Archives des mots-clés : biomedical research

Reproducibility of COVID-19 pre-prints

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Authors : Annie Collins, Rohan Alexander

To examine the reproducibility of COVID-19 research, we create a dataset of pre-prints posted to arXiv, bioRxiv, medRxiv, and SocArXiv between 28 January 2020 and 30 June 2021 that are related to COVID-19.

We extract the text from these pre-prints and parse them looking for keyword markers signalling the availability of the data and code underpinning the pre-print. For the pre-prints that are in our sample, we are unable to find markers of either open data or open code for 75 per cent of those on arXiv, 67 per cent of those on bioRxiv, 79 per cent of those on medRxiv, and 85 per cent of those on SocArXiv.

We conclude that there may be value in having authors categorize the degree of openness of their pre-print as part of the pre-print submissions process, and more broadly, there is a need to better integrate open science training into a wide range of fields.

URL : https://arxiv.org/abs/2107.10724

Grand challenges and emergent modes of convergence science

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Authors : Alexander M. Petersen, Mohammed E. Ahmed, Ioannis Pavlidis

To address complex problems, scholars are increasingly faced with challenges of integrating diverse domains. We analyzed the evolution of this convergence paradigm in the ecosystem of brain science, a research frontier that provides a contemporary testbed for evaluating two modes of cross-domain integration: (a) cross-disciplinary collaboration among experts from academic departments associated with disparate disciplines; and (b) cross-topic knowledge recombination across distinct subject areas.

We show that research involving both modes features a 16% citation premium relative to a mono-domain baseline. We further show that the cross-disciplinary mode is essential for integrating across large epistemic distances.

Yet we find research utilizing cross-topic exploration alone—a convergence shortcut—to be growing in prevalence at roughly 3% per year, significantly outpacing the more essential cross-disciplinary convergence mode.

By measuring shifts in the prevalence and impact of different convergence modes in the 5-year intervals up to and after 2013, we find that shortcut patterns may relate to competitive pressures associated with Human Brain funding initiatives launched that year.

Without policy adjustments, flagship funding programs may unintentionally incentivize suboptimal integration patterns, thereby undercutting convergence science’s potential in tackling grand challenges.

URL : Grand challenges and emergent modes of convergence science

DOI : https://doi.org/10.1057/s41599-021-00869-9

Day-to-day discovery of preprint–publication links

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Authors : Guillaume Cabanac, Theodora Oikonomidi, Isabelle Boutron

Preprints promote the open and fast communication of non-peer reviewed work. Once a preprint is published in a peer-reviewed venue, the preprint server updates its web page: a prominent hyperlink leading to the newly published work is added.

Linking preprints to publications is of utmost importance as it provides readers with the latest version of a now certified work. Yet leading preprint servers fail to identify all existing preprint–publication links.

This limitation calls for a more thorough approach to this critical information retrieval task: overlooking published evidence translates into partial and even inaccurate systematic reviews on health-related issues, for instance.

We designed an algorithm leveraging the Crossref public and free source of bibliographic metadata to comb the literature for preprint–publication links. We tested it on a reference preprint set identified and curated for a living systematic review on interventions for preventing and treating COVID-19 performed by international collaboration: the COVID-NMA initiative (covid-nma.com).

The reference set comprised 343 preprints, 121 of which appeared as a publication in a peer-reviewed journal. While the preprint servers identified 39.7% of the preprint–publication links, our linker identified 90.9% of the expected links with no clues taken from the preprint servers.

The accuracy of the proposed linker is 91.5% on this reference set, with 90.9% sensitivity and 91.9% specificity. This is a 16.26% increase in accuracy compared to that of preprint servers. We release this software as supplementary material to foster its integration into preprint servers’ workflows and enhance a daily preprint–publication chase that is useful to all readers, including systematic reviewers.

This preprint–publication linker currently provides day-to-day updates to the biomedical experts of the COVID-NMA initiative.

URL : Day-to-day discovery of preprint–publication links

DOI : https://doi.org/10.1007/s11192-021-03900-7

Publication by association: how the COVID-19 pandemic has shown relationships between authors and editorial board members in the field of infectious diseases

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Authors : Clara Locher, David Moher, Ioana Alina Cristea, Florian Naudet

During the COVID-19 pandemic, the rush to scientific and political judgements on the merits of hydroxychloroquine was fuelled by dubious papers which may have been published because the authors were not independent from the practices of the journals in which they appeared.

This example leads us to consider a new type of illegitimate publishing entity, ‘self-promotion journals’ which could be deployed to serve the instrumentalisation of productivity-based metrics, with a ripple effect on decisions about promotion, tenure and grant funding, but also on the quality of manuscripts that are disseminated to the medical community and form the foundation of evidence-based medicine.

DOI : http://dx.doi.org/10.1136/bmjebm-2021-111670

Exploring factors that influence the practice of Open Science by early career health researchers: a mixed methods study

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Authors : Ksenija Zečević, Catherine Houghton, Chris Noone, Hopin Lee, Karen Matvienko-Sikar, Elaine Toomey

Background

There is a growing global movement towards open science and ensuring that health research is more transparent. It is vital that the researchers are adequately prepared for this research environment from early in their careers.

However, limited research has been conducted on the barriers and enablers to practicing open science for early career researchers. This study aimed to explore the views, experiences and factors influencing open science practices amongst ECRs working in health research.

Methods

Semi-structured individual interviews were conducted with a convenience sample of ECRs working in health research. Participants also completed surveys regarding the factors influencing open science practices. Thematic analysis was used to analyse the qualitative data and descriptive statistical analyses were used to analyse survey data.

Results

14 ECRs participated. Two main themes were identified from interview data; Valuing Open Science and Creating a Culture for Open Science. Within ‘Valuing Open Science’, participants spoke about the conceptualisation of open science to be open across the entire research cycle, and important for producing better and more impactful research for patients and the public.

Within ‘Creating a Culture of Open Science’ participants spoke about a number of factors influencing their practice of open science. These included cultural and academic pressures, the positives and negatives of increased accountability and transparency, and the need for more training and supporting resources to facilitate open science practices.

Conclusion

ECRs see the importance of open science for beneficially impacting patient and public health but many feel that they are not fully supported to practice open science.

Resources and supports including education and training are needed, as are better incentives for open science activities. Crucially, tangible engagement from institutions, funders and researchers is needed to facilitate the development of an open science culture.

URL : Exploring factors that influence the practice of Open Science by early career health researchers: a mixed methods study

DOI : https://doi.org/10.12688/hrbopenres.13119.2

Investigating the division of scientific labor using the Contributor Roles Taxonomy (CRediT)

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Authors : Vincent Larivière, David Pontille, Cassidy R. Sugimoto

Contributorship statements were introduced by scholarly journals in the late 1990s to provide more details on the specific contributions made by authors to research papers.

After more than a decade of idiosyncratic taxonomies by journals, a partnership between medical journals and standards organizations has led to the establishment, in 2015, of the Contributor Roles Taxonomy (CRediT), which provides a standardized set of 14 research contributions.

Using the data from Public Library of Science (PLOS) journals over the 2017–2018 period (N = 30,054 papers), this paper analyzes how research contributions are divided across research teams, focusing on the association between division of labor and number of authors, and authors’ position and specific contributions.

It also assesses whether some contributions are more likely to be performed in conjunction with others and examines how the new taxonomy provides greater insight into the gendered nature of labor division. The paper concludes with a discussion of results with respect to current issues in research evaluation, science policy, and responsible research practices.

URL : Investigating the division of scientific labor using the Contributor Roles Taxonomy (CRediT)

DOI : https://doi.org/10.1162/qss_a_00097

The evolving role of preprints in the dissemination of COVID-19 research and their impact on the science communication landscape

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Authors : Nicholas Fraser, Liam Brierley, Gautam Dey, Jessica K. Polka, Máté Pálfy, Federico Nann, Jonathon Alexis Coates

The world continues to face a life-threatening viral pandemic. The virus underlying the Coronavirus Disease 2019 (COVID-19), Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has caused over 98 million confirmed cases and 2.2 million deaths since January 2020.

Although the most recent respiratory viral pandemic swept the globe only a decade ago, the way science operates and responds to current events has experienced a cultural shift in the interim.

The scientific community has responded rapidly to the COVID-19 pandemic, releasing over 125,000 COVID-19–related scientific articles within 10 months of the first confirmed case, of which more than 30,000 were hosted by preprint servers.

We focused our analysis on bioRxiv and medRxiv, 2 growing preprint servers for biomedical research, investigating the attributes of COVID-19 preprints, their access and usage rates, as well as characteristics of their propagation on online platforms.

Our data provide evidence for increased scientific and public engagement with preprints related to COVID-19 (COVID-19 preprints are accessed more, cited more, and shared more on various online platforms than non-COVID-19 preprints), as well as changes in the use of preprints by journalists and policymakers.

We also find evidence for changes in preprinting and publishing behaviour: COVID-19 preprints are shorter and reviewed faster.

Our results highlight the unprecedented role of preprints and preprint servers in the dissemination of COVID-19 science and the impact of the pandemic on the scientific communication landscape.

URL : The evolving role of preprints in the dissemination of COVID-19 research and their impact on the science communication landscape

DOI : https://doi.org/10.1371/journal.pbio.3000959