Archives des mots-clés : Preprint

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

Peer reviewers equally critique theory, method, and writing, with limited effect on the final content of accepted manuscripts

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Author : Dimity Stephen

The primary aims of peer review are to detect flaws and deficiencies in the design and interpretation of studies, and ensure the clarity and quality of their presentation. However, it has been questioned whether peer review fulfils this function.

Studies have highlighted a stronger focus of reviewers on critiquing methodological aspects of studies and the quality of writing in biomedical sciences, with less focus on theoretical grounding. In contrast, reviewers in the social sciences appear more concerned with theoretical underpinnings.

These studies also found the effect of peer review on manuscripts’ content to be variable, but generally modest and positive. I qualitatively analysed 1430 peer reviewers’ comments for a sample of 40 social science preprint-publication pairs to identify the key foci of reviewers’ comments.

I then quantified the effect of peer review on manuscripts by examining differences between the preprint and published versions using the normalised Levenshtein distance, cosine similarity, and word count ratios for titles, abstracts, document sections and full-texts.

I also examined changes in references used between versions and linked changes to reviewers’ comments. Reviewers’ comments were nearly equally split between issues of methodology (30.7%), theory (30.0%), and writing quality (29.2%).

Titles, abstracts, and the semantic content of documents remained similar, although publications were typically longer than preprints.

Two-thirds of citations were unchanged, 20.9% were added during review and 13.1% were removed. These findings indicate reviewers equally attended to the theoretical and methodological details and communication style of manuscripts, although the effect on quantitative measures of the manuscripts was limited.

URL : Peer reviewers equally critique theory, method, and writing, with limited effect on the final content of accepted manuscripts

DOI : https://doi.org/10.1007/s11192-022-04357-y

Open Access in Geochemistry from Preprints to Data Sharing: Past, Present, and Future

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Authors : Olivier Pourret, Dasapta Erwin Irawan

In this short communication, we discuss the latest advances regarding Open Access in the earth sciences and geochemistry community from preprints to findable, accessible, interoperable, and reusable data following the 14f session held at Goldschmidt conference (4–9 July 2021) dedicated to “Open Access in Earth Sciences”.

URL : Open Access in Geochemistry from Preprints to Data Sharing: Past, Present, and Future

DOI : https://doi.org/10.3390/publications10010003

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

Preprints in times of COVID19: the time is ripe for agreeing on terminology and good practices

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Authors : Raffaella Ravinetto, Céline Caillet, Muhammad H. Zaman, Jerome Amir Singh, Philippe J. Guerin, Aasim Ahmad, Carlos E. Durán, Amar Jesani, Ana Palmero, Laura Merson, Peter W. Horby, E. Bottieau, Tammy Hoffmann, Paul N. Newton

Over recent years, the research community has been increasingly using preprint servers to share manuscripts that are not yet peer-reviewed. Even if it enables quick dissemination of research findings, this practice raises several challenges in publication ethics and integrity.

In particular, preprints have become an important source of information for stakeholders interested in COVID19 research developments, including traditional media, social media, and policy makers.

Despite caveats about their nature, many users can still confuse pre-prints with peer-reviewed manuscripts. If unconfirmed but already widely shared first-draft results later prove wrong or misinterpreted, it can be very difficult to “unlearn” what we thought was true. Complexity further increases if unconfirmed findings have been used to inform guidelines.

To help achieve a balance between early access to research findings and its negative consequences, we formulated five recommendations: (a) consensus should be sought on a term clearer than ‘pre-print’, such as ‘Unrefereed manuscript’, “Manuscript awaiting peer review” or ‘’Non-reviewed manuscript”; (b) Caveats about unrefereed manuscripts should be prominent on their first page, and each page should include a red watermark stating ‘Caution—Not Peer Reviewed’; (c) pre-print authors should certify that their manuscript will be submitted to a peer-review journal, and should regularly update the manuscript status; (d) high level consultations should be convened, to formulate clear principles and policies for the publication and dissemination of non-peer reviewed research results; (e) in the longer term, an international initiative to certify servers that comply with good practices could be envisaged.

URL : Preprints in times of COVID19: the time is ripe for agreeing on terminology and good practices

DOI : https://doi.org/10.1186/s12910-021-00667-7