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Tracking changes between preprint posting and journal publication during a pandemic
Amid the Coronavirus Disease 2019 (COVID-19) pandemic, preprints in the biomedical sciences are being posted and accessed at unprecedented rates, drawing widespread attention from the general public, press, and policymakers for the first time. This phenomenon has sharpened long-standing questions about the reliability of information shared prior to journal peer review. Does the information shared in preprints typically withstand the scrutiny of peer review, or are conclusions likely to change in the version of record? We assessed preprints from bioRxiv and medRxiv that had been posted and subsequently published in a journal through April 30, 2020, representing the initial phase of the pandemic response. We utilised a combination of automatic and manual annotations to quantify how an article changed between the preprinted and published version. We found that the total number of figure panels and tables changed little between preprint and published articles. Moreover, the conclusions of 7.2% of non-COVID-19–related and 17.2% of COVID-19–related abstracts undergo a discrete change by the time of publication, but the majority of these changes do not qualitatively change the conclusions of the paper.
Journal Article
Gender gap in journal submissions and peer review during the first wave of the COVID-19 pandemic. A study on 2329 Elsevier journals
During the early months of the COVID-19 pandemic, there was an unusually high submission rate of scholarly articles. Given that most academics were forced to work from home, the competing demands for familial duties may have penalized the scientific productivity of women. To test this hypothesis, we looked at submitted manuscripts and peer review activities for all Elsevier journals between February and May 2018-2020, including data on over 5 million authors and referees. Results showed that during the first wave of the pandemic, women submitted proportionally fewer manuscripts than men. This deficit was especially pronounced among more junior cohorts of women academics. The rate of the peer-review invitation acceptance showed a less pronounced gender pattern with women taking on a greater service responsibility for journals, except for health & medicine, the field where the impact of COVID-19 research has been more prominent. Our findings suggest that the first wave of the pandemic has created potentially cumulative advantages for men.
Journal Article
Bitcoin for the biological literature
[...]ScienceMatters is different in another way, too: it's developing a peer-review process based on the Bitcoin blockchain technology - a public, but tamper-proof database of transactions shared across thousands of computers around the world. Reviewers will be compensated for their time with Eureka tokens - a cryptocurrency tied to the Eureka network that can be exchanged for other currencies, as Bitcoin can be. Because all data around a submission are open, immutable and time stamped, Eureka will provide a public and trusted research management service, says Lawrence Rajendran, a neuroscientist at King's College London, who founded ScienceMatters and Eureka. According to Dave Kochalko, co-founder of the collaboration and citation platform Artifacts in Cambridge, Massachusetts, research produces a wealth of interesting material - such as data sets, single observations and hypotheses - in the long run-up to publication that doesn't get cited until the final peer-reviewed article appears, if it does at all. [...]whatever the application, it is likely to be some time before scientists reap the rewards, says Joris van Rossum, who authored the report Blockchain for Research (see go.nature. com/2wqqvrg) for Digital Science, a Londonbased technology firm (operated by the Holtzbrinck Publishing Group, which also has a majority share in Nature's publisher).
Journal Article
Social media usage to share information in communication journals: An analysis of social media activity and article citations
Social media has surrounded every area of life, and social media platforms have become indispensable for today’s communication. Many journals use social media actively to promote and disseminate new articles. Its use to share the articles contributes many benefits, such as reaching more people and spreading information faster. However, there is no consensus in the studies that to evaluate between tweeted and non-tweeted papers regarding their citation numbers. Therefore, it was aimed to show the effect of social media on the citations of articles in the top ten communication-based journals. For this purpose, this work evaluated original articles published in the top 10 communication journals in 2018. The top 10 communication-based journals were chosen based on SCImago Journal & Country Rank (cited in 2019). Afterward, it was recorded the traditional citation numbers (Google Scholar and Thompson-Reuters Web of Science) and social media exposure of the articles in January 2021 (nearly three years after the articles’ publication date). It was assumed that this period would allow the impact of the published articles (the citations and Twitter mentions) to be fully observed. Based on this assessment, a positive correlation between exposure to social media and article citations was observed in this study.
Journal Article
The case for open computer programs
Scientific reproducibility now very often depends on the computational method being available to duplicate, so here it is argued that all source code should be freely available.
The open road for computer programs
Most scientific papers published today rely on computer programs for data collection and manipulation. Writing in the Perspective pages in this issue of
Nature
, Darrel Ince and colleagues argue that the policies of most journals and funding bodies towards the release of computer codes as part of the publication process are obsolete. They say that the full release of actual source code should be the norm for any scientific results dependent on computation, with an agreed list of exceptions applicable only to rare cases. Current policies range from a requirement for release of the relevant computer programs on request to
Nature
's less stringent stipulation of a 'natural language' description of computer algorithms.
Scientific communication relies on evidence that cannot be entirely included in publications, but the rise of computational science has added a new layer of inaccessibility. Although it is now accepted that data should be made available on request, the current regulations regarding the availability of software are inconsistent. We argue that, with some exceptions, anything less than the release of source programs is intolerable for results that depend on computation. The vagaries of hardware, software and natural language will always ensure that exact reproducibility remains uncertain, but withholding code increases the chances that efforts to reproduce results will fail.
Journal Article
On the value of preprints: An early career researcher perspective
Peer-reviewed journal publication is the main means for academic researchers in the life sciences to create a permanent public record of their work. These publications are also the de facto currency for career progress, with a strong link between journal brand recognition and perceived value. The current peer-review process can lead to long delays between submission and publication, with cycles of rejection, revision, and resubmission causing redundant peer review. This situation creates unique challenges for early career researchers (ECRs), who rely heavily on timely publication of their work to gain recognition for their efforts. Today, ECRs face a changing academic landscape, including the increased interdisciplinarity of life sciences research, expansion of the researcher population, and consequent shifts in employer and funding demands. The publication of preprints, publicly available scientific manuscripts posted on dedicated preprint servers prior to journal-managed peer review, can play a key role in addressing these ECR challenges. Preprinting benefits include rapid dissemination of academic work, open access, establishing priority or concurrence, receiving feedback, and facilitating collaborations. Although there is a growing appreciation for and adoption of preprints, a minority of all articles in life sciences and medicine are preprinted. The current low rate of preprint submissions in life sciences and ECR concerns regarding preprinting need to be addressed. We provide a perspective from an interdisciplinary group of ECRs on the value of preprints and advocate their wide adoption to advance knowledge and facilitate career development.
Journal Article
Scholarly Context Not Found: One in Five Articles Suffers from Reference Rot
The emergence of the web has fundamentally affected most aspects of information communication, including scholarly communication. The immediacy that characterizes publishing information to the web, as well as accessing it, allows for a dramatic increase in the speed of dissemination of scholarly knowledge. But, the transition from a paper-based to a web-based scholarly communication system also poses challenges. In this paper, we focus on reference rot, the combination of link rot and content drift to which references to web resources included in Science, Technology, and Medicine (STM) articles are subject. We investigate the extent to which reference rot impacts the ability to revisit the web context that surrounds STM articles some time after their publication. We do so on the basis of a vast collection of articles from three corpora that span publication years 1997 to 2012. For over one million references to web resources extracted from over 3.5 million articles, we determine whether the HTTP URI is still responsive on the live web and whether web archives contain an archived snapshot representative of the state the referenced resource had at the time it was referenced. We observe that the fraction of articles containing references to web resources is growing steadily over time. We find one out of five STM articles suffering from reference rot, meaning it is impossible to revisit the web context that surrounds them some time after their publication. When only considering STM articles that contain references to web resources, this fraction increases to seven out of ten. We suggest that, in order to safeguard the long-term integrity of the web-based scholarly record, robust solutions to combat the reference rot problem are required. In conclusion, we provide a brief insight into the directions that are explored with this regard in the context of the Hiberlink project.
Journal Article
Clustering Scientific Publications Based on Citation Relations: A Systematic Comparison of Different Methods
Clustering methods are applied regularly in the bibliometric literature to identify research areas or scientific fields. These methods are for instance used to group publications into clusters based on their relations in a citation network. In the network science literature, many clustering methods, often referred to as graph partitioning or community detection techniques, have been developed. Focusing on the problem of clustering the publications in a citation network, we present a systematic comparison of the performance of a large number of these clustering methods. Using a number of different citation networks, some of them relatively small and others very large, we extensively study the statistical properties of the results provided by different methods. In addition, we also carry out an expert-based assessment of the results produced by different methods. The expert-based assessment focuses on publications in the field of scientometrics. Our findings seem to indicate that there is a trade-off between different properties that may be considered desirable for a good clustering of publications. Overall, map equation methods appear to perform best in our analysis, suggesting that these methods deserve more attention from the bibliometric community.
Journal Article
Do you have AI dependency? The roles of academic self-efficacy, academic stress, and performance expectations on problematic AI usage behavior
Although previous studies have highlighted the problematic artificial intelligence (AI) usage behaviors in educational contexts, such as overreliance on AI, no study has explored the antecedents and potential consequences that contribute to this problem. Therefore, this study investigates the causes and consequences of AI dependency using ChatGPT as an example. Using the Interaction of the Person-Affect-Cognition-Execution (I-PACE) model, this study explores the internal associations between academic self-efficacy, academic stress, performance expectations, and AI dependency. It also identifies the negative consequences of AI dependency. Analysis of data from 300 university students revealed that the relationship between academic self-efficacy and AI dependency was mediated by academic stress and performance expectations. The top five negative effects of AI dependency include increased laziness, the spread of misinformation, a lower level of creativity, and reduced critical and independent thinking. The findings provide explanations and solutions to mitigate the negative effects of AI dependency.
Journal Article