relief, to restore joint func-
tionality and to prevent progression of joint destruction,
especially in severely altered joints. In some instances
drastic measures like total TMJ replacement by TMJ pros-
thesis are necessary to achieve clinical success, but such
measures impose the problem of long term complications
(material failure, scull base perforation) especially when
used in younger patients. The use of alloplastic materials
is therefore a matter of controversy in maxillofacial sur-
gery [1]. Dimitroulis [2] stresses in his review on TMJ sur-
gery the demands of a close adaptation to natural tissues
when a long term success is envisioned. Most of the exper-
imental and clinical attempts that have hence been made
to restore articular cartilage structure aim at re-establish-
ment of biomechanically competent tissue of an enduring
nature [31]. The surgical measures to improve temporo-
mandibular joint structure and function without the use
of biologically active substances can be conceptualised as
methods to improve the condition of the joint fluids (lav-
age), to mechanically remove diseased or necrotic superfi-
cial chondral tissue (shaving, debridement, laser - mechanical disruption of articular cartilage limited to
articular cartilage - damage to the cells and matrices of articular cartilage and
subchondral bone - mechanical disruption of articular cartilage and bone - mechanical disruption of articular cartilage and bone Each type of tissue damage initiates a distinct cell driven
repair response [21-23]. The ability of chondrocytes to
sense changes in matrix composition and synthesise new
molecules are the basis for repair processes [24-27]. The
two features that are assumed to play main roles in the
limited repair response of articular cartilage are the lack of
blood supply and a lack of undifferentiated cells that can
promote repair. Cartilage regeneration Cartilage is a metabolically active tissue that under nor-
mal conditions is maintained in a relatively slow state of
turnover by a sparse population of chondrocytes distrib-
uted throughout the tissue. Despite the activity of these
cells, cartilage has a limited capacity for intrinsic repair,
and even minor lesions or injuries may lead to progressive
damage (and in case of articular cartilage leads to subse-
quent joint degeneration) [18-20]. Isolated chondral or
osteochondral lesions also may be a significant source of
pain and loss of function, and will heal spontaneously
only under some circumstances. The repair of cartilage is
critically dependent on the extent of tissue destruction. Based on the extent of tissue damage, articular defects can
be classified into three types: http://www.head-face-med.com/content/4/1/3 http://www.head-face-med.com/content/4/1/3 Head & Face Medicine 2008, 4:3 of the repair and remodeling responses is critically
dependant on the desintegration of the subchondral tis-
sue. Defects that extend into subchondral bone cause, in
contrast to superficial defects, bleeding into the defect
area. Soon after full thickness defects are present, blood
escaping from the damaged subchondral bone forms a
hematoma that fills the injury site. The final outcome of
the repair tissue typically has a composition and structure
intermediate between hyaline cartilage and fibrocartilage,
imposing an impaired biomechanical competence. The
newly formed tissue is in structure and biomechanical
competence different to normal articular cartilage
[21,22,24,25,29] imposing decreased stiffness and
increased permeability. The impact of load on cartilage
structure and function is of outermost importance. Physi-
ologic TMJ loading maintains cartilage structure and func-
tion. In the context of articular cartilage repair, it is
important to recognise that stresses in a cartilage defect or
the surrounding tissue may be altered significantly from
their normal mechanical environment, and therefore
impairs tissue integrity before and after cell/scaffold
implantation. fibrils and non-collagenous proteins that form an exten-
sive network. Many of the molecules play a structural role,
whereas others may be involved in regulating cell func-
tion. The ground substance of articular cartilage contains
also a large variety of noncollagenous proteins and
polysaccharides. The molecules vary in their abundance
and structure with anatomical site or the person's age. There are no common features of non-collagenous pro-
teins in respect to their distribution, structure and func-
tion. Many of the molecules are proteoglycans, bearing
glycosaminoglycan chains, whereas others are glycopro-
teins or even nonglycosylated proteins. Cartilage histology As cartilage defects are typi-
cally seen in arthrotic or arthritic patients, cartilage
engineering may be today of special relevance in these
patient groups but may be in future also used to repair
more complex cases. At its free (superficial) surface, which is contacted by syn-
ovial fluid, the chondrocytes are flattened and aligned
parallel to the surface (for review see Poole et al. [15]). Below the superficial zone is the midzone where cell den-
sity is lower. The ultrastructure of the midzone reveals
more typical morphologic features of a hyaline cartilage
with more rounded cells and an extensive extracellular
matrix. Between this midzone and the layer of calcified
cartilage is the deep zone. Deep to the articular cartilage,
and separated from it, is a layer of calcified cartilage. The
calcified cartilage is not very vascular normally, and the
remodeling process is therefore not as effective as in vas-
cularised locations. Cell density is lowest in this zone. The
chondrocytes in the calcified zone usually express the
hypertrophic phenotype, reaching a stage of differentia-
tion that can also be found in fracture repair. The calcified
interface provides excellent structural integration with the
subchondral bone. Subchondral trabecular bone is under-
lying the subchondral plate. The structure and appearance
of subchondral bone, being critically dependent on the
load situation of the TMJ [16], changes its density by
remodelling [17]. The extracellular matrix of fibrocarti-
lage is composed of differentially distributed collagen It is important to note that in contrast to maxillofacial sur-
gery, where recently the economically most important
skeletal tissue substitute is bone, cartilage plays the most
prominent role in orthopaedics [10]. Cartilage engineer-
ing therapies were mainly invented and tested in the
orthopaedic field but are now introduced in maxillofacial
surgery. Based on a multitude of valuable basic scientific,
pre-clinical as well as clinical studies, advances have been
made in all fields of cartilage tissue engineering. The
review is intended to give an updated overview of cartilage
tissue engineering. To understand the evolving field of Page 2 of 7
(page number not for citation purposes) Page 2 of 7
(page number not for citation purposes) Page 3 of 7
(page number not for citation purposes) Surgical repair strategies Chondrocytes can repair defects ad inte-
grum in circumstances where the loss of matrix proteogly-
cans does not exceed what the cells can rapidly produce, if
the fibrillar collagen meshwork remains intact, and if
enough chondrocytes remain capable of responding to
the matrix damage. The repair and remodeling of osteochondral defects dif-
fers from the events that follow injuries that cause only
cell and matrix injury or disruption of the articular surface
limited to articular cartilage [28]. The extent and outcome Page 3 of 7
(page number not for citation purposes) Page 3 of 7
(page number not for citation purposes) Head & Face Medicine 2008, 4:3 http://www.head-face-med.com/content/4/1/3 surgery due to the significant functional impairment in
the harvesting region. abrasion) and to gain access to the subchondral bone
(abrasion chondroplasty, pridie drilling, microfracture
techniques and spongialisation). The underlying reason
for lavage or debridement is the removal of inflamed or
diseased tissue, whereas the method to gain access to
subchondral bone is aimed at initiating a spontaneous
healing response. Arthroscopic lavage and debridement
are often used to alleviate joint pain. Lavage is mainly per-
formed by arthroscopy. Various other methods like free
[32] or vascularised tissue transfer [33] are clinically used,
but some of these approaches impose unexpected clinical
outcomes [34]. In contrast to the orthopeadic field, where
an ankylosis of a joint may be the ultimate treatment ratio
for complicated cases, iatrogenic ankylosis seems not to
be indicated for the TMJ in any clinical situation. Articular chondrocytes are responsible for the unique fea-
tures of articular cartilage; hence, it seemed rational to use
committed chondrocytes to repair a cartilaginous defect. As cells were demonstrated to impose the ability to be
expanded in culture the re-transplantation of ex-vivo mul-
tiplicated cells (autologous chondrocyte transplantation
(ACT)) seemed to be a promising treatment strategy. Over
the last decade autologous chondrocyte transplantation
has gained much scientific and commercial interests. ACT
and its several modifications are the most widespread
applications of cartilage tissue engineering. In the clinical
use of in vitro expanded autologous chondrocytes for car-
tilage repair the aim seemed to be to have an adequate
number of expanded cells to implant and an overlying
membrane to avoid cell and matrix loss. Brittberg etal. [38] successfully reported in 1994 on autologous
chondrocyte implantation using a monolayer culture sys-
tem to treat cartilage defects. Surgical repair strategies In this procedure, harvested
autologous chondrocytes, expanded in a monolayer cul-
ture system were transplanted to an osteochondral lesion
which was covered by a periosteal flap. The rationale
behind this approach was the finding that chondrocytes
can, after harvesting, be isolated by enzymatic digestion
and expanded in culture 20 to 50 times the initial number
of cells [39]. It is known that cells, cultured in monolayers
with serum supplementation in the culture media, com-
mence to dedifferentiate. The dedifferentiated chondro-
cytes share features of primitive mesenchymal cells and
on implantation at high density the in-vitro expanded
primitive immature chondrocytes imitate prechondroge-
neic cell condensation and cartilage formation [40,41]. This findings and the initial report by Brittberg had a high
impact on cartilage surgery and was regarded as a break-
through for cell-based cartilage repair strategies. The
United States Food and Drug Administration approved in
1997 the cell technology that uses the patient's own
chondrocytes to repair cartilage injuries in the knee [42]. This was the first type of cell technology that was regulated
by industry for use in expanding autologous cells for
human transplantation. In the U.S.A. and Europe, cell
processing in a monolayer culture is now been carried out
on a commercial basis. The use of autologous chondro-
cytes was primarily performed in traumatically damaged
knee joints [43]. Based on the sum of the experience
gained in orthopaedics, preclinical and clinical studies
tended to expand the indications to joints others than the
knee. To date ACT is clinically used to treat also non-trau-
matic cartilage defects (arthrosis, arthritis defects), and to
repair complex tissue defects (osteochondral defects) by a
combination of bone and cartilage products. As a conse-
quence, ACT is now under investigation as a clinical treat-
ment modality also in TMJ surgery http://www.head-face-med.com/content/4/1/3 Head & Face Medicine 2008, 4:3 http://www.head-face-med.com/content/4/1/3 Whereas ACT is now routinely done some issues must be
stressed. In contrast to the clinical outcome rates, limited
information is present on the histogenesis of the cell-
driven human repair tissue. Biopsy specimens from
grafted areas in individuals obtained after autologous
chondrocyte transplantation (in the orthopaedic field)
indicated that the ACT procedure helps to build up a tis-
sue with hyaline and fibrocartilage-like features [44,45]. Transarthroscopic biopsy specimens obtained from
grafted areas demonstrated in general a heterogeneity
throughout the repair tissue. Although beneficial short- or
middle-term clinical results were reported on a clinical
basis [45,46], the ACT procedure has potential disadvan-
tages, such as the risk of leakage of transplanted chondro-
cytes from the cartilage defects and an uneven distribution
of chondrocytes in the transplanted site [47]. Addition-
ally, ACT transplantation is not able to regenerated larger
defects. These limitations explain to some extent the find-
ing of a heterogenous tissue formation in the defect site. To overcome these limitations, further developments
focus therefore on the ex-vivo growth of a three dimen-
sional cartilage-like tissue, which integrates intimately in
the defect site after being implanted. Other possible
sources of cells for tissue engineering include beneath
autologous cells allogenic and xenogenic cells. Each cate-
gory can be subdivided according to whether the cells are
in a more or less differentiated stage. Various mature cell
lines as well as multipotential so-called mesenchymal
progenitors have been successfully established [48] in
bone tissue engineering approches. Moreover, there are
some reports using totipotent embryonic stem cells for tis-
sue engineering of bone [49,50]. Another group of cells,
which is a special focus of scientific and clinical studies
today, is believed to contain multipotential stem cells
which are often called "mesenchymal stem cells (MSCs)"
[51,52] or "adult stem cells" [53]. Whereas the situation
of determined cells is well known to researchers and clini-
cians in TMJ reconstruction, not only the origin, but also
the destiny and clinical usefulness of MSCs in TMJ surgery
has not been entirely resolved to date. ferentiation and three dimensional assembly [54]. In bio-
reactors outside the body the cellular device is ideally
matured to a cartilage-like tissue. New approaches in
extracorporal tissue engineering strategies are aimed to
improve chondrocyte cell lines and to fabricate scaffold-
free three-dimensional micro-tissue constructs. Page 5 of 7
(page number not for citation purposes) http://www.head-face-med.com/content/4/1/3 Whether
the cell containing device contains an artificial scaffold or
not [4], the construct has to be implanted in the defect site
to promote cartilage healing. An appropriate method to
gain this scaffold-free three-dimensional micro-tissue
might be the micromass technology. Cells are dissociated
and the dispersed cells are then reaggregated into cellular
spheres. The micromass technology relies to a great extend
on the presence of proteinacious extracellular matrix. The
extracellular matrix may exert direct and indirect influ-
ences on cells and consequently modulate their behav-
iour. In contrast to conventional monolayer cell cultures,
the three-dimensional spheres exert higher proliferation
rates and their differentiation more closely resembles that
seen in situ [55]. Most chondrocyte transplantation studies have, to date,
predominantly focussed on the use of an unselected
source of chondrocytes [38]. In the ongoing search to
improve chondrocyte cell lines, the use of specific
chondrocyte populations are now being considered to
investigate whether an improved cartilaginous structure
would be generated in-vivo and in-vitro by these specifi-
cally selected populations of determined chondrocytes
[56]. As distinct phenotypic and functional properties of
chondrocytes across the zones of articular cartilage are
present, it seemed reasonable to search for the best source
of chondrocyte subpopulations [57]. It was reported in
this respect that a combination of mid and deep zone
chondrocytes seems to be more suitable for the ex-vivo
generation of a hyaline-like cartilage tissue. Dowthwaite et
al. [58], have recently reported on an isolation technique
for chondrocytes that reside in the superficial zone of
immature bovine articular cartilage. These cells, character-
ised as determined chondrogenic cells, were shown to
allow appositional growth of the articular cartilage from
the articular surface [59]. Therefore, when chondrocytes
are aimed to generate a cartilage-like structure ex-vivo, it
seems to be reasonable not to gain full thickness cartilage
implants but to use subpopulations of chondrocytes. Sep-
aration of cartilage zones after the explantation and before
cultivation with a selective subpopulation may provide a
tool to improve tissue engineering strategies using deter-
mined cells. Phenotypic plasticity was tested by a series of
in-ovo injections where colony-derived populations of
these chondroprogenitors were engrafted into a variety of
connective tissue lineages thus confirming that this popu-
lation of cells have properties akin to those of a progenitor
cell. The high colony forming ability and the capacity to
successfully expand these progenitor populations in-vitro Cellular repair strategies The use of cells or cell-containing devices, considered to
be tissue engineering strategies, can be performed by dif-
ferent measures [35-37]. Tissue engineering techniques
have seen rapid advances and refinements during the last
years. Whereas these techniques have been elaborated
mainly by orthopaedics, their principle application refers
also to the maxillofacial field. Transplants from either
autologous or allogenic origin can be harvested in the
form of perichondrial or periosteal tissue and as a bulk
osteochondral part. Perichondrial or periosteal autotrans-
plantation as a single procedure has been exploited in a
variety of protocols elaborated for the treatment of articu-
lar cartilage defects. Other tissue engineering concepts
such as autologous chondrocyte transplantation (ACT)
delivers chondrogenic precursor cells to the defect site. The basic biological principle behind the use of these cell
based techniques is the fact that perichondrial and perio-
steal tissue as well as isolated cell suspensions (ACT) con-
tains cells that possess a life-long chondrogenic potential. A pool of precursor or adult-type stem cells is assumed to
be present in these tissues that render self-renewable
capacity and are able to induce tissue healing. Implanta-
tion of explanted bulk chondral or osteochondral tissue
(mosaicplasty), routinely used in orthopaedic joint and
bone surgery but seldom applied in the TMJ region [4], is
aimed to repair mid-size chondral or osteochondral
defects. Experimental studies revealed that graft material
persisted for a short time, however, long-term effects are
not extensively evaluated. It was demonstrated by retro-
spective studies that clinical outcomes were acceptable in
sense of improved joint functionality and pain relief. Despite the short-term clinical success, the use of non
expanded autografts possess a number of disadvantages. The donor site may experience severe morbidity since the
explantation site will loose as much chondral or osteo-
chondral tissue as the diseased implantation site will get. Transplantation of extended cartilage containing speci-
mens (iliac crest, digits) [33] are seldom performed in TMJ Page 4 of 7
(page number not for citation purposes) Page 4 of 7
(page number not for citation purposes) In-vitro engineering strategies In-vitro engineering strategies
In order to prevent the loss of chondrocytes after cell
implantation (in the case of ACT) and to increase the size
of a cellular device, extracorporal tissue engineering tech-
niques were considered an alternative pathway [7]. Extra-
corporal cartilage engineering requires not only living
chondrocytes, but additionally the interaction of two
other components: extracellular scaffolds and in some
instances growth factors. For engineering cartilage tissue
in-vitro cultured cartilage cells are cultured as described for
the ACT procedure in monolayer to increase the cell
number. Later on they are grown on two-dimensional or
three dimensional bioactive degradable biomaterials that
provide the physical and chemical basis to guide their dif- Page 5 of 7
(page number not for citation purposes) http://www.head-face-med.com/content/4/1/3 http://www.head-face-med.com/content/4/1/3 Head & Face Medicine 2008, 4:3 [59] may further aid our knowledge of cartilage develop-
ment and growth and may provide novel solutions in ex-
vivo cartilage tissue engineering strategies. 3. Allen KD, Athanasiou KA: Tissue Engineering of the TMJ Disk:
A Review. Tissue Eng 2006, 12(5):1183-1196. 4. Schek RM, Taboas JM, Hollister SJ, Krebsbach PH: Tissue enginner-
ing osteochondral implants for temporomandibular joint
repair. Orthod Craniofac Res 2005, 8:313-319. p
5. Kaufmann MR, Tobias GW: Engineering cartilage growth and
development. Clin Plast Surg 2003, 30:539-546. Many attempts have been successfully undertaken to
refine procedures for the propagation and differentiation
of cells by the use of bioreactors [60] or by the use of pre-
cursor cells. The use of stem cells offers new perspectives
in cell propagation techniques. At present, adult stem cells
are able to differentiate into chondrocyte-like cells which
are competent to synthesise a cartilage-like extracellular
matrix under in vitro conditions. Despite the various
advantages of using tissue-derived adult stem cells over
other sources of cells, there is some debate as to whether
large enough populations of differentiated cells can be
grown in-vitro rapidly enough when needed clinically. The
alternative approach of using embryonic stem cells is
advantageous in respect to the nearly unlimited capacity
of cell multiplication but the clinical use of embryonic
stem cells is restricted through legal and ethical issues. The
use of unrestricted somatic stem cells (USSC's) gained
through umbilical cord blood seems, from a clinical per-
spective the most promising stem cell approach to date
[61]. These cells can be gained from stem cell banks, indi-
vidually matched prior transplantation, and transplanted
without major medical or legal restrictions. In-vitro engineering strategies Whereas vari-
ous problems must be considered as a limitation for the
use of stem cells in extracorporal cartilage tissue engineer-
ing, the use of USSC's is in the clinical testing phase. Whereas more basic research is necessary to assess the full
potential of stem cell therapy to reconstitute chondral
defects, such therapies may be one treatment option in
the near future. In this respect it is important to note that
many basic research and preclinical studies are today
directed toward the development of gene therapy proto-
cols employing gene insertion strategies [62]. 6. Lohmander LS: Tissue engineering of cartilage: do we need it,
can we do it, is it good and can we prove it? Novartis Found Symp
2003, 249:2-10. 7. Almarza AJ, Athanasiou KA: Design charachterisrics for the tis-
sue engineering of cartilaginous tissues. Ann Biomed Eng 2004,
32:2-17. 8. Stamm T, Hohoff A, Van Meegen A, Meyer U: On the three-dimen-
sional physiological position of the temporomandibular
joint. J Orofac Orthop 2004, 65:280-289. j
J
p
9. Feinberg SE, Hollister SJ, Halloran JW, Chu TM, Krebsbach PH:
Image-based biomimetric approach to reconstruction of the
temporomandibular
joint. Cells
Tissues
Organs
2001,
169:309-321. 10. Meyer U, Wiesmann HP: Bone and cartilage engineering. Berlin,
Springer; 2006. 11. Stratmann U, Schaarschmidt K, Santamaria P: Morphometric inves-
tigation of condylar cartilage and disc thickness in the human
temporomandibular joint: significance for the definition of
ostearthrothic changes. J Oral Pathol Med 1996, 25:200-2005. g
J
12. Luder HU: Frequency and distribution of articular tissue fea-
tures in adult human mandibular condyles: a semiquantita-
tive light microscopy study. Anat Rec 1997, 248:18-28. g
py
y
13. Behonick DJ, Werb Z: A bit of give and take: the relationship
between the extracellular matrix and the developing
chondrocyte. Mech Dev 2003, 120:1327-1336. 14. Von der Mark K, Conrad G: Cartilage cell differentiation:
review. Clin Orthop Relat Res 1979, 139:185-205. 15. Poole AR, Kojima T, Yasuda T, Mwale F, Kobayashi M, Laverty S:
Composition and structure of articular cartilage: a template
for tissue repair. Clin Orthop Relat Res 2001, (391 Suppl):26-33. p
p
(
pp )
16. Kruse-Losler B, Meyer U, Floren C, Joos U: Influence of distrac-
tion rates on the temporomandibular joint position and car-
tilage morphology in a rabbit model of mandibular
lengthening. J Oral Maxillofac Surg 2001, 59:1452-1459. g
g
J
f
g
17. 1.
Dimitroulist T: The role of surgery in the management of dis-
orders of the Temporomandibular Joint: a critical review of
the literature. Part 1. Int J Oral Maxillofac Surg 2005, 34:107-113.
2.
Dimitroulis T: The role of surgery in the management of dis-
orders of the Temporomandibular Joint: a critical review of
the literature. Part 2. Int J Oral Maxillofac Surg 2005, 34:231-237. Conclusion Cartilage tissue engineering has seen significant improve-
ments in the basic research field as well as in pre-clinical
applications. Whereas a lot of these techniques are rou-
tinely used (or at least) have gained entrance in clinical tri-
als in orthopaedic surgery, less acceptance can be found in
maxillofacial surgery [63]. This may be based to some
extent on the specific requirements in TMJ surgery, but
from a biological perspective it can be assumed that it may
be approached more often in maxillofacial surgery in the
next future. g
(
pp
)
21. Buckwalter JA, Mankin HJ: Articular cartilage: I. Tissue design
and chondrocyte-matrix interactions. J Bone Joint Surg Am 1997,
79A:600-611. 22. Buckwalter JA, Mankin HJ: Articular cartilage: II. Degeneration
and osteoarthrosis, repair, regeneration and transplanta-
tion. J Bone Joint Surg Am 1997, 79A:612-632. J
J
g
23. Buckwalter JA, Brown TD: Joint injury, repair, and remodeling:
roles in post-traumatic osteoarthritis. Clin Orthop Relat Res
2004, 423:7-16. 24. Meyer U, Wiesmann HP, Meyer T, Stratmann U, Szulczewski D, Joos
U: Mechanical tension regulates differentiation of chondro-
cytes to osteoblast-like cells in distraction osteogenesis. Int J
Oral and Maxillofac Surg 2001, 12:522-530. 25. 25. Hollmiund A, Hellsing G: Arthroscopy of the temporomandibu-
lar joint. A comparative study of arthroscopic and tomo-
graphic findings. Int J Oral Maxillofac Surg 1988, 17:128-133. In-vitro engineering strategies Hu K, Radhakrishnan P, Patel RV, Mao JJ: Regional structural and
viscoelastic properties of fibrocartilage upon nanoindenta-
tion of the articular condyle. J Struct Biol 2001, 136:46-52. y
J
18. Coutts RD, Healey RM, Ostrander R, Sah RL, Goomer R, Amiel D:
Matrices for cartilage repair. Clin Orthop Relat Res 2001, (391
Suppl):271-279. pp )
19. Roughley PJ: Age-associated changes in cartilage matrix:
implications for tissue repair. Clin Orthop Relat Res 2001, (391
Suppl):153-160. pp )
20. Burr DB: Anatomy and physiology of the mineralized tissues:
role in the pathogenesis of osteoarthrosis. Osteoarthritis Carti-
lage 2004, 12(Suppl A):20-30. 1.
Dimitroulist T: The role of surgery in the management of dis-
orders of the Temporomandibular Joint: a critical review of
the literature. Part 1. Int J Oral Maxillofac Surg 2005, 34:107-113. J
f
g
2.
Dimitroulis T: The role of surgery in the management of dis-
orders of the Temporomandibular Joint: a critical review of
the literature. Part 2. Int J Oral Maxillofac Surg 2005, 34:231-237. References Shenaq SM, Klebuc MJ: The iliac crest microsurgical free flap in
mandibular reconstruction. Clin Plast Surg 1994, 21:37-44. g
g
J
p
58. Dowthwaite GP, Bishop JC, Redman SN, Khan IM, Rooney P, Evans
DJ, Haugthon L, Bayram Z, Boyer S, Thomson B, Wolf MS, Archer
CW: The surface of articular cartilage contains a progenitor
cell population. J Cell Sci 2004, 117:889-897. g
34. Baek RM, Song YT: Overgrowth of a costochondral graft in
reconstruction of the temporomandibular joint. Scand J Plast
Reconstr Surg Hand Surg 2006, 40:179-185. g
g
35. Meyer U, Berr K, Wiesmann HP, Kubler N, Handschel J: Cell based
bone reconstruction
therapies. Principles
of
clinical
approaches. Int J Oral Maxillofac Implants 2006, 21(6):899-906. 59. Hayes DW, Averett RK: Articular cartilage transplantation. Current and future limitations and solutions. Clin Podiatr Med
Surg 2001, 18:161-176. pp
J
p
( )
36. Handschel J, Depprich R, Kubler N, Wiesmann HP, Meyer U: Cell
based bone reconstruction therapies. Cell sources. Int J Oral
Maxillofac Implants 2006, 21(6):890-898. g
60. Meyer U, Buchter A, Nazer N, Wiesmann HP: Design and per-
formance of a bioreactor to mechanically promote bone and
cartilage tissue formation. Br J Oral Maxillofac Surg 2005,
44:134-140. 37. Edwards PC, Mason JM: Gene enhanced tissue engineering for
dental hard tissue regeneration. (1) Overview and practical
considerations. Head Face Med 2006, 2:12. 61. Kogler G, Sensken S, Airey JA, Trapp T, Mueschen M, Fedhahn N,
Liedtke S, Sorg RV, Fischer J, Rosenbaum C, Greschat S, Knipper A,
Bender J, Degistrici O, Gao J, Caplan AI, Coletti EJ, Almeida-Porada
G, Muller HW, Zanjani E, Wernet P: A new human somatic stem
cell from placental cord blood with intrinsic pluripotent dif-
ferentiation potential. J Exp Med 2004, 200:123-135. 38. Brittberg M, Lindahl A, Nilsson A, Ohlsson C, Isaksson O, Peterson
L: Treatment of deep cartilage defects in the knee with autol-
ogous chondrocyte transplantation. N Engl J Med 1994,
331:889-895. 62. p
J
p
62. Evans CH, Robbins PD: Possible orthopaedic applications of
gene therapy. J Bone Joint Surg Am 1995, 77:1103-1114. 39. Wie X, Messnerr K: Maturation-dependent durability of spon-
taneous cartilage repair in rabbit knee joint. J Biomed Mater Res
1999, 46:539-548. 63. g
p
J
J
g
63. Yang C, Wang XD, Qui WL, Cai XY, Ha Q: A experimental study
on arthroscopic auricular cartilage transplantation for repair
of osteochondral defect of temporomandibular joint. References g
p
g
J
g
26. Martin JA, Buckwalter JA: The role of chondrocyte-matrix inter-
actions in maintaining and repairing articular cartilage. Bior-
heology 2006, 37(1–2):129-140. 27. Martin I, Obradovic B, Treppo S, Grodzinsky AJ, Langer R, Freed LE,
Vunjak-Nonakovic G: Modulation of the mechanical properties
of
tissue
engineered
cartilage. Biorheology
2001,
37(1–2):141-147. Page 6 of 7
(page number not for citation purposes) Page 6 of 7
(page number not for citation purposes) Head & Face Medicine 2008, 4:3 http://www.head-face-med.com/content/4/1/3 http://www.head-face-med.com/content/4/1/3 28. Buckwalter JA: Mechanical Injuries of Articular Cartilage. In
Biology and Biomechanics of the Traumatized Synovial Joint Edited by: Fin-
erman G. Park Ridge, IL, American Academy of Orthopaedic Sur-
geons; 1992:83-96. 52. Pittenger MF, Mackay AM, Beck SC, et al.: Multilineage potential
of adult human mesenchymal stem cells. Science 1999,
284(5411):143-147. (
)
53. Moosmann S, Hutter J, Moser C, Krombach F, Huss R: Milieu-
adopted in vitro and in vivo differentiation of mesenchymal
tissues derived from different adult human CD34-negative
progenitor cell clones. Cells Tissues Organs 2005, 179(3):91-101. g
29. Buckwalter JA, Martin JA, Olmstead M, Athansiou K, Rosenwasser
MP, Mow VC: Osteochondral repair of primate knee femoral
and patellar articular surfaces: implications for preventing
post-traumatic osteoarthritis. Iowa Orthop J 2003, 23:66-74. 54. Handschel J, Depprich RA, Kubler NR, Wiesmann HP, Ommerborn
M, Meyer U: Prospects of micromass culture technology in tis-
sue engineering. Head & Face Medicine 2007:4. p
p J
30. Reinholz GG, Lu L, Saris DB, Yaszemski MJ, O'Driscoll SW: Animal
models for cartilage reconstruction. Biomaterials 2004,
25:1511-1521. g
g
55. Springer IN, Fleiner B, Jepsen S, Acil Y: Culture of cells gained
from temporomandibular joint cartilage of non-absorbable
scaffolds. Biomaterials 2001, 22:2569-2577. 31. Macintosh RB: The use of autogenous tissues for temporoman-
dibular joint reconstuction. J Oral Maxillofac Surg 2000, 58:63-69. 56. Redman SN, Oldfield SF, Archer CW: Current strategies for
articular cartilage repair. Eur Cell Mater 2005, 9:23-32. 32. Zhu SS, Hu J, Li N, Zhou HX, Luo E: Autogenous coronoid proc-
ess as a new donor source for reconstruction of mandibular
condyle: an experimental study on goats. Oral Sug Oral Med
Oral Pathol Oral Radio Endod 2006, 101:572-580. g
p
57. Waldman SD, Grynpas MD, Pilliar RM, Kandel RA: The use of spe-
cific chondrocyte populations to modulate the properties of
tissue-engineered cartilage. J Orthop Res 2003, 21:132-138. ,
33. References Shang-
hai Kou Quiang Yi Xue 2001, 10:260-262. 40. Anderer A, Libera J: In vitro engineering of human autogenous
cartilage. J Bone Miner Res 2002, 17:1420-9. 41. Brittberg M: Autologous chondrocyte transplantation. Clin
Orthop Relat Res 1999, 367:S147-155. p
42. Hauselmann HJ, Flura T, Marti C, Hauser N, Hedbom E: From
chondrocyte culture to joint cartilage replacement. Devel-
opment of de novo cartilage in vitro. Schweiz Med Wochenschr
1998, 128:824-832. 43. Vangsness CT, Kurzweil PR, Liebermann JR: Restoring articular
cartilage in the knee. Am J Orthop 2004, 33(2 Suppl):S29-34. g
J
p
(
pp )
44. Richardson JB, Caterson B, Evans EH, Ashton BA, Roberts S: Repair
of human articular cartilage after implantation of autologous
chondrocytes. J Bone Joint Surg Br 1999, 81:1064-1068. 45. Peterson LT, Minas T, Brittberg M, Nilsson A, Sjogren-Jansson E, Lin-
dahl A: Two- to 9-year outcome after autologous chondro-
cyte transplantation of the knee. Clin Orthop Relat Res 2000,
374:212-234. 46. Minas T: Autologous chondrocyte implantation for focal
chondral defects of the knee. Clin Orthop Relat Res 2001,
391:S349-361. 47. Sohn DH, Lottmann LM, Lum LY, Kim SG, Pedowitz RA, Coutts RD,
Sah RL: Effect of gravity on localization of chondrocytes
implanted in cartilage defects. Clin Orthop Relat Res 2002,
394:254-262. Publish with BioMed Central and every
scientist can read your work free of charge
"BioMed Central will be the most significant development for
disseminating the results of biomedical research in our lifetime."
Sir Paul Nurse, Cancer Research UK
Your research papers will be:
available free of charge to the entire biomedical community
peer reviewed and published immediately upon acceptance
cited in PubMed and archived on PubMed Central
yours — you keep the copyright
Submit your manuscript here:
http://www.biomedcentral.com/info/publishing_adv.asp
BioMedcentral
Page 7 of 7
(page number not for citation purposes) Publish with BioMed Central and every
scientist can read your work free of charge
"BioMed Central will be the most significant development for
disseminating the results of biomedical research in our lifetime."
Sir Paul Nurse, Cancer Research UK
Your research papers will be:
available free of charge to the entire biomedical community
peer reviewed and published immediately upon acceptance
cited in PubMed and archived on PubMed Central
yours — you keep the copyright
Submit your manuscript here:
http://www.biomedcentral.com/info/publishing_adv.asp
BioMedcentral Publish with BioMed Central and every
scientist can read your work free of charge Publish with BioMed Central and every
scientist can read your work free of charge 48. Yamaguchi M, Hirayama F, Murahashi H, et al.: Ex vivo expansion of
human UC blood primitive haematopoetic progenitors and
transplantable stem cells using human primary BM stromal
cells and human AB serum. Cytotherapy 2002, 4(2):109-118. y
py
( )
49. Heng BC, Cao T, Stanton LW, Robson P, Olsen B: Strategies for
directing the differentiation of stem cells into the osteogenic
lineage in vitro. J Bone Miner Res 2004, 19(9):1379-1394. g
J
( )
50. Zur Nieden NI, Kempka G, Rancourt DE, Ahr HJ: Induction of
chondro-, osteo-, and adipogenesis in embryonic stem cells
by bone morphogenetic protein-2: effect of cofactors on dif-
ferentiating lineages. BMC Dev Biol 2005, 5(1):1. g
g
( )
51. Halleux C, Sottile V, Gasser JA, Seuwen K: Multi-lineage potential
of human mesenchymal stem cells following clonal expan-
sion. J Musculoskelet Neuronal Interact 2001, 2(1):71-76. g
g
( )
51. Halleux C, Sottile V, Gasser JA, Seuwen K: Multi-lineage potential
of human mesenchymal stem cells following clonal expan-
sion. J Musculoskelet Neuronal Interact 2001, 2(1):71-76.
|
https://openalex.org/W4317941164
|
https://www.research-collection.ethz.ch/bitstream/20.500.11850/596663/2/PhysRevE.107.015307.pdf
|
English
| null |
Voronoi tessellation-based algorithm for determining rigorously defined classical and generalized geometric pore size distributions
|
Physical review. E
| 2,023
|
cc-by
| 17,299
|
ETH Library ETH Library Voronoi tessellation-based
algorithm for determining
rigorously defined classical and
generalized geometric pore size
distributions Voronoi tessellation-based algorithm for determining rigorously defined classical
and generalized geometric pore size distributions Samarth Agrawal,1,2,* Sandra Galmarini
,1,† and Martin Kröger
2,3,‡
1Laboratory for Building Energy Materials and Components, Swiss Federal Laboratories for Science and Technology,
Empa, Überlandstrasse 129, 8600 Dübendorf, Switzerland
2Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
3Magnetism and Interface Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland (Received 25 September 2022; accepted 6 January 2023; published 25 January 2023) (Received 25 September 2022; accepted 6 January 2023; published 25 January 2023) The geometric pore size distribution (PSD) P(r) as function of pore radius r is an important characteristic
of porous structures, including particle-based systems, because it allows us to analyze adsorption behavior,
the strength of materials, etc. Multiple definitions and corresponding algorithms, particularly in the context of
computational approaches, exist that aim at calculating a PSD, often without mentioning the employed definition
and therefore leading to qualitatively very different and apparently incompatible results. Here, we analyze the
differences between the PSDs introduced by Torquato et al. and the more widely accepted one provided by Gelb
and Gubbins, here denoted as T-PSD and G-PSD, respectively, and provide rigorous mathematical definitions
that allow us to quantify the qualitative differences. We then extend G-PSD to incorporate the ideas of coating,
which is significant for nanoparticle-based systems, and of finite probe particles, which is crucial to micro and
mesoporous particles. We derive how the extended and classical versions are interrelated and how to calculate
them properly. We next analyze various numerical approaches used to calculate classical G-PSDs and may
be used to calculate the generalized G-PSD. To this end, we propose a simple yet sufficiently complicated
benchmark for which we calculate the different PSDs analytically. This approach allows us to completely rule out
a recently proposed algorithm based on radical Voronoi tessellation. Instead, we find and prove that the output of
a grid-free classical Voronoi tessellation, namely, the properties of its triangulated faces, can be used to formulate
an algorithm, which is capable of calculating the generalized G-PSD for a system of monodisperse spherical
particles (or points) to any precision, using analytical expressions. The Voronoi-based algorithm developed and
provided here has optimal scaling behavior and outperforms grid-based approaches. DOI: 10.1103/PhysRevE.107.015307 Author(s): This page was generated automatically upon download from the ETH Zurich Research Collection. For more information, please consult the Terms of use. PHYSICAL REVIEW E 107, 015307 (2023) DOI: 10.1103/PhysRevE.107.015307 I. INTRODUCTION To avoid this
issue, methods have been developed which extract a PSD In the present work we focus on the definition provided
by Gelb and Gubbins [31], also referred to as geometric pore
size distribution P(r), and denoted as classical G-PSD in the
remainder of this paper because it provides results consistent
with indirect methods such as Barrett-Joyner-Halenda (BJH)
[17] and nonlocal density-functional theory (NLDFT) [20] *samarth.agrawal@empa.ch
†sandra.galmarini@empa.ch
‡mk@mat.ethz.ch
2470-0045/2023/107(1)/015307(16) 015307-1 ©2023 American Physical Society PHYSICAL REVIEW E 107, 015307 (2023) AGRAWAL, GALMARINI, AND KRÖGER Examples for the classical case of V (r|0) and its geometrical
construction for a 2D system composed of N = 20 circular
material particles of radius r◦= 0.1 are shown in Fig. 1. The
centers of the circular pores of radius r are located in a region
whose points are further away than r from the surface of
the material. To visualize this region, we show the euclidean
distance maps (EDM) in the first column. Each point in an
EDM map carries the distance to the closest center of a ma-
terial circle. The Voronoi tessellation is an EDM map where
only those points are shown as Voronoi edges that have equal
distance to more than a single material circle. Each Voronoi
cell surrounding a material circle then represents all points
that are closer to this material circle than to any other material
circle. Examples for the classical case of V (r|0) and its geometrical
construction for a 2D system composed of N = 20 circular
material particles of radius r◦= 0.1 are shown in Fig. 1. The
centers of the circular pores of radius r are located in a region
whose points are further away than r from the surface of
the material. To visualize this region, we show the euclidean
distance maps (EDM) in the first column. Each point in an
EDM map carries the distance to the closest center of a ma-
terial circle. The Voronoi tessellation is an EDM map where
only those points are shown as Voronoi edges that have equal
distance to more than a single material circle. Each Voronoi
cell surrounding a material circle then represents all points
that are closer to this material circle than to any other material
circle. for simple geometries such as cylinders, spheres while also
providing meaningful results for more complex structures
such as porous glasses [31]. I. INTRODUCTION It was demonstrated with ex-
traordinary clarity that the T-PSDs defined by Torquato et al. [30] should not be used if a physically meaningful PSD is
targeted [28]. Most literature available in the context of PSD,
including computational approaches, consider the adsorbate
gas molecule (used for studying the adsorption isotherm), to
be a point sized sphere (probe radius rp = 0). However, for
the case of micro- and mesoporous materials such as metal
organic frameworks, aerogels, etc. [32], the size of the adsor-
bate gas molecule is comparable to the size of cavities present
in the adsorbent material and therefore has a significant effect
on the adsorption isotherms and derived quantities such as
SASA and PSDs [33]. Pinheiro et al. [34] have studied the
probe-size dependent G-PSD for computationally generated
Zeolite structures, but have not provided the equivalent math-
ematical expression for the Monte Carlo scheme used. For the
class of nanoparticles and their porous composites the PSD
is affected by a temperature- or solvent quality-depending
coating thickness [35,36]. Such stabilizing coatings usually
contain thermoresponsive polymers [37]. We revisit and eventually generalize existing algorithms,
and provide a new one that is particularly suited for the
calculation of the generalized P(r; rp|rc) = P(r −rp|reff) for
monodisperse systems composed of spherical particles of ra-
dius r◦. This gives rise to a second relevant radius we use later,
the radius of the effectively coated particle, rs = r◦+ reff. (2) (2) The calculation of G-PSD is not straightforward, and var-
ious approaches have been suggested. For all such methods,
the distribution is obtained at finite resolution: using M ran-
dom insertions or M grid nodes. Algorithms that aim to fill
the void space based on pixelated images of the material,
have been suggested previously [38,39]. Various Monte Carlo
schemes have also been proposed, including Bhattacharya
et al. [40], wherein each Monte Carlo step is formulated as
a constrained maximization problem and found it to be a
computationally cheap. However, given the nature of opti-
mization algorithms it is susceptible to locating local extrema
as opposed to optimal solutions. Pinheiro et al. [34] sug-
gested a semi-analytical solution to this problem by utilizing
a radical Voronoi partition of the porous system. However,
as we explain later, this method is actually erroneous and
not suitable for calculating the G-PSD. I. INTRODUCTION Given its extensive
use to characterize porous materials, the development of a
fast algorithm which provides correct results is imperative. We adapt the existing numerical methods to generate probe
size dependent G-PSD, and also present a Voronoi-based
numerical method which can be used to calculate the same
specifically for monodisperse systems composed of spherical
particles. Furthermore, we compare the accuracy of the nu-
merical algorithms presented for some simple configurations. Here, we derive the analytical expression for probe radius
rp and coating-thickness rc-dependent generalized G-PSD
P(r; rp|rc). We examine how it changes qualitatively for a
simple benchmark case, for which the analytic solution is
derived as well. We consider both finite coating thickness rc
and probe particle radius rp mainly for the reason that they
can be treated using identical methods. The G-PSD P(r; rp|0)
for a naked system (uncoated, rc = 0) with finite probe size
rp can be mapped onto the problem P(r; 0|rc) of a rc-coated
system with vanishing probe radius. The G-PSD for the coated
system, in turn, is the P(r) for the modified, rc-coated original
material, which we denote by P(r|rc). There are several im-
portant points to realize: (i) the G-PSD for a coated system is
qualitatively different from the G-PSD for the original system
and does not correspond to a simply r-shifted P(r); (ii) the
generalized P(r; rp|rc) can be obtained from P(r|reff) with an
effective coating thickness (1) reff = rc + rp,
(1) as we going to explain; (iii) the two versions of T-PSDs intro-
duced by Torquato et al. can be expressed in terms of a shifted
P(0|r) and are therefore qualitatively completely different to
P(r|0), as we will discuss in detail. Different definitions of the PSD can be expressed in terms
of the void volume accessible to a full r sphere in an reff-
coated system denoted by The definition of G-PSD and its generalization, as well
as its connection to accessible volumes is provided in
Sec. II. Existing numerical methods are revisited in Sec. III,
along with a complete description of the new proposed
Voronoi-based O(M) algorithm for calculating the G-PSD
for two-dimensional (2D) systems. Section IV presents our
recommended benchmark, for which we derive analytic ex-
pressions in Sec. IV A. The benchmark serves to rule out
the radial Voronoi approach in Sec. IV B. The differences
between T-PSDs and the G-PSD are worked out in Sec. I. INTRODUCTION from adsorption isotherms [17–19]. These methods typically
assume the geometry of pores and shape of the distribution
before fitting with the experimental data to estimate a PSD. The major drawback of such approaches is the assumption
of pore geometry, and even state-of-the-art methods based
on nonlocal density-functional theory [20,21] have shown to
produce spurious results for some cases [22]. Therefore, an
alternative approach wherein a PSD is directly calculated from
the microstructure of the material serves as a viable solution. The microstructure in question can be either generated using
nonintrusive high-resolution microscopy techniques [23–25]
or via computational methods [26]. The mathematical defini-
tion of a pore size distribution, however, is not unique [27–29]. Definitions provided by Torquato et al. [30] and by Gelb et al. [31] differ significantly. While the former is based on the
nearest-neighbor statistics, the latter derives the concept of
a pore from the total accessible volume to a probe of given
radius. The characterization of the void region in porous materials
is an important aspect for understanding their behavior and
for engineering purposes. The role of the void region has
been studied in the context of glassy systems [1–3], mechan-
ical behavior of cellular solids [4], hydrophobicity in amino
acids [5], phase transition in two-dimensional (2D) colloids
[6], strength of concrete [7], etc. The void regions are char-
acterized in terms of quantities such as solvent accessible
surface area (SASA) [8,9] and pore size distribution (PSD)
[10–12]. The latter is an important parameter for designing
mesoporous and microporous materials which can be used
for engineering applications such as gas storage [13–15] and
separation of different components [16]. Experimentally, a
PSD can be estimated using mercury porosimetry [11,12],
however this method is intrusive and could potentially damage
the sample during the measurement process. II. GEOMETRIC PORE SIZE DISTRIBUTIONS G-PSD For an arbitrary porous system in D dimensions, the space
can be divided into rc-coated material and void regions. Here,
we denote by rc-coated material the expanded material, whose
outer surface is at distance rc away from the original surface;
rc = 0 corresponds to the classical naked case. These coatings
may overlap with themselves, and may also be regarded as
hypothetical coatings for the purpose of this paper. Then, the
size of a spherical pore for a given point p inside the void
space is defined by the largest sphere that resides completely
in the void region and contains this point p [40]. Such a
D-dimensional sphere is termed as largest enclosing sphere
(LES) and is represented as r(p|rc), where r is its radius which
is a function of the chosen point p subject to the condition that
the material is rc coated. y
q
p
0
Generalized G-PSD. For the case of micro- and meso-
porous materials such as metal organic frameworks, aerogels,
etc. [32], the size of the adsorbate gas molecule (used for
studying the adsorption isotherm) is comparable to the size
of cavities present in the adsorbent material [33]. The total
pore volume that is accessible experimentally to finitely sized
probe particles is not necessarily the entirety of the void
region, and hence the concept of the size of the pore at a
point p is redefined as—the largest sphere that resides in the
void region and completely contains the probe sphere centered
at p with radius rp. Such a sphere is hereby termed as the
largest probe enclosing sphere (LPES) and is represented by
r(p; rp|rc) because it is a function of the chosen point p as
well as of the spherical probe radius rp, within the rc-coated
material. A schematic figure showing the LES r(p) = r(p|0)
and LPES r(p; rp) = r(p; rp|0) for a given p and rp, in an
arbitrary naked landscape, are respectively shown in Figs. 2(a)
and 2(b). The dashed lines around the material particles in
Fig. 2(d) to form the surface of the hypothetically rp-coated
material, and the region marked by the dashed circle, of radius
r −rp inside the LPES is the total volume accessible to the
center position p of the finitely sized probe particle, while the Classical G-PSD. I. INTRODUCTION IV C. The convergence behavior and computational efficiency of
the Voronoi-based algorithm is discussed in Sec. IV D, for
the benchmark and also for a more “realistic” system, where
computational approaches are the only means to estimate V (r|reff),
(r ⩾0, reff ⩾−r◦). This volume is significantly larger and more difficult to esti-
mate than the volume accessible to the center of an r sphere;
V (r|reff) is the most fundamental quantity in this work. The
generalized G-PSD is expressed in terms of V (r|reff) in Eq. (4)
below. All PSDs treated in this work and related quantities
can be derived from V (r|reff), as we show later. However, it
should be noted that this does not imply that an algorithm that
determines a PSD must focus on calculating V (r|reff). Nega-
tively coated particles appear in connection with the T-PSDs
and the classical G-PSD requires knowledge of V (r|0) only. 015307-2 VORONOI TESSELLATION-BASED ALGORITHM FOR … PHYSICAL REVIEW E 107, 015307 (2023) FIG. 1. Multidisk setup. Construction, shape and size of the volume V (r) = V (r|0) for a 2D system consisting of 20 noncoated circles of
radius r◦= 0.1 (filled circles) in a periodic box of side length L = 1 for two selected cases: (a) r = 0.1, and (b) r = 0.3. The first column
shows the euclidean distance map (EDM, colored) constructed from the particles center positions (dark blue), as well as a single contour line
(black) at altitude r + r◦. The second column highlights the region (green) enclosed by the EDM contour line; it carries all possible center
coordinates of circular pores of radius r. The last column shows the volume V (r|0) (green). FIG. 1. Multidisk setup. Construction, shape and size of the volume V (r) = V (r|0) for a 2D system consisting of 20 noncoated circles of
radius r◦= 0.1 (filled circles) in a periodic box of side length L = 1 for two selected cases: (a) r = 0.1, and (b) r = 0.3. The first column
shows the euclidean distance map (EDM, colored) constructed from the particles center positions (dark blue), as well as a single contour line
(black) at altitude r + r◦. The second column highlights the region (green) enclosed by the EDM contour line; it carries all possible center
coordinates of circular pores of radius r. I. INTRODUCTION The last column shows the volume V (r|0) (green). the PSD. Conclusions based on these results are provided in
Sec. V. spheres of radius r, and V ′(r) represents the derivative with
respect to r. The denominator V (0) is then the total volume of
the void region as the entirety of the void region is accessible
to a point-sized sphere. As seen readily, P(r) is normalized
because, as V (∞) = 0 for any finitely sized—or periodic—
system, Eq. (3) implies
∞
0 P(r)dr = 1. II. GEOMETRIC PORE SIZE DISTRIBUTIONS G-PSD 3 shows the change in the EDM for finite reff. Based on
these considerations, the generalized G-PSD is We can find the expression for the generalized G-PSD,
P(r; rp|rc), by reducing it to a class of problem treated by
Eq. (3). The point p cannot be chosen within a distance of
rp from the rc-coated material region to prevent the probe par-
ticle from overlapping. Hence, we can operate in a modified
system wherein all the material elements are hypothetically
coated with an additional thickness of rp. For the rc-coated
system, the volume accessible to a sphere of radius r is de-
noted by V (r|rc). Therefore the entirety of the void region of
the reff ≡rc + rp-coated material is represented by V (0|reff);
any possible probe particle center resides within this volume. With Eq. (4) at hand, the cumulative distribution,
Pcum(r; rp|rc) =
∞
rp P(ρ; rp|rc)dρ corresponding to the gen-
eralized G-PSD is Pcum(r + rp; rp|rc) = 1 −V (r|reff)
V (0|reff)
(r ⩾0),
(6) (6) where V (0|reff) is the total void volume in the effectively or
hypothetically reff-coated system. As seen the proper limits
are Pcum(rp; rp|rc) = 0 and limr→∞Pcum(r; rp|rc) = 1, for any
rc and any rp, confirming that P(r; rp|rc) is indeed a properly
normalized probability density. The mean pore radius as func-
tion of rp and rc is ⟨r⟩=
∞
rp
rP(r; rp|rc)dr = rp +
∞
0 V (r|reff)dr
V (0|reff)
. (7) P(r; rp|rc) = −V ′(r −rp|reff)
V (0|reff)
(r ⩾rp),
(4) (7) (4) These expressions allow us to calculate the G-PSD from V ,
which is the easier quantity for analytic calculations. We now
calculate the G-PSD for some regular shaped geometries. In
case of a reff-coated cylinder of radius r⃝> reff and length
L, we have V (r|reff) = π(r⃝−reff)2L for r ⩽r⃝−reff, and
V (r|reff) = 0 otherwise. According to Eq. (4), P(r; rp|rc) =
δ(r⃝−rc −r) has a single dirac-distributed peak as long as
reff ⩽r⃝and vanishes otherwise. This examples highlights
the fact that reff = rc + rp can be freely distributed over probe
radius and coating layer thickness, and how this splitting
affects the G-PSD. II. GEOMETRIC PORE SIZE DISTRIBUTIONS G-PSD The classical G-PSD, P(r), is the prob-
ability density function of r(p) = r(p|0) of the LES for
uniformly chosen p in the void region of the naked material. It has been shown that P(r) is defined as [31] P(r) = −V ′(r)
V (0)
(r ⩾0),
(3) (3) wherein V (r) denotes the accessible pore volume, which is
the total volume of the void region that is within reach to 015307-3 PHYSICAL REVIEW E 107, 015307 (2023) AGRAWAL, GALMARINI, AND KRÖGER c
rc
r = 0
p
r = 0
p
r(p|r)
c
r(p;r)
p
r
r-rp
r(p)
rp
(a)
(d)
(c)
(b)
p
rp
rp
ro
FIG. 2. Enclosing spheres for a material with just two solid 3D spheres. (a) Largest enclosing sphere (LES, black empty circle, actually
representing a sphere) of radius r(p), centered at c (cyan), containing the probe point particle centered at p (green). (b) Largest probe enclosing
sphere (LPES, black empty circle) of radius r(p; rp) centered at another c, containing the probe sphere (radius rp > 0) centered at p. (c) LES
of radius r(p|rc) within the rc-coated material. (d) A hypothetical material shell of size rp can be used to calculate r(p; rp) −rp = r(p|rp), cf. Eq. (4), and to reduce the LPES problem to the setup shown in panel (c), where rc is replaced by an effective radius reff = rc + rp, cf. Eq. (1). The distance R(c) between c and the center of the nearest material particle (radius r◦) is different in panels (a)–(c). For sufficiently large probe
particles, there are regions in the void space (coating overlap) that cannot host a finitely sized probe particle. Note that the surface of the probe
particle must not touch the LES or LPES in general, if there are more than two material spheres. This will become obvious later below. rc
r = 0
p
r(p|r)
c
(c) r
r-rp
(d)
rp
rp (b) (c) (d) rc FIG. 2. Enclosing spheres for a material with just two solid 3D spheres. (a) Largest enclosing sphere (LES, black empty circle, actually
representing a sphere) of radius r(p), centered at c (cyan), containing the probe point particle centered at p (green). (b) Largest probe enclosing
sphere (LPES, black empty circle) of radius r(p; rp) centered at another c, containing the probe sphere (radius rp > 0) centered at p. II. GEOMETRIC PORE SIZE DISTRIBUTIONS G-PSD (c) LES
of radius r(p|rc) within the rc-coated material. (d) A hypothetical material shell of size rp can be used to calculate r(p; rp) −rp = r(p|rp), cf. Eq. (4), and to reduce the LPES problem to the setup shown in panel (c), where rc is replaced by an effective radius reff = rc + rp, cf. Eq. (1). The distance R(c) between c and the center of the nearest material particle (radius r◦) is different in panels (a)–(c). For sufficiently large probe
particles, there are regions in the void space (coating overlap) that cannot host a finitely sized probe particle. Note that the surface of the probe
particle must not touch the LES or LPES in general, if there are more than two material spheres. This will become obvious later below. either the case P(r; 0|rc) of point-like probe particles in the
original material with variable coating, or the case P(r; rp|0)
of rp-sized probe particles in the naked system, to obtain
the full P(r; rp|rc). If the material consists of monodisperse
spheres of equal radius r◦, these particles can also be regarded
as r◦-coated points. For the special case of point-like probe
particles in naked material, Eq. (4) reduces to Eq. (3). volume accessible to the probe particle itself also includes
the portions of the hypothetical coating. We can find the expression for the generalized G-PSD,
P(r; rp|rc), by reducing it to a class of problem treated by
Eq. (3). The point p cannot be chosen within a distance of
rp from the rc-coated material region to prevent the probe par-
ticle from overlapping. Hence, we can operate in a modified
system wherein all the material elements are hypothetically
coated with an additional thickness of rp. For the rc-coated
system, the volume accessible to a sphere of radius r is de-
noted by V (r|rc). Therefore the entirety of the void region of
the reff ≡rc + rp-coated material is represented by V (0|reff);
any possible probe particle center resides within this volume. Any LES which contains the center of the probe particle is
then effectively the LPES, as extension into the imaginary
coating is permissible. Therefore the problem of finding the
LPES is now reduced to the original problem of finding the
LES in the coated system. Figure 2 illustrates the idea of
finding the LES and the LPES via hypothetical coating, while
Fig. II. GEOMETRIC PORE SIZE DISTRIBUTIONS G-PSD The first column shows the euclidean distance map (EDM, colored) constructed from the particles center positions (dark blue), as
well as a single contour line (black) at altitude r + rs. The second column highlights the region (green) enclosed by the EDM contour line; it
carries all possible center coordinates of circular pores of radius r. The black circles in panel (b) mark the outer surface of reff-coated particles. The last column shows the volume V (r|reff) (green), i.e., V (0.2, 0) in panel (a) and V (0.1, 0.1) in panel (b). All variants of PSD’s are encoded
in the two-parametric V (r|reff). The numerical result for V (r|reff) over the whole range of semipositive r and reff for this setup is shown in
Fig. 6, along with the corresponding results for the generalized G-PSD. keeping in mind that these quantities contain the generalized
G-PSD and cumulative G-PSD as function of rc and rp via
Eqs. (5) and (6). To be clear, the generalized G-PSD is ob-
tained from the two-parametric V (r|reff) via On the other hand, for a hollow cube, P(r; rp|rc) is very
sensitive to rp and rc, as the fraction of void region ac-
cessible to the probe in the neighborhood of the corners
changes considerably with rp and rc. Some cases for which
all the quantities V (r|reff) and P(r; rp|rc) can be calculated
analytically, are collected in Appendix. For more compli-
cated systems, such as those generated using methods such
as molecular dynamics, calculating the geometric G-PSD an-
alytically is impossible [31,41] and numerical methods must
be employed. In the following section, we briefly describe
existing numerical methods that can, or cannot be used to
calculate geometric G-PSD P(r; rp|rc) and also propose a new
method based on Voronoi tessellation that can be used for
systems made of monodisperse spherical particles. P(r; rp|rc) = P(r −rp|reff),
(9)
Pcum(r; rp|rc) = Pcum(r −rp|reff). (10) (9) (10) Pcum(r; rp|rc) = Pcum(r −rp|reff). (10) With the help of Pcum(r|reff) the mean pore radius can also be
written as ⟨r⟩= rp +
∞
0 [1 −Pcum(r|reff)] dr.
0
T-PSDs. Using unchanged notation, we can provide a
mathematical definition of the two T-PSD versions suggested
by Torquato et al. [30], which are only applicable for the spe-
cial case of rc = rp = reff = 0 (for a derivation see Sec. II. GEOMETRIC PORE SIZE DISTRIBUTIONS G-PSD where the prime denotes a derivative with respect to r, and
where we recall that V (r|reff) is the fundamental void volume
in the reff-coated system that is accessible to a full r sphere. A special case is the naked version (3) since V (r) =
V (r|0). If we write Eq. (4) as P(r + rp; rp|rc) = −V ′(r|reff)
V (0|reff)
(r ⩾0),
(5) (5) with the effective coating reff = rc + rp, assumes the same
form as Eq. (1), therefore indicating that G-PSD depends on
r and reff only. It is therefore in every case sufficient to study 015307-4 PHYSICAL REVIEW E 107, 015307 (2023) VORONOI TESSELLATION-BASED ALGORITHM FOR … FIG. 3. Multidisk setup. Construction, shape and size of the volume V (r|reff) for the system treated already by Fig. 1, here for two selected
cases which share their sum r + reff = 0.2: (a) r = 0.2, reff = 0, (b) r = reff = rc + rp = 0.1 (for example rc = 0.1 and rp = 0 or rc = 0 and
rp = 0.1). The first column shows the euclidean distance map (EDM, colored) constructed from the particles center positions (dark blue), as
well as a single contour line (black) at altitude r + rs. The second column highlights the region (green) enclosed by the EDM contour line; it
carries all possible center coordinates of circular pores of radius r. The black circles in panel (b) mark the outer surface of reff-coated particles. The last column shows the volume V (r|reff) (green), i.e., V (0.2, 0) in panel (a) and V (0.1, 0.1) in panel (b). All variants of PSD’s are encoded
in the two-parametric V (r|reff). The numerical result for V (r|reff) over the whole range of semipositive r and reff for this setup is shown in
Fig. 6, along with the corresponding results for the generalized G-PSD. FIG. 3. Multidisk setup. Construction, shape and size of the volume V (r|reff) for the system treated already by Fig. 1, here for two selected
cases which share their sum r + reff = 0.2: (a) r = 0.2, reff = 0, (b) r = reff = rc + rp = 0.1 (for example rc = 0.1 and rp = 0 or rc = 0 and
rp = 0.1). A. Brute force scan using a grid The possibly most straightforward approach to directly
estimate P(r|reff) rather than V (r|reff) for a fixed coating
thickness reff at high memory and computational cost is by
considering a regular lattice of M coordinates {pi} in the void
space of the reff-coated structure, with an initially zeroed LES
field r(pi|reff). Note here already that the LES r(p|reff) for the
coated system is not identical to the LPES r(p; reff) for the
naked system, and that this difference matters, if one is not
only interested in the classical P(r). For each of the lattice
points c ∈{pi} all the nodes residing within the volume of
the largest sphere centered at c, with radius R(c|reff), are
visited and the r values of all those nodes are updated to
max(r, R(c|reff)). R(c|reff) is determined by the distance be-
tween c and coated material surface next to c. For a substrate
consisting of N polydisperse spheres of radius rk
◦, centered at
xk, the radius R(c|reff) of the largest sphere at c fully residing
in the void is given by R(c|reff) = R(c) −reff with the usual
smallest distance provided in Fig. 4. While the first example [Figs. 4(a)–4(c)]
is a simple triangle whose edges consist of infinitely many
material points (r◦= 0), the second example [Figs. 4(d)–4(f)]
will become our benchmark case composed of a single ma-
terial point subject to periodic boundary conditions, to be
discussed in detail in Sec. IV. It is interesting to note that
the T-PSDs are linear in r for empty cylinders and spheres,
while the G-PSD to which we focus in this work considers a
spherical inclusion of radius r⃝to be a well-defined pore with
unique radius r⃝. As this Fig. 4 attempts to explain by show-
ing the relevant volumes entering the PSD definitions, the
versions produce qualitatively different pore size distributions
(Sec. IV C). R(c) = mink=1,...,N
|c −xk| −rk
◦
,
(12) (12) where | · ·| represents the Euclidean distance between two
points. For other types of substrates, R(c) can be calculated
from the shape of the material surface, and R(c) ⩾reff by
construction. At the end of this procedure one is left with a list
of size M whose entries are r(pi|reff) values. The histogram of
all these r values is P(r|reff) multiplied by a constant, and this
constant is simply given by Pcum(∞|reff) = 1. II. GEOMETRIC PORE SIZE DISTRIBUTIONS G-PSD IV C;
to avoid any confusion we label them by P instead of
P). There is on one hand a center-based Tc-PSD, Pc(r) =
dPc
cum(r)/dr with As discussed in detail, we can analyze the case of
point-sized probe particle in reff-coated material instead of
considering nonvanishing rp and rc separately. To this end we
finally define, using Eqs. (5) and (6), Pc
cum(r) = 1 −V (0|r −r◦)
V (0| −r◦)
(r ⩾0),
(11) (11) Pcum(r|reff) ≡Pcum(r; 0|reff) = 1 −V (r|reff)
V (0|reff)
(r ⩾0),
P(r|reff) ≡dPcum(r|reff)
dr
= −V ′(r|reff)
V (0|reff)
(r ⩾0),
(8) and on the other a surface-based Ts-PSD, defined via
Ps
cum(r) = Pc
cum(r + r◦) for r ⩾0. The qualitative differences
between the three PSDs (G versus center-based Tc-PSD and
surface-based Ts-PSD) are highlighted by the two examples 015307-5 AGRAWAL, GALMARINI, AND KRÖGER PHYSICAL REVIEW E 107, 015307 (2023) G
r
G
(a)
(b)
(d)
(e)
r
r -r
(c)
T
r
r
(f)
+r
Tc
Ts
Ts
Tc
FIG. 4. Relevant PSD volumes for the triangle and our bench-
mark setup. Drastic differences between the relevant (gray-shaded)
areas used to define the G-PSD P(r) of Gelb & Gubbins (G) [31]
as well as the Tc-PSD and Ts-PSD of Torquato et al. [30]. While
for the Tc-PSD (Ts-PSD) the red circle touches at least one center
(one surface) of a material particle, for the G-PSD it touches at least
two surfaces of material particles. (a)–(c) Naked triangle serving as
material. Its edges can be thought of consisting of infinitely many
circles of radius r◦= 0. (d)–(f) Our naked benchmark setup, con-
sisting of a single material particle of radius r◦subject to periodic
boundary conditions, i.e., tangent to its periodic image. (a) Shaded
area V (r|0) accessible to a circle of radius r, relevant for the G-PSD. (b), (c) Shaded area V (0|r −r◦) = V (0|r) enclosed by r-coated tri-
angle, relevant for both Tc-PSD and Ts-PSD, because r◦= 0 for the
triangle. (d) One quarter of the area V (r|0) (gray-shaded) accessible
to a circle of radius r, relevant for the G-PSD. (e) One quarter of
the area V (0|r −r◦) (gray-shaded) created by the material circle
coated by a shell of thickness r −r◦(for this particular example,
negatively coated), relevant for the Tc-PSD. II. GEOMETRIC PORE SIZE DISTRIBUTIONS G-PSD (f) One quarter of the
area V (0|r) (gray-shaded) created by the material circle coated by
a shell of thickness r, relevant for the Ts-PSD. While the Tc- and
Ts-PSDs are both trivially calculated at minor computational effort,
the efficient calculation of the G-PSD still poses a challenge, as these
simple examples might already suggest. r
(b)
(e)
(c)
(f)
Ts
Tc (c)
T
r
r
(f)
+r
Ts
Ts (c)
(f)
Ts r
(b)
Tc is either not well-defined, or as easy to compute as the T-
PSDs, while the calculation of the most useful G-PSD is much
more difficult to compute without making approximations or
introducing a finite grid resolution. After revisiting possible
approaches we derive an algorithm that is approximation-
and grid-free, efficient as it finds the coordinates of the
LPES semi-analytically, and exhibits the best possible O(M)
scaling. (a) T
r
r
(f)
+r
Ts (e)
r -r
Tc (f) (e) (d) III. EXISTING NUMERICAL METHODS FOR
GEOMETRIC AND GENERALIZED GEOMETRIC G-PSDs Most numerical methods proposed in literature focus on
determining the G-PSD P(r) = P(r|0) for the naked material
via a Monte Carlo scheme wherein large number of p is
chosen uniformly in the void region and the corresponding
LES is determined to build the histogram and subsequently,
the approximate distribution. Past works have mostly focused
on finding fast and accurate algorithms to determine the LES. We briefly explain the existing methods, mention how they
can be adapted to calculate LPES or the generalized P(r|reff)
based on LES for the coated material, and propose a new
algorithm for determining P(r|reff) for a material consisting
of N monodisperse spheres in Sec. IV. FIG. 4. Relevant PSD volumes for the triangle and our bench-
mark setup. Drastic differences between the relevant (gray-shaded)
areas used to define the G-PSD P(r) of Gelb & Gubbins (G) [31]
as well as the Tc-PSD and Ts-PSD of Torquato et al. [30]. While
for the Tc-PSD (Ts-PSD) the red circle touches at least one center
(one surface) of a material particle, for the G-PSD it touches at least
two surfaces of material particles. (a)–(c) Naked triangle serving as
material. Its edges can be thought of consisting of infinitely many
circles of radius r◦= 0. (d)–(f) Our naked benchmark setup, con-
sisting of a single material particle of radius r◦subject to periodic
boundary conditions, i.e., tangent to its periodic image. (a) Shaded
area V (r|0) accessible to a circle of radius r, relevant for the G-PSD. (b), (c) Shaded area V (0|r −r◦) = V (0|r) enclosed by r-coated tri-
angle, relevant for both Tc-PSD and Ts-PSD, because r◦= 0 for the
triangle. (d) One quarter of the area V (r|0) (gray-shaded) accessible
to a circle of radius r, relevant for the G-PSD. (e) One quarter of
the area V (0|r −r◦) (gray-shaded) created by the material circle
coated by a shell of thickness r −r◦(for this particular example,
negatively coated), relevant for the Tc-PSD. (f) One quarter of the
area V (0|r) (gray-shaded) created by the material circle coated by
a shell of thickness r, relevant for the Ts-PSD. While the Tc- and
Ts-PSDs are both trivially calculated at minor computational effort,
the efficient calculation of the G-PSD still poses a challenge, as these
simple examples might already suggest. B. Constrained local numerical optimization The problem of finding the LES radius and its center posi-
tion c for a given p and effective coating thickness reff can
also be formulated as a nonlinear constrained optimization
problem, using R(c) from the previous section, as ∀j=1,...,N
|r −xi|2 −
ri
◦
2 ⩽|r −x j|2 −
r j
◦
2,
(16) (16) where ri
◦corresponding to p is rp, when the radical Voronoi is
applied to N + 1 points via Eq. (15). The metric |r −xi|2 −
(ri
◦)2 is essentially square of the tangential length. It was
suggested that this metric is used instead of a more intuitive
|r −xi| −ri
◦because it results in irregular polyhedra much
like the standard Voronoi tessellation. Using this approach,
the center c of the LPES is then assumed to lie either on
one of the radical Voronoi vertices of the ghost cell, or on
one of the radical Voronoi vertices using N spheres. We can,
however, show that this approach exhibits a major deficiency
in methodology and is not suitable for all but the simplest
geometries. In particular, one can show analytically, that the
center of the LPES cannot coincide with the vertices of the
ghost cell. maximize
R(c|reff) = R(c) −reff,
constraint
R(c|reff) ⩾|c −p|,
(13) (13) wherein the constraint guarantees that point probe particle is
completely covered by the R sphere and does not overlap with
the coating. A main difference with the grid-based approach
is that c and p must both not reside on a grid, and c can
reside anywhere within the void space. As for most off-lattice
problems of this kind, this system of equation and inequal-
ity cannot be strictly solved using a nonlinear programming
module, as the landscape can be highly nontrivial. While the
grid-based approach cannot miss the constrained extremum
within the given resolution, the off-lattice version does not
guarantee a certain resolution, but can potentially lead to
correct results at infinitely large resolution. The optimization
procedure is repeated M times to result in a G-PSD P(r|reff)
that has a resolution comparable with the grid-based approach. The P(r; rp|rc) is then obtained from P(r|reff) via Eq. (10). As
opposed to the grid-based approach, R(c) cannot be calculated
once and stored but must also be calculated each time it is
required. If the average step size of the solver is denoted by δ,
the computational effort is MN⟨r⟩/δ. B. Constrained local numerical optimization Let cp be a vertex of Vp, then as per the definition of radical
Voronoi tessellation, it satisfies |cp −p|2 −r2
p = |cp −xi|2 −r2
◦,
(17) (17) where i is index of all particles which share the vertex cp, and
where we assumed monodisperse material particles, ri
◦= r◦,
only to shorten the following expressions. Then, the LPES
radius r(p; rp) = R(cp) must be large enough to completely
cover the probe particle. Mathematically, these conditions
can be represented as R(cp) −rp ⩾|cp −p| and R(cp) + r◦⩽
|cp −xi|, where we basically reiterated Eqs. (12) and (13). These inequalities imply C. Radical Voronoi tessellation Voronoi tessellation techniques partition the space using
a distance metric. In the standard method, given a set of N
points {xk}, the physical space can be divided into regions
based on the Euclidean distance from each point. In the
current context, the space is partitioned into N regions each
corresponding to one of the points. These regions are also
known as Voronoi cells. The Voronoi cell of point i contains
the set of all positions, r, which satisfy 0 ⩽|cp −xi| −r◦−|cp −p| −rp. (18) (18) Upon multiplying Eq. (18) with the positive |cp −xi| + r◦one
obtains with the help of Eq. (17) 0 ⩽|cp −xi|2 −r2
◦−(|cp −p| + rp)(|cp −xi| + r◦)
= |cp −p|2 −r2
p −(|cp −p| + rp)(|cp −xi| + r◦). (19) Upon dividing by the positive |cp −p| + rp, this inequality
implies Upon dividing by the positive |cp −p| + rp, this inequality
implies ∀j=1,...,N
|r −xi| ⩽|r −x j|. (14) (14) Such a partition of space results in cells shaped as irregular
polyhedra, with the faces, edges and vertices being sets of
points that are equidistant with respect to adjacent particle
centers. To find the LES of yet unknown radius r(p) cen-
tered at some c, Pinheiro et al. [34] proposed to consider,
in addition, the Voronoi tessellation for the (N + 1) points
(p, x1, . . . , xN ). Then, the cell corresponding to the point p,
hereby denoted as Vp, termed the “ghost cell,” contains the
set of all coordinates r which satisfy |cp −p| −rp ⩾|cp −xi| + r◦. (20) (20) This last inequality, however, negates inequality (18) and is
only possible when r◦= rp = 0 and |cp −p| = |cp −xi|. The
latter equality is ensured by the radical Voronoi construction,
if the former is fulfilled. As the radical Voronoi reduces to
the classical Voronoi construction for r◦= rp = 0, the radical
Voronoi construction can simply not be used for calculating
the classical or generalized G-PSD. We are going to calculate
the radical Voronoi vertices for the benchmark used within This last inequality, however, negates inequality (18) and is
only possible when r◦= rp = 0 and |cp −p| = |cp −xi|. The
latter equality is ensured by the radical Voronoi construction,
if the former is fulfilled. A. Brute force scan using a grid Having provided proper mathematical definitions of the
existing PSDs, explained their differences, and added the
definition of the generalized G-PSD, it is an apparently
straightforward exercise to calculate all these quantities nu-
merically, e.g., by evaluating the two-parametric function
V (r|reff) defined in Sec. I. Many previous works have reported
PSD curves, however, a careful inspection of the literature
shows that most so-called PSD curves show something that The accuracy of the method depends on the resolution of
the lattice and eventually requires large amounts of memory
to store the details of the lattice. If an upper limit for a pore
radius is determined in advance, memory can be saved and
resolution increased upon applying the grid-based approach
to regions of a size smaller than a multiple of the limiting 015307-6 PHYSICAL REVIEW E 107, 015307 (2023) VORONOI TESSELLATION-BASED ALGORITHM FOR … pore radius. The lattice can also be displaced and the proce-
dure repeated to increase the resolution. If the grid spacing
is δ, the computational effort of the grid-based approach is
≈M × N for the generation of the R grid, and ≈M(⟨r⟩/δ)D
for the accumulation of the D-dimensional r grid, for each
reff. If M ≫N, the overall computational effort is therefore
somewhere between O(M) and O(M2), and the details of the
PSD can only be obtained up to finite resolution δ. For the case of naked point particles (ri
◦= rc = 0), and point
probe particles (rp = 0), the center c of the largest included
sphere that contains p then resides on either the vertices of
the N- or (N + 1)-Voronoi meshes; the vertex with the largest
R(c) serves as the solution to the LES problem. Given this
property, it was further proposed [34] that the radical Voronoi
tessellation could be adapted to find the center and radius
of the LPES if both the material and the probe particle are
composed of spheres with finite radii, i.e., for ri
◦> 0 and
rp > 0. In the case of radical Voronoi tessellation, the space
is partitioned according to modified Eq. (14): C. Radical Voronoi tessellation The candidate
pore radius is re = |A + t0C| −rs and the corresponding pore
center is at ce = x + A + t0C because the two additional can-
didates to be derived next cannot lead to a larger re anymore. The so far unused 1 −t0 we have to keep in mind. If the two
terminals did not yet give rise to a final candidate pore radius
re, we need to continue and calculate at most the two solutions
t± to the effectively quadratic equation c −rs = |A −P + tC| FIG. 5. The Voronoi-based algorithm locates the center c (blue
point) and radius of the pore (black open circle) for a given point p
(green) either on (a) a vertex or (b) an edge of the Voronoi diagram
(black straight lines) corresponding to the material circles (black
solid circles). We calculate the position of c analytically, t ∈{0, 1}
for vertex-centered pores, and t ∈(0, 1) for edge-centered pores in
Sec. III D. FIG. 5. The Voronoi-based algorithm locates the center c (blue
point) and radius of the pore (black open circle) for a given point p
(green) either on (a) a vertex or (b) an edge of the Voronoi diagram
(black straight lines) corresponding to the material circles (black
solid circles). We calculate the position of c analytically, t ∈{0, 1}
for vertex-centered pores, and t ∈(0, 1) for edge-centered pores in
Sec. III D. this work in Sec. IV B to confirm that they do not lead to the
correct R(c|reff). C. Radical Voronoi tessellation As the radical Voronoi reduces to
the classical Voronoi construction for r◦= rp = 0, the radical
Voronoi construction can simply not be used for calculating
the classical or generalized G-PSD. We are going to calculate
the radical Voronoi vertices for the benchmark used within ∀j=1,...,N
|r −p| ⩽|r −x j|. (15) ∀j=1,...,N
|r −p| ⩽|r −x j|. (15) 015307-7 AGRAWAL, GALMARINI, AND KRÖGER PHYSICAL REVIEW E 107, 015307 (2023) (a) vertex-centered
pore
(b) edge-centered
pore
FIG. 5. The Voronoi-based algorithm locates the center c (blue
point) and radius of the pore (black open circle) for a given point p
(green) either on (a) a vertex or (b) an edge of the Voronoi diagram
(black straight lines) corresponding to the material circles (black
solid circles). We calculate the position of c analytically, t ∈{0, 1}
for vertex-centered pores, and t ∈(0, 1) for edge-centered pores in
Sec. III D. (a) vertex-centered
pore
(b) edge-centered
pore (a) vertex-centered
pore
(b) edge-centered
pore (a) vertex-centered
pore point p all possible candidate edges, we can visit each of
the T triangular regions and its finite number of candidate
edges just once. To this end we randomly pick a known
but triangle-dependent number m of points p within each
triangle ∈{1, . . . , T }, such that mj equals M times the void
area covered by the triangle within the system of reff-coated
material circles, divided by the total void area V (0|reff) avail-
able in the reff-coated system. This implies that, if a given
triangle does not have any overlap with the void space, no p
have to be placed in this region because this triangle does not
contribute to V (r|reff). For each of the m different positions
p located within a triangle (whose three vertices are respec-
tively at the center position x of the material particle to which
it belongs and at two adjacent vertices of the Voronoi face
belonging to x; the two relative vectors A and B point from
x to the other two vertices), we have to calculate a center c and
radius r of the LES that includes the point p and does not over-
lap with the reff-coated material circles. Once calculated, the
G-PSD P(r|reff) is the probability density constructed from
the M different r values. C. Radical Voronoi tessellation There are now two equally important
ingredients of our proposed algorithm left to be described, that
are key to the speed of execution and optimal scaling of CPU
time ∝M: (i) the generation of static subsets E of potentially
relevant Voronoi edges for the given triangle , and (ii) an
analytic expression for a candidate re value (and its ce) for the
given Voronoi edge e ∈E and point p. The final pore radius
for p is then given by the largest candidate re with e ∈E. (i)
The generation of static subsets E ⊂{1, . . . , T } is useful as
the number of pore-relevant edges for points p located inside
any of the T triangles is usually much smaller than both m
and N. A list E is obtained by first calculating the shortest
distances {se} between the triangle and all the T/2 different
Voronoi edges e (connecting Ae with Be). All those edges e
for which max(|Ae|, |Be|) −rs ⩾se are added to E. Because
max(|Ae|, |Be|) −rs is finite, the computational effort is at
most O(N) and therefore does not affect the scaling ∝M for
sufficiently large M. (ii) The given Voronoi edge e ∈E is a
line connecting two Voronoi vertices at A ≡Ae and B ≡Be,
that form a triangle with the corresponding material center
at x. Hence ce −x = A + tC with C ≡B −A and yet un-
known t ∈[0, 1]. The pore radius in the reff-coated system
is given by the maximum R(c|reff) = |c −x| −rs = c −rs
subject to the constraint R(c|reff) ⩾|c −p| = |A −P + tC|,
where c ≡|ce −x| and P ≡p −x. Since R(c|reff) ⩾0, max-
imizing R2(c|reff) presents an optimal solution for R(c|reff) as
well. We observe that ∂2[rs + R(c|reff)]2/∂c2 = 2 > 0, which
indicates that R2(c|reff) and by implication R(c|reff) has a
local minimum only and no local maximum. Hence, for any
given interval t ∈[t1,t2], the maximum lies on either of the
endpoints provided where the above inequality is satisfied. Consequently, we first test one of the two extremal values
t ∈{0, 1} corresponding to the edge terminals [Fig. 5(a)]. If
|A −P| ⩾|B −P|, we set t0 = 1, otherwise we set t0 = 0. If
|A + t0C| −rs ⩾|A −P + t0C|, we are done. D. Voronoi-based global analytical optimization We have already seen that the radical Voronoi construction
cannot be used to calculate the G-PSD, except where it re-
duces to the classical Voronoi, i.e., for the case of point-like
probe and point-like, uncoated material particles. However,
the information contained in the Voronoi network of the
N material particles alone can be used devise an algorithm
that greatly improves over the suitably adapted classical ap-
proaches (Sec. III B). Finding the center c of the LES or LPES for a given p
can be simplified by considering the fact that they must touch
at least two spheres at the same time (Fig. 5). In the case of
D = 2 dimensions, this amounts to the center c residing on an
edge of any of the N Voronoi cells, and on any of the Voronoi
faces in case of D = 3. Instead of randomly walking through
continuous D-dimensional space as done within constrained
optimization in its original form, we can restrict the algorithm
to inspect a number of relevant (D −1)-dimensional faces. For each such face, the optimum solution satisfying the con-
straints can be solved analytically not only in 2D but also in
three dimensions (3D). Each face gives rise to a candidate pore
radius; the largest among those candidate pore radii is the pore
radius for the given p. Here, we are limiting ourselves to derive and describe the
2D algorithm that returns the generalized G-PSD P(r|reff) for
a probe circle (radius rp) in a system of eventually overlapping
monodisperse material circles (radius r◦, coating thickness rc). The corresponding algorithm for the 3D case can be treated
in an analogous fashion. Once P(r; reff) has been computed,
P(r; rc|rp) is immediately available via Eq. (10). As a first
step, we make use of an existing algorithm to calculate, for
each material particle center x ∈{xk}, the vertex coordinates
of its Voronoi cell. Each Voronoi cell can be uniquely sub-
divided into nonoverlapping adjacent triangles that all meet
at x. D. Voronoi-based global analytical optimization Importantly, as the T = O(N) triangles corresponding
to the N material circles are all known from the Voronoi
construction at minor O(N) effort, to subsequently calculate
the G-PSD using M ≫T probe particle insertions efficiently,
and with proper statistics, without searching for each insertion 015307-8 VORONOI TESSELLATION-BASED ALGORITHM FOR … PHYSICAL REVIEW E 107, 015307 (2023) (a)
0
0.1
0.2
0.3
0
0.05
0.1
0.15
0.2
0.25
0.3
0
0.1
0.2
0.3
0.4
0.5
0.6
(b)
0
0.1
0.2
0.3
0
0.05
0.1
0.15
0.2
0.25
0.3
0
0.2
0.4
0.6
0.8
1
(c)
0
0.1
0.2
0.3
0
0.05
0.1
0.15
0.2
0.25
0.3
-5
0
5
FIG. 6. Multidisk setup. Results from the presented algorithm for the configuration inspected in Figs. 1 and 3. The former figures provided
visual information on how to obtain 4 selected points (marked by red bullets) in the present quantitative plots (a) V (r|reff), (b) the cumulative
G-PSD Pcum(r|reff), and (c) the G-PSD P(r|reff) defined in Eq. (8). Beyond a certain r + reff (the radius of the LES), there is no contour
line anymore in the left column of Fig. 1, and therefore vanishing V (r|reff) = 0, P(r|reff) = 0, and Pcum(r|reff) = 1. For the uncoated system
(rc = 0), the classical PSD P(r) for point-like probe particles (rp = 0) is contained in panel (c) on the x axis, i.e., at reff = rc + rp = 0. (c)
0
0.1
0.2
0.3
0
0.05
0.1
0.15
0.2
0.25
0.3
-5
0
5 (a)
0
0.1
0.2
0.3
0
0.05
0.1
0.15
0.2
0.25
0.3
0
0.1
0.2
0.3
0.4
0.5
0.6 (b)
0
0.1
0.2
0.3
0
0.05
0.1
0.15
0.2
0.25
0.3
0
0.2
0.4
0.6
0.8
1 FIG. 6. Multidisk setup. Results from the presented algorithm for the configuration inspected in Figs. 1 and 3. The former figures provided
visual information on how to obtain 4 selected points (marked by red bullets) in the present quantitative plots (a) V (r|reff), (b) the cumulative
G-PSD Pcum(r|reff), and (c) the G-PSD P(r|reff) defined in Eq. (8). Beyond a certain r + reff (the radius of the LES), there is no contour
line anymore in the left column of Fig. 1, and therefore vanishing V (r|reff) = 0, P(r|reff) = 0, and Pcum(r|reff) = 1. D. Voronoi-based global analytical optimization It ensures that we
find the LES (rp = 0, reff = rc) or LPES (rc = 0, reff = rp),
i.e., the global optimum of the constrained optimization prob-
lem stated in Eq. (13). Each of the analytically calculated r
values, whose ensemble with M members gives rise to a prob-
ability distribution G-PSD P(r|reff), has computational effort
O(1). The number of required calculations for the G-PSD is
therefore strictly proportional to M, apart from the relatively
cheap Voronoi and list Ej constructions that have to be done
only once at O(N) effort for all subsequent choices of system
parameters r◦, rc, and rp. As opposed to the other mentioned
strategies, the algorithm proposed here is unaffected by a
mean pore radius. where A = |A|,C = |C|, and P = |P|. These expressions for a
and b in Eq. (21) that determine the three remaining candidate
t in the set {1 −t0,t−,t+} can be derived most conveniently
by first subtracting c2 + r2
s from both sides of the squared
equation c −rs = |c −p|, and then squaring it again. Out
of these three t, the t∗∈[0, 1] leading to the largest c∗=
|A + t∗C| solves the problem, i.e., the candidate pore radius
is re = c∗−rs and the candidate pore center is located at
ce = x + A + t∗C. To summarize, this algorithm relies on the
Voronoi network for a given configuration. It ensures that we
find the LES (rp = 0, reff = rc) or LPES (rc = 0, reff = rp),
i.e., the global optimum of the constrained optimization prob-
lem stated in Eq. (13). Each of the analytically calculated r
values, whose ensemble with M members gives rise to a prob-
ability distribution G-PSD P(r|reff), has computational effort
O(1). The number of required calculations for the G-PSD is
therefore strictly proportional to M, apart from the relatively
cheap Voronoi and list Ej constructions that have to be done
only once at O(N) effort for all subsequent choices of system
parameters r◦, rc, and rp. As opposed to the other mentioned
strategies, the algorithm proposed here is unaffected by a
mean pore radius. A. Benchmark with analytically known G-PSD We consider a simple geometry wherein the pore size dis-
tribution can be calculated analytically, and therefore serves
as a validation case for the algorithms to be tested. The idea
for this benchmark is derived from simple reasoning—if the
phase of a given setup is flipped then the algorithm should be
able to correctly compute the geometric pore size distribution
of the “negative material.” A figure of the setup is shown in
Fig. 7. While the setup is essentially two dimensional, it is
trivially extended to three dimensions. We therefore keep the
symbol V for areas within the remainder of this paper. To calculate the generalized G-PSD P(r; rp|rc) which con-
tains the classical G-PSD P(r) for point-like particles in the
naked benchmark setup as a special case, we need to derive
an expression for V (r|reff), the void area accessible to circles
of radius r in the reff-coated setup for the only nontrivial case
of rs = r◦+ reff ⩾0. Given the symmetry of the benchmark
setup, it is sufficient to focus on calculating V (r|reff)/8, the
shaded area in Fig. 8. It corresponds to the area accessible
to a sphere of radius r in the reff-coated configuration. One
selected circle of radius r is shown, with its center coordinate
at x on the y axis marking its outermost position in the void
space. The cylinder is gray, the actual coating is blueish, the The 2D code just described is part of our Supplemental
Material [42]. The slightly more complicated analytic expres-
sions for the 3D case we are planning to publish along with a
2D + 3D code elsewhere, as mentioned in the conclusion. D. Voronoi-based global analytical optimization For the uncoated system
(rc = 0), the classical PSD P(r) for point-like probe particles (rp = 0) is contained in panel (c) on the x axis, i.e., at reff = rc + rp = 0. over the domain t± ∈(0, 1) [Fig. 5(b)]. Some basic algebraic
operations lead to t± = a ± (a2 + b)1/2, with discussion that makes, apart from the development of the
algorithm presented in Sec. III D, the core of our results. To
this end, Fig. 6 displays V (r|reff) as well as Pcum(r|reff) and
P(r|reff) versus r and reff for the configuration shown as filled
black circles in Figs. 1 and 3. a = 1
2
2P · A + r2
s −P2
P · C −2r2
s A · C
(rsC)2 −(P · C)2
,
b = 1
4
2P · A + r2
s −P22 −(2rsA)2
(rsC)2 −(P · C)2
, The remainder of this section has two parts: In the first part
we develop the analytic expression for the generalized G-PSD
(which includes T-PSDs as special cases) of an extremely
simple, but not too simple, configuration because it allows us
to test G-PSD algorithms rigorously. The strategy turns out
useful in falsifying the radical Voronoi approach. In the sec-
ond part we present a new G-PSD algorithm, which improves
over the local numerical optimization approach because it al-
lows us to make sure that the global optimum is found exactly,
and also efficiently, as we provide analytic expressions that
solely require the coordinates of the N-Voronoi network. (21) where A = |A|,C = |C|, and P = |P|. These expressions for a
and b in Eq. (21) that determine the three remaining candidate
t in the set {1 −t0,t−,t+} can be derived most conveniently
by first subtracting c2 + r2
s from both sides of the squared
equation c −rs = |c −p|, and then squaring it again. Out
of these three t, the t∗∈[0, 1] leading to the largest c∗=
|A + t∗C| solves the problem, i.e., the candidate pore radius
is re = c∗−rs and the candidate pore center is located at
ce = x + A + t∗C. To summarize, this algorithm relies on the
Voronoi network for a given configuration. IV. RESULTS AND DISCUSSION The
colored filled circles represent two possible largest circles that can be
inscribed within the (white) void space enclosed by the large circles. The blue circle with radius rmax (24), represents the circle with largest
possible radius that can be inscribed within this setup. This situation
is realized in a periodic simulation cell (black square) of side length
L, carrying a single circle of radius r◦. FIG. 7. Naked (uncoated) benchmark setup. The setup consists
of identical circles of radius r◦= 1 or, equivalently, infinitely long
and aligned cylinders, that just touch each other (L = 2r◦). The
colored filled circles represent two possible largest circles that can be
inscribed within the (white) void space enclosed by the large circles. The blue circle with radius rmax (24), represents the circle with largest
possible radius that can be inscribed within this setup. This situation
is realized in a periodic simulation cell (black square) of side length
L, carrying a single circle of radius r◦. V (r|reff) = 4
r◦x(r) −r2
s γ (r) + r2α(r)
(rmax −r), V (r|reff) = 4
r◦x(r) −r2
s γ (r) + r2α(r)
(rmax −r), (25) (25) with α(r) = π/2 −β(r), γ (r) = α(r) −π/4, and
denotes
the Heaviside step function. One has V (rmax|reff) = πr2
max, as
the largest pore of radius rmax is located in the center of the
setup, where it occupies a large fraction of the void space. To
express the G-PSD, we need the total area of the void space in
the reff-coated setup which is already known from Eq. (25) as V (0|reff) = 4
r◦x(0) −r2
s γ (0)
,
(26) (26) r
r
r+rc
0
x
L/2
r+reff
rp
V(r r )/8
eff
L
2
FIG. 8. Benchmark geometry. First quadrant of the rc-coated
benchmark setup (Fig. 7). Here we introduce radius r of the circle
centered at (x, 0), radius rp of the probe particle, and some inter-
related angles α, β, and γ . The shaded area V (r|reff) is the area
that needs to be calculated as function of r, for given effective
shell thickness, reff = rc + rp to obtain the generalized G-PSD. The
classical G-PSD is adsorbed by the special case reff = 0. where reff is again hidden in rs, x(0) and γ (0) via Eq. (2). IV. RESULTS AND DISCUSSION As we have exemplified the definition of the two-
parametric volume V (r|reff) in Figs. 1 and 3 by inspecting
just four different (r|reff) pairs, we start with completing this
numerical example first, before we enter a more fundamental 015307-9 AGRAWAL, GALMARINI, AND KRÖGER PHYSICAL REVIEW E 107, 015307 (2023) L
L
r
FIG. 7. Naked (uncoated) benchmark setup. The setup consists
of identical circles of radius r◦= 1 or, equivalently, infinitely long
and aligned cylinders, that just touch each other (L = 2r◦). The
colored filled circles represent two possible largest circles that can be
inscribed within the (white) void space enclosed by the large circles. The blue circle with radius rmax (24), represents the circle with largest
possible radius that can be inscribed within this setup. This situation
is realized in a periodic simulation cell (black square) of side length
L, carrying a single circle of radius r◦. additional virtual coating of thickness rp required to perform
the calculation for probe particles of radius rp is white. Some
angles α, β, and γ have been added to help writing down the
equations. One has β + γ = π/4 and α + β = π/2, more-
over tan β = (r◦−x)/r◦and sin β = (r◦−x)/(r◦+ reff + r). This implies L
L
r x(r) = r◦−
(rs + r)2 −r2◦,
(22)
β(r) = tan−1
1 −x(r)
r◦
,
(23) (22) (23) where we have re-introduced rs = r◦+ reff, Eq. (2). The
largest possible circle that can be placed in the void space is
centered at the origin with radius rmax =
√
2 r◦−rs. (24) (24) The shaded area can be seen as a difference between two
areas—a large triangle with base length x and height r◦and
the fraction γ /2π of the circle of radius r◦+ reff = rs—plus
a fraction α/2π of the r circle. Putting this together gives The shaded area can be seen as a difference between two
areas—a large triangle with base length x and height r◦and
the fraction γ /2π of the circle of radius r◦+ reff = rs—plus
a fraction α/2π of the r circle. Putting this together gives FIG. 7. Naked (uncoated) benchmark setup. The setup consists
of identical circles of radius r◦= 1 or, equivalently, infinitely long
and aligned cylinders, that just touch each other (L = 2r◦). IV. RESULTS AND DISCUSSION By
now, we have calculated all ingredients to write down the final
results for the benchmark setup, with and without coating, for
point-like and finitely sized probe particles. Point of departure
is the final cumulative G-PSD for a point-like probe particle
in the reff-coated material: r
r
r+rc
0
x
L/2
r+reff
rp
V(r r )/8
eff
L
2 Pcum(r|reff) = 1 −r2α(r) + r◦x(r) −r2
s γ (r)
r◦x(0) −r2s γ (0)
(rmax −r),
(27) (27) with α(r), γ (r) given in terms of x(r) and β(r) specified by
Eqs. (22) and (23), and rmax given by Eq. (24). The classical
cumulative G-PSD is Pcum(r) = Pcum(r|0), which amounts to
replacing rs by r◦in the derived expression. This yields also
the simple V (0) = V (0|0) = (4 −π)r2
◦. p
◦
It is important to recall once again the meaning of
reff = rp + rc and the identities P(r|reff) = P(r + rp; rp|rc) =
dPcum(r|reff)/dr as stated in Eq. (8). The general result (27)
contains three special cases: (i) the classical G-PSD for point-
like probe particles in the naked setup, P(r) = P(r|0) for r ⩾
0, (ii) the generalized G-PSD for a finitely sized probe particle
of radius rp > 0 in the naked setup, P(r; rp|0) = P(r −rp|rp)
for r ⩾rp, and (iii) the generalized G-PSD for a point probe
in the rc-coated setup, P(r; 0|rc) = P(r|rc) for r ⩾0. Addi-
tionally the analytical expression for the mean pore radius ⟨r⟩
can be derived from Eq. (7). We are plotting ⟨r⟩for various
cases in Fig. 9. x FIG. 8. Benchmark geometry. First quadrant of the rc-coated
benchmark setup (Fig. 7). Here we introduce radius r of the circle
centered at (x, 0), radius rp of the probe particle, and some inter-
related angles α, β, and γ . The shaded area V (r|reff) is the area
that needs to be calculated as function of r, for given effective
shell thickness, reff = rc + rp to obtain the generalized G-PSD. The
classical G-PSD is adsorbed by the special case reff = 0. FIG. 8. Benchmark geometry. First quadrant of the rc-coated
benchmark setup (Fig. 7). Here we introduce radius r of the circle
centered at (x, 0), radius rp of the probe particle, and some inter-
related angles α, β, and γ . IV. RESULTS AND DISCUSSION 0
0.2
0.4
0.6
0.8
1
0.2
0.25
0.3
0.35
0.4 (a)
0
0.1
0.2
0.3
0.4
0.5
0
0.1
0.2
0.3
0.4
0.5 (a) ( )
(b)
0
0.1
0.2
0.3
0.4
0.5
0.1
0.15
0.2
0.25
0.3
0.35
0.4
0.45 FIG. 11. Benchmark. The largest pore radius rmax is covering a
significant portion V (rmax|reff) of the total pore volume V (0|reff) for
the reff-coated benchmark setup, leading to a jump in the cumulative
G-PSD Pcum(r|reff) from the value Pcum(rmax|reff) to unity for r >
rmax. The effect of reff on this value is displayed here because it is an
important characteristics of the whole benchmark G-PSD. Because
reff can only take values between 0 and (
√
2 −1)r◦for the benchmark
(Fig. 8), we here plotted versus the scaled a dimensionless reff that
resides on the interval [0,1]. FIG. 11. Benchmark. The largest pore radius rmax is covering a FIG. 11. Benchmark. The largest pore radius rmax is covering a
significant portion V (rmax|reff) of the total pore volume V (0|reff) for
the reff-coated benchmark setup, leading to a jump in the cumulative
G-PSD Pcum(r|reff) from the value Pcum(rmax|reff) to unity for r >
rmax. The effect of reff on this value is displayed here because it is an
important characteristics of the whole benchmark G-PSD. Because
reff can only take values between 0 and (
√
2 −1)r◦for the benchmark
(Fig. 8), we here plotted versus the scaled a dimensionless reff that
resides on the interval [0,1]. The Pcum(r; rp|0) (Fig. 10) starts being nonzero at r = rp,
then increases monotonically until it jumps from its value
Pcum(rmax|reff) to unity at r > rmax. There are two values that
are particularly useful when comparing a numerical imple-
mentation of the G-PSD with the analytical solution. The
magnitude of Pcum(rmax|reff) (Fig. 11), and the mean pore
radius (Fig. 9). For reff = 0, we obtain Pcum(rmax) = 2[2 −
(2 −
√
2)π]/(4 −π) ≈0.37208 and ⟨r⟩≈0.3383 r◦. (b) FIG. 9. Benchmark (analytic results). Mean pore radius ⟨r⟩for
the benchmark configuration, obtained analytically. (a) ⟨r⟩versus
rc for various probe particle radii rp. (b) ⟨r⟩versus rc for various
coating thickness values rc. The sum reff = rc + rp is limited by rmax
for reff = 0, which is (
√
2 −1)r◦≈0.41 r◦. IV. RESULTS AND DISCUSSION As there are no spurious local minima, the analytic results
are fully consistent with the solution to the benchmark prob-
lem of aforementioned numerical algorithms (constrained
local optimization, grid-based brute force), according to the
chosen resolution of the numerical methods. 0
0.1
0.2
0.3
0.4
0
0.2
0.4
0.6
0.8
1
(a)
0
0.1
0.2
0.3
0.4
0
0.2
0.4
0.6
0.8
1
(c) 0
0.1
0.2
0.3
0.4
0
0.2
0.4
0.6
0.8
1
(a)
0
0.1
0.2
0.3
0.4
10
10
10
10
10
(b)
0
0.1
0.2
0.3
0.4
0
0.2
0.4
0.6
0.8
1
(c)
0
0.1
0.2
0.3
0.4
0
0.2
0.4
0.6
0.8
1
(d)
FIG. 10. Benchmark. Analytic distribution functions for the
benchmark, Eq. (27), all exactly reproduced with the numerical
scheme of Sec. III D. (a) Pcum(r; rp|0) = Pcum(r −rp|rp) for various
probe radii rp in the naked setup. (b) G-PSD P(r; rp|0) corresponding
to the cumulative G-PSD shown in panel (a). (c) Pcum(r; 0|rc) =
Pcum(r|rc) for point-like probe particle at various coating thickness
values rc. (d) Pcum(r; rp|rc) = Pcum(r −rp|rp + rc) for probe particles
of radius rp = 0.1 at various coating thickness values rc. 0
0.1
0.2
0.3
0.4
10
10
10
10
10
(b) To summarize, in this section we have derived and pre-
sented analytic expressions for the interrelated V (r|reff),
P(r|reff), Pcum(r|reff) for the benchmark with probe particles
of arbitrary radius rp and arbitrary coating thickness rc, while
reff = rc + rp, Eq. (1). The classical G-PSD P(r) is absorbed
by reff = 0. IV. RESULTS AND DISCUSSION The shaded area V (r|reff) is the area
that needs to be calculated as function of r, for given effective
shell thickness, reff = rc + rp to obtain the generalized G-PSD. The
classical G-PSD is adsorbed by the special case reff = 0. 015307-10 VORONOI TESSELLATION-BASED ALGORITHM FOR … PHYSICAL REVIEW E 107, 015307 (2023) (a)
0
0.1
0.2
0.3
0.4
0.5
0
0.1
0.2
0.3
0.4
0.5
0.15
0.2
0.25
0.3
0.35
0.4
0.45
0
0.2
0.4
0.6
0.8
1
0.2
0.25
0.3
0.35
0.4
FIG. 11. Benchmark. The largest pore radius rmax is covering a
significant portion V (rmax|reff) of the total pore volume V (0|reff) for
the reff-coated benchmark setup, leading to a jump in the cumulative
G-PSD Pcum(r|reff) from the value Pcum(rmax|reff) to unity for r >
rmax. The effect of reff on this value is displayed here because it is an
important characteristics of the whole benchmark G-PSD. Because
reff can only take values between 0 and (
√
2 −1)r◦for the benchmark
(Fig. 8), we here plotted versus the scaled a dimensionless reff that
resides on the interval [0,1]. 0
0.2
0.4
0.6
0.8
1
0.2
0.25
0.3
0.35
0.4
FIG. 11. Benchmark. The largest pore radius rmax is covering a
significant portion V (rmax|reff) of the total pore volume V (0|reff) for
the reff-coated benchmark setup, leading to a jump in the cumulative
G-PSD Pcum(r|reff) from the value Pcum(rmax|reff) to unity for r >
rmax. The effect of reff on this value is displayed here because it is an
important characteristics of the whole benchmark G-PSD. Because
reff can only take values between 0 and (
√
2 −1)r◦for the benchmark
(Fig. 8), we here plotted versus the scaled a dimensionless reff that
resides on the interval [0,1]. (a)
0
0.1
0.2
0.3
0.4
0.5
0
0.1
0.2
0.3
0.4
0.5
(b)
0
0.1
0.2
0.3
0.4
0.5
0.1
0.15
0.2
0.25
0.3
0.35
0.4
0.45
FIG. 9. Benchmark (analytic results). Mean pore radius ⟨r⟩for
the benchmark configuration, obtained analytically. (a) ⟨r⟩versus
rc for various probe particle radii rp. (b) ⟨r⟩versus rc for various
coating thickness values rc. The sum reff = rc + rp is limited by rmax
for reff = 0, which is (
√
2 −1)r◦≈0.41 r◦. D. Performance of the various G-PSD algorithms Finally, we demonstrate how the newly proposed Voronoi-
based algorithm performs in practice, and how it compares
with the classical, grid-based approach, for both, the bench-
mark with N = 1, and a larger system with N = 1000. The
larger system is chosen in addition, as one might be still in
doubt about the relevance of the benchmark for the general
case. We begin by inspecting the benchmark (Fig. 13). This
figure quantitatively compares both the speed and quality of
the two algorithms at either identical values for M, or identical
computational cost. The Voronoi-based method outperforms
the grid-based algorithm in all aspects. The deviation analyzed
in panels (a) and (c) is measured against the analytical solu-
tion. Figure 13(b) highlights the CPU scaling behavior with
M. While the Voronoi-based algorithm has a computational
cost ∝M, the grid-based approach scales as M5/3 for this
example, and is more generally superlinear in M. To confirm
that all observations for the benchmark overtake to real sys-
tems made of a large number of particles, we inspect such
a configuration in Fig. 14. Indeed, the grid-based result con-
verges only slowly against the exact result, which is (at least
by eye) obtained using the Voronoi-based version at relatively
small M = 10N already. Still, a much larger M of the order
of 107 is required to generate a smooth P(r|0) for this system
(result not shown). While such a value for M is easily within
reach for the Voronoi-based method (several seconds), it poses
both a memory problem for the grid-based version, as well
as significantly enlarged computational cost (several hours). Pc
cum(r) = 1 −V (0|r −r◦)
V (0| −r◦)
(r ⩾0),
(29) (29) noting that V (0|r −r◦) = L2 −πr2 if r ⩽r◦for our bench-
mark, i.e., if the particle is negatively coated. The situation
was shown in Fig. 4(e). The often-employed surface-based
version of the above center-based Tc-PSD is just the r◦-shifted
variant of Pc
cum(r), Ps
cum(r) = 1 −V (0|r)
V (0|0) = Pc
cum(r + r◦)
(r ⩾0). (30) (30) The Tc-PSD based on area Tc in Fig. 4(e), and the Ts-PSD
based on area Ts in Fig. 4(f) are both qualitatively differ-
ent from the G-PSD not only in general, but also for the
benchmark, and the analytic expression is given by Eq. (11)
or Eq. (30) with Eq. (26). C. Difference between G-PSD and T-PSD Torquato’s cumulative center-based Tc-PSD Pc
cum(r) =
1 −EV (r) is the probability of finding a region, which is a
spherical cavity of radius r (centered at some arbitrary point),
containing one or more particle centers [30]. Using our nota-
tion, we can write this as B. Radical Voronoi applied to the benchmark The same is true for our benchmark, cf. Eq. (31) versus
Eq. (27) for rs = r◦. g
p
p
Inserting c = (cx, 0), p = (px, 0) and xi = (1, ±1) into
Eq. (17) yields (cx −px)2 −r2
p = (cx −1)2, further replacing
cx by px + rp −r(p; rp) shows that the equation defining the
vertices of the (N + 1)-Voronoi produces a vertex position at
the proper c only for the single case of px = 1 −rp. All other
points with px > rmax on the x axis are not capturing the LPES
radius correctly. Even worse, this single point px = 1 −rp is
the irrelevant point for which the pore radius vanishes, and
therefore does not exceed a finite rp. The radical Voronoi
does fail completely not only if p is located on the x axis,
but whenever the probe particle covers a point outside the
rmax circle. In general, the vertices of the (N + 1)-Voronoi
are located inside the material, except for the special case
of rp = r◦, that was most likely for this reason chosen in the
original work [34]. largest radius rmax by 341% while the largest radius according
to Ps(r) is the same as for the G-PSD, however contrary to the
G-PSD, the volume accessible to the probe V (0|rmax) = 0. largest radius rmax by 341% while the largest radius according
to Ps(r) is the same as for the G-PSD, however contrary to the
G-PSD, the volume accessible to the probe V (0|rmax) = 0. For systems made of point-like particles, r◦= 0, such as
the equilateral triangle treated in Fig. 4(a), the two T-PSDs
are identical by definition. The enormous differences between
the G- and T-PSDs we quantify in Fig. 12 for this particularly
simple example, for which analytic expressions are also avail-
able (Appendix 3). For systems made of point-like particles, r◦= 0, such as
the equilateral triangle treated in Fig. 4(a), the two T-PSDs
are identical by definition. The enormous differences between
the G- and T-PSDs we quantify in Fig. 12 for this particularly
simple example, for which analytic expressions are also avail-
able (Appendix 3). B. Radical Voronoi applied to the benchmark x(r) + r = px + rp, hence
r(p; rp) = (px + rp −1)2
2(px + rp)
(px > rmax, py = 0),
(28) x(r) + r = px + rp, hence
r(p; rp) = (px + rp −1)2
2(px + rp)
(px > rmax, py = 0),
(28) x(r) + r = px + rp, hence 0
0.05
0.1
0.15
0.2
0.25
0
0.2
0.4
0.6
0.8
1
(a)
G-PSD
T-PSDs 0
0.05
0.1
0.15
0.2
0.25
0
2
4
6
8
(b)
G-PSD
T-PSDs (28) while c = (cx, cy) with cx = px + rp −r(p; rp) and cy = 0 is
the center of the LPES sphere. If the radical Voronoi were ap-
plicable, this point c must be a vertex of either the N-Voronoi
or the (N + 1)-Voronoi networks. The N-Voronoi network has
a single vertex at the origin in Fig. 8 and is therefore ruled out. The (N + 1)-Voronoi network has four vertices, only one of
them located on the positive x axis. It is sufficient to show that
the above c does not fulfill Eq. (17) to disqualify the radical
Voronoi method for calculating a proper G-PSD. FIG. 12. Triangle. For the equilateral triangle with unit side FIG. 12. Triangle. For the equilateral triangle with unit side
length and a straight edges (r◦= 0), the volume V (r|reff) can be
calculated analytically, cf. Eq. (A4) and leads to the G-PSD quanti-
ties (a) Pcum(r) = [4(9 −
√
3π)r2
1]/3, (b) P(r) = [8(9 −
√
3π)r1]/3,
while both T-PSDs are identical in that case, (a) Pc
cum(r) =
Ps
cum(r) = 4(
√
3 −3r1)r1, and (b) P(r) = 4(
√
3 −6r1). This fig-
ure demonstrates the huge qualitative difference between G-PSD and
T-PSDs. The same is true for our benchmark, cf. Eq. (31) versus
Eq. (27) for rs = r◦. g
q
g
length and a straight edges (r◦= 0), the volume V (r|reff) can be
calculated analytically, cf. Eq. (A4) and leads to the G-PSD quanti-
ties (a) Pcum(r) = [4(9 −
√
3π)r2
1]/3, (b) P(r) = [8(9 −
√
3π)r1]/3,
while both T-PSDs are identical in that case, (a) Pc
cum(r) =
Ps
cum(r) = 4(
√
3 −3r1)r1, and (b) P(r) = 4(
√
3 −6r1). This fig-
ure demonstrates the huge qualitative difference between G-PSD and
T-PSDs. B. Radical Voronoi applied to the benchmark Consider a point p inside the void space of our naked
benchmark (Fig. 8) with r◦= 1 and a probe particle radius
rp ⩽rmax. For all p residing inside the largest inscribed cir-
cle of radius rmax, the radical N-Voronoi results in c = 0
and r(p; rp) = rmax, which is correct. Now consider a point
p = (px, py) with px > rmax located outside the central re-
gion, but for simplicity on the x axis, py = 0. Since x(r) =
1 −√(2 + r)r is the position of the center of the r circle
that touches the naked material according to Eq. (22) with
rs = r◦= 1, and because this r circle must just touch the
probe circle to make sure the probe is contained within the
r circle, and the r circle maximally large, we know that
the correct LPES radius r(p; rp) is given by the solution to FIG. 10. Benchmark. Analytic distribution functions for the
benchmark, Eq. (27), all exactly reproduced with the numerical
scheme of Sec. III D. (a) Pcum(r; rp|0) = Pcum(r −rp|rp) for various
probe radii rp in the naked setup. (b) G-PSD P(r; rp|0) corresponding
to the cumulative G-PSD shown in panel (a). (c) Pcum(r; 0|rc) =
Pcum(r|rc) for point-like probe particle at various coating thickness
values rc. (d) Pcum(r; rp|rc) = Pcum(r −rp|rp + rc) for probe particles
of radius rp = 0.1 at various coating thickness values rc. 015307-11 PHYSICAL REVIEW E 107, 015307 (2023) AGRAWAL, GALMARINI, AND KRÖGER 0
0.05
0.1
0.15
0.2
0.25
0
0.2
0.4
0.6
0.8
1
(a)
G-PSD
T-PSDs
0
0.05
0.1
0.15
0.2
0.25
0
2
4
6
8
(b)
G-PSD
T-PSDs
FIG. 12. Triangle. For the equilateral triangle with unit side
length and a straight edges (r◦= 0), the volume V (r|reff) can be
calculated analytically, cf. Eq. (A4) and leads to the G-PSD quanti-
ties (a) Pcum(r) = [4(9 −
√
3π)r2
1]/3, (b) P(r) = [8(9 −
√
3π)r1]/3,
while both T-PSDs are identical in that case, (a) Pc
cum(r) =
Ps
cum(r) = 4(
√
3 −3r1)r1, and (b) P(r) = 4(
√
3 −6r1). This fig-
ure demonstrates the huge qualitative difference between G-PSD and
T-PSDs. The same is true for our benchmark, cf. Eq. (31) versus
Eq. (27) for rs = r◦. D. Performance of the various G-PSD algorithms This yields for our benchmark,
recalling rs = r◦+ reff, and using ξ = r/r◦, Pc
cum(r) =
ξ 2 −1 −πξ 2
4
+ ξ 2 csc−1 (ξ )
(ξ ⩽
√
2). (31 (31) Note that Eq. (31) simplifies to Pc
cum(r) = πξ 2/4 for ξ ⩽1;
this expression is confirmed visually by Fig. 4(e). The largest
pore radius is r =
√
2 r◦using Pc(r), exceeding the true 015307-12 PHYSICAL REVIEW E 107, 015307 (2023) VORONOI TESSELLATION-BASED ALGORITHM FOR … 101
102
103
104
shots = grid nodes
0
10
20
30
40
50
60
deviation %
voronoi-based
grid-based (a)
100
101
102
103
104
105
shots = grid nodes
10-4
10-2
100
102
cpu seconds
voronoi-based
grid-based (b)
slope 0.98
slope 1.65
10-4
10-3
10-2
10-1
100
101
102
cpu seconds
0.5
1
5
10
50
100
deviation %
voronoi-based
grid-based (c)
FIG. 13. Benchmark. Comparison (quality and speed) between methods to calculate the cumulative G-PSD Pcum(r|reff) for the benchmark
setup with reff = 0: (i) the Voronoi-based global analytical optimization developed in this work (Sec. III D) with M shots, (ii) regular grid-
based brute force scan (Sec. III A) with M nodes. The deviation is a standard deviation calculated against the analytical solution (27). The
computational effort is strictly linear in M for the Voronoi-based version, and generally independent of N, while the grid-based approach is
∝M5/3 for this case, and also independent of N. The local constrained optimization approach is almost linear in M, but in addition linear in N
except for systems with very small pores, where a neighbor list can remove the dependency on N (Sec. III B). 100
101
102
103
104
105
shots = grid nodes
10-4
10-2
100
102
cpu seconds
voronoi-based
grid-based (b)
slope 0.98
slope 1.65 10-4
10-3
10-2
10-1
100
101
102
cpu seconds
0.5
1
5
10
50
100
deviation %
voronoi-based
grid-based (c) 101
102
103
104
shots = grid nodes
0
10
20
30
40
50
60
deviation %
voronoi-based
grid-based (a) 10
10
1
shots = grid nodes cpu seconds FIG. 13. Benchmark. Comparison (quality and speed) between methods to calculate the cumulative G-PSD Pcum(r|reff) for the benchmark
setup with reff = 0: (i) the Voronoi-based global analytical optimization developed in this work (Sec. III D) with M shots, (ii) regular grid-
based brute force scan (Sec. D. Performance of the various G-PSD algorithms III A) with M nodes. The deviation is a standard deviation calculated against the analytical solution (27). The
computational effort is strictly linear in M for the Voronoi-based version, and generally independent of N, while the grid-based approach is
∝M5/3 for this case, and also independent of N. The local constrained optimization approach is almost linear in M, but in addition linear in N
except for systems with very small pores, where a neighbor list can remove the dependency on N (Sec. III B). These aspects rule out the grid-based approach completely for
systems with millions of particles. and the T-PSDs analytically. With this at hand, we concluded
that the method based on radical Voronoi tessellation is un-
fit for calculating the G-PSD for complex geometries. The
grid-based approach and constrained optimization provide an-
swers but are computationally expensive. The latter fails to
locate the maxima at times especially in the case of com-
plex geometries, while the former becomes highly time- and
memory-consuming for high resolution. V. CONCLUSIONS We have presented a proper definition of the generalized G-
PSD, following the notions introduced by Gelb and Gubbins
[31]. Additionally we have described the relation of the G-
PSD to other definitions in particular the different definitions
based on the work of Torquato et al. [30], termed T-PSDs. Calculating the generalized G-PSD and classical G-PSD is
a long-standing problem, as all known methods come with
severe limitations. Therefore, to shed light on this problem,
we set up a simple benchmark that is complex enough to
test implementations, and calculated the generalized G-PSD We proposed a novel approach within the spirit of con-
strained optimization, which becomes a simpler problem to
solve by considering an additional constraint. This reduces
the search space of solutions for the optimization problem
considerably. We were also able to calculate the solution to the
optimization problem analytically for a given triangle located
on a Voronoi face, which could prove crucial to a significant 5
. 0
0
5
. 0
-
-0.5
-0.4
-0.3
-0.2
-0.1
0
0.1
0.2
0.3
0.4
0.5
0
0.01
0.02
0.03
0.04
0.05
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
grid-based M=10000
voronoi-based M=10000
grid-based M=40000
voronoi-based M=40000
grid-based M=90000
voronoi-based M=90000
FIG. 14. Multidisk. Comparison of convergence behavior for Voronoi-based and grid-based methods during the calculation of the
cumulative G-PSD Pcum(r|reff) for the multidisk N = 1000 setup shown on the left. The right panel displays Pcum(r|0) versus r for various
choices of M, for both methods. While the grid-based result slowly converges against the Voronoi-based result, the latter remains basically
unaffected by M for sufficiently large M ≫N. The underlying reason is the absence of a grid for the Voronoi-based method. At the same time
it runs more efficiently and does not suffer from memory limitations. The present result just confirms the trends already available from our
benchmark (Fig. 13). 0
0.01
0.02
0.03
0.04
0.05
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
grid-based M=10000
voronoi-based M=10000
grid-based M=40000
voronoi-based M=40000
grid-based M=90000
voronoi-based M=90000 5
. 0
0
5
. 0
-
-0.5
-0.4
-0.3
-0.2
-0.1
0
0.1
0.2
0.3
0.4
0.5 FIG. 14. Multidisk. Comparison of convergence behavior for Voronoi-based and grid-based methods during the calculation of the
cumulative G-PSD Pcum(r|reff) for the multidisk N = 1000 setup shown on the left. ACKNOWLEDGMENTS V□(r|reff) = [(L −2reff)2 −(2r)2 + πr2]
(L −2reff −2r). (A3) V□(r|reff) = [(L −2reff)2 −(2r)2 + πr2]
(L −2reff −2r). This work was supported by Project IZCOZ0_189872 of
the Swiss National Science Foundation (SNSF). M.K. would
like to thank Yéléna Luap for creating Fig. 4. (A3) Here (L −2reff)2 is the void area of the coated square, and
r2 −πr2/4 is the area not reachable by an r circle in any of
the four corners of the square. The area vanishes as soon as r
exceeds L/2 −reff, giving rise to the Heaviside contribution. Inserting this V□(r|rp) into Eqs. (4) and (8) yields the G-PSD
P□(r; rp|rc) and all related quantities analytically. 1. Circular or cylindrical void (A4) The generalized G-PSD P⃝(r|reff) for a circular void with
radius r⃝, or equivalently, an infinitely long cylindrical three-
dimensional void with cylinder radius r⃝, is with V (0|0) =
√
3/4. This implies Pcum
△
(r|reff) = 4(9 −
√
3π)r2
1
3(1 −2
√
3reff)2 ,
(A5) (A5) P⃝(r|reff) = δ(r −r⃝+ reff)
(r ⩾0),
(A1) (A1) because the full circle is available to circles of any radius r as
long as r ⩽r⃝−reff. The same result is obtained if we start
from V⃝(r|reff), the area accessible to circles of radius r in the
reff-coated substance. This is the area of a circle with radius
r⃝−reff as long as r ⩽r⃝−reff, more formally, and P△(r|reff) =
dPcum
△
(r|reff)
dr
=
8(9 −
√
3π)r
3(1 −2
√
3reff)2 . (A6) (A6) The special case of reff = 0 is shown in Fig. 12. V⃝(r|reff) = π(r⃝−reff)2
(r⃝−reff −r). (A2) V⃝(r|reff) = π(r⃝−reff)2
(r⃝−reff −r). (A2)
The special case of ref (A2) (A2) of cellular solids like aerogels, Phys. Rev. E 103, 043001
(2021). of cellular solids like aerogels, Phys. Rev. E 103, 043001
(2021). of cellular solids like aerogels, Phys. Rev. E 103, 043001
(2021). [1] S. Sastry, D. S. Corti, P. G. Debenedetti, and F. H. Stillinger,
Statistical geometry of particle packings. I. Algorithm for exact
determination of connectivity, volume, and surface areas of void
space in monodisperse and polydisperse sphere packings, Phys. Rev. E 56, 5524 (1997). (
)
[5] M. A. Moret and G. F. Zebende, Amino acid hydrophobic-
ity and accessible surface area, Phys. Rev. E 75, 011920
(2007). [6] J. Kim and B. J. Sung, Dynamics and spatial correlation of voids
in dense two dimensional colloids, J. Chem. Phys. 141, 014502
(2014). [6] J. Kim and B. J. Sung, Dynamics and spatial correlation of voids
in dense two dimensional colloids, J. Chem. Phys. 141, 014502
(2014). [2] S. Sastry, P. G. Debenedetti, and F. H. Stillinger, Statistical
geometry of particle packings. II. “Weak spots” in liquids, Phys. Rev. E 56, 5533 (1997). [7] R. Kumar and B. Bhattacharjee, Porosity, pore size distribution
and in situ strength of concrete, Cem. Concr. Res. 33, 155
(2003). [3] N. V. Priezjev and M. A. Makeev, Evolution of the pore size
distribution in sheared binary glasses, Phys. Rev. E 96, 053004
(2017). [8] T. J. 3. Triangular void For an equilateral triangle with unit side lengths, one finds V△(r|reff) = V△(0|0) −(3
√
3 −π)r2 −3reff(1 −
√
3reff),
(A4)
with V (0|0) =
√
3/4 This implies 2. Square-shaped and cubic void The pore radius distribution for a square-shaped two-
dimensional void with linear size L, or equivalently, an
infinitely long rectangular three-dimensional void with square
cross-sectional area L2, is most conveniently obtained from
V□(r|reff), the area accessible to circles of radius r in the
reff-coated square, given by While the 2D code is part of our Supplemental Material
[42], we are planning to make the 3D code available as a
LAMMPS [43] option, and as a stand-alone C++ application
that makes use of the VORO++ library [44]. V. CONCLUSIONS The right panel displays Pcum(r|0) versus r for various
choices of M, for both methods. While the grid-based result slowly converges against the Voronoi-based result, the latter remains basically
unaffected by M for sufficiently large M ≫N. The underlying reason is the absence of a grid for the Voronoi-based method. At the same time
it runs more efficiently and does not suffer from memory limitations. The present result just confirms the trends already available from our
benchmark (Fig. 13). FIG. 14. Multidisk. Comparison of convergence behavior for Voronoi-based and grid-based methods during the calculation of the
cumulative G-PSD Pcum(r|reff) for the multidisk N = 1000 setup shown on the left. The right panel displays Pcum(r|0) versus r for various
choices of M, for both methods. While the grid-based result slowly converges against the Voronoi-based result, the latter remains basically
unaffected by M for sufficiently large M ≫N. The underlying reason is the absence of a grid for the Voronoi-based method. At the same time
it runs more efficiently and does not suffer from memory limitations. The present result just confirms the trends already available from our
benchmark (Fig. 13). 015307-13 AGRAWAL, GALMARINI, AND KRÖGER PHYSICAL REVIEW E 107, 015307 (2023) increase in the efficiency and accuracy of determining gener-
alized G-PSD for any given spherical monodisperse system. Instead of scanning the D-dimensional space in a random or
deterministic fashion, which comes with the inherent danger
of missing the global optimum, we can walk over a limited
number of relevant triangles, those in the neighborhood of the
test particle position. The size of the neighborhood is known
a priori from the radius of the largest pore, and the global
optimum is therefore found exactly (analytically) at relatively
low computational cost. Inserting this V⃝(r|reff) into Eq. (8) reproduces Eq. (A1). To
complete this, Eqs. (4), (8) then imply P⃝(r; rp|rc) = P⃝(r −
rp|rc + rp) = δ(r −rp −r⃝+ reff) = δ(r −r⃝+ rc)
for
r ⩾rp, just highlighting the fact that the only effect of probe
radius rp on the G-PSD for this simple example is its absence
for r ⩽rp. APPENDIX: ANALYTICS RESULTS FOR THE
GENERALIZED PSD Analytical results for the benchmark configuration have
been provided in Sec. IV A. Here we add additional results
for simple configurations that serve to test the accuracy of
the algorithms. As we have shown, the G-PSD, and also T-
PSDs, are trivially calculated from an analytic expression for
V (r|reff). [4] A. Rege, S. Aney, and B. Milow, Influence of pore-size distri-
butions and pore-wall mechanics on the mechanical behavior U.S.A. 7, 115 (1921). [12] L. Drake, Pore-size distribution in porous materials, Ind. Eng. Chem. 41, 780 (1949). [28] V. Sorichetti, V. Hugouvieux, and W. Kob, Determining the
mesh size of polymer solutions via the pore size distri-
bution, Macromolecules (Washington, DC, U.S.) 53, 2568
(2020). [13] C. M. Simon, J. Kim, D. A. Gomez-Gualdron, J. S. Camp, Y. G. Chung, R. L. Martin, R. Mercado, M. W. Deem, D. Gunter,
M. Haranczyk et al., The materials genome in action: Iden-
tifying the performance limits for methane storage, Energy
Environ. Sci. 8, 1190 (2015). [29] K. Trepte and S. Schwalbe, porE: A code for deterministic and
systematic analyses of porosities, J. Comput. Chem. 42, 630
(2021). [14] S.-Y. Lee and S.-J. Park, Determination of the optimal pore
size for improved CO2 adsorption in activated carbon fibers,
J. Colloid Interface Sci. 389, 230 (2013). [30] S. Torquato, B. Lu, and J. Rubinstein, Nearest-neighbor distri-
bution functions in many-body systems, Phys. Rev. A 41, 2059
(1990). [15] K. Kwac, J. H. Lee, J. W. Choi, and Y. Jung, Computa-
tional analysis of pressure-dependent optimal pore size for CO2
capture with graphitic surfaces, J. Phys. Chem. C 120, 3978
(2016). [31] L. D. Gelb and K. Gubbins, Pore size distributions in porous
glasses: A computer simulation study, Langmuir 15, 305
(1999). [16] P. Nugent, Y. Belmabkhout, S. D. Burd, A. J. Cairns, R. Luebke, K. Forrest, T. Pham, S. Ma, B. Space, L. Wojtas et al.,
Porous materials with optimal adsorption thermodynamics
and kinetics for CO2
separation, Nature (London) 495, 80
(2013). [32] F.-X. Coudert and A. H. Fuchs, Computational characterization
and prediction of metal–organic framework properties, Coord. Chem. Rev. 307, 211 (2016). [33] J. Rouquerol, P. Llewellyn, F. Rouquerol et al., Is the bet
equation applicable to microporous adsorbents, Stud. Surf. Sci. Catal. 160, 49 (2007). [17] E. P. Barrett, L. G. Joyner, and P. P. Halenda, The determination
of pore volume and area distributions in porous substances. I. Computations from nitrogen isotherms, J. Am. Chem. Soc. 73,
373 (1951). [34] M. Pinheiro, R. L. Martin, C. H. Rycroft, A. Jones, E. Iglesia,
and M. Haranczyk, Characterization and comparison of pore
landscapes in crystalline porous materials, J. Mol. Graphics
Modell. 44, 208 (2013). [18] J. Villarroel-Rocha, D. Barrera, and K. Sapag, Introduc-
ing a self-consistent test and the corresponding modifica-
tion in the Barrett, Joyner and Halenda method for pore-
size determination, Microporous Mesoporous Mater. 1. Circular or cylindrical void Richmond, Solvent accessible surface area and ex-
cluded volume in proteins: Analytical equations for overlapping [4] A. Rege, S. Aney, and B. Milow, Influence of pore-size distri-
butions and pore-wall mechanics on the mechanical behavior [4] A. Rege, S. Aney, and B. Milow, Influence of pore-size distri-
butions and pore-wall mechanics on the mechanical behavior 015307-14 PHYSICAL REVIEW E 107, 015307 (2023) VORONOI TESSELLATION-BASED ALGORITHM FOR … [25] A. Kaestner, E. Lehmann, and M. Stampanoni, Imaging and
image processing in porous media research, Adv. Water Resour. 31, 1174 (2008). spheres and implications for the hydrophobic effect, J. Mol. Biol. 178, 63 (1984). [9] S. W. Cranford and M. J. Buehler, Packing efficiency and ac-
cessible surface area of crumpled graphene, Phys. Rev. B 84,
205451 (2011). [26] L. D. Gelb and K. Gubbins, Characterization of porous
glasses: Simulation models, adsorption isotherms, and the
Brunauer-Emmett-Teller analysis method, Langmuir 14, 2097
(1998). [10] E. W. Washburn, The dynamics of capillary flow, Phys. Rev. 17,
273 (1921). [27] V. Sorichetti, V. Hugouvieux, and W. Kob, Structure and dy-
namics of a polymer-nanoparticle composite: Effect of nanopar-
ticle size and volume fraction, Macromolecules (Washington,
DC, U.S.) 51, 5375 (2018). [11] E. W. Washburn, Note on a method of determining the distri-
bution of pore sizes in a porous material, Proc. Natl. Acad. Sci. U S A 7 115 (1921) [44] C. H. Rycroft, Voro++: A three-dimensional Voronoi cell li-
brary in C++, Chaos 19, 041111 (2009). U.S.A. 7, 115 (1921). 200, 68
(2014). [35] D. Vollath and D. V. Szabó, Coated nanoparticles: A new
way to improved nanocomposites, J. Nanopart. Res. 1, 235
(1999). [36] Y. Li, M. Kröger, and W. K. Liu, Endocytosis of pegylated
nanoparticles accompanied by structural changes of the grafted
polyethylene glycol, Biomaterials 35, 8467 (2014). [19] D. Dollimore and G. Heal, An improved method for the calcu-
lation of pore size distribution from adsorption data, J. Appl. Chem. (London, U.K.) 14, 109 (1964). [37] A. Halperin,
M. Kröger,
and
F. M. Winnik,
Poly(n-
isopropylacrylamide) phase diagrams: Fifty years of research,
Angew. Chem., Int. Ed. 54, 15342 (2015). [20] P. I. Ravikovitch, G. L. Haller, and A. V. Neimark, Density
functional theory model for calculating pore size distributions:
Pore structure of nanoporous catalysts, Adv. Colloid Interface
Sci. 76-77, 203 (1998). [38] B. Münch and L. Holzer, Contradicting geometrical con-
cepts in pore size analysis attained with electron microscopy
and mercury intrusion, J. Am. Ceram. Soc. 91, 4059
(2008). [21] P. I. Ravikovitch and A. V. Neimark, Density functional theory
model of adsorption on amorphous and microporous silica ma-
terials, Langmuir 22, 11171 (2006). [39] S. Song, Q. Ding, and J. Wei, Improved algorithm for estimating
pore size distribution from pore space images of porous media,
Phys. Rev. E 100, 053314 (2019). [22] G. Kupgan, T. P. Liyana-Arachchi, and C. M. Colina, NLDFT
pore size distribution in amorphous microporous materials,
Langmuir 33, 11138 (2017). [40] S. Bhattacharya and K. E. Gubbins, Fast method for computing
pore size distributions of model materials, Langmuir 22, 7726
(2006). [23] S. Hemes, G. Desbois, J. L. Urai, B. Schröppel, and J.-O. Schwarz, Multi-scale characterization of porosity in Boom Clay
(HADES-level, Mol, Belgium) using a combination of X-ray
μ-CT, 2D BIB-SEM and FIB-SEM tomography, Microporous
Mesoporous Mater. 208, 1 (2015). [41] T. Ng, J. Yeo, and Z. Liu, A molecular dynamics study of
the thermal conductivity of nanoporous silica aerogel, obtained
through negative pressure rupturing, J. Non-Cryst. Solids 358,
1350 (2012). [24] D. Wildenschild and A. P. Sheppard, X-ray imaging and
analysis techniques for quantifying pore-scale structure and
processes in subsurface porous medium systems, Adv. Water
Resour. 51, 217 (2013). [42] See Supplemental Material at http://link.aps.org/supplemental/
10.1103/PhysRevE.107.015307 for the codes for the calcula-
tion of the G-PSD and Ts-PSD using the Voronoi-based and 015307-15 AGRAWAL, GALMARINI, AND KRÖGER PHYSICAL REVIEW E 107, 015307 (2023) C. Trott, and S. J. U.S.A. 7, 115 (1921). Plimpton, LAMMPS - a flexible simulation
tool for particle-based materials modeling at the atomic, meso,
and continuum scales, Comput. Phys. Commun. 271, 108171
(2022). C. Trott, and S. J. Plimpton, LAMMPS - a flexible simulation
tool for particle-based materials modeling at the atomic, meso,
and continuum scales, Comput. Phys. Commun. 271, 108171
(2022). C. Trott, and S. J. Plimpton, LAMMPS - a flexible simulation
tool for particle-based materials modeling at the atomic, meso,
and continuum scales, Comput. Phys. Commun. 271, 108171
(2022). grid-based methods. We offer routines that allow us to redo the
figures shown in this paper, as well as codes that can be used to
investigate user-defined 2D structures. grid-based methods. We offer routines that allow us to redo the
figures shown in this paper, as well as codes that can be used to
investigate user-defined 2D structures. [43] A. P. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu,
W. M. Brown, P. S. Crozier, P. J. in ’t Veld, A. Kohlmeyer, S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, [44] C. H. Rycroft, Voro++: A three-dimensional Voronoi cell li-
brary in C++, Chaos 19, 041111 (2009). 015307-16
|
https://openalex.org/W3048167911
|
https://journalimplantdent.springeropen.com/track/pdf/10.1186/s40729-020-00235-5
|
English
| null |
Immediate implant placement in molar extraction sockets: a systematic review and meta-analysis
|
International journal of implant dentistry
| 2,020
|
cc-by
| 6,568
|
© 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/. Abstract Background: Immediate implants are frequently employed in the anterior maxillary area. However, the installation
of dental implants simultaneously with tooth extraction can also provide with benefits in the posterior areas with a
reduction in time prior the recovery of the masticatory function. Results previously reported in the literature show
high-survival and success rates for implants placed in extraction sockets in molar areas; however, this topic has
received limited systematic analysis. Material and methods: Electronic and manual literature searches were performed by two independent reviewers
in several data-bases, including MEDLINE, EMBASE, and Cochrane Oral Health Group Trials Register, for articles up to
January 2019 reporting outcomes of immediate implants placed in molar areas. Primary outcomes included survival
and success rates, as well as marginal bone loss. Secondary outcomes included the influence of implant position,
type of implant connection, grafting protocol, flap or flapless approach, implant diameter, surgical phase, presence
of buccal plate, and loading protocol. Results: Twenty studies provided information on the survival rate, with a total sample of 1.106 implants. The
weighted mean survival rate of immediate implants after 1 year of follow-up was 96.6%, and the success rate was
93.3%. On the other hand, marginal bone loss was 1.29 ± 0.24 mm. Secondary outcomes demonstrated that
grafting the gap and the loading protocol have an effect on survival and success rates. Similarly, the presence or
absence of the buccal bone affect crestal bone levels. Meta-analysis of 4 investigations showed a weighted mean
difference of 0.31 mm ± 0.8 IC 95% (0.15–0.46) more marginal bone loss at immediate implant placement versus
implants in healed sites (p < 0.001) I2 = 15.2%. Conclusion: In selected scenarios, immediate implant placement in molar extraction socket might be considered a
predictable technique as demonstrated by a high survival and success rates, with minimal marginal bone loss. healing period of 6–12 months before loading was rec-
ommended [1]. Immediate implant placement in molar
extraction sockets: a systematic review and
meta-analysis Gian Maria Ragucci1*, Basel Elnayef1, Elena Criado-Cámara2, Fernando Suárez-López Del Amo2 and
Federico Hernández-Alfaro1 * Correspondence: gian1@uic.es
1Department of Oral and Maxillofacial Surgery, International University of
Catalonia, Josep Trueta, s/n, 08195 Sant Cugat del Vallès, Barcelona, Spain
Full list of author information is available at the end of the article Introduction As implant therapy evolves, new challenges are faced as
result of higher functional and esthetics demands. Ori-
ginal protocols during the late 1970s and 1980s advo-
cated the placement of dental implants exclusively in
completely healed edentulous ridges. Additionally, a Fortunately, as a consequence of continuous research,
new surface technologies, and new implant designs,
more recent protocols have arisen shortening the time
intervals by means of immediate implant placement (IIP)
and/or immediate restorations (IR). Although different
definitions have been proposed for the terms immediate,
early and conventional implant placement, in 2004, a
consensus
statement
by
Hämmerle
and
coworkers * Correspondence: gian1@uic.es
1Department of Oral and Maxillofacial Surgery, International University of
Catalonia, Josep Trueta, s/n, 08195 Sant Cugat del Vallès, Barcelona, Spain
Full list of author information is available at the end of the article (2020) 6:40 (2020) 6:40 Ragucci et al. International Journal of Implant Dentistry
https://doi.org/10.1186/s40729-020-00235-5 International Journal of
Implant Dentistry International Journal of
Implant Dentistry Page 2 of 12 Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 2019 by two independent examiners (G.M.R and B.E)
aiming at answering the following PICO (Patient, Inter-
vention, Comparison and Outcome) question: In pa-
tients over 18 years of age, does the placement of
immediate implants in molar areas result in similar im-
plant survival rate, success rate, and marginal bone loss
as implants installed in healed sites, after 6 months of
healing from tooth extraction? When necessary, dis-
agreements were resolved by discussion with a third
examiner (F.H.A). Search terms included “Jaw, edentu-
lous”[mh] OR “Alveolar process”[mh] OR “Alveolar
bone loss”[mh] OR “Dental implantation”[mh] OR “Den-
tal implants”[mh] OR “Dental prosthesis design”[mh]
OR “Denture”[mh] OR “Dental prosthesis, implant-
supported”[mh] OR “molar”[tiab] OR “Fresh socket”[-
tiab] AND (“Immediate”[tiab] OR “Immediate non-
occlusal”[tiab] OR “Functional”[tiab] OR “Non-functio-
nal”[tiab]) AND (“Provisionalization”[tiab] OR “Restora-
tion”[tiab] OR “Loading”[tiab]) described 4 different protocols for implant placement in
the extraction socket. Type 1 refers to IIP after tooth ex-
traction, type 2 is considered when implants are placed
after 4 to 8 weeks, achieving complete soft tissue cover-
age, type 3 consists in implants placed after 12 to 16
weeks when substantial clinical and/or radiographic
bone fill has occurred, and type 4 refers to implants
placed in healed sites [2]. IIP is a therapeutic approach introduced in 1976 as an
alternative to the classic delayed implant placement de-
scribed by Branemark [3]. This treatment alternative
offers several advantages; including a reduction in both
treatment time and the number of surgical interventions,
therefore increasing patient satisfaction. In addition to
these advantages, survival and success rates of immedi-
ate implants have shown favorable results, proving simi-
lar outcomes to implants installed in healed edentulous
ridges. A systematic review on implants installed imme-
diately after tooth extraction demonstrated survival rates
of more than 98% after a minimum of 1-year follow up. These results are comparable to conventional implant
placement in healed sites which showed 5-year survival
rates of up to 95% [4]. This is also in agreement with a
randomized controlled clinical trial that demonstrated
adequate hard and soft tissue healing with stable mar-
ginal bone levels after 3 years of follow-up for immediate
implants placed in the anterior area [5]. The esthetic ad-
vantages of IIP in combination with IR for patients that
have lost anterior teeth becomes obvious when treat-
ment time is reduced; decreasing the waiting period
prior delivery of a fixed restoration. However, IIP in pos-
terior areas may also represent a beneficial approach in
selected scenarios providing with a faster recovery of the
masticatory function. g
In addition, a review of the references of the included
investigations was performed. Finally, hand search (Jan
2000–Jan 2019) was carried out in dental journals, includ-
ing Journal of Oral and Maxillofacial Implants, Clinical
Implant Dentistry and Related Research, Clinical Oral Im-
plants Research, Implant Dentistry, European Journal of
Oral Implantology, Journal of Oral Implantology, Inter-
national Journal of Oral and Maxillofacial Surgery, Jour-
nal of Oral and Maxillofacial Surgery, Journal of Dental
Research, International Journal of Prosthodontics, Journal
of Prosthetic Dentistry, Journal of Clinical Periodontology,
Journal of Periodontology, and The International Journal
of Periodontics and Restorative Dentistry. Articles were included if they met the following inclu-
sion criteria: human randomized controlled trials, pro-
spective cohort studies, retrospective studies, and case
series with a minimum of 10 subjects; studies with at
least 1 year of follow-up; studies reporting data on mar-
ginal bone loss and survival rates of immediate implants
placed in molar sites. On the other hand, articles were
excluded if they present with any of the following char-
acteristics: implants placed following early protocol; un-
known survival rate, success rate or marginal bone loss;
less than 1 year of follow-up; less than 10 subjects for
the immediate implant group, interventions involving
simultaneous lateral or crestal sinus floor elevation, in-
ferior nerve transposition or sandwich osteotomy, ani-
mal studies, and implant placement in non-molar areas. Results reported in the literature have shown high sur-
vival (99.1–100) and success rates (93.9–100%) for im-
plants placed in extraction sockets on molar areas. Similarly, a systematic review published in 2010 reported
up to 99% survival rate for implants placed in posterior
areas. Nevertheless, multitude of new investigations have
emerged since this review was conducted. These recent
studies could offer further information on the outcomes
and considerations for this treatment alternative [6–12]. The aim of this systematic review was to assess the
survival and success rates, as well as the marginal bone
loss (MBL) of IIP in molars extraction sockets after a
minimum follow up of 1 year. Primary outcomes in this systematic review included
(1) survival rate (defined as implant present in the oral
cavity independent of biological or technical complica-
tions), (2) success rate (defined as implants free of all
complications); and (3) marginal bone loss. Secondary
outcomes included: implant position, type of implant
connection, grafting protocol, flap or flapless approach, Selection of studies Two independent reviewers (G.M.R and B.E) screened
all titles and determined the number of abstracts to be
evaluated. All selected abstracts were screened for pos-
sible inclusion in the systematic review. The full texts of
all studies of relevance were then obtained for independ-
ent assessment by the reviewers, and any disagreement
was resolved by discussion with a third examiner. Quality assessment The criteria used to evaluate the quality of the selected
randomized controlled trials (RCTs) were modified from
the randomized clinical trial checklist of the Cochrane
Center and the CONSORT (Consolidated Standards of
Reporting Trials) statement, which provided guidelines
for the following parameters: (1) sequence generation;
(2) allocation concealment method; (3) masking of the
examiner; (4) address of incomplete outcome data; and
(5) free of selective outcome reporting. Two independent
reviewers (G.M.R and B.E) evaluated all the included ar-
ticles. On the other hand, for non-randomized clinical
trials, the Newcastle-Ottawa Scale (NOS) was used to
rank risk of bias of included studies. Primary outcomes in this systematic review included
survival, success rates, and MBL. Secondary outcomes
included the analysis of the influence of: implant pos-
ition, type of connection, grafting protocol, flap or flaw-
less surgery, implant diameter, surgical phase, presence
of buccal plate, and loading protocols. Study of heterogeneity Heterogeneity was assessed based on calculation of the
I2 statistic (percentage variability of estimated effect that
can be attributed to the heterogeneity of the effects) and
the null statistic test. Galbraith graphs displayed the de-
gree of heterogeneity. Funnel plots and the Egger test
were used to assess risk of bias of the accepted statistical
significance level was 5% (p = 0.05). Implant survival Survival was defined as implants remaining in situ at the
follow-up examinations, irrespective of their conditions. All 20 studies reported survival rates, leading to a
weighted mean survival rate of 96.6% with 95% CI
(93.5–99.7) [13–32]. Certain considerations must be
taken into account when interpreting the estimates of
the individual studies: the study by Atieh et al. shows a
greater standard deviation, due to the small sample size,
only 12 implants [13]. For this reason, it is considered
appropriate to exclude this study from the meta-analysis. The model is re-estimated, obtaining: a weighted sur-
vival rate of 97.8% with an IC 95% (95.8-99.9) (Fig. 2) Statistical analysis The R 3.0.2 software package was used to perform the
meta-analysis. The pooled weighted mean (WM) and the
95% confidence interval (IC) of each variable were esti-
mated using a computer program (Comprehensive Meta-
analysis version 2, Biostat). Random effects meta-analyses
of the selected studies were applied to account for poten-
tial bias arising from methodology. The analysis consists
in the estimation of the survival and success rates, as well
as the weighted average MBL for the whole of the studies,
using a random effects model. Estimates of mean propor-
tions and bone loss, both individual, for each investigation
and global, are accompanied by the 95% confidence inter-
val and are represented by a Forest graph. Results The search resulted in 2759 titles. Following the first
stage of screening, 44 potentially relevant studies were
identified. After the second stage of screening, full text
publications were obtained and analyzed, resulting in 20
articles fulfilling the inclusion criteria (Fig. 1). Reasons
for exclusion of articles after full text analysis were: ab-
sence of report of data on MBL, studies with less than
10 subject, studies on implants placed in the anterior
zone, studies that included anterior and posterior im-
plants within the same groups, and studies that failed to
specify timing of implant placement (Table 1). All of the
included investigations had a follow up of at least 1 year;
7 studies reported a follow-up of more than 18 months
and one study showed an observational period up to 5
years. The majority of studies were conducted in an in-
stitutional environment. A total of 990 patients were an-
alyzed in this review, including 1.106 implants Table 2. Material and methods
Search strategy Three electronic databases were used including PubMed,
Ovid (MEDLINE), and Cochrane Central for relevant
studies published in the English language without any
time limitation. The search was conducted up to January Page 3 of 12 Page 3 of 12 Page 3 of 12 Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 Ragucci et al. International Journal of Implant Dentistry implant diameter, surgical phase, presence or absence of
buccal plate, and loading protocol. implant diameter, surgical phase, presence or absence of
buccal plate, and loading protocol. Meta-analysis For the study of the survival rate, odds ratios were esti-
mated for each study, as well as the overall effect meas-
ure in a meta-analysis of random effects, always with
95% confidence intervals. For the analysis of MBL, the
difference between the average value of the test group:
immediate implants in molar extraction socket, and the
control group: implants in healed sites, after 6 months of
healing from tooth extraction were calculated. The
weighted mean difference (WMD) was the overall effect
measure, estimated by a random effects meta-analysis. Type of implant-abutment connection Table 1 Articles excluded and reasons for exclusion
Reason for exclusion
Study
No report on data of MBL
Ormanier et al. 2012, Carlino et al. 2008,
Acocella et al. 2010
Less than 10 subjects
included
Youself et al. 2012, Block et al. 2011
Implants placed in
anterior area
De Angelis et al. 2011, Gómez Roman et al. 2001, Paoloantonio et al. 2001, Harel et al. 2014, McAllister et al. 2012, Malchiodi et al. 2010, Siepnkothen et al. 2007
Implant placement timing
not specified. Cavallaro et al. 2011 Table 1 Articles excluded and reasons for exclusion The studies included in this systematic review that ana-
lyzed survival and success rates as well as MBL depend-
ing on the type of implant-abutment connection [13,
15–32] reported no statistically significant for implant
survival rate (p = 0.511) success rate (p = 0.463) and
MBL (p = 0.393) around implants with internal or exter-
nal connections. Implant position Six investigations were included for the analysis of im-
plant position, four studies reported implants placed in Marginal bone loss the mandible [13, 14, 19, 20], two studies reported im-
plants placed in maxilla [25, 26]. Studies assessing im-
plant survival in the posterior maxilla yielded a 100%
survival rate. Implant survival in the posterior mandible
yielded a 97.4% survival rate and an 97.5% success rate. No statistically significant difference in survival and suc-
cess rates were detected according to the implant pos-
ition (p = 0.233). MBL assessed according to implant
location, also revealed no significant differences when
comparing maxilla and mandible (p = 0.991). Eleven studies reported on MBL, analyzed through the
use of periapical radiography, including data of 372 im-
plants [13, 16, 22, 18–21, 24, 25, 27, 29, 32]. The esti-
mated global MBL over 1 year of follow-up was 1.29 ±
0.24 mm with 95% CI (0.81–1.76) (Fig. 4). Implant success
Th The success rate was only analyzed in 6 studies [13, 16,
20, 22, 28, 30] leading to a weighted mean success rate
of 93.3% with 95% CI (83.7–100). Excluding again the
study of Atieh, the success rate increases to 98.1% with
95% CI (96.1–100) (Fig. 3) [16, 20, 22, 28, 30]. Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 Page 4 of 12 Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 Fig. 1 PISMA flowchart of the screening process Fig. 1 PISMA flowchart of the screening process Grafting protocol Out of the 20 included investigations for this analysis, 16
studies used grafting materials [14, 16–20, 23, 24, 26–32] Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 Page 5 of 12 Table 2 Characteristics of the included articles Table 2 Characteristics of the included articles and 4 did not perform any grafting [13–22]. Implant sur-
vival was 92.2% with 95% CI (85.1-99.2) for studies that
did not graft the gap, while studies that grafted the gap
presented with 97.7% with 95% CI (94.3–100). There were
no significant differences in survival according to presence
or absence of grafting material (p = 0.168). Implant suc-
cess was reported in 6 studies, reporting 83.8% with 95%
CI (68.0–99.6) in the graftless group and 97.9% with 95%
CI (87.0–100) for the grafted group. There were no statis-
tically significant differences in success according to pres-
ence or absence of graft (p = 0.150) [13, 16, 20, 22, 28, 30]. Although
statistical
significance
difference
was
not
reached, results showed that grafting favors survival and
success rates. With regards to the effect of grafting on MBL, no significant differences were observed between
studies using biomaterials 1.39 ± 0.63 mm with 95% CI
(0.87–1.92) versus those that did not perform grafting
0.79 ± 0.55 mm. There were no statistically significant dif-
ferences in MBL according to presence or absence of graft
(p = 0.333) [13, 16, 18–21, 24, 25, 27, 29, 32]. Flap/flapless surgery Fourteen studies reported a flapless technique [2, 3, 13, 14,
17, 20–22, 24–28, 30, 31] while the remaining 6 investiga-
tions reported the use of a full thickness flap for implant
placement [15, 16, 18, 19, 29, 32]. No significant differences
were observed in implant survival (p = 0.742), implant suc-
cess (p = 0.932) and MBL. MBL was 1.41± 0.38mm with Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 Page 6 of 12 Fig. 2 Statistical analysis of implant survival Fig. 2 Statistical analysis of implant survival 23, 24, 28, 30] diameter. Implant survival rate for < 5
mm group was 96.1% with 95% CI (88.9–100), and
94.5% with 95% CI (88.2–100) for > 5 mm. MBL was
assessed in 6 studies reporting a mean bone loss of 0.74
± 0.32 mm with 95% CI (0.13–1.35) [19, 27, 29] for > 5
mm group, and 1.41 ± 0.38 mm with 95% CI (0.66–2.15)
for < 5 mm group [13, 21, 23], without statistical signifi-
cant difference (p = 0.205). 95% CI (0.66 2.15) when a flap was elevated for implant
placement and 1.19 ±0.34 mm with 95% CI (0.53 1.85) with
a flapless approach. Flap elevation also showed no effect on
survival and success rates. (p = 0.667) Implant diameter Analyzed implants were divided into two groups: < 5
mm [15, 19, 22, 26, 27, 29] and > 5 mm [13, 14, 17, 21, Fig. 3 Statistical analysis of implant success Fig. 3 Statistical analysis of implant success Ragucci et al. International Journal of Implant Dentistry (2020) 6:40
Page 7 of 12 Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 Page 7 of 12 Fig. 4 Statistical analysis of marginal bone loss significant differences in MBL according to the presence
or absence of the buccal bone (p < 0.001) (Fig. 5). significant differences in MBL according to the presence
or absence of the buccal bone (p < 0.001) (Fig. 5). Surgical protocol The influence of surgical protocol on implant survival was
assessed in 19 studies showing 97.1% with 95% CI (92.9–
100) for implant placed in one surgical stage, in which a
healing abutment or immediate restoration has been
placed on the day of surgery. For implants placed in 2 sur-
gical phases was 95.3% with 95% CI (89.8–100) [13, 14,
16, 18, 20–22, 25, 28–30, 32]; without statistical significant
difference (p = 0.616) [15, 19, 23, 24, 26, 27, 31] Implant loading protocol Eighteen studies [15–28, 30, 31] reported loading at least
3 months after implant placement, and two studies re-
ported immediate aesthetic restoration placement [13,
14]. The loading protocol significantly influenced sur-
vival rates (p = 0.007) with immediate loaded implants
showing 84.1% with 95% CI (74.6–98.6) survival rate,
and studies that used delayed loading protocols showed
97.7% with 95% CI (94.3–100). Implant success and
MBL could not be analyzed due to small sample size. p
MBL was assessed in 11 studies, reporting 1.43 ± 0.92
mm with 95% CI (0.87–1.99) mean MBL for implants
placed in one surgical stage [13, 16, 18, 20, 21, 25, 29,
32] and 0.91 ± 0.46 mm with 95% CI (0.01–1.81) mean
MBL for implants placed in two stages [19, 24, 27]. Meta-analysis Nine studies were included in this analysis, with three
reporting the absence of the buccal bone (assessed clin-
ically using a periodontal probe) after tooth extraction
[27, 29, 31] and six installing implants only when the
buccal bone wall was present [13, 14, 16, 23, 24, 28]. Survival rate was 100% with 95% CI (89.1–100) for stud-
ies without buccal bone and 92.1% with 95% CI (84.3–
99.9) for studies with buccal bone. There were no sig-
nificant differences in success according to presence or
absence of buccal plate (p = 0.247). Five studies analyzed
MBL and showed 1.56 ± 0.10 mm with 95% CI (1.37–
1.76) when no buccal bone was present [27, 29] and 0.56
± 0.11 mm with 95% CI (0.79–1.21) MBL when buccal
plate was present [13, 16, 24]. There were statistical Four RCTs compared immediate implants versus im-
plants installed in healed molar sites after 6 months
from tooth extraction in terms of survival rates and
MBL. The risk of bias has been found to be moderate
among these investigations (Fig. 6) [13, 23, 24, 27]. Implant survival rate The overall effect measure of the meta-analysis was
OR = 0.41 (95% CI 0.13–1.30) I2 = 0%; without statis-
tical significant difference (p = 0.131). This indicated
that the probability of survival with immediate im-
plants was reduced by 59% compared to implants in
healed sites (Fig. 7). Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 Page 8 of 12 Fig. 5 Influence of buccal bone presence on marginal bone loss Marginal bone loss Eleven studies
rendered information on MBL showing an average of
1.29 ± 0.24 mm; these results are comparable with those
of a prospective clinical study performed on 30 patients
which received immediate implants in the anterior zone,
where the mean peri-implant bone loss seen after 3 years
of follow-up was 1.00 mm [33]. However, the meta-
analysis showed a weighted mean difference of 0.31 ±
0.8 mm; finding statistical significant more marginal
bone loss at implants installed immediately (p < 0.001). The reported bone loss is probably influenced by a var-
iety of different factors including the resorption process
occurring after tooth extraction. This resorption can
reach 1.53 mm during the first 12 months [34]. In order
to minimize the volumetric changes after tooth extrac-
tion, a flapless implant placement is recommended; how-
ever, no significant differences were seen in MBL when
comparing flap and flapless approaches. These results
also coincide with the data reported in a meta-analysis
performed by Chcranovic et al. who reported no statisti-
cally significant differences in implant failure or MBL
around implants placed after flap elevation versus flap-
less implants placement [35]. Aspects favoring the use of
a flapless technique could include minimization of post-
operative peri-implant tissue loss, decreased operative
time, more rapid post-surgical healing, fewer postopera-
tive
complications,
and
increased
patient
comfort. Nevertheless, flap elevation can allow the clinician to
better visualize the area in which the implant should be
installed as well as better access to proper regenerative
procedures. In the present study, the loading protocol also signifi-
cantly influenced implant survival rates (p = 0.007). Im-
mediately loaded implants showed 84.1% survival rate,
while the delayed loading protocol showed 97.7%. Con-
versely, Benic et al. in a recent systematic review con-
cluded
that
immediately
and
conventionally
loaded
single-implant crowns are equally successful regarding
implant survival and MBL [37]. Also, Meloni et al. ana-
lyzed immediate non-occlusal versus delayed loading of
mandibular first molars during a 5-year follow up, find-
ing 100% implant survival rate for both groups; and a
mean marginal bone loss of 0.62 ± 0.45 mm in the im-
mediate loading group and 0.69 ± 0.33 mm for the de-
layed group [38]. Marginal bone loss Four investigations showed a weighted mean difference
of 0.31 ± 0.8 mm with 95% CI (0.15–0.46) finding statis-
tically significant more marginal bone loss at immediate
implant placement versus implants in healed sites. (p <
0.001) I2 = 15.2% (Fig. 8). The purpose of this investigation was to systematically
analyze the available literature reporting on the survival
and success rates as well as the MBL of implants placed
immediately in molar areas. Although a systematic re-
view was previously performed on this topic years ago, Fig. 6 Risk of bias analysis Ragucci et al. International Journal of Implant Dentistry (2020) 6:40
Page 9 of 12 Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 Ragucci et al. International Journal of Implant Dentistry Page 9 of 12 Fig. 7 Meta-analysis of implant survival rate between immediate and conventional implants and that other factors can also strongly influence thera-
peutic results, including but not limited to implant
location,
implant
connection,
smoking,
as
well
as
implant-socket gap grafting and flap elevation. These
variables potentially influencing treatment outcomes are
also analyzed in this review. implant therapy has rapidly evolved and new evidence
has emerged. Hence, this study aimed at updating the
previously mentioned review given that multiple studies
have been performed on this topic since 2010 [6]. Previous investigations revealed that timing of implant
placement plays a critical role in treatment outcomes Fig. 8 Meta-analysis of marginal bone loss between immediate and conventional implants Page 10 of 12 Page 10 of 12 Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 This study revealed that implants installed in fresh ex-
traction sockets on molar sites yielded survival rates of
96.6% over a minimum 1 year follow up period. These
results are in concordance to those achieved by Lang
et al. where immediate implants placed in extraction
sockets of anterior teeth yielded a 98.4% survival rate
after a 2-year follow up [4]. A successful treatment
should be considered when the implant is free of tech-
nical and/or biological complications and, in addition,
aesthetic outcomes are satisfactory. In this systematic re-
view the average success rate was 93.3%. Marginal bone loss Limitations of the present systematic review include
the analysis of small sample sizes, heterogeneities in the
included investigations, and low number of randomized
controlled clinical trial comparing implants installed in
healed ridges vs implant immediately placed after extrac-
tion. An analysis evaluating the influence of implant pos-
ition (i.e., mandible vs maxilla) would be interesting in
order to elucidate the influence of different anatomical
aspects such as the maxillary sinus and/or bone quality,
on the survival and success rates of immediate implants. In addition, more RCTs are needed comparing immedi-
ate implants versus early implant placement and im-
plants installed in healed ridges. In addition, future
investigations should focus on the long-term results of
this treatment protocol. Conclusions
I
l
d In selected scenarios, immediate implant in molar ex-
traction sockets might be considered a predictable tech-
nique, as demonstrated by a high implant survival and
success rates, with minimal MBL. The ideal treatment
protocol consists on a flapless approach, a one-stage im-
plant placement, without performing immediate loading,
grafting the gap and the use of implants with < 5 mm
diameter. More studies are needed focused in the role of
implant surfaces, biomaterials in the gap, and the ana-
tomical characteristics of the recipient sites. The effect of grafting protocol on MBL also showed
no significant differences between studies using biomate-
rials for the gap, versus those with a graftless approach. In addition, although statistically significance difference
was not reached, it appeared that grafting the gap re-
ported higher survival and success rates. A recent study
conducted by Tarnow et al. also suggested that grafting
the gap at immediate implant sites combined with a con-
toured healing abutment or a provisional restoration re-
sulted in reduction of ridge contour change. Therefore,
it is recommended to graft the gap and use contoured
healing abutment or provisional restorations at the time
of immediate implant placement [36]. Authors contributions
Dr. Gian Maria Ragucci and Dr. Basel Elnayef performed the search strategy
and article analysis. Disagreements were resolved by discussion with Dr.
Hernández Alfaro that along with Dr. Fernando Suárez-López del Amo
formed an active part of the systematic review in the revision and correction
of the article Abbreviations
IIP I
di
i Abbreviations
IIP: Immediate implant placement; IR: Immediate restorations; MBL: Marginal
bone loss; RCTs: Randomized controlled trials; NOS: Newcastle-Ottawa Scale;
IC: Confidence interval Consent for publication
Not applicable Consent for publication
Not applicable 18. Cafiero C, Annibali S, Gherlone E, Grassi FR, Gualini F, Magliano A, Salvi GE,
ITI study group Italia, et al. Immediate transmucosal implant placement in
molar extraction sites: a 12-month prospective multicenter cohort study. Clin Oral Implants Res. 2008;19(5):476–82. References 1. Adell R, Lekholm U, Rockler B, Brånemark PI. A 15-year study of
osseointegrated implants in the treatment of the edentulous jaw. Int J Oral
Surg. 1981;10(6):387–416. 1. Adell R, Lekholm U, Rockler B, Brånemark PI. A 15-year study of
osseointegrated implants in the treatment of the edentulous jaw. Int J Oral
Surg. 1981;10(6):387–416. 23. Checchi V, Felice P, Zucchelli G, Barausse C, Piattelli M, Pistilli R, et al. Wide
diameter immediate post-extractive implants vs delayed placement of
normal-diameter implants in preserved sockets in the molar region: 1-year
post-loading outcome of a randomised controlled trial. Eur J Oral Implantol. 2017;10(3):263–78. 2. Hämmerle CH, Chen ST, Wilson TG Jr. Consensus statements and
recommended clinical procedures regarding the placement of implants in
extraction sockets. Int J Oral Maxillofac Implants. 2004;19(4):26–38. p
3. Schulte W, Heimke G. The Tübinger immediate implant. Quintessenz. 1976;
27(6):17–23. 24. Tallarico M, Xhanari E, Pisano M, Gatti F, Meloni SM. Molar replacement with
7 mm-wide diameter implants: to place the implant immediately or to wait
4 months after socket preservation? 1 year after loading results from a
randomised controlled trial. Eur J Oral Implantol. 2017;10(2):169–78. 4. Lang NP, Pun L, Lau KY, Li KY, Wong MC. A systematic review on survival
and success rates of implants placed immediately into fresh extraction
sockets after at least 1 year. Clin Oral Implants Res. 2012;2(5):39–66. 4. Lang NP, Pun L, Lau KY, Li KY, Wong MC. A systematic review on survival
and success rates of implants placed immediately into fresh extraction
sockets after at least 1 year. Clin Oral Implants Res. 2012;2(5):39–66. 25. Chen Y, Yuan S, Zhou N, Man Y. Transcrestal sinus floor augmentation with
immediate implant placement applied in three types of fresh extraction
sockets: a clinical prospective study with 1-year follow-up. Clin Implant Dent
Relat Res. 2017;19(6):1034–43. 5. Sanz M, Cecchinato D, Ferrus J, Salvi GE, Ramseier C, Lang NP, et al. Implants placed in fresh extraction sockets in the maxilla: clinical and
radiographic outcomes from a 3-year follow-up examination. Clin Oral
Implants Res. 2014;25(3):321–7. 26. Wychowanski P, Wolinski J, Kacprzak M, Tomkiewicz W, Bartlomiej I,
Szubinska-Lelonkiewicz D, et al. Immediate palatal molar implants: a simple,
safe, minimally invasive technique. Int J Periodontics Restorative Dent. 2017;
37(37):297–301. 6. Atieh MA, Payne AG, Duncan WJ, de Silva RK. Cullinan MP immediate
placement or immediate restoration/loading of single implants for molar
tooth replacement: a systematic review and meta-analysis. Received: 24 February 2020 Accepted: 2 June 2020 22. Amato F, Polara G. Immediate implant placement in single-tooth molar
extraction sockets: a 1- to 6-year retrospective clinical study. Int J
Periodontics Restorative Dent. 2018;38(4):495–501. Competing interests The authors do not have any financial interests, either directly or indirectly,
in the products or information listed in the paper. The authors declare that
they have no competing interests. 19. Hamouda NI, Mourad SI, El-Kenawy MH, Maria OM. Immediate implant
placement into fresh extraction socket in the mandibular molar sites: a
preliminary study of a modified insertion technique. Clin Implant Dent Relat
Res. 2015;17(1):107–16. Authors’ contributions Dr. Gian Maria Ragucci and Dr. Basel Elnayef performed the search strategy
and article analysis. Disagreements were resolved by discussion with Dr. Hernández Alfaro that along with Dr. Fernando Suárez-López del Amo
formed an active part of the systematic review in the revision and correction
of the article Page 11 of 12 Page 11 of 12 Page 11 of 12 Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 Dra. Elena Criado-Cámara has made the tables and figures and contributed
to the writing of the article. All colleagues mentioned took part in the devel-
opment of this article. All authors read and approved the final manuscript. 14. Prosper L, Crespi R, Valenti E, Capparé P, Gherlone E. Five-year follow-up of
wide-diameter implants placed in fresh molar extraction sockets in the
mandible: immediate versus delayed loading. Int J Oral Maxillofac Implants. 2010;25(3):607–12. 15. Urban T, Kostopoulos L, Wenzel A. Immediate implant placement in molar
regions: a 12-month prospective, randomized follow-up study. Clin Oral
Implants Res. 2012;23(12):1389–97. References Int J Oral
Maxillofac Implants. 2010;25(2):401–15. 27. Santana RB, Santana CM, Dibart S. Platelet-derived growth factor-mediated
guided bone regeneration in immediate implant placement in molar sites
with buccal bone defects. Int J Periodontics Restorative Dent. 2015;35(6):
825–33. 7. Fugazzotto PA. Implant placement at the time of maxillary molar extraction:
treatment protocols and report of results. J Periodontol. 2008;79(2):216–23. 8. Fugazzotto PA. Implant placement at the time of mandibular molar
extraction: description of technique and preliminary results of 341 cases. J
Periodontol. 2008;79(4):737–47. 28. Vandeweghe S, Hattingh A, Wennerberg A, Bruyn HD. Surgical protocol
and short-term clinical outcome of immediate placement in molar
extraction sockets using a wide body implant. J Oral Maxillofac Res. 2011;2(3):1–8. 9. Bianchi AE, Sanfilippo F. Single-tooth replacement by immediate implant
and connective tissue graft: a 1-9-year clinical evaluation. Clin Oral Implants
Res. 2004;15(3):269–77. 9. Bianchi AE, Sanfilippo F. Single-tooth replacement by immediate implant
and connective tissue graft: a 1-9-year clinical evaluation. Clin Oral Implants
Res. 2004;15(3):269–77. 29. Siciliano VI, Salvi GE, Matarasso S, Cafiero C, Blasi A, Lang NP. Soft tissues
healing at immediate transmucosal implants placed into molar extraction
sites with buccal self-contained dehiscences. A 12-month controlled clinical
trial. Clin Oral Implants Res. 2009;20(5):482–8. 10. Fugazzotto PA. Treatment options following single-rooted tooth removal: a
literature review and proposed hierarchy of treatment selection. J
Periodontol. 2005;76(5):821–31. 10. Fugazzotto PA. Treatment options following single-rooted tooth removal: a
literature review and proposed hierarchy of treatment selection. J
Periodontol. 2005;76(5):821–31. 11. Fugazzotto PA. Implant placement at the time of maxillary molar extraction:
technique and report of preliminary results of 83 sites. J Periodontol. 2006;
77(2):302–9. 30. Jiansheng H, Dongying X, Xianfeng W, Baoyi X, Qiong L, Jincai Z. Clinical
evaluation of short and wide-diameter implants immediately placed into
extraction sockets of posterior areas: a 2-year retrospective study. J Oral
Implantol. 2012;38(6):729–37. 12. Fugazzotto PA. Implant placement in maxillary first premolar fresh
extraction sockets: description of technique and report of preliminary
results. J Periodontol. 2002;73(6):669–74. 12. Fugazzotto PA. Implant placement in maxillary first premolar fresh
extraction sockets: description of technique and report of preliminary
results. J Periodontol. 2002;73(6):669–74. 31. Hu C, Gong T, Lin W, Yuan Q, Man Y. Immediate implant placement into
posterior sockets with or without buccal bone dehiscence defects: a
retrospective cohort study. J Dent. 2017;65:95–100. 13. Atieh MA, Alsabeeha NH, Duncan WJ, de Silva RK, Cullinan MP, Schwass D,
Payne AG. Funding Not applicable 16. Peñarrocha-Oltra D, Demarchi CL, Maestre-Ferrín L, Peñarrocha-Diago M,
Peñarrocha-Diago M. Comparison of immediate and delayed implants in
the maxillary molar region: a retrospective study of 123implants. Int J Oral
Maxillofac Implants. 2012;27(3):604–10. Availability of data and materials
Not applicable Ethics approval and consent to participate 17. Peñarrocha-Diago M, Carrillo-Garcîa C, Boronat-Lopez A, García-Mira B. Comparative study of wide-diameter implants placed after dental extraction
and implantspositioned in mature bone for molar replacement. Int J Oral
Maxillofac Implants. 2008;23(3):497–501. Author details
1D
f 20. Hayacibara RM, Gonçalves CS, Garcez-Filho J, Magro-Filho O, Esper H,
Hayacibara MF. The success rate of immediate implant placement of
mandibular molars: a clinical and radiographic retrospective evaluation
between 2 and 8 years. Clin Oral Implants Res. 2013;24(7):806–11. 1Department of Oral and Maxillofacial Surgery, International University of
Catalonia, Josep Trueta, s/n, 08195 Sant Cugat del Vallès, Barcelona, Spain. 2Tacoma, WA, USA. 21. Hattingh A, Hommez G, De Bruyn H, Huyghe M, Vandeweghe S. A
prospective study on ultra-wide diameter dental implants for immediate
molar replacement. Clin Implant Dent Relat Res. 2018;20(6):1009–101. References Immediate single implant restorations in mandibular molar
extraction sockets: a controlled clinical trial. Clin Oral Implants Res. 2013;
24(5):484–96. 32. Cafiero C, Marenzi G, Blasi A, Siciliano VI, Nicolò M, Sammartino G. Soft and
hard tissues healing at immediate transmucosal implants placed into molar Page 12 of 12 Ragucci et al. International Journal of Implant Dentistry (2020) 6:40 extraction sites with collagen membrane uncovered: a 12-month
prospective study. Implant Dent. 2013;22(5):474–80. extraction sites with collagen membrane uncovered: a 12-month
prospective study. Implant Dent. 2013;22(5):474–80. 33. Cosyn J, Eghbali A, De Bruyn H, Collys K, Cleymaet R, De Rouck T. Immediate single-tooth implants in the anterior maxilla: 3-year results of a
case series on hard and soft tissue response and aesthetics. J Clin
Periodontol. 2011;38(8):746–53. 34. Schropp L, Kostopoulos L, Wenzel A, Isidor F. Clinical and radiographic
performance of delayed-immediate single-tooth implant placement
associated with peri-implant bone defects. A 2-year prospective, controlled,
randomized follow-up report. J Clin Periodontol. 2005;32(5):480–7. 35. Chrcanovic BR, Albrektsson T, Wennerberg A. Flapless versus conventional
flapped dental implant surgery: a meta-analysis. PLoS One. 2014;9(6):1006–
10024. 36. Tarnow DP, Chu SJ, Salama MA, Stappert CF, Salama H, Garber DA, et al. Flapless postextraction socket implant placement in the esthetic zone: part
1. The effect of bone grafting and/or provisional restoration on facial-palatal
ridge dimensional change-a retrospective cohort study. Int J Periodontics
Restorative Dent. 2014;34(3):323–31. 37. Benic GI, Mir-Mari J, Hämmerle CH. Loading protocols for single-implant
crowns: a systematic review and meta-analysis. Int J Oral Maxillofac
Implants. 2014;29:222–38. 37. Benic GI, Mir-Mari J, Hämmerle CH. Loading protocols for single-implant
crowns: a systematic review and meta-analysis. Int J Oral Maxillofac
Implants. 2014;29:222–38. 38. Meloni SM, Baldoni E, Duvina M, Pisano M, De Riu G, Tallarico M. Immediate
non-occlusal versus delayed loading of mandibular first molars. Five-year
results from a randomised controlled trial. Eur J Oral Implantol. 2018;11(4):
409–18. 38. Meloni SM, Baldoni E, Duvina M, Pisano M, De Riu G, Tallarico M. Immediate
non-occlusal versus delayed loading of mandibular first molars. Five-year
results from a randomised controlled trial. Eur J Oral Implantol. 2018;11(4):
409–18. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations.
|
https://openalex.org/W4236978371
|
https://www.researchsquare.com/article/rs-264432/latest.pdf
|
English
| null |
The mirror mechanism in schizophrenia spectrum disorders: Protocol for a systematic review and meta-synthesis
|
Research Square (Research Square)
| 2,021
|
cc-by
| 4,556
|
Amir Valizadeh
(
thisisamirv@gmail.com
) Amir Valizadeh
(
thisisamirv@gmail.com
) The mirror mechanism in schizophrenia spectrum
disorders: Protocol for a systematic review and
meta-synthesis p
p
disorders: Protocol for a systematic review and
meta-synthesis
Amir Valizadeh
(
thisisamirv@gmail.com
)
Tehran University of Medical Sciences
https://orcid.org/0000-0001-5983-8527
Nazanin Hedayati Amlashi
Tehran University of Medical Sciences
https://orcid.org/0000-0003-0804-0018
Anita Rasooli
Tehran University of Medical Sciences
https://orcid.org/0000-0002-5963-1419
Mathew Mbwogge
London School of Hygiene and Tropical Medicine
https://orcid.org/0000-0003-0594-1937
Ainaaz Haadi
Tehran University of Medical Sciences
https://orcid.org/0000-0002-6613-1877
Systematic Review
Keywords: Schizophrenia, Mirror Neurons
Posted Date: March 1st, 2021
DOI: https://doi.org/10.21203/rs.3.rs-264432/v5
License:
This work is licensed under a Creative Commons Attribution 4.0 International
License. Read Full License Systematic Review Page 1/14 Page 1/14 Page 1/14 Abstract Rationale: Mirror neurons are visuomotor neurons that perform mirror mechanisms, meaning each time
an individual observes another individual performing an action, these neurons which encode that action,
are activated in the observer’s cortical motor system. One of the cognitive domains of controversy in
schizophrenia is Motor Resonance, also known as the Mirror Neuron System (MNS). In the current paper,
we aim to review all the available literature regarding mirror mechanism examination in patients with
schizophrenia and present an explicit summary of the available findings up to this date. Objectives: To investigate the mirror mechanism in patients with schizophrenia and related disorders
(psychosis spectrum disorder) and present an explicit view of available findings regarding this manner up
to the date. Data sources: We will search MEDLINE (through PubMed), Embase, Science Citation Index – Expanded
(Web of Science), and Conference Proceedings Citation Index – Science (Web of Science). We won’t
consider any timeframe, language, or geographical restrictions. Methods: Standard systematic review protocol methodology is employed. Eligibility criteria is reported in
line with SPIDER guideline. Sample is limited to Adults of any age and sex with the diagnosis of
schizophrenia, schizoaffective disorder, and psychosis spectrum disorders in general confirmed by a
physician according to International Classification of Diseases (ICD) or Diagnostic and Statistical Manual
of Mental Disorders (DSM) guidelines, irrespective of the severity of disease and duration of illness. Participants with any other confirmed structural or functional neurologic disorders will be excluded. Phenomenon of interest is the mirror neuron system (MNS) functional integrity. Study designs will be
restricted to observational cohort and cross-sectional studies. Means of evaluation will be
Electroencephalography (EEG), Magnetoencephalography (MEG), Transcranial magnetic stimulation
(TMS), Functional magnetic resonance imaging (fMRI), near-infrared spectroscopy (NIRS), Eye-tracking,
and muscle activation (EMG). Research types of interest will be qualitative, quantitative, and mixed-
methods researches. All included studies will be assessed for the risk of bias using NIH Quality
Assessment Tool for Observational Cohort and Cross-Sectional Studies. We will perform a meta-synthesis
based on vote counting methods on the included studies. We will also evaluate the publication bias using
Funnel plots and assess the confidence in cumulative evidence using CERQual. Rationale Schizophrenia is one of the most debilitating and common neuropsychiatric disorders in the world, with
an estimated incidence of 1% in the population worldwide (2). Deficits in a variety of cognitive domains
are well-known for this disorder (3-5) and they are listed as specifiers for schizophrenia in the 11th
revision of the International Classification of Diseases (ICD) (6). One of the cognitive domains of Page 2/14 Page 2/14 controversy in schizophrenia is Motor Resonance, also known as the Mirror Neuron System (MNS). Mirror
neurons are visuomotor neurons that perform mirror mechanisms, meaning each time an individual
observes another individual performing an action, these neurons which encode that action, are activated
in the observer’s cortical motor system (7, 8). These neurons were first discovered in the premotor area F5
of macaque monkeys (9-12). Later, similar neurons were found in the inferior parietal lobule, area PF, of
macaque monkeys and the concept of ‘mirror system’ was established. Since the discovery of mirror
neurons, some studies have claimed the discovery of similar neurons in various regions of the human
brain, including the ventral premotor cortex (13, 14), inferior frontal gyrus (15-19), and inferior parietal
lobule (14, 20). Meta-analyses of fMRI studies have demonstrated that there might be other brain regions
too with mirror neurons including the dorsal premotor cortex, superior parietal lobe, temporal gyrus, and
cerebellum (21, 22). Several important functions beyond the action domain have been theorized for the mirror neuron system
(MNS). For example, it has been posited as a fundamental building block for understanding others’
actions (23). It is suggested that the possible specific cognitive role of mirror neurons might be that of
encoding the intentions of the actor (8, 24, 25). Also, the act of imitation has been suggested to rely on
MNS (7, 26, 27). This idea seems eligible, considering that the parieto-frontal motor regions are known to
be typically involved in the planning and execution of actions (21, 28-30). Iacoboni has suggested a ‘‘core
circuit’’ for imitation that includes three regions, two of which include parts of MNS (31), although
because monkeys are relatively poor in the task of imitation has brought arguments in this regard. Considering these findings there is an idea that the direct goal encoding feature of MNS provides a
primary mechanism both for understanding other people and for imitating them (32). Rationale More recently,
researchers suggest that MNS may play a role in human infants’ ability to map similarities between self
and others, and thus may be involved in providing a foundation for social–cognitive development (33). Additionally, there has been emphasis’ on ties between MNS and empathy (34, 35), and MNS and
language (36, 37). To date, there has never been a systematic review of the studies which examine mirror mechanism in
patients with schizophrenia. Based on a recent narrative review in Nature Reviews journal (38), findings in
this regard are mixed and not compatible. This stresses the necessity of a systematic examination of the
studies in this subject. In the current paper, we aim to review all the available literature regarding mirror
mechanism examination in patients with schizophrenia and present an explicit summary of the available
findings up to this date. (PI) Phenomenon of Interest: The mirror neuron system (MNS) functional integrity. (PI) Phenomenon of Interest: The mirror neuron system (MNS) functional integrity. (D) Design: Observational cohort and cross-sectional studies. (E) Evaluation: Electroencephalography (EEG), Magnetoencephalography (MEG), Transcranial magnetic
stimulation (TMS), Functional magnetic resonance imaging (fMRI), Near-infrared spectroscopy (NIRS),
Eye-tracking, and muscle activation (EMG). (E) Evaluation: Electroencephalography (EEG), Magnetoencephalography (MEG), Transcranial magnetic
stimulation (TMS), Functional magnetic resonance imaging (fMRI), Near-infrared spectroscopy (NIRS),
Eye-tracking, and muscle activation (EMG). (R) Research type: Qualitative, quantitative, and mixed-methods research can be searched for. (R) Research type: Qualitative, quantitative, and mixed-methods research can be searched for. Methods Design and methods used for this protocol review comply with Centre for Reviews and Dissemination
(CRD’s) Guidance For Undertaking Reviews in Healthcare (39), Meta-analyses of Observational Studies in
Epidemiology (MOOSE) (40) and is reported in line with Preferred Reporting Items for Systematic Reviews
and Meta-Analysis Protocols (PRISMA-P) (1). Eligibility criteria were informed using the SPIDER (41) and
MOOSE guidelines. Objectives To investigate the mirror mechanism in patients with schizophrenia and related disorders (psychosis
spectrum disorder) and present an explicit view of available findings regarding this manner up to the
date. Page 3/14 Eligibility criteria (S) Sample: Adults of any age and sex with the diagnosis of schizophrenia, schizoaffective disorder, and
psychosis spectrum disorders in general confirmed by a physician according to International
Classification of Diseases (ICD) (6, 42, 43) or Diagnostic and Statistical Manual of Mental Disorders
(DSM) (44, 45) guidelines, irrespective of the severity of disease and duration of illness. Participants with
any other confirmed structural or functional neurologic disorders will be excluded. Information sources The search will employ sensitive topic-based strategies designed for each database with no time frame
limitations. There will be no language or geographical restrictions either. We will perform our search on
the 10th of February, 2021. Selection process Two reviewers (NH and AH) will independently screen the title and abstract of identified studies for
inclusion. We will link publications from the same study to avoid including data from the same study
more than once. If any study cannot be clearly excluded based on its title and abstract, its full text will be
reviewed. A study will be included when both reviewers independently assess it as satisfying the inclusion
criteria from the full text. A third reviewer (AV) will act as arbitrator in the event of disagreement following
discussion. Data management Records will be managed through EndNote (RRID:SCR_014001) version X9 (46); specific software for
managing bibliographies. Databases: Databases: MEDLINE through PubMed (RRID:SCR_004846) Embase (RRID:SCR_001650) Science Citation Index – Expanded (Web of Science) (RRID:SCR_017657) Science Citation Index – Expanded (Web of Science) (RRID:SCR_017657) Conference Proceedings Citation Index – Science (Web of Science) (RRID:SCR_017657) Conference Proceedings Citation Index – Science (Web of Science) (RRID:SCR_017657) Page 4/14 Search strategy Our search strategies for all the databases included in our study, namely MEDLINE (through PubMed),
Embase, Science Citation Index – Expanded (Web of Science), and Conference Proceedings Citation
Index – Science (Web of Science) are presented in appendix A. Data collection process Using a standardized form, two reviewers (AR and MM) will extract the data independently. A third
reviewer (AV) will independently check the data for consistency and clarity. We will attempt to extract data
presented only in graphs and figures whenever possible but will include such data only if two reviewers
independently obtain the same result. If studies are multi-center, then where possible we will extract data
relevant to each. If necessary, we will attempt to contact study authors through an open-ended request to
obtain missing information or for clarification. Data items Data extracted will include the following summary data: sample characteristics, sample size, type of
modality used for examining MNS in participants, the task that was used for the study, founding sources,
declarations of interests, results, and summary of the findings as either normal, abnormal, and mixed
(indicating that different components of the data suggest different things, or that the reported results are
not entirely statistically robust). Page 5/14 Outcomes and prioritization Studies will be grouped according to the different modalities used, which may include
Electroencephalography (EEG), Magnetoencephalography (MEG), Transcranial magnetic stimulation
(TMS), Functional magnetic resonance imaging (fMRI), near-infrared spectroscopy (NIRS), Eye-tracking,
and muscle activation (EMG). However, studies using general behavioral measures (e.g. imitation tasks)
and studies of reaction time during automatic imitation will be excluded. In the end, we will review other
approaches that did not fit in the standard categorization of tasks, and also the findings from structural
MRI studies. Risk of bias in individual studies Two authors (AR and MM) will independently evaluate the included studies for risks of bias. We will
discuss any disagreement and document our decisions, and a third author (AV) will act as arbitrator in
such a case. Cohen's κ will be used to assess agreement between reviewers. All tools and processes will
be piloted before use. We will use the NIH Quality Assessment Tool for Observational Cohort and Cross-
Sectional Studies (47). This tool consists of fourteen questions which will address the following: 1-
Research question, 2 and 3- Study population, 4- Study eligibility criteria, 5- Sample size justification, 6-
Whether the exposure assessed prior to outcome measurement, 7- Wether sufficient timeframe was given
to see an effect, 8- Different levels of the exposure of interest, 9- Exposure measures and assessment, 10-
Repeated exposure assessment, 11- Outcome measures, 12- Blinding of outcome assessors, 13- Followup
rate, and 14- Statistical analysis. There are five possible answers to each question: yes, no, cannot
determine, not applicable, and not reported. Finally, there are three possible judgments for the quality
rating of each study: high quality, fair quality, and low quality. A high risk of bias translates to a rating of
poor quality, while a low risk of bias translates to a rating of good quality. The tool, with the authors’
judgment for a “yes” answer to each question, is presented in Appendix B. Data synthesis We will use R version 4 (48) as the software for our data synthesis. A meta-synthesis will be performed
based on vote counting methods and results will be presented as a harvest plot. A summary of all studies
included in the synthesis will also be presented. In this table we will present the following: Modality of the study (EEG, fMRI, etc.) Study ID Number of schizophrenia participants Mean age of participants (in years) Task: the task that was used with the modality. Results Results Page 6/14 Meta-bias To evaluate the risk of reporting bias across studies, a test for funnel plot asymmetry will be conducted. This test examines whether the relationship between estimated effect size and study size is greater than
chance (49). Funnel plots will be generated for visual inspection of potential publication bias. In the
presence of publication bias, the plot will be symmetrical at the top, and data points will increasingly be
missing from the middle to the bottom parts of the plot (50). Page 6/14 Summary: the results of each study will be summarized in terms of whether the paper provides
evidence for an abnormal MNS in schizophrenia, a normal MNS, or evidence that is mixed. Mixed
evidence can mean either that different components of the data suggest different things, or because
the reported results are not entirely statistically robust. Summary: the results of each study will be summarized in terms of whether the paper provides
evidence for an abnormal MNS in schizophrenia, a normal MNS, or evidence that is mixed. Mixed
evidence can mean either that different components of the data suggest different things, or because
the reported results are not entirely statistically robust. Confidence in cumulative evidence The strength of the overall body of evidence will be assessed using the Confidence in Evidence from
Reviews of Qualitative research method (CERQual) (51). This approach uses four components to
evaluate confidence in the review findings. These include the methodological limitations of included
studies, the relevance of the included studies to review questions, the coherence of the review findings,
and the adequacy of the data that contributes to each review finding. In the first instance, MM will
evaluate each finding using the four components of CERQual and a four-point scoring system ranging
from 'no or very minor concerns' to 'substantial concerns'; AV then checks the evaluation. The review
authors will meet and discuss the scores and assign each finding an overall CERQual assessment score. Each finding starts with a 'high confidence' score which could be downgraded to 'moderate confidence',
'low confidence', or 'very low confidence' if the CERQual process revealed concerns. Embase #1. 'mirror neuron system':ab,ti
#2. 'mirror system':ab,ti
#3. 'motor resonance':ab,ti Page 7/14 Page 7/14 #4. (neuron NEAR/5 mirror):ab,ti
#5. (brain NEAR/5 mirror):ab,ti
#6. 'mirror neuron'/exp
#7. #1 OR #2 OR #3 OR #4 OR #5 OR #6
#8. 'schizophrenia spectrum disorder'/exp
#9. schizo*:ab,ti
#10. (psychosis NEAR/5 spectrum):ab,ti
#11. #8 OR #9 OR #10
#12. #7 AND #11
#13. #12 AND [embase]/lim #5. (brain NEAR/5 mirror):ab,ti MEDLINE (through PubMed) (mirror neuron system[tw] OR Mirror Neurons[mh] OR mirror neuron*[tw] OR mirror system[tw] OR motor
resonance[tw]) AND (schizo*[tw] OR Schizophrenia[mh] OR psychosis [tw]) Web of Science Page 8/14 #9. #7 OR #8
#10. #6 AND #9 #9. #7 OR #8
#10. #6 AND #9 #9. #7 OR #8 #10. #6 AND #9 Support No sources of support or funding were provided for this review. Contributions AV is the leading author for protocol development, analyses, and dissemination. AV is also the first
reviewer and the corresponding author. All authors will contribute to data interpretation and article drafts. Conflicts of interest All authors declare there are no conflicts of interest regarding this study or its possible results. Amendments Important protocol amendments post registration will be recorded and included in dissemination. Appendix B NIH Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies (47) Page 9/14 Number
Question
Authors’ judgment for “yes”
#1
Was the research question or objective in this
paper clearly stated? “Assessment of MNS in
schizophrenia spectrum disorders
patients” is clearly defined as an
objective. #2
Was the study population clearly specified and
defined? Baseline characteristics of the study
population, specifically the definite
diagnosis of schizophrenia spectrum
disorders are stated. #3
Was the participation rate of eligible persons at
least 50%? More than 50% of the eligible
population participated in the study. #4
Were all the subjects selected or recruited from
the same or similar populations (including the
same time period)? Were inclusion and exclusion
criteria for being in the study prespecified and
applied uniformly to all participants? Inclusion and exclusion criteria were
developed before recruitment or
selection of the study population and
the same underlying criteria were
used for all of the subjects involved. #5
Was a sample size justification, power
description, or variance and effect estimates
provided? No: Most of our targeted studies will
be explanatory in nature. #6
For the analyses in this paper, were the
exposure(s) of interest measured prior to the
outcome(s) being measured? In cohort studies, MNS evaluation
was done after the diagnosis. In cross-sectional studies, the answer
is “No”. #7
Was the timeframe sufficient so that one could
reasonably expect to see an association between
exposure and outcome if it existed? In cohort studies, at least one year is
passed after the diagnosis when
MNS is evaluated. In cross-sectional studies, the answer
is “No”. #8
For exposures that can vary in amount or level,
did the study examine different levels of the
exposure as related to the outcome (e.g.,
categories of exposure, or exposure measured as
continuous variable)? Not applicable: Our exposure
(diagnosis of the disease) does not
have variation in amount. #9
Were the exposure measures (independent
variables) clearly defined, valid, reliable, and
implemented consistently across all study
participants? Diagnosis of the disease was made
by a trained physician based on the
DSM or ICD criteria. #10
Was the exposure(s) assessed more than once
over time? Not applicable: Multiple times of
diagnosis of the disease I not
necessary. ( Baseline characteristics of the study
population, specifically the definite
diagnosis of schizophrenia spectrum
disorders are stated. exposure status of participants? diagnosis of patients. #13
Was loss to follow-up after baseline 20% or less? Appendix B In cohort studies, loss to follow-up
was less than 20%. In cross-sectional the answer is “Not
applicable”. #14
Were key potential confounding variables
measured and adjusted statistically for their
impact on the relationship between exposure(s)
and outcome(s)? Regression methods were used for
adjustment for baseline differences. exposure status of participants? diagnosis of patients. References 1. Moher D, Shamseer L, Clarke M, Ghersi D, Liberati A, Petticrew M, et al. Preferred reporting items for
systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Systematic reviews. 2015;4(1):1-9. 2. McGrath J, Saha S, Chant D, Welham J. Schizophrenia: a concise overview of incidence, prevalence,
and mortality. Epidemiologic reviews. 2008;30(1):67-76. 2. McGrath J, Saha S, Chant D, Welham J. Schizophrenia: a concise overview of incidence, prevalence,
and mortality. Epidemiologic reviews. 2008;30(1):67-76. 3. Bora E, Yucel M, Pantelis C. Theory of mind impairment in schizophrenia: meta-analysis. Schizophrenia research. 2009;109(1-3):1-9. 4. Gold JM. Cognitive deficits as treatment targets in schizophrenia. Schizophrenia research. 2004 72(1) 21 8 4. Gold JM. Cognitive deficits as treatment targets in schizophrenia. Schizophrenia research. 2004;72(1):21-8. Page 11/14 Page 11/14 5. Green MF, Harvey PD. Cognition in schizophrenia: Past, present, and future. Schizophrenia Research:
Cognition. 2014;1(1):e1-e9. 6. Organization WH. International classification of diseases 11th Revision [CID-11]. Recuperado de
https://icd. who. int; 2018. 7. Rizzolatti G, Craighero L. The mirror-neuron system. Annu Rev Neurosci. 2004;27:169-92. 8. Rizzolatti G, Sinigaglia C. The functional role of the parieto-frontal mirror circuit: interpretations and
misinterpretations. Nature reviews neuroscience. 2010;11(4):264-74. 9. Di Pellegrino G, Fadiga L, Fogassi L, Gallese V, Rizzolatti G. Understanding motor events: a
neurophysiological study. Experimental brain research. 1992;91(1):176-80. 10. Gallese V, Fadiga L, Fogassi L, Rizzolatti G. Action recognition in the premotor cortex. Brain. 1996;119(2):593-609. 11. Rizzolatti G, Fogassi L, Gallese V. Neurophysiological mechanisms underlying the understanding and
imitation of action. Nature reviews neuroscience. 2001;2(9):661-70. 11. Rizzolatti G, Fogassi L, Gallese V. Neurophysiological mechanisms underlying the understanding and
imitation of action. Nature reviews neuroscience. 2001;2(9):661-70. 12. Umilta MA, Kohler E, Gallese V, Fogassi L, Fadiga L, Keysers C, et al. I know what you are doing: A
neurophysiological study. Neuron. 2001;31(1):155-65. 12. Umilta MA, Kohler E, Gallese V, Fogassi L, Fadiga L, Keysers C, et al. I know what you are doing: A
neurophysiological study. Neuron. 2001;31(1):155-65. 13. Dinstein I, Hasson U, Rubin N, Heeger DJ. Brain areas selective for both observed and executed
movements. Journal of neurophysiology. 2007;98(3):1415-27. 13. Dinstein I, Hasson U, Rubin N, Heeger DJ. Brain areas selective for both observed and executed
movements. Journal of neurophysiology. 2007;98(3):1415-27. 14. Gazzola V, Keysers C. The observation and execution of actions share motor and somatosensory
voxels in all tested subjects: single-subject analyses of unsmoothed fMRI data. Cerebral cortex. 2009;19(6):1239-55. 15. References Kilner JM, Neal A, Weiskopf N, Friston KJ, Frith CD. Evidence of mirror neurons in human inferior
frontal gyrus. Journal of Neuroscience. 2009;29(32):10153-9. 15. Kilner JM, Neal A, Weiskopf N, Friston KJ, Frith CD. Evidence of mirror neurons in human inferior
frontal gyrus. Journal of Neuroscience. 2009;29(32):10153-9. 16. Rizzolatti G, Fadiga L, Gallese V, Fogassi L. Premotor cortex and the recognition of motor actions. Cognitive brain research. 1996;3(2):131-41. 16. Rizzolatti G, Fadiga L, Gallese V, Fogassi L. Premotor cortex and the recognition of motor actions. Cognitive brain research. 1996;3(2):131-41. 17. Decety J, Grezes J, Costes N, Perani D, Jeannerod M, Procyk E, et al. Brain activity during observation
of actions. Influence of action content and subject's strategy. Brain: a journal of neurology. 1997;120(10):1763-77. 18. Buccino G, Binkofski F, Fink GR, Fadiga L, Fogassi L, Gallese V, et al. Action observation activates
premotor and parietal areas in a somatotopic manner: an fMRI study. European journal of
neuroscience. 2001;13(2):400-4. 19. Grèzes J, Armony JL, Rowe J, Passingham RE. Activations related to “mirror” and “canonical”
neurones in the human brain: an fMRI study. Neuroimage. 2003;18(4):928-37. 20. Chong TTJ, Cunnington R, Williams MA, Kanwisher N, Mattingley JB. fMRI adaptation reveals mirror
neurons in human inferior parietal cortex. Current biology. 2008;18(20):1576-80. 20. Chong TTJ, Cunnington R, Williams MA, Kanwisher N, Mattingley JB. fMRI adaptation reveals mirror
neurons in human inferior parietal cortex. Current biology. 2008;18(20):1576-80. 21. Molenberghs P, Cunnington R, Mattingley JB. Brain regions with mirror properties: a meta-analysis of
125 human fMRI studies. Neuroscience & Biobehavioral Reviews. 2012;36(1):341-9. Page 12/14 Page 12/14 22. Grezes J, Decety J. Functional anatomy of execution, mental simulation, observation, and verb
generation of actions: a meta‐analysis. Human brain mapping. 2001;12(1):1-19. 23. Rizzolatti G, Fabbri-Destro M. The mirror system and its role in social cognition. Current opinion in
neurobiology. 2008;18(2):179-84. 24. Bonini L, Rozzi S, Serventi FU, Simone L, Ferrari PF, Fogassi L. Ventral premotor and inferior parietal
cortices make distinct contribution to action organization and intention understanding. Cerebral
Cortex. 2010;20(6):1372-85. 25. Fogassi L, Ferrari PF, Gesierich B, Rozzi S, Chersi F, Rizzolatti G. Parietal lobe: from action
organization to intention understanding. Science. 2005;308(5722):662-7. 26. Brass M, Heyes C. Imitation: is cognitive neuroscience solving the correspondence problem? Trends
in cognitive sciences. 2005;9(10):489-95. 27. Buccino G, Vogt S, Ritzl A, Fink GR, Zilles K, Freund H-J, et al. Neural circuits underlying imitation
learning of hand actions: an event-related fMRI study. Neuron. References 2004;42(2):323-34. 28. Rizzolatti G, Sinigaglia C. The mirror mechanism: a basic principle of brain function. Nature Reviews
Neuroscience. 2016;17(12):757-. 29. Bonini L. The extended mirror neuron network: Anatomy, origin, and functions. The Neuroscientist. 2017;23(1):56-67. 30. Caspers S, Zilles K, Laird AR, Eickhoff SB. ALE meta-analysis of action observation and imitation in
the human brain. Neuroimage. 2010;50(3):1148-67. 31. Iacoboni M, Dapretto M. The mirror neuron system and the consequences of its dysfunction. Nature
Reviews Neuroscience. 2006;7(12):942-51. 32. Hamilton AF. The mirror neuron system contributes to social responding. Cortex. 2013;49(10):2957-9. 33 Marshall PJ Meltzoff AN Neural mirroring mechanisms and imitation in human infants 32. Hamilton AF. The mirror neuron system contributes to social responding. Cortex. 2013;49(10):2957-9. 33. Marshall PJ, Meltzoff AN. Neural mirroring mechanisms and imitation in human infants. Philosophical Transactions of the Royal Society B: Biological Sciences. 2014;369(1644):20130620-. g
Philosophical Transactions of the Royal Society B: Biological Sciences. 2014;369(1644):20130620-. 34. Carr L, Iacoboni M, Dubeau M-C, Mazziotta JC, Lenzi GL. Neural mechanisms of empathy in humans:
a relay from neural systems for imitation to limbic areas. Proceedings of the national Academy of
Sciences. 2003;100(9):5497-502. 35. Iacoboni M. Imitation, empathy, and mirror neurons. Annual review of psychology. 2009;60:653-70. 36. Théoret H, Pascual-Leone A. Language acquisition: Do as you hear. Current Biology. 35. Iacoboni M. Imitation, empathy, and mirror neurons. Annual review of psychology. 2009;60:653-70. 35. Iacoboni M. Imitation, empathy, and mirror neurons. Annual review of psychology. 2009;60:653-70. 36. Théoret H, Pascual-Leone A. Language acquisition: Do as you hear. Current Biology. 2002;12(21):R736-R7. 36. Théoret H, Pascual-Leone A. Language acquisition: Do as you hear. Current Biology. 2002;12(21):R736-R7. 37. Wolf NS, Gales ME, Shane E, Shane M. The developmental trajectory from amodal perception to
empathy and communication: The role of mirror neurons in this process. Psychoanalytic Inquiry. 2001;21(1):94-112. 38. Green MF, Horan WP, Lee J. Social cognition in schizophrenia. Nature Reviews Neuroscience. 2015;16(10):620-31. 38. Green MF, Horan WP, Lee J. Social cognition in schizophrenia. Nature Reviews Neuroscience. 2015;16(10):620-31. 39. Reviews Cf, Dissemination. CRD's guidance for undertaking reviews in healthcare: York Publ. Services; 2009. 39. Reviews Cf, Dissemination. CRD's guidance for undertaking reviews in healthcare: York Publ. Services; 2009. Page 13/14 Page 13/14 Page 13/14 40. Stroup DF, Berlin JA, Morton SC, Olkin I, Williamson GD, Rennie D, et al. Meta-analysis of
observational studies in epidemiology: a proposal for reporting. Jama. 2000;283(15):2008-12. 41. Cooke A, Smith D, Booth A. References Beyond PICO: the SPIDER tool for qualitative evidence synthesis. Qualitative health research. 2012;22(10):1435-43. 42. Organization WH. INTERNATIONAL CLASSIFICATION OF DISEASES—NINTH REVISION (ICD-9). Weekly Epidemiological Record= Relevé épidémiologique hebdomadaire. 1988;63(45):343-4. 43. Organization WH. International classification of diseases, 10th revision. Geneva: World Health
Organization; Available: http. icd9cm chrisendres com/ Accessed July 8th. 2008. 44. Association AP. DSM-IV: Diagnostic and statistical manual of mental disorders. 1980. 45. Association AP. Diagnostic and statistical manual of mental disorders (DSM-5®): American
Psychiatric Pub; 2013. 46. Hupe M. EndNote X9. Journal of Electronic Resources in Medical Libraries. 2019;16(3-4):117-9. 46. Hupe M. EndNote X9. Journal of Electronic Resources in Medical Librarie 47. National Heart L, Institute B. Quality assessment tool for observational cohort and cross-sectional
studies. Bethesda: National Institutes of Health, Department of Health and Human Services. 2014:103-11. 48. Team RC. R: A language and environment for statistical computing. 2013. 49. Higgins JPT, Thomas J, Chandler J, Cumpston M, Li T, Page MJ, et al. Cochrane handbook for
systematic reviews of interventions: John Wiley & Sons; 2019. 50. Borenstein M, Hedges LV, Higgins JPT, Rothstein HR. Introduction to meta-analysis: John Wiley &
Sons; 2011. 50. Borenstein M, Hedges LV, Higgins JPT, Rothstein HR. Introduction to meta-analysis: John Wiley &
Sons; 2011. 51. Lewin S, Glenton C, Munthe-Kaas H, Carlsen B, Colvin CJ, Gülmezoglu M, et al. Using qualitative
evidence in decision making for health and social interventions: an approach to assess confidence in
findings from qualitative evidence syntheses (GRADE-CERQual). PLoS Med. 2015;12(10):e1001895. 51. Lewin S, Glenton C, Munthe-Kaas H, Carlsen B, Colvin CJ, Gülmezoglu M, et al. Using qualitative
evidence in decision making for health and social interventions: an approach to assess confidence in
findings from qualitative evidence syntheses (GRADE-CERQual). PLoS Med. 2015;12(10):e1001895. Page 14/14 Page 14/14 Page 14/14
|
https://openalex.org/W4206740981
|
https://revmaterialeplastice.ro/pdf/19 STOICHIOIU 4 21.pdf
|
English
| null |
In-plane Shear Response of a Flax Fiber-epoxy Resin Composite Subjected to Repeated Loading and Creep-recovery Cycles
|
Materiale plastice
| 2,022
|
cc-by
| 4,252
|
MATERIALE PLASTICE
https://revmaterialeplastice.ro
https://doi.org/10.37358/Mat.Plast.1964 In-plane Shear Response of a Flax Fiber-epoxy Resin Composite
Subjected to Repeated Loading and Creep-recovery Cycles
CONSTANTIN STOCHIOIU1, ANCA DECA1, ANTON HADAR1,2,3*, HORIA GHEORGHIU1
1University Politehnica of Bucharest, 313 Splaiul Independentei, 060042, Bucharest, Romania
2Academy of Romanian Scientists, 125 Calea Victoriei, 010071, Bucharest, Romania
3Technical Sciences Academy of Romania, 26 Dacia Blvd, Bucharest, 010413, Romania In-plane Shear Response of a Flax Fiber-epoxy Resin Composite
Subjected to Repeated Loading and Creep-recovery Cycles
CONSTANTIN STOCHIOIU1, ANCA DECA1, ANTON HADAR1,2,3*, HORIA GHEORGHIU1
1University Politehnica of Bucharest, 313 Splaiul Independentei, 060042, Bucharest, Romania
2Academy of Romanian Scientists, 125 Calea Victoriei, 010071, Bucharest, Romania
3Technical Sciences Academy of Romania, 26 Dacia Blvd, Bucharest, 010413, Romania CONSTANTIN STOCHIOIU1, ANCA DECA1, ANTON HADAR1,2,3*, HORIA
1University Politehnica of Bucharest, 313 Splaiul Independentei, 060042, Bucharest, Romania
2Academy of Romanian Scientists, 125 Calea Victoriei, 010071, Bucharest, Romania
3Technical Sciences Academy of Romania, 26 Dacia Blvd, Bucharest, 010413, Romania Abstract: The present paper is aimed at studying the in-plane shear response of a flax fiber - epoxy resin
composite laminate. Rectangular specimens, with ±45° laminate orientation with respect to loading
direction were used for the experimental procedure. Tensile testing up to failure allowed to extract the
shear strain-shear stress curve, which have shown a linear domain, up to approximately 25 MPa, where
a shear modulus was calculated, of 1.67 GPa and a Poisson ratio of 0.7, value which is typical for off
axis laminates. Strain measurement during these tests, using Digital Image Correlation, have shown
that, at high stress levels, concentrators occur in the specimen in the region of failure. Repeated loading
tests have shown that the material stiffens approximately 9% when increasing loading speed, leading to
conclude that a viscoelastic component of the deformation is present during loading. Repeated creep-
recovery tests showed that, for longer periods of time, viscoplastic deformations appear as well, with an
exponential evolution with respect to the creep duration. *email: anton.hadar@upb.ro 1. Introduction Nowadays, society is seeing a pronounced shift in perspective, towards low emission technologies
[1, 2], a shift that is making a mark in all areas of the industry. For the composite materials field, it is
entraining the search for alternatives to the current popular options, such as carbon and glass fiber
reinforcements, which are the most common reinforcements for laminate composites. Viable options are
proving to be bio-based, such as the use of plant fibers, which have an innate low environmental
footprint. While a great diversity exists among the proposed alternatives, studies have shown that
composites with flax fiber reinforcement tend to have the best mechanical properties among the bio-
based reinforcement fibers [3, 4]. The low density of flax fibers, of approximately 1.5 kg/cm3 [3] results
in high specific strength and stiffness for the resulting material, higher than that of glass-fiber reinforced
laminates [5], with which they are often compared. Furthermore, the flax plant has a long tradition of
cultivation in Europe, making it an accessible local source of raw materials [6] on the continent,
especially in the temperate to cold regions. Additionally, current fiber reinforced composites present a
difficulty in the end-of-life cycle, pyrolysis having been proven to be the only viable method of disposal
or recycling [7], a solution which alters the reinforcement fiber’s mechanical properties.These arguments
fuel the research for green sourced materials, with flax fiber reinforced composites, currently being on
the forefront. Several industrial applications have already been proposed, ranging from car body elements [8], to
musical instruments or furniture [5]. They prove the usability of flax fiber reinforced materials for non-
structural applications. However, several unknowns are still under scope before high load applications
are to be considered in an industrial scale. The microscopic structure of the flax fibers, which broadly consists of a cellulose crystalline structure
embedded in a hemicellulose matrix [9], gives it a complex mechanical response. The stress-strain curve
is associated with a bi-linear or a tri-linear evolution [10, 11]. Studies conducted by Keryvin et al. [12]
and Charlet et al. [13] have shown that a time dependant component is present in the elementary flax
fiber’s mechanical behavior. Mater. Plast., 58 (4), 2021, 179-186 179 https://doi.org/10.37358/MP.21.4.5543 MATERIALE PLASTICE
https://revmaterialeplastice.ro
https://doi.org/10.37358/Mat.Plast.1964 MATERIALE PLASTICE
https://revmaterialeplastice.ro
https://doi.org/10.37358/Mat.Plast.1964 Studies conducted by Poilane et al. 2. Materials and methods The composite material used in this study is an epoxy resin reinforced with unidirectional flax fibers
oriented to ±45°, alternating and symmetrical to a middle plane. This stacking sequence allows for
analyzing the in-plane shear response of the laminated material. Sheets of pre-impregnated fiber were
stacked, 20 in number, and placed in a heated press. The material was manufactured using a
thermocompression process at 3 bars and 130°C for 60 min, followed by a post-curing cycle at 130°C
for 60 min, destined to eliminate residual stress caused by resin curing. From the resulting composite
plates, 280 mm x 280 mm in size and approximately 3.25 mm thick, specimens were cut at dimensions
200 mm x 25 mm (Figure 1) through a laser cutter. g
g
The mechanical characterization was conducted in accordance with ASTM D3518 [18]. Deformation
was recorded using a Dantec Dynamics Digital Image Correlation (DIC) equipment and the load was
applied using an INSTRON 8872 universal testing machine (UTM), with a speed of 2 mm/min. Five
specimens were selected for this procedure and painted on one of the surfaces with a stochastic pattern
of black dots on a white background (Figure 2) to allow deformation recording by the DIC. A sample, which was equipped with aluminum end tabs, was subjected to repeated loading-unloading
tests, to determine the loading speed influence on the material response. Strain measurement was
performed with strain gauges, as they are highly versatile in recording data with either high or low
frequencies. The specimen was equipped with four transducers, two on the direction of the load and two
perpendiculars to it, mounted back-to-back, as can be seen in Figure 3. Four more strain gauges on each
direction, which were equipped on a dummy sample, were added to the connection, to form complete
Wheatstone bridges for each of the two strain gauge directions. This type of connection was chosen to
compensate for both bending and temperature-induced parasite strains. The load was applied using the
same INSTRON 8872 UTM, with speeds ranging in several orders of magnitude, as can be extracted
from Table 1 and data was recorded with a frequency of 50 Hz. 1. Introduction [14, 15] have shown that it also is inherited by the composite
material in which the fibers and introduced, regardless of fiber orientation or length. Composites with
the reinforcement on the load direction have proven to display both a viscoelastic and a viscoplastic
component, behavior exhibited in repeated loading-unloading and creep-recovery tests [16]. They are
both recorded starting from low stress levels. For a laminate composite to be used in conception, behavior on other directions needs to be studied
as well. In a previous work, the authors have shown, using samples with ±45° fiber reinforcement, that
in shear [17], a viscoelastic component is present, but modeling the composite behavior only considering
has proven insufficient. The present work is aimed to further fuel those results, by identifying a possible
viscoplastic component, through repeated loading-unloading and creep-recovery tests. 2. Materials and methods At the end of each loading phase, one of the grips of the machine was opened and a period of time
was allowed to pass between two consecutive tests, to permit the unhindered recovery of the sample
until strain stabilization, which was continuously monitored. It is worth noting that, this modification to
a regular loading-unloading test, which are common in material testing, was necessary as the unloading
component of the test cycle is usually with the sample in the grips of the machine, which dictates the
deformation of the sample and viciates it. Furthermore, sample integrity was evaluated with low-stress level cycles conducted between
consecutive tests. Damage appearing in the sample during loading phases would result in loss of
modulus. A description of the testing procedure is presented in Figure 4. The third type of test was that of repeated creep-recovery with a variable creep duration. The purpose
was to determine how the material behaves under long periods of loading. Four cycles were conducted
on the same sample, with a constant creep stress level, but increasing creep duration. The recovery period
was constant, of 24 h, considered sufficient for deformations to be stabilized. The procedure is
represented in Figure 5. The strain was constantly recorded with the same method that was described for
the previous test, but with a lower frequency, of 0.1 Hz, to allow for long periods of data recording. Mater. Plast., 58 (4), 2021, 179-186 180 https://doi.org/10.37358/MP.21.4.5543 3.1. Tensile tests Image data collected during the tensile testing through the DIC equipment was processed with
ISTRA 4D Software to calculate the deformation distribution during loading (Figure 6) which, due to
geometry and ply lay-up of the sample, is uniform. From the processed data, principal strains were
extracted as an average of the processed surface. They represent the longitudinal deformation, 𝜀𝐿, and
the transverse one, 𝜀𝑇. The deformation distribution calculated by ISTRA 4D allows to observe that, when close to
rupturing, deformation distribution is no longer uniform and concentrators appear on the sample in the
failure area, (Figure 7) making Eq. (1) and (2) inappropriate for shear stress and strain calculation at that
level. For this reason, analysis is limited to the domain where strain distribution is uniform. Shear strain and shear stress were plotted in Figure 8 for the five samples to obtain the characteristic
curve in shear, up to 5% shear strain, and in Figure 9 the transverse strain was plotted with respects to
longitudinal strains. ongitudinal strains. Figure 6. Example of deformation Figure 7. Concentrators
distribution during loading: principal strain 1 at high load levels
The shear stress-strain curves show a linear domain, up to approximately 25 MPa. For this region, a
chord shear modulus, G, is calculated, between 0.2% and 0.6% shear strain, obtaining a value of
1.67±0.01 GPa. The linear region is followed by a reduction in stiffness, where the maximum shear
tress is achieved, at 37.78 ± 0.5 GPa, before failure. Longitudinal strain versus transverse strain plots
hows a linear evolution, leading to the conclusion of a constant Poisson’s ratio, calculated to be 0.7 ±
0.01 in the same 0.2% - 0.6% shear strain interval. It is worth noting that the value is higher than 0.5
maximum possible value for an isotropic material) due to the layup of the reinforcement material in the
matrix and is common for off-axis reinforced composites [18]. Figure 6. Example of deformation
distribution during loading: principal strain 1 Figure 7. Concentrators
at high load levels Figure 6. Example of deformation
distribution during loading: principal strain 1 Figure 7. Concentrators
at high load levels g
p
distribution during loading: principal strain 1 The shear stress-strain curves show a linear domain, up to approximately 25 MPa. For this region, a
chord shear modulus, G, is calculated, between 0.2% and 0.6% shear strain, obtaining a value of
1.67±0.01 GPa. MATERIALE PLASTICE https://revmaterialeplastice.ro https://revmaterialeplastice.ro
https://doi.org/10.37358/Mat.Plast.1964 p
p
https://doi.org/10.37358/Mat.Plast.1964 3. Results and discussions Strain data, obtained with both DIC and strain gauges was recorded on the direction of loading, or
longitudinal, and perpendicular to the loading direction, or transverse. Due to the layer layup, at ±45°
and symmetrical to a middle plane, shear strain is equal to the difference between the two, Eq. (1) and
shear stress is equal to the force divided by the double of the cross-section area, Eq. (2). 𝛾= 𝜀𝐿 −𝜀𝑇 (1)
𝜏=
𝐹
2𝐴 (2) (1)
(2) (2) MATERIALE PLASTICE https://revmaterialeplastice.ro p
p
https://doi.org/10.37358/Mat.Plast.1964 Loading was managed with dead weights, amplified by a lever mechanism which enabled constant stress
levels for extended periods of time. Figure 1. Composite sample
Figure 2. Sample prepared for mechanical testing
Figure 3. Sample equipped for loading-unloading and creep-recovery tests Figure 1. Composite sample
Figure 2. Sample prepared for mechanical testing
Figure 3. Sample equipped for loading-unloading and creep-recovery tests Figure 1. Composite sample Figure 1. Composite sample Figure 2. Sample prepared for mechanical testing Figure 3. Sample equipped for loading-unloading and creep-recovery tests Figure 3. Sample equipped for loading-unloading and creep-recovery tests Mater. Plast., 58 (4), 2021, 179-186 181 https://doi.org/10.37358/MP.21.4.5543
Table 1. Repeated loading
tests parameters
Cycle
no. Load speed
[kN/min]
τ
[MPa]
1
1
15
2
5
3
10
4
50
5
100
6
500
7
1000
Figure 4. Repeated loading tests procedure
Figure 5. Repeated creep-recovery procedure Table 1. Repeated loading
tests parameters
Cycle
no. Load speed
[kN/min]
τ
[MPa]
1
1
15
2
5
3
10
4
50
5
100
6
500
7
1000
Figure 4. Repeated loading tests procedure Figure 4. Repeated loading tests procedure Figure 4. Repeated loading tests procedure Figure 4. Repeated loading tests procedure Figure 5. Repeated creep-recovery procedure Mater. Plast., 58 (4), 2021, 179-186 181 https://doi.org/10.37358/MP.21.4.5543 MATERIALE PLASTICE 3.1. Tensile tests The linear region is followed by a reduction in stiffness, where the maximum shear
stress is achieved, at 37.78 ± 0.5 GPa, before failure. Longitudinal strain versus transverse strain plots
shows a linear evolution, leading to the conclusion of a constant Poisson’s ratio, calculated to be 0.7 ±
0.01 in the same 0.2% - 0.6% shear strain interval. It is worth noting that the value is higher than 0.5
(maximum possible value for an isotropic material) due to the layup of the reinforcement material in the
matrix and is common for off-axis reinforced composites [18]. Mater. Plast., 58 (4), 2021, 179-186 182 https://doi.org/10.37358/MP.21.4.5543 https://revmaterialeplastice.ro p
p
https://doi.org/10.37358/Mat.Plast.1964 https://doi.org/10.37358/Mat.Plast.1964 Figure 8. Shear strain - Shear stress curve Figure 9. Longitudinal strain versus
transverse strain Figure 8. Shear strain - Shear stress curve Figure 8. Shear strain - Shear stress curve Figure 9. Longitudinal strain versus
transverse strain Figure 9. Longitudinal strain versus
transverse strain Figure 9. Longitudinal strain versus
transverse strain Figure 8. Shear strain - Shear stress curve 3.2. Repeated loading tests The deformation response during the repeated loading tests is presented in Figure 10. It can be
noticed that, after releasing from the grips, the sample fully recovers in a period of time. This shows the
presence of a visco-elastic behavior and the absence of residual deformations. Loading phases are cut
and presented in shear strain-shear stress coordinates, in Figure 11. They show a variance of the curve,
dependent on loading speed, confirming that visco-elastic deformations occur during loading. p
g p
g
g
g
Shear modulus G is calculated for each curve, in the same domain as for the previously tests and is
presented in Figure 12, on a logarithmic scale. An increase of approximately 9% is observed, from 1.69
GPa to 1.84 GPa, which stabilizes for the highest loading speeds. This leads to the conclusion that, if a
sufficiently high speed is applied, a purely elastic response can be obtained. However, it can also be
extracted that, in the case of high loading speeds, due to machine limitations, an overshoot is produced,
which is undesirable in either laboratory conditions or industrial applications. Lastly, during the
evaluation cycles, no loss in modulus has been detected, concluding that no damage has been produced
in the sample. Figure 10. Deformation response during repeated loading tests Figure 10. Deformation response during repeated loading tests Mater. Plast., 58 (4), 2021, 179-186 183 https://doi.org/10.37358/MP.21.4.5543 MATERIALE PLASTICE https://doi.org/10.37358/Mat.Plast.1964 https://doi.org/10.37358/Mat.Plast.1964
Figure 11. Shear stress-shear strain Figure 12. Shear modulus versus
curves with respects to loading speed to loading speed Figure 12. Shear modulus versus
to loading speed Figure 11. Shear stress-shear strain
curves with respects to loading speed Figure 12. Shear modulus versus
to loading speed 3.3. Repeated creep-recovery tests The deformation response during the entire testing period is presented in Figure 13. It can be
observed that a time-dependent deformation is present during creep, as expected and confirmed by the
previous tests. However, at the end of each cycle, plastic deformations are present. The recovery phases are extracted in Figure 14. Viscoelastic deformations tend to recover but, at the
end of each phase, plastic deformations tend to increase. Since no load is applied during recovery, it can
be concluded that they are produced by the load during creep and that they are constant during the entire
recovery phase. Thus, they can be considered time-dependent plastic deformations, or viscoplastic, and
that they increase with creep duration. Furthermore, it is possible to dissociate them during recovery,
when viscoplastic strains are constant, but impossible during the creep phase, when they are both varying
in time. Figure 13. Shear strain response during the creep-recovery test
0.5 h
1 h
1.5 h
2 h Figure 13. Shear strain response during the creep-recovery test This viscoplastic strain, recorded at the end of the recovery phases, is depicted in Figure 15 in a
logarithmic time scale, where the cumulated creep duration is used for the abscissa axis. A linear
evolution can be traced, which signifies, on a linear scale, an exponential evolution with respects to time. This viscoplastic strain, recorded at the end of the recovery phases, is depicted in Figure 15 in a
logarithmic time scale, where the cumulated creep duration is used for the abscissa axis. A linear
evolution can be traced, which signifies, on a linear scale, an exponential evolution with respects to time. This viscoplastic strain, recorded at the end of the recovery phases, is depicted in Figure 15 in a
logarithmic time scale, where the cumulated creep duration is used for the abscissa axis. A linear
evolution can be traced, which signifies, on a linear scale, an exponential evolution with respects to time. Mater. Plast., 58 (4), 2021, 179-186 184 https://doi.org/10.37358/MP.21.4.5543 p
p
https://doi.org/10.37358/Mat.Plast.1964 Figure 14. Recovery phases Figure 15. Cumulated plastic deformations
versus cumulated creep duration Figure 14. Recovery phases Figure 15. 1. *** United Nations Framework Convention on Climate Change, Paris Agreement, 2015.
2. *** EUR-Lex, Directive 2005/64/EC of the European Parliament and of the Council of 26 October
2005, Official Journal of the European Union, 2005, L 310, p. 10-27.
3. BLEDZKI A.K., REIHMANE S., GASSAN J., Properties and modification methods for vegetable
fibers for natural fiber composites, Journal of Applied Polymer Science, 1996, 59(8), p. 1329-1336.
4. GAY D., Composite Materials Design and Applications, CRC press, 2016.
5. PIL L., BENSADOUN F., PARISET J., VERPOEST I., Why are designers fascinated by flax and
hemp fibre composites? Composites Part A: Applied Science and Manufacturing, 2016, 83, p. 193-205.
6. FAOSTAT Report, Top 10 producers of flax for 2010-2016, 2018. 3.3. Repeated creep-recovery tests Cumulated plastic deformations
versus cumulated creep duration
When considering the repeated loading tests and the creep recovery tests, it can be concluded that the
overall shear behavior of the material is a sum of viscoelasticity and viscoplasticity, with the latter being
present only when the load is maintained for a longer period of time. These results show that a laminated composite material with flax fiber reinforcement will have a time-
dependent behavior even in normal environmental conditions. Figure 15. Cumulated plastic deformations
versus cumulated creep duration Figure 14. Recovery phases Figure 14. Recovery phases Figure 15. Cumulated plastic deformations
versus cumulated creep duration Figure 15. Cumulated plastic deformations
versus cumulated creep duration When considering the repeated loading tests and the creep recovery tests, it can be concluded that the
overall shear behavior of the material is a sum of viscoelasticity and viscoplasticity, with the latter being
present only when the load is maintained for a longer period of time. When considering the repeated loading tests and the creep recovery tests, it can be concluded that the
overall shear behavior of the material is a sum of viscoelasticity and viscoplasticity, with the latter being
present only when the load is maintained for a longer period of time. These results show that a laminated composite material with flax fiber reinforcement will have a time- p
y
g
p
These results show that a laminated composite material with flax fiber reinforcement will have a time-
dependent behavior even in normal environmental conditions. p
y
g
p
These results show that a laminated composite material with flax fiber reinforcement will have a time-
dependent behavior even in normal environmental conditions. 4. Conclusions A set of experimental data for a laminated composite of flax fiber and epoxy resin has been presented. The lay-up of the laminates, arranged at ± 45°, with respect to the loading direction and symmetrically
with respect to a middle plane allowed to analyze the in-plane shear response of the material. Through tensile testing, the shear strain - shear stress curve was extracted up to 5% shear strain. It
presents a linear domain, where a shear modulus was calculated and a transition region where maximum
shear stress was extracted. The longitudinal strain versus transverse strain plot showed a linear evolution,
leading to the conclusion of a constant Poisson’s ratio. The repeated loading test have shown that, by increasing the loading speed, the material stiffens, up
to an asymptote, leading to the conclusion that a viscoelastic component is present in the material
response, even during loading. It can be reduced and, possibly eliminated by increasing the loading
speed. Furthermore, no significant plastic deformations were recorded due to the short duration of the
applied loads. The creep-recovery tests showed that, for long periods of loading, plastic deformations
accumulate, dependent on load duration, in an exponential evolution. Acknowledgments: This work is supported by the project ANTREPRENORDOC, in the framework of
Human Resources Development Operational Programme 2014-2020, financed from the European Social
Fund under the contract number 36355/23.05.2019 HRD OP /380/6/13 - SMIS Code: 123847 References Mater. Plast., 58 (4), 2021, 179-186 185 https://doi.org/10.37358/MP.21.4.5543 MATERIALE PLASTICE
https://revmaterialeplastice.ro
https://doi.org/10.37358/Mat.Plast.1964 MATERIALE PLASTICE
https://revmaterialeplastice.ro
https://doi.org/10.37358/Mat.Plast.1964 7. JODY B.J., POMYKALA J.A., DANIELS E.J., GREMINGER J.L., A process to recover carbon fibers
from polymer-matrix composites in end-of-life vehicles, JOM, 2004, 56(8), p. 43-47. 7. JODY B.J., POMYKALA J.A., DANIELS E.J., GREMINGER J.L., A process to recover carbon fibers
from polymer-matrix composites in end-of-life vehicles, JOM, 2004, 56(8), p. 43-47. 8. AKAMPUMUZA O., WAMBUA P.M., AHMED A., LI W., QIN X.H., Review of the applications of
biocomposites in the automotive industry, Polymer Composites, 2017, 38(11), p. 2553-2569. 9. BOURMAUD A., BEAUGRAND J., SHAH D.U., PLACET V., BALEY C., Towards the design of
high-performance plant fibre composites, Progress in Materials Science, 2018, 97, p. 347-408. 10.CHARLET K., EVE S., JERNOT J.P., GOMINA M., BREARD J., Tensile deformation of a flax fiber,
Procedia Engineering, 2009, 1(1), p. 233-236. 11.LEFEUVRE A., BOURMAUD A., MORVAN C., BALEY C., Elementary flax fibre tensile 8. AKAMPUMUZA O., WAMBUA P.M., AHMED A., LI W., QIN X.H., Review of the applications of
biocomposites in the automotive industry, Polymer Composites, 2017, 38(11), p. 2553-2569. 9 BOURMAUD A BEAUGRAND J SHAH D U PLACET V BALEY C To ards the design of high-performance plant fibre composites, Progress in Materials Science, 2018, 97, p. 347-408. 10.CHARLET K., EVE S., JERNOT J.P., GOMINA M., BREARD J., Tensile deformation of a flax fiber,
Procedia Engineering, 2009, 1(1), p. 233-236. g
p
p
p
p
10.CHARLET K., EVE S., JERNOT J.P., GOMINA M., BREARD J., Tensile deformati
Procedia Engineering, 2009, 1(1), p. 233-236. ., EVE S., JERNOT J.P., GOMINA M., BREARD J., Tensile deformation of a flax fiber,
ering, 2009, 1(1), p. 233-236. 11.LEFEUVRE A., BOURMAUD A., MORVAN C., BALEY C., Elementary flax fibre tensile
properties: Correlation between stress-strain behaviour and fibre composition, Industrial Crops and
Products, 2014, 52, p. 762-769. p
12. KERYVIN V., LAN M., BOURMAUD A., PARENTEAU T., CHARLEUX L., BALEY C., Analysis
of flax fibres viscoelastic behaviour at micro and nano scales, Composites Part A: Applied Science and
Manufacturing, 2015, 68, p. 219-225. 13. CHARLET K., Contribution à l’étude de composites unidirectionnels renforcés par des fibres de lin :
relation entre la microstructure de la fibre et ses propriétés mécaniques, Thèse de Doctorat, Université de
Caen/Basse-Normandie, 2008. Â 14. POILÂNE C., Z. Mater. Plast., 58 (4), 2021, 179-186 Manuscript received: 2.12.2021 https://doi.org/10.37358/MP.21.4.5543 References CHERIF E., RICHARD F., VIVET A., BEN DOUDOU B., CHEN J., Polymer
reinforced by flax fibres as a viscoelastoplastic material, Composite Structures, 2014, 112(1), p. 100-112. 15.VARNA J., ROZITE L., JOFFE R., PUPURE A., Non-linear behaviour of PLA based flax composites,
Plastics, Rubber and Composites, 2012, 41(2), p. 49-60. p
( ) p
16. STOCHIOIU C., GHEORGHIU H.M., ARTIMON F.P.G., Visco-elastoplastic characterization of a
flax-fiber reinforced biocomposite, Mater. Plast., 58(1), 2021, p. 78-84. 17. STOCHIOIU C., PIEZEL B., CHETTAH A., FONTAINE S., GHEORGHIU H.M., Basic modeling 16. STOCHIOIU C., GHEORGHIU H.M., ARTIMON F.P.G., Visco-elastoplastic characterization of a
flax-fiber reinforced biocomposite, Mater. Plast., 58(1), 2021, p. 78-84. 17. STOCHIOIU C., PIEZEL B., CHETTAH A., FONTAINE S., GHEORGHIU H.M., Basic modeling
of the visco elastic behavior of flax fiber composites, Industria Textila, 2019, 70(4), p. 331-335. 18. ***STANDARD A.S.T.M. D3518/D3518M-94, Standard Test Method for In-Plane Shear Response
of Polymer Matrix Composite Materials by Tensile Test of a ±45° Laminate, Annual Book of ASTM 17. STOCHIOIU C., PIEZEL B., CHETTAH A., FONTAINE S., GHEORGHIU H.M., Basic modeling
of the visco elastic behavior of flax fiber composites, Industria Textila, 2019, 70(4), p. 331-335. 17. STOCHIOIU C., PIEZEL B., CHETTAH A., FONTAINE S., GHEORGHIU H.M., Basic modeling
of the visco elastic behavior of flax fiber composites, Industria Textila, 2019, 70(4), p. 331-335. 18. ***STANDARD A.S.T.M. D3518/D3518M-94, Standard Test Method for In-Plane Shear Response 18. ***STANDARD A.S.T.M. D3518/D3518M-94, Standard Test Method for In-Plane Shear Response
of Polymer Matrix Composite Materials by Tensile Test of a ±45° Laminate, Annual Book of ASTM
Standards, 2007, 94, p. 1-7. Manuscript received: 2.12.2021 186 Mater. Plast., 58 (4), 2021, 179-186
|
https://openalex.org/W3080143045
|
https://www.researchsquare.com/article/rs-30147/v1.pdf?c=1591058635000
|
English
| null |
Associations of socioeconomic factors with cause-specific Mortality and burden of cardiovascular diseases: findings from the vital registration in urban Shanghai, China, during 1974–2015
|
BMC public health
| 2,020
|
cc-by
| 7,767
|
Original article for the collection of CVD Original article for the collection of CVD Associations of Socioeconomic Factors with Cause-specific Mortality and
Burden of Cardiovascular Diseases: Findings from the Vital Registration in
Urban Shanghai, China, during 1974-2015 Lijuan Zhang1,*, Qi Li1,*, Xue Han2,*, Shuo Wang3*, Peng Li4*, Yibo Ding4, Tao Zhang2, Jia
Zhao2, Yifan Chen4, Jiluo Liu4, Jue Li1, Xiaojie Tan4, Wenbin Liu4, Rong Zhang2, Guangwen
Cao4 * These authors contribute equally to this work. * These authors contribute equally to this work. Correspondence Prof. Guangwen Cao (2 supplementary Figures and 5 supplementary tables) 1 Background Although cardiovascular disease (CVD) is preventable and treatable, the number of global
CVD death has increased by 12.5% during the last decade. CVD accounts for one third of
global human death (17.7/55 millions) in 2017 [1, 2]. In the Western world, the mortality rate
of CVD has decreased since the mid-1990s due to improvements in acute care and the
efficacy of secondary prevention [3]. In low- and middle-income countries (LMICs), a
substantial number of CVD death are attributed to tobacco abuse, physical inactivity,
unhealthy diet, harmful alcohol use, air pollution, poor food supply, low education level,
uncontrolled blood pressure, and psychosocial aspects [4-7]. China is one of the largest
LMICs. Population in mainland China experienced dramatic sufferings and alterations after
the First Opium War (1840-1842). Since the founding of the People's Republic of China in
1949, several demographic and socioeconomic challenges accompanied by social
development have been reported: a rapid population swell (1952-1982) [8], the rapid
economic expansion started in 1978 [9], life expectancy increases (since 1981) [10], aging
society (since 1999) [11], unhealthy lifestyle (since 1990) [9], environmental pollution [12,
13], and increases in conventional CVD risk factors such as hypertension, dyslipidemia,
diabetes mellitus, overweight, and obesity [14-17]. Thereafter, specific steps and responses
were taken to meet these challenges including a series of programs to promote healthy
lifestyles targeting to the risk factors of CVD, improvement of primary care since 1997, basic
medical insurance coverage in 2008, hospital care, and public health actions such as air
pollution control action plan [9]. However, the mortality rate of CVD has increased
significantly during the last 2 decades and CVD is still the top cause of human death in China
[18]. There is a large gap between medical / public health actions and effective prophylaxis of
CVD in China. The influence of socioeconomic improvements and national health plans on Although cardiovascular disease (CVD) is preventable and treatable, the number of global
CVD death has increased by 12.5% during the last decade. CVD accounts for one third of
global human death (17.7/55 millions) in 2017 [1, 2]. In the Western world, the mortality rate
of CVD has decreased since the mid-1990s due to improvements in acute care and the
efficacy of secondary prevention [3]. Abstract Background: Cardiovascular disease (CVD) is the leading cause of mortality worldwide. The
effect of socioeconomic factors on cause-specific mortality and burden of CVD is rarely
evaluated in low- and middle-income countries, especially in a rapidly changing society. Methods: Original data were derived from the vital registration system in Yangpu, a
representative, population-stable district of urban Shanghai, China, during 1974-2015. Temporal trends for the mortality rates and burden of CVD during 1974-2015 were evaluated
using Joinpoint Regression Software. The burden was evaluated using age-standardized
person years of life loss per 100,000 persons (SPYLLs). Age-sex-specific CVD mortality
rates were predicted by using age-period-cohort Poisson regression model. Results: A total of 101,822 CVD death occurred during 1974-2015, accounting for 36.95% of
total deaths. Hemorrhagic stroke, ischemic heart disease, and ischemic stroke were the 3
leading causes of CVD death. The age-standardized CVD mortality decreased from
144.5/100,000 to 100.7/100,000 in the residents (average annual percentage change [AAPC]
-1.0, 95% confidence interval [CI] -1.7 to -0.2), which was mainly contributed by women
(AAPC -1.3, 95% CI -2.0 to -0.7), not by men. Hemorrhagic stroke, the major CVD death in
the mid-aged population, decreased dramatically after 1991. The crude mortality of ischemic
heart disease kept increasing but its age-adjusted mortality decreased continually after 1997. SPYLLs of CVD death increased from 1974 to 1986 (AAPC 2.1, 95% CI 0.4 to 3.8) and
decreased after 1986 (AAPC 1.8, 95% CI -2.3 to -1.3). These changes were in concert with
the implementation of policies including extended medical insurance coverage, pollution
control, active prophylaxis of CVD including lifestyle promotion, and national health
programs. The mortality of CVD increased in those born during 1937-1945, a period of the
Japanese military occupation, and during 1958-1965, a period including the Chinese Famine. Sequelae of CVD and ischemic heart disease are predicted to be the leading causes of CVD 2 death in 2029. death in 2029. Conclusions: Exposure to serious malnutrition in early life might increase CVD mortality in
later life. Improvements in medical services, pollution control, and lifestyle could decrease
CVD death. New strategy is needed to prevent the aging-related CVD death and burden in the
future. Keywords: Cardiovascular disease; mortality; medical insurance; burden; malnutrition;
lifestyle; pollution control; sociodemographic index; low- and middle-income countries 3 Background In low- and middle-income countries (LMICs), a
substantial number of CVD death are attributed to tobacco abuse, physical inactivity,
unhealthy diet, harmful alcohol use, air pollution, poor food supply, low education level,
uncontrolled blood pressure, and psychosocial aspects [4-7]. China is one of the largest
LMICs. Population in mainland China experienced dramatic sufferings and alterations after
the First Opium War (1840-1842). Since the founding of the People's Republic of China in
1949, several demographic and socioeconomic challenges accompanied by social
development have been reported: a rapid population swell (1952-1982) [8], the rapid
economic expansion started in 1978 [9], life expectancy increases (since 1981) [10], aging
society (since 1999) [11], unhealthy lifestyle (since 1990) [9], environmental pollution [12,
13], and increases in conventional CVD risk factors such as hypertension, dyslipidemia,
diabetes mellitus, overweight, and obesity [14-17]. Thereafter, specific steps and responses
were taken to meet these challenges including a series of programs to promote healthy
lifestyles targeting to the risk factors of CVD, improvement of primary care since 1997, basic
medical insurance coverage in 2008, hospital care, and public health actions such as air
pollution control action plan [9]. However, the mortality rate of CVD has increased
significantly during the last 2 decades and CVD is still the top cause of human death in China
[18]. There is a large gap between medical / public health actions and effective prophylaxis of
CVD in China. The influence of socioeconomic improvements and national health plans on 4 the CVD-caused immature death has not been systemically evaluated. Data Sources Information on CVD death during 1974-2015 was derived from the vital registration system,
covering the all registered residents of Yangpu district, Shanghai [21]. The details of each
CVD patient including age, gender, CVD types, date and causes of death were collected. The
majority (97.94%) of CVD death were diagnosed with solid clinical and laboratory evidence
or morphologic verification. Death from each CVD cause during 1974-2001 was classified
based on the International Classification of Disease-9th version (ICD-9) codes. Since 2002,
causes of CVD death were classified according to the ICD-10 codes (Table S1 in Additional
file). Causes of CVD death were estimated for a comprehensive category that combined CVD
and circulatory conditions. These causes included ischemic heart disease (IHD), hemorrhagic
stroke (HS), ischemic stroke (IS), hypertensive disease (HD), rheumatic heart disease (RHD),
sequelae of cerebrovascular disease (SCD), other forms of heart diseases (heart failure,
pericarditis and other diseases of pericardium, acute and subacute endocarditis, heart valve
diseases, myocarditis and cardiomyopathy, conduction diseases, cardiac arrest, cardiac
arrhythmias), and other cardiovascular and circulatory diseases. For stroke death estimates,
the GBD defined stroke ICD codes as HS, IS or non-specific as to type, non-specific codes
were redistributed to HS or IS using a regression model [22]. The study was performed in
accordance with the 2000 Declaration of Helsinki and was approved by the ethics committee
of the Naval Medical University. Information on CVD death during 1974-2015 was derived from the vital registration system,
covering the all registered residents of Yangpu district, Shanghai [21]. The details of each
CVD patient including age, gender, CVD types, date and causes of death were collected. The
majority (97.94%) of CVD death were diagnosed with solid clinical and laboratory evidence
or morphologic verification. Death from each CVD cause during 1974-2001 was classified
based on the International Classification of Disease-9th version (ICD-9) codes. Since 2002,
causes of CVD death were classified according to the ICD-10 codes (Table S1 in Additional
file). Causes of CVD death were estimated for a comprehensive category that combined CVD
and circulatory conditions. These causes included ischemic heart disease (IHD), hemorrhagic
stroke (HS), ischemic stroke (IS), hypertensive disease (HD), rheumatic heart disease (RHD),
sequelae of cerebrovascular disease (SCD), other forms of heart diseases (heart failure,
pericarditis and other diseases of pericardium, acute and subacute endocarditis, heart valve
diseases, myocarditis and cardiomyopathy, conduction diseases, cardiac arrest, cardiac
arrhythmias), and other cardiovascular and circulatory diseases. Data Sources For stroke death estimates,
the GBD defined stroke ICD codes as HS, IS or non-specific as to type, non-specific codes
were redistributed to HS or IS using a regression model [22]. The study was performed in
accordance with the 2000 Declaration of Helsinki and was approved by the ethics committee
of the Naval Medical University. the CVD-caused immature death has not been systemically evaluated. As the economic center in China, Shanghai belonged to low-income region before 1994,
lower-middle income region between 1996-2005, and upper-middle income region after 2006
[19]. Shanghai stands at the forefront of the national strategic initiatives and responds quickly
to these policies. Therefore, Shanghai is one of the most suitable places to clarify the effects
of socioeconomic changes and national actions on CVD death in China. We selected Yangpu
district of Shanghai as a study district based on the following reasons. First, highly polluting
industries including coal-fired power generation, textiles, steel metallurgy, electroplating, and
coal gas production were introduced since the old municipal government established in
Yangpu in 1933 and were shut down in the 1980s due to resultant heavy pollution. Second,
the permanent residents in Yangpu, rather than in whole Shanghai, have been quite stable
during 1974-2015, without immigration influx or efflux. Effects of changing risk factor
exposures on the causes of CVD deaths can be only evaluated in a stable population. The
epidemiological transition in CVD mortality occurred earlier and slower in western countries,
but it has been compressed to just a few decades in China, that is, the main cause of
population death has shifted from infectious diseases and perinatal diseases to chronic
diseases [20]. Third, the vital registration system in Yangpu was established 14 years prior to
the national one established in 1987 [21]. In the present study, we characterized the effect of socioeconomic alterations during 1974 and
2015 on long-term trends in the mortality and burden of CVD in Yangpu, a representative
district of urban Shanghai, to evaluate the influence of socioeconomic events and health
actions on cause-specific CVD death, which may help in improving CVD control strategy in
the other countries in the world, especially in LMICs. 5 Estimation of CVD Mortality and Burden 6 The mortality rates from 1974 to 2015 stratified by sexes and eighteen 5-year age groups were
calculated. All the rates were calculated as per 100,000 persons per year. Age standardized
mortality rates were calculated using Segi's world standard population [21, 23]. Age-standardized mortality and birth cohort were applied to characterize the temporal trends
of CVD mortality. Person years of life lost (PYLL), age-standardized person years of life loss
per 100,000 persons (SPYLLs) and average years of life lost (AYLL) were applied to
estimate CVD burden. All analyses were performed separately by sex and aggregated by
5-year age categories. Burden of all-cardiovascular and each underlying CVD cause were
estimated using PYLL, SPYLLs and AYLL. Formula and calculation for disease burden were
as follows: PYLL=∑
𝑎𝑖
𝑒
𝑖=1
𝑑𝑖
SPYLLs = PYLL × 100 000
𝑛
AYLL=
PYLL
∑𝑑𝑖 PYLL=∑
𝑎𝑖
𝑒
𝑖=1
𝑑𝑖 e=the life expectancy in Shanghai (Table S2 in Additional file); i=median age of the death
group; ai=e-(i+0.5); di=number of deaths at age; n=general population. Sociodemographic Index Sociodemographic Index (SDI) was applied to examine changes in the major causes of CVD
death burden as a function of epidemiological transition [24]. SDI was estimated using
equally weighted age-sex-state-year-specific geometric means of income per capita,
educational attainment, and total fertility rate. 7 7 Statistical Analysis CVD mortality in time trends can theoretically be attributed to aging, characterized by
changes in cumulative exposure to risk factors over time (age effects), changes occurring
during specific calendar periods irrespective of age (a period effect), or changes affecting
persons born in specific or successive generations irrespective of age (a cohort effect). An
age-period-cohort (APC) model was fitted to better understand the effects of the three factors
on disease rates [25]. Segmented package in R software (Version 3.3.3) was applied to
conduct the APC model [21]. Leslie matrices were applied to predict cause of CVD death
cases and person-years by age (a), period (p) and cohort (c) on mortality and predict mortality
trend from 2015 to 2029 [26]. Temporal trends for the crude, log-transformed and
age-standardized mortality rates and the burden of CVD from 1974 to 2015 were carried out
using Joinpoint Regression Software, version 4.7.0.0, provided by the Surveillance Research
Program of the National Cancer Institute (Bethesda, MD). The trend was expressed as an
average annual percentage change (AAPC). The z test was employed to assess whether APC
was statistically different from zero; 95% confidence interval (95% CI) for each segment was
calculated. Other statistical analyses were conducted using SPSS 23.0 (SPSS, Chicago, IL). General information All registered permanent residents in Yangpu, with a total of 41,879,864 person-years, were
analyzed. A total of 101,822 CVD deaths (51,423 women vs. 50,399 men) occurred,
accounting for 36.95% of all deaths. Age-standardized mortality rate for all CVD was higher 8 in men than in women (155.2/105 vs.121.4/105, P=4.6×10-6). IHD, HS and IS and SCD were
the 4 leading causes of CVD deaths in both sexes (Figure S1 in Additional file), accounting
for 80.16% in crude mortality and 82.01% in age-standardized mortality for all CVD. Composition of CVD death IHD and IS deaths increased with aging and SCD death increased after 50 years in all
populations (Figure 1A); RHD was the main cause of CVD deaths in women within 10-39
years (Figure 1B); HS was the leading cause of CVD deaths at 35-69 years in both women
and men (Figure 1B and 1C). Trends in CVD death Average age of CVD death was 68.13±12.93 years in 1974 and increased consecutively
during 1974-2015 (AAPC 0.5, 95% CI 0.3 to 0.6 in women; AAPC 0.4, 95% CI, 0.4 to 0.5 in
men) (Figure 2A). Men died from CVD earlier than women (72.26±11.41 vs. 75.75±10.45
years, P=0.001). RHD was the top CVD type that caused earlier death in both men and
women (Figure 2B-2D). The age-standardized mortality rate of total CVD decreased in all the residents (AAPC -1.0,
95% CI -1.7 to -0.2) and in women (AAPC -1.3, 95% CI -2.0 to -0.7) during 1974-2015;
however, it did not alter in men (AAPC -0.7, 95% CI -1.5 to 0.1) (Table S3 in Additional
file). The crude mortality rate of IHD consecutively increased whereas the rate of HS
decreased sharply after 1997. The crude mortality curves of HS and IHD, the two major CVD
types, converged at 1997-1998 (Figure 3A, 3C, 3E). The age-standardized mortality rate of 9 HS increased during 1974-1991 (AAPC 0.9, 95% CI 0.1 to1.7) and then decreased
dramatically during 1991-2003 (AAPC -14.5, 95% CI -18.1 to -10.8); the age-standardized
mortality rate of IHD increased dramatically during 1984-1997 and then decreased (AAPC
-1.6, 95% CI -2.1 to -1.1). The age-standardized mortality curves of HS and IHD also
converged at 1997-1998 (Figure 3B, 3D, 3F). The age-standardized mortality rates of IS and
RHD kept decreasing during 1974-2015 (AAPC -2.5, 95% CI -3.1 to -1.8 and AAPC -6.0, 95%
CI -7.1 to -4.9, respectively) (Table S3 in Additional file). Association of SDI with the main causes of CVD death With an increase in SDI, the age-standardized mortality for all CVD declined during the study
period and the regression coefficient (β) was -0.690 (P=4.3×10-7). RHD and hemorrhagic
disease showed gradual declines with an increase of SDI during 1974-2015, with the β value
of -0.927 for RHD, -0.796 for HS, and -0.781 for HD, respectively (all P<0.001). The same
was true for IS (β= -0.684, P=5.9×10-7). However, IHD mortality rates increased with
increasing SDI (β=0.646, P=4.0×10-5). Other causes of CVD deaths did not display
association with the change of SDI (all P>0.05) (Table S4 in Additional file). Age, period and cohort effects on the main causes of CVD death We reclassified the causes of CVD into hemorrhagic disease (HS and HD) and ischemic
disease (IHD and IS), and myocardial valvular diseases (RHD, other forms of heart disease,
and other cardiovascular and circulatory diseases). Deaths from hemorrhagic disease
increased sharply during 1974-1982, increased slightly during 1982-1992, and greatly
decreased after 1992-2000 in the age groups of 50~70 years (Figure 4A1). Deaths from
ischemic disease increased consecutively in the age groups above 70 years (Figure 4B1). Birth cohort analysis indicated that deaths from all CVD increased in population born during
1937-1945 and increased again in those born during 1958-1965 (Figure 4A2, 4B2, 4C2). The
fitting trend of the birth cohort indicated that the risks of death from hemorrhagic disease
increased for 4 fold in the population born during 1885-1920, and then decreased sharply in
the population born after 1935 (Figure 4A3); whereas the risks of death from ischemic
disease increased for 33 fold in the population born during 1885-1935, and then decreased
slightly in the population born after 1935 (Figure 4B3). The data of myocardial valvular
diseases were in a jumble, indicating the heterogenicity in their etiology (Figure 4C3). 10 Burden of CVD death during 1974-2015 SPYLLs of CVD death were 17,187 person years in 1974 and increased in the following 12
years (AAPC 2.1, 95% CI 0.4 to 3.8), then decreased at an annual average rate of 1.8 (95% CI
-2.3 to -1.3) during 1986-2015 (Figure 5A). This reduction mainly came from women
(Figure 5B), not from men (Figure 5C). Using the Shanghai life table as a reference, AYLL
were 13.4 years for CVD deaths. AYLL did not change over time, with a mean change of 0.2
years (95% CI -0.1 to 0.4). PYLLs for IHD kept increasing (Table S5 in Additional file), whereas SPYLLs for IHD kept
stable during 1974-2015 (Table 1), indicating aging is the major determinant. SPYLLs for HS
increased before 1994 and then decreased rapidly during 1994-2005. However, HS and IHD
remained the first 2 causes for SPYLLs and AYLL of CVD in 1974 and subsequent two 20
years (1974-1995 and 1995-2015). RHD was one of the 3 leading causes for SPYLLs and
AYLL in 1974, but fell by annual average percent of -2.6 (95% CI -4.0 to -1.2) during 11 1974-1995 before rapidly falling off after 1995. IS became the 3rd leading cause for SPYLLs
during 1995-2015. The annual average percent of SPYLLs for other forms of heart disease
increased after 1982 (AAPC 4.2, 95% CI 3.0 to 5.4) (Figure 6). Total CVD burden decreased over the 42 years in women. The largest annual percentage
decrease occurred from 1998 to 2001 (AAPC -10.9, 95% CI -19.1 to -1.7), further decreased
at an annual average rate of -3.0 (95% CI -4.7 to -1.3) in the following 15 years. In women,
HS contributed to 30%-50% of CVD SPYLLs before 1998 while HS, IHD and IS became the
3 major sources of CVD SPYLLs after 1998 (Figure 7A). In men, total CVD burden kept
stable during 1974-2015, slightly increased during 1974-1998 and 2001-2015. HS, IHD and
IS remained to be the major causes of CVD SPYLLs during 1974-2015 (Figure 7B). Projecting causes of CVD death in 2025-2029 A total of 16,753 women and 22,690 men are predicted to die of CVD during 2020-2029 in
the study population. The proportion of SCD kept increasing during 1974-2014 and will be
the top cause of CVD death in both sexes during 2025-2029. IHD will be the second leading
cause during 2025-2029 in both sexes. HS and IS, the top 2 causes of CVD death during
1975-1979, will drop to the fifth and fourth causes of CVD death during 2025-2029,
respectively (Figure 8). RHD accounted for less and less CVD death in the 3 consecutive
time periods. chronic diseases, CVD is now the leading cause of mortality and morbidity worldwide Discussion 12
Of the chronic diseases, CVD is now the leading cause of mortality and morbidity worldwide 12 [27]. In this study, we evaluated the trends and burden of major CVD death in a rapidly
developing society. HS, IHD and IS were the top 3 leading causes of CVD death during
1974-2015. These data are useful in elucidating the causes of each CVD. As the leading cause
of CVD immature death, HS death mainly occurred among occupational population aged
35-69 years in both sexes. Except for those unmodifiable HS risk factors include age, sex,
race-ethnicity and genetics, modifiable risk factors such as hypertension, smoking,
waist-to-hip ratio, diet and heavy alcohol consumption were well established [28]. HS is
highly prevalent in LMICs, where the burdens of hypertensive disorders are greater [28]. HS
accounts for <30% of stroke death in USA, whereas it accounts for 30-40% of all stroke death
in China [29]. Alcohol and smoking consumptions have direct relationships with HS. The
consumptions are strongly related to a specific worksite and time of shift, job stressors, and
air pollution [30, 31]. Heavy alcohol and smoking consumptions are linked to hypertension
and poor blood pressure control in hypertensive patients [32, 33]. Air pollution factors such as
nitrogen dioxide and ozone also increase the risk of HS death via increasing the incidence of
hypertension [34-36]. HS death started to decrease from 1995, possibly due to 4 reasons: first,
hypertension was under the control because anti-hypertensives were covered by medical
insurance since 1992; second, effective control of blood pressure owing to the World
Bank-supported mass health program in 1996 decreased HS-related death; third, polluting
industries were removed during the 1980s, which greatly reduced ambient pollution; fourth,
medical insurance and medical reform since 1990 have got initial achievements. IHD, the 2nd cause of CVD-related immature death during 1974-1995, ranked the leading
cause of CVD deaths after 1995, which was in accord with that in the whole Chinese
population [37]. Marked regional differences have been observed in epidemiological trends in
age-standardized mortality of IHD in China. In 2015, the mortality from IHD in Heilongjiang 13 province located in the north east region and Shanghai in the southeast region of China was
187.4 per 100 000 and 44.2 per 100 000, respectively [38]. This difference might be caused
by relatively higher SDI, better health education, and more advanced health care systems in
Shanghai. Discussion The crude mortality of IHD kept increasing in both sexes, possibly because of the
increase in the aged population [10]. Ambient pollution and consumption of red and
processed meat are positively associated with the risk of IHD, possibly because of high serum
non-high-density lipoprotein cholesterol concentration and systolic blood pressure; whereas
regular excise like cycling is inversely associated the risk of IHD [38-41]. The
age-standardized IHD mortality began to decline slowly after 1998 although population in
Shanghai is aging at unprecedented levels since 1995. Improvements in medical service and
healthy lifestyle promotion should be effective in decreasing IHD death. IS has been
associated with low income, low education levels, hypercholesterolemia, physical inactivity,
smoking, and obesity [42-44]. IHD and IS had been recognized as a single type of CVD
called ischemic disease in international guidelines because they shared pathologies and risk
factors, and shared strategies for primary and secondary prevention [18]. Ischemic disease
increased with increased total cholesterol and decreased with elevated high-density
lipoprotein cholesterol [45]. The trend in ischemic disease is affected by population aging,
SDI, lifestyle change, and the quality of medical care. Smoking led to a 63% higher risk of
ischemic disease in urban male smokers [46]. A study of the China Kadoorie Biobank based
on approximate 500,000 Chinese has demonstrated that individuals in the top quintiles of
physical activity have a 23% lower risk of major ischemic events than those in the bottom
quintiles [47]. Compared to people who never or rarely ate fresh fruit, people who consumed
fresh fruit daily had a 34% lower risk of IHD and a 25% lower risk of IS [48]. Total IHD
death had been decreased significantly since the Chinese government issued the “National
Physical Fitness Program” in 1995, pledging sports and health-building services would be 14 aligned with national economic development. Residents in Shanghai kept the habit of daily
consumption of fresh vegetables and fruits during the studied 42 years, the proportion of daily
consumption varied from 34% to 39%, which may contribute to changes in CVD mortality
curves (Figure S2 in Additional file). The mechanisms by which fruits and vegetables
protected CVD death include not only some known bioactive nutrient effects, but also their
functional properties including reducing antioxidant stress, improving plasma lipoproteins,
lowering blood pressure, improving insulin sensitivity, regulating hemostasis [49]. Discussion These
evidences indicate that ischemic CVD should be prevented via improving lifestyles such as
quitting smoking, increasing physical inactivity, and consuming fresh vegetables and fruits. RHD, the main cause of CVD deaths in children and young adults in developing countries,
results from an abnormal autoimmune response to a group A streptococcal infection [50]. Preventive measures, based on antibiotic treatment especially penicillin use, are very efficient. Thus, RHD reflects poor socioeconomic development, resulting in lack of medical resources. With steady socioeconomic growth during 1974-2015 in Shanghai, death from RHD kept
decreasing. Death of CVD (hemorrhagic CVD, ischemic CVD, and myocardial valvular diseases)
increased in population born during 1937-1945 and increased again in those born during
1958-1965. This might be caused by early life malnutrition during the Japanese military
occupation (1937-1945) and the Chinese Famine (1958-1961), respectively. Exposures to
adverse living condition and malnutrition in early life are often associated with metabolic
syndrome in later life and aggravate the association of CVD with hyperglycemia,
hypertension, and type 2 diabetes [51-54]. Thus, nutrition in early life should be important for
the prevention of the major types of CVD in later life. 15 15 Over the 42-year study period, a reduction in the age-standardized CVD mortality was greater
in women than in men. The age-standardized mortality rate and SYPLL of CVD kept
decreasing in women after 1977 and declining sharply after 1998 but did not decline anymore
in men, which is consistent with a previous observation [55]. In the 21st century, HS, IHD
and IS have become the 3 main threats to men lifetime and shown a growing trend, suggesting
that specific research and health strategies of CVD for men need to be brought to attention. This sex disparity is possibly caused by different levels of risk factor exposure. In China, men
are more likely to be exposed to factory air pollution, tobacco smoking and alcohol abuse [56]. Smoking cessation and alcohol restriction should be effective in controlling more
CVD-caused immature death in men. Further, SCD will be the leading cause of CVD during 2025-2029. Discussion This suggests that with the
improvement of medical services, the first episode of CVD rarely lead to death, and turn into
sequelae stage, which will prolong lifetime but may reduce the healthy life year, it also
weakens the quality of life and aggravates the burden, hence the urgent need for effective
rehabilitation care in the future to prevent disability caused by sequelae of CVD. This study has major strengths including a stable and large sample size population, a social
context of rapid economic development and intensive change of policies, and stringent
mortality ascertainment. However, there are certain limitations to be acknowledged. First,
although death registration in Yangpu is one of the high-quality systems in China, the death
certification was too precise to assign CVD subtypes using ICD codes, only 7 causes of CVD
deaths were demonstrated, other CVD subtypes were grouped as “other cardiovascular and
circulatory diseases”. Second, lifestyle, disease history, and medical care data were not 16 included in this system, so it was impossible to quantitate the associations of the risk factors
with CVD death. Conclusively, although the trends in cause-specific mortality and burden of CVD in urban
Shanghai have generally declined during 1974-2015,the threat of CVD to human life is still
the primary concern. Exposure to adverse event and malnutrition in early life contributed to
an increase in CVD death. It is necessary to improve air quality, strengthen health education,
advocate smoking cessation, restrict alcohol consumption, and popularize reasonable diet. Medical insurance and medical reform are important for the prevention and control of CVD
death. Effective rehabilitation is needed to prevent the disability caused by sequelae of CVD. Supplementary information All the additional files in Supplementary information affiliated to this paper are deposited in
the journal website. Author details 1 Shanghai East Hospital, Key Laboratory of Arrhythmias, Ministry of Education, School of
Medicine, Tongji University, Shanghai, China; 2 Division of Chronic Diseases, Center for
Disease Control and Prevention of Yangpu District, Shanghai, China; 3 Division of Chronic
Diseases, Center for Disease Control and Prevention of Hongkou District, Shanghai, China;
4 Department of Epidemiology, Second Military Medical University, Shanghai, China. Conclusions Exposure to serious malnutrition in early life might increase CVD mortality in later life. Improvements in medical services, pollution control, and lifestyle could decrease CVD death. New strategy is needed to prevent the aging-related CVD death and burden in the future. 17 Abbreviations AAPC: average annual percentage change; APC: age-period-cohort; AYLL: average years of
life lost; CVD: Cardiovascular disease; CI: confidence interval; ICD: International
Classification of Disease; IHD: ischemic heart disease; HD: hypertensive disease; HS:
hemorrhagic stroke; IS: ischemic stroke; LMICs: low- and middle-income countries; PYLL:
Person years of life lost; RHD rheumatic heart disease; SCD: sequelae of cerebrovascular
disease; SDI: Sociodemographic Index; SPYLLs: age-standardized person years of life loss
per 100,000 persons; Ethics approval and consent to participate The study was performed in accordance with the 2000 Declaration of Helsinki and was
approved by the ethics committee of the Naval Medical University. 18 Funding This work was supported by the National Key Basic Research Program (973 program) of
China (2015CB554000 to GC) and the National Natural Science Foundation of China
(91529305, 81520108021, 81673250, and 81521091 to GC; 81872720 to LJ Z). The study
was completed by the author independently, and the funding unit did not intervene. Authors’ contributions GC presented the study concept, designed the study, and revised and finalized the manuscript. LZ, QL,WL and SW analyzed the data and drafted the manuscript. XH provided the original
data. YD, TZ, JZ, XT,and RZ took parts in organizing original data. PL, YC, JL, and JL joined
the statistical analysis. All authors read the manuscript and approved the submission. Consent for publication Not applicable. Competing interests The authors declare that they have no competing interests. Availability of data and materials All the data are provided in the manuscript and additional file. Acknowledgements Not applicable. 19 20 20 References 1. Collaborators GBDCoD, Naghavi M, Abajobir AA, Abbafati C, Abbas KM,
Abd-Allah F, Abera SF, Aboyans V, Adetokunboh O, Afshin A et al: Global, regional,
and national age-sex specific mortality for 264 causes of death, 1980-2016: a
systematic analysis for the Global Burden of Disease Study 2016. Lancet 2017,
390(10100):1151-1210. 1. Collaborators GBDCoD, Naghavi M, Abajobir AA, Abbafati C, Abbas KM,
Abd-Allah F, Abera SF, Aboyans V, Adetokunboh O, Afshin A et al: Global, regional,
and national age-sex specific mortality for 264 causes of death, 1980-2016: a
systematic analysis for the Global Burden of Disease Study 2016. Lancet 2017,
390(10100):1151-1210. 2. Collaborators GBDCoD: Global, regional, and national age-sex-specific mortality for
282 causes of death in 195 countries and territories, 1980-2017: a systematic analysis
for the Global Burden of Disease Study 2017. Lancet 2018, 392(10159):1736-1788. 2. Collaborators GBDCoD: Global, regional, and national age-sex-specific mortality for
282 causes of death in 195 countries and territories, 1980-2017: a systematic analysis
for the Global Burden of Disease Study 2017. Lancet 2018, 392(10159):1736-1788. 3. Bansilal S, Castellano JM, Fuster V: Global burden of CVD: focus on secondary
prevention of cardiovascular disease. Int J Cardiol 2015:7. 4. Bowry AD, Lewey J, Dugani SB, Choudhry NK: The Burden of Cardiovascular
Disease in Low- and Middle-Income Countries: Epidemiology and Management. Can
J Cardiol 2015, 31(9):1151-1159. 5. Lear SA, Hu W, Rangarajan S, Gasevic D, Leong D, Iqbal R, Casanova A,
Swaminathan S, Anjana RM, Kumar R et al: The effect of physical activity on
mortality and cardiovascular disease in 130 000 people from 17 high-income,
middle-income, and low-income countries: the PURE study. Lancet 2017,
390(10113):2643-2654. 5. Lear SA, Hu W, Rangarajan S, Gasevic D, Leong D, Iqbal R, Casanova A,
Swaminathan S, Anjana RM, Kumar R et al: The effect of physical activity on
mortality and cardiovascular disease in 130 000 people from 17 high-income,
middle-income, and low-income countries: the PURE study. Lancet 2017,
390(10113):2643-2654. 6. Yusuf S, Joseph P, Rangarajan S, Islam S, Mente A, Hystad P, Brauer M, Kutty VR,
Gupta R, Wielgosz A et al: Modifiable risk factors, cardiovascular disease, and
mortality in 155 722 individuals from 21 high-income, middle-income, and
low-income
countries
(PURE):
a
prospective
cohort
study. Lancet
2020;395(10226):795-808.. 6. References Yusuf S, Joseph P, Rangarajan S, Islam S, Mente A, Hystad P, Brauer M, Kutty VR,
Gupta R, Wielgosz A et al: Modifiable risk factors, cardiovascular disease, and
mortality in 155 722 individuals from 21 high-income, middle-income, and
low-income
countries
(PURE):
a
prospective
cohort
study. Lancet
2020;395(10226):795-808.. 21 21 7. Teo KK, Dokainish H: The Emerging Epidemic of Cardiovascular Risk Factors and
Atherosclerotic Disease in Developing Countries. Can J Cardiol 2017, 33(3):358-365. 8. McN G, Coale AJ: Rapid Population Change in China, 1952-1982. Population and
Development Review 1984, 10(4):1. 9. Wu Y, Benjamin EJ, MacMahon S: Prevention and Control of Cardiovascular Disease
in the Rapidly Changing Economy of China. Circulation 2016, 133(24):2545-2560. 10. National Bureau of Statistics of People’s Republic of China. China life expectancy. http://datastatsgovcn/easyqueryhtm?cn=C01&zb=A0304&sj=2014 Accessed July 20,
2015. 11. Fang EF, Scheibye-Knudsen M, Jahn HJ, Li J, Ling L, Guo H, Zhu X, Preedy V, Lu H,
Bohr VA et al: A research agenda for aging in China in the 21st century. Ageing Res
Rev 2015, 24(Pt B):197-205. 12. Snider G, Carter E, Clark S, Tseng JTW, Yang X, Ezzati M, Schauer JJ, Wiedinmyer C,
Baumgartner J: Impacts of stove use patterns and outdoor air quality on household air
pollution and cardiovascular mortality in southwestern China. Environ Int 2018,
117:116-124. 13. Chen R, Samoli E, Wong C-M, Huang W, Wang Z, Chen B, Kan H, Group CC:
Associations between short-term exposure to nitrogen dioxide and mortality in 17
Chinese cities: the China Air Pollution and Health Effects Study (CAPES). Environ Int
2012, 45:32-38. 14. Bundy JD, He J: Hypertension and Related Cardiovascular Disease Burden in China. Ann Glob Health 2016, 82(2):227-233. 22
15. Pan XR, Yang WY, Li GW, Liu J: Prevalence of diabetes and its risk factors in China,
1994. National Diabetes Prevention and Control Cooperative Group. Diabetes Care 22 1997, 20(11):1664-1669. 16. Shi Z: Prevalence of diabetes among men and women in China. The New England
journal of medicine 2010, 362(25):2425; author reply 2426. 17. Wu Y: Overweight and obesity in China. BMJ (Clinical research ed ) 2006,
333(7564):362-363. 18. Zhao D, Liu J, Wang M, Zhang X, Zhou M: Epidemiology of cardiovascular disease in
China: current features and implications. Nat Rev Cardiol 2019, 16(4):203-212. 19. Statistics
SBo:
Shanghai
Statistical
Yearbook
[DB/OL]. Available
from:
http://wwwstats-shgovcn/ 2016. 20. References Yang G, Kong L, Zhao W, Wan X, Zhai Y, Chen LC, Koplan JP: Emergence of chronic
non-communicable diseases in China. Lancet 2008, 372(9650):1697-1705. 21. Wang S, Du X, Han X, Yang F, Zhao J, Li H, Li M, Zhang H, Liu W, Song J et al:
Influence of socioeconomic events on cause-specific mortality in urban Shanghai,
China, from 1974 to 2015: a population-based longitudinal study. CAMJ 2018,
190(39):E1153-E1161. 22. Roth GA, Johnson CO, Nguyen G, Naghavi M, Feigin VL, Murray CJ, Forouzanfar
MH, Vos T: Methods for Estimating the Global Burden of Cerebrovascular Diseases. Neuroepidemiology 2015, 45(3):146-151. 23. Kim HJ, Fay MP, Feuer EJ, Midthune DN: Permutation tests for joinpoint regression
with applications to cancer rates. Stat Med 2000, 19(3):335-351. 24. Mortality GBD, Causes of Death C: Global, regional, and national life expectancy,
all-cause mortality, and cause-specific mortality for 249 causes of death, 1980-2015: a
systematic analysis for the Global Burden of Disease Study 2015. Lancet 2016, 23 388(10053):1459-1544. 388(10053):1459-1544. 25. Clayton D, Schifflers E: Models for temporal variation in cancer rates. II:
Age-period-cohort models. Stat Med 1987, 6(4):469-481. 26. Caceres MO, Caceres-Saez I: Random Leslie matrices in population dynamics. J Math
Biol 2011, 63(3):519-556. 27. Joseph P, Leong D, McKee M, Anand SS, Schwalm JD, Teo K, Mente A, Yusuf S:
Reducing the Global Burden of Cardiovascular Disease, Part 1: The Epidemiology and
Risk Factors. Circulation research 2017, 121(6):677-694. 28. Boehme AK, Esenwa C, Elkind MSV: Stroke Risk Factors, Genetics, and Prevention. Circ Res 2017, 120(3):472-495. 29. Zhang L-F, Yang J, Hong Z, Yuan G-G, Zhou B-F, Zhao L-C, Huang Y-N, Chen J, Wu
Y-F, Collaborative Group of China Multicenter Study of Cardiovascular E: Proportion
of different subtypes of stroke in China. Stroke 2003, 34(9):2091-2096. 30. Ragland DR, Greiner BA, Krause N, Holman BL, Fisher JM: Occupational and
nonoccupational correlates of alcohol consumption in urban transit operators. Prev
Med 1995, 24(6):634-645. 31. Xu L, Schooling CM, Chan WM, Lee SY, Leung GM, Lam TH: Smoking and
hemorrhagic stroke mortality in a prospective cohort study of older Chinese. Stroke
2013, 44(8):2144-2149. 32. Rantakomi SH, Laukkanen JA, Sivenius J, Kauhanen J, Kurl S: Alcohol consumption
and the risk of stroke among hypertensive and overweight men. J Neurol 2013,
260(2):534-539. 33. Kelly TN, Gu D, Chen J, Huang J-F, Chen J-C, Duan X, Wu X, Chen C-S, He J: 24 Cigarette smoking and risk of stroke in the chinese adult population. Stroke 2008,
39(6):1688-1693. 34. Wilker EH, Mostofsky E, Fossa A, Koutrakis P, Warren A, Charidimou A, Mittleman
MA, Viswanathan A: Ambient Pollutants and Spontaneous Intracerebral Hemorrhage
in Greater Boston. Stroke 2018:2764-2766. 35. Bo Y, Guo C, Lin C, Chang LY, Chan TC, Huang B, Lee KP, Tam T, Lau AKH, Lao
XQ et al: Dynamic Changes in Long-Term Exposure to Ambient Particulate Matter
and Incidence of Hypertension in Adults. Hypertension 2019, 74(3):669-677. 36. Han MH, Yi HJ, Kim YS, Kim YS: Effect of seasonal and monthly variation in
weather and air pollution factors on stroke incidence in Seoul, Korea. Stroke 2015,
46(4):927-935. 37. Yang G, Wang Y, Zeng Y, Gao GF, Liang X, Zhou M, Wan X, Yu S, Jiang Y, Naghavi
M et al: Rapid health transition in China, 1990-2010: findings from the Global Burden
of Disease Study 2010. Lancet 2013, 381(9882):1987-2015. 38. 388(10053):1459-1544. Zhang G, Yu C, Zhou M, Wang L, Zhang Y, Luo L: Burden of Ischaemic heart disease
and attributable risk factors in China from 1990 to 2015: findings from the global
burden of disease 2015 study. BMC Cardiovasc Disord 2018, 18(1):18. 39. Key TJ, Appleby PN, Bradbury KE, Sweeting M, Wood A, Johansson I, et al. Consumption of Meat, Fish, Dairy Products, and Eggs and Risk of Ischemic Heart
Disease. Circulation 2019;139(25):2835-45. 40. Fan M, Lv J, Yu C, Guo Y, Bian Z, Yang S, et al. Association Between Active Commuting
and Incident Cardiovascular Diseases in Chinese: A Prospective Cohort Study. J Am
Heart Assoc 2019;8(20):e012556. 25 Crossover Study of the Association of Outdoor Ambient Air Pollution With the Risk of
Acute Myocardial Infarction in the Context of Seasonal Exposure to the Southeast
Asian Haze Problem. J Am Heart Assoc. 2019;8(6):e011272. Crossover Study of the Association of Outdoor Ambient Air Pollution With the Risk of
Acute Myocardial Infarction in the Context of Seasonal Exposure to the Southeast
Asian Haze Problem. J Am Heart Assoc. 2019;8(6):e011272. 42. O'Donnell MJ, Xavier D, Liu L, Zhang H, Chin SL, Rao-Melacini P, Rangarajan S, Islam
S, Pais P, McQueen MJ et al: Risk factors for ischaemic and intracerebral
haemorrhagic stroke in 22 countries (the INTERSTROKE study): a case-control study. Lancet 2010, 376(9735):112-123. 42. O'Donnell MJ, Xavier D, Liu L, Zhang H, Chin SL, Rao-Melacini P, Rangarajan S, Islam
S, Pais P, McQueen MJ et al: Risk factors for ischaemic and intracerebral
haemorrhagic stroke in 22 countries (the INTERSTROKE study): a case-control study. Lancet 2010, 376(9735):112-123. 43. Wang Y, Liao X, Zhao X, Wang DZ, Wang C, Nguyen-Huynh MN, Zhou Y, Liu L,
Wang X, Liu G et al: Using recombinant tissue plasminogen activator to treat acute
ischemic stroke in China: analysis of the results from the Chinese National Stroke
Registry (CNSR). Stroke 2011, 42(6):1658-1664. 44. Liu L, Wang D, Wong KS, Wang Y: Stroke and stroke care in China: huge burden,
significant workload, and a national priority. Stroke 2011, 42(12):3651-3654. 45. Tirschwell DL, Smith NL, Heckbert SR, Lemaitre RN, Longstreth WT, Jr., Psaty BM:
Association of cholesterol with stroke risk varies in stroke subtypes and patient
subgroups. Neurology 2004, 63(10):1868-1875. 46. Du H, Li L, Bennett D, Guo Y, Key TJ, Bian Z, Sherliker P, Gao H, Chen Y, Yang L et 388(10053):1459-1544. Chen Z, Peto R, Zhou M, Iona A, Smith M, Yang L, Guo Y, Chen Y, Bian Z, Lancaster
G et al: Contrasting male and female trends in tobacco-attributed mortality in China:
evidence from successive nationwide prospective cohort studies. Lancet 2015,
386(10002):1447-1456. 47. Bennett DA, Du H, Clarke R, Guo Y, Yang L, Bian Z, Chen Y, Millwood I, Yu C, He P
et al: Association of Physical Activity With Risk of Major Cardiovascular Diseases in
Chinese Men and Women. JAMA Cardiol 2017, 2(12):1349-1358. 48. Du H, Li L, Bennett D, Guo Y, Key TJ, Bian Z, Sherliker P, Gao H, Chen Y, Yang L et 26
48. Du H, Li L, Bennett D, Guo Y, Key TJ, Bian Z, Sherliker P, Gao H, Chen Y, Yang L et 26 al: Fresh Fruit Consumption and Major Cardiovascular Disease in China. The New
England journal of medicine 2016, 374(14):1332-1343. 49. Alissa EM, Ferns GA: Dietary fruits and vegetables and cardiovascular diseases risk. Crit Rev Food Sci Nutr 2017, 57(9):1950-1962. 50. Marijon E, Mirabel M, Celermajer DS, Jouven X: Rheumatic heart disease. Lancet
2012, 379(9819):953-964. 51. Zhang Y, Ying Y, Zhou L, Fu J, Shen Y, Ke C: Exposure to Chinese famine in early
life modifies the association between hyperglycaemia and cardiovascular disease. Nutr
Metab Cardiovasc Dis 2019, 29(11):1230-1236. 52. Shi Z, Ji L, Ma RCW, Zimmet P: Early life exposure to 1959-1961 Chinese famine
exacerbates association between diabetes and cardiovascular disease. J Diabetes 2020,
12(2):134-141. 53. Shi Z, Nicholls SJ, Taylor AW, Magliano DJ, Appleton S, Zimmet P: Early life
exposure to Chinese famine modifies the association between hypertension and
cardiovascular disease. J Hypertens 2018, 36(1):54-60. 54. Han C, Hong YC: Fetal and childhood malnutrition during the Korean War and
metabolic syndrome in adulthood. Nutrition 2019, 62:186-193. 55. Wang W, Jiang B, Sun H, Ru X, Sun D, Wang L, Wang L, Jiang Y, Li Y, Wang Y et al:
Prevalence, Incidence, and Mortality of Stroke in China: Results from a Nationwide
Population-Based Survey of 480 687 Adults. Circulation 2017, 135(8):759-771. 56. Li Q, Hsia J, Yang G: Prevalence of smoking in China in 2010. N Engl J Med 2011,
364(25):2469-2470. 27 27 Figure Legends Figure Legends Figure 1. Proportion of age-standardized mortality rates per 100,000 persons for major CVD
causes in Yangpu, Shanghai, China, 1974-2015 Figure 2. Average age of the residents died of each subtype of cardiovascular diseases in
Yangpu district, Shanghai, China, 1974-2015
Note: AAPC, average annual percentage change Figure 2. Average age of the residents died of each subtype of cardiovascular diseases in
Yangpu district, Shanghai, China, 1974-2015 Figure 2. Average age of the residents died of each subtype of cardiovascular diseases in
Yangpu district, Shanghai, China, 1974-2015
Note: AAPC, average annual percentage change Note: AAPC, average annual percentage change Figure 3. Trends in crude and age-standardized mortality rates for major cause of CVD death
in both sexes in Yangpu, Shanghai, China, 1974-2015 Note: (A) trend in crude mortality rates of all residents; (B) trend in age-standardized
mortality rates of all residents; (C) trend in crude mortality rates of women; (D) trend in
age-standardized mortality rates of women; (E) trend in crude mortality rates of men; (F)
trend in age-standardized mortality rates of men. Figure 4. Age-specific mortality rates (per 100,000) by period and birth cohort and age,
period, and cohort effects for the mortality rates of major CVD in Yangpu, Shanghai, China,
1974-2015 Note: Each row of plots, from left to right, are age-specific mortality rates by period,
age-specific mortality by birth cohort, and an age-period-cohort Poisson (APC) regression
plot. The APC regression plot has 3 curves depicting, from left to right, trends in mortality
rate by age (yr) for the reference birth cohort (1949), the risk ratio of the cohort effect 28 compared with the reference birth cohort (1949), and the risk ratio of the calendar period
effect compared with the reference cohort (1980). Dotted lines show the 95% confidence
intervals of the 3 components (solid lines). compared with the reference birth cohort (1949), and the risk ratio of the calendar period
effect compared with the reference cohort (1980). Dotted lines show the 95% confidence
intervals of the 3 components (solid lines). Figure 5. Trends of age-standardized CVD person years of life lost (SPYLLs) per 100,000
persons in Yangpu district, Shanghai, China, 1974-2015 Note: Solid lines, mean value; dotted lines, standard error. Figure 6. Main causes of CVD SPYLLs and AYLL for 1974, 1995, and 2015, with change in
AYLL and percent change in SPYLLs in Yangpu, Shanghai, China Note: Solid lines are “increases” and dashed lines are “decreases”. Figure Legends For the time period
1974-1995 and 1995-2015, two measures of change are shown: percent change in SPYLLs,
change in SPYLLs, change in AYLL. Statistically significant changes are shown with *. SPYLLs=age-standardized person years of life lost. AYLL=average years of life lost. Figure 7. Age-standardized CVD person years of life lost (SPYLLs) per 100,000 persons of
the major causes of CVD death in both sexes in Yangpu district, Shanghai, China, 1974-2015. Figure 8. Pie charts of cause-specific CVD death in women and men from 1976 to 1980 and
from 2011 to 2015, and predicted from 2025 to 2030, scaled to the number of deaths during
each period, (A) for women; (B) for men. 29
|
https://openalex.org/W3036406937
|
https://scholars.direct/Articles/orthopedic-surgery/jost-3-022.pdf?jid=orthopedic-surgery
|
English
| null |
Salvage Procedure Salvaged by External Fixation: A Case Report
|
Journal of orthopedic surgery and techniques
| 2,020
|
cc-by
| 2,066
|
Keywords One-bone forearm, Distal radio-ulnar joint, External fixation, Forearm non-union, Darrach failure List of Abreviations
DRUJ: Distal Radio-Ulnar Joint; OBF: One-Bone Forearm List of Abreviations
DRUJ: Distal Radio-Ulnar Joint; OBF: One-Bone Forearm List of Abreviations
DRUJ: Distal Radio-Ulnar Joint; OBF: One-Bone Forearm List of Abreviations Salvage Procedure Salvaged by External Fixation: A Case
Report Ingrid Tuzi1*, Nader Chahidi2 and Konstantinos Drossos2
1Faculty of Medicine, Free University of Brussels (ULB), Belgium
2Centre for Hand Surgery, Park Leopold Medical Centre, Belgium Journal of Orthopedic Surgery and Techniques
Vol 3 | Issue 1 | Pages 120-122
ISSN: 2578-7187 Journal of Orthopedic Surgery and Techniques
Vol 3 | Issue 1 | Pages 120-122
ISSN: 2578-7187 Vol 3 | Issue 1 | Pages 120-122 Journal of Orthopedic Surgery and Techniques ISSN: 2578-7187 Abstract Background: The one-bone forearm is a salvage procedure that can be used in chronic distal radio-ulnar joint instability,
therefore sacrificing pronation-supination in order to reduce pain. Failed consolidation is a common complication and
associated with several risk factors. Many authors insist on the need for rigid fixation, combining bone grafting, internal
fixation and external fixation together when faced with complicated upper-limb reconstruction. Case presentation: A 56-year-old woman presents chronic right-forearm pain following serious trauma to the distal
radio-ulnar joint. Multiple surgical interventions were performed, including a Darrach procedure, extensive resection
of the distal ulna, and latero-lateral arthrodesis. Several years later in 2017, considering the persistence of symptoms
and the limited amount of alternative solutions, reconstruction using the one-bone forearm salvage procedure was
performed. However, consolidation was not successfully achieved until the third retake, when an external fixator was
used instead of an above-elbow plaster cast to immobilize the forearm after surgery. Conclusion: Our hypothesis is that the new biomechanical constraints created in a one-bone forearm can be so high that
they exceed the stabilizing capacities of an internal plate and traditional plaster cast, resulting in repeated non-union. Systematic use of an external fixator would therefore ensure optimal consolidation and avoid such complications. Background dure or radio-ulnar fusion. They were able to identify several
factors associated with poor results (including non-union):
Traumatic primary pathology, ≥ 2 previous major reconstruc-
tive procedures, severe nerve injury, and previous infection. Jacoby, et al. [5] report a similar non-union rate of 37.5% in 8
patients after an OBF procedure, with an average of 4.2 previ-
ous procedures for patients with non-union compared to 3.4
for patients with union. They equally suggest that smoking
and the type of osteotomy (transverse vs. oblique) could play
a role in bone union. Initially used to treat complicated post-traumatic forearm
injuries, the one-bone forearm (OBF) is an unconventional
yet effective solution to a variety of complicated situations
involving chronic pain and instability of the forearm. Despite
acceptable functional and esthetical results [1-3], it remains
a salvage technique that should not be the first line of treat-
ment for the simple reason that it eliminates forearm prona-
tion/supination. This loss of supination/pronation, though seemingly rad-
ical at first, is a small sacrifice that restores forearm stability
and use of the hand, ultimately improving one’s quality of life. Patients are also able to adapt by using the shoulder joint in
order to partially compensate this loss of range of motion [4]. The exact fusion angle is chosen based on the patient’s life-
style and personal preferences, and cannot be determined by
a surgical team alone, despite various recommendations [4]. *Corresponding author: Ingrid Tuzi, Faculty of Medicine, Free
University of Brussels (ULB), Belgium
Accepted: May 21, 2020
Published online: May 23, 2020
Citation: Tuzi I, Chahidi N, Drossos K (2020) Salvage Procedure
Salvaged by External Fixation: A Case Report. J Orthop Surg
Tech 3(1):120-122
Open Access | Page 120 |
© 2020 Tuzi I, et al. This is an open-access article distributed under the terms of
e Commons Attribution License, which permits unrestricted use, distribution, and i
n in any medium, provided the original author and source are credited. Scholarly Pages
SCHOLARS.DIRECTi
the hand, ultimately improving one’s quality of life. e also able to adapt by using the shoulder joint in
artially compensate this loss of range of motion [4]. fusion angle is chosen based on the patient’s life-
ersonal preferences, and cannot be determined by
eam alone, despite various recommendations [4]. consolidation of the OBF is a common complica-
son, et al. Background Figure 1: Persistence of a significant gap between the ulnar stump and the mid-radial diaphysis (1A; September 2008). Significant
displacement of the hard ware (1B; January 2017). Broken internal plate after the patient’s fall (1C; June 2017). Internal and external
osteosynthes is with early signs of consolidation (1D; July 2017). End result after consolidation of the one-bone forearm (1E; July 2018). One-month later, X-ray images showed no signs of consol-
idation and significant displacement of the internal hardware
(Figure 1B). The same procedure was repeated using a longer
plate, but in June 2017, despite continued immobilisation,
the internal plate failed following a fall (Figure 1C). Though several authors emphasize the importance of
bone grafting [4], the most important factor for any bone
union is correct osteosynthesis. When considering the OBF,
Jacoby, et al. [5] conclude that “it is difficult to recommend
one form of internal fixation over another because of reports
based on small case series, heterogeneous patient popu-
lations, and differences in outcome assessment tools”. Our
case shows that internal osteosynthesis a lone, even when
combined with an above-elbow plaster cast, is not sufficient. After the third retake, an external fixator was used for
more rigid immobilisation. Early signs of consolidation were
visible on X-ray images just one month later (Figure 1D) and
complete consolidation was achieved by January 2018 (Figure
1E). One year later, the patient is extremely satisfied with the
results. Bessy, et al. [1] insist on the need for rigid fixation with
bone grafting, and use an external fixator in combination with
internal osteosynthesis techniques in two cases of complex
upper member reconstruction. Dell and Sheppard recognize
the potential importance of such external fixation, stating
that “an external fixator is essential to supplement the recog-
nized marginal internal fixation” [6]. Case Presentation A 56-year-old woman presents chronic right-forearm pain
after an aggression resulted in important distal radio-ulnar
joint (DRUJ) instability. Following the initial Darrach proce-
dure, she developed painful ulnar impingement and increased
forearm instability. Multiple retakes including soft-tissue re-
construction, further ulnar resection, and latero-lateral ar-
throdesis were unsuccessful (Figure 1A). Background [4] found a primary non-union rate of
patients having undergone either an OBF proce- *Corresponding author: Ingrid Tuzi, Faculty of Medicine, Free
University of Brussels (ULB), Belgium
Accepted: May 21, 2020
Published online: May 23, 2020
Citation: Tuzi I, Chahidi N, Drossos K (2020) Salvage Procedure
Salvaged by External Fixation: A Case Report. J Orthop Surg
Tech 3(1):120-122
Open Access | Page 120 |
uted under the terms of
ed use, distribution, and
e credited. Scholarly Pages
SCHOLARS.DIRECT *Corresponding author: Ingrid Tuzi, Faculty of Medicine, Free
University of Brussels (ULB), Belgium
Accepted: May 21, 2020
Published online: May 23, 2020
Citation: Tuzi I, Chahidi N, Drossos K (2020) Salvage Procedure
Salvaged by External Fixation: A Case Report. J Orthop Surg
Tech 3(1):120-122 *Corresponding author: Ingrid Tuzi, Faculty of Medicine, Free
University of Brussels (ULB), Belgium Citation: Tuzi I, Chahidi N, Drossos K (2020) Salvage Procedure
Salvaged by External Fixation: A Case Report. J Orthop Surg
Tech 3(1):120-122 Failed consolidation of the OBF is a common complica-
tion. Peterson, et al. [4] found a primary non-union rate of
32% in 19 patients having undergone either an OBF proce- Copyright: © 2020 Tuzi I, 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. Scholarly Pages
SCHOLARS.DIRECT Open Access | Page 120 | Open Access | Page 120 | Citation: Tuzi I, Chahidi N, Drossos K (2020) Salvage Procedure Salvaged by External Fixation: A Case Report. J Orthop Surg Tech 3(1):120-122 Figure 1: Persistence of a significant gap between the ulnar stump and the mid-radial diaphysis (1A; September 2008). Significant
displacement of the hard ware (1B; January 2017). Broken internal plate after the patient’s fall (1C; June 2017). Internal and external
osteosynthes is with early signs of consolidation (1D; July 2017). End result after consolidation of the one-bone forearm (1E; July 2018). Figure 1: Persistence of a significant gap between the ulnar stump and the mid-radial diaphysis (1A; September 2008). Significant
displacement of the hard ware (1B; January 2017). Broken internal plate after the patient’s fall (1C; June 2017). Internal and external
osteosynthes is with early signs of consolidation (1D; July 2017). End result after consolidation of the one-bone forearm (1E; July 2018). Declaration of Interests None. Our team was consulted in September 2016 and the one-
bone forearm (OBF) salvage procedure was performed in
January 2017. Forearm bones were exposed using ananteri-
or Henry approach, the ulnar stump was slightly shortened
and the proximal radial diaphysis was partially resected, then
the proximal ulna and distal radius was joined end-to-end at
40° of pronation. A compressive plate with 3.5 mm diame-
ter screws ensured solid internal osteosynthesis, cancellous
bone graft was packed in the junction, and an above-elbow
plaster cast was used for post-operative immobilisation. Conclusion Our hypothesis is that the new biomechanical constraints
created by the OBF procedure can be so high that they exceed
the stabilizing capacities of an internal plate and traditional
plaster cast, resulting in repeated non-union. This is espe-
cially true for patients with traumatic aetiology or multiples
previous surgical procedures, where bone vascularisation has
been compromised by scar tissue. Considering that the OBF
is a salvage procedure, most patients belong to this category,
therefore we recommend immediate external fixation in all
patients. Tuzi et al. J Orthop Surg Tech 2020, 3(1):120-122 1. Bessy H, Leemrijse Th, Cadot B, et al. (1996) La reconstruction
des pertes de substance osseuse de l’avant-bras par cubitalisa-
tion du radius (one bone forearm) : A propos de six observations.
Ann Chir Main Memb Supér 15: 199-211. 2. Kim SY, Chim H, Bishop AT, et al. (2017) Complications and out-
comes of one-bone forearm reconstruction. Hand (N Y) 12: 140-
144. 3. Tong CWC, Hung LK, Cheng JCY (1998) Lengthening of a one-
bone forearm: a sequel of neonatal osteomyelitis. J Hand Surg
Br 23: 453-456. 5. Jacoby SM, Bachoura A, DiPrinzio EV, et al. (2013) Complications
Following One-Bone Forearm Surgery for Posttraumatic Forearm
and Distal Radioulnar Joint Instability. J Hand Surg Am 38: 976-
982. 4. Peterson CA, Maki S, Wood MB (1995) Clinical results of the one-
bone forearm. J Hand Surg Am 20: 609-618. 6. Dell PC, Sheppard JE (1984) Vascularized bone grafts in the treat-
ment of infected forearm nonunions. J Hand Surg Am 9: 653-658. Citation: Tuzi I, Chahidi N, Drossos K (2020) Salvage Procedure Salvaged by External Fixation: A Case Report. J Orthop Surg Tech 3(1):120-122 Tuzi et al. J Orthop Surg Tech 2020, 3(1):120-122 References 1. Bessy H, Leemrijse Th, Cadot B, et al. (1996) La reconstruction
des pertes de substance osseuse de l’avant-bras par cubitalisa-
tion du radius (one bone forearm) : A propos de six observations. Ann Chir Main Memb Supér 15: 199-211. 2. Kim SY, Chim H, Bishop AT, et al. (2017) Complications and out-
comes of one-bone forearm reconstruction. Hand (N Y) 12: 140-
144. Open Access | Page 121 | Tuzi et al. J Orthop Surg Tech 2020, 3(1):120-122 Tuzi et al. J Orthop Surg Tech 2020, 3(1):120-122
Open Access | Page 122 |
Copyright: © 2020 Tuzi I, 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. SCHOLARS.DIRECT
DOI: 10.36959/453/533 DOI: 10.36959/453/533 Copyright: © 2020 Tuzi I, 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 Tuzi I, 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. SCHOLARS.DIRECT Tuzi et al. J Orthop Surg Tech 2020, 3(1):120-122 Open Access | Page 122 |
|
https://openalex.org/W1998900332
|
https://europepmc.org/articles/pmc4258650?pdf=render
|
English
| null |
Development of hybrid materials based on sponge supported reduced graphene oxide and transition metal hydroxides for hybrid energy storage devices
|
Scientific reports
| 2,014
|
cc-by
| 8,034
|
OPEN Received
11 September 2014
Accepted
11 November 2014
Published
8 December 2014 Deepak P. Dubal1,2, Rudolf Holze2 & Pedro Gomez-Romero1,3 1Catalan Institute of Nanoscience and Nanotechnology, CIN2, ICN2 (CSIC-ICN), Campus UAB, E-08193 Bellaterra, Barcelona,
Spain, 2Technische Universita¨t Chemnitz, Institut fu¨r Chemie, AG Elektrochemie, D-09107 Chemnitz, Germany, 3Consejo Superior
de Investigaciones Cientı´ficas (CSIC), Spain. Earnest efforts have been taken to design hybrid energy storage devices using hybrid electrodes based on
capacitive (rGO) and pseudocapacitive (Ni(OH)2 and Co(OH)2) materials deposited on the skeleton of 3D
macroporous (indicate sponge material) sponge support. Conducting framework was formed by coating
rGO on macroporous sponge on which subsequent deposition of Ni(OH)2 and Co(OH)2 was carried out. The synergetic combination of rGO and Ni(OH)2 or Co(OH)2) provides dual charge-storing mechanisms
whereas 3D framework of sponge allows excellent accessibility of electrolyte to hybrid electrodes. Moreover,
to further increase the energy density, hybrid devices have been fabricated with SP@rGO@Ni or SP@rGO@
Co and SP@rGO as positive and negative electrodes, respectively. These hybrid devices operate with
extended operating voltage windows and achieve remarkable electrochemical supercapacitive properties
which make them truly promising energy storage devices for commercial production. Correspondence and
requests for materials
should be addressed to
D.P.D. (dubaldeepak2@
gmail.com) or P.G.-R. (pedro.gomez@cin2. es) N N
owadays, energy-related science and technology are benefiting from a big tsunami of hybridization,
starting from hybrid materials to hybrid devices1. In hybrid materials, there are synergistic effects of
materials properties whereas hybrid devices combine the different mechanisms of devices in a single one. The field of hybrid energy storage devices is no exception. Among different energy storage systems playing on the
chessboard of Ragone plot, supercapacitors are getting increasing attention from scientists and industrialists alike
due to their excellent performance at high power rates2,3. Indeed, supercapacitors are intrinsically well suited to
provide high power density by storing charge non-faradically at the electrode/electrolyte interface (electrochem-
ical double layer capacitor, EDLC) or through redox mechanism at the electrode surface (pseudocapacitor) hence
allowing for high power, fast charge-discharge rates and excellent cycling life4. As we look back, supercapacitors
are highly effective and are integrated in many of our daily-live applications from portable devices such as mobile-
phones, laptops, cameras to hybrid electric vehicles etc. Despite this success these systems still have boundaries
such as low energy density in EDLC, or short cycle life and limited power capability in pseudocapacitors5. Development of hybrid materials based
on sponge supported reduced graphene
oxide and transition metal hydroxides for
hybrid energy storage devices Development of hybrid materials based
on sponge supported reduced graphene
oxide and transition metal hydroxides for
hybrid energy storage devices Correspondence and
requests for materials
should be addressed to
D.P.D.
(dubaldeepak2@
gmail.com) or P.G.-R.
(pedro.gomez@cin2.
es) Results
h 2(a, b) reveal, the 3D open porous
nature of the sponge substrate is maintained even after the coating of
rGO and deposition of Ni(OH)2 and Co(OH)2 nanostructures. Fig. 2(c and d) shows hierarchically porous well networked structure
of thin b-Ni(OH)2 nanosheets and b-Co(OH)2 nanoflakes. These
nanostructures are interconnected with each other, providing open
porous structure which enables the full exposure of the arrays to the
electrolyte. The open geometry between the arrays allows easier elec-
trolyte penetration into the inner region of the electrode, increasing
the utilization of the active materials. The skeleton of the sponge is
fully covered by both Ni(OH)2 and Co(OH)2 nanostructures so that
no rGO is exposed to the surface (Supporting information S3). The
thicknesses of the Ni(OH)2 and Co(OH)2 coatings were found to be
,1.2 and ,1.3 mm, respectively which can be measured by the cross-
section SEM images in Fig. 2(e–f). A possible growth process will be
as follows: Initially, dissolved ammonia forms a complex with metal
ions (Ni21 and Co21), which decreases the free metal ion concentra-
tion and reduces the rate of crystal growth. Formation of metal
ammine complex avoids homogeneous nucleation in the solution
due to the binding of metal ions and provides priority to heterogen-
eous nucleation on the substrate. Further, as the reaction time
increases (at a constant temperature), hydrolysis of HMT molecules
takes place. This increases the concentration of OH2 in the solution
which encourages the formation of thin Ni(OH)2 nanosheets and
Co(OH)2 nanoflakes15. Here, HMT provides controlled supply of
ammonia via the hydrolysis reaction, while unreacted HMT selec-
tively adsorbs on the metal hydroxide nanoparticles due to its high
binding capacity16, resulting in the formation of nanosheets/nano- In this work we have successfully used both of those possible
optimization pathways (CBD on foam substrates) to improve the
performance of supercapacitors in aqueous system. According to
the equation for energy storage i.e. E 5 0.5 CV2, the performance
of the supercapacitors can be enhanced by increasing capacitance
and extending the operational voltage window using different con-
figurations. Results
h graphene frameworks10–13. To this list of possible substrates for
hybrid supercapacitive electrodes, a new very practical contender
has been recently added, namely, commercially available sponges
with 3D porous structure coated with carbon. The sponge substrate
provides smooth inner and outer sides of the skeleton for the depos-
ition of materials and its soft, lightweight, flexible and cost-effective
nature makes it more attractive for flexible devices. Moreover,
macroporosity and high surface area of sponge provide an easy path
to the electrolyte to reach the entire surface of the electrodes where
redox reactions can take place. graphene frameworks10–13. To this list of possible substrates for
hybrid supercapacitive electrodes, a new very practical contender
has been recently added, namely, commercially available sponges
with 3D porous structure coated with carbon. The sponge substrate
provides smooth inner and outer sides of the skeleton for the depos-
ition of materials and its soft, lightweight, flexible and cost-effective
nature makes it more attractive for flexible devices. Moreover,
macroporosity and high surface area of sponge provide an easy path
to the electrolyte to reach the entire surface of the electrodes where
redox reactions can take place. Synthesis of SP@rGO@Ni and SP@rGO@Co hybrid electrodes
involves two steps: first, coating of rGO onto the sponge substrate
by ‘‘dip and dry’’ method and subsequently, depositions of nanos-
tructured Ni(OH)2 and Co(OH)2 carried out by CBD method (see
Fig. 1). The bare sponge was first coated with rGO nanosheets via
dipping into rGO ink in aqueous solution and subsequent drying in
an oven. By this way, 3D macroporous conducting framework with
high surface area was formed which provides enough space for the
heavy and uniform deposition of nanostructured Ni(OH)2 and
Co(OH)2 onto the skeleton of the sponge easily. Sponge surface
was uniformly covered with aggregates of rGO sheets (see
Supporting information S2) with almost completely transparent
and crumpled to a curly, wavy shape. In the long list of possible chemical methods, the chemical bath
deposition (CBD) method is best suited to prepare large-scale thin
coatings of different materials with diverse and controllable
morphologies at low temperature and low cost on any type of sub-
strate. Moreover, direct growth of material by CBD method enhances
the interfacial contacts and avoids the use of unnecessary binders and
additives. SEM images as shown in Fig. OPEN Looking
at both systems, the demerits of one type are the strengths of the other and vice-versa. Thus, the hybridization of
EDLC and pseudocapacitor materials is an appealing path to solve the problems related to both systems6. p
p
pp
g p
p
y
There are two kinds of hybrids; one is the ‘‘hybrid electrode’’ in which pseudocapacitive/faradic and non-
faradic materials are combined in single electrode in order to take the advantage of both charge storing mechan-
isms7, whereas the second is the ‘‘hybrid device or hybrid combination’’ in which a pseudocapacitive/faradic
electrode and non-faradic one are combined in a single cell8. The most promising approach to develop hybrid
electrodes is to integrate non-faradaic (carbon based) and pseudocapacitive/faradic materials (transition metal
oxides/hydroxides, polyoxometalates, conducting polymers and Li-intercalates). Simple mixing of two different
materials will not be an effective mode to fabricate hybrid electrodes due to difficulties in interfacial contacts
between them. The proper hybridization of components through rational design with control over morphology,
size and uniformity of active material, as well as facile processing are key parameters to obtain inexpensive yet
high-performance hybrid electrodes9. An emerging new concept to fabricate hybrid electrodes is designing
carbon supported substrates with pseudocapacitive materials under the control of their morphologies and sizes
such as carbon nanofiber textile, carbon nanotube/graphene coated textile, and three dimensional macroporous SCIENTIFIC REPORTS | 4 : 7349 | DOI: 10.1038/srep07349 1 www.nature.com/scientificreports Figure 1 | Schematic representation with digital photographs of fabrication of hybrid materials based on rGO and transition metal hydroxides
(Ni(OH)2 and Co(OH)2) onto skeleton of 3D macroporous sponge. Figure 1 | Schematic representation with digital photographs of fabrication of hybrid materials based on rGO and transition metal hydroxides
(Ni(OH)2 and Co(OH)2) onto skeleton of 3D macroporous sponge. Results
h The work we present here deals with: 1)
Construction of unique hybrid electrodes to improve capacit-
ance: Using macroporous 3D sponge (SP) substrate coated with
reduced graphene oxide (rGO), we have deposited two different
materials Ni(OH)2 and Co(OH)2 by inexpensive CBD method
to fabricate open porous, high surface area hybrid electrodes to
achieve synergistic effects of EDLC and pseudocapacitive mate-
rials at low cost. 2)
Fabrication of hybrid device to extend working potential win-
dow: The hybrid device is configured by using hybrid electrode
(above mentioned) as positive with rGO coated sponge as nega-
tive electrodes in single cell to extend working potential
window. Thus, we have presented an integrated approach from hybrid
materials to hybrid devices. These hybrid materials effectively
increase the capacitance and hybrid configurations extend the
working potential windows of device in aqueous system which con-
sequently enhances the supercapacitive properties of the devices. SCIENTIFIC REPORTS | 4 : 7349 | DOI: 10.1038/srep07349 2 Figure 2 | SEM images of (a), (c) and (e) SP@rGO@Ni and (b), (d) and (f) SP@rGO@Co hybrid at two different magnifications with corresponding
cross-sectional images showing a thick layer of Ni(OH)2 and Co(OH)2 coated on SP@rGO support. Figure 2 | SEM images of (a), (c) and (e) SP@rGO@Ni and (b), (d) and (f) SP@rGO@Co hybrid at two different magnifications with corresponding
cross-sectional images showing a thick layer of Ni(OH)2 and Co(OH)2 coated on SP@rGO support. flakes. According to thermodynamics, the surface energy of an indi-
vidual nanosheet or nanoflake is high therefore they aggregate per-
pendicularly to the surface planes in order to decrease the surface
energy17. Therefore, as the reaction proceeds, the thin sheets and
flakes would self-aggregate to form interconnected Ni(OH)2
nanosheets and Co(OH)2 nanoflakes clusters for minimizing the
overall surface energy. line in nature. Due to the small content of rGO coated on the sponge
substrate, the corresponding peak for rGO was not detected in XRD. Further, to investigate the oxidation states of elements, XPS analysis
was carried out. The XPS Ni2p peak (Fig. 3(c)) consisted of two spin-
orbit doublets characteristic of Ni21 and Ni31 and two shake-up
satellites. The binding energy of Ni2p3/2 was about 855.2 eV, which
is consistent with the previously reported value18. The XPS Co2p
peak (Fig. 3(d)) consisted of two spin-orbit doublets characteristic
of Co21 and Co31 and two shake-up satellites. The binding energy
corresponding to Co2p3/2 was about 780.2 eV18. Results
h The most of the pores are observed in the range of 2–10 nm, with
a centered pore distributions at around 3.57 nm, and 2.29 nm for
Ni(OH)2 and Co(OH)2 samples, respectively indicating that pores of
hierarchical nanosheets and nanoflakes are mainly mesopores with
some micropores. This mesoporous structure of Ni(OH)2 and
Co(OH)2 could provide easy access for the ions in the electrolyte
as well as short diffusion path for intercalation and de-intercalation. The porosity of samples is an amalgamation of internal space of the
agglomerated nanosheets/nanoflakes and the porosity due to
internal space of bunch of nanosheets/nanoflakes. The pore size
distribution of Ni(OH)2 and Co(OH)2 samples is slightly narrow
which further supports the better homogeneity in the surface mor-
phology and porosity of samples. These surface properties directly
affect the electrochemical properties of electrode materials. with high accessible surface area and macroporous open pore struc-
tures were acted as electrode as well as current collector which also
provides highly porous channels for the full access of electrolytes to
active materials. The cyclic voltammetry (CV) curves (Fig. 5(a)) indi-
cate that the SP@rGO devices can be operated over a wide range of
scan rates: from 5 up to 500 mV/s. Even at the scan rate of 500 mV/s,
the cyclic voltammograms retain the rectangular shape showing the
ideal electrochemical double layer behavior of rGO coated sponge
electrode. The high scan rate that SP@RGO can achieve implies that
ultrahigh power density can be obtained in this device. The galvano-
static charge/discharge curve at a specific current of 5 A/g (Fig. 5(b))
shows an ultrafast charge discharge rate, linear dependence on volt-
age and time, and very small voltage drop demonstrating that the
SP@rGO electrodes can work at high specific current. Thus, the
results demonstrate that SP@rGO electrode exhibit high EDLC per-
formance and would be a promising energy storage substrate. p
g
gy
g
To demonstrate the advantages of hybrid electrodes (SP@rGO@
Ni and SP@rGO@Co) which are obtained by hybridization of pseu-
docapacitive and non-faradic materials, we have investigated the
electrochemical properties in two electrode configuration devices. The SP@rGO@Ni and SP@rGO@Co served as electrodes as well as
current collectors with binder-free, highly porous and conductive
framework which provides full access to electrolyte ions. The shapes
of the CV curves of SP@rGO@Ni and SP@rGO@Co symmetric
devices (Fig. Results
h line in nature. Due to the small content of rGO coated on the sponge
substrate, the corresponding peak for rGO was not detected in XRD. Further, to investigate the oxidation states of elements, XPS analysis
was carried out. The XPS Ni2p peak (Fig. 3(c)) consisted of two spin-
orbit doublets characteristic of Ni21 and Ni31 and two shake-up
satellites. The binding energy of Ni2p3/2 was about 855.2 eV, which
is consistent with the previously reported value18. The XPS Co2p
peak (Fig. 3(d)) consisted of two spin-orbit doublets characteristic
of Co21 and Co31 and two shake-up satellites. The binding energy
corresponding to Co2p3/2 was about 780.2 eV18. Fig. 3(a, b) shows the XRD patterns of SP@rGO@Ni and SP@
rGO@Co, respectively. As seen from the XRD patterns, it is evi-
denced that both materials are polycrystalline in nature. The diffrac-
tion peaks (001), (100), (101), (102), (110) and (111) in Fig. 3(a) are
readily indexed to a pure single phase of b-Ni(OH)2 with the hexa-
gonal brucite structure [JCPDS 14-0117] whereas the peaks (100),
(101), (110) and (111) correspond to pure hexagonal b-Co(OH)2
according to JCPDS 30-0443 (Fig. 3(b)). Moreover, broadened dif-
fraction peaks evidence that both deposited materials are nanocystal- TEM analysis is further carried out to provide more insight into
the detailed microstructures of the Ni(OH)2 and Co(OH)2 samples. TEM image shown in Fig. 4(a) presents a panoramic view of thin
nanosheets of Ni(OH)2. It is further seen that, the nanosheets are
loosely packed and have separate existence. Fig. 4(b) shows the TEM
image of a representative flowerlike Co(OH)2 nanostructure which is Figure 3 | (a), (b) XRD patterns and (c), (d) core level XPS of Ni2p and Co2p spectra for SP@rGO@Ni and SP@rGO@Co hybrid materials, respectively. Figure 3 | (a), (b) XRD patterns and (c), (d) core level XPS of Ni2p and Co2p spectra for SP@rGO@Ni and SP@rGO@Co hybrid materials, respectively. d) core level XPS of Ni2p and Co2p spectra for SP@rGO@Ni and SP@rGO@Co hybrid materials, respectively. Figure 3 | (a), (b) XRD patterns and (c), (d) core level XPS of Ni2p and Co2p spectra for SP@rGO@Ni and SP@r (b) XRD patterns and (c), (d) core level XPS of Ni2p and Co2p spectra for SP@rGO@Ni and SP@rGO@Co hybrid ma SCIENTIFIC REPORTS | 4 : 7349 | DOI: 10.1038/srep07349 SCIENTIFIC REPORTS | 4 : 7349 | DOI: 10.1038/srep07349 3 www.nature.com/scientificreports in good agreement with the results from the FESEM image. Results
h In addi-
tion to this the edge of the hierarchical Ni(OH)2 nanosheets and
Co(OH)2 nanoflakes further indicates the ultrathin nature of a single
component with almost transparent feature. Fig. 4(c–d) shows the
nitrogen adsorption and desorption isotherms and the correspond-
ing pore size distributions (inset) of Ni(OH)2 and Co(OH)2 samples,
respectively. The specific surface areas were calculated from the
Brunauer-Emmett-Teller (BET) method and the pore size distribu-
tions (PSD) were obtained by means of the Barrett-Joyner-Halenda
(BJH) equation using the adsorption isotherm branch. The BET
specific surface areas of Ni(OH)2 and Co(OH)2 samples were found
to be 91 and 87 m2/g, respectively. The pore size distribution curves
of Ni(OH)2 and Co(OH)2 samples are also shown in inset of Fig. 4(c–
d). The most of the pores are observed in the range of 2–10 nm, with
a centered pore distributions at around 3.57 nm, and 2.29 nm for
Ni(OH)2 and Co(OH)2 samples, respectively indicating that pores of
hierarchical nanosheets and nanoflakes are mainly mesopores with
some micropores. This mesoporous structure of Ni(OH)2 and
Co(OH)2 could provide easy access for the ions in the electrolyte
as well as short diffusion path for intercalation and de-intercalation. The porosity of samples is an amalgamation of internal space of the
agglomerated nanosheets/nanoflakes and the porosity due to
internal space of bunch of nanosheets/nanoflakes. The pore size
distribution of Ni(OH)2 and Co(OH)2 samples is slightly narrow
which further supports the better homogeneity in the surface mor-
phology and porosity of samples. These surface properties directly
affect the electrochemical properties of electrode materials. in good agreement with the results from the FESEM image. In addi-
tion to this the edge of the hierarchical Ni(OH)2 nanosheets and
Co(OH)2 nanoflakes further indicates the ultrathin nature of a single
component with almost transparent feature. Fig. 4(c–d) shows the
nitrogen adsorption and desorption isotherms and the correspond-
ing pore size distributions (inset) of Ni(OH)2 and Co(OH)2 samples,
respectively. The specific surface areas were calculated from the
Brunauer-Emmett-Teller (BET) method and the pore size distribu-
tions (PSD) were obtained by means of the Barrett-Joyner-Halenda
(BJH) equation using the adsorption isotherm branch. The BET
specific surface areas of Ni(OH)2 and Co(OH)2 samples were found
to be 91 and 87 m2/g, respectively. The pore size distribution curves
of Ni(OH)2 and Co(OH)2 samples are also shown in inset of Fig. 4(c–
d). Results
h 6(A, B)) indicate that the capacitance characteristic is
different from that of electric double layer capacitance in which the
shape is normally close to an ideal rectangular shape. Each CV curve
consists of a pair of strong redox peaks, which indicates that the
capacitance characteristics are mainly governed by redox reactions. It must also be noted that as the scan rate increased, the potential of
the anodic and cathodic peaks shift to more positive and negative To evaluate the electrochemical performance SP@rGO electrodes,
a typical two electrode configuration was constructed. Two pieces of
SP@rGO sponge as electrodes, one piece of separator and 2 M KOH
as electrolyte was used. The sponges based conductive framework Figure 4 | (a), (b) TEM images of Ni(OH)2 and Co(OH)2 samples with corresponding high magnified TEM images (inset), respectively, (c), (d) Nitrogen
adsorption/desorption isotherm of Ni(OH)2 and Co(OH)2 samples and inset shows the corresponding BJH pore size distribution plots. Figure 4 | (a), (b) TEM images of Ni(OH)2 and Co(OH)2 samples with corresponding high magnified TEM images (inset), respectively, (c), (d) Nitrogen
adsorption/desorption isotherm of Ni(OH)2 and Co(OH)2 samples and inset shows the corresponding BJH pore size distribution plots. SCIENTIFIC REPORTS | 4 : 7349 | DOI: 10.1038/srep07349 SCIENTIFIC REPORTS | 4 : 7349 | DOI: 10.1038/srep07349 4 Figure 5 | (a) Cyclic voltammetry curves of SP@rGO electrodes collected at different scanning rates in 2 M KOH electrolyte, respectively (b)
Galvanostatic charge/discharge curves of SP@rGO electrodes at different current densities. Figure 5 | (a) Cyclic voltammetry curves of SP@rGO electrodes collected at different scanning rates in 2 M KOH electrolyte, respectively (b)
Galvanostatic charge/discharge curves of SP@rGO electrodes at different current densities. directions, respectively. The possible charge storing mechanisms for
Ni(OH)2 and Co(OH)2 are as follows19: directions, respectively. The possible charge storing mechanisms for
Ni(OH)2 and Co(OH)2 are as follows19: the inner-pore surfaces of the hybrid electrode materials are effec-
tively utilized for the intercalation20. The highest specific capacitance
values obtained for symmetric SP@rGO@Ni and SP@rGO@Co
devices were 812 F/g (1.7 F/cm2) for mass loading of 4.2 mg/cm2
whereas 752 F/g (1.46 F/cm2) for mass loading of 3.9 mg/cm2 at a
potential scan rate of 5 mV/s, respectively. The galvanostatic charge-
discharge curves of both hybrid symmetric devices are shown in
Fig. 6(C–D) at different current densities. Results
h The curves show that these
hybrid systems can be operated at a wide range of current densities
with small voltage drop, further demonstrating the excellent electro-
chemical performance of SP@rGO@Ni and SP@rGO@Co nanos-
tructured hybrid electrodes. The charge-discharge curves reflect Ni(OH)2zOH{uNiOOHzH2Oze{
ð1Þ
Co(OH)2zOH{uCoOOHzH2Oze{
ð2Þ ð2Þ As expected, there is an increase in current with the scan rate while
the CV curves retain the shape when the applied scan rate is very high
(200 mV/s). This indicates a proper hybridization of (Ni(OH)2 or
Co(OH)2) with rGO which allows efficient ion transport at the inter-
face of hybrid electrodes and electrolyte. Moreover, both outer- and Figure 6 | (A), (B) Cyclic voltammetry curves of SP@rGO@Ni and SP@rGO@Co hybrid electrodes collected at different scanning rates in 2 M KOH
electrolyte, respectively (C), (D) Galvanostatic charge/discharge curves of SP@rGO@Ni and SP@rGO@Co hybrid electrodes at different current densities,
respectively. Figure 6 | (A), (B) Cyclic voltammetry curves of SP@rGO@Ni and SP@rGO@Co hybrid electrodes collected at different scanning rates in 2 M KOH
electrolyte, respectively (C), (D) Galvanostatic charge/discharge curves of SP@rGO@Ni and SP@rGO@Co hybrid electrodes at different current densities,
respectively. SCIENTIFIC REPORTS | 4 : 7349 | DOI: 10.1038/srep07349 5 Figure 7 | CV curves of the (a) SP@rGO//SP@rGO@Ni and (b) SP@rGO//SP@rGO@Co hybrid devices at different working voltages at a scan rate of
100 mV/s. CV curves of (c) SP@rGO//SP@rGO@Ni and (d) SP@rGO//SP@rGO@Co hybrid devices at different scan rates. Variation of specific and areal
capacitances of (e) SP@rGO//SP@rGO@Ni and (f) SP@rGO//SP@rGO@Co devices as function of the scan rate. Figure 7 | CV curves of the (a) SP@rGO//SP@rGO@Ni and (b) SP@rGO//SP@rGO@Co hybrid devices at different working voltages at a scan rate of
100 mV/s. CV curves of (c) SP@rGO//SP@rGO@Ni and (d) SP@rGO//SP@rGO@Co hybrid devices at different scan rates. Variation of specific and areal
capacitances of (e) SP@rGO//SP@rGO@Ni and (f) SP@rGO//SP@rGO@Co devices as function of the scan rate. order to reach the highest cell voltage, the charges stored in both
electrodes must be balanced by adjusting the mass loading of the
electrodes. The positive to negative electrode mass ratio was calcu-
lated by the following equation to achieve a charge balance q1 5 q2. the faradic behavior of the Ni(OH)2 and Co(OH)2 samples. It should
also be noted that the small voltage-drop at the start of discharge
indicates a low internal resistance, excellent conductivity, and the
capability for a quick charge. Results
h This may be attributed to the inclusion
of rGO in Ni(OH)2 and Co(OH)2 nanostructures. The estimated
specific capacitance values of SP@rGO@Ni and SP@rGO@Co
hybrid electrodes were found to be 806 and 747 F/g at a current
density of 2 A/g. The good capacitive behavior of SP@rGO@Ni
and SP@rGO@Co electrodes is due to the combined contribution
of rGO with Ni(OH)2 and Co(OH)2 nanostructures which provides
large internal accessible surface sample matrix, decrease the ion dif-
fusion resistance and enhance the electro-active surface utilization
during the redox process. Moreover, the 3D macroporous framework
of the sponge and numerous nano-channels in Ni(OH)2 nanosheets
and Co(OH)2 nanoflakes act as ‘‘ion-buffering reservoirs’’ which
reduce the mean free path of the ions and facilitate faster ionic and
electronic kinetics, thus maximizing the reversible insertion/de-
insertion reactions21. mz
m{
~ (C{|DE{)
(Cz|DEz)
ð3Þ ð3Þ where q1, q2, m1, m2, C1, C2, E1, and E2 are the charge, mass,
specific capacitance and potential windows for the cathode (1) and
anode (2). Hence, the mass ratio between the positive and negative
electrodes of the SP@rGO//SP@rGO@Ni and SP@rGO//SP@rGO@
Co hybrid devices should be 3.19 and 2.37, respectively. Accordingly,
the charge balance between positive and negative electrodes,
the optimal positive-to-negative mass ratio was determined to
be 4.12 mg/cm251.28 mg/cm2 and 3.23 mg/cm251.33 mg/cm2 for
SP@rGO//SP@rGO@Ni
and
SP@rGO//SP@rGO@Co
hybrid
devices, respectively. Fig. 7(a–b) show the CV curves at different
voltage windows for SP@rGO//SP@rGO@Ni and SP@rGO//SP@
rGO@Co hybrid devices respectively at a scan rate of 100 mV/s. It
can be clearly seen that the fabricated hybrid devices show a good
capacitive behavior and expand their potential windows up to 1.5 and
1.4 V for SP@rGO//SP@rGO@Ni and SP@rGO//SP@rGO@Co
cells, respectively. Further increase in voltage window causes some
irreversible reaction since sudden increase in current has been
observed (see Fig. 7(a–b)). It was further found that the current
and consequently the specific capacitance greatly increase as the
operating voltage window is increased, which indicates the improve-
ment in stored energy and delivered power. As a consequence, the
overall performance of the supercapacitor could also be remarkably
improved. As is generally known, operating at higher voltage will be
favorable for reducing the number of devices in series required to
reach the desired output voltage in practical applications. Results
h Very
small voltage-drop is observed at initial discharge curve indicating
excellent conductivity and fast I–V response. SP@rGO@Ni and SP@rGO//SP@rGO@Co hybrid devices mea-
sured at various scan rates of 10–500 mV/s. These CV curves
exhibit a non-rectangular current response on voltage reversal
with small redox peaks. The shapes of CV curves remain
unchanged even at a high scan rate of 500 mV/s, suggesting that
the cell possesses excellent rate capability which is desirable for
high-power supercapcitors. The specific capacitances of hybrid
devices (based on the total mass of the active materials of the
two electrodes) at different scan rates calculated from the CV
curves is presented in Fig. 7(e–f). The highest gravimetric capa-
citance (areal capacitance) for SP@rGO//SP@rGO@Ni and SP@
rGO//SP@rGO@Co hybrid devices were found to be 185 (0.49 F/
cm2) and 158 (0.35 F/cm2) at 10 mV/s, which are greatly larger
than the values reported for hydroxide based asymmetric super-
capacitors25–28. The specific capacitances decrease gradually with
increasing scan rate as diffusion limits the movement of electro-
lyte ions at high scan rates because of the time constraint and only
the outer active surface can be utilized for charge storage, resulting
in a lower electrochemical utilization of electroactive materials29. The higher specific capacitance could be obtained at higher opera-
tion voltage windows thanks to the redox reactions of Ni(OH)2
and Co(OH)2. Importantly, it should be pointed out that the
specific capacitance is calculated based on the total mass of the
active material on both electrodes. The excellent performance of
the hybrid devices can thus be attributed to the high capacitance
and rate performance as well as the synergistic effects of both the
SP@rGO and SP@rGO@Ni/SP@rGO@Co hybrid electrodes. Finally, a long cycling life is an important requirement for super-
capacitor applications. Long cycling-life tests were carried out for the
SP@rGO//SP@rGO@Ni and SP@rGO//SP@rGO@Co hybrids by
repeating the CV test at a scan rate of 100 mV/s for 2000 cycles
(see inset of Fig. 8(C–D)). Fig. 8(C–D) shows the capacitance reten-
tion ratio of the hybrid devices as a function of the cycle number. It is
worth noting that the specific capacitance decreases suddenly after
the initial 50 cycles, which is probably related to pulverization and
loss of electrical contact between the active material and the current
as well as wettability issues. Results
h Thus, we
chose an operation voltage window of 1.5 V and 1.4 V for SP@rGO//
SP@rGO@Ni and SP@rGO//SP@rGO@Co cells in 2 M KOH aque-
ous electrolyte to further investigate the electrochemical perform-
ance, respectively. Fig. 7(c–d) shows the CV curves of the SP@rGO// In order to further increase the specific energy without sacrificing
power delivery and cycle life in the aqueous electrolyte; supercapa-
citors have been proposed to reach a higher cell voltage through the
asymmetric mode where one electrode is made of a faradaic material
and the other of a non-faradaic one. Several reports are available on
this approach22,23. Here, we are going to demonstrate somewhat dif-
ferent hybrid design which is comprised of one non-faradic electrode
(SP@rGO) with other hybrid electrode which combines non-faradic
and pseudocapacitive characteristics (SP@rGO@Ni or SP@rGO@
Co) in aqueous system. Due to the high hydrogen evolution over-
potential of rGO in aqueous media24 and the excellent capacitive
features of SP@rGO@Ni and SP@rGO@Co synthesized in this work,
hybrid configuration is tested for achieving the goal of high-energy
and high-power densities. In this hybrid device, charges are stored
non-faradically in rGO electrodes, and through redox reactions in
the hybrid metal hydroxide electrodes. The specific capacitances of
the SP@rGO@Ni, SP@rGO@Co and SP@rGO electrode were calcu-
lated to be 812 F/g (4.2 mg/cm2), 752 F/g (3.9 mg/cm2) and 127 F/g
(1.9 mg/cm2) at the scan rates of 5 mV/s, respectively. Note that in SCIENTIFIC REPORTS | 4 : 7349 | DOI: 10.1038/srep07349 6 www.nature.com/scientificreports Figure 8 | Galvanostatic charge-discharge curves of (A) SP@rGO//SP@rGO@Ni and (B) SP@rGO//SP@rGO@Co hybrid devices at different current
densities. Variation of capacity retention of (C) SP@rGO//SP@rGO@Ni and (D) SP@rGO//SP@rGO@Co hybrid devices with number of cycles at
100 mV/s scan rate along with corresponding CV curves (inset) at 1st and 2000th cycles. Figure 8 | Galvanostatic charge-discharge curves of (A) SP@rGO//SP@rGO@Ni and (B) SP@rGO//SP@rGO@Co hybrid devices at different current
densities. Variation of capacity retention of (C) SP@rGO//SP@rGO@Ni and (D) SP@rGO//SP@rGO@Co hybrid devices with number of cycles at
100 mV/s scan rate along with corresponding CV curves (inset) at 1st and 2000th cycles. all of the curves are not ideal straight lines, indicating the involve-
ment of a redox reaction process. Furthermore, there is an initial
drop in potential, which may be caused by the internal resistance
as well as different rates of oxidation and reduction reactions. Results
h After 2000 cycles, the SP@rGO//SP@
rGO@Ni and SP@rGO//SP@rGO@Co hybrid devices display an
excellent long cycle life with 90% and 87% retention of their initial
specific capacitance, respectively, demonstrating superior long-term
electrochemical stability. Moreover, excellent stability confirms the
proper hybridization of two different (pseudocapacitive and non-
faradic) materials. Such a stable and connecting structure helps to
alleviate the structure damage caused by volume expansion during
cycling process, resulting in an enhanced stability. Thus, such a cyc-
ling performance is highly competitive with those of some other
asymmetric supercapacitors, such as Ni(OH)2//activated carbon
(82% retention after 1000 cycles)30, LiNi1/3Co1/3Mn1/3O2//AC (ca. 80% retention after 1000 cycles)31, graphene-MnO2//graphene
(79% retention after 1000 cycles)32, and porous NiO//carbon devices
(50% after 1000 cycles)33. y
Galvanostatic charge/discharge curves of hybrid cells were
recorded with various current densities to further evaluate the elec-
trochemical performance as shown in Fig. 8(A–B). It can be seen that SCIENTIFIC REPORTS | 4 : 7349 | DOI: 10.1038/srep07349 7 Figure 9 | The power density versus energy density of SP@rGO//SP@
rGO@Ni and SP@rGO//SP@rGO@Co hybrid devices in a Ragone plot. an energy density .10 Wh/kg even at a high power density. The
energy density demonstrated in this work is significantly higher than
those obtained for other carbon-based symmetric capacitors in aque-
ous electrolytes, such as activated carbon (,10 Wh/kg)34, carbon
nanotubes (,10 Wh/kg)35, graphene (9.1 Wh/kg)36. The excellent
performance is also comparable or superior to other asymmetric cells
with mild aqueous electrolytes, such as Co(OH)2//GO (11.94 Wh/
kg)25, Co(OH)2//AC (92.7 Wh/kg)26, Ni(OH)2//AC (32.7 Wh/kg)27,
b-Ni(OH)2//AC (36.2 Wh/kg)37, Ni(OH)2-graphene//porous gra-
phene (77.8 Wh/kg)38, a-Ni(OH)2//AC (42.3 Wh/kg)28, Ni(OH)2//
AC (35.7 Wh/kg)39, Ni(OH)2/ultrathin graphite foam//activated
microwave exfoliated graphite oxide (13.4 Wh/kg)40. Discussion
b SCIENTIFIC REPORTS | 4 : 7349 | DOI: 10.1038/srep07349 8 The SP@rGO was washed with water to get rid of the surfactant after drying in an
electrical oven for 2 h. Then the surfactant-free SP@rGO was put in a vacuum oven
for another 3 h to remove the water completely. working potential window for the entire system (DVmax) will be the
sum of potentials across rGO electrode (DVNF) and hybrid electrode
(DVHy). Thus the total amount of energy stored in this hybrid system
is the sum of energy stored in rGO electrode (ENF) and that of the
hybrid electrode (EHy). The hybrid electrode system has advantage at
high power density due to the structural characteristics of the system
compared to those of typical asymmetric capacitors41. In effect, the
rGO electrode, which can store electrochemical energy by electro-
static force, enhances the electron transfer to the Ni(OH)2 and
Co(OH)2 in the hybrid electrode system, causing a better charge
transfer reaction at a high rate. To show high energy density of hybrid
device for example SP@rGO//SP@rGO@Ni, the device was charged
to light an LED as a demonstration for real application (Fig. 10(c–e)). After a quick charge of around 20 seconds the cell can light one LED
for ,5 min. This result further demonstrates the successful utility of
hybrid devices with aqueous electrolyte to realize high performance
supercapacitors. Development of SP@rGO@Ni and SP@rGO@Co hybrid electrodes. Subsequent
depositions of nanostructured Ni(OH)2 and Co(OH)2 on to SP@rGO support
substrate were carried out by simple chemical bath deposition (CBD) method. Briefly,
solutions of 0.1 M NiSO4 and 0.1 M CoCl2 complexed with ammonia solution and
0.1 M hexamethylenetetramine (HMT) were prepared in de-ionized water separately
in order to synthesize Ni(OH)2 and Co(OH)2 thin films, respectively. Further the
pieces of SP@rGO support substrates were immersed in these baths and the bath was
heated. When the bath attained the temperature of 343 K, the precipitation started in
the bath. During the precipitation, a heterogeneous reaction occurs and
nanostructured Ni(OH)2 and Co(OH)2 thin coatings were deposited on the SP@rGO
substrates. The deposition time for both materials placed at 343 K was kept constant
at 4 h. At the end, SP@rGO coated with Ni(OH)2 and Co(OH)2 are referred to as SP@
rGO@Ni and SP@rGO@Co, respectively. Materials characterization. Discussion
b For a better understanding of the working of hybrid device with
hybrid electrode, the schematic of hybrid device is sketched in
Fig. 10(a). The characteristic of hybrid electrode is hybridization of
pseudocapacitive component (Ni(OH)2 and Co(OH)2) and non-
faradic component (rGO) in a single electrode so that energy can
be stored through both mechanisms. For example, in case of SP@
rGO@Ni hybrid electrode, the rGO is charged by electrostatic force
in the initial state until the electrode potential attains the redox
reaction potential of the Ni(OH)2 till q1 as seen in Fig 10(b). Then
the Ni(OH)2 is charged by the redox reaction while maintaining the
redox reaction potential of the hybrid electrode, until the component
reaches the full-charge state (QF). After the full charge of the
Ni(OH)2, the rGO is charged again (q2) to reach the maximum
potential of hybrid electrode storing the charge on the surface. Hence the total charge stored in the hybrid electrode is due to both
components ((q1 1 q2) 1 QF). In addition to this the maximum Figure 9 | The power density versus energy density of SP@rGO//SP@
rGO@Ni and SP@rGO//SP@rGO@Co hybrid devices in a Ragone plot. Energy density and power density are two key factors for evalu-
ating the performance of supercapacitors. A high performance
supercapacitor is expected to provide high energy density or high
specific capacitance at high discharge rates. Fig. 9 presents the
Ragone plot of the SP@rGO//SP@rGO@Ni and SP@rGO//SP@
rGO@Co hybrid devices. The as-assembled SP@rGO//SP@rGO@
Ni hybrid device with a cell voltage of 1.5 V can deliver a high specific
energy of 42.02 Wh/kg with maximum specific power of 11 kW/kg
whereas SP@rGO//SP@rGO@Co cell exhibits 33.01 Wh/kg with
specific power of 8 kW/kg. Furthermore, these devices can retain Figure 10 | (a), (b) Schematic representation of hybrid combination (device) of hybrid electrode (SP@rGO@Ni or SP@rGO@Co) and SP@rGO electrode
with propylene carbonate paper as separator along with charge-potential profile. (c)–(e) Demonstration of the use of the SP@rGO//SP@rGO@Ni hybrid
device is given with a light emitting diode (LED). Figure 10 | (a), (b) Schematic representation of hybrid combination (device) of hybrid electrode (SP@rGO@Ni or SP@rGO@Co) and SP@rGO electrode
with propylene carbonate paper as separator along with charge-potential profile. (c)–(e) Demonstration of the use of the SP@rGO//SP@rGO@Ni hybrid
device is given with a light emitting diode (LED). Discussion
b The X-ray diffraction (XRD) of samples was carried out
using a Bruker AXS D8 Advance diffractometer with copper radiation (Ka of l 5
1.54 A˚). The X-ray photoelectron spectra (XPS) data were obtained by X-ray
photoelectron spectroscopy (XPS, Perkin-Elmer model PHI 1600). The
microstructures of the samples were investigated by scanning electron microscope
(SEM, Nova NanoSEM 200). Transmission electron microscopy observations were
conducted using JEOL JEM-2100 operated at 200 kV. N2 adsorption/desorption was
determined by Brunauer-Emmett-Teller (BET) measurements using Micromeritics
instrument. p
p
The superior electrochemical performance of the fabricated
hybrid devices (SP@rGO//SP@rGO@Ni and SP@rGO//SP@rGO@
Ni) can be reasonably attributed to the synergistic contribution of
both materials (hybrid electrode) as well as that between the positive
and negative electrodes in single device. The energy density of the
hybrid devices is significantly improved because of the extended wide
operation voltage window. On the other hand, the rGO in both
electrodes demonstrate their distinctive features such as excellent
electrochemical stability and superior conductivity due to the fact
that rGO not only acts as the support for the Ni(OH)2 nanosheets
and Co(OH)2 nanoflakes, but also maintains the mechanical integ-
rity and high electrical conductivity of the overall electrode. Additionally, 3D macroporous framework as the negative electrode
facilitates the transport of electrolyte ions and provides a larger sur-
face area for charge-transfer reactions, ensuring high power density
and excellent rate performance. Thus, pairing up SP@rGO@Ni or
SP@rGO@Co and SP@rGO hybrid materials for hybrid devices
represents a new approach to high-performance energy storage
devices. Our future research will be focused on the use of organic
and ionic liquid based electrolytes for such hybrid-electrode based
hybrid devices. Supercapacitors cell fabrication and electrochemical characterization. Two
identical pieces of hybrid electrode (SP@rGO@Ni and SP@rGO@Co) each with an
area of 1 cm2 were sandwiched by porous polypropylene film separator soaked with
2 M KOH electrolyte and assembled into a coin cell. The mass of the active materials
was calculated by the mass difference method. Hybrid devices were assembled with
hybrid electrode (SP@rGO@Ni and SP@rGO@Co) as the positive electrode (cathode)
and SP@rGO as the negative electrode (anode). The electrodes were separated by
polypropylene film separator soaked with 2 M KOH electrolyte and assembled into a
coin cell. All electrochemical characteristics were evaluated by cyclic voltammetry
(CV) and galvanostatic charge/discharge (CD) measurements on IviumStat and
Atlas-0961 multichannel battery interface. 1. Dubal, D. P. et al. Discussion
b p
p
p
11. Yu, G. et al. Solution-processed Graphene/MnO2 nanostructured textiles for high-
performance electrochemical capacitors. Nano Lett. 11, 2905–2911 (2011). 12. Shen, L., Che, Q., Li, H. & Zhang, X. Mesoporous NiCo2O4 nanowire arrays grown
on carbon textiles as binder-free flexible electrodes for energy storage. Adv. Funct. Mater. 24, 2630–2637 (2014). 13. Lu, X. et al. Oxygen-deficient hematite nanorods as high-performance and novel
negative electrodes for flexible asymmetric supercapacitors. Adv. Mater. 26,
3148–3155 (2014). 14. Weng, Z. et al. Graphene-cellulose paper flexible supercapacitors. Adv. Energy
Mater. 1, 917–922 (2011). 15. Dubal, D. P. & Holze, R. Self-assembly of stacked layers of Mn3O4 nanosheets
using a scalable chemical strategy for enhanced, flexible, electrochemical energy
storage. J. Power Sources 238, 274–282 (2013). Discussion
b Supercapacitors based on flexible substrates: An overview. Energy Technol., 2, 325–341 (2014). 2. Simon, P. & Gogotsi, Y. Materials for electrochemical capacitors. Nat. Mater. 7,
845–854 (2008). 3. Lu, X., Yu, M., Wang, G., Tong, Y. & Li, Y. Flexible solid-state supercapacitors:
design, fabrication and applications. Energy Environ. Sci., 7, 2160–2181 (2014). y
With our earnest efforts, we have designed stunning hybrid mate-
rials based on sponge-supported rGO and transition metal hydro-
xides for hybrid energy storage devices. By taking into account, the
processing and fabrication cost of hybrid materials and hybrid
devices, inexpensive and scalable ‘dip and dry’ and CBD methods
with aqueous electrolyte system have been utilized. The synergic
combination of non-faradic (rGO) and redox (Ni(OH)2 and
Co(OH)2) materials provides dual charge-storing mechanisms
whereas 3D porous framework of sponge support allows good
accessibility of electrolyte to hybrid electrodes resulting in excellent
electrochemical performance. Moreover, hybrid devices using SP@
rGO and SP@rGO@Ni or SP@rGO@Co as the negative and positive
electrodes, respectively have been demonstrated as a bolstering
approach. The proper hybridization of rGO and Ni(OH)2/
Co(OH)2 improves interfacial contacts which delivers high energy
as well as sustains the volume expansion during the long term char-
ging/discharging reactions in an extended operating voltage. These
encouraging findings open up the possibility of hybrid electrodes for
numerous applications in hybrid energy storage devices to meet the
diverse demands where high power and energy storage systems are
required. 4. Arico, A. S. et al. Nanostructured materials for advanced energy conversion and
storage devices. Nat. Mater. 4, 366–377 (2005). 5. Zhang, L. L. & Zhao, X. S. Carbon-based materials as supercapacitor electrodes. Chem. Soc. Rev. 38, 2520–2531 (2009). 6. Suarez-Guevara, J., Ruiz, V. & Gomez-Romero, P. Hybrid energy storage: high
voltage aqueous supercapacitors based on activated carbon-phosphotungstate
hybrid materials. J. Mater. Chem. A, 2, 1014–1021 (2014). 7. Fedorkova, A., Nacher-Alejos, A., Gomez-Romero, P., Orinakova, R. &
Kaniansky, D. Structural and electrochemical studies of PPy/PEG-LiFePO4
cathode material for Li-ion batteries. Electrochim. Acta 55, 943–947 (2010 8. Dubal, D. P., Gund, G. S., Lokhande, C. D. & Holze, R. Controlled growth of CoSx
nanostrip arrays (CoSx-NSA) on nickel foam for asymmetric supercapacitors. Energy Technol. 2, 401–408 (2014). 9. Chen, W. et al. High performance nanostructured supercapacitors on a sponge. Nano Lett. 11, 5165–5171 (2011). 10. Lu, X. et al. WO3-x@Au@MnO2 core-shell nanowires on carbon fabric for high-
performance flexible supercapacitors Adv. Mater. 24, 938–944 (2012). Methods Fabrication of sponge@rGO (SP@rGO) composite. At first, rGO was prepared by
the modified Hummer’s method (supporting information S1) reported elsewhere14. Briefly, rGO ink with concentration of 2 mg/ml in 10 mg/ml of sodium
dodecylbenzenesulfonate (SDBS) water solution was prepared by applying a 30 min
bath sonication. A piece of commercially available macroporous cellulose sponge
previously cleaned with water and ethanol several times was dipped into this rGO ink. 16. Chen, F. et al. Large-scale and shape-controlled syntheses of three-dimensional
CdS nanocrystals with flowerlike structure. J. Phys. Chem. C 112, 1001–1007
(2008). (
)
17. Gund, G. S., Dubal, D. P., Jambure, S. B., Shinde, S. S. & Lokhande, C. D. Temperature influence on morphological progress of Ni(OH)2 thin films and its SCIENTIFIC REPORTS | 4 : 7349 | DOI: 10.1038/srep07349 9 subsequent effect on electrochemical supercapacitive properties. J. Mater. Chem. A 1, 4793–4803 (2013). 36. Wang, H. et al. Advanced asymmetrical supercapacitors based on graphene
hybrid materials. Nano Res. 4, 729–736 (2011). subsequent effect on electrochemical supercapacitive properties. J. Mater. Chem. A 1, 4793–4803 (2013). 18. Chen, W., Yang, Y. & Shao, H. Cation-exchange induced high power
electrochemical properties of core-shell Ni(OH)2@CoOOH. J. Power Sources 196,
488–494 (2011). y
37. Huang, J. et al. Asymmetric supercapacitors based on b-Ni(OH)2 nanosheets and
activated carbon with high energy density. J. Power Sources 246, 371–376 (2014). 38. Yan, J. et al. Advanced asymmetric supercapacitors based on Ni(OH)2/graphene
and porous graphene electrodes with high energy density. Adv. Funct. Mater. 22,
2632–2641 (2012). 19. Salunkhe, R. R., Jang, K., Lee, S. & Ahn, H. Aligned nickel-cobalt hydroxide
nanorod arrays for electrochemical pseudocapacitor applications. RSC Advances
2, 3190–3193 (2012). 39. Li, H. B. et al. Amorphous nickel hydroxide nanospheres with ultrahigh
capacitance and energy density as electrochemical pseudocapacitor materials. Nat. Commun. 4, 1894 (2013). 20. Zhang, G. Q. & Lou, X. W. Controlled growth of NiCo2O4 nanorods and ultrathin
nanosheets on carbon nanofibers for high-performance supercapacitors. Sci. Rep. 3, 1470 (2013). 40. Ji, J. et al. Nanoporous Ni(OH)2 thin film on 3D ultrathin-graphite foam for
asymmetric supercapacitor. ACS Nano 7, 6237–6243 (2013). 21. Dubal, D. P., Kim, J. G., Kim, Y., Holze, R. & Kim, W. B. Demonstrating the
highest supercapacitive performance of branched MnO2 nanorods grown directly
on flexible substrates using controlled chemistry at ambient temperature. Energy
Technol. 1, 125–130 (2013). 41. Choi, H. S. & Park, C. R. Author contributions D.P.D. and P.G.R. designed the experiments, analyzed the data and wrote the manuscript. D.P.D. carried out synthesis and characterization of hybrid thin films. D.P.D. and R.H. designed and carried out electrochemical measurements. To the preparation and reviewing
manuscript, all authors contributed equally. 28. Lang, J. W., Kong, L. B., Liu, M., Luo, Y. C. & Kang, L. Asymmetric supercapacitors
based on stabilized a-Ni(OH)2 and activated carbon. J. Solid State Electrochem. 14,
1533–1539 (2010). 29. Shinde, S. K., Dubal, D. P., Ghodake, G. S., Kim, D. Y. & Fulari, V. J. Nanoflower-
like CuO/Cu(OH)2 hybrid thin films: Synthesis and electrochemical
supercapacitive properties. J. Electroanal Chem. 732, 80–85 (2014). Acknowledgments 24. Hsu, C. T. & Hu, C. C. Synthesis and characterization of mesoporous spinel
NiCo2O4 using surfactant-assembled dispersion for asymmetric supercapacitors. J. Power Sources 242, 662–671 (2013). Authors appreciate the award to DPD of a Humboldt Fellowship of the Alexander von
Humboldt Foundation (AvH), Germany and the award of a Marie-Curie Fellowship
through Beatriu de Pinos Program (BP-DGR-2013) for Catalan system of science and
technology, Spain. Partial funding from Spanish Grant MAT2012-39199-C02-01 is
gratefully acknowledged. ICN2 acknowledges support from the Severo Ochoa Program
(MINECO, Grant SEV-2013-0295). Authors appreciate the award to DPD of a Humboldt Fellowship of the Alexander von
Humboldt Foundation (AvH), Germany and the award of a Marie-Curie Fellowship
through Beatriu de Pinos Program (BP-DGR-2013) for Catalan system of science and
technology, Spain. Partial funding from Spanish Grant MAT2012-39199-C02-01 is
gratefully acknowledged. ICN2 acknowledges support from the Severo Ochoa Program
(MINECO, Grant SEV-2013-0295). 25. Salunkhe, R. R. et al. Direct growth of cobalt hydroxide rods on nickel foam and its
application for energy storage. Chem. Eur. J. 20, 3084–3088 (2014). 26. Kong, L. B., Liu, M., Lang, J. W., Luo, Y. C. & Kang, L. Asymmetric supercapacitor
based on loose-packed cobalt hydroxide nanoflake materials and activated
carbon. J. Electrochem. Soc. 156, A1000–A1004 (2009). 27. Tang, Y. et al. Hydrothermal synthesis of a flower-like nano-nickel hydroxide for
high performance supercapacitors. Electrochim. Acta 123, 158–166 (2014). Methods Theoretical guidelines to designing high performance
energy storage device based on hybridization of lithium-ion battery and
supercapacitors. J. Power Sources 259, 1–14 (2014). 22. Wang, F. et al. Electrode materials for aqueous asymmetric supercapacitors. RSC
Adv. 3, 13059–13084 (2013). 23. Zhai, T. et al. A New Benchmark Capacitance for Supercapacitor Anodes by
Mixed-Valence Sulfur-Doped V6O13-x. Adv. Mater. 26, 5869–5875 (2014). Additional information 30. Lang, J. W., Kong, L. B., Liu, M., Luo, Y. C. & Kang, L. Asymmetric supercapacitors
based on stabilized a-Ni(OH)2 and activated carbon. J. Solid State Electrochem. 14,
1533–1539 (2010). Supplementary information accompanies this paper at http://www.nature.com/
scientificreports Supplementary information accompanies this paper at http://www.nature.com/
scientificreports Competing financial interests: The authors declare no competing financial interests. Competing financial interests: The authors declare no competing financial interests. 31. Zhao, Y. et al. Pseudocapacitance properties of AC/LiNi1/3Co1/3Mn1/3O2
asymmetric supercapacitor in aqueous electrolyte. Synth. Met. 159, 331–337
(2009). How to cite this article: Dubal, D.P., Holze, R. & Gomez-Romero, P. Development of
hybrid materials based on sponge supported reduced graphene oxide and transition metal
hydroxides for hybrid energy storage devices. Sci. Rep. 4, 7349; DOI:10.1038/srep07349
(2014). 32. Wu, Z. S. et al. High-energy MnO2 nanowire/graphene and graphene asymmetric
electrochemical capacitors. ACS Nano 4, 5835–5842 (2010). 33. Wang, D. W., Li, F. & Cheng, H. M. Hierarchical porous nickel oxide and carbon
as electrode materials for asymmetric supercapacitor. J. Power Sources 185,
1563–1568 (2008). This work is licensed under a Creative Commons Attribution 4.0 International
License. The images or other third party material in this article are included in the
article’s Creative Commons license, unless indicated otherwise in the credit line; if
the material is not included under the Creative Commons license, users will need
to obtain permissionfrom the licenseholderin order toreproduce the material. To
view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ 34. Wang, D. W., Li, F., Liu, M., Lu, G. Q. & Cheng, H. M. 3D aperiodic hierarchical
porous graphitic carbon material for high-rate electrochemical capacitive energy
storage. Ang. Chem. International Ed. 47, 373–376 (2008). g
g
35. Yu, C., Masarapu, C., Rong, J., Wei, B. & Jiang, H. Stretchable supercapacitors
based on buckled single-walled carbon-nanotube macrofilms. Adv. Mater. 21,
4793–4797 (2009). SCIENTIFIC REPORTS | 4 : 7349 | DOI: 10.1038/srep07349 10
|
https://openalex.org/W4300197948
|
https://zenodo.org/record/3706486/files/6315ijwsc02.pdf
|
English
| null |
AN ADAPTIVE APPROACH FOR DYNAMIC RECOVERY DECISIONS IN WEB SERVICE COMPOSITION USING SPACE BASED QOS FACTOR
|
Zenodo (CERN European Organization for Nuclear Research)
| 2,015
|
cc-by
| 8,517
|
ABSTRACT Service Oriented Architecture facilitates automatic execution and composition of web services in
distributed environment. This service composition in the heterogeneous environment may suffer from
various kinds of service failures. These failures interrupt the execution of composite web services and
lead towards complete system failure. The dynamic recovery decisions of the failed services are
dependent on non-functional attributes of the services. In the recent years, various methodologies
have been presented to provide recovery decisions based on time related QoS (Quality of Service)
factors. These QoS attributes can be categorized further. Our paper categorized these attributes as
space and time. In this paper, we have proposed an affinity model to quantify the location affinity for
composition of web services. Furthermore, we have also suggested a replication mechanism and
algorithm for taking recovery decisions based on time and space based QoS parameters and usage
pattern of the services by the user. Dr. Ravi Shankar Pandey, Richa Pathak Department of Computer Engineering, BIT Mesra , Ranchi, India International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 KEYWORDS Failure recovery, QoS Factors, Location Affinity, Recovery Decisions AN ADAPTIVE APPROACH FOR DYNAMIC RECOVERY
DECISIONS IN WEB SERVICE COMPOSITION USING
SPACE BASED QOS FACTOR Dr. Ravi Shankar Pandey, Richa Pathak 1. INTRODUCTION DOI : 10.5121/ijwsc.2015.6302 11
Enterprises are using information technology to automate their business activities within the
organization as well as with other organizations. They are using different software and hardware
platforms for automating these activities. In general these business activities consist of more than
one smaller sub activities. These activities may reside at same geographical location or at different
geographical location. Internet provides an infrastructure for integrating such activities. A new
paradigm is developed to facilitate these integrations known as Service Oriented Architecture
(SOA). In this architecture software’s are viewed as services. This architecture contains
description of the service using WSDL (Web Service Description Language), communication
protocol SOAP (Simple Object Access Protocol) for providing interaction among the services and
UDDI (Universal Description, Discovery and Integration) storage mechanism for these services. All they are based on open source mechanism provided by XML (Extensible Markup Language). These services are loosely coupled in nature and may be integrated at run time dynamically. This
architecture facilitates three types of entities; these are service requester, service provider and
service broker. The main role of the service providers are to host their services in storage
area(UDDI) and requester searches the desired service through broker in automated environment. 11 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 Different service providers may publish the same services in the UDDI registry. So it become
strenuous to select a single service from the same service domain based on their functional
features. In these view non-functional properties of the services play an important role in service
selection. These non functional properties are known as QoS attributes. The service providers
consider these parameters as QoS attribute for their published services while service requester uses
these parameters as non-functional requirement for their desired services. These parameters are
availability, execution time, cost, reliability, latency. All these parameters are primarily based on
time factor. .[24] have proposed QoS attributes which are based o the usability of the services in
their composition other than time related QoS (dominant role, dominant operations).Web services
are hosted at different geographical locations and are used by people situated at different
geographical regions. In this scenario services may be preferred by their geographical location or
they may be frequently used for a particular region. Thus we have concluded that for service
selection location is also a non-functional attribute of a service. 1. INTRODUCTION We are categorizing all the non-
functional attributes or features of web service in two categories. One is the QoS based on time
factor (reliability, cost, latency, execution time) and other is the QoS based on location that is
location affinity of the service. We have introduced a term “location affinity” with respect to the
web services as a space based quality of service factor. We are describing the location affinity as
the degree or extent to which user likes and utilize the service of a particular geographical location. When a service execution takes place in atomic manner it is less susceptible to failure. Service
composition is prone to failure due to lack of availability, semantic mismatching and other
functional attributes. Several research efforts have been made to model non-functional parameters
and provide a recovery mechanism in case of the failure occurred during compositions. In this paper, we have proposed a methodology for taking the recovery decisions to handle the
failure in service composition based on time as well as location based QoS attributes together. We
are also proposing finite state machine model for the web service composition. This model
includes their QoS parameters, input parameters, set of operations, transition function for transition
from one state to another and evaluating impact on Overall QoS factors of our model. We are also
suggesting a methodology to take recovery decisions dynamically. This paper is organized as follows. The section 2, introduces the related work on service
composition, service failure, QoS evaluation using finite state machines. In section 3, we
represented the location affinity based meta-model and finite state machine model for service
composition using QoS attributes. In the last section, we presented a replication strategy and
algorithm to take recovery decision in the presence of fault. 2. RELATED WORK Now a day’s web based services are being capturing the IT market completely. With the growth of
use of Internet user’s requirement is also growing explosively and single service fails to meet this
requirement. Thus service composition came in to the existence. Various methods for service
composition have been presented whether it is dynamic or static. Sunil R Dhore et al [1] have
discussed the semantic composer that uses enhanced ant colony optimization mechanism to
provide service composition in efficient manner by finding optimal composition length in each set
of candidate web service proposed for service composition. Zhou Xiangbing et al [2] have
presented a web service modeling ontology for service composition using genetic algorithm. In
this paper they have considered four non functional attributes, these are: information exchange, 12 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 13
time, matching reasoning and cost. Finite state machine based composition solutions have also
been proposed by different authors.Olga et al [4] have estimated the quality of service and quality
of experience of web service using the finite state machine concept. Jun Sun et al [25] have
suggested the finite state machine synthesis for software systems. Number of methods has been
proposed to monitor and identify faults in service based systems. Jocelyn Simmonds et al [9] have
presented an approach to monitor and recover web service based applications using three stage
phenomenons. In first stage of preprocessing BPEL code is converted in to labeled transition
systems and properties supplied by the user are converted in to monitor code .In monitor phase
application is checked for an error and In recovery phase compensation plan are ranked and
applied. Compensation allows a web service to go-back to the previous stage if an error occurred. Thirumaran.M et al [6] have proposed a QoS based run time exception handler. This handler first
takes exception information as an input and on the basis of that calculates the time and space
complexity. Decidability evaluator than categorize the problem in to, NP-Complete solvable
problem set, NP-Hard may be solvable problem set. They have also used turning machine to find
the solution of the problem in a specified time using audit log that contains some predefined
solutions for particular problem. Services composed at run time are more prone to failure. 2. RELATED WORK These
failures could occur due to various reasons .Hadi Saboohi et al [11] have figured out reasons for
the failures. This paper identifies the functional as well as non functional causes of service
composition failure. Functional causes includes service unavailability, service malfunctioning and
non functional causes includes unexpected data, network delay, response time-out. Abdelkarem
Erradi et al [17] have proposed various recovery policies (retry, substitution, parallel execution,
dynamic update of service composition). They have also proposed MASC (Manageable &
Adaptive Service Composition) model for monitoring failure and providing recovery from failure. H. Elfawal Mansour et al [14] have proposed a model that calculates the reliability at run time and
uses roll back mechanism to recover services from failure. They have used a broker that decides
that the result computed by a particular web service is relevant or not. If it is relevant process of
computation continues otherwise the service is roll backed and another service having same
functionality is been called to complete the execution of the complete web service based system. Suchi Gupta et al [8] have presented subset replacement mechanism to handle service failure. According to this paper failed set of services are first identified by the middle agent and then
replaced by another set of services providing the similar functionality. Keting Yin [15] have also
used replacement mechanism to recover service from failure. They have also presented a ranking
mechanism to select the service that could replace the failed service based on non functional QoS
parameters. Guisheng Fan et al[16] has categorized the service failure as failure of available
service, failure of component service, Failure of operating environment and model the composite
web services using petri-nets. Cao et al [18] have presented in which firstly, the service execution
graph (SEG) is introduced and a service execution solution selection algorithm is proposed to
choose one from the solution set of TSSA which has the highest success rate of recovery. Then,
the concepts of execution backup path and switch cost are introduced and a search algorithm is
presented to search for the optimal backup path when current service failure occurs.Rafael
Angarita et al [10] have categorized the recovery mechanism in to two parts based on the ACID
properties of a transaction. These categories are forward and backward recovery mechanism. In
forward recovery mechanism replacement, compensation and replication strategies are included. In
backward recovery mechanism roll-back strategy is included. 2. RELATED WORK All the recovery mechanism has
been tested based on the execution cost and execution time in different failure conditions and
dynamic recovery decisions could be taken on the basis of experimental result. Replication of the
web service is the preferable solution of handling failure of the services in distributed
environment. Marwa F. Mohamed et al [21] have provided a framework for the dynamic 13
time, matching reasoning and cost. Finite state machine based composition solutions have also
been proposed by different authors.Olga et al [4] have estimated the quality of service and quality
of experience of web service using the finite state machine concept. Jun Sun et al [25] have
suggested the finite state machine synthesis for software systems. Number of methods has been
proposed to monitor and identify faults in service based systems. Jocelyn Simmonds et al [9] have
presented an approach to monitor and recover web service based applications using three stage
phenomenons. In first stage of preprocessing BPEL code is converted in to labeled transition
systems and properties supplied by the user are converted in to monitor code .In monitor phase
application is checked for an error and In recovery phase compensation plan are ranked and
applied. Compensation allows a web service to go-back to the previous stage if an error occurred. Thirumaran.M et al [6] have proposed a QoS based run time exception handler. This handler first
takes exception information as an input and on the basis of that calculates the time and space
complexity. Decidability evaluator than categorize the problem in to, NP-Complete solvable
problem set, NP-Hard may be solvable problem set. They have also used turning machine to find
the solution of the problem in a specified time using audit log that contains some predefined
solutions for particular problem. Services composed at run time are more prone to failure. These
failures could occur due to various reasons .Hadi Saboohi et al [11] have figured out reasons for
the failures. This paper identifies the functional as well as non functional causes of service
composition failure. Functional causes includes service unavailability, service malfunctioning and
non functional causes includes unexpected data, network delay, response time-out. Abdelkarem
Erradi et al [17] have proposed various recovery policies (retry, substitution, parallel execution,
dynamic update of service composition). They have also proposed MASC (Manageable &
Adaptive Service Composition) model for monitoring failure and providing recovery from failure. H. 2. RELATED WORK Elfawal Mansour et al [14] have proposed a model that calculates the reliability at run time and
uses roll back mechanism to recover services from failure. They have used a broker that decides
that the result computed by a particular web service is relevant or not. If it is relevant process of
computation continues otherwise the service is roll backed and another service having same
functionality is been called to complete the execution of the complete web service based system. Suchi Gupta et al [8] have presented subset replacement mechanism to handle service failure. According to this paper failed set of services are first identified by the middle agent and then
replaced by another set of services providing the similar functionality. Keting Yin [15] have also
used replacement mechanism to recover service from failure. They have also presented a ranking
mechanism to select the service that could replace the failed service based on non functional QoS
parameters. Guisheng Fan et al[16] has categorized the service failure as failure of available
service, failure of component service, Failure of operating environment and model the composite
web services using petri-nets. Cao et al [18] have presented in which firstly, the service execution
graph (SEG) is introduced and a service execution solution selection algorithm is proposed to
choose one from the solution set of TSSA which has the highest success rate of recovery. Then,
the concepts of execution backup path and switch cost are introduced and a search algorithm is
presented to search for the optimal backup path when current service failure occurs.Rafael
Angarita et al [10] have categorized the recovery mechanism in to two parts based on the ACID
properties of a transaction. These categories are forward and backward recovery mechanism. In
forward recovery mechanism replacement, compensation and replication strategies are included. In
backward recovery mechanism roll-back strategy is included. All the recovery mechanism has
been tested based on the execution cost and execution time in different failure conditions and
dynamic recovery decisions could be taken on the basis of experimental result. Replication of the
web service is the preferable solution of handling failure of the services in distributed
environment. Marwa F. Mohamed et al [21] have provided a framework for the dynamic 13
Suchi Gupta et al [8] have presented subset replacement mechanism to handle service failure. 2. RELATED WORK According to this paper failed set of services are first identified by the middle agent and then
replaced by another set of services providing the similar functionality. Keting Yin [15] have also
used replacement mechanism to recover service from failure. They have also presented a ranking
mechanism to select the service that could replace the failed service based on non functional QoS
parameters. Guisheng Fan et al[16] has categorized the service failure as failure of available
service, failure of component service, Failure of operating environment and model the composite
web services using petri-nets. Cao et al [18] have presented in which firstly, the service execution
graph (SEG) is introduced and a service execution solution selection algorithm is proposed to
choose one from the solution set of TSSA which has the highest success rate of recovery. Then,
the concepts of execution backup path and switch cost are introduced and a search algorithm is
presented to search for the optimal backup path when current service failure occurs.Rafael
Angarita et al [10] have categorized the recovery mechanism in to two parts based on the ACID
properties of a transaction. These categories are forward and backward recovery mechanism. In
forward recovery mechanism replacement, compensation and replication strategies are included. In
backward recovery mechanism roll-back strategy is included. All the recovery mechanism has
been tested based on the execution cost and execution time in different failure conditions and
dynamic recovery decisions could be taken on the basis of experimental result. Replication of the
web service is the preferable solution of handling failure of the services in distributed
environment. Marwa F. Mohamed et al [21] have provided a framework for the dynamic 13 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 replication of the web services .This framework automatically replicates a service based on it’s
consumption and reduces the service response time as well. They have taken sensor based
mechanism to identify the service failure and then take replication decision for the failed web
service. Mario Bravetti et al [22] computed the system performance after replicating the web
service using SOCK calculus. An Liu et al [26] have proposed a framework named as “FACTS” to
provide highly reliable and fault tolerant service composition. 2. RELATED WORK They have also used BPEL to
elaborate their proposed architecture.Johannes Behl et al [27] have presented architecture to
replicate the BPEL engine as well as web service using proxy servers (input and output proxy
servers) to enhance the availability and reliability of the services in cloud computing platform. Ivona Brandic et al [23] location affinity QoS with respect to the Grid Computing environment. It
is basically used for providing the security to the users of the grid and giving the grid resources of
particular domain (organization, home) based on the user’s willingness. R.S.Pandey et al [24] has
proposed a methodology to estimate the minimum and maximum value of the Quality of service
attributes (reliability, availability, latency, security). We have analyzed that all the above
researches basically emphasis upon the time based Quality of Service factors for composing the
service and also for recovery decision. In [10] recovery decisions were taken dynamically on the
basis of the execution time and execution cost. None of the author considered the geographical
location factor to take recovery decisions at run time. In our paper we are selecting recovery
strategy among all the available strategies (replacement, roll-back, replacement) based on
geographical location .In this paper we are also advocating the need of the replication mechanism
and suggested a methodology to decide which service from the same location affinity and similar
set of functionality should be replicate in distributed environment to avoid failure. In our proposed
work we are including location factor for the composition of services based on finite state
machine. Dynamic recovery concept has also been extended with location necessity. 3. MODELING LOCATION AFFINITY In [23] location affinity is modeled to benefit the grid computing users. The authors of this paper
mainly concerned with security and legal issues, while using grid technology. They have also
discussed that grid users hesitate to use this technology everywhere rather they wanted to use this
technology within a specific domain or range. They have modeled location affinity for grid user
with in a specific domain of their choice for the security purpose. QoWL (QoS-aware Grid Flow
Language) that is a XML based language is developed and used for modeling the location affinity. In [23] location affinity is modeled for the security purposes but in our paper we are modeling
location affinity with a different perspective. We are considering affinity as the user’s preference
to use a particular service that belongs to a certain geographical boundary. For example a user
weekly visits to the Mumbai city and requires hotel service of Mumbai city frequently. Thus user’s
location affinity is Mumbai city. In this model, we have considered that universe is divided into the
continents, continents are divided into countries, countries are divided into the states, states are
divided into the district and districts are divided into cities and villages respectively. This model
uses various attributes to distinguish among countries, states, cities and villages. As per our model
city is specialized geographical area of the district and has several villages. Similarly, state is an
aggregation of all the districts which belongs to the same state. In this model, we have not
distinguished different types of states for simplicity. We have not further detailed city and village
to make the model simple.Fig1 is representing the meta-model of location affinity. We are going to
use this model in web service composition. In web service composition several operators are used
(sequential, parallel, loop and switch). Service may be composed one after other which is called as 14 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 sequential execution of the services or two services may execute simultaneously in parallel mode. One service may execute more than one time or under any defined condition. The proposed model
has some pre-assumptions for service composition based on our proposed geographical criteria’s. If two services are executing in the same state than their affinity is considered to be the city or
district affinity. 3. MODELING LOCATION AFFINITY Similarly, if these services are composing from different states than their affinity is
considered as state affinity. Consider that service1’s location affinity is Allahabad city of Uttar
Pradesh state and services2’s location affinity is the Banaras city of the state Uttar Pradesh. Then,
while composing their affinity is city since lying in the same state or region of our model. Similarly, we have considered that service1’s location affinity is Allahabad city of Uttar Pradesh
state and Service 2’s location affinity is Mumbai city of the State Mumbai then compositely their
affinity would be state since lying in different boundaries of our model. Figure 1. Modeling Location Affinity Figure 1. Modeling Location Affinity Figure 1. Modeling Location Affinity 4. FINITE STATE MACHINE FOR REPRESENTING WEB SERVICES Every web service consists of several input and output operations. A service changes its state due
to the invocation of various available operations. These invocations may affect the parameters of
quality of service attributes. For example: if the invocation is successful then reliability of web
service will be higher. The other attributes also may change due to the state change like cost. For
example: In ticket Reservation system if we invoke bookTicket operation, in this scenario the cost
of the web service may change. In the case of single web service execution, the space related QoS
attributes like affinity will not change. Several research efforts have been made to incorporate
time-based QoS attributes to model web service using finite state machine [4], [24]. We are
arguing that the space related QoS attribute will play a dominant role in the case of web service
composition. We have modeled a web service as finite state machine that includes set of input
operations, initial state, final state, transition function and quality of service parameters. Our 15 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 model is based on time as well as space related QoS attributes, so it is a vector which has two
different types of values one is based on geographical location and other is based on time. These
component services have been modeled using finite state machine concept. A component web
service is a finite state machine having touple (I, O, F, S0 , SF, δ, Q).Where I is representing the set of input. O is representing the set operations
δ is the transition function that is represented as :
δ: I × O × S× QS
SF is the final state of the finite state machine. F is the subset of S and represents the set of final states. Q is the quality of service factor which is categorized on the basis of the time and
space dimensions i.e. Qs ɛ Q and QT ɛ Q as well as
Q=QT × QS
QT=QE × QR × QA I is representing the set of input. Where QE is the execution time, QR is for reliability and QA for availability. Where QE is the execution time, QR is for reliability and QA for availability. Affinity is the quality of service attribute based on location of the web service. It is computed by
the user’s usability of web service based on user’s location preferences. 4. FINITE STATE MACHINE FOR REPRESENTING WEB SERVICES O is representing the set operations δ is the transition function that is represented as :
δ I
O
S
QS δ is the transition function that is represented as :
δ: I × O × S× QS SF is the final state of the finite state machine. F is the subset of S and represents the set of final states. Q is the quality of service factor which is categorized on the basis of the time and
space dimensions i.e. Qs ɛ Q and QT ɛ Q as well as
Q=QT × QS
QT=QE × QR × QA 5. MODELING COMPOSITION OF WEB SERVICES BASED ON LOCATION
AFFINITY 5. MODELING COMPOSITION OF WEB SERVICES BASED ON LOCATION
AFFINITY In [4] a finite state machine based model is proposed to evaluate QoS parameters of service
composition. They have also elaborated how machine learning algorithms can be used for
evaluating QoS of service composition. [25] have proposed a model for synthesizing finite state
machine. We are synthesizing finite machine based on time as well as space based QoS
parameters. A service could individually serve the user or it could be the composition of two or more services. Thus, overall system output is dependent on the successful execution of the each component web
service existing in composition plan. To give rules for composition of web services we are considering two state machines M1 and M2
i.e. M1= (I1, O1, F1, S01, SF1, δ1, Q1) and M2 = (I2, O2, F2, S02 , SF2, δ2, Q2). Resultant machine can
be expressed as, M = (I, O, F, S01 ,SF1, δ, Q) .Where I=I1 U I2
O=O1 U O2
F = F1 × F2
δ: I1 × I2 ×O1 ×O2 × Q × S1× S2 F1 × F2
Q Q1 composition Q2 I=I1 U I2
O=O1 U O2
F = F1 × F2
δ: I1 × I2 ×O1 ×O2 × Q × S1× S2 F1 × F2
Q Q1 composition Q2 I=I1 U I2
O=O1 U O2
F = F1 × F2
δ: I1 × I2 ×O1 ×O2 × Q × S1× S2 F1 × F2
Q Q1 composition Q2 In composition model services may execute in sequential manner, parallel manner, in the form of
loop and choice [24], [29]. 16 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 Thus quality of service attributes composition depends upon the composition operators. We are
using the composition rules for all the composition operators as given in [24], [29]. We are
summarizing these rules as given below with respect to the two services S1 and S2. We have assumed that (r1, A1, E1) is the reliability, availability and execution time of the service S1
and (r2, A2, E2) is the reliability, availability and execution time of the service S2 respectively. InventoryCheck: This service is responsible for checking the quantity of the product ordered by the Buyer. This
service ensures that the quantity of item requested by the Buyer is available in the stock, if not it
sends a negative acknowledgement to the Seller service to maintain the consistency. Seller: This service receives the item request from Buyer service and process the request by initiating the
execution of InventoryCheck and CreditCheck services. After receiving the response returned by
both the services Seller acknowledge the Buyer about the status of his request of product purchase. 5. MODELING COMPOSITION OF WEB SERVICES BASED ON LOCATION
AFFINITY Consider that services S1 and S2 are executing based on choice than according to the rules [24],[29]
resultant reliability is the minimum of the reliabilities of both the services, resultant availability is
the minimum of availabilities of both the services and resultant execution time is the maximum of 17 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 the execution time of both the services respectively. In choice operator the affinity is the affinity of
the web service that is selected for the execution among all available choices. QT=QT1 choice QT2 = (r1,A1,E1)or( (r2,A2,E2)=(r,A,E)
r =min (r1, r2)
A=min (A1, A2)
E=max (E1, E2) Example 1. Consider the Figure 2, which represents the composite execution of the purchase order service. This service uses four services for completing the execution plan. These services are defined as: Buyer: This service is agent service that initiates the composition plan and invokes seller service after
giving the request of particular product to purchase. 5. MODELING COMPOSITION OF WEB SERVICES BASED ON LOCATION
AFFINITY Consider that services S1 and S2 are executing in sequential manner than according to the rules
given in [24],[29] resultant reliability is the product of reliabilities of both the services, resultant
availability is the product of availabilities of both the services and resultant execution time is the
summation of the execution times of both the services respectively. Our affinity rule suggests that
if two services have same level of affinity than the resultant affinity will be one level higher than
the previous level affinity. QT=QT1 × QT2= (r1, A1, E1), (r2, A2, E2) =(r, A, E)
r= r1 × r2
A=A1 × A2
E=E1+E2 Consider that services S1 and S2 are executing in parallel manner than according to the rules
[24,29] resultant reliability is the minimum of the reliabilities of both the services, resultant
availability is the minimum of the availabilities of both the services and resultant execution time is
the maximum of the execution times of both the services respectively. If the parallel execution of
web services is taking place during composition than the resultant affinity level is considered to be
at same affinity level. QT=QT1 || QT2 = (r1,A1,E1)||( (r2,A2,E2)=(r,A,E)
r = r1|| r2=minimum (r1, r2)
A=A1||A2=minimum (A1, A2)
E=maximum (E1, E2) QT=QT1 || QT2 = (r1,A1,E1)||( (r2,A2,E2)=(r,A,E)
r = r1|| r2=minimum (r1, r2)
A=A1||A2=minimum (A1, A2)
E=maximum (E1, E2) Consider that services S1 and S2 are executing in loop than according to the rules given in [24,29]
resultant reliability is the minimum of the reliabilities of both the services, resultant availability is
the minimum of availabilities of both the services and resultant execution time is the multiple of
the number of times loop is executing a service respectively. In loop based execution of web
services the resultant affinity level is considered to be as before the execution of the service. QT=QT1 loopQT2 = (r1,A1,E1)loop( (r2,A2,E2)=(r,A,E)
r= r1= r2
A= A1=A2
E=n × E
Where n is the number of times loop is executing. Where n is the number of times loop is executing. Where n is the number of times loop is executing. 5.1. Aaa Finite State Machine for Buyer Service Finite state machine takes the name of the product as an input and request product order. In this
description of the finite state machine pro_name is representing name of the product ordered by
Buyer. Here reqOrder () operation is used to send the product order request to the Seller. Few
variables are also used to represent the communication process among services. In this finite state
machine representation poreqstate variable is used to store the status of the request whether it is
sent from the Buyer’s end to the Seller’s end or not and r1,a1,e1,la1 variables are used to store
reliability, availability, execution time and location affinity of the Buyer service. •
I= {pro_name}
•
O= {reqOrder ()}
•
δ = {pro_name} × {reqOrder()} × S11{poreqstate, r1, a1,e1, la1}S12{poreqstate =”Sent”,
r1=.7, a1=.8 ,e1=8, la1= “Lucknow”}
•
QT= {.7, .8, 8}
•
QS= {“Lucknow”} •
I= {pro_name} •
O= {reqOrder ()} •
QT= {.7, .8, 8} •
QS= {“Lucknow”} CreditCheck: This service checks the Buyer’s balance and acknowledge the seller, whether Buyer is having
sufficient amount to purchase the item or not. 18 18 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 Figure 2. Composite Purchase Order Service Figure 2. Composite Purchase Order Service •
O= {processOrder ()} 5.2. Bbb Finite State Machine for Seller Service Finite state machine of Seller service takes the name of the product and quantity of the product as
an input. In this description of the finite state machine pro_name and quantity are representing
name of the product and quantity of the product ordered by Buyer. processOrder () operation is
used for further processing in the composite system. Variables poreqstate, ccrequeststate,
ivreqstate,poack are used to store the status of the product order request state, credit check request
state, inventory check request state In this scenario.r2,A2,E2,la2 variables are used to store
reliability, availability, execution time and location affinity of the Seller service. •
I= {pro_name, quantity} •
O= {processOrder ()} 19 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 •
δ={pro_name,quantity}×{processOrder()}×S21{poeqstate,ccrequeststate,ivreqstate,poack,
r2,A2,E2,la2}S22{poreqstate=”received”,ccreqstate=”sent”,ivreqstate=”sent”,poack=”sen
t”, r2=.60,A2=.55,E2=5,la2= “Allahabad” } •
δ={pro_name,quantity}×{processOrder()}×S21{poeqstate,ccrequeststate,ivreqstate,poack,
r2,A2,E2,la2}S22{poreqstate=”received”,ccreqstate=”sent”,ivreqstate=”sent”,poack=”sen
t”, r2=.60,A2=.55,E2=5,la2= “Allahabad” } •
QT= {.60, .55, 5} •
QS= {“Allahabad”} 5.4. Ddd Finite State Machine for CreditCheck Service Finite state machine takes the account detail of the buyer as an input. In this finite state machine
checkAvailability () operation is used to check the required balance for purchasing the product. In
this scenario ccreqstate, ccavailablestate, ccack, r4, A4, E4, la4 notations are used to describe credit
check request state, credit availability state, credit acknowledgement state, reliability, availability,
execution time, location affinity of Credit Check service. •
I= {account_detail} •
O={creditAvailability ()} •
δ = {account_detail}× {checkAvailability() }× S41{ ccreqstate,ccavailablestate,
ccAck,r4,A4,E4,la4}
S42{ccreqstate=”recieved”,ccavailablestate=”true”,ccack=”sent”,r4=
.9,A4=
.8
,E4=11,la4=” Banaras” } .8 •
QT= {.9,.8,11} •
QT= {.9,.8,11} •
QS= {“Banaras”} •
QS= {“Banaras”} •
QS= {“Banaras”} 5.3. Ccc Finite State Machine for InventoryCheck Service Finite state machine takes the quantity of the product as an input. checkInvAvailability ()
operation is used to check whether the required quantity of the product is available in inventory
stock or not. In this context ivreqstate, invavailablestate, invack, r3, A3, E3, la3 notations are used
to describe inventory request state, inventory availability state, inventory acknowledgement state,
reliability, availability, execution time, location affinity of InventoryCheck service. •
I= {quantity} •
I= {quantity}
•
O={checkInvAvailability()}
•
δ
=
{quantity}×
{checkInvAvailability()}
×
S31{
ivreqstate
,invavailablestate,invack,r3,A3,E3,la3}
S32{ivreqstate=”received”,inavailablestate=”true”,invack=”sent”, r3=.7,.A3=.6, E3=7,
la3= “Mumbai” }
•
QT= {.7, .6, 7}
•
QS= {“Mumbai”} •
I= {quantity}
•
O={checkInvAvailability()}
•
δ
=
{quantity}×
{checkInvAvailability()}
×
S31{
ivreqstate
,invavailablestate,invack,r3,A3,E3,la3}
S32{ivreqstate=”received”,inavailablestate=”true”,invack=”sent”, r3=.7,.A3=.6, E3=7,
la3= “Mumbai” }
•
QT= {.7, .6, 7}
•
QS= {“Mumbai”} •
O={checkInvAvailability() •
QT= {.7, .6, 7} •
QS= {“Mumbai”} 5.5. Eee Service Composition These Services have been composed to complete the system execution. In this example Buyer
service is executing first in sequential manner with Seller service. Seller service than invoke the
InventoryCheck and CreditCheck services in parallel to give desired output. 20 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 Buyer.Seller.InventoryCheck||CreditCheck The resultant Quality of service and finite state machine of composite service purchase order can
be represented as given below. Where IB.S , QTB.QTS, QSB.QSS are representing input , time based
QoS, space based QoS of Buyer andSeller together. •
I B.S= {IB U IS} = {pro_name, quantity} •
I B.S= {IB U IS} = {pro_name, quantity} •
OB .OS= {OBUOS} = {reqOrder (), processOrder ()} •
δB.δS=IB×IS×OB×OS× S11×S21S12×S22= {pro_name} × {quantity} × {reqOrder()} × {
processOrder()} ×S11{poreqstate , r1 , A1 , E1 , la1} × S 21{poreqstate , ccrequeststate ,
ivreqstate , poack , r2 , A2 , E2 , la2} S12{poreqstate=”Sent”, r1=.7, A1=.8, E1=8,
la1=”Lucknow”} × S22{poreqstate=”received”, ccreqstate=”sent”, ivreqstate=”sent”,
poack=”sent”, r2=.6, A2=.55, E2=5, la2=” Allahabad“} •
QTB.QTS= {.42, .44, 13} •
QSB.QSS = {“STATE AFFINITY”} •
QSB.QSS = {“STATE AFFINITY”} Since Inventory and Credit Check services are executing in parallel manner
WI||WC Since Inventory and Credit Check services are executing in parallel manner
WI||WC Finite Sate machine for composition have been represented as: Finite Sate machine for composition have been represented as: •
I CI.CC= {ICI U ICC} = {quantity, account_detail} •
O CI.CC= {OCI U OCC } = {checkInvAvailability() , checkAvailability ()} •
δCI .δCC=ICI × ICC × OCI×OCC× S31×S41S32×S42={Quantity} × { Account_detail } × {
checkInvAvailability()} ×{checkAvailability ()} × S31 { ivreqstate , invavailablestate,
invack , r3, A3, E3, la3} × S41{ ccreqstate , ccavailablestate, ccack , r4 , A4 , E4 ,
la4}S32{ivreqstate=”received”, inavailablestate=”true”, invack=”sent”, r3=.7, A3= .6,
E3=7 , la3= “Mumbai”} × S42{ccreqstate=”received”, ccavailablestate=”true”,
ccack=”sent” , r4= .9 , A4= .8 , E4=11 , la4=”Banaras” } •
QTS.QTC={ .7, .6, 11 } •
QSI.QSC= {“STATE AFFINITY”} •
QSI.QSC= {“STATE AFFINITY”} In this finite state model ICI.CC , O CI.CC , δCI .δCC , QTI.QTC , QSI.QSC are representing the
composite input, output, transition function ,time based QoS and space based QoS of the
composite Inventory and Credit check services. Complete composite finite state machine for
purchase order service is given below: •
I= {pro_name, quantity, account_detail} •
I= {pro_name, quantity, account_detail} {p
q
y
}
•
O= {reqOrder (), processOrder (), checkInvAvailability(),checkAvailability ()} •
δ = {pro_name, quantity, account_detail}×{ reqOrder (), processOrder (),
checkInvAvailability(), checkAvailability()} ×S1f{poreqstate, r1, A1, E1, la1,
ccrequeststate, ivreqstate, poack, r2, A2, E2, la2, ivreqstate , invavailablestate, ccreqstate,
ccavailablestate, ccack, r4, A4, E4, la4, invack, r3, A3, E3, la3} S2f{ poreqstate=”Sent”,
r1=.7,A1=.8,E1=8, la1=”Lucknow”, poreqstate=”received”, ccreqstate=”sent”,
ivreqstate=”sent”, poack=”sent”, r2=.6,A2=.55,E2=5,la2= “Allahabad”, ivreqstate
=”received”, inavailablestate=”true”, invack=”sent”,r3=.7, A3=.6, E3=7, la3= “Mumbai”,
ccreqstate=”received” , ccavailablestate=”true” , ccack=”sent”,r4= .9,A 4= .8, E4=11,
la4=”Banaras”} 4
}
•
QTB.QTS= {.29, .26, 24} 21 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 •
QSB.QSS = {“COUNTRY AFFINITY”} •
QSB.QSS = {“COUNTRY AFFINITY”} •
QSB.QSS = {“COUNTRY AFFINITY”} of the service having similar functionality and similar affinity than we send the replica
copy for the location affinity of the complete composite service execution is considered to be
“Country” and in case of the failure service providing the same functionality from the country
affinity is suggested to replace with failed service. 6. REPLICATION POLICY In the view of advancement in distributed computing, need of replication is also growing rapidly
Service replication is also the most popular remedy to avoid failures during service execution. In
the scenario where a system contains only three and four services full replication gives 90% fault
tolerance. In case of the system having thousands of services, replication is not a feasible choice
for us due to storage and processing overhead. So in distributed computing full replication is a very costly affair. It generally added measurable
amount of cost in total composition cost. We are providing a methodology according to which
only one service from the same functionality domain as well as location affinity is replicated to
reduce the storage overhead of the system. Replication of a service is done on the basis of the
threshold value. This threshold value is considered as the popularity factor of the service from the
same location affinity. This threshold value is calculated on the basis of the service usage pattern
of the user. Definition 1. Popularity index is the index according to which replica of a service is being
created. This popularity is dependent upon the average usage amount of the service by the users in the System. Notation
for popularity factor is P and U for average service usage amount. P ∝ U (1)
P= RU (2) P ∝ U (2) Where R is the constant and depends upon the ratio of the number of users of service and total
users of the system. [28] have also modeled replication manager concept to assign jobs to the web
services based on round robin algorithm for proper utilization of resources. In this research we are
proposing replication manger concept to calculate the popularity index and creating replica of
most popular service. Consider a system that contains the five users of the seller services from the same location affinity
that is Mumbai (Maharashtra).There are five seller services from the same location affinity that are
providing similar set of functions to the user. These services are Seller1, Seller2, Seller3, Seller4,
and Seller5 respectively. In the system there are 500 users. Replicating all the services will increase
the performance as well as storage overhead .Solution of this problem is the calculation of
popularity factor. Service having highest population factor is being replicated to avoid the fault in
the system. 6. REPLICATION POLICY 22 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015
Table 1. Service Usage Frequency
Popularity factor is calculated for all the service given in table 1. Service
/User
Seller1
(MUM)
Seller 2
(MUM)
Seller3
(MUM)
Seller4
(MUM)
Seller5
(MUM)
User1
(MUM)
100
100
300
100
100
User2
(MUM)
200
50
100
100
100
User3
(MUM)
300
30
300
100
50
User4
(MUM)
50
150
100
100
50
User5
(MUM)
100
50
50
100
100 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015
Table 1. Service Usage Frequency Popularity factor is calculated for all the service given in table 1. P SELLER1 = (5/500)×(750/5)=1.5
PSELLER2 = (5/500) ×(380/5)=.76
PSELLER3= (5/500) × (850/5) =1.7
PSELLER4= (5/500) × (500/5) =1
PSELLER5= (5/500) × (400/5) =.80 P SELLER1 = (5/500)×(750/5)=1.5
PSELLER2 = (5/500) ×(380/5)=.76
PSELLER3= (5/500) × (850/5) =1.7
PSELLER4= (5/500) × (500/5) =1
PSELLER5= (5/500) × (400/5) =.80 P SELLER1 = (5/500)×(750/5)=1.5
PSELLER2 = (5/500) ×(380/5)=.76
PSELLER3= (5/500) × (850/5) =1.7
PSELLER4= (5/500) × (500/5) =1
PSELLER5= (5/500) × (400/5) =.80 From the calculations given above Seller3 is identified as the highest popularity service. This
service is replicated in the distributed environment. Periodic update in the service usage pattern is
performed by replication manager to find out the highest popular service in the service domain and
particular location affinity. 7. CONCLUSION In this paper we have modeled geographical locations for computing location affinity of the
services. We have also integrated time based QoS attributes and space based QoS attributes to
model failure. A service failure recovery policy is also introduced that takes recovery decisions
dynamically based on our suggested QoS attributes. Replication is the basic demand of
distributed systems but it is a costlier effort to implement. Thus we have initially included a
popularity value to decide the service that should be replicated. We also suggested the algorithm
that takes recovery decisions based on time as well as space based QoS parameters. 6.1. Aaa PROPOSED ALGORITHM Taking in to consideration the concept given in the replication policy we are assuming that we
have already a replica of the service providing similar services from the same affinity as a failure
handling mechanism. Our suggested algorithm is taking three types of the recovery decisions
.Firstly it checks the replica copy of the failed service if we found the replica execution. If it found
replica copy as unavailable as it takes the replacement approach as a remedy of failure. Lastly if
both the foresaid operations are unsuccessful it just roll-back the execution of the service.In this
scenario r1,a1,E1, is representing the reliability, availability ,execution time of the failed service
and r2,a2,E2 reliability, availability ,execution time of the service to be replaced. 23 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015
Algorithm 1. Service Recovery Based on time as well as space QoS
Input: Failed Service
Output:Selected Recovery Mechanism
1. Check for the availability of the replica of the service. 2. If (Replica Available) then
3. Provide replica of the most popular service providing similer functionality from the same
location affinity to the user. 4. Else
5. If (r1<r2 && a1<a2 && E1 >E2&& user’s
location affinity==location Affinity of Service)
Then
6. replace the service
7. Else
8. Rollback the failed service REFERENCES [1]
Sunil R Dhore, M U Kharat,”QoS Based Web Service Composition using Ant Colony Optimization:
Mobile Agent Approach”, International Journal of Advance Research in Computer and
Communication Engineering, vol. 1, issue 7, pp. 519-527, September 2012. [2]
Zhou Xiangbing, Ma Hongjiang, Miao Fang “An Optimal Approach to the QoS-Based WSMO Web
Service Composition Using Genetic Algorithm”, Workshops Lecture volume 7759, pp 127-139,
Springer, 2013. [3]
Quan Z. Sheng a, xiaoqiang Qiao b,, Athanasios V. Vasilakos c, Claudia Szabo a,Scott Bourne a,
xiaofei xu d ,“Web services composition: A decade’s overview”, Information Sciences 280 ,pp. 218–
238,Elsevier,2014. [4]
Olga kondratyeva,Natalia Kushik ,Ana Cavalli,Nina Yevtushenko,” Evaluating Web Service Quality
using Finite State Models”, Proc. 13th International Conference on Quality Software, pp.95 – 102,
IEEE, 2013. [5]
Kevin Wiesner, Roman Vacul´ın, Martin Kollingbaum, and Katia Sycara, ”Recovery Mechanisms for
Semantic Web Services”, Distributed Applications and Interoperable Systems ,Lecture Notes in
Computer Science, volume 5053, pp 100-105,Springer,2008. [6]
Thirumaran.Ma,Dhavachelvan.Pb,Shanmugapriya.Rc, Kiran Kumar Reddyd,” A Novel Approach for
Web Service Run Time Exception Handling”, In the proc. of 2nd International Conference on
Communication, Computing & Security, volume 6, pp.145–152, Elsevier,2012. 24 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 [7]
Jocelyn Simmonds, Shoham Ben-David, Marsha Chechik,” Guided Recovery for Web Service
Applications”, Proc. eighteenth ACM SIGSOFT international symposium on foundations of software
engineering, pp. 247-256, 2010. g
g pp
[8]
Suchi Gupta, Praveen Bhanodia,”A Fault Tolerant Mechanism for composition of Web Services using
Subset Replacement”, International Journal of Advance Research in Computer and Communication
Engineering, vol. 2, issue 8, pp. 3080-3085, August 2013. g
g
pp
g
[9]
Jocelyn Simmonds, Shoham Ben-David, Marsha Chechik, “Monitoring and Recovery of Web Service
Applications”, volume 95,issue 3,pp. 223-267,computing ,2012. [10] Rafael Angarita, Yudith Cardinale, Marta Rukoz,”Reliable Composite Web Services Execution:
Towards a Dynamic Recovery Decision”, Electronic Notes in Theoretical Computer Science, vol.302,
pp.5-28, Elsevier, 2014. [11] Hadi Saboohi, Sameem Abdul Kareem,” Requirements of a Recovery Solution for Failure of
Composite Web Services”, International Journal of Web & Semantic Technology, vol.3, issue 4, pp. 3-19, October 2012. [12] Zho Wu,Naixue xiong,Wenlin Han,Yan N. Huang,Chun Y. Hu,Qiong Gu, Bo Hang, ”A Fault-
Tolerant Method for Enhancing Reliability of Service Composition Application in WSNs Based on
BPEL”, International Journal of Distributed Sensor Networks ,volume 2013,arcticle id 493678,II
page. [13] Hossein Rahmani, Hassanabolhassani, ”Composite Web Service Failure Recovery Considering User
Non-Functional Preferences “, Proc. REFERENCES 25 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 International Journal on Web Service Computing (IJWSC), Vol.6, No.2/3, September 2015 [25] Jun Sun, Jin Song Dong,”Design Synthesis from Interaction and State-Based Specifications “,
Transactions on Software Engineering, vol. 32, issue 6, pp. 349 - 364 IEEE, 2006. [25] Jun Sun, Jin Song Dong,”Design Synthesis from Interaction and State-Based Specifications “, [26] An Liu, Qing Li, Senior Member, IEEE, Liusheng Huang, and Mingjun Xiao, “FACTS: A
Framework for Fault-Tolerant Composition of Transactional Web Services”, IEEE Transactions On
Services Computing, vol. 3, issue 1, pp. 46 - 59, 2010. p
g
pp
[27] Johannes Behl, Rüdiger Kapitza, Matthias Schunter , “Providing Fault-tolerant Execution of Web-
service–based Workflows within Clouds “, Proc. 2nd International Workshop on Cloud Computing
Platforms. Bern, Switzerland, article no. 7, ACM, 2012. Platforms. Bern, Switzerland, article no. 7, ACM, 2012. [28] Pat. P. W. Chan, Michael R. Lyu,” Reliable Web Services: Methodology, Experiment and Modeling”,
Proc. IEEE International Conference on Web Services, pp. 679 - 686 2007. [29] Huiyuan Zheng, WeiliangZhao, Jian Yang , Bouguettaya, A.,” QoS Analysis for Web Service
Compositions with Complex Structures” , IEEE Transactions on Services Computing, vol. 6,issue 3,
pp.373 – 386,2007. REFERENCES of 4th International Conference on Next Generation Web
Services Practices, pp. 39 – 45, IEEE, 2008. pp
[14] H. Elfawal Mansour and T. Dillon, Fellow, IEEE,” Dependability and Rollback Recovery for
Composite Web Services”, IEEE TRANSACTIONS ON SERVICE COMPUTING, vol. 4, pp. 328 –
339, October-December 2011. [15] Keting Yin , Bo Zhou , Shuai Zhang , Bin Xu “QoS-Aware Services Replacement of Web Service
Composition”, Proc. of Internal Conference on Information Technology and Computer Science,
pp.271 – 274, IEEE,2009. pp
[16] Guisheng Fan, Huiqun Yu, Liqiong Chen, Chunhua Gu1,” An Approach to Handling Failure
Recovery in Service Composition and Its Analysis”, Proc. of Fifth IEEE International Conference on
Theoretical Aspects of Software Engineering, pp. 153 – 160,2011. p
g
g pp
[17] Abdelkarim Erradi, Piyush Maheshwari2, Vladimir Tosic,”Recovery Policies for Enhancing Web
Services Reliability”, Proc. IEEE International Conference on Web Services, pp. 189 – 196, 2006. [18] Cao Jiuxin, Zhou Tao, Zhu Gongrui, Liu Bo, Luo Junzhou, “Execution Recovery in Transactional
Composite Service”, Proc. 20th International Conference on Web Services, pp.276-283, IEEE,2013. [19] Joyce El Haddad, Maude Manouvrie, Marta Rukoz, “TQoS-Transactional and QoS-Aware Selection
Algorithm for Automatic Web Service Composition”, IEEE Transactions on Services Computing,
vol. 3, issue1, pp.73-85, 2010. [20] Mohamed Sellami, Samir Tata, ZakariaMaamar, and Bruno Defude,”Recommender System for Web
Services Discovery in a Distributed Registry Environment”. Proc. Fourth International Conference on
Internet and Web Applications and Services, pp.418 - 423, IEEE, 2009. pp
pp
[21] Marwa F. Mohamed, Hany F, ElYamany, Mohamed K. Hussien, Nashwa, M. Yhiea2 and Hamed M. Nassar,”An Adaptive Replication Framework For Improving The QoS Of Web Services”, vol. 2,
issue 1,SpringerPlus ,2013. p
g
[22] Mario Bravetti, Stephen Gilmore, Claudio Guidi , and Mirco Tribastone, ” Replicating Web Services
for Scalability”, Proc. of Third Symposium on Trustworthy Global Computing Lecture Notes in
Computer Science, Springer, Volume 4912, 2008, pp. 204-221. [23] Ivona Brandic, Sabri Pllana, Siegfried Benkner, “High-level composition of QoS-aware Grid
workflows: An approach that considers location affinity”, Proc. Workflows In Support Of Large-
Scale Science, pp. 1 - 10, IEEE, 2006. pp
[24] R.S. Pandey, B.D. Chaudhary, “An estimation of min-max of QoS attributes of a choreography”, In
proc. of International Conference on Advances in Engineering, Science and Management , pp. 872 -
878 ,IEEE ,2012 . Richa Pathak M.Tech.(Computer Science and Engineering ) from Birla Institute of Technology.MCA
from U.P. technical University.Worked as Lecturer at Shri Ramswaroop Memorial College of Engineering
and Technology,Lucknow (U.P.Technical University) from 2010 to 2013. AUTHORS Dr. R. S. Pandey PhD. (Computer Science and Engineering) from Motilal National Institute of
Technology (MNNIT). M.Tech. (Computer Science and Engineering) from Motilal National Institute of Dr. R. S. Pandey PhD. (Computer Science and Engineering) from Motilal National Institute of
Technology (MNNIT). M.Tech. (Computer Science and Engineering) from Motilal National Institute of
Technology (MNNIT). M.Sc (Computer Science) from J.K Institute of Applied Physics (Allaahabad
University) . Working as Assitant Professor at Birla Institute of Technology since 2000. gy (
)
(
p
g
g)
Technology (MNNIT). M.Sc (Computer Science) from J.K Institute of Applied Physics (Allaahabad
University) . Working as Assitant Professor at Birla Institute of Technology since 2000. Richa Pathak M.Tech.(Computer Science and Engineering ) from Birla Institute of Technology.MCA
from U.P. technical University.Worked as Lecturer at Shri Ramswaroop Memorial College of Engineering
and Technology,Lucknow (U.P.Technical University) from 2010 to 2013. Richa Pathak M.Tech.(Computer Science and Engineering ) from Birla Institute of Technology.MCA
from U.P. technical University.Worked as Lecturer at Shri Ramswaroop Memorial College of Engineering
and Technology,Lucknow (U.P.Technical University) from 2010 to 2013. 26
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.