E-Prints – DigitalKoans

Reviewed Preprints Published Change: "eLife New Model at Six Months: An ICOR analysis"

Submissions are steady, and the proportion of papers sent for review is similar in the two models.

Reviewed Preprints are visible earlier than traditionally peer-reviewed articles, which provides a middle ground between unreviewed preprints and published VORs.

Author demographics have not changed significantly with regard to discipline or geography.

Authors, Senior Editors, and Reviewing Editors are reporting largely favorable experiences with the new model, with some concerns about quality and suggestions regarding process being voiced.

https://tinyurl.com/3u9w46fe

"Transforming Scholarly Communications: The Part Played by the Pandemic and the Contribution of Early Career Researchers"

Investigates whether junior researchers believe that the scholarly communication system is changing in a significant way, whether they have contributed to the changes they envisaged, whether the pandemic has fast-forwarded change and what they thought a transformed system might look like. The data are drawn from the Harbingers-2 project, which investigated the impact of the pandemic on the scholarly communications attitudes and behaviours of early career researchers (ECRs). . . . A majority of ECRs thought that there had been significant changes in the scholarly system, and a large minority thought that the pandemic was responsible. Most of them wanted a system that was more open in terms of open access and open data, with a third taking personal action to bring about change.

https://doi.org/10.1002/leap.1576

"The State of Scientific PDF Accessibility in Repositories: A Survey in Switzerland"

This survey analyzes the quality of the portable document format (PDF) documents in online repositories in Switzerland, examining their accessibility for people with visual impairments. Two minimal accessibility features were analysed: the PDFs had to have tags and a hierarchical heading structure. The survey also includes interviews with the managers or heads of multiple Swiss universities’ repositories . . . An analysis of interviewee responses indicates an overall lack of awareness of PDF accessibility, and shows that online repositories currently have no concrete plans to address the issue. This paper concludes by presenting a set of recommendations for online repositories to improve the accessibility of their PDF documents.

https://doi.org/10.1002/leap.1581

"PreprintResolver: Improving Citation Quality by Resolving Published Versions of ArXiv Preprints using Literature Databases"

The growing impact of preprint servers enables the rapid sharing of time-sensitive research. Likewise, it is becoming increasingly difficult to distinguish high-quality, peer-reviewed research from preprints. Although preprints are often later published in peer-reviewed journals, this information is often missing from preprint servers. To overcome this problem, the PreprintResolver was developed, which uses four literature databases (DBLP, SemanticScholar, OpenAlex, and CrossRef / CrossCite) to identify preprint-publication pairs for the arXiv preprint server. . . . Experiments were performed on a sample of 1,000 arXiv-preprints from the research field of computer science and without any publication information. . . . The results show that the PreprintResolver was able to resolve 603 out of 1,000 (60.3 %) arXiv-preprints from the research field of computer science and without any publication information. . . . In conclusion the PreprintResolver is suitable for individual, manually reviewed requests, but less suitable for bulk requests. The PreprintResolver tool (this https URL, Available from 2023-08-01) and source code (this https URL, Accessed: 2023-07-19) is available online.

https://arxiv.org/abs/2309.01373

"The Experiences of COVID-19 Preprint Authors: A Survey of Researchers about Publishing and Receiving Feedback on Their Work during the Pandemic"

The COVID-19 pandemic caused a rise in preprinting, triggered by the need for open and rapid dissemination of research outputs. We surveyed authors of COVID-19 preprints to learn about their experiences with preprinting their work and also with publishing their work in a peer-reviewed journal. Our research had the following objectives: 1. to learn about authors’ experiences with preprinting, their motivations, and future intentions; 2. to consider preprints in terms of their effectiveness in enabling authors to receive feedback on their work; 3. to compare the impact of feedback on preprints with the impact of comments of editors and reviewers on papers submitted to journals. In our survey, 78% of the new adopters of preprinting reported the intention to also preprint their future work. The boost in preprinting may therefore have a structural effect that will last after the pandemic, although future developments will also depend on other factors, including the broader growth in the adoption of open science practices. A total of 53% of the respondents reported that they had received feedback on their preprints. However, more than half of the feedback was received through "closed" channels–privately to the authors. This means that preprinting was a useful way to receive feedback on research, but the value of feedback could be increased further by facilitating and promoting "open" channels for preprint feedback. Almost a quarter of the feedback received by respondents consisted of detailed comments, showing the potential of preprint feedback to provide valuable comments on research. Respondents also reported that, compared to preprint feedback, journal peer review was more likely to lead to major changes to their work, suggesting that journal peer review provides significant added value compared to feedback received on preprints.

https://doi.org/10.7717/peerj.15864

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Paywall: "Proactive Institutional Repository Collection Development Techniques: Archiving Gold Open Access Articles and Metadata Retrieved with Web Scraping"

This article describes a method for copying open access articles and corresponding descriptive metadata from open repositories for archiving in an institutional repository using Beautiful Soup and Selenium as web scraping tools. This method quickly added hundreds of articles to an IR without relying on faculty participation or consulting publisher policies, increasing repository downloads and usage.

https://doi.org/10.1080/01930826.2023.2240190

"The Emergence of Preprints: Comparing Publishing Behaviour in the Global South and the Global North"

Purpose: The recent proliferation of preprints could be a way for researchers worldwide to increase the availability and visibility of their research findings. Against the background of rising publication costs caused by the increasing prevalence of article processing fees, the search for other ways to publish research results besides traditional journal publication may increase. This could be especially true for lower-income countries. Design/methodology/approach: Therefore, we are interested in the experiences and attitudes towards posting and using preprints in the Global South as opposed to the Global North. To explore whether motivations and concerns about posting preprints differ, we adopted a mixed-methods approach, combining a quantitative survey of researchers with focus group interviews. Findings: We found that respondents from the Global South were more likely to agree to adhere to policies and to emphasise that mandates could change publishing behaviour towards open access. They were also more likely to agree posting preprints has a positive impact. Respondents from the Global South and the Global North emphasised the importance of peer-reviewed research for career advancement. Originality: The study has identified a wide range of experiences with and attitudes towards posting preprints among researchers in the Global South and the Global North. To our knowledge, this has hardly been studied before, which is also because preprints only have emerged lately in many disciplines and countries.

https://arxiv.org/abs/2308.04186

"How Many Preprints Have Actually Been Printed and Why: A Case Study of Computer Science Preprints on arXiv"

In this paper, a case study of computer science preprints submitted to arXiv from 2008 to 2017 is conducted to quantify how many preprints have eventually been printed in peer-reviewed venues. Among those published manuscripts, some are published under different titles and without an update to their preprints on arXiv. In the case of these manuscripts, the traditional fuzzy matching method is incapable of mapping the preprint to the final published version. In view of this issue, we introduce a semantics-based mapping method with the employment of Bidirectional Encoder Representations from Transformers (BERT). With this new mapping method and a plurality of data sources, we find that 66% of all sampled preprints are published under unchanged titles and 11% are published under different titles and with other modifications. A further analysis was then performed to investigate why these preprints but not others were accepted for publication. Our comparison reveals that in the field of computer science, published preprints feature adequate revisions, multiple authorship, detailed abstract and introduction, extensive and authoritative references and available source code.

https://arxiv.org/abs/2308.01899

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"The Future of Academic Publishing"

Ultimately, we might be forced to rethink publication. If scientific research is mostly read by machines, the question arises of whether it is relevant to package it into a single coherent narrative that is adapted to the limitations of human cognition. This seems like a lot of busywork for scientists. We could unbundle scientific research from the constraints of journal formatting, as suggested by Neuromatch Open Publishing. In this view, research will be a living compendium of code, datasets, graphs and narrative content remixable and always up to date. Open and freely accessible research will be more valuable and influential because it will be seen by LLMs.

https://doi.org/10.1038/s41562-023-01637-2

"Unreviewed Science in the News: The Evolution of Preprint Media Coverage from 2014-2021"

It has been argued that preprint coverage during the COVID-19 pandemic constituted a paradigm shift in journalism norms and practices. This study examines whether, in what ways, and to what extent this is the case using a sample of 11,538 preprints posted on four preprint servers—bioRxiv, medRxiv, arXiv, and SSRN—that received coverage in 94 English-language media outlets between 2014-2021. We compared mentions of these preprints with mentions of a comparison sample of 397,446 peer reviewed research articles indexed in the Web of Science to identify changes in the share of media coverage that mentioned preprints before and during the pandemic. We found that preprint media coverage increased at a slow but steady rate pre-pandemic, then spiked dramatically. This increase applied only to COVID-19-related preprints, with minimal or no change in coverage of preprints on other topics. In addition, the rise in preprint coverage was most pronounced among health and medicine-focused media outlets, which barely covered preprints before the pandemic but mentioned more COVID-19 preprints than outlets focused on any other topic. These results suggest that the growth in coverage of preprints seen during the pandemic period may imply a shift in journalistic norms, including a changing outlook on reporting preliminary, unvetted research.

https://doi.org/10.1101/2023.07.10.548392

Paywall: The Strategic Marketing of Science, Technology, and Medical Journals: A Business History of a Dynamic Marketplace, 2000–2020

This book analyzes the various economic and marketing strategies utilized by the five major STM commercial scholarly journal publishers since 2000. This period has witnessed tremendous economic, marketing, and technological growth including the migration from a print only to a hybrid publishing format. With this growth, the industry has also seen the rise of open access publishing, copyright challenges by websites such as Sci-Hub, the emergence of sharing platforms such as ResearchGate and Academia.edu, as well as the impact of Plan S on publishers, universities, and authors.. . . Scrutinizing the different managerial, marketing, technology, and economic-financial strategies crafted by scholarly journal publishers between 2000-2020, this book offers a comprehensive assessment of the industry’s attempts to identify, understand, cope with, and minimize or defeat the herculean threats to its business model.

https://tinyurl.com/5n6rd8xy

"The Status of Open Access Repositories in the Field of Technology: Insights from OpenDOAR"

The study found that 125 nations contributed a total of 4,045 repositories in the field of research, with the USA leading the list with the most repositories. Maximum repositories were operated by institutions having multidisciplinary approaches. The DSpace and Eprints were the preferred software types for repositories. The preferred upload content by contributors was "research articles" and "electronic thesis and dissertations."

https://doi.org/10.1108/IDD-11-2022-0119

Japanese Preprint Server: "Guest Post — A Year of Jxiv — Warming the Preprints Stone"

However, this anomaly was corrected with the launch in March 2022 of Jxiv — the first fully-fledged Japanese-born preprint server — by the Japan Science and Technology Agency (JST), one of the largest public funders of research in the country that sits under the administrative and policy behemoth, the Ministry of Education, Culture, Sports, Science and Technology (MEXT). . . . JST also manages J-STAGE, the national online platform for Japanese journals launched in 1999, which hosts more than 3,500 journals containing almost 5.38 million articles, as well as J-STAGE Data launched in 2020.

https://tinyurl.com/388vd3y3

"A Scoping Review on the Use and Acceptability of Preprints"

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.

https://doi.org/10.31235/osf.io/nug4p

"Open Access at a Crossroads: Library Publishing and Bibliodiversity"

The open access movement has gained momentum since the Budapest Open Access Initiative (BOAI) first launched twenty years ago. Notably, there has been a drastic increase in the number of open access articles. Concerns have been raised about equality and diversity issues, however, for researchers without an affiliation (e.g. independent, unemployed and retired researchers) and researchers on the "scientific periphery" who are excluded from the gold open access model. This article argues that the gold open access model is destructive to the knowledge production ecosystem by addressing the importance of bibliodiversity and the ways in which library publishing can contribute to sustainable and equitable knowledge production.

https://doi.org/10.1629/uksg.613

Academic Publishing and Open Access. What Does Economics Teach Us?

While the gold regime seems the most natural way to achieve open access, a generalized switch to open access may also have undesired consequences: projections indeed suggest that a massive move towards the gold regime would generate an explosion in the amount of APC unless there are controls to limit market power. Beside the sharp increase in APC, the shift to gold open access may create conflicts of interest for publishers given that their income comes from authors and may alter the quality of publications. The green regime, by introducing competition between the journal’s version of an article and a free public version, seems an efficient way to reduce market power while expanding access.

https://shs.hal.science/halshs-04080573

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

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.

https://doi.org/10.55835/6442f782b2b5580ba561406b

"Do Open Access Mandates Work? A Systematized Review of the Literature on Open Access Publishing Rates"

To encourage the sharing of research, various entities—including public and private funders, universities, and academic journals—have enacted open access (OA) mandates or data sharing policies. It is unclear, however, whether these OA mandates and policies increase the rate of OA publishing and data sharing within the research communities impacted by them. A team of librarians conducted a systematized review of the literature to answer this question. A comprehensive search of several scholarly databases and grey literature sources resulted in 4,689 unique citations. However, only five articles met the inclusion criteria and were deemed as having an acceptable risk of bias. This sample showed that although the majority of the mandates described in the literature were correlated with a subsequent increase in OA publishing or data sharing, the presence of various confounders and the differing methods of collecting and analyzing the data used by the studies’ authors made it impossible to establish a causative relationship.

https://doi.org/10.31274/jlsc.15444

"The Transformation of the Green Road to Open Access"

(1) Background: The 2002 Budapest Open Access Initiative recommended on self-archiving of scientific articles in open repositories as the "green road" to open access. Twenty years later, only one part of the researchers deposits their publications in open repositories; moreover, one part of the repositories’ content is not based on self-archived deposits but on mediated nonfaculty contributions. The purpose of the paper is to provide more empirical evidence on this situation and to assess the impact on the future of the green road. (2) Methods: We analyzed the contributions on the French national HAL repository from more than 1,000 laboratories affiliated to the ten most important French research universities, with a focus on 2020, representing 14,023 contributor accounts and 166,939 deposits. (3) Results: We identified seven different types of contributor accounts, including deposits from nonfaculty staff and import flows from other platforms. Mediated nonfaculty contribution accounts for at least 48% of the deposits. We also identified difference between institutions and disciplines. (4) Conclusions: Our empirical results reveal a transformation of open repositories from self-archiving and direct scientific communication towards research information management. Repositories like HAL are somewhere in the middle of the process. The paper describes data quality as the main issue and major challenge of this transformation.

https://doi.org/10.20944/preprints202302.0268.v1

Only 10% Fully Understand "Preprint": "Framing COVID-19 Preprint Research as Uncertain: A Mixed-Method Study of Public Reactions"

Unlike hedging, preprint disclosure had no impact on audience message evaluations, nor vaccine attitudes and intentions. In one sense, this is a positive finding in that transparency about preprint status is unlikely to produce negative public reactions. Yet a likely explanation for the null effects is that most participants lacked the knowledge to differentiate between preprints and peer-reviewed research and did not understand this disclosure as an indicator of preliminary science. The qualitative data supported this explanation. When asked how they interpret the term "preprint" when they see it in a scientific news article, participants’ responses indicated that most had a limited understanding of the concept, even among those who received the preprint disclosure message with a brief explanation of the term. In total, only 10% of participants provided definitions of preprint that aligned with those accepted by the scholarly community. Only 15% described the term as an indicator of uncertain or preliminary evidence.

https://doi.org/10.1080/10410236.2023.2164954

"PreprintMatch: A Tool for Preprint to Publication Detection Shows Global Inequities in Scientific Publication"

Preprints, versions of scientific manuscripts that precede peer review, are growing in popularity. They offer an opportunity to democratize and accelerate research, as they have no publication costs or a lengthy peer review process. Preprints are often later published in peer-reviewed venues, but these publications and the original preprints are frequently not linked in any way. To this end, we developed a tool, PreprintMatch, to find matches between preprints and their corresponding published papers, if they exist. This tool outperforms existing techniques to match preprints and papers, both on matching performance and speed. PreprintMatch was applied to search for matches between preprints (from bioRxiv and medRxiv), and PubMed. The preliminary nature of preprints offers a unique perspective into scientific projects at a relatively early stage, and with better matching between preprint and paper, we explored questions related to research inequity. We found that preprints from low income countries are published as peer-reviewed papers at a lower rate than high income countries (39.6% and 61.1%, respectively), and our data is consistent with previous work that cite a lack of resources, lack of stability, and policy choices to explain this discrepancy. Preprints from low income countries were also found to be published quicker (178 vs 203 days) and with less title, abstract, and author similarity to the published version compared to high income countries. Low income countries add more authors from the preprint to the published version than high income countries (0.42 authors vs 0.32, respectively), a practice that is significantly more frequent in China compared to similar countries. Finally, we find that some publishers publish work with authors from lower income countries more frequently than others.

https://doi.org/10.1371/journal.pone.0281659

"Lack of Sustainability Plans for Preprint Services Risks Their Potential to Improve Science"

Despite successfully building a revenue model that shares the burden between Cornell University, the Simons Foundation and several members and supporters, arXiv’s “funding is still outpaced by [their] growth” – the server hosts over 2 million preprints already and is growing by 10% each year. And while arXiv has been supporting more and more scholars to share and discover preprints, the team behind it has been through significant changes in leadership and is dealing with the urgent need to modernize their 30-year-old technology. As a former Executive Director of arXiv noted, “[arXiv’s success] may not last forever”. Similarly, the recent news that Chan Zuckerberg Initiative has renewed its financial support for the leading preprint servers in biology and medicine, bioRxiv and medRxiv is welcome relief, but this support is temporary, and the team must find a way to continue in the long run.

bit.ly/3y745Ji

2.6 Billion Total Downloads: arXiv Annual Report 2022

Our critical priorities during 2022 were to secure additional funding, hire technical and program directors, and ramp up our efforts to modernize arXiv’s software by moving it to the cloud, which will provide better stability, scalability and maintainability. I’m pleased to report that we were able to make significant progress on all of these fronts. arXiv brought in more funding than expected in the form of grants, memberships, and donations, and we hired Stephanie Orphan as program director and Charles Frankston as technical director. Both bring strong and complementary expertise to the team. Moving the technical operations of arXiv—a service with a 30 year history—off of Cornell’s on-premises servers is a major, complicated task. The move to the cloud is currently in progress and on track

bit.ly/41exRsX

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"The Preprint Revolution — Implications for Bibliographic Databases"

In the box below, we present six recommendations for optimizing the indexing of preprints in bibliographic databases. As we will discuss later, implementing these recommendations requires close collaboration between bibliographic databases and other actors in the scholarly publishing system.

Recommendation 1: Cover all relevant preprint servers.

A bibliographic database should index preprints from all relevant preprint servers. A disciplinary database (e.g., PubMed and Europe PMC) should index preprints from all preprint servers relevant in a particular discipline. A multidisciplinary database (e.g., Dimensions, the Lens, Scopus, and Web of Science) should index preprints from all preprint servers across all disciplines.

Recommendation 2: Provide comprehensive preprint metadata.

A bibliographic database should provide metadata for preprints that is as comprehensive as metadata for journal articles. The metadata should at least include the title and abstract of a preprint, the names and affiliations of the authors, the reference list, and funding information. It should also include a version history.

Recommendation 3: Provide links between preprints and journal articles.

If an article has been published both on a preprint server and in a journal, a bibliographic database should provide a link between the preprint and the journal article. The link establishes that the preprint and the journal article are different versions of the same article. The preprint and the journal article belong to the same publication family.

Recommendation 4: Provide links between preprints and peer reviews.

If a preprint has been peer reviewed and the reviews have been made openly available, a bibliographic database should index the reviews and should provide links between the preprint and the reviews.

Recommendation 5: Provide deduplicated citation links between publication families.

A bibliographic database should provide deduplicated citation links at the level of publication families. If there are multiple citation links from publications in one publication family (e.g., from a preprint and from a journal article) to publications in another publication family, these citation links should be deduplicated.

Recommendation 6: Do not make arbitrary distinctions between publication types (preprints, journal articles, and others).

A bibliographic database should not make arbitrary distinctions between preprints, journal articles, and other publication types. A database may inform its users about relevant differences between publications of different types (e.g., whether publications have been peer reviewed or not), but otherwise it should treat all publications in the same way, regardless of their publication type.

bit.ly/3KtuWXl

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Clarivate: "The Preprint Citation Index: Linking Preprints to the Trusted Web of Science Ecosystem"

After many months of planning, we are launching the Preprint Citation Index, a multidisciplinary collection of preprints from leading repositories that helps researchers stay current with the newest research while maintaining confidence in the resources they rely on. . . . The Preprint Citation Index currently provides nearly two million preprints from arXiv, bioRxiv, chemRxiv, medRxiv and Preprints.org. We plan to add preprints from a dozen additional repositories as well as display open peer reviews on Preprint Citation Index throughout 2023.

bit.ly/3YxPcuw

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