Category Archives: oa.preprints

Why preprint? | Zavarka

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“Preprints have been around and used extensively (particularly in maths and physics) for over 30 years at this point (arXiv was founded in 1991). Most major funders and journals recognise preprints, probably the majority of funders now have open access requirements that can be fulfilled with preprints, and a few are even mandating their use. It’s actually not much younger than the widespread use of peer review, which didn’t become a de facto standard until the 1960s-1970s (Nature didn’t use it until 1973 for example).

Preprinting papers is a huge advantage to authors, and the data is stark. Papers in biology which originally appeared as preprints get 36% more citations and the advantage is immediate and long lasting.

To make the argument clearer, let’s break it down into the different roles that preprints can have….”

Making science public: a review of journalists’ use of Open Science research

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Abstract:  Science journalists are uniquely positioned to increase the societal impact of open science by contextualizing and communicating research findings in ways that highlight their relevance and implications for non-specialist audiences. Through engagement with and coverage of open research outputs, journalists can help align the ideals of openness, transparency, and accountability with the wider public sphere and its democratic potential. Yet, it is unclear to what degree journalists use open research outputs in their reporting, what factors motivate or constrain this use, and how the recent surge in openly available research seen during the COVID-19 pandemic has affected the relationship between open science and science journalism. This literature review thus examines journalists’ use of open research outputs, specifically open access publications and preprints. We focus on literature published from 2018 onwards—particularly literature relating to the COVID-19 pandemic—but also include seminal articles outside the search dates. We find that, despite journalists’ potential to act as critical brokers of open access knowledge, their use of open research outputs is hampered by an overreliance on traditional criteria for evaluating scientific quality; concerns about the trustworthiness of open research outputs; and challenges using and verifying the findings. We also find that, while the COVID-19 pandemic encouraged journalists to explore open research outputs such as preprints, the extent to which these explorations will become established journalistic practices remains unclear. Furthermore, we note that current research is overwhelmingly authored and focused on the Global North, and the United States specifically. Finally, given the dearth of research in this area, we conclude with recommendations for future research that attend to issues of equity and diversity, and more explicitly examine the intersections of open science and science journalism.

 

SocArXiv Papers | A scoping review on the use and acceptability of preprints

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Abstract:  Background: Preprints are open and accessible scientific manuscript or report that has not been submitted to a peer reviewed journal. The value and importance of preprints has grown since its contribution during the public health emergency of the COVID-19 pandemic. Funders and publishers are establishing their position on the use of preprints, in grant applications and publishing models. However, the evidence supporting the use and acceptability of preprints varies across funders, publishers, and researchers. The purpose of this scoping review was to explore the current evidence on the use and acceptability of preprints by publishers, funders, and the research community throughout the research lifecycle.

  Methods: A scoping review was undertaken with no study or language limits. The search strategy was limited to the last five years (2017-2022) to capture changes influenced by COVID-19 (e.g., accelerated use and role of preprints in research). The review included international literature, including grey literature, and two databases were searched: Scopus and Web of Science (24 August 2022). Results: 379 titles and abstracts and 193 full text articles were assessed for eligibility. Ninety-eight articles met eligibility criteria and were included for full extraction. For barriers and challenges, 26 statements were grouped under four main themes (e.g., volume/growth of publications, quality assurance/trustworthiness, risks associated to credibility, and validation). For benefits and value, 34 statements were grouped under six themes (e.g., openness/transparency, increased visibility/credibility, open review process, open research, democratic process/systems, increased productivity/opportunities). Conclusions: Preprints provide opportunities for rapid dissemination but there is a need for clear policies and guidance from journals, publishers, and funders. Cautionary measures are needed to maintain the quality and value of preprints, paying particular attention to how findings are translated to the public. More research is needed to address some of the uncertainties addressed in this review.

Rapid, accurate publication and dissemination of clinical trial results: benefits and challenges | European Heart Journal | Oxford Academic

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Abstract:  Large-scale clinical trials are essential in cardiology and require rapid, accurate publication, and dissemination. Whereas conference presentations, press releases, and social media disseminate information quickly and often receive considerable coverage by mainstream and healthcare media, they lack detail, may emphasize selected data, and can be open to misinterpretation. Preprint servers speed access to research manuscripts while awaiting acceptance for publication by a journal, but these articles are not formally peer-reviewed and sometimes overstate the findings. Publication of trial results in a major journal is very demanding but the use of existing checklists can help accelerate the process. In case of rejection, procedures such as easing formatting requirements and possibly carrying over peer-review to other journals could speed resubmission. Secondary publications can help maximize benefits from clinical trials; publications of secondary endpoints and subgroup analyses further define treatment effects and the patient populations most likely to benefit. These rely on data access, and although data sharing is becoming more common, many challenges remain. Beyond publication in medical journals, there is a need for wider knowledge dissemination to maximize impact on clinical practice. This might be facilitated through plain language summary publications. Social media, websites, mainstream news outlets, and other publications, although not peer-reviewed, are important sources of medical information for both the public and for clinicians. This underscores the importance of ensuring that the information is understandable, accessible, balanced, and trustworthy. This report is based on discussions held on December 2021, at the 18th Global Cardiovascular Clinical Trialists meeting, involving a panel of editors of some of the top medical journals, as well as members of the lay press, industry, and clinical trialists.

 

The Preprint Club: A blueprint for community?based peer review: EMBO reports: Vol 0, No 0

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“Here, we would like to discuss how journal clubs could play a role in reviewing preprints. Journal clubs are ubiquitous in academia as nearly every department, institute, or even research group organize one to discuss the latest published research; in fact, journal clubs may be better served by discussing and reviewing preprints instead of already peer-reviewed research. Moreover, it provides a safe environment for ECRs to train their peer reviewing skills (Avasthi et al, 2018). With that in mind, we, a group of ECRs from the immunology departments of the Icahn School of Medicine at Mount Sinai and the University of Oxford—later joined by peers from the Karolinska Institute and the University of Toronto—established the Preprint Club in 2020 to discuss manuscripts from the field of immunology….”

To Preprint or Not to Preprint: Experience and Attitudes of Researchers Worldwide

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Abstract:  The pandemic has underlined the significance of open science and spurred further growth of preprinting. Nevertheless, preprinting has been adopted at varying rates across different countries/regions. To investigate researchers’ experience with and attitudes toward preprinting, we conducted a survey of authors of research papers published in 2021 or 2022. We find that respondents in the US and Europe had a higher level of familiarity with and adoption of preprinting than those in China and the rest of the world. Respondents in China were most worried about the lack of recognition for preprinting and the risk of getting scooped. US respondents were very concerned about premature media coverage of preprints, the reliability and credibility of preprints, and public sharing of information before peer review. Respondents identified integration of preprinting in journal submission processes as the most important way to promote preprinting.

 

Current concerns on journal article with preprint: Korean Journal of Internal Medicine perspectives

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Abstract:  Preprints are preliminary research reports that have not yet been peer-reviewed. They have been widely adopted to promote the timely dissemination of research across many scientific fields. In August 1991, Paul Ginsparg launched an electronic bulletin board intended to serve a few hundred colleagues working in a subfield of theoretical high-energy physics, thus launching arXiv, the first and largest preprint platform. Additional preprint servers have since been implemented in different academic fields, such as BioRxiv (2013, Biology; www.biorxiv.org) and medRxiv (2019, Health Science; www.medrxiv.org). While preprint availability has made valuable research resources accessible to the general public, thus bridging the gap between academic and non-academic audiences, it has also facilitated the spread of unsupported conclusions through various media channels. Issues surrounding the preprint policies of a journal must be addressed, ultimately, by editors and include the acceptance of preprint manuscripts, allowing the citation of preprints, maintaining a double-blind peer review process, changes to the preprint’s content and authors’ list, scoop priorities, commenting on preprints, and preventing the influence of social media. Editors must be able to deal with these issues adequately, to maintain the scientific integrity of their journal. In this review, the history, current status, and strengths and weaknesses of preprints as well as ongoing concerns regarding journal articles with preprints are discussed. An optimal approach to preprints is suggested for editorial board members, authors, and researchers.

 

OSF Preprints | Advancing the culture of peer review with preprints

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Abstract:  Preprints enable new forms of peer review that have the potential to be more thorough, inclusive, and collegial. In December 2022, 80 researchers and representatives of funders, institutions, preprint servers, journals, indexers, and review services were invited to gather online and at the Janelia Research Campus for a workshop on Recognizing Preprint Peer Review. Sponsored by HHMI, ASAPbio, and EMBO, this meeting aimed to catalyze community consensus and support for preprint peer review and to create model funder, institutional, and journal policies that recognize both preprints with reviews, and reviews of preprints. Here, we make a call to action to stakeholders in the community to help capture the growing momentum of preprint sharing and empower researchers to provide open and constructive peer review for preprints.

arXiv OSTP memorandum response – arXiv info

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“Funding Agencies can expedite public access to research results through the distribution of electronic preprints of results in open repositories, in particular existing preprint distribution servers such as arXiv,2 bioRxiv,3 and medRxiv.4 Distribution of preprints of research results enables rapid and free accessibility of the findings worldwide, circumventing publication delays of months, or, in some cases, years. Rapid circulation of research results expedites scientific discourse, shortens the cycle of discovery and accelerates the pace of discovery.5

Distribution of research findings by preprints, combined with curation of the archive of submissions, provides universal access for both authors and readers in perpetuity. Authors can provide updated versions of the research, including “as accepted,” with the repositories openly tracking the progress of the revision of results through the scientific process. Public access to the corpus of machine readable research manuscripts provides innovative channels for discovery and additional knowledge generation, including links to the data behind the research, open software tools, and supplemental information provided by authors.

Preprint repositories support a growing and innovative ecosystem for discovery and evaluation of research results, including tools for improved accessibility and research summaries. Experiments in open review and crowdsourced commenting can be layered over preprint repositories, providing constructive feedback and alternative models to the increasingly archaic process of anonymous peer review….”

bioRxiv and medRxiv response to the OSTP memo – an open letter to US funding agencies

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“Agencies can enable free public access to research results simply by mandating that reports of federally funded research are made available as “preprints” on servers such as arXiv, bioRxiv, medRxiv, and chemRxiv, before being submitted for journal publication. This will ensure that the findings are freely accessible to anyone anywhere in the world. An important additional benefit is the immediate availability of the information, avoiding the long delays associated with evaluation by traditional scientific journals (typically around one year). Scientific inquiry then progresses faster, as has been particularly evident for COVID research during the pandemic.

Prior access mandates in the US and elsewhere have focused on articles published by academic journals. This complicated the issue by making it a question of how to adapt journal revenue streams and led to the emergence of new models based on article-processing charges (APCs). But APCs simply move the access barrier to authors: they are a significant financial obstacle for researchers in fields and communities that lack the funding to pay them. A preprint mandate would achieve universal access for both authors and readers upstream, ensuring the focus remains on providing access to research findings, rather than on how they are selected and filtered.

Mandating public access to preprints rather than articles in academic journals would also future-proof agencies’ access policies. The distinction between peer-reviewed and non-peer-reviewed material is blurring as new approaches make peer review an ongoing process rather than a judgment made at a single point in time. Peer review can be conducted independently of journals through initiatives like Review Commons. And traditional journal-based peer review is changing: for example, eLife, supported by several large funders, peer reviews submitted papers but no longer distinguishes accepted from rejected articles. The author’s “accepted” manuscript that is the focus of so-called Green Open Access policies may therefore no longer exist. Because of such ongoing change, mandating the free availability of preprints would be a straightforward and strategically astute policy for US funding agencies.

A preprint mandate would underscore the fundamental, often overlooked, point that it is the results of research to which the public should have access. The evaluation of that research by journals is part of an ongoing process of assessment that can take place after the results have been made openly available. Preprint mandates from the funders of research would also widen the possibilities for evolution within the system and avoid channeling it towards expensive APC-based publishing models. Furthermore, since articles on preprint servers can be accompanied by supplementary data deposits on the servers themselves or linked to data deposited elsewhere, preprint mandates would also provide mechanisms to accomplish the other important OSTP goal: availability of research data.”

Open science in health psychology and behavioral medicine: A statement from the Behavioral Medicine Research Council.

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Abstract:  Open Science practices include some combination of registering and publishing study protocols (including hypotheses, primary and secondary outcome variables, and analysis plans) and making available preprints of manuscripts, study materials, de-identified data sets, and analytic codes. This statement from the Behavioral Medicine Research Council (BMRC) provides an overview of these methods, including preregistration; registered reports; preprints; and open research. We focus on rationales for engaging in Open Science and how to address shortcomings and possible objections. Additional resources for researchers are provided. Research on Open Science largely supports positive consequences for the reproducibility and reliability of empirical science. There is no solution that will encompass all Open Science needs in health psychology and behavioral medicine’s diverse research products and outlets, but the BMRC supports increased use of Open Science practices where possible.

 

ASAPbio’s response to the NIH Plan to Enhance Public Access – ASAPbio

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“ASAPbio is a 501(c)(3) organization working to promote innovation and transparency in life sciences communication. 

We are fully supportive of the 2022 OSTP directive to make all federally-funded research immediately accessible upon publication. Based on the public access plan the NIH has proposed in response to this memo, we appreciate the NIH’s desire to ensure equitable access to research for diverse stakeholders, and to ensure that this is provided at reasonable costs that do not exacerbate existing disparities. Furthermore, we support the need to ensure that research outputs are findable and discoverable through robust infrastructure and standards.

Many of these goals can be supported by moving toward a model where preprints are the primary form of sharing; this would also provide a strong foundation for aligning researchers’ incentives with the goals set out in the RFI. Many researchers now experience a disconnect between wanting to share work with the community and existing incentives for keeping data private. In a preprint-centric model, researchers would be recognized for sharing their work early and completely, which would also accelerate scientific discovery. Preprints also support rigor, reproducibility, and integrity by allowing broad engagement in public commenting and peer review. Given these benefits, we offer the following suggestions for using preprints to promote equitable, cost-effective, and discoverable publishing….”

Trends in preprint, data, and code sharing, 2019-2022

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“PLOS recently introduced Open Science Indicators (OSIs), a large public dataset identifying and quantifying Open Science practices like preprint posting, data sharing and code sharing in PLOS articles, as well as a selection of comparator articles published elsewhere. Now, we are delighted to release another six months of data from the second half of 2022, providing a new view of Open Science practices by researchers, over four years. The latest results continue to show incremental growth in all three areas. Read on for more details on the project, detailed numbers, and a closer look at preprints….”

Science Publishing Innovation: Why Do So Many Good Ideas Fail? – Science Editor

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“Over a decade ago, BioMed Central (BMC) recognized the importance of postpublication discussion. Prepublication review can improve papers and catch errors, but only time and subsequent work of other scientists can truly show which results in a publication are robust and valid. Unlike a print journal (or print as a medium, in general), the Internet permits the readers to comment on published papers over time. So in 2002 BMC developed and enabled commenting on every one of its articles across its suite of journals. Not only does this allow for postpublication review, but it enables readers to easily ask authors and other readers a question, with public responses enriching the original manuscript, clarifying, and helping to improve the comprehension of the work.

This is a terrific idea, but it didn’t really catch on….

Remarkably, despite the creation of arXiv for physicists in 1990 and despite the enthusiastic embrace of preprints by the physics community, it has been assumed this is impossible for biology. The common argument is that biologists are different from physicists and the arXiv success is not informative. What many did find telling is the death of the 2007 preprint initiative from the Nature Publishing Group (NPG). NPG tried preprints with Nature Precedings, but adoption was low and in 2012 NPG pulled the plug on the experiment.3 This triggered some skepticism about the prospects of the bioRxiv preprint effort from Cold Spring Harbor Lab (CSHL) Press.4 Critics told the director of CSHL Press, John Inglis, that a preprint for biologists simply couldn’t work.5

Once again, we must ask the cause of the Nature Precedings failure. Did NPG kill it because biologists wouldn’t behave in the same way as physicists? We know that isn’t the case. Preprints in biology are all the rage today….

In the winter of 2012, Alexei Stoliartchouk and I came up with the idea for protocols.io—a central place where scientists can share and discover science methods. We wanted to create a site where corrections and the constant tweaking of science methods could be shared, even after publication in a journal….

Few people know about bioprotocols.com, but many know about OpenWetWare (OWW) and Nature Protocol Exchange—both open-access community resources for sharing protocols. Both have been mentioned to me countless times as evidence that protocols.io wouldn’t work. As with preprints, the problems that OWW and Protocol Exchange faced seemed to be proof that biologists would not share details of their methods on such a platform. As with bioRxiv, we are in the early days of protocols.io, but judging from the growth in the figure below, it’s hard to argue that biologists don’t need this or that they won’t take the time to publicly share their methods….”