bims-skolko Biomed News
on Scholarly communication
Issue of 2020‒08‒16
twenty-four papers selected by
Thomas Krichel
Open Library Society


  1. Am J Pharm Educ. 2020 Jul;84(7): ajpe7846
    Rivkin A.
      It is imperative that articles published in reputable peer-reviewed journals provide balanced, fair, objective, and accurate references. However, studies on the accuracy of references in various scientific disciplines demonstrate an error rate of 25%-54%. These errors can range from minor errors in citation accuracy to major errors that alter the original content and meaning of the material referenced. This article discusses importance of citation accuracy, reviews principles of good citation practices, and offers recommendations aimed to decrease citation error rates.
    Keywords:  citations; references
    DOI:  https://doi.org/10.5688/ajpe7846
  2. BMJ Open. 2020 Aug 13. 10(8): e035600
    Glonti K, Boutron I, Moher D, Hren D.
      OBJECTIVE: To generate an understanding of the communication practices that might influence the peer-review process in biomedical journals.METHOD: Recruitment was based on purposive maximum variation sampling. We conducted semistructured interviews. Data were analysed using thematic analysis method.
    PARTICIPANTS: 56 journal editors from general medicine (n=13) and specialty (n=43) biomedical journals. Most were editor-in-chiefs (n=39), men (n=40) and worked part time (n=50).
    RESULTS: Our analysis generated four themes (1) providing minimal guidance to peer reviewers-two subthemes described the way journal editors rationalised their behaviour: (a) peer reviewers should know without guidelines how to review and (b) detailed guidance and structure might have a negative effect; (2) communication strategies of engagement with peer reviewers-two opposing strategies that journal editors employed to handle peer reviewers: (a) use of direct and personal communication to motivate peer reviewers and (b) use of indirect communication to avoid conflict; (3) concerns about impact of review model on communication-maintenance of anonymity as a means of facilitating critical and unburdened communication and minimising biases and (4) different practices in the moderation of communication between authors and peer reviewers-some journal editors actively interjected themselves into the communication chain to guide authors through peer reviewers' comments, others remained at a distance, leaving it to the authors to work through peer reviewers' comments.
    CONCLUSIONS: These journal editors' descriptions reveal several communication practices that might have a significant impact on the peer-review process. Editorial strategies to manage miscommunication are discussed. Further research on these proposed strategies and on communication practices from the point of view of authors and peer reviewers is warranted.
    Keywords:  education & training (see medical education & training); epidemiology; medical journalism
    DOI:  https://doi.org/10.1136/bmjopen-2019-035600
  3. Res Integr Peer Rev. 2020 ;5 11
    Horbach SPJM, Halffman W.
      Background: Triggered by a series of controversies and diversifying expectations of editorial practices, several innovative peer review procedures and supporting technologies have been proposed. However, adoption of these new initiatives seems slow. This raises questions about the wider conditions for peer review change and about the considerations that inform decisions to innovate. We set out to study the structure of commercial publishers' editorial process, to reveal how the benefits of peer review innovations are understood, and to describe the considerations that inform the implementation of innovations.Methods: We carried out field visits to the editorial office of two large academic publishers housing the editorial staff of several hundreds of journals, to study their editorial process, and interviewed editors not affiliated with large publishers. Field notes were transcribed and analysed using coding software.
    Results: At the publishers we analysed, the decision-making structure seems to show both clear patterns of hierarchy and layering of the different editorial practices. While information about new initiatives circulates widely, their implementation depends on assessment of stakeholder's wishes, impact on reputation, efficiency and implementation costs, with final decisions left to managers at the top of the internal hierarchy. Main tensions arise between commercial and substantial arguments. The editorial process is closely connected to commercial practices of creating business value, and the very specific terms in which business value is understood, such as reputation considerations and the urge to increase efficiency. Journals independent of large commercial publishers tend to have less hierarchically structured processes, report more flexibility to implement innovations, and to a greater extent decouple commercial and editorial perspectives.
    Conclusion: Our study demonstrates that peer review innovations are partly to be understood in light of commercial considerations related to reputation, efficiency and implementations costs. These arguments extend beyond previously studied topics in publishing economics, including publishers' choice for business or publication models and reach into the very heart of the editorial and peer review process.
    Keywords:  Commercial publishers; Editorial process; In situ interviews; Innovation; Peer review; Publishing
    DOI:  https://doi.org/10.1186/s41073-020-00097-w
  4. J Clin Apher. 2020 Aug 07.
    Weinstein R.
      The process of publishing original work in a peer review journal is not complete at the point where the manuscript is first submitted. The journal editors will submit the manuscript to peer review whereby outside experts are asked to vet the manuscript for scientific merit, originality and quality. Reviewers' comments are meant to help authors strengthen their manuscripts for potential publication. Authors benefit from this feedback and should approach the reviewers as volunteer consultants rather than as critics. Authors should respond to all reviewers' comments, completely and politely addressing the points raised. This article is meant to assist junior or inexperienced authors to understand the process of peer review and to function effectively within the process in order to succeed in having their manuscripts published.
    Keywords:  editor; manuscript revision; manuscript writing; publication; reviewer
    DOI:  https://doi.org/10.1002/jca.21822
  5. Indian J Pathol Microbiol. 2020 Jul-Sep;63(3):63(3): 347-349
    Agrawal R.
      
    DOI:  https://doi.org/10.4103/IJPM.IJPM_793_20
  6. Nature. 2020 08;584(7820): 192
    Sutherland WJ, Lythgoe KA.
      
    Keywords:  Peer review; Public health; Publishing; SARS-CoV-2
    DOI:  https://doi.org/10.1038/d41586-020-02333-1
  7. Vet J. 2020 Aug;pii: S1090-0233(20)30094-0. [Epub ahead of print]262 105517
    Rishniw M.
      
    Keywords:  Citation; Funding; Letters; Peer review; Scientific literature
    DOI:  https://doi.org/10.1016/j.tvjl.2020.105517
  8. Nature. 2020 08;584(7820): 192
    Dhar V, Brand A.
      
    Keywords:  Peer review; Publishing; SARS-CoV-2
    DOI:  https://doi.org/10.1038/d41586-020-02330-4
  9. Nature. 2020 Aug 14.
    Van Noorden R.
      
    Keywords:  Mathematics and computing; Peer review; Publishing
    DOI:  https://doi.org/10.1038/d41586-020-02378-2
  10. PLoS One. 2020 ;15(8): e0236927
    Park B, Sohn E, Kim S.
      Although the peer review system of academic journals is seen as fundamental to scientific achievement, a major threat to the validity of the system is a potential evaluation bias resulting from constraints at the journal level. In this study, we examine how the time pressure to maintain a fixed periodical quota for journal publication can influence a journal editor's decision to accept or reject a paper at any given point in time. We find that an increase in publication backlog, proxied as the average delay between paper acceptance and print publication, is correlated with an increase in the subsequent rejection rates of new submissions. Our findings suggest that time pressures inherent in the peer review system may be a source of potential evaluator bias, calling for a need to reconsider the current quota system.
    DOI:  https://doi.org/10.1371/journal.pone.0236927
  11. Phys Ther. 2020 Aug 10. pii: pzaa145. [Epub ahead of print]
    Araujo AC, Gonzalez GZ, Nascimento DP, Costa LOP.
      
    Keywords:  altmetric; altmetrics; social impact; social media; visibility
    DOI:  https://doi.org/10.1093/ptj/pzaa145
  12. An Acad Bras Cienc. 2020 ;pii: S0001-37652020000300908. [Epub ahead of print]92(2): e20200328
    McManus CM, Neves AAB, MaranhÃo AQ.
      Publishing profiles can help institutions and financing agencies understand the different needs of knowledge areas and regions for development within a country. Incites ® (Web of Science) was used to see where Brazilian authors were publishing, the impact, and the cost of this publishing. The USA was the country of choice for publishing journals, along with Brazil, England, and the Netherlands. While Brazilian authors continue to publish in hybrid journals, they are more often opting for closed access, with 89% of the papers published in Brazil being open access, compared with 21% of papers published abroad. The correlation between the cost of publishing and the number of citations was positive and significant. Publishing patterns were different depending on the area of knowledge and the Brazilian region. Stagnation or reduction in publications with international collaboration, industry collaboration, or in high impact open access journals may be the cause of a reduction in citation impact. These data can help in elaborating public and institutional policies for financing publications in Brazil, especially when looking at unfavourable changes in currency exchange rates.
    DOI:  https://doi.org/10.1590/0001-3765202020200328
  13. Brief Bioinform. 2020 Aug 14. pii: bbaa152. [Epub ahead of print]
    Porubsky V, Smith L, Sauro HM.
      Publishing repeatable and reproducible computational models is a crucial aspect of the scientific method in computational biology and one that is often forgotten in the rush to publish. The pressures of academic life and the lack of any reward system at institutions, granting agencies and journals means that publishing reproducible science is often either non-existent or, at best, presented in the form of an incomplete description. In the article, we will focus on repeatability and reproducibility in the systems biology field where a great many published models cannot be reproduced and in many cases even repeated. This review describes the current landscape of software tooling, model repositories, model standards and best practices for publishing repeatable and reproducible kinetic models. The review also discusses possible future remedies including working more closely with journals to help reviewers and editors ensure that published kinetic models are at minimum, repeatable. Contact: hsauro@uw.edu.
    Keywords:  SBML; kinetic modeling; reproducibility; standards; systems biology
    DOI:  https://doi.org/10.1093/bib/bbaa152
  14. Nature. 2020 Aug 12.
    Madsen R.
      
    Keywords:  Funding; Publishing; Research management
    DOI:  https://doi.org/10.1038/d41586-020-02395-1
  15. J Proteome Res. 2020 Aug 13.
    Boekweg H, McCown MA, Payne SH.
      Scientific progress comes as we build upon the work of others. Implicit in this advance is that we have access to and can thoroughly examine the work of others. It is important to recognize that our scholarly work as scientists encompasses not only experimental design and data collection, but also our analytical methods. Thus, when communicating biology experiments, especially those that utilize molecular omics data, the analysis methods which connect raw data to scientific conclusions must be presented with sufficient clarity that others can reproduce our exact work. Although there are many resources for sharing raw data files, there is currently not a widely utilized method for sharing analysis methods. We present a semi-structured pattern for sharing analysis methods that is simple, efficient and can be implemented by individual labs using existing software. This pattern requires three types of files in a publicly accessible repository, such as GitHub: 1) data files, 2) a universal I/O script that parses all data files, and 3) analysis scripts creating figures and metrics reported in the manuscript. We suggest additional conventions to improve readability and provide a template repository for the pattern. Sharing our exact analysis methods as software, in addition their narrative description in a manuscript, will ensure reproducibility and transparency. Importantly, the pattern we present does not require new infrastructure and can be achieved without advanced computing skills.
    DOI:  https://doi.org/10.1021/acs.jproteome.0c00454
  16. Nature. 2020 08;584(7820): 192
    Ohno-Machado L, Xu H.
      
    Keywords:  Databases; Publishing; SARS-CoV-2
    DOI:  https://doi.org/10.1038/d41586-020-02331-3
  17. Prog Rehabil Med. 2020 ;5 20200005
    Takashi A, Daichi I.
      Objectives: The purpose of this study was to evaluate the quality of reporting of systematic reviews published in Japanese in the field of physical therapy.Methods: The study design was a bibliometric analysis of systematic reviews. Two Japanese physical therapy journals (Physical Therapy Japan and Rigakuryoho Kagaku) were analysed using J-STAGE. The inclusion criterion was that articles were systematic reviews. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist was used to score the reporting quality of eligible systematic reviews. The quality assessment was performed by two reviewers independently.
    Results: Of the 1578 articles identified, thirteen articles were included in this study. The median score of checklist items adequately adhered to across the included studies was 12 (range, 7-17). None of the studies adhered to the structured summary or additional analysis PRISMA items. The intention of bias assessment across studies was reported in only three studies (23%), and only two of these three reported the results.
    Conclusions: The reporting quality of systematic reviews published in Japanese physical therapy journals was suboptimal. Therefore, readers should critically appraise the contents of systematic reviews. It is recommended that journals should strictly require their authors to adhere to reporting guidelines.
    Keywords:  PRISMA; critical appraisal; physical therapy; reporting guideline; transparency
    DOI:  https://doi.org/10.2490/prm.20200005
  18. Health Sci Rep. 2020 Sep;3(3): e175
    FitzGibbon H, King K, Piano C, Wilk C, Gaskarth M.
      Background and Aims: Plain-language summaries (PLS) are being heralded as a tool to improve communication of scientific research to lay audiences and time-poor or nonspecialist healthcare professionals. However, this relies on PLS being intuitively located and accessible. This research investigated the "discoverability" of PLS in biomedical journals.Methods: The eLIFE list of journals/organizations that produce PLS was consulted on July 12, 2018, for biomedical journals (based on title). Internet research, primarily focusing on information provided by the journal websites, explored PLS terminology (what do the journals call PLS), requirements (what articles are PLS generated for, who writes/reviews them, and at what stage), and location and sharing mechanisms (where/how the PLS are made available, are they free to access, and are they visible on PubMed).
    Results: The methodology identified 10 journals from distinct publishers, plus eLIFE itself (N = 11). Impact factors ranged from 3.768 to 17.581. Nine different terms were used to describe PLS. Most of the journals (8/11) required PLS for at least all research articles. Authors were responsible for writing PLS in 9/11 cases. Seven journals required PLS on article submission; of the other four, one required PLS at revision and three on acceptance. The location/sharing mechanism for PLS varied: within articles, alongside articles (separate tab/link), and/or on separate platforms (eg, social media, dedicated website). PLS were freely available when they were published with articles; however, PLS were only included within conventional abstracts on PubMed for 2/11 journals.
    Conclusion: Across the few biomedical journals producing PLS, our research suggests there is wide variation in terminology, location, sharing mechanisms, and PubMed visibility. We advocate a more consistent approach to ensure that PLS have appropriate prominence and can be easily found by their intended audiences.
    Keywords:  biomedical research; communication; lay summaries; patient summaries; plain English summaries; plain‐language summaries
    DOI:  https://doi.org/10.1002/hsr2.175
  19. J Urol. 2020 Aug 12. 101097JU0000000000001326
    Smith JA.
      
    DOI:  https://doi.org/10.1097/JU.0000000000001326
  20. J Med Ethics. 2020 Aug 13. pii: medethics-2020-106140. [Epub ahead of print]
    Bülow W, Godskesen TE, Helgesson G, Eriksson S.
      The purpose of retracting published papers is to maintain the integrity of academic research. Recent work in research ethics has devoted important attention to how to improve the system of paper retraction. In this context, the focus has primarily been on how to handle fraudulent or flawed research papers and how to encourage the retraction of papers based on honest mistakes. Less attention has been paid to whether papers that report unethical research-for example, research performed without appropriate concern for the moral rights and interests of the research participants-should be retracted. The aim of this paper is to examine to what extent retraction policies of academic journals and publishers address retractions of unethical research and to discuss critically various policy options and the reasons for accepting them. The paper starts by reviewing retraction policies of academic publishers. The results show that many journals do not have explicit policies for how to handle unethical research. Against this background, we then discuss four normative arguments for why unethical research should be retracted. In conclusion, we suggest a retraction policy in light of our empirical and normative investigations.
    Keywords:  applied and professional ethics; publication ethics; research ethics
    DOI:  https://doi.org/10.1136/medethics-2020-106140