Preprints: Accelerating Research

“What are preprints, and how are they changing how biomedical research results are shared? Should you use information from preprints? Should you share your own research results in a preprint? This course from the National Library of Medicine® explains the basics of preprints, and explores the benefits and considerations of using and submitting preprints….”

bioRxiv & medRxiv; Communicating at the Speed of Science

“Preprint servers bioRxiv & medRxiv have experienced unprecedented growth and attention during these past 18 months as they have contributed to the scientific community’s collaborative response to the present international health crisis. The frequent reports in mass-media outlets alone, after January 2020, demonstrate that bioRxiv and medRxiv are becoming recognized Open Science digital repositories that are at the center of rapidly disseminating scientific research freely throughout the world.

Please join us on Oct 26th at 11am for our inaugural session during Open Access Week 2021 as the Harvard Library welcomes Richard Sever, Assistant Director Cold Spring Harbor Laboratory Press & Co-founder of the preprint servers bioRxiv and medRxiv. Dr. Sever will share his observations and reflections on the exponential growth and impact that preprints have had on advancing scientific communication during this unprecedented time.”

‘New journals concept’ from CUP’s Research Directions | The Bookseller

“Cambridge University Press is launching an initiative it describes as a “new concept” for the journal, bringing researchers from different fields together to explore fundamental questions which cut across traditional disciplines.

Research Directions is the brainchild of Fiona Hutton, CUP executive publisher and its head of STM Open Access publishing. A former research scientist, Hutton wants to provide alternatives to traditional journal formats and bring communities together to frame research to problems that no one discipline would be able to tackle alone, said the publisher.

CUP said the approach would “speed discovery by fostering collaboration and knowledge sharing between subject communities” as well as provide “opportunities to publish research from areas not well served by traditional, discipline-specific journals”. 

The first titles under the Research Directions banner will be published in 2022, with an initial set of questions to answer, informed by feedback from hundreds of researchers. The publishing model will “mirror the research lifecycle”, with the results, analysis and impact reviews all published as separate, Open Access, peer-reviewed and citable outputs on CUP’s Cambridge Core platform….”

All Things PrePrints: An Introduction

“The last year has seen a global spike in health and life science preprints. In June of 2020 the NIH even launched a pilot project to include COVID-19 related preprints in PubMed search results. This librarian shop talk will cover preprint definitions, how to locate them, and their impact as part of the biomedical research corpus. The event will conclude with discussion and myth busting of common concerns so librarians can talk knowledgeably with their users all things preprints at their own institutions. Two brief interactive break-outs will encourage participants to review the scope of preprints at their own institutions and address other common elements of concern.”

 

A Checklist for Submitting Your Research to arXiv | by Liz Maag-Capriotti | Oct, 2021 | Towards Data Science

arXiv is a popular open-access archive of scholarly articles that has operated for the last 30 years and includes research in the fields of physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering and systems science, and economics. arXiv has helped open science through pre-prints and improved global collaboration by allowing authors to share knowledge earlier in the scientific process and gain feedback on their research and ideas. Today arXiv remains one of the largest and exponentially growing preprint services.

Lessons from the pandemic: Embrace ‘open science,’ confront exclusion of investigators

“Will this trend to freely disseminate research papers prior to peer review and their acceptance by journals be sustained after the pandemic, when the sense of urgency recedes? I certainly hope so. This would be a lasting, beneficial consequence of the pandemic. By reducing the power of the journals to hold research hostage through long and often unnecessarily contentious peer review, preprints not only speed up the process but also democratize science for some in other parts the world who do not have access to expensive journal subscriptions.”

Four years of chemistry preprints | Feature | Chemistry World

“Then, in August 2017, two things happened. First, the SSRN preprint server (originally for social sciences and currently run by publishing giant Elsevier) launched an offshoot called the Chemistry Research Network (ChemRN). Then, a week or so later, ChemRxiv was launched by the American Chemical Society (ACS) – it is now run as a collaboration between the ACS, the Royal Society of Chemistry and the chemical societies of China, Japan and Germany….

Neither was initially welcomed with wholly open arms into the chemistry community. An insistence – especially from some journal editors – that depositing work caused it to lose the required novelty to warrant publication in their journals was the biggest issue, explains Donna Blackmond, a professor of chemistry at the Scripps Research Institute in California, US, and a member of the ChemRxiv scientific advisory board.

 

At the start, some chemistry journals accepted submissions that had been preprinted, some did not and many others left authors guessing by not having a preprint policy at all. It took about year for all the chemistry journals to accept preprints, says Blackmond. The ACS flagship journal, the Journal of the American Chemical Society, held out the longest….

Four years after their launch, the preprint servers are now finding their feet in the chemistry community. In 2020, 5137 preprints were posted on ChemRxiv and 3538 on ChemRN. The same year, ChemRxiv preprints were accessed a total of 16,120,921 times and ChemRN pre-prints downloaded 499,553 times….”

 

Frontiers | Open Science for Veterinary Education Research | Veterinary Science

“The manifesto for reproducible science (15) details a range of approaches that can be used to support more open research practices. For veterinary education, there are a number that can be integrated into our current practice….

Data sharing is another aspect of reporting which supports openness within education research. While data sharing is highly prevalent in some fields, there are complex ethical considerations regarding human data within social science contexts (32, 36). Where participants are informed and have consented to share their data, and where reasonable precautions are taken regarding ethical concerns (37), sharing data can help reduce unnecessary data collection, support the development of researchers in areas like the Global South (38), and help to catch errors within the research process (39).

Finally, dissemination and reporting can be further improved through pre-printing, the process of making articles available prior to peer-review. Pre-printing has a host of benefits (40, 41) including enhancing sight of the findings and facilitating open review, improving the transparency of peer review, and facilitating the publication of controversial findings. Pre-printing also allows for the sharing of author’s final version manuscripts, as they can be updated post peer-review. This will support the availability of research beyond paywalls. Unfortunately, not all journals support pre-printing. In the author’s experience, both Medical Teacher and Journal of Veterinary Medical Education have in 2020–2021 discouraged the use of pre-printing by considering it prior-publication, thus making pre-printed papers unable to be published by those journals. However, other journals, such as Frontiers in Veterinary Science support the use of open publishing approaches. Researchers must be cautious in pre-printing to ensure they are not inadvertently cutting themselves off from their desired audience, but should also participate in journal communities to encourage pre-printing where appropriate….”

Australian funder backflips on controversial preprint ban

“Australia’s major research funding body has backtracked on a rule that banned the mention of preprints in grant applications, under pressure from researchers who decried the ruling as “astonishing” and “outdated”.

The policy adjustment by the Australian Research Council (ARC) comes nearly four weeks after an anonymous researcher behind the ARC Tracker account on Twitter revealed that dozens of applications for early-career funding schemes had been rejected for citing preprints. More than 30 applications, worth Aus$22 million (US$16 million), were ruled ineligible.

Several rejected applicants, who can’t apply again because fellowship-application attempts are limited, told Nature last month that the decision had effectively ended their careers….”

An Open-Publishing Response to the COVID-19 Infodemic

Abstract:  The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures present unique challenges to collaborative science. We applied a massive online open publishing approach to this problem using Manubot. Through GitHub, collaborators summarized and critiqued COVID-19 literature, creating a review manuscript. Manubot automatically compiled citation information for referenced preprints, journal publications, websites, and clinical trials. Continuous integration workflows retrieved up-to-date data from online sources nightly, regenerating some of the manuscript’s figures and statistics. Manubot rendered the manuscript into PDF, HTML, LaTeX, and DOCX outputs, immediately updating the version available online upon the integration of new content. Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1,500 sources and developed seven literature reviews. While many efforts from the computational community have focused on mining COVID-19 literature, our project illustrates the power of open publishing to organize both technical and non-technical scientists to aggregate and disseminate information in response to an evolving crisis.

 

The Journal of Craniofacial Surgery Advances to Preprint Ser… : Journal of Craniofacial Surgery

“It is indeed a pleasure now that I have the chance to communicate with you all, readers, authors, fans and customers, to tell you what is going to happen in the future in the brave new digital world as regards preprints and post-prints, changes that will be arriving soon and not in the distant future – preprint servers will soon be mobile and accessible to all. This will indeed require some sacrifice and attention, making you feel part of the family with a matrix base and principled pillars that cannot be shaken, stirred, or disturbed by any negativity. We are bringing this to you knowing that there will be some growing pains such as those that we have experienced previously in all the advances that we have made. We do not expect less this time as regards those who are used to burning bridges of collaboration and who are already armed with their matches ready to use at any time; our advice to them is to start their fires with their tails….

The solution for quicker presentation and dissemination of knowledge comes with preprint servers, which we are working on for our journal but which are not yet not perfected. We have seen some ugly instances of misuse of the process during the pandemic; we cannot blame particular groups of people, it is purely a matter of human nature….

What is a preprint? The paper will be submitted as a preprint contribution, there will be a ledger fee for its submission and the paper will directly progress to the submission process and to the server, which is totally separate, and within 24 hours it will have a DOI and will be available globally for viewing, downloading and dissemination of knowledge, and it will have “preprint” stamped on each page. This means it is not peer-reviewed and not cross-checked; it is there on the basis of the integrity of the author and its authenticity; this is not a process that will guarantee publication at all. A second copy will go through the process noted above and this may take 6–9 months, based on and including the revisions required, and will depend on the multifactorial processes involved in regular publication. At the end of the road the preprint will meet at high noon with the standard print; if accepted the preprint will move to PAP or if rejected it will be stamped “rejected” and removed from the preprint server; that is the ugly black eye that may result. Of course the good ones are happily in print format and are now in the cloud and access around the global medical arena will be infinite….”

Elsevier’s Scopus expands to include SSRN preprints

“Elsevier, a global leader in research publishing and information analytics, today announces that preprints from SSRN, its world-leading early stage research and preprint platform, are now available through Scopus, Elsevier’s abstract and citation database. This follows preprints from arXiv, ChemRxiv, bioRxiv and medRxiv being indexed in Scopus earlier this year.

This development comes in reaction to feedback and requests from the researcher community, as demand for and use of preprints has jumped in recent years. At present, over 1 million Author Profiles in Scopus have 900,000 preprints indexed to them dating back to 2017. By the end of this year, approximately 170,000 SSRN preprints, from 2017 onwards will be included in Scopus….”

The impact of the COVID-19 pandemic on academic productivity

Abstract:  ‘Publish or perish’ is an expression describing the pressure on academics to consistently publish research to ensure a successful career in academia. With a global pandemic that has changed the world, how has it changed academic productivity? Here we show that academics are posting just as many publications on the arXiv pre-print server as if there were no pandemic: 168,630 were posted in 2020, a +12.6% change from 2019 and +1.4? deviation above the predicted 162,577 ± 4,393. However, some immediate impacts are visible in individual research fields. Conference cancellations have led to sharp drops in pre-prints, but laboratory closures have had mixed effects. Only some experimental fields show mild declines in outputs, with most being consistent on previous years or even increasing above model expectations. The most significant change is a 50% increase (+8?) in quantitative biology research, all related to the COVID-19 pandemic. Some of these publications are by biologists using arXiv for the first time, and some are written by researchers from other fields (e.g., physicists, mathematicians). While quantitative biology pre-prints have returned to pre-pandemic levels, 20% of the research in this field is now focussed on the COVID-19 pandemic, demonstrating a strong shift in research focus.

Over?promotion and caution in abstracts of preprints during the COVID?19 crisis – Bordignon – – Learned Publishing – Wiley Online Library

“The abstract is known to be a promotional genre where researchers tend to exaggerate the benefit of their research and use a promotional discourse to catch the reader’s attention. The COVID-19 pandemic has prompted intensive research and has changed traditional publishing with the massive adoption of preprints by researchers. Our aim is to investigate whether the crisis and the ensuing scientific and economic competition have changed the lexical content of abstracts. We propose a comparative study of abstracts associated with preprints issued in response to the pandemic relative to abstracts produced during the closest pre-pandemic period. We show that with the increase (on average and in percentage) of positive words (especially effective) and the slight decrease of negative words, there is a strong increase in hedge words (the most frequent of which are the modal verbs can and may). Hedge words counterbalance the excessive use of positive words and thus invite the readers, who go probably beyond the ‘usual’ audience, to be cautious with the obtained results. The abstracts of preprints urgently produced in response to the COVID-19 crisis stand between uncertainty and over-promotion, illustrating the balance that authors have to achieve between promoting their results and appealing for caution.