Archives des mots-clés : biomedical research

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

Examining linguistic shifts between preprints and publications

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Authors : David N. Nicholson, Vincent Rubinetti, Dongbo Hu, Marvin Thielk, Lawrence E. Hunter, Casey S. Greene

Preprints allow researchers to make their findings available to the scientific community before they have undergone peer review. Studies on preprints within bioRxiv have been largely focused on article metadata and how often these preprints are downloaded, cited, published, and discussed online.

A missing element that has yet to be examined is the language contained within the bioRxiv preprint repository. We sought to compare and contrast linguistic features within bioRxiv preprints to published biomedical text as a whole as this is an excellent opportunity to examine how peer review changes these documents.

The most prevalent features that changed appear to be associated with typesetting and mentions of supporting information sections or additional files. In addition to text comparison, we created document embeddings derived from a preprint-trained word2vec model.

We found that these embeddings are able to parse out different scientific approaches and concepts, link unannotated preprint–peer-reviewed article pairs, and identify journals that publish linguistically similar papers to a given preprint.

We also used these embeddings to examine factors associated with the time elapsed between the posting of a first preprint and the appearance of a peer-reviewed publication. We found that preprints with more versions posted and more textual changes took longer to publish.

Lastly, we constructed a web application (https://greenelab.github.io/preprint-similarity-search/) that allows users to identify which journals and articles that are most linguistically similar to a bioRxiv or medRxiv preprint as well as observe where the preprint would be positioned within a published article landscape.

URL : Examining linguistic shifts between preprints and publications

DOI : https://doi.org/10.1371/journal.pbio.3001470

Publishing of COVID-19 preprints in peer-reviewed journals, preprinting trends, public discussion and quality issues

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Authors : Ivan Kodvanj, Jan Homolak, Vladimir Trkulja

COVID-19-related (vs. non-related) articles appear to be more expeditiously processed and published in peer-reviewed journals.

We aimed to evaluate: (i) whether COVID-19-related preprints were favored for publication, (ii) preprinting trends and public discussion of the preprints, and (iii) the relationship between the publication topic (COVID-19-related or not) and quality issues.

Manuscripts deposited at bioRxiv and medRxiv between January 1 and September 27 2020 were assessed for the probability of publishing in peer-reviewed journals, and those published were evaluated for submission-to-acceptance time. The extent of public discussion was assessed based on Altmetric and Disqus data.

The Retraction Watch Database and PubMed were used to explore the retraction of COVID-19 and non-COVID-19 articles and preprints. With adjustment for the preprinting server and number of deposited versions, COVID-19-related preprints were more likely to be published within 120 days since the deposition of the first version (OR = 1.96, 95% CI: 1.80–2.14) as well as over the entire observed period (OR = 1.39, 95% CI: 1.31–1.48). Submission-to-acceptance was by 35.85 days (95% CI: 32.25–39.45) shorter for COVID-19 articles.

Public discussion of preprints was modest and COVID-19 articles were overrepresented in the pool of retracted articles in 2020. Current data suggest a preference for publication of COVID-19-related preprints over the observed period.

URL : https://doi.org/10.1007/s11192-021-04249-7

Characteristics of retracted editorial articles in the biomedical literature

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Author : Bakthavachalam Elango

The main purpose of this short communication is to identify and analyze retracted editorials in the biomedical literature. Twenty-five of the 33 editorials are chosen for further analysis. All of the editorials were published as commentaries and concise reviews between 1998 and 2021.

Due to plagiarism and data-related issues, the majority of the editorial articles were retracted. Alarmingly, one-fifth of the editorials were funded by external agencies, with the USA leading the list of retracted editorials.

The average time between the publication of the editorials and their retraction is 2.48 years, and two editorials were retracted with the longest durations; both were written by the same author.

The conclusion is that, at the very least, editorial articles should be devoid of research/scientific misconduct.

DOI : https://doi.org/10.1007/s11192-021-04263-9