[ { "key": "MXTNREYM", "version": 499, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/MXTNREYM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/MXTNREYM", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2887239, "username": "anne_lassailly", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/anne_lassailly", "type": "text/html" } } }, "creatorSummary": "Brives and Latour", "parsedDate": "2022-01-01", "numChildren": 0 }, "data": { "key": "MXTNREYM", "version": 499, "itemType": "book", "title": "Face à l antibiorésistance : une écologie politique des microbes / Charlotte Brives; préface de Bruno Latour", "creators": [ { "creatorType": "author", "firstName": "Charlotte", "lastName": "Brives" }, { "creatorType": "author", "firstName": "Bruno", "lastName": "Latour" } ], "abstractNote": "", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2022-01-01", "publisher": "", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "numPages": "", "ISBN": "978-2-35480-254-7", "DOI": "", "citationKey": "", "url": "https://search.ebscohost.com/login.aspx?direct=true&db=cat03336a&AN=msip.ISO00083873&site=eds-live", "accessDate": "2023-10-06", "ISSN": "", "archive": "Catalogue de la médiathèque", "archiveLocation": "msip.ISO00083873", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "NAXLZUTB" ], "relations": {}, "dateAdded": "2023-10-06T10:10:09Z", "dateModified": "2023-10-06T10:10:09Z" } }, { "key": "MZ622PDQ", "version": 493, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/MZ622PDQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/MZ622PDQ", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/385213/items/PYLNF722", "type": "application/json" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "MZ622PDQ", "version": 493, "parentItem": "PYLNF722", "itemType": "attachment", "linkMode": "imported_file", "title": "Beam et al. - 2021 - A data-driven framework for mapping domains of hum.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Beam et al. - 2021 - A data-driven framework for mapping domains of hum.pdf", "md5": "23120730a6d5fc12ac0609d219753e30", "mtime": 1646420809000, "tags": [], "relations": {}, "dateAdded": "2022-03-04T19:06:38Z", "dateModified": "2022-03-04T19:06:50Z" } }, { "key": "PYLNF722", "version": 492, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/PYLNF722", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/PYLNF722", "type": "text/html" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "creatorSummary": "Beam et al.", "parsedDate": "2021", "numChildren": 1 }, "data": { "key": "PYLNF722", "version": 492, "itemType": "journalArticle", "title": "A data-driven framework for mapping domains of human neurobiology", "creators": [ { "creatorType": "author", "firstName": "Elizabeth", "lastName": "Beam" }, { "creatorType": "author", "firstName": "Christopher", "lastName": "Potts" }, { "creatorType": "author", "firstName": "Russell A.", "lastName": "Poldrack" }, { "creatorType": "author", "firstName": "Amit", "lastName": "Etkin" } ], "abstractNote": "", "publicationTitle": "Nature Neuroscience", "publisher": "", "place": "", "date": "12/2021", "volume": "24", "issue": "12", "section": "", "partNumber": "", "partTitle": "", "pages": "1733-1744", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Neurosci", "DOI": "10.1038/s41593-021-00948-9", "citationKey": "", "url": "https://www.nature.com/articles/s41593-021-00948-9", "accessDate": "2022-03-04T19:06:49Z", "PMID": "", "PMCID": "", "ISSN": "1097-6256, 1546-1726", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "FVJR4VH6" ], "relations": {}, "dateAdded": "2022-03-04T19:06:49Z", "dateModified": "2022-03-04T19:06:49Z" } }, { "key": "4MDG46WL", "version": 494, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/4MDG46WL", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/4MDG46WL", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/385213/items/CGCFKTTJ", "type": "application/json" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "4MDG46WL", "version": 494, "parentItem": "CGCFKTTJ", "itemType": "attachment", "linkMode": "imported_file", "title": "Loiodice et al. - 2021 - Mismatch negativity as EEG biomarker supporting CN.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Loiodice et al. - 2021 - Mismatch negativity as EEG biomarker supporting CN.pdf", "md5": "6cf317b12b02a89e2ee7fb92d9111c0a", "mtime": 1646420807000, "tags": [], "relations": {}, "dateAdded": "2022-03-04T19:06:36Z", "dateModified": "2022-03-04T19:06:47Z" } }, { "key": "CGCFKTTJ", "version": 492, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/CGCFKTTJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/CGCFKTTJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "creatorSummary": "Loiodice et al.", "parsedDate": "2021", "numChildren": 1 }, "data": { "key": "CGCFKTTJ", "version": 492, "itemType": "journalArticle", "title": "Mismatch negativity as EEG biomarker supporting CNS drug development: a transnosographic and translational study", "creators": [ { "creatorType": "author", "firstName": "Simon", "lastName": "Loiodice" }, { "creatorType": "author", "firstName": "Wilhelmus H.", "lastName": "Drinkenburg" }, { "creatorType": "author", "firstName": "Abdallah", "lastName": "Ahnaou" }, { "creatorType": "author", "firstName": "Andrew", "lastName": "McCarthy" }, { "creatorType": "author", "firstName": "Geoffrey", "lastName": "Viardot" }, { "creatorType": "author", "firstName": "Emilie", "lastName": "Cayre" }, { "creatorType": "author", "firstName": "Bertrand", "lastName": "Rion" }, { "creatorType": "author", "firstName": "Valérie", "lastName": "Bertaina-Anglade" }, { "creatorType": "author", "firstName": "Marsel", "lastName": "Mano" }, { "creatorType": "author", "firstName": "Philippe", "lastName": "L’Hostis" }, { "creatorType": "author", "firstName": "Christophe", "lastName": "Drieu La Rochelle" }, { "creatorType": "author", "firstName": "Martien J.", "lastName": "Kas" }, { "creatorType": "author", "firstName": "Philippe", "lastName": "Danjou" } ], "abstractNote": "Abstract\n The lack of translation from basic research into new medicines is a major challenge in CNS drug development. The need to use novel approaches relying on (i) patient clustering based on neurobiology irrespective to symptomatology and (ii) quantitative biomarkers focusing on evolutionarily preserved neurobiological systems allowing back-translation from clinical to nonclinical research has been highlighted. Here we sought to evaluate the mismatch negativity (MMN) response in schizophrenic (SZ) patients, Alzheimer’s disease (AD) patients, and age-matched healthy controls. To evaluate back-translation of the MMN response, we developed EEG-based procedures allowing the measurement of MMN-like responses in a rat model of schizophrenia and a mouse model of AD. Our results indicate a significant MMN attenuation in SZ but not in AD patients. Consistently with the clinical findings, we observed a significant attenuation of deviance detection (~104.7%) in rats subchronically exposed to phencyclidine, while no change was observed in APP/PS1 transgenic mice when compared to wild type. This study provides new insight into the cross-disease evaluation of the MMN response. Our findings suggest further investigations to support the identification of neurobehavioral subtypes that may help patients clustering for precision medicine intervention. Furthermore, we provide evidence that MMN could be used as a quantitative/objective efficacy biomarker during both preclinical and clinical stages of SZ drug development.", "publicationTitle": "Translational Psychiatry", "publisher": "", "place": "", "date": "12/2021", "volume": "11", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "253", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Transl Psychiatry", "DOI": "10.1038/s41398-021-01371-1", "citationKey": "", "url": "http://www.nature.com/articles/s41398-021-01371-1", "accessDate": "2022-03-04T19:06:47Z", "PMID": "", "PMCID": "", "ISSN": "2158-3188", "archive": "", "archiveLocation": "", "shortTitle": "Mismatch negativity as EEG biomarker supporting CNS drug development", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "FVJR4VH6" ], "relations": {}, "dateAdded": "2022-03-04T19:06:47Z", "dateModified": "2022-03-04T19:06:47Z" } }, { "key": "ZS3NCZ97", "version": 495, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/ZS3NCZ97", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/ZS3NCZ97", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/385213/items/TMURME99", "type": "application/json" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "ZS3NCZ97", "version": 495, "parentItem": "TMURME99", "itemType": "attachment", "linkMode": "imported_file", "title": "Baevski et al. - data2vec A General Framework for Self-supervised .pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Baevski et al. - data2vec A General Framework for Self-supervised .pdf", "md5": "010093163d46f9d8ed7517884a59ae8f", "mtime": 1646420805000, "tags": [], "relations": {}, "dateAdded": "2022-03-04T19:06:34Z", "dateModified": "2022-03-04T19:06:45Z" } }, { "key": "TMURME99", "version": 492, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/TMURME99", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/TMURME99", "type": "text/html" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "creatorSummary": "Baevski et al.", "numChildren": 1 }, "data": { "key": "TMURME99", "version": 492, "itemType": "journalArticle", "title": "data2vec: A General Framework for Self-supervised Learning in Speech, Vision and Language", "creators": [ { "creatorType": "author", "firstName": "Alexei", "lastName": "Baevski" }, { "creatorType": "author", "firstName": "Wei-Ning", "lastName": "Hsu" }, { "creatorType": "author", "firstName": "Qiantong", "lastName": "Xu" }, { "creatorType": "author", "firstName": "Arun", "lastName": "Babu" }, { "creatorType": "author", "firstName": "Jiatao", "lastName": "Gu" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Auli" } ], "abstractNote": "While the general idea of self-supervised learning is identical across modalities, the actual algorithms and objectives differ widely because they were developed with a single modality in mind. To get us closer to general self-supervised learning, we present data2vec, a framework that uses the same learning method for either speech, NLP or computer vision. The core idea is to predict latent representations of the full input data based on a masked view of the input in a selfdistillation setup using a standard Transformer architecture. Instead of predicting modality-specific targets such as words, visual tokens or units of human speech which are local in nature, data2vec predicts contextualized latent representations that contain information from the entire input. Experiments on the major benchmarks of speech recognition, image classification, and natural language understanding demonstrate a new state of the art or competitive performance to predominant approaches. Models and code are available at www.github.com/pytorch/fairseq/ tree/master/examples/data2vec.", "publicationTitle": "", "publisher": "", "place": "", "date": "", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "13", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "Zotero", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "FVJR4VH6" ], "relations": {}, "dateAdded": "2022-03-04T19:06:45Z", "dateModified": "2022-03-04T19:06:45Z" } }, { "key": "SF5NZ2CA", "version": 505, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/SF5NZ2CA", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/SF5NZ2CA", "type": "text/html" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "creatorSummary": "Helmer et al.", "parsedDate": "2020-08-25", "numChildren": 1 }, "data": { "key": "SF5NZ2CA", "version": 505, "itemType": "report", "title": "On stability of Canonical Correlation Analysis and Partial Least Squares with application to brain-behavior associations", "creators": [ { "creatorType": "author", "firstName": "Markus", "lastName": "Helmer" }, { "creatorType": "author", "firstName": "Shaun", "lastName": "Warrington" }, { "creatorType": "author", "firstName": "Ali-Reza", "lastName": "Mohammadi-Nejad" }, { "creatorType": "author", "firstName": "Jie Lisa", "lastName": "Ji" }, { "creatorType": "author", "firstName": "Amber", "lastName": "Howell" }, { "creatorType": "author", "firstName": "Benjamin", "lastName": "Rosand" }, { "creatorType": "author", "firstName": "Alan", "lastName": "Anticevic" }, { "creatorType": "author", "firstName": "Stamatios N.", "lastName": "Sotiropoulos" }, { "creatorType": "author", "firstName": "John D.", "lastName": "Murray" } ], "abstractNote": "Abstract\n \n Associations between datasets, each comprising many features, can be discovered through multivariate methods like Canonical Correlation Analysis (CCA) or Partial Least Squares (PLS). Application of CCA/PLS to high-dimensional datasets raises critical questions about reliability and interpretability. To study this, we developed a generative modeling framework to simulate synthetic datasets, parameterized by dimensionality, variance structure, and association strength. We found that CCA/PLS associations could be highly inaccurate when the number of samples per feature is relatively small. For PLS, profiles of feature weights exhibit detrimental bias toward leading principal component axes. We confirmed these trends in state-of-the-art neuroimaging datasets, Human Connectome Project (n\n ≈\n 1000) and UK Biobank (n=20000), finding that only the latter comprised sufficient samples for stable estimates. Analysis of the neuroimaging literature using CCA to map brain-behavior relationships revealed also that the commonly employed sample sizes yield unstable CCA solutions. Finally, we provide a calculator of dataset properties required for CCA/PLS stability. Collectively, we characterize how to limit detrimental effects of overfitting on CCA/PLS stability, and provide recommendations for future studies.", "reportNumber": "", "reportType": "preprint", "institution": "Neuroscience", "place": "", "date": "2020-08-25", "seriesTitle": "", "seriesNumber": "", "pages": "", "DOI": "10.1101/2020.08.25.265546", "ISBN": "", "citationKey": "", "url": "http://biorxiv.org/lookup/doi/10.1101/2020.08.25.265546", "accessDate": "2022-03-04T19:06:43Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "FVJR4VH6" ], "relations": {}, "dateAdded": "2022-03-04T19:06:43Z", "dateModified": "2022-03-04T19:06:43Z" } }, { "key": "YRCC5TSN", "version": 496, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/YRCC5TSN", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/YRCC5TSN", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/385213/items/SF5NZ2CA", "type": "application/json" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "YRCC5TSN", "version": 496, "parentItem": "SF5NZ2CA", "itemType": "attachment", "linkMode": "imported_file", "title": "Helmer et al. - 2020 - On stability of Canonical Correlation Analysis and.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Helmer et al. - 2020 - On stability of Canonical Correlation Analysis and.pdf", "md5": "ba3a68519fe32cff54644b765d738a73", "mtime": 1646420803000, "tags": [], "relations": {}, "dateAdded": "2022-03-04T19:06:32Z", "dateModified": "2022-03-04T19:06:43Z" } }, { "key": "8AUXX2SL", "version": 490, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/8AUXX2SL", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/8AUXX2SL", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/385213/items/Y4TD22AU", "type": "application/json" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "8AUXX2SL", "version": 490, "parentItem": "Y4TD22AU", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text PDF", "accessDate": "2022-03-04T19:05:55Z", "url": "https://osf.io/preprints/metaarxiv/b9qaw/download?format=pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Pontika et al. - 2022 - Indicators of research quality, quantity, openness.pdf", "md5": "b7ac17569878fad41f79405de96466d8", "mtime": 1646420755000, "tags": [], "relations": {}, "dateAdded": "2022-03-04T19:05:55Z", "dateModified": "2022-03-04T19:05:55Z" } }, { "key": "Y4TD22AU", "version": 505, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/Y4TD22AU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/Y4TD22AU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "creatorSummary": "Pontika et al.", "parsedDate": "2022-03-03", "numChildren": 1 }, "data": { "key": "Y4TD22AU", "version": 505, "itemType": "report", "title": "Indicators of research quality, quantity, openness and responsibility in institutional promotion, review and tenure policies across seven countries", "creators": [ { "creatorType": "author", "firstName": "Nancy", "lastName": "Pontika" }, { "creatorType": "author", "firstName": "Thomas", "lastName": "Klebel" }, { "creatorType": "author", "firstName": "Antonia", "lastName": "Correia" }, { "creatorType": "author", "firstName": "Hannah", "lastName": "Metzler" }, { "creatorType": "author", "firstName": "Petr", "lastName": "Knoth" }, { "creatorType": "author", "firstName": "Tony", "lastName": "Ross-Hellauer" } ], "abstractNote": "The need to reform research assessment processes related to career advancement at research institutions has become increasingly recognised in recent years, especially to better foster open and responsible research practices. Current assessment criteria are believed to focus too heavily on inappropriate criteria related to productivity and quantity as opposed to quality, collaborative open research practices, and the socio-economic impact of research. Evidence of the extent of these issues is urgently needed to inform actions for reform, however. We analyse current practices as revealed by documentation on institutional review, promotion and tenure processes in seven countries (Austria, Brazil, Germany, India, Portugal, United Kingdom and United States of America). Through systematic coding and analysis of 143 RPT policy documents from 107 institutions for the prevalence of 17 criteria (including those related to qualitative or quantitative assessment of research, service to the institution or profession, and open and responsible research practices), we compare assessment practices across a range of international institutions to significantly broaden this evidence-base. Although prevalence of indicators varies considerably between countries, overall we find that currently open and responsible research practices are minimally rewarded and problematic practices of quantification continue to dominate.", "reportNumber": "", "reportType": "", "institution": "MetaArXiv", "place": "", "date": "2022-03-03T13:09:12.713Z", "seriesTitle": "", "seriesNumber": "", "pages": "", "DOI": "10.31222/osf.io/b9qaw", "ISBN": "", "citationKey": "", "url": "https://osf.io/preprints/metaarxiv/b9qaw/", "accessDate": "2022-03-04T19:05:52Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en-us", "libraryCatalog": "OSF Preprints", "callNumber": "", "rights": "", "extra": "type: article", "tags": [ { "tag": "Open Science", "type": 1 }, { "tag": "Other Social and Behavioral Sciences", "type": 1 }, { "tag": "RRI", "type": 1 }, { "tag": "Research assessment", "type": 1 }, { "tag": "Social and Behavioral Sciences", "type": 1 } ], "collections": [ "FVJR4VH6" ], "relations": {}, "dateAdded": "2022-03-04T19:05:52Z", "dateModified": "2022-03-04T19:05:52Z" } }, { "key": "NVNGAGV4", "version": 485, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/NVNGAGV4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/NVNGAGV4", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/385213/items/DVTZQ5KI", "type": "application/json" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "NVNGAGV4", "version": 485, "parentItem": "DVTZQ5KI", "itemType": "attachment", "linkMode": "imported_url", "title": "Kathawalla_et_al-2021-Easing_Into_Open_Science.pdf", "accessDate": "2021-01-28T18:23:48Z", "url": "https://online.ucpress.edu/collabra/article-pdf/7/1/18684/450844/collabra_2021_7_1_18684.pdf", "note": "

Contents

", "contentType": "application/pdf", "charset": "", "filename": "Kathawalla_et_al-2021-Easing_Into_Open_Science.pdf", "md5": "93b2fbc5bf18afcd5e0f824303211b37", "mtime": 1611858228000, "tags": [], "relations": {}, "dateAdded": "2021-01-28T18:23:48Z", "dateModified": "2021-01-28T18:23:49Z" } }, { "key": "DVTZQ5KI", "version": 484, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/DVTZQ5KI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/DVTZQ5KI", "type": "text/html" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "creatorSummary": "Kathawalla et al.", "parsedDate": "2021-01-26", "numChildren": 1 }, "data": { "key": "DVTZQ5KI", "version": 484, "itemType": "journalArticle", "title": "Easing Into Open Science: A Guide for Graduate Students and Their Advisors", "creators": [ { "creatorType": "author", "firstName": "Ummul-Kiram", "lastName": "Kathawalla" }, { "creatorType": "author", "firstName": "Priya", "lastName": "Silverstein" }, { "creatorType": "author", "firstName": "Moin", "lastName": "Syed" } ], "abstractNote": "This article provides a roadmap to assist graduate students and their advisors to engage in open science practices. We suggest eight open science practices that novice graduate students could begin adopting today. The topics we cover include journal clubs, project workflow, preprints, reproducible code, data sharing, transparent writing, preregistration, and registered reports. To address concerns about not knowing how to engage in open science practices, we provide a difficulty rating of each behavior (easy, medium, difficult), present them in order of suggested adoption, and follow the format of what, why, how, and worries. We give graduate students ideas on how to approach conversations with their advisors/collaborators, ideas on how to integrate open science practices within the graduate school framework, and specific resources on how to engage with each behavior. We emphasize that engaging in open science behaviors need not be an all or nothing approach, but rather graduate students can engage with any number of the behaviors outlined.", "publicationTitle": "Collabra: Psychology", "publisher": "", "place": "", "date": "January 26, 2021", "volume": "7", "issue": "18684", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Collabra: Psychology", "DOI": "10.1525/collabra.18684", "citationKey": "", "url": "https://doi.org/10.1525/collabra.18684", "accessDate": "2021-01-28T18:23:46Z", "PMID": "", "PMCID": "", "ISSN": "2474-7394", "archive": "", "archiveLocation": "", "shortTitle": "Easing Into Open Science", "language": "", "libraryCatalog": "Silverchair", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "FVJR4VH6" ], "relations": {}, "dateAdded": "2021-01-28T18:23:46Z", "dateModified": "2021-01-28T18:23:46Z" } }, { "key": "H3SYKV2K", "version": 482, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/H3SYKV2K", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/H3SYKV2K", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/385213/items/U4WBIR8E", "type": "application/json" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "H3SYKV2K", "version": 482, "parentItem": "U4WBIR8E", "itemType": "attachment", "linkMode": "imported_url", "title": "Wintermute_et_al-2021-A_survival_model_for_course-course_interactions_in_a_Massive_Open_Online_Course.pdf", "accessDate": "2021-01-28T14:42:07Z", "url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0245718&type=printable", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Wintermute_et_al-2021-A_survival_model_for_course-course_interactions_in_a_Massive_Open_Online_Course.pdf", "md5": "6bfdc7d8659bd0132311267ac36b89e3", "mtime": 1611844927000, "tags": [], "relations": {}, "dateAdded": "2021-01-28T14:42:07Z", "dateModified": "2021-01-28T14:42:08Z" } }, { "key": "U4WBIR8E", "version": 505, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/U4WBIR8E", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/U4WBIR8E", "type": "text/html" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "creatorSummary": "Wintermute et al.", "parsedDate": "2021-01-22", "numChildren": 1 }, "data": { "key": "U4WBIR8E", "version": 505, "itemType": "journalArticle", "title": "A survival model for course-course interactions in a Massive Open Online Course platform", "creators": [ { "creatorType": "author", "firstName": "Edwin H.", "lastName": "Wintermute" }, { "creatorType": "author", "firstName": "Matthieu", "lastName": "Cisel" }, { "creatorType": "author", "firstName": "Ariel B.", "lastName": "Lindner" } ], "abstractNote": "Massive Open Online Course (MOOC) platforms incorporate large course catalogs from which individual students may register multiple courses. We performed a network-based analysis of student achievement, considering how course-course interactions may positively or negatively affect student success. Our data set included 378,000 users and 1,000,000 unique registration events in France Université Numérique (FUN), a national MOOC platform. We adapt reliability theory to model certificate completion rates with a Weibull survival function, following the intuition that students “survive” in a course for a certain time before stochastically dropping out. Course-course interactions are found to be well described by a single parameter for user engagement that can be estimated from a user’s registration profile. User engagement, in turn, correlates with certificate rates in all courses regardless of specific content. The reliability approach is shown to capture several certificate rate patterns that are overlooked by conventional regression models. User engagement emerges as a natural metric for tracking student progress across demographics and over time.", "publicationTitle": "PLOS ONE", "publisher": "Public Library of Science", "place": "", "date": "Jan 22, 2021", "volume": "16", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "e0245718", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLOS ONE", "DOI": "10.1371/journal.pone.0245718", "citationKey": "", "url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245718", "accessDate": "2021-01-28T14:42:04Z", "PMID": "", "PMCID": "", "ISSN": "1932-6203", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "PLoS Journals", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Complex systems", "type": 1 }, { "tag": "France", "type": 1 }, { "tag": "Human learning", "type": 1 }, { "tag": "Internet", "type": 1 }, { "tag": "Probability density", "type": 1 }, { "tag": "Reliability", "type": 1 }, { "tag": "Statistical models", "type": 1 }, { "tag": "Survival analysis", "type": 1 } ], "collections": [ "J5WHMTMX" ], "relations": {}, "dateAdded": "2021-01-28T14:42:04Z", "dateModified": "2021-01-28T14:42:04Z" } }, { "key": "XD22IEVY", "version": 479, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/XD22IEVY", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/XD22IEVY", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/385213/items/8EUTJ8NC", "type": "application/json" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "XD22IEVY", "version": 479, "parentItem": "8EUTJ8NC", "itemType": "attachment", "linkMode": "imported_url", "title": "Gorgolewski_et_al-2017-BIDS_apps.pdf", "accessDate": "2021-01-19T14:25:54Z", "url": "https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005209&type=printable", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Gorgolewski_et_al-2017-BIDS_apps.pdf", "md5": "7e55c2a25880e8233e61e9875e119bda", "mtime": 1611066354000, "tags": [], "relations": {}, "dateAdded": "2021-01-19T14:25:54Z", "dateModified": "2021-01-19T14:25:55Z" } }, { "key": "8EUTJ8NC", "version": 505, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/8EUTJ8NC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/8EUTJ8NC", "type": "text/html" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "creatorSummary": "Gorgolewski et al.", "parsedDate": "2017-03-09", "numChildren": 1 }, "data": { "key": "8EUTJ8NC", "version": 505, "itemType": "journalArticle", "title": "BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods", "creators": [ { "creatorType": "author", "firstName": "Krzysztof J.", "lastName": "Gorgolewski" }, { "creatorType": "author", "firstName": "Fidel", "lastName": "Alfaro-Almagro" }, { "creatorType": "author", "firstName": "Tibor", "lastName": "Auer" }, { "creatorType": "author", "firstName": "Pierre", "lastName": "Bellec" }, { "creatorType": "author", "firstName": "Mihai", "lastName": "Capotă" }, { "creatorType": "author", "firstName": "M. Mallar", "lastName": "Chakravarty" }, { "creatorType": "author", "firstName": "Nathan W.", "lastName": "Churchill" }, { "creatorType": "author", "firstName": "Alexander Li", "lastName": "Cohen" }, { "creatorType": "author", "firstName": "R. Cameron", "lastName": "Craddock" }, { "creatorType": "author", "firstName": "Gabriel A.", "lastName": "Devenyi" }, { "creatorType": "author", "firstName": "Anders", "lastName": "Eklund" }, { "creatorType": "author", "firstName": "Oscar", "lastName": "Esteban" }, { "creatorType": "author", "firstName": "Guillaume", "lastName": "Flandin" }, { "creatorType": "author", "firstName": "Satrajit S.", "lastName": "Ghosh" }, { "creatorType": "author", "firstName": "J. Swaroop", "lastName": "Guntupalli" }, { "creatorType": "author", "firstName": "Mark", "lastName": "Jenkinson" }, { "creatorType": "author", "firstName": "Anisha", "lastName": "Keshavan" }, { "creatorType": "author", "firstName": "Gregory", "lastName": "Kiar" }, { "creatorType": "author", "firstName": "Franziskus", "lastName": "Liem" }, { "creatorType": "author", "firstName": "Pradeep Reddy", "lastName": "Raamana" }, { "creatorType": "author", "firstName": "David", "lastName": "Raffelt" }, { "creatorType": "author", "firstName": "Christopher J.", "lastName": "Steele" }, { "creatorType": "author", "firstName": "Pierre-Olivier", "lastName": "Quirion" }, { "creatorType": "author", "firstName": "Robert E.", "lastName": "Smith" }, { "creatorType": "author", "firstName": "Stephen C.", "lastName": "Strother" }, { "creatorType": "author", "firstName": "Gaël", "lastName": "Varoquaux" }, { "creatorType": "author", "firstName": "Yida", "lastName": "Wang" }, { "creatorType": "author", "firstName": "Tal", "lastName": "Yarkoni" }, { "creatorType": "author", "firstName": "Russell A.", "lastName": "Poldrack" } ], "abstractNote": "The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). The portability of these applications (BIDS Apps) is achieved by using container technologies that encapsulate all binary and other dependencies in one convenient package. BIDS Apps run on all three major operating systems with no need for complex setup and configuration and thanks to the comprehensiveness of the BIDS standard they require little manual user input. Previous containerized data processing solutions were limited to single user environments and not compatible with most multi-tenant High Performance Computing systems. BIDS Apps overcome this limitation by taking advantage of the Singularity container technology. As a proof of concept, this work is accompanied by 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.", "publicationTitle": "PLOS Computational Biology", "publisher": "Public Library of Science", "place": "", "date": "Mar 9, 2017", "volume": "13", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "e1005209", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLOS Computational Biology", "DOI": "10.1371/journal.pcbi.1005209", "citationKey": "", "url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005209", "accessDate": "2021-01-19T14:25:52Z", "PMID": "", "PMCID": "", "ISSN": "1553-7358", "archive": "", "archiveLocation": "", "shortTitle": "BIDS apps", "language": "en", "libraryCatalog": "PLoS Journals", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Computational pipelines", "type": 1 }, { "tag": "Computer software", "type": 1 }, { "tag": "Diffusion weighted imaging", "type": 1 }, { "tag": "Functional magnetic resonance imaging", "type": 1 }, { "tag": "Magnetic resonance imaging", "type": 1 }, { "tag": "Neuroimaging", "type": 1 }, { "tag": "Operating systems", "type": 1 }, { "tag": "Software tools", "type": 1 } ], "collections": [ "P2745HHW" ], "relations": {}, "dateAdded": "2021-01-19T14:25:52Z", "dateModified": "2021-01-19T14:25:52Z" } }, { "key": "HDNVFIHU", "version": 476, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/HDNVFIHU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/HDNVFIHU", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/385213/items/F4TPFGXJ", "type": "application/json" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "HDNVFIHU", "version": 476, "parentItem": "F4TPFGXJ", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text PDF", "accessDate": "2021-01-12T20:31:52Z", "url": "https://www.frontiersin.org/articles/10.3389/fninf.2011.00037/pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Das et al. - 2012 - LORIS a web-based data management system for mult.pdf", "md5": "89fb7c3b9c520805bbd79a01852a8111", "mtime": 1610483512000, "tags": [], "relations": {}, "dateAdded": "2021-01-12T20:31:52Z", "dateModified": "2021-01-12T20:31:52Z" } }, { "key": "F4TPFGXJ", "version": 505, "library": { "type": "group", "id": 385213, "name": "Imaginons la recherche", "links": { "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/385213/items/F4TPFGXJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imaginons_la_recherche/items/F4TPFGXJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 288746, "username": "Guillaume Dumas", "name": "Guillaume Dumas", "links": { "alternate": { "href": "https://www.zotero.org/guillaume_dumas", "type": "text/html" } } }, "creatorSummary": "Das et al.", "parsedDate": "2012", "numChildren": 1 }, "data": { "key": "F4TPFGXJ", "version": 505, "itemType": "journalArticle", "title": "LORIS: a web-based data management system for multi-center studies", "creators": [ { "creatorType": "author", "firstName": "Samir", "lastName": "Das" }, { "creatorType": "author", "firstName": "Alex P.", "lastName": "Zijdenbos" }, { "creatorType": "author", "firstName": "Dario", "lastName": "Vins" }, { "creatorType": "author", "firstName": "Jonathan", "lastName": "Harlap" }, { "creatorType": "author", "firstName": "Alan C.", "lastName": "Evans" } ], "abstractNote": "LORIS (Longitudinal Online Research and Imaging System) is a modular and extensible web-based data management system that integrates all aspects of a multi-center study: from heterogeneous data acquisition (imaging, clinical, behavior, genetics) to storage, processing and ultimately dissemination. It provides a secure, user-friendly, and streamlined platform to automate the flow of clinical trials and complex multi-center studies. A subject-centric internal organization allows researchers to capture and subsequently extract all information, longitudinal or cross-sectional, from any subset of the study cohort. Extensive error-checking and quality control procedures, security, data management, data querying and administrative functions provide LORIS with a triple capability (i) continuous project coordination and monitoring of data acquisition (ii) data storage/cleaning/querying, (iii) interface with arbitrary external data processing “pipelines”. LORIS is a complete solution that has been thoroughly tested through the full life cycle of a multi-center longitudinal project# and is now supporting numerous neurodevelopment and neurodegeneration research projects internationally.", "publicationTitle": "Frontiers in Neuroinformatics", "publisher": "Frontiers", "place": "", "date": "2012", "volume": "5", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Front. 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Contents

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