Publishing of COVID-19 preprints in peer-reviewed journals, preprinting trends, public discussion and quality issues
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ABSTRACT: Supplementary Information
The online version contains supplementary material available at 10.1007/s11192-021-04249-7.
SUBMITTER: Kodvanj I
PROVIDER: S-EPMC8801281 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundPreprint usage is growing rapidly in the life sciences; however, questions remain on the relative quality of preprints when compared to published articles. An objective dimension of quality that is readily measurable is completeness of reporting, as transparency can improve the reader's ability to independently interpret data and reproduce findings.MethodsIn this observational study, we initially compared independent samples of articles published in bioRxiv and in PubMed-indexed journals in 2016 using a quality of reporting questionnaire. After that, we performed paired comparisons between preprints from bioRxiv to their own peer-reviewed versions in journals.ResultsPeer-reviewed articles had, on average, higher quality of reporting than preprints, although the difference was small, with absolute differences of 5.0% [95% CI 1.4, 8.6] and 4.7% [95% CI 2.4, 7.0] of reported items in the independent samples and paired sample comparison, respectively. There were larger differences favoring peer-reviewed articles in subjective ratings of how clearly titles and abstracts presented the main findings and how easy it was to locate relevant reporting information. Changes in reporting from preprints to peer-reviewed versions did not correlate with the impact factor of the publication venue or with the time lag from bioRxiv to journal publication.ConclusionsOur results suggest that, on average, publication in a peer-reviewed journal is associated with improvement in quality of reporting. They also show that quality of reporting in preprints in the life sciences is within a similar range as that of peer-reviewed articles, albeit slightly lower on average, supporting the idea that preprints should be considered valid scientific contributions.
| S-EPMC7706207 | biostudies-literature
Project description:This article discusses the open-identity label, i.e., the practice of disclosing reviewers' names in published scholarly books, a common practice in Central and Eastern European countries. This study's objective is to verify whether the open-identity label is a type of peer-review label (like those used in Finland and Flanders, i.e., the Flemish part of Belgium), and as such, whether it can be used as a delineation criterion in various systems used to evaluate scholarly publications. We have conducted a two-phase sequential explanatory study. In the first phase, interviews with 20 of the 40 largest Polish publishers of scholarly books were conducted to investigate how Polish publishers control peer reviews and whether the open-identity label can be used to identify peer-reviewed books. In the other phase, two questionnaires were used to analyze perceptions of peer-review and open-identity labelling among authors (n = 600) and reviewers (n = 875) of books published by these 20 publishers. Integrated results allowed us to verify publishers' claims concerning their peer-review practices. Our findings reveal that publishers actually control peer reviews by providing assessment criteria to reviewers and sending reviews to authors. Publishers rarely ask for permission to disclose reviewers' names, but it is obvious to reviewers that this practice of disclosing names is part of peer reviewing. This study also shows that only the names of reviewers who accepted manuscripts for publication are disclosed. Thus, most importantly, our analysis shows that the open-identity label that Polish publishers use is a type of peer-review label like those used in Flanders and Finland, and as such, it can be used to identify peer-reviewed scholarly books.
| S-EPMC6433260 | biostudies-literature
Project description:ObjectiveWe undertook this investigation to characterize conflict of interest (COI) policies of biomedical journals with respect to authors, peer-reviewers, and editors, and to ascertain what information about COI disclosures is publicly available.MethodsWe performed a cross-sectional survey of a convenience sample of 135 editors of peer-reviewed biomedical journals that publish original research. We chose an international selection of general and specialty medical journals that publish in English. Selection was based on journal impact factor, and the recommendations of experts in the field. We developed and pilot tested a 3-part web-based survey. The survey included questions about the presence of specific policies for authors, peer-reviewers, and editors, specific restrictions on authors, peer-reviewers, and editors based on COI, and the public availability of these disclosures. Editors were contacted a minimum of 3 times.ResultsThe response rate for the survey was 91 (67%) of 135, and 85 (93%) of 91 journals reported having an author COI policy. Ten (11%) journals reported that they restrict author submissions based on COI (e.g., drug company authors' papers on their products are not accepted). While 77% report collecting COI information on all author submissions, only 57% publish all author disclosures. A minority of journals report having a specific policy on peer-reviewer 46% (42/91) or editor COI 40% (36/91); among these, 25% and 31% of journals state that they require recusal of peer-reviewers and editors if they report a COI. Only 3% of respondents publish COI disclosures of peer-reviewers, and 12% publish editor COI disclosures, while 11% and 24%, respectively, reported that this information is available upon request.ConclusionMany more journals have a policy regarding COI for authors than they do for peer-reviewers or editors. Even author COI policies are variable, depending on the type of manuscript submitted. The COI information that is collected by journals is often not published; the extent to which such "secret disclosure" may impact the integrity of the journal or the published work is not known.
| S-EPMC1924760 | biostudies-literature
Project description:MotivationReproducing the results from a scientific paper can be challenging due to the absence of data and the computational tools required for their analysis. In addition, details relating to the procedures used to obtain the published results can be difficult to discern due to the use of natural language when reporting how experiments have been performed. The Investigation/Study/Assay (ISA), Nanopublications (NP), and Research Objects (RO) models are conceptual data modelling frameworks that can structure such information from scientific papers. Computational workflow platforms can also be used to reproduce analyses of data in a principled manner. We assessed the extent by which ISA, NP, and RO models, together with the Galaxy workflow system, can capture the experimental processes and reproduce the findings of a previously published paper reporting on the development of SOAPdenovo2, a de novo genome assembler.ResultsExecutable workflows were developed using Galaxy, which reproduced results that were consistent with the published findings. A structured representation of the information in the SOAPdenovo2 paper was produced by combining the use of ISA, NP, and RO models. By structuring the information in the published paper using these data and scientific workflow modelling frameworks, it was possible to explicitly declare elements of experimental design, variables, and findings. The models served as guides in the curation of scientific information and this led to the identification of inconsistencies in the original published paper, thereby allowing its authors to publish corrections in the form of an errata.AvailabilitySOAPdenovo2 scripts, data, and results are available through the GigaScience Database: http://dx.doi.org/10.5524/100044; the workflows are available from GigaGalaxy: http://galaxy.cbiit.cuhk.edu.hk; and the representations using the ISA, NP, and RO models are available through the SOAPdenovo2 case study website http://isa-tools.github.io/soapdenovo2/.Contactphilippe.rocca-serra@oerc.ox.ac.uk and susanna-assunta.sansone@oerc.ox.ac.uk.
| S-EPMC4495984 | biostudies-literature
Project description:To increase transparency in science, some scholarly journals are publishing peer review reports. But it is unclear how this practice affects the peer review process. Here, we examine the effect of publishing peer review reports on referee behavior in five scholarly journals involved in a pilot study at Elsevier. By considering 9,220 submissions and 18,525 reviews from 2010 to 2017, we measured changes both before and during the pilot and found that publishing reports did not significantly compromise referees' willingness to review, recommendations, or turn-around times. Younger and non-academic scholars were more willing to accept to review and provided more positive and objective recommendations. Male referees tended to write more constructive reports during the pilot. Only 8.1% of referees agreed to reveal their identity in the published report. These findings suggest that open peer review does not compromise the process, at least when referees are able to protect their anonymity.
| S-EPMC6338763 | biostudies-literature
Project description:BACKGROUND:Vaccine hesitancy is a growing threat to national and global health security. The current study was undertaken to provide insights into the global scientific literature on vaccine hesitancy in peer-reviewed journals. METHOD:The current study was a descriptive bibliometric study. A validated search strategy on vaccine hesitancy was implemented using SciVerse Scopus. Bibliometric indicators such as (1) annual growth of publications, (2) key players, (3) research themes, (4) pathogens/diseases encountered, (5) top-cited documents, and (6) annual growth of publications stratified by world region and by age category were presented. The study period was from 1990 to 2019. RESULTS:Search strategy found 2791 documents. The h-index of the retrieved literature was 89. The leading journal was Vaccine (369; 13.2%%) followed by Human Vaccines and Immunotherapeutics (129; 4.6%). Authors from the USA led with 1125 (40.3%) followed by authors from Italy (234; 8.4%) and the UK (204; 7.3%). The US CDC led with 140 (5.0%) documents followed by Emory University (USA) (81, 2.9%). The list of active authors included six from the USA while the remaining were from France, Australia, and Canada. Research themes in the retrieved literature focused on influenza, human papillomavirus, and the role of parents in immunization of their children. The region of the Americas and the European region had the greatest share of publications and showed steep growth of publications lately. Vaccine hesitancy research on adolescents was most noticed after 2007 while that on children was present all the time but escalated lately. Titles/abstracts analysis indicated that 621(22.3%) documents focused on influenza, 392 (14.0%) focused on Human papillomavirus, and 292 (10.5%) focused on measles. The top-cited documents in literature published after 2015 focused on the definition and strategies to overcome vaccine hesitancy. CONCLUSION:The last decade witnessed a noticeable increase in the number of publications. Influenza vaccine and parental concerns about the human papillomavirus vaccine were the main focus of the retrieved literature. Information on vaccine hesitancy needs to be collected from all countries to build a better coalition against the anti-vaccination groups. Re-building trust in vaccines requires targeting parents by providing adequate information on the vaccines.
| S-EPMC7433157 | biostudies-literature
Project description:Accessible sources of clinical information have proliferated over the past decade. Although these new sources that contextualize information for practice are user friendly, there are questions about their accuracy because much of the material is not peer reviewed. On the other hand, traditional peer-reviewed material can be somewhat removed from the needs of practicing dentists, and recently questions have been raised about the accuracy of journals. This study assessed the accuracy of cone beam computed tomography (CBCT) radiation safety information in both professional media and peer-reviewed journals. Articles introducing CBCT technology to dentists and published in peer-reviewed journals were compared to articles appearing in professional magazines, clinically oriented news sites, and blogs written by clinicians for clinicians. The reported radiation doses of CBCT and conventional dental radiographs were recorded, as were conclusions about the comparative doses of these 2 imaging modalities. The proportion of articles reporting CBCT dose to be greater than, equal to, or less than that of conventional dental radiographs was not different between the peer-reviewed and professional media articles during the period 2003-2016. There is weak evidence that the conclusions of peer-reviewed journal articles, but not professional media sources, became more conservative after the 2010 publication of an article in The New York Times that was critical of misinformation concerning the safety and efficacy of CBCT in dentistry. Professional media articles that were not peer reviewed were as accurate as peer-reviewed journals for this topic and during the time period assessed. However, the method used here necessitated a narrow focus, and more studies are needed to broaden understanding.
| S-EPMC7189219 | biostudies-literature
Project description:BackgroundOutdoor air pollution is a major threat to global public health that needs responsible participation of researchers at all levels. Assessing research output is an important step in highlighting national and international contribution and collaboration in a certain field. Therefore, the aim of this study was to analyze globally-published literature in outdoor air pollution - related respiratory health.MethodOutdoor air pollution documents related to respiratory health were retrieved from Scopus database. The study period was up to 2017. Mapping of author keywords was carried out using VOSviewer 1.6.6.ResultsSearch query yielded 3635 documents with an h-index of 137. There was a dramatic increase in the number of publications in the last decade of the study period. The most frequently encountered author keywords were: air pollution (835 occurrences), asthma (502 occurrences), particulate matter (198 occurrences), and children (203 occurrences). The United States of America ranked first (1082; 29.8%) followed by the United Kingdom (279; 7.7%) and Italy (198; 5.4%). Annual research productivity stratified by income and population size indicated that China ranked first (22.2) followed by the USA (18.8). Analysis of regional distribution of publications indicated that the Mediterranean, African, and South-East Asia regions had the least contribution. Harvard University (92; 2.5%) was the most active institution/organization followed the US Environmental Protection Agency (89; 2.4%). International collaboration was restricted to three regions: Northern America, Europe, and Asia. The top ten preferred journals were in the field of environmental health and respiratory health. Environmental Health Perspective was the most preferred journal for publishing documents in outdoor pollution in relation to respiratory health.ConclusionResearch on the impact of outdoor air pollution on respiratory health had accelerated lately and is receiving a lot of interest. Global research networks that include countries with high level of pollution and limited resources are highly needed to create public opinion in favor of minimizing outdoor air pollution and investing in green technologies.
| S-EPMC5984296 | biostudies-literature
Project description:Delays in peer reviewed publication may have consequences for both assessment of scientific prowess in academics as well as communication of important information to the knowledge receptor community. We present an analysis on the perspectives of authors publishing in conservation biology journals regarding their opinions on the importance of speed in peer-review as well as how to improve review times. Authors were invited to take part in an online questionnaire, of which the data was subjected to both qualitative (open coding, categorizing) and quantitative analyses (generalized linear models). We received 637 responses to a total of 6,547 e-mail invitations sent. Peer-review speed was generally perceived as slow, with authors experiencing a typical turnaround time of 14 weeks while their perceived optimal review time is six weeks. Male and younger respondents seem to have higher expectations of review speed than females and older respondents. Majority of participants attributed lengthy review times to the 'stress' on the peer-review system (i.e., reviewer and editor fatigue), while editor persistence and journal prestige were believed to speed up the review process. Negative consequences of lengthy review times appear to be greater for early career researchers and can also have impact on author morale (e.g. motivation or frustration). Competition among colleagues were also of concern to respondents. Incentivizing peer review was among the top suggested alterations to the system along with training graduate students in peer review, increased editorial persistence, and changes to the norms of peer-review such as opening the peer-review process to the public. It is clear that authors surveyed in this study view the peer-review system as under stress and we encourage scientists and publishers to push the envelope for new peer review models.
| S-EPMC4533968 | biostudies-literature
Project description:Publishing peer review materials alongside research articles promises to make the peer review process more transparent as well as making it easier to recognise these contributions and give credit to peer reviewers. Traditionally, the peer review reports, editors letters and author responses are only shared between the small number of people in those roles prior to publication, but there is a growing interest in making some or all of these materials available. A small number of journals have been publishing peer review materials for some time, others have begun this practice more recently, and significantly more are now considering how they might begin. This article outlines the outcomes from a recent workshop among journals with experience in publishing peer review materials, in which the specific operation of these workflows, and the challenges, were discussed. Here, we provide a draft as to how to represent these materials in the JATS and Crossref data models to facilitate the coordination and discoverability of peer review materials, and seek feedback on these initial recommendations.
| S-EPMC6206614 | biostudies-literature