Enabling preprint discovery, evaluation, and analysis with Europe PMC.

Preprints provide an indispensable tool for rapid and open communication of early research findings. Preprints can also be revised and improved based on scientific commentary uncoupled from journal-organised peer review. The uptake of preprints in the life sciences has increased significantly in recent years, especially during the COVID-19 pandemic, when immediate access to research findings became crucial to address the global health emergency. With ongoing expansion of new preprint servers, improving discoverability of preprints is a necessary step to facilitate wider sharing of the science reported in preprints. To address the challenges of preprint visibility and reuse, Europe PMC, an open database of life science literature, began indexing preprint abstracts and metadata from several platforms in July 2018. Since then, Europe PMC has continued to increase coverage through addition of new servers, and expanded its preprint initiative to include the full text of preprints related to COVID-19 in July 2020 and then the full text of preprints supported by the Europe PMC funder consortium in April 2022. The preprint collection can be searched via the website and programmatically, with abstracts and the open access full text of COVID-19 and Europe PMC funder preprint subsets available for bulk download in a standard machine-readable JATS XML format. This enables automated information extraction for large-scale analyses of the preprint corpus, accelerating scientific research of the preprint literature itself. This publication describes steps taken to build trust, improve discoverability, and support reuse of life science preprints in Europe PMC. Here we discuss the benefits of indexing preprints alongside peer-reviewed publications, and challenges associated with this process.

Altmetric Attention Scores and Citations of Published Research With or Without Preprints.

This cross-sectional study assesses how frequently research articles published in the clinical journals with high impact factors are preprinted and whether preprinting is associated with changes in media attention and citation counts.

Describing the Landscape of Medical Education Preprints on MedRxiv: Current Trends and Future Recommendations.

PURPOSE: A preprint is a version of a research manuscript posted to a preprint server prior to peer review. Preprints enable authors to quickly and openly share research, afford opportunities for expedient feedback, and enable immediate listing of research on grant and promotion applications. In medical education, most journals welcome preprints, which suggests that preprints play a role in the field's discourse. Yet, little is known about medical education preprints, including author characteristics, preprint use, and ultimate publication status. This study provides an overview of preprints in medical education to better understand their role in the field's discourse. METHOD: The authors queried medRxiv, a preprint repository, to identify preprints categorized as "medical education" and downloaded related metadata. CrossRef was queried to gather information on preprints later published in journals. Data were analyzed using descriptive statistics. RESULTS: Between 2019 and 2022, 204 preprints were classified in medRxiv as "medical education," with most deposited in 2021 (n = 76; 37.3%). On average, preprint full-texts were downloaded 1,875.2 times, and all were promoted on social media. Preprints were authored, on average, by 5.9 authors. Corresponding authors were based in 41 countries, with 45.6% in the United States, the United Kingdom, and Canada. Almost half (n = 101; 49.5%) became published articles in predominantly peer-reviewed journals. Preprints appeared in 65 peer-reviewed journals, with BMC Medical Education (n = 9; 8.9%) most represented. CONCLUSIONS: Medical education research is being deposited as preprints, which are promoted, heavily accessed, and subsequently published in peer-reviewed journals, including medical education journals. Considering the benefits of preprints and the slowness of medical education publishing, it is likely that preprint depositing will increase and preprints will be integrated into the field's discourse. The authors propose next steps to facilitate responsible and effective creation and use of preprints.

Comparison of effect estimates between preprints and peer-reviewed journal articles of COVID-19 trials.

BACKGROUND: Preprints are increasingly used to disseminate research results, providing multiple sources of information for the same study. We assessed the consistency in effect estimates between preprint and subsequent journal article of COVID-19 randomized controlled trials. METHODS: The study utilized data from the COVID-NMA living systematic review of pharmacological treatments for COVID-19 (covid-nma.com) up to July 20, 2022. We identified randomized controlled trials (RCTs) evaluating pharmacological treatments vs. standard of care/placebo for patients with COVID-19 that were originally posted as preprints and subsequently published as journal articles. Trials that did not report the same analysis in both documents were excluded. Data were extracted independently by pairs of researchers with consensus to resolve disagreements. Effect estimates extracted from the first preprint were compared to effect estimates from the journal article. RESULTS: The search identified 135 RCTs originally posted as a preprint and subsequently published as a journal article. We excluded 26 RCTs that did not meet the eligibility criteria, of which 13 RCTs reported an interim analysis in the preprint and a final analysis in the journal article. Overall, 109 preprint-article RCTs were included in the analysis. The median (interquartile range) delay between preprint and journal article was 121 (73-187) days, the median sample size was 150 (71-464) participants, 76% of RCTs had been prospectively registered, 60% received industry or mixed funding, 72% were multicentric trials. The overall risk of bias was rated as 'some concern' for 80% of RCTs. We found that 81 preprint-article pairs of RCTs were consistent for all outcomes reported. There were nine RCTs with at least one outcome with a discrepancy in the number of participants with outcome events or the number of participants analyzed, which yielded a minor change in the estimate of the effect. Furthermore, six RCTs had at least one outcome missing in the journal article and 14 RCTs had at least one outcome added in the journal article compared to the preprint. There was a change in the direction of effect in one RCT. No changes in statistical significance or conclusions were found. CONCLUSIONS: Effect estimates were generally consistent between COVID-19 preprints and subsequent journal articles. The main results and interpretation did not change in any trial. Nevertheless, some outcomes were added and deleted in some journal articles.

Using an expert survey and user feedback to construct PRECHECK: A checklist to evaluate preprints on COVID-19 and beyond.

Background: The quality of COVID-19 preprints should be considered with great care, as their contents can influence public policy. Surprisingly little has been done to calibrate the public's evaluation of preprints and their contents. The PRECHECK project aimed to generate a tool to teach and guide scientifically literate non-experts to critically evaluate preprints, on COVID-19 and beyond. Methods: To create a checklist, we applied a four-step procedure consisting of an initial internal review, an external review by a pool of experts (methodologists, meta-researchers/experts on preprints, journal editors, and science journalists), a final internal review, and a Preliminary implementation stage. For the external review step, experts rated the relevance of each element of the checklist on five-point Likert scales, and provided written feedback. After each internal review round, we applied the checklist on a small set of high-quality preprints from an online list of milestone research works on COVID-19 and low-quality preprints, which were eventually retracted, to verify whether the checklist can discriminate between the two categories. Results: At the external review step, 26 of the 54 contacted experts responded. The final checklist contained four elements (Research question, study type, transparency and integrity, and limitations), with 'superficial' and 'deep' evaluation levels. When using both levels, the checklist was effective at discriminating a small set of high- and low-quality preprints. Its usability for assessment and discussion of preprints was confirmed in workshops with Bachelors students in Psychology and Medicine, and science journalists. Conclusions: We created a simple, easy-to-use tool for helping scientifically literate non-experts navigate preprints with a critical mind and facilitate discussions within, for example, a beginner-level lecture on research methods. We believe that our checklist has potential to help guide decisions about the quality of preprints on COVID-19 in our target audience and that this extends beyond COVID-19.

What are preprints?

Preprints are a way in which a manuscript containing scientific results can be rapidly communicated from one scientist, or a a group of scientists, to the entire scientific community. This video by ASAPbio (Accelerating Science and Publication in biology) explains what preprints are and their benefits, how they differ from journal publications, and how scientists can use both mechanisms to communicate their work

Examining linguistic shifts between preprints and publications.

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.

Preprint servers in lipidology: current status and future role.

PURPOSE OF REVIEW: Preprinting, or the sharing of non-peer reviewed, unpublished scholarly manuscripts, has exploded in all fields of science and medicine over the past 5 years. We searched the literature and evaluated the posting and uptake of preprint publications in the field of lipidology in bioRxiv and medRxiv servers. We also contacted the editorial offices of 20 journals that publish original research in lipidology to gauge their policies on preprints. RECENT FINDINGS: All 20 journals contacted indicated that they accepted preprints. As of 31 May 2021, 473 and 231 preprints in lipidology had been submitted to bioRxiv and medRxiv, respectively. About half of all lipidology preprints were related to cardiovascular, cardiometabolic, and/or metabolic diseases (CVMD) and their risk factors, but at least 12 other disease categories were also represented. 16.9% and 1.08% of medRxiv and bioRxiv preprints, respectively, were related to coronavirus disease 2019 (COVID-19). SUMMARY: All identified journals accept lipidology themed preprints for submission, removing any barriers authors may have had regarding preprinting. Based on growing experience with preprinting, this trend should encourage increased community feedback and facilitate higher quality lipidology research in the future.