From amazing work to I beg to differ – analysis of bioRxiv preprints that received one public comment till September 2019 | bioRxiv

Abstract:  While early commenting on studies is seen as one of the advantages of preprints, the nature of such comments, and the people who post them, have not been systematically explored. We analysed comments posted between 21 May 2015 and 9 September 2019 for 1,983 bioRxiv preprints that received only one comment. Sixty-nine percent of comments were posted by non-authors (n=1,366), and 31% by preprint authors (n=617). Twelve percent of non-author comments (n=168) were full review reports traditionally found during journal review, while the rest most commonly contained praises (n=577, 42%), suggestions (n=399, 29%), or criticisms (n=226, 17%). Authors’ comments most commonly contained publication status updates (n=354, 57%), additional study information (n=158, 26%), or solicited feedback for the preprints (n=65, 11%). Our study points to the value of preprint commenting, but further studies are needed to determine the role that comments play in shaping preprint versions and eventual journal publications.

 

Quantifying and contextualizing the impact of bioRxiv preprints through automated social media audience segmentation

Abstract:  Engagement with scientific manuscripts is frequently facilitated by Twitter and other social media platforms. As such, the demographics of a paper’s social media audience provide a wealth of information about how scholarly research is transmitted, consumed, and interpreted by online communities. By paying attention to public perceptions of their publications, scientists can learn whether their research is stimulating positive scholarly and public thought. They can also become aware of potentially negative patterns of interest from groups that misinterpret their work in harmful ways, either willfully or unintentionally, and devise strategies for altering their messaging to mitigate these impacts. In this study, we collected 331,696 Twitter posts referencing 1,800 highly tweeted bioRxiv preprints and leveraged topic modeling to infer the characteristics of various communities engaging with each preprint on Twitter. We agnostically learned the characteristics of these audience sectors from keywords each user’s followers provide in their Twitter biographies. We estimate that 96% of the preprints analyzed are dominated by academic audiences on Twitter, suggesting that social media attention does not always correspond to greater public exposure. We further demonstrate how our audience segmentation method can quantify the level of interest from nonspecialist audience sectors such as mental health advocates, dog lovers, video game developers, vegans, bitcoin investors, conspiracy theorists, journalists, religious groups, and political constituencies. Surprisingly, we also found that 10% of the preprints analyzed have sizable (>5%) audience sectors that are associated with right-wing white nationalist communities. Although none of these preprints appear to intentionally espouse any right-wing extremist messages, cases exist in which extremist appropriation comprises more than 50% of the tweets referencing a given preprint. These results present unique opportunities for improving and contextualizing the public discourse surrounding scientific research.

 

Meta-Research: International authorship and collaboration across bioRxiv preprints | eLife

Abstract:  Preprints are becoming well established in the life sciences, but relatively little is known about the demographics of the researchers who post preprints and those who do not, or about the collaborations between preprint authors. Here, based on an analysis of 67,885 preprints posted on bioRxiv, we find that some countries, notably the United States and the United Kingdom, are overrepresented on bioRxiv relative to their overall scientific output, while other countries (including China, Russia, and Turkey) show lower levels of bioRxiv adoption. We also describe a set of ‘contributor countries’ (including Uganda, Croatia and Thailand): researchers from these countries appear almost exclusively as non-senior authors on international collaborations. Lastly, we find multiple journals that publish a disproportionate number of preprints from some countries, a dynamic that almost always benefits manuscripts from the US.

 

Preprint Servers in Kidney Disease Research | American Society of Nephrology

Abstract:  Preprint servers, such as arXiv and bioRxiv, have disrupted the scientific communication landscape by providing rapid access to research before peer review. medRxiv was launched as a free online repository for preprints in the medical, clinical, and related health sciences in 2019. In this review, we present the uptake of preprint server use in nephrology and discuss specific considerations regarding preprint server use in medicine. Distribution of kidney-related research on preprint servers is rising at an exponential rate. Survey of nephrology journals identified that 15 of 17 (88%) are publishing original research accepted submissions that have been uploaded to preprint servers. After reviewing 52 clinically impactful trials in nephrology discussed in the online Nephrology Journal Club (NephJC), an average lag of 300 days was found between study completion and publication, indicating an opportunity for faster research dissemination. Rapid review of papers discussing benefits and risks of preprint server use from the researcher, publisher, or end user perspective identified 53 papers that met criteria. Potential benefits of biomedical preprint servers included rapid dissemination, improved transparency of the peer review process, greater visibility and recognition, and collaboration. However, these benefits come at the risk of rapid spread of results not yet subjected to the rigors of peer review. Preprint servers shift the burden of critical appraisal to the reader. Media may be especially at risk due to their focus on “late-breaking” information. Preprint servers have played an even larger role when late-breaking research results are of special interest, such as during the global coronavirus disease 2019 pandemic. Coronavirus disease 2019 has brought both the benefits and risks of preprint servers to the forefront. Given the prominent online presence of the nephrology community, it is poised to lead the medicine community in appropriate use of preprint servers.

 

The relationship between bioRxiv preprints, citations and altmetrics | Quantitative Science Studies | MIT Press Journals

Abstract:  A potential motivation for scientists to deposit their scientific work as preprints is to enhance its citation or social impact. In this study we assessed the citation and altmetric advantage of bioRxiv, a preprint server for the biological sciences. We retrieved metadata of all bioRxiv preprints deposited between November 2013 and December 2017, and matched them to articles that were subsequently published in peer-reviewed journals. Citation data from Scopus and altmetric data from Altmetric.com were used to compare citation and online sharing behavior of bioRxiv preprints, their related journal articles, and nondeposited articles published in the same journals. We found that bioRxiv-deposited journal articles had sizably higher citation and altmetric counts compared to nondeposited articles. Regression analysis reveals that this advantage is not explained by multiple explanatory variables related to the articles’ publication venues and authorship. Further research will be required to establish whether such an effect is causal in nature. bioRxiv preprints themselves are being directly cited in journal articles, regardless of whether the preprint has subsequently been published in a journal. bioRxiv preprints are also shared widely on Twitter and in blogs, but remain relatively scarce in mainstream media and Wikipedia articles, in comparison to peer-reviewed journal articles.

 

 

Preprinting a pandemic: the role of preprints in the COVID-19 pandemic | bioRxiv

Abstract:  The world continues to face an ongoing viral pandemic that presents a serious threat to human health. The virus underlying the COVID-19 disease, SARS-CoV-2, has caused over 3.2 million confirmed cases and 220,000 deaths between January and April 2020. Although the last pandemic of respiratory disease of viral origin swept the globe only a decade ago, the way science operates and responds to current events has experienced a paradigm shift in the interim. The scientific community has responded rapidly to the COVID-19 pandemic, releasing over 16,000 COVID-19 related scientific articles within 4 months of the first confirmed case, of which at least 6,000 were hosted by preprint servers. We focused our analysis on bioRxiv and medRxiv, two growing preprint servers for biomedical research, investigating the attributes of COVID-19 preprints, their access and usage rates, characteristics of their sharing on online platforms, and the relationship between preprints and their published articles. Our data provides evidence for increased scientific and public engagement (COVID-19 preprints are accessed and distributed at least 15 times more than non-COVID-19 preprints) and changes in journalistic practice with reference to preprints. We also find evidence for changes in preprinting and publishing behaviour: COVID-19 preprints are shorter, with fewer panels and tables, and reviewed faster. Our results highlight the unprecedented role of preprints and preprint servers in the dissemination of COVID-19 science, and the likely long-term impact of the pandemic on the scientific publishing landscape.

 

All that’s fit to preprint | Nature Biotechnology

“The uptake of preprints during the COVID-19 pandemic has been nothing short of remarkable. In April, the clinical preprint repository medRxiv published between 50 and 100 SARS-CoV-2-related posts daily. The burgeoning adoption of preprints by the medical community in recent months underscores their importance as a means for rapid sharing and updating of research findings during an outbreak. In the longer term, it also may prove a watershed moment, signaling the arrival of preprints as a legitimate complement to peer-reviewed journals, broadening their acceptance among a wider community of researchers, and accelerating their integration into journal publishing workflows.

Preprints — unvetted versions of research papers — offer open publication, establish precedence of research, enable rapid dissemination of results, provide early recognition and visibility for work (especially for early-career researchers) and avoid the selection bias against negative findings commonly associated with traditional peer review. Although they are not a new idea, they only took off in the life sciences after the 2013 launch of bioRxiv; today, at least 44 different archives host biology preprints; most are non-profit, community-based repositories, although traditional publishers, such as Elsevier (SSSN), are also getting into the game….

At medRxiv, all preprints carry a disclaimer indicating that they have “not been certified by peer review” and “should not be used to guide clinical practice.” Submissions also have to pass two types of prescreening: first, a set of clerical checks for author consent, plagiarism, clinical trial registration and ethics compliance (institutional review board approvals and privacy protections), along with declarations of competing interests, funding sources, and data and code availability; and second, a check by affiliated experts to determine whether a post is spam, nonsense or pseudoscience, is dual-use research, or has the potential to cause harm by changing public behavior (for example, a claim cigarettes don’t cause cancer or vaccines cause autism)….”

All that’s fit to preprint | Nature Biotechnology

“The uptake of preprints during the COVID-19 pandemic has been nothing short of remarkable. In April, the clinical preprint repository medRxiv published between 50 and 100 SARS-CoV-2-related posts daily. The burgeoning adoption of preprints by the medical community in recent months underscores their importance as a means for rapid sharing and updating of research findings during an outbreak. In the longer term, it also may prove a watershed moment, signaling the arrival of preprints as a legitimate complement to peer-reviewed journals, broadening their acceptance among a wider community of researchers, and accelerating their integration into journal publishing workflows.

Preprints — unvetted versions of research papers — offer open publication, establish precedence of research, enable rapid dissemination of results, provide early recognition and visibility for work (especially for early-career researchers) and avoid the selection bias against negative findings commonly associated with traditional peer review. Although they are not a new idea, they only took off in the life sciences after the 2013 launch of bioRxiv; today, at least 44 different archives host biology preprints; most are non-profit, community-based repositories, although traditional publishers, such as Elsevier (SSSN), are also getting into the game….

At medRxiv, all preprints carry a disclaimer indicating that they have “not been certified by peer review” and “should not be used to guide clinical practice.” Submissions also have to pass two types of prescreening: first, a set of clerical checks for author consent, plagiarism, clinical trial registration and ethics compliance (institutional review board approvals and privacy protections), along with declarations of competing interests, funding sources, and data and code availability; and second, a check by affiliated experts to determine whether a post is spam, nonsense or pseudoscience, is dual-use research, or has the potential to cause harm by changing public behavior (for example, a claim cigarettes don’t cause cancer or vaccines cause autism)….”

Coronavirus Research Moves Faster than Medical Journals

“Many of the coronavirus-related papers being posted on MedRxiv are rushed and flawed, and some are terrible. But a lot report serious research findings, some of which will eventually find their way into prestigious journals, which have been softening their stance on previously released research. (“We encourage posting to preprint servers as a way to share information immediately,” emails Jennifer Zeis, director of communications at the New England Journal of Medicine.) In the meantime, the research is out there, being commented on and followed up on by other scientists, and reported on in the news media. The journals, which normally keep their content behind steep paywalls, are also offering coronavirus articles outside of it. New efforts to sort through the resulting bounty of available research are emerging, from a group of Johns Hopkins University scholars sifting manually through new Covid-19 papers to a 59,000-article machine-readable data set, requested by the White House Office of Science and Technology Policy and enabled by an assortment of tech corporations and academic and philanthropic organizations, that is meant to be mined for insights using artificial intelligence and other such means.

This is the future for scientific communication that has been predicted since the spread of the internet began to enable it in the early 1990s (and to some extent long before then), yet proved slow and fitful in its arrival. It involves more or less open access to scientific research and data, and a more-open review process with a much wider range of potential peers than the peer review offered by journals. For its most enthusiastic boosters, it is also an opportunity to break through disciplinary barriers, broaden and improve the standards for research success and generally just make science work better. To skeptics, it means abandoning high standards and a viable economic model for research publishing in favor of a chaotic, uncertain new approach.

I’m mostly on the side of the boosters here, but have learned during five years of writing on and off about academic publishing that the existing way of doing things is quite well entrenched, and that would-be innovators often misunderstand the challenges involved in displacing or replacing it….”

Technical and social issues influencing the adoption of preprints in the life sciences

Abstract:  Preprints are gaining visibility in many fields. Thanks to the exponential growth in submissions to bioRxiv, an online server for preprints in biology, versions of manuscripts prior to the completion of journal-organized peer review are poised to become a standard component of the publishing experience in the life sciences. Here, we provide an overview of current challenges facing preprints, both technical and social, and a vision for their future development.