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https://openalex.org/W2112223494
https://europepmc.org/articles/pmc4318176?pdf=render
English
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Clinical and cost effectiveness of computer treatment for aphasia post stroke (Big CACTUS): study protocol for a randomised controlled trial
Trials
2,015
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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. 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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. 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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. 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Understanding Activation Patterns in Shared Circuits: Toward a Value Driven Model
Frontiers in human neuroscience
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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. 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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. 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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
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Performance of HbA1c versus oral glucose tolerance test (OGTT) as a screening tool to diagnose dysglycemic status in high-risk Thai patients
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(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. 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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. 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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. 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https://openalex.org/W3046224654
https://zenodo.org/records/3969272/files/RaTG13%20anomalies.pdf
English
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Anomalies in BatCoV/RaTG13 sequencing and provenance
Zenodo (CERN European Organization for Nuclear Research)
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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
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The impacts of interaction of audit litigation and ownership structure on audit quality
Future business journal
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cc-by
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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://​creat​iveco​ mmons.​org/​licen​ses/​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://​creat​iveco​ mmons.​org/​licen​ses/​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.​audit​analy​tics.​com/​conta​ct?​subje​ct=​ 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=​33512​30 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. 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Interferometric and fluorescence analysis of shock wave effects on cell membrane
Communications physics
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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. 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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. 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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. 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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
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Cause and preventability of in-hospital mortality after PCI: A statewide root-cause analysis of 1,163 deaths
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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. 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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. 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Fine mapping of a recessive leaf rust resistance locus on chromosome 2BS in wheat accession CH1539
Molecular breeding
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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. 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(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
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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. 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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
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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
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  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. 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Aberrant Proliferation in CXCR7+ Endothelial Cells via Degradation of the Retinoblastoma Protein
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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. 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Optimal deterministic and robust selection of electricity contracts
Journal of global optimization
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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. 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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.
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Volatile compounds of Bacillus pseudomycoides induce growth and drought tolerance in wheat (Triticum aestivum L.)
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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. 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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. 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https://zenodo.org/records/4729657/files/THE%20STALEMATE%20OF%20COMMUNITY%20POLICING%20IN%20SOUTH%20AFRICA.pdf
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The stalemate of community policing in South Africa
Eureka, Social and Humanities./Eureka, Social and Humanities
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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. 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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. 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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
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PALAVRA CANTADA: A POTÊNCIA COMUNICATIVA, O ENCANTO ESTÉTICO E USO PEDAGÓGICO DO ACALANTO NA FORMAÇÃO DE LEITORES INFANTIS
Revista Ifes Ciência
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cc-by
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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,
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Towards Interoperable Blockchains: A Survey on the Role of Smart Contracts in Blockchain Interoperability
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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. 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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. 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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
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PENGARUH TEH DAUN KELOR (Moringa oleifera L) TERHADAP PENINGKATAN KADAR HEMOGLOBIN PENDERITA ANEMIA
Avicenna
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cc-by-sa
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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)
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The Role of Brand Reputation on Customer Retention of Social Media Users
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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. 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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
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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. 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The Effect of Therapeutic Group Therapy to Mother’s Knowledge about Cognitive and Psychosocial of Preschool-age Children
International journal of research in nursing
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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. ■■
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Multimode quantum states with single photons carrying orbital angular momentum
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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. 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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. 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Fine-needle aspiration to improve diagnosis of melioidosis of the head and neck in children: a study from Sarawak, Malaysia
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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://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​ mmons.​org/​publi​cdoma​in/​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://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​ mmons.​org/​publi​cdoma​in/​zero/1.​0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
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Convergence Rate of the Modified Landweber Method for Solving Inverse Potential Problems
Mathematics
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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/).
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Effect of Fineness and Heat Treatment on the Pozzolanic Activity of Natural Volcanic Ash for Its Utilization as Supplementary Cementitious Materials
Crystals
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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. 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https://www.repository.cam.ac.uk/bitstream/1810/326060/2/41386_2020_Article_780.pdf
English
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Synaptic control of DNA-methylation involves activity-dependent degradation of DNMT3a1 in the nucleus
bioRxiv (Cold Spring Harbor Laboratory)
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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. 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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
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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
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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
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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. 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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. 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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. 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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.
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Emotion concepts for representing the vicissitudes of fate in Markus Zusak’s “Bridge of Clay”
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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
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Baptist Theological Seminary - An Example of Integrity and Assertion of Freedoms of Conscience
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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
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Sediment Transport Modeling at the Oued Fodda Watershed Level Using HEC-RAS 1D Software
GeoScience Engineering
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cc-by
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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. 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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. 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Dutch guideline for clinical foetal-neonatal and paediatric post-mortem radiology, including a review of literature
European journal of pediatrics
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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. 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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. 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Determinants of Pregnancy Outcomes After Assisted Reproductive Therapy: A Sample From the West Bank, Palestine
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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
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Dynamic Gesture Classification for Vietnamese Sign Language Recognition
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(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
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English
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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. 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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.
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Regulation of mouse hepatic genes in response to diet induced obesity, insulin resistance and fasting induced weight reduction
Nutrition & metabolism
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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. 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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. 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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." 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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. 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https://openalex.org/W2131581112
https://ricerca.uniba.it/bitstream/11586/148105/2/NanomatNanotech_Carlucci2015.pdf
English
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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
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The eruption of Timor in 1638: 350 years of plagiarism, embellishments and misunderstandings
Volcanica
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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. Colle ed 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. Colle ed 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). 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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. 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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
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Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq
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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. 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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
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Anatomy and Connectivity of the Subthalamic Nucleus in Humans and Non-human Primates
Frontiers in neuroanatomy
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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. 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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. 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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
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Development of an Extended RAMS Framework for Railway Networks
Proceedings of the 29th European Safety and Reliability Conference (ESREL)
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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
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The Absence of CYP3A5*3 Is a Protective Factor to Anticonvulsants Hypersensitivity Reactions: A Case-Control Study in Brazilian Subjects
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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. 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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
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A Personalized Self-Management Rehabilitation System with an Intelligent Shoe for Stroke Survivors: A Realist Evaluation
JMIR rehabilitation and assistive technologies
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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. 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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. 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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
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Impacts of seawater level and human activities on Yeh Gangga Beach’s coastal area at Tabanan Town
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© 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
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Peer Review #1 of "Epigenetic considerations in aquaculture (v0.1)"
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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. 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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)
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Buddhist-like opposite diminishing and non-judging during ketamine infusion are associated with antidepressant response: an open-label personalized-dosing study
Frontiers in pharmacology
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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). 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Inhibition of amyloid beta toxicity in zebrafish with a chaperone-gold nanoparticle dual strategy
Nature communications
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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. 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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. 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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. 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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. 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Clinical outcomes and prognostic factors in bloodstream infections due to extended-spectrum β-lactamase-producing Enterobacteriaceae among patients with malignancy: a meta-analysis
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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. 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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
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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. 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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. 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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/).
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Key factors in the internationalization process of born global Romanian software companies: an exploratory study
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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. 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https://openalex.org/W4382137956
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English
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Trajectory optimization for arbitrary layered geometries in wire-arc additive manufacturing
Optimization and engineering
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cc-by
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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, vw t}, 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 = α t ( 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 = α t ( 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 vw t . 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 vm t . 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
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Modular and Generic Control Software System for Scalable Automation
IFIP advances in information and communication technology
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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
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Optimization of the ISP Parameters of a Camera Through Differential Evolution
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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
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https://revistia.com/index.php/ejmn/article/view/5018/4871
English
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Qualitative Data Regarding the Macrophytic Communities Structure in the Wave Breaking Zone at the Romanian Black Sea Littoral
European journal of interdisciplinary studies
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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. 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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
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Garra dampaensis, a new ray-finned fish species (Cypriniformes: Cyprinidae) from Mizoram, northeastern India
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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
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Health care seeking behaviour and financial protection of patients with hypertension: A cross-sectional study in rural West Bengal, India
PloS one
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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. 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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. 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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. 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Author Correction: Myxozoan infection in thinlip mullet Chelon ramada (Mugiliformes: Mugilidae) in the Sea of Galilee
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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://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. https://doi.org/10.1038/s41598-023-31318-z Scientific Reports | (2023) 13:4565 |
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Peer Review #1 of "Gene expression in Tribolium castaneum life stages: Identifying a species-specific target for pest control applications (v0.1)"
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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 28C, 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 95C, 30 cycles of 95C for 30 182 sec, primer annealing at Tm 55.5C for 30 sec, and extension at 68C for 30 sec, final extension 183 at 68C for 5 min, and hold at 4C). 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 95C, 5 cycles of 95C for 30 sec, primer Tm for 30 sec, 72C for 30 193 sec, 29 cycles of 95C for 30 sec, primer Tm plus 5C for 30 sec, and 72C for 30 sec, extension 194 for 5 min at 68C and hold at 4C. The secondary PCR primers had a T7 construct attached to 195 the 5’ end (TAATACGACTCACTATAGGG), and thus 5C 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 37C 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 28C, 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 37C 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 95C, 30 cycles of 95C for 30 182 sec, primer annealing at Tm 55.5C for 30 sec, and extension at 68C for 30 sec, final extension 183 at 68C for 5 min, and hold at 4C). 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 95C, 5 cycles of 95C for 30 sec, primer Tm for 30 sec, 72C for 30 193 sec, 29 cycles of 95C for 30 sec, primer Tm plus 5C for 30 sec, and 72C for 30 sec, extension 194 for 5 min at 68C and hold at 4C. The secondary PCR primers had a T7 construct attached to 195 the 5’ end (TAATACGACTCACTATAGGG), and thus 5C 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. 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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. 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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
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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. 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Photogrammetry applied to Problematic artefacts
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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
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Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests: A Randomized Clinical Trial
PLoS medicine
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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. 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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. 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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
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E-Mail Network Patterns and Body Language Predict Risk-Taking Attitude
Future internet
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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. 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Correlation of macular sensitivity measures and visual acuity to vision-related quality of life in patients with age-related macular degeneration
BMC ophthalmology
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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. 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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
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Normalising comparative effectiveness trials as clinical practice
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© 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.
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https://www.degruyter.com/document/doi/10.1515/jisys-2018-0020/pdf
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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. 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Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema
BMC infectious diseases
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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. 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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
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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
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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
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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
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A new species of Demidospermus Suriano, 1983 (Monogenea) parasite of gills of Auchenipterus osteomystax (Auchenipteridae), from the upper Paraná river floodplain, Brazil
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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
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Changes in canine serum N-glycosylation as a result of infection with the heartworm parasite Dirofilaria immitis
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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. 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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. 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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. 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Studenten strooien hete centen voor het volk. Stedelijke identiteit en de geschiedenis van een omstreden herinnering in Leiden (1841-2016)
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* 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
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Alternate-locus aware variant calling in whole genome sequencing
Genome medicine
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cc-by
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© 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. 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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. 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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:
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Targeted-Gene Sequencing and Bioinformatics Analysis of Patients with Gallbladder Neuroendocrine Carcinoma: A Case Report and Literature Review
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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. 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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
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Testing hypotheses for maternal effects in <i>Daphnia magna</i>
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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. 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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:
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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
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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. 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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/).
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Depleted depletion drives polymer swelling in poor solvent mixtures
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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
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Intron-assisted, viroid-based production of insecticidal circular double-stranded RNA in<i>Escherichia coli</i>
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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
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An Archaeal Chitinase With a Secondary Capacity for Catalyzing Cellulose and Its Biotechnological Applications in Shell and Straw Degradation
Frontiers in microbiology
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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. 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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
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Spiritual Well-Being and Quality of Life of Iranian Adults with Type 2 Diabetes
Evidence-based complementary and alternative medicine
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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. 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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. 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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. 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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.
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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. 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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.
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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
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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
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Medico-ethnobotanical investigations in Parbat district of Western Nepal
Journal of medicinal plant research
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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.
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UM ESTUDO SOBRE A FORMAÇÃO DE TRADUTORES E INTÉRPRETES DE LÍNGUAS DE SINAIS
Trabalhos em Lingüística Aplicada
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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
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Controlled Nanoconfinement of Polyimide Networks in Mesoporous γ-Alumina Membranes for Molecular Separation of Organic Dyes
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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 CO bond, and the band at 1365 cm−1, which is related to CNC 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 AlOSi 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 (CH3CH2OSi) 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 SiOAl 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 CO 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. 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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). 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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. 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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. 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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
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Managing clustering effects and learning effects in the design and analysis of randomised surgical trials: a review of existing guidance
Trials
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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://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​ mmons.​org/​publi​cdoma​in/​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://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. The Creative Commons Public Domain Dedication waiver (http://​creat​iveco​ mmons.​org/​publi​cdoma​in/​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.​equat​or-​netwo​rk.​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. 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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.​
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Use of Self-Selected Postures to Regulate Multi-Joint Stiffness During Unconstrained Tasks
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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. 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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
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The Relationship between Vital Statistics with Pregnant Body Weight of Etawah Cross Bred Goat in Malang District, Indonesia
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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.
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Author Correction: Atmosphere similarity patterns in boreal summer show an increase of persistent weather conditions connected to hydro-climatic risks
Scientific reports
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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://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/. © The Author(s) 2021 | https://doi.org/10.1038/s41598-021-03671-4 Scientific Reports | (2021) 11:24242
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Principles of cartilage tissue engineering in TMJ reconstruction
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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. 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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. 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Voronoi tessellation-based algorithm for determining rigorously defined classical and generalized geometric pore size distributions
Physical review. E
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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. 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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. 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Rycroft, Voro++: A three-dimensional Voronoi cell li- brary in C++, Chaos 19, 041111 (2009). 015307-16
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https://journalimplantdent.springeropen.com/track/pdf/10.1186/s40729-020-00235-5
English
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Immediate implant placement in molar extraction sockets: a systematic review and meta-analysis
International journal of implant dentistry
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© 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. 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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.
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The mirror mechanism in schizophrenia spectrum disorders: Protocol for a systematic review and meta-synthesis
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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. 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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. 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In-plane Shear Response of a Flax Fiber-epoxy Resin Composite Subjected to Repeated Loading and Creep-recovery Cycles
Materiale plastice
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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
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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
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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. 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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
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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 |
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Development of hybrid materials based on sponge supported reduced graphene oxide and transition metal hydroxides for hybrid energy storage devices
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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
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AN ADAPTIVE APPROACH FOR DYNAMIC RECOVERY DECISIONS IN WEB SERVICE COMPOSITION USING SPACE BASED QOS FACTOR
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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. 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[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