Dynamic causal modelling of COVID-19.
Identifieur interne : 001104 ( Main/Exploration ); précédent : 001103; suivant : 001105Dynamic causal modelling of COVID-19.
Auteurs : Karl J. Friston [Royaume-Uni] ; Thomas Parr [Royaume-Uni] ; Peter Zeidman [Royaume-Uni] ; Adeel Razi [Royaume-Uni, Australie] ; Guillaume Flandin [Royaume-Uni] ; Jean Daunizeau [France] ; Ollie J. Hulme [Danemark, Royaume-Uni] ; Alexander J. Billig [Royaume-Uni] ; Vladimir Litvak [Royaume-Uni] ; Rosalyn J. Moran [Royaume-Uni] ; Cathy J. Price [Royaume-Uni] ; Christian Lambert [Royaume-Uni]Source :
- Wellcome open research [ 2398-502X ] ; 2020.
Abstract
This technical report describes a dynamic causal model of the spread of coronavirus through a population. The model is based upon ensemble or population dynamics that generate outcomes, like new cases and deaths over time. The purpose of this model is to quantify the uncertainty that attends predictions of relevant outcomes. By assuming suitable conditional dependencies, one can model the effects of interventions (e.g., social distancing) and differences among populations (e.g., herd immunity) to predict what might happen in different circumstances. Technically, this model leverages state-of-the-art variational (Bayesian) model inversion and comparison procedures, originally developed to characterise the responses of neuronal ensembles to perturbations. Here, this modelling is applied to epidemiological populations-to illustrate the kind of inferences that are supported and how the model per se can be optimised given timeseries data. Although the purpose of this paper is to describe a modelling protocol, the results illustrate some interesting perspectives on the current pandemic; for example, the nonlinear effects of herd immunity that speak to a self-organised mitigation process.
DOI: 10.12688/wellcomeopenres.15881.2
PubMed: 32832701
PubMed Central: PMC7431977
Affiliations:
- Australie, Danemark, France, Royaume-Uni
- Angleterre, Grand Londres
- Londres
- University College de Londres
Links toward previous steps (curation, corpus...)
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Friston</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Parr, Thomas" sort="Parr, Thomas" uniqKey="Parr T" first="Thomas" last="Parr">Thomas Parr</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Zeidman, Peter" sort="Zeidman, Peter" uniqKey="Zeidman P" first="Peter" last="Zeidman">Peter Zeidman</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Razi, Adeel" sort="Razi, Adeel" uniqKey="Razi A" first="Adeel" last="Razi">Adeel Razi</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>Turner Institute for Brain and Mental Health & Monash Biomedical Imaging, Monash University, Clayton, VIC, 3800, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Turner Institute for Brain and Mental Health & Monash Biomedical Imaging, Monash University, Clayton, VIC, 3800</wicri:regionArea><wicri:noRegion>3800</wicri:noRegion></affiliation></author><author><name sortKey="Flandin, Guillaume" sort="Flandin, Guillaume" uniqKey="Flandin G" first="Guillaume" last="Flandin">Guillaume Flandin</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Daunizeau, Jean" sort="Daunizeau, Jean" uniqKey="Daunizeau J" first="Jean" last="Daunizeau">Jean Daunizeau</name><affiliation wicri:level="1"><nlm:affiliation>Institut du Cerveau et de la Moelle épinière, INSERM UMRS, Paris, 1127, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut du Cerveau et de la Moelle épinière, INSERM UMRS, Paris, 1127</wicri:regionArea><wicri:noRegion>1127</wicri:noRegion><wicri:noRegion>1127</wicri:noRegion></affiliation></author><author><name sortKey="Hulme, Ollie J" sort="Hulme, Ollie J" uniqKey="Hulme O" first="Ollie J" last="Hulme">Ollie J. 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Moran</name><affiliation wicri:level="3"><nlm:affiliation>Centre for Neuroimaging Science, Department of Neuroimaging, IoPPN, King's College London, London, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Neuroimaging Science, Department of Neuroimaging, IoPPN, King's College London, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Price, Cathy J" sort="Price, Cathy J" uniqKey="Price C" first="Cathy J" last="Price">Cathy J. 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Friston</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Parr, Thomas" sort="Parr, Thomas" uniqKey="Parr T" first="Thomas" last="Parr">Thomas Parr</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Zeidman, Peter" sort="Zeidman, Peter" uniqKey="Zeidman P" first="Peter" last="Zeidman">Peter Zeidman</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Razi, Adeel" sort="Razi, Adeel" uniqKey="Razi A" first="Adeel" last="Razi">Adeel Razi</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>Turner Institute for Brain and Mental Health & Monash Biomedical Imaging, Monash University, Clayton, VIC, 3800, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Turner Institute for Brain and Mental Health & Monash Biomedical Imaging, Monash University, Clayton, VIC, 3800</wicri:regionArea><wicri:noRegion>3800</wicri:noRegion></affiliation></author><author><name sortKey="Flandin, Guillaume" sort="Flandin, Guillaume" uniqKey="Flandin G" first="Guillaume" last="Flandin">Guillaume Flandin</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Daunizeau, Jean" sort="Daunizeau, Jean" uniqKey="Daunizeau J" first="Jean" last="Daunizeau">Jean Daunizeau</name><affiliation wicri:level="1"><nlm:affiliation>Institut du Cerveau et de la Moelle épinière, INSERM UMRS, Paris, 1127, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut du Cerveau et de la Moelle épinière, INSERM UMRS, Paris, 1127</wicri:regionArea><wicri:noRegion>1127</wicri:noRegion><wicri:noRegion>1127</wicri:noRegion></affiliation></author><author><name sortKey="Hulme, Ollie J" sort="Hulme, Ollie J" uniqKey="Hulme O" first="Ollie J" last="Hulme">Ollie J. Hulme</name><affiliation wicri:level="1"><nlm:affiliation>Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Hvidovre</wicri:regionArea><wicri:noRegion>Hvidovre</wicri:noRegion></affiliation><affiliation wicri:level="3"><nlm:affiliation>London Mathematical Laboratory, Hammersmith, London, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>London Mathematical Laboratory, Hammersmith, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Billig, Alexander J" sort="Billig, Alexander J" uniqKey="Billig A" first="Alexander J" last="Billig">Alexander J. Billig</name><affiliation wicri:level="4"><nlm:affiliation>Ear Institute, University College London, London, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Ear Institute, University College London, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName><orgName type="university">University College de Londres</orgName></affiliation></author><author><name sortKey="Litvak, Vladimir" sort="Litvak, Vladimir" uniqKey="Litvak V" first="Vladimir" last="Litvak">Vladimir Litvak</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Moran, Rosalyn J" sort="Moran, Rosalyn J" uniqKey="Moran R" first="Rosalyn J" last="Moran">Rosalyn J. Moran</name><affiliation wicri:level="3"><nlm:affiliation>Centre for Neuroimaging Science, Department of Neuroimaging, IoPPN, King's College London, London, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Neuroimaging Science, Department of Neuroimaging, IoPPN, King's College London, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Price, Cathy J" sort="Price, Cathy J" uniqKey="Price C" first="Cathy J" last="Price">Cathy J. Price</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Lambert, Christian" sort="Lambert, Christian" uniqKey="Lambert C" first="Christian" last="Lambert">Christian Lambert</name><affiliation wicri:level="4"><nlm:affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG</wicri:regionArea><orgName type="university">University College de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author></analytic><series><title level="j">Wellcome open research</title><idno type="ISSN">2398-502X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">This technical report describes a dynamic causal model of the spread of coronavirus through a population. The model is based upon ensemble or population dynamics that generate outcomes, like new cases and deaths over time. The purpose of this model is to quantify the uncertainty that attends predictions of relevant outcomes. By assuming suitable conditional dependencies, one can model the effects of interventions (e.g., social distancing) and differences among populations (e.g., herd immunity) to predict what might happen in different circumstances. Technically, this model leverages state-of-the-art variational (Bayesian) model inversion and comparison procedures, originally developed to characterise the responses of neuronal ensembles to perturbations. Here, this modelling is applied to epidemiological populations-to illustrate the kind of inferences that are supported and how the model <i>per se</i> can be optimised given timeseries data. Although the purpose of this paper is to describe a modelling protocol, the results illustrate some interesting perspectives on the current pandemic; for example, the nonlinear effects of herd immunity that speak to a self-organised mitigation process.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" VersionID="2" VersionDate="2020/08/07" Owner="NLM"><PMID Version="2">32832701</PMID><DateRevised><Year>2020</Year><Month>08</Month><Day>25</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2398-502X</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>Wellcome open research</Title><ISOAbbreviation>Wellcome Open Res</ISOAbbreviation></Journal><ArticleTitle>Dynamic causal modelling of COVID-19.</ArticleTitle><Pagination><MedlinePgn>89</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.12688/wellcomeopenres.15881.2</ELocationID><Abstract><AbstractText>This technical report describes a dynamic causal model of the spread of coronavirus through a population. The model is based upon ensemble or population dynamics that generate outcomes, like new cases and deaths over time. The purpose of this model is to quantify the uncertainty that attends predictions of relevant outcomes. By assuming suitable conditional dependencies, one can model the effects of interventions (e.g., social distancing) and differences among populations (e.g., herd immunity) to predict what might happen in different circumstances. Technically, this model leverages state-of-the-art variational (Bayesian) model inversion and comparison procedures, originally developed to characterise the responses of neuronal ensembles to perturbations. Here, this modelling is applied to epidemiological populations-to illustrate the kind of inferences that are supported and how the model <i>per se</i> can be optimised given timeseries data. Although the purpose of this paper is to describe a modelling protocol, the results illustrate some interesting perspectives on the current pandemic; for example, the nonlinear effects of herd immunity that speak to a self-organised mitigation process.</AbstractText><CopyrightInformation>Copyright: © 2020 Friston KJ et al.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Friston</LastName><ForeName>Karl J</ForeName><Initials>KJ</Initials><Identifier Source="ORCID">https://orcid.org/0000-0001-7984-8909</Identifier><AffiliationInfo><Affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Parr</LastName><ForeName>Thomas</ForeName><Initials>T</Initials><Identifier Source="ORCID">https://orcid.org/0000-0001-5108-5743</Identifier><AffiliationInfo><Affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zeidman</LastName><ForeName>Peter</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Razi</LastName><ForeName>Adeel</ForeName><Initials>A</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-0779-9439</Identifier><AffiliationInfo><Affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Turner Institute for Brain and Mental Health & Monash Biomedical Imaging, Monash University, Clayton, VIC, 3800, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Flandin</LastName><ForeName>Guillaume</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Daunizeau</LastName><ForeName>Jean</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institut du Cerveau et de la Moelle épinière, INSERM UMRS, Paris, 1127, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hulme</LastName><ForeName>Ollie J</ForeName><Initials>OJ</Initials><AffiliationInfo><Affiliation>Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>London Mathematical Laboratory, Hammersmith, London, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Billig</LastName><ForeName>Alexander J</ForeName><Initials>AJ</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-4531-8616</Identifier><AffiliationInfo><Affiliation>Ear Institute, University College London, London, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Litvak</LastName><ForeName>Vladimir</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Moran</LastName><ForeName>Rosalyn J</ForeName><Initials>RJ</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-2736-2621</Identifier><AffiliationInfo><Affiliation>Centre for Neuroimaging Science, Department of Neuroimaging, IoPPN, King's College London, London, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Price</LastName><ForeName>Cathy J</ForeName><Initials>CJ</Initials><AffiliationInfo><Affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lambert</LastName><ForeName>Christian</ForeName><Initials>C</Initials><Identifier Source="ORCID">https://orcid.org/0000-0001-8281-4611</Identifier><AffiliationInfo><Affiliation>Wellcome Centre for Human Neuroimaging, University College London, London, WC1N 3BG, UK.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>figshare</DataBankName><AccessionNumberList><AccessionNumber>10.6084/m9.figshare.12174006.v1</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>08</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Wellcome Open Res</MedlineTA><NlmUniqueID>101696457</NlmUniqueID><ISSNLinking>2398-502X</ISSNLinking></MedlineJournalInfo><KeywordList 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