Archives des mots-clés : Preprint

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

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

Over-promotion and caution in abstracts of preprints during the COVID-19 crisis

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Authors : Frederique Bordignon, Liana Ermakova, Marianne Noel

The abstract is known to be a promotional genre where researchers tend to exaggerate the benefit of their research and use a promotional discourse to catch the reader’s attention. The COVID-19 pandemic has prompted intensive research and has changed traditional publishing with the massive adoption of preprints by researchers.

Our aim is to investigate whether the crisis and the ensuing scientific and economic competition have changed the lexical content of abstracts. We propose a comparative study of abstracts associated with preprints issued in response to the pandemic relative to abstracts produced during the closest pre-pandemic period.

We show that with the increase (on average and in percentage) of positive words (especially effective) and the slight decrease of negative words, there is a strong increase in hedge words (the most frequent of which are the modal verbs can and may).

Hedge words counterbalance the excessive use of positive words and thus invite the readers, who go probably beyond the ‘usual’ audience, to be cautious with the obtained results.

The abstracts of preprints urgently produced in response to the COVID-19 crisis stand between uncertainty and over-promotion, illustrating the balance that authors have to achieve between promoting their results and appealing for caution.

DOI : https://doi.org/10.1002/leap.1411

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

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