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.

 

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….”

Preprint servers: a ‘rush to publish’ or ‘just in time delivery’ for science? | Thorax

“At Thorax [a journal from BMJ] we embrace this new pathway to publishing medical research findings and we welcome the submission of manuscripts which have previously appeared on a preprint server. We do, however, ask all submitting authors to make this clear in the covering letter at the time of submission. The first batch of 10 articles, which previously appeared as preprints, have been through peer review with Thorax. The acceptance of articles which have previously appeared as a preprint is now widespread among medical journals.5 6 Acceptance of preprints is, however, not universal and authors are well advised to check the guidelines of their target journals before they post a preprint….

In due course, when the COVID-19 curve (flattened or otherwise) hits baseline, researchers and journals must use the preprint literature wisely and as it is intended—as a way to share research data rapidly before formal expert review in a journal. Any individual claims should be treated with healthy scepticism, until verified by peer review. …”

An XML Repository of All bioRxiv Articles is Now Available for Text and Data Mining

“bioRxiv and medRxiv provide free and unrestricted access to all articles posted on their servers. We believe this should apply not only to human readers but also to machine analysis of the content. A growing variety of resources have been created to facilitate this access.

bioRxiv and medRxiv metadata are made available via a number of dedicated RSS feeds and APIs. Simplified summary statistics covering the content and usage are also available. For bioRxiv, this information is available here’

Bulk access to the full text of bioRxiv articles for the purposes of text and data mining (TDM) is available via a dedicated Amazon S3 resource. Click here for details of this TDM resource and how to access it….”

Covid-19 Changed How the World Does Science, Together – The New York Times

“While political leaders have locked their borders, scientists have been shattering theirs, creating a global collaboration unlike any in history. Never before, researchers say, have so many experts in so many countries focused simultaneously on a single topic and with such urgency. Nearly all other research has ground to a halt….

One small measure of openness can be found on the servers of medRxiv and bioRxiv, two online archives that share academic research before it has been reviewed and published in journals. The archives have been deluged with coronavirus research from across the globe. Despite the nationalistic tone set by the Chinese president, Xi Jinping, Chinese researchers have contributed a significant portion of the coronavirus research available in the archive….”

Covid-19 Changed How the World Does Science, Together – The New York Times

“While political leaders have locked their borders, scientists have been shattering theirs, creating a global collaboration unlike any in history. Never before, researchers say, have so many experts in so many countries focused simultaneously on a single topic and with such urgency. Nearly all other research has ground to a halt….

One small measure of openness can be found on the servers of medRxiv and bioRxiv, two online archives that share academic research before it has been reviewed and published in journals. The archives have been deluged with coronavirus research from across the globe. Despite the nationalistic tone set by the Chinese president, Xi Jinping, Chinese researchers have contributed a significant portion of the coronavirus research available in the archive….”

Covid-19 Changed How the World Does Science, Together

Never before, scientists say, have so many of the world’s researchers focused so urgently on a single topic. Nearly all other research has ground to a halt.