Biology subjects

Moher, D.

Publications and source records attributed to Moher, D..

10 recordsLinked to original sources

bioRxiv2025

Funders' expectations for open science in cardiovascular research: A Scoping review of the largest cardiovascular research funders

Open science practices, including data sharing, open access, and prospective study registration, have been increasingly recognized to improve transparency, reproducibility, and accessibility in research, yet their uptake and implementation by cardiovascular research funders is unclear. We conducted a scoping review of publicly available policies, guidance, and grant instructions from 12 members of the Global Cardiovascular Research Funders Forum to assess expectations, monitoring, and support for open science in cardiovascular research. We included 105 documents from 9 funders; no relevant documents were identified for 3 funders. Data sharing (75%) and open access (67%) were the most common mandates by funders, followed by prospective registration (50%). Requirements for other practices, including code sharing, use of reporting guidelines, preprints, and open peer review, were uncommon. Monitoring compliance was inconsistent, with many funders not specifying any mechanisms, even for widely required practices. Where available, support was most often provided through financial assistance, guidance, or infrastructure, particularly for open access, data sharing, and patient or public involvement. These findings suggest that while cardiovascular funders are engaging with open science, policies remain uneven in scope, monitoring, and support. Navigating the open science implementation gap in cardiovascular research will be essential to reap the benefits of transparency and innovation, only possible through the sharing of information and data.

scientific communication and education↗

bioRxiv2023

COVID-19-related research data availability and quality according to the FAIR principles: A meta-research study

BackgroundAs per the FAIR principles (Findable, Accessible, Interoperable, and Reusable), scientific research data should be findable, accessible, interoperable, and reusable. The COVID-19 pandemic has led to massive research activities and an unprecedented number of topical publications in a short time. There has not been any evaluation to assess if this COVID-19-related research data complied with FAIR principles (or FAIRness) so far. ObjectiveOur objective was to investigate the availability of open data in COVID-19-related research and to assess compliance with FAIRness. MethodsWe conducted a comprehensive search and retrieved all open-access articles related to COVID-19 from journals indexed in PubMed, available in the Europe PubMed Central database, published from January 2020 through June 2023, using the metareadr package. Using rtransparent, a validated automated tool, we identified articles that included a link to their raw data hosted in a public repository. We then screened the link and included those repositories which included data specifically for their pertaining paper. Subsequently, we automatically assessed the adherence of the repositories to the FAIR principles using FAIRsFAIR Research Data Object Assessment Service (F-UJI) and rfuji package. The FAIR scores ranged from 1-22 and had four components. We reported descriptive analysis for each article type, journal category and repository. We used linear regression models to find the most influential factors on the FAIRness of data. Results5,700 URLs were included in the final analysis, sharing their data in a general-purpose repository. The mean (standard deviation, SD) level of compliance with FAIR metrics was 9.4 (4.88). The percentages of moderate or advanced compliance were as follows: Findability: 100.0%, Accessibility: 21.5%, Interoperability: 46.7%, and Reusability: 61.3%. The overall and component-wise monthly trends were consistent over the follow-up. Reviews (9.80, SD=5.06, n=160), and articles in dental journals (13.67, SD=3.51, n=3) and Harvard Dataverse (15.79, SD=3.65, n=244) had the highest mean FAIRness scores, whereas letters (7.83, SD=4.30, n=55), articles in neuroscience journals (8.16, SD=3.73, n=63), and those deposited in GitHub (4.50, SD=0.13, n=2,152) showed the lowest scores. Regression models showed that the most influential factor on FAIRness scores was the repository (R2=0.809). ConclusionThis paper underscored the potential for improvement across all facets of FAIR principles, with a specific emphasis on enhancing Interoperability and Reusability in the data shared within general repositories during the COVID-19 pandemic.

bioinformatics↗

bioRxiv2023

Biomedical researchers perspectives on the reproducibility of research: a cross-sectional international survey

We conducted an international cross-sectional survey of biomedical researchers perspectives on the reproducibility of research. This study builds on a widely cited 2016 survey on reproducibility, and provides a biomedical-specific and contemporary perspective on reproducibility. To sample the community, we randomly selected 400 journals indexed in MEDLINE, from which we extracted the author names and e-mails from all articles published between October 1, 2020 and October 1, 2021. We invited participants to complete an anonymous online survey which collected basic demographic information, perceptions about a reproducibility crisis, perceived causes of irreproducibility of research results, experience conducting replication studies, and knowledge of funding and training for research on reproducibility. A total of 1924 participants accessed our survey, of which 1630 provided useable responses (response rate 7% of 23,234). Key findings include that 72% of participants agreed there was a reproducibility crisis in biomedicine, with 27% of participants indicating the crisis was significant. The leading perceived cause of irreproducibility was a pressure to publish with 62% of participants indicating it always or very often contributes. About half of the participants (54%) had run a replication of their own previously published study while slightly more (57%) had run a replication of another researchers study. Just 16% of participants indicated their institution had established procedures to enhance the reproducibility of biomedical research; and 67% felt their institution valued new research over replication studies. Participants also reported few opportunities to obtain funding to attempt to reproduce a study and 83% perceived it would be harder to do so than to get funding to do a novel study. Our results may be used to guide training and interventions to improve research reproducibility and to monitor rates of reproducibility over time. The findings are also relevant to policy makers and academic leadership looking to create incentives and research cultures that support reproducibility and value research quality.

scientific communication and education↗

bioRxiv2023

Cardiology researchers' practices and perceived barriers related to open science: an international cross-sectional survey

BackgroundOpen science is a movement and set of practices to conduct research more transparently. Implementing open science will significantly improve public access and supports equity. It also has the potential to foster innovation and reduce duplication through data and materials sharing. Here, we survey an international group of researchers publishing in cardiovascular journals regarding their perceptions and practices related to open science. MethodsWe identified the top 100 "Cardiology and Cardiovascular Medicine" subject category journals from the SCImago journal ranking platform. This is a publicly available portal that draws from Scopus. We then extracted the corresponding authors name and e-mail from all articles published in these journals between March 1, 2021 - March 1, 2022. Participants were sent a purpose-built survey about open science. The survey contained primarily multiple choice and scale-based questions for which we report count data and percentages. For the few text-based responses we conducted thematic content analysis. Results198 participants responded to our survey. Participants had a mean response of 6.8 (N=197, SD=1.8) on a 9-point scale with endpoints, not at all familiar (1) and extremely familiar (9), when indicating how familiar they were with open science. When asked about where they obtained open science training, most participants indicated this was done on the job self-initiated while conducting research (n=103, 52%), or that they had no formal training with respect to open science (n=72, 36%). More than half of the participants indicated they would benefit from practical support from their institution on how to perform open science practices (N=106, 54%). A diversity of barriers to each of the open science practices presented to participants were acknowledged. Participants indicated that funding was the most essential incentive to adopt open science. DiscussionIt is clear that policy alone will not lead to the effective implementation of open science. This survey serves as a baseline for the cardiovascular research communitys open science performance and perception and can be used to inform future interventions and monitoring.

scientific communication and education↗

bioRxiv2021

Sex and Gender Considerations in Reporting Guidelines of Health Research: A Systematic Review

BackgroundDespite growing recognition of the importance of sex and gender considerations in health research, they are rarely integrated into research design and reporting. We sought to assess the integration of sex, as a biological attribute and gender as a socially constructed identity in published reporting guidelines. Methods and FindingsWe conducted a systematic review of published reporting guidelines listed on the EQUATOR website (www.equator-nework.org) from inception until December 2018. We selected all reporting guidelines (original and extensions) listed on the EQUATOR library. We used EndNote Citation Software to build a database of the statement of each guideline identified as full bibliographic reference and retrieved the full texts. Reviewers independently extracted the data from the checklist/abstract/main text of guidelines. Data were analyzed using descriptive statistics and narrative synthesis. A total of 407 reporting guidelines were included; they were published between 1995 and 2018. Of the 407 guidelines, 159 (39%) mentioned "sex" and/or "gender" in the checklist/abstract/main text. Of these, 90 (22.1%) mentioned only "sex", and 91 (22.4%) mentioned only "gender". In the checklist of the reporting guidelines (n = 363), "sex" and "gender" were mentioned in 50 (13.8%) and 39 (10.7%), respectively. Only one reporting guideline met the three criteria of correct use of sex and gender concepts. Trends in the use of sex and gender in the checklists showed that the use of "sex" only started in 2003, while "gender" has been used since 1996. ConclusionsWe assessed the integration of sex and gender considerations in reporting guidelines based on the use of sex- and gender-related words. Our findings showed a low use and integration of sex and gender concepts in reporting guidelines. Authors of reporting guidelines should reduce this gap for a better use of research knowledge. Registration: PROSPERO no. CRD42019136491.

scientific communication and education↗

bioRxiv2021

'Nepotistic journals: a survey of biomedical journals.

ContextConvergent analyses in different disciplines support the use of the Percentage of Papers by the Most Prolific author (PPMP) as a red flag to identify journals that can be suspected of questionable editorial practices. We examined whether this index, complemented by the Gini index, could be useful for identifying cases of potential editorial bias, using a large sample of biomedical journals. MethodsWe extracted metadata for all biomedical journals referenced in the National Library of Medicine, with any attributed Broad Subject Terms, and at least 50 authored (i.e. by at least one author) articles between 2015 and 2019, identifying the most prolific author (i.e. the person who signed the most papers in each particular journal). We calculated the PPMP and the 2015-2019 Gini index for the distribution of articles across authors. When the relevant information was reported, we also computed the median publication lag (time between submission and acceptance) for articles authored by any of the most prolific authors and that for articles not authored by prolific authors. For outlier journals, defined as a PPMP or Gini index above the 95th percentile of their respective distributions, a random sample of 100 journals was selected and described in relation to status on the editorial board for the most prolific author. Results5 468 journals that published 4 986 335 papers between 2015 and 2019 were analysed. The PPMP 95th percentile was 10.6% (median 2.9%). The Gini index 95th percentile was 0.355 (median 0.183). Correlation between the two indices was 0.35 (95CI 0.33 to 0.37). Information on publication lag was available for 2 743 journals. We found that 277 journals (10.2%) had a median time lag to publication for articles by the most prolific author(s) that was shorter than 3 weeks, versus 51 (1.9%) journals with articles not authored by prolific author(s). Among the random sample of outlier journals, 98 provided information about their editorial board. Among these 98, the most prolific author was part of the editorial board in 60 cases (61%), among whom 25 (26% of the 98) were editors-in-chief. DiscussionIn most journals publications are distributed across a large number of authors. Our results reveal a subset of journals where a few authors, often members of the editorial board, were responsible for a disproportionate number of publications. The papers by these authors were more likely to be accepted for publication within 3 weeks of their submission. To enhance trust in their practices, journals need to be transparent about their editorial and peer review practices.

scientific communication and education↗

bioRxiv2020

A systematic examination of preprint platforms for use in the medical and biomedical sciences setting

ABSTRACTObjectives The objective of this review is to identify all preprint platforms with biomedical and medical scope and to compare and contrast the key characteristics and policies of these platforms. We also aim to provide a searchable database to enable relevant stakeholders to compare between platforms.Study Design and Setting Preprint platforms that were launched up to 25th June 2019 and have a biomedical and medical scope according to MEDLINE’s journal selection criteria were identified using existing lists, web-based searches and the expertise of both academic and non-academic publication scientists. A data extraction form was developed, pilot-tested and used to collect data from each preprint platform’s webpage(s). Data collected were in relation to scope and ownership; content-specific characteristics and information relating to submission, journal transfer options, and external discoverability; screening, moderation, and permanence of content; usage metrics and metadata. Where possible, all online data were verified by the platform owner or representative by correspondence.Results A total of 44 preprint platforms were identified as having biomedical and medical scope, 17 (39%) were hosted by the Open Science Framework preprint infrastructure, six (14%) were provided by F1000 Research Ltd (the Open Research Central infrastructure) and 21 (48%) were other independent preprint platforms. Preprint platforms were either owned by non-profit academic groups, scientific societies or funding organisations (n=28; 64%), owned/partly owned by for-profit publishers or companies (n=14; 32%) or owned by individuals/small communities (n=2; 5%). Twenty-four (55%) preprint platforms accepted content from all scientific fields although some of these had restrictions relating to funding source, geographical region or an affiliated journal’s remit. Thirty-three (75%) preprint platforms provided details about article screening (basic checks) and 14 (32%) of these actively involved researchers with context expertise in the screening process. The three most common screening checks related to the scope of the article, plagiarism and legal/ethical/societal issues and compliance. Almost all preprint platforms allow submission to any peer-reviewed journal following publication, have a preservation plan for read-access, and most have a policy regarding reasons for retraction and the sustainability of the service. Forty-one (93%) platforms currently have usage metrics, with the most common metric being the number of downloads presented on the abstract page.Conclusion A large number of preprint platforms exist for use in biomedical and medical sciences, all of which offer researchers an opportunity to rapidly disseminate their research findings onto an open-access public server, subject to scope and eligibility. However, the process by which content is screened before online posting and withdrawn or removed after posting varies between platforms, which may be associated with platform operation, ownership, governance and financing.In concurrence with an increase in the number of preprint servers and platforms supporting biomedical and medical sciences research since 2013, there has been substantial growth in the number of preprints posted in this research area.The significant benefits of accelerated dissemination of research that preprints offer has attracted the support of many major funders.The raised profile of preprints has led to their wider acceptance in institutional and individual level assessment.This is the first full examination of the characteristics and policies of 44 preprint platforms with biomedical and medical scope. We use a robust methodological approach to extract relevant information from web-based material with input from preprint platform owners.Despite concerns regarding the permanence and quality of preprints, most preprint platforms have long-term preservation strategies and many have screening checks (for example, a basic check for the relevance of content) in place. For some platforms, these checks are performed by researchers with content expertise.We provide a searchable database as a valuable resource for researchers, funders and policymakers in the biomedical and medical science field to determine which preprint platforms are relevant to their research scope and which have the functionality and policies that they value most.Competing Interest StatementJessica Polka is Executive Director of ASAPbio.View Full Text

scientific communication and education↗

bioRxiv2020

Inflated citations and metrics of journals discontinued from Scopus for publication concerns: the GhoS(t)copus Project

Background Scopus is considered a leading bibliometric database. It contains the largest number of abstracts and articles cited in peer reviewed publications. The journals included in Scopus are periodically re-evaluated to ensure they meet indexing criteria. Afterwards, some journals might be discontinued for publication concerns. Despite their discontinuation, previously published articles remain indexed and continue to be cited. The metrics and characteristics of journals discontinued for publication concerns have yet to be studied. This study aimed (1) to evaluate the main features and citation metrics of journals discontinued from Scopus for publication concerns, before and after discontinuation, and (2) to determine the extent of predatory journals among the discontinued journals.Materials and Methods Eight authors surveyed a list of discontinued journals from Scopus (version July 2019). Data regarding metrics, citations and indexing were extracted from Scopus or other scientific databases, for the journals discontinued for publication concerns.Results A total of 317 journals were evaluated. The mean number of citations per year after discontinuation was significantly higher than before (median of difference 64 citations, p<0.0001), and so was the number of citations per document (median of difference 0.4 citations, p<0.0001). The total number of citations after discontinuation was 607,261, with a median of 713 citations (IQR 254-2056, range 0-19468) per journal. The open access publishing model was declared for 93% (294/317) of the journals, but only nine of these are currently indexed in the Directory of Open Access Journals (DOAJ). Twenty-two percent (72/317) of the journals were included in the Cabell blacklist.Conclusions The citation count of journals discontinued for publication concerns, increases despite discontinuation. Countermeasures should be taken to ensure the validity and reliability of Scopus metrics both at journal- and author-level for the purpose of scientific assessment of publishing.View Full Text

scientific communication and education↗

bioRxiv2019

Academic criteria for promotion and tenure in faculties of biomedical sciences: a cross-sectional analysis of 146 universities

ObjectivesTo determine the presence of a set of pre-specified traditional and progressive criteria used to assess scientists for promotion and tenure in faculties of biomedical sciences among universities worldwide. DesignCross-sectional study. SettingNot applicable. Participants170 randomly selected universities from the Leiden Ranking of world universities list were considered. Main outcome measuresTwo independent reviewers searched for all guidelines applied when assessing scientists for promotion and tenure for institutions with biomedical faculties. Where faculty-level guidelines were not available, institution-level guidelines were sought. Available documents were reviewed and the presence of 5 traditional (e.g., number of publications) and 7 progressive (e.g., data sharing) criteria was noted in guidelines for assessing assistant professors, associate professors, professors, and the granting of tenure. ResultsA total of 146 institutions had faculties of biomedical sciences with 92 having eligible guidelines available to review. Traditional criteria were more commonly reported than progressive criteria (t(82)= 15.1, p= .001). Traditional criteria mentioned peer-reviewed publications, authorship order, journal impact, grant funding, and national or international reputation in 95%, 37%, 28%, 67%, and 48% of the guidelines, respectively. Conversely, among progressive criteria only citations (any mention in 26%) and accommodations for extenuating circumstances (37%) were relatively commonly mentioned; while there was rare mention of alternative metrics for sharing research (2%) and data sharing (1%), and 3 criteria (publishing in open access mediums, registering research, and adhering to reporting guidelines) were not found in any institution reviewed. We observed notable differences across continents on whether guidelines are accessible or not (Australia 100%, North America 97%, Europe 50%, Asia 58%, South America 17%), and more subtle differences on the use of specific criteria. ConclusionsThis study demonstrates that the current evaluation of scientists emphasizes traditional criteria as opposed to progressive criteria. This may reinforce research practices that are known to be problematic while insufficiently supporting the conduct of better-quality research and open science. Institutions should consider incentivizing progressive criteria. RegistrationOpen Science Framework (https://osf.io/26ucp/) What is already known on this topicO_LIAcademics tailor their research practices based on the evaluation criteria applied within their academic institution. C_LIO_LIEnsuring that biomedical researchers are incentivized by adhering to best practice guidelines for research is essential given the clinical implications of this work. C_LIO_LIWhile changes to the criteria used to assess professors and confer tenure have been recommended, a systematic assessment of promotion and tenure criteria being applied worldwide has not been conducted. C_LI What this study addsO_LIAcross countries, university guidelines focus on rewarding traditional research criteria (peer-reviewed publications, authorship order, journal impact, grant funding, and national or international reputation). C_LIO_LIThe minimum requirements for promotion and tenure criteria are predominantly objective in nature, although several of them are inadequate measures to assess the impact of researchers. C_LIO_LIDeveloping and evaluating more appropriate, progressive indicators of research may facilitate changes in the evaluation practices for rewarding researchers. C_LI

scientific communication and education↗

bioRxiv2019

What difference do retractions make? An estimate of the epistemic impact of retractions on recent meta-analyses.

Every year, several hundred publications are retracted due to fabrication and falsification of data or plagiarism and other breeches of research integrity and ethics. Despite considerable research on this phenomenon, the extent to which a retraction requires revising previous scientific estimates and beliefs - which we define as the epistemic impact - is unknown. We collected a representative sample of recently retracted studies that had been included in recent meta-analyses, and compared the summary effect size of these meta analyses with and without the refracted studies. On average, the retractions had occurred about six years prior to the publication of the corresponding meta-analyses.\n\nOur results suggest that retractions have varying impacts depending on their causes. In particular, removing from an analysis a study retracted because of issues with data, methods or results, led to a statistically significant reduction of the estimated effect size. Assuming that the results of these retracted studies are completely false, then the meta-analyses that had included them had overestimated the summary effect sizes by, averaging across effect size metrics, 30% (median, 13%). However, retractions due to plagiarism or other issues not related to data, methods or results had no impact on the conclusions of meta-analyses.\n\nSince retractions due to plagiarism or other non-data related issues typically constitute over 75% of total retractions, our results suggest that the epistemic impact of most retractions is likely to be null. However, our results also suggest that retractions due to issues with data, methods or results should be accompanied by a revision of relevant meta-analyses, and by extension a downwards revision of prior scientific beliefs.

scientific communication and education↗