Archives des mots-clés : biomedical research

Science in motion: A qualitative analysis of journalists’ use and perception of preprints

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Authors : Alice Fleerackers, Laura L. Moorhead, Lauren A. Maggio, Kaylee Fagan, Juan Pablo Alperin

This qualitative study explores how and why journalists use preprints—unreviewed research papers—in their reporting. Through thematic analysis of interviews conducted with 19 health and science journalists in the second year of the COVID-19 pandemic, it applies a theoretical framework that conceptualizes COVID-19 preprint research as a form of post-normal science, characterized by high scientific uncertainty and societal relevance, urgent need for political decision-making, and value-related policy considerations.

Findings suggest that journalists approach the decision to cover preprints as a careful calculation, in which the potential public benefits and the ease of access preprints provided were weighed against risks of spreading misinformation.

Journalists described viewing unreviewed studies with extra skepticism and relied on diverse strategies to find, vet, and report on them. Some of these strategies represent standard science journalism, while others, such as labeling unreviewed studies as preprints, mark a departure from the norm. However, journalists also reported barriers to covering preprints, as many felt they lacked the expertise or the time required to fully understand or vet the research.

The findings suggest that coverage of preprints is likely to continue post-pandemic, with important implications for scientists, journalists, and the publics who read their work.

URL : Science in motion: A qualitative analysis of journalists’ use and perception of preprints

DOI : https://doi.org/10.1371/journal.pone.0277769

Forecasting the publication and citation outcomes of COVID-19 preprints

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Authors : Michael Gordon, Michael Bishop, Yiling Chen, Anna Dreber, Brandon Goldfedder, Felix Holzmeister, Magnus Johannesson, Yang Liu, Louisa Tran, Charles Twardy, Juntao Wang, Thomas Pfeiffer

Many publications on COVID-19 were released on preprint servers such as medRxiv and bioRxiv. It is unknown how reliable these preprints are, and which ones will eventually be published in scientific journals.

In this study, we use crowdsourced human forecasts to predict publication outcomes and future citation counts for a sample of 400 preprints with high Altmetric score. Most of these preprints were published within 1 year of upload on a preprint server (70%), with a considerable fraction (45%) appearing in a high-impact journal with a journal impact factor of at least 10.

On average, the preprints received 162 citations within the first year. We found that forecasters can predict if preprints will be published after 1 year and if the publishing journal has high impact. Forecasts are also informative with respect to Google Scholar citations within 1 year of upload on a preprint server.

For both types of assessment, we found statistically significant positive correlations between forecasts and observed outcomes. While the forecasts can help to provide a preliminary assessment of preprints at a faster pace than traditional peer-review, it remains to be investigated if such an assessment is suited to identify methodological problems in preprints.

URL : Forecasting the publication and citation outcomes of COVID-19 preprints

DOI : https://doi.org/10.1098/rsos.220440

Publication practices during the COVID-19 pandemic: Expedited publishing or simply an early bird effect?

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Authors : Yulia V. Sevryugina, Andrew J. Dicks

This study explores the evolution of publication practices associated with the SARS-CoV-2 research papers, namely, peer-reviewed journal and review articles indexed in PubMed and their associated preprints posted on bioRxiv and medRxiv servers: a total of 4,031 journal article-preprint pairs.

Our assessment of various publication delays during the January 2020 to March 2021 period revealed the early bird effect that lies beyond the involvement of any publisher policy action and is directly linked to the emerging nature of new and ‘hot’ scientific topics.

We found that when the early bird effect and data incompleteness are taken into account, COVID-19 related research papers show only a moderately expedited speed of dissemination as compared with the pre-pandemic era.

Medians for peer-review and production stage delays were 66 and 15 days, respectively, and the entire conversion process from a preprint to its peer-reviewed journal article version took 109.5 days.

The early bird effect produced an ephemeral perception of a global rush in scientific publishing during the early days of the coronavirus pandemic. We emphasize the importance of considering the early bird effect in interpreting publication data collected at the outset of a newly emerging event.

URL : Publication practices during the COVID-19 pandemic: Expedited publishing or simply an early bird effect?

DOI : https://doi.org/10.1002/leap.1483

Preprint citation practice in PLOS

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Authors : Marc Bertin, Iana Atanassova

The role of preprints in the scientific production and their part in citations have been growing over the past 10 years. In this paper we study preprint citations in several different aspects: the progression of preprint citations over time, their relative frequencies in relation to the IMRaD structure of articles, their distributions over time, per preprint database and per PLOS journal.

We have processed the PLOS corpus that covers 7 journals and a total of about 240,000 articles up to January 2021, and produced a dataset of 8460 preprint citation contexts that cite 12 different preprint databases.

Our results show that preprint citations are found with the highest frequency in the Method section of articles, though small variations exist with respect to journals. The PLOS Computational Biology journal stands out as it contains more than three times more preprint citations than any other PLOS journal.

The relative parts of the different preprint databases are also examined. While ArXiv and bioRxiv are the most frequent citation sources, bioRxiv’s disciplinary nature can be observed as it is the source of more than 70% of preprint citations in PLOS Biology, PLOS Genetics and PLOS Pathogens.

We have also compared the lexical content of preprint citation contexts to the citation content to peer-reviewed publications. Finally, by performing a lexicometric analysis, we have shown that preprint citation contexts differ significantly from citation contexts of peer-reviewed publications.

This confirms that authors make use of different lexical content when citing preprints compared to the rest of citations.

URL : Preprint citation practice in PLOS

DOI : https://doi.org/10.1007/s11192-022-04388-5

Biosecurity in an age of open science

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Authors : James Andrew Smith, Jonas B. Sandbrink

The risk of accidental or deliberate misuse of biological research is increasing as biotechnology advances. As open science becomes widespread, we must consider its impact on those risks and develop solutions that ensure security while facilitating scientific progress.

Here, we examine the interaction between open science practices and biosecurity and biosafety to identify risks and opportunities for risk mitigation. Increasing the availability of computational tools, datasets, and protocols could increase risks from research with misuse potential.

For instance, in the context of viral engineering, open code, data, and materials may increase the risk of release of enhanced pathogens. For this dangerous subset of research, both open science and biosecurity goals may be achieved by using access-controlled repositories or application programming interfaces. While preprints accelerate dissemination of findings, their increased use could challenge strategies for risk mitigation at the publication stage.

This highlights the importance of oversight earlier in the research lifecycle. Preregistration of research, a practice promoted by the open science community, provides an opportunity for achieving biosecurity risk assessment at the conception of research.

Open science and biosecurity experts have an important role to play in enabling responsible research with maximal societal benefit.

URL : Biosecurity in an age of open science

DOI : https://doi.org/10.1371/journal.pbio.3001600

Peer reviewers’ dilemmas: a qualitative exploration of decisional conflict in the evaluation of grant applications in the medical humanities and social sciences

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Authors : Gaëlle Vallée-Tourangeau, Ana Wheelock, Tushna Vandrevala, Priscilla Harris

Independent evaluations of grant applications by subject experts are an important part of the peer-review system. However, little is known about the real-time experiences of peer reviewers or experts who perform reviews of a grant application independently.

This study sought to gain insight into this stage of the grant evaluation process by observing how experts conduct an independent review in near real time. Using the think aloud approach and Critical Decision Method of interviewing, in-depth interviews were conducted with 16 peer reviewers from a range of roles and disciplines within the medical humanities and social sciences.

Participants were asked to think aloud while reviewing applications to different grant schemes from a single prestigious funder. The analysis shows reviewers encountered five dilemmas during the evaluation process.

These dilemmas were related to whether or not one should (1) accept an invitation to review, (2) rely exclusively on the information presented in the application, (3) pay attention to institutional prestige, (4) offer comments about aspects that are not directly related to academics’ area of expertise, and (5) to take risks and overlook shortcomings rather than err on the side of caution.

In order to decide on the appropriate course of action, reviewers often engaged in a series of deliberations and trade-offs—varying in length and complexity.

However, their interpretation of what was ‘right’ was influenced by their values, preferences and experiences, but also by relevant norms and their understanding of the funder’s guidelines and priorities.

As a result, the way reviewers approached the identified dilemmas was idiosyncratic and sometimes diametrically opposed to other reviewers’ views, which could lead to variation in peer-review outcomes.

The dilemmas we have uncovered suggest that peer reviewers engage in thoughtful considerations during the peer-review process.

We should, therefore, be wary of reducing the absence of consensus as resulting from biased, instinctive thinking. Rather, these findings highlight the diversity of values, priorities and habits and ways of working each reviewer brings to the fore when reviewing the applicants and their project proposals and call for further reflection on, and study of, this “invisible work” to better understand and continue to improve the peer-reviewing process.

URL : Peer reviewers’ dilemmas: a qualitative exploration of decisional conflict in the evaluation of grant applications in the medical humanities and social sciences

DOI : https://doi.org/10.1057/s41599-022-01050-6

L’impact de la crise de la COVID-19 sur les pratiques et usages des prépublications des chercheurs en sciences du vivant et de la médecine : questionner leur légitimité

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Autrice/Author : Marie Vial–Bonacci

La COVID-19, pandémie mondiale, apparue dans la ville de Wuhan en Chine en novembre 2019, a engendré un bouleversement sans précédent de la communication scientifique. Cette crise sanitaire a incité les chercheurs à utiliser les serveurs de prépublications afin de communiquer plus rapidement les résultats scientifiques dans l’objectif de faire avancer la science.

Le présent mémoire tentera d’analyser et de mettre en lumière ces changements majeurs à travers une étude des modifications des pratiques et usages des prépublications depuis le début de la pandémie, à l’échelle internationale.

Cette perspective sera également étudiée à l’échelle nationale, à travers une enquête de terrain. Ce travail de recherche sera centré sur le secteur des sciences du vivant et de la médecine, un secteur qui n’utilise que très peu les prépublications mais qui connait une explosion de cette pratique avec la crise sanitaire. Plus encore ce mémoire tentera d’étudier l’évolution de leur légitimité pendant la pandémie.

URL: L’impact de la crise de la COVID-19 sur les pratiques et usages des prépublications des chercheurs en sciences du vivant et de la médecine : questionner leur légitimité

Original location : https://www.enssib.fr/bibliotheque-numerique/notices/70354-l-impact-de-la-crise-de-la-covid-19-sur-les-pratiques-et-usages-des-prepublications-des-chercheurs-en-sciences-du-vivant-et-de-la-medecine-questionner-leur-legitimite