Archives des mots-clés : biomedical research

Assessment of transparency indicators across the biomedical literature: How open is open?

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Authors : Stylianos Serghiou, Despina G. Contopoulos-Ioannidis, Kevin W. Boyack, Nico Riedel, Joshua D. Wallach, John P. A. Ioannidis

Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic.

We present an open-source, automated approach to identify 5 indicators of transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures, and protocol registration) and apply it across the entire open access biomedical literature of 2.75 million articles on PubMed Central (PMC).

Our results indicate remarkable improvements in some (e.g., conflict of interest [COI] disclosures and funding disclosures), but not other (e.g., protocol registration and code sharing) areas of transparency over time, and map transparency across fields of science, countries, journals, and publishers.

This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand, and promote transparency and reproducibility in science.

URL : Assessment of transparency indicators across the biomedical literature: How open is open?

DOI : https://doi.org/10.1371/journal.pbio.3001107

Publication rate and citation counts for preprints released during the COVID-19 pandemic: the good, the bad and the ugly

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Authors : Diego Añazco, Bryan Nicolalde, Isabel Espinosa, Jose Camacho , Mariam Mushtaq, Jimena Gimenez, Enrique Teran

Background

Preprints are preliminary reports that have not been peer-reviewed. In December 2019, a novel coronavirus appeared in China, and since then, scientific production, including preprints, has drastically increased. In this study, we intend to evaluate how often preprints about COVID-19 were published in scholarly journals and cited.

Methods

We searched the iSearch COVID-19 portfolio to identify all preprints related to COVID-19 posted on bioRxiv, medRxiv, and Research Square from January 1, 2020, to May 31, 2020. We used a custom-designed program to obtain metadata using the Crossref public API.

After that, we determined the publication rate and made comparisons based on citation counts using non-parametric methods. Also, we compared the publication rate, citation counts, and time interval from posting on a preprint server to publication in a scholarly journal among the three different preprint servers.

Results

Our sample included 5,061 preprints, out of which 288 were published in scholarly journals and 4,773 remained unpublished (publication rate of 5.7%). We found that articles published in scholarly journals had a significantly higher total citation count than unpublished preprints within our sample (p < 0.001), and that preprints that were eventually published had a higher citation count as preprints when compared to unpublished preprints (p < 0.001).

As well, we found that published preprints had a significantly higher citation count after publication in a scholarly journal compared to as a preprint (p < 0.001). Our results also show that medRxiv had the highest publication rate, while bioRxiv had the highest citation count and shortest time interval from posting on a preprint server to publication in a scholarly journal.

Conclusions

We found a remarkably low publication rate for preprints within our sample, despite accelerated time to publication by multiple scholarly journals. These findings could be partially attributed to the unprecedented surge in scientific production observed during the COVID-19 pandemic, which might saturate reviewing and editing processes in scholarly journals.

However, our findings show that preprints had a significantly lower scientific impact, which might suggest that some preprints have lower quality and will not be able to endure peer-reviewing processes to be published in a peer-reviewed journal.

URL : Publication rate and citation counts for preprints released during the COVID-19 pandemic: the good, the bad and the ugly

DOI : https://doi.org/10.7717/peerj.10927

From Old School to Open Science: The Implications of New Research Norms for Educational Psychology and Beyond

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Authors : Hunter Gehlbach, Carly Robinson

Recently, scholars have noted how several “old school” practices—a host of well-regarded, long-standing scientific norms—in combination, sometimes compromise the credibility of research.

In response, other scholarly fields have developed several “open science” norms and practices to address these credibility issues. Against this backdrop, this special issue explores the extent to which and how these norms should be adopted and adapted for educational psychology and education more broadly.

Our introductory article contextualizes the special issue’s goals by: overviewing the historical context that led to open science norms (particularly in medicine and psychology); providing a conceptual map to illustrate the interrelationships between various old school as well as open science practices; and then describing educational psychologists’ opportunity to benefit from and contribute to the translation of these norms to novel research contexts.

We conclude by previewing the articles in the special issue.

DOI : https://doi.org/10.35542/osf.io/za7p5

Linguistic Analysis of the bioRxiv Preprint Landscape

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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 supplementary 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.

DOI : https://doi.org/10.1101/2021.03.04.433874

Publication practices during the COVID-19 pandemic: Biomedical preprints and peer-reviewed literature

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Authors : Yulia V. Sevryugina, Andrew J. Dicks

The coronavirus pandemic introduced many changes to our society, and deeply affected the established in biomedical sciences publication practices. In this article, we present a comprehensive study of the changes in scholarly publication landscape for biomedical sciences during the COVID-19 pandemic, with special emphasis on preprints posted on bioRxiv and medRxiv servers.

We observe the emergence of a new category of preprint authors working in the fields of immunology, microbiology, infectious diseases, and epidemiology, who extensively used preprint platforms during the pandemic for sharing their immediate findings. The majority of these findings were works-in-progress unfitting for a prompt acceptance by refereed journals.

The COVID-19 preprints that became peer-reviewed journal articles were often submitted to journals concurrently with the posting on a preprint server, and the entire publication cycle, from preprint to the online journal article, took on average 63 days. This included an expedited peer-review process of 43 days and journal’s production stage of 15 days, however there was a wide variation in publication delays between journals. Only one third of COVID-19 preprints posted during the first nine months of the pandemic appeared as peer-reviewed journal articles.

These journal articles display high Altmetric Attention Scores further emphasizing a significance of COVID-19 research during 2020. This article will be relevant to editors, publishers, open science enthusiasts, and anyone interested in changes that the 2020 crisis transpired to publication practices and a culture of preprints in life sciences.

DOI : https://doi.org/10.1101/2021.01.21.427563

Être chercheur, devenir expert ? L’économie morale du rapport à l’expertise dans un laboratoire de toxicologie

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Auteur/Author : David Demortain

Le rapport entre système de recherche et action publique s’est institutionnalisé ces dernières années, à travers un entrelacs de comités d’expertise, de groupes de travail ou de conseils scientifiques, souvent supervisés par des agences gouvernementales, qui permettent la mobilisation systématique de chercheurs pour la sécurité sanitaire.

Le système d’expertise ne peut toutefois collecter l’ensemble des connaissances scientifiques produites par les chercheurs, ne serait-ce que parce qu’une partie de cette profession considère que l’expertise ne fait pas partie de son métier.

Cet article cherche à comprendre comment et dans quelle mesure les chercheurs deviennent experts, à partir d’une analyse des activités des chercheurs d’un laboratoire de toxicologie, et des motifs et modalités variées d’engagement dans l’expertise parmi ceux-ci.

Il dégage trois économies morales distinctes du rapport à l’expertise, pour montrer que l’engagement dans l’expertise est lié à différentes manières de définir et valoriser le travail de recherche toxicologique.

DOI : https://doi.org/10.4000/rac.19302

Preprints in motion: tracking changes between posting and journal publication

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

Amidst the COVID-19 pandemic, preprints in the biomedical sciences are being posted and accessed at unprecedented rates, drawing widespread attention from the general public, press and policymakers for the first time.

This phenomenon has sharpened longstanding questions about the reliability of information shared prior to journal peer review. Does the information shared in preprints typically withstand the scrutiny of peer review, or are conclusions likely to change in the version of record?

We assessed preprints that had been posted and subsequently published in a journal between 1st January and 30th April 2020, representing the initial phase of the pandemic response. We utilised a combination of automatic and manual annotations to quantify how an article changed between the preprinted and published version.

We found that the total number of figure panels and tables changed little between preprint and published articles. Moreover, the conclusions of 6% of non-COVID-19-related and 15% of COVID-19-related abstracts undergo a discrete change by the time of publication, but the majority of these changes do not reverse the main message of the paper.

DOI : https://doi.org/10.1101/2021.02.20.432090